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DEFAULT_SS_COIL_IDENTIFIER module-attribute 

DEFAULT_SS_COIL_IDENTIFIER = 'C'

Secondary structure identifier mapping Stride B/b:Isolated bridge E:Strand/Extended conformation G:3-10 helix H:Alpha helix I:PI-helix T:Turn C:Coil (none of the above) SS_TURN_IDENTIFIERS = 'T' SS_DISORDER_IDENTIFIERS = 'C'

DSSP B:beta bridge E:strand/beta bulge G:310 helix H:α helix I:π helix T:turns S:high curvature (where the angle between i-2, i, and i+2 is at least 70°) " "(space):loop SS_DISORDER_IDENTIFIERS = ' ' SS_TURN_IDENTIFIERS = 'TS'

alpha_helix_15_atoms module-attribute 

alpha_helix_15_atoms = Atoms([Atom(0, 1, 'N', ' ', 'ALA', 'A', 1, ' ', 27.128, 20.897, 37.943, 1.0, 0.0, 'N', ''), Atom(1, 2, 'CA', ' ', 'ALA', 'A', 1, ' ', 27.933, 21.94, 38.546, 1.0, 0.0, 'C', ''), Atom(2, 3, 'C', ' ', 'ALA', 'A', 1, ' ', 28.402, 22.92, 37.481, 1.0, 0.0, 'C', ''), Atom(3, 4, 'O', ' ', 'ALA', 'A', 1, ' ', 28.303, 24.132, 37.663, 1.0, 0.0, 'O', ''), Atom(4, 5, 'CB', ' ', 'ALA', 'A', 1, ' ', 29.162, 21.356, 39.234, 1.0, 0.0, 'C', ''), Atom(5, 6, 'N', ' ', 'ALA', 'A', 2, ' ', 28.914, 22.392, 36.367, 1.0, 0.0, 'N', ''), Atom(6, 7, 'CA', ' ', 'ALA', 'A', 2, ' ', 29.395, 23.219, 35.278, 1.0, 0.0, 'C', ''), Atom(7, 8, 'C', ' ', 'ALA', 'A', 2, ' ', 28.286, 24.142, 34.793, 1.0, 0.0, 'C', ''), Atom(8, 9, 'O', ' ', 'ALA', 'A', 2, ' ', 28.508, 25.337, 34.61, 1.0, 0.0, 'O', ''), Atom(9, 10, 'CB', ' ', 'ALA', 'A', 2, ' ', 29.857, 22.365, 34.102, 1.0, 0.0, 'C', ''), Atom(10, 11, 'N', ' ', 'ALA', 'A', 3, ' ', 27.092, 23.583, 34.584, 1.0, 0.0, 'N', ''), Atom(11, 12, 'CA', ' ', 'ALA', 'A', 3, ' ', 25.956, 24.355, 34.121, 1.0, 0.0, 'C', ''), Atom(12, 13, 'C', ' ', 'ALA', 'A', 3, ' ', 25.681, 25.505, 35.079, 1.0, 0.0, 'C', ''), Atom(13, 14, 'O', ' ', 'ALA', 'A', 3, ' ', 25.488, 26.639, 34.648, 1.0, 0.0, 'O', ''), Atom(14, 15, 'CB', ' ', 'ALA', 'A', 3, ' ', 24.703, 23.49, 34.038, 1.0, 0.0, 'C', ''), Atom(15, 16, 'N', ' ', 'ALA', 'A', 4, ' ', 25.662, 25.208, 36.38, 1.0, 0.0, 'N', ''), Atom(16, 17, 'CA', ' ', 'ALA', 'A', 4, ' ', 25.411, 26.214, 37.393, 1.0, 0.0, 'C', ''), Atom(17, 18, 'C', ' ', 'ALA', 'A', 4, ' ', 26.424, 27.344, 37.27, 1.0, 0.0, 'C', ''), Atom(18, 19, 'O', ' ', 'ALA', 'A', 4, ' ', 26.055, 28.516, 37.29, 1.0, 0.0, 'O', ''), Atom(19, 20, 'CB', ' ', 'ALA', 'A', 4, ' ', 25.519, 25.624, 38.794, 1.0, 0.0, 'C', ''), Atom(20, 21, 'N', ' ', 'ALA', 'A', 5, ' ', 27.704, 26.987, 37.142, 1.0, 0.0, 'N', ''), Atom(21, 22, 'CA', ' ', 'ALA', 'A', 5, ' ', 28.764, 27.968, 37.016, 1.0, 0.0, 'C', ''), Atom(22, 23, 'C', ' ', 'ALA', 'A', 5, ' ', 28.497, 28.876, 35.825, 1.0, 0.0, 'C', ''), Atom(23, 24, 'O', ' ', 'ALA', 'A', 5, ' ', 28.602, 30.096, 35.937, 1.0, 0.0, 'O', ''), Atom(24, 25, 'CB', ' ', 'ALA', 'A', 5, ' ', 30.115, 27.292, 36.812, 1.0, 0.0, 'C', ''), Atom(25, 26, 'N', ' ', 'ALA', 'A', 6, ' ', 28.151, 28.278, 34.682, 1.0, 0.0, 'N', ''), Atom(26, 27, 'CA', ' ', 'ALA', 'A', 6, ' ', 27.871, 29.032, 33.478, 1.0, 0.0, 'C', ''), Atom(27, 28, 'C', ' ', 'ALA', 'A', 6, ' ', 26.759, 30.04, 33.737, 1.0, 0.0, 'C', ''), Atom(28, 29, 'O', ' ', 'ALA', 'A', 6, ' ', 26.876, 31.205, 33.367, 1.0, 0.0, 'O', ''), Atom(29, 30, 'CB', ' ', 'ALA', 'A', 6, ' ', 27.429, 28.113, 32.344, 1.0, 0.0, 'C', ''), Atom(30, 31, 'N', ' ', 'ALA', 'A', 7, ' ', 25.678, 29.586, 34.376, 1.0, 0.0, 'N', ''), Atom(31, 32, 'CA', ' ', 'ALA', 'A', 7, ' ', 24.552, 30.444, 34.682, 1.0, 0.0, 'C', ''), Atom(32, 33, 'C', ' ', 'ALA', 'A', 7, ' ', 25.013, 31.637, 35.507, 1.0, 0.0, 'C', ''), Atom(33, 34, 'O', ' ', 'ALA', 'A', 7, ' ', 24.652, 32.773, 35.212, 1.0, 0.0, 'O', ''), Atom(34, 35, 'CB', ' ', 'ALA', 'A', 7, ' ', 23.489, 29.693, 35.478, 1.0, 0.0, 'C', ''), Atom(35, 36, 'N', ' ', 'ALA', 'A', 8, ' ', 25.814, 31.374, 36.543, 1.0, 0.0, 'N', ''), Atom(36, 37, 'CA', ' ', 'ALA', 'A', 8, ' ', 26.321, 32.423, 37.405, 1.0, 0.0, 'C', ''), Atom(37, 38, 'C', ' ', 'ALA', 'A', 8, ' ', 27.081, 33.454, 36.583, 1.0, 0.0, 'C', ''), Atom(38, 39, 'O', ' ', 'ALA', 'A', 8, ' ', 26.874, 34.654, 36.745, 1.0, 0.0, 'O', ''), Atom(39, 40, 'CB', ' ', 'ALA', 'A', 8, ' ', 27.193, 31.773, 38.487, 1.0, 0.0, 'C', ''), Atom(40, 41, 'N', ' ', 'ALA', 'A', 9, ' ', 27.963, 32.98, 35.7, 1.0, 0.0, 'N', ''), Atom(41, 42, 'CA', ' ', 'ALA', 'A', 9, ' ', 28.75, 33.859, 34.858, 1.0, 0.0, 'C', ''), Atom(42, 43, 'C', ' ', 'ALA', 'A', 9, ' ', 27.834, 34.759, 34.042, 1.0, 0.0, 'C', ''), Atom(43, 44, 'O', ' ', 'ALA', 'A', 9, ' ', 28.052, 35.967, 33.969, 1.0, 0.0, 'O', ''), Atom(44, 45, 'CB', ' ', 'ALA', 'A', 9, ' ', 29.621, 33.061, 33.894, 1.0, 0.0, 'C', ''), Atom(45, 46, 'N', ' ', 'ALA', 'A', 10, ' ', 26.807, 34.168, 33.427, 1.0, 0.0, 'N', ''), Atom(46, 47, 'CA', ' ', 'ALA', 'A', 10, ' ', 25.864, 34.915, 32.62, 1.0, 0.0, 'C', ''), Atom(47, 48, 'C', ' ', 'ALA', 'A', 10, ' ', 25.23, 36.024, 33.448, 1.0, 0.0, 'C', ''), Atom(48, 49, 'O', ' ', 'ALA', 'A', 10, ' ', 25.146, 37.165, 33.001, 1.0, 0.0, 'O', ''), Atom(49, 50, 'CB', ' ', 'ALA', 'A', 10, ' ', 24.752, 34.012, 32.097, 1.0, 0.0, 'C', ''), Atom(50, 51, 'N', ' ', 'ALA', 'A', 11, ' ', 24.783, 35.683, 34.66, 1.0, 0.0, 'N', ''), Atom(51, 52, 'CA', ' ', 'ALA', 'A', 11, ' ', 24.16, 36.646, 35.544, 1.0, 0.0, 'C', ''), Atom(52, 53, 'C', ' ', 'ALA', 'A', 11, ' ', 25.104, 37.812, 35.797, 1.0, 0.0, 'C', ''), Atom(53, 54, 'O', ' ', 'ALA', 'A', 11, ' ', 24.699, 38.97, 35.714, 1.0, 0.0, 'O', ''), Atom(54, 55, 'CB', ' ', 'ALA', 'A', 11, ' ', 23.81, 36.012, 36.887, 1.0, 0.0, 'C', ''), Atom(55, 56, 'N', ' ', 'ALA', 'A', 12, ' ', 26.365, 37.503, 36.107, 1.0, 0.0, 'N', ''), Atom(56, 57, 'CA', ' ', 'ALA', 'A', 12, ' ', 27.361, 38.522, 36.37, 1.0, 0.0, 'C', ''), Atom(57, 58, 'C', ' ', 'ALA', 'A', 12, ' ', 27.477, 39.461, 35.177, 1.0, 0.0, 'C', ''), Atom(58, 59, 'O', ' ', 'ALA', 'A', 12, ' ', 27.485, 40.679, 35.342, 1.0, 0.0, 'O', ''), Atom(59, 60, 'CB', ' ', 'ALA', 'A', 12, ' ', 28.73, 37.9, 36.625, 1.0, 0.0, 'C', ''), Atom(60, 61, 'N', ' ', 'ALA', 'A', 13, ' ', 27.566, 38.89, 33.974, 1.0, 0.0, 'N', ''), Atom(61, 62, 'CA', ' ', 'ALA', 'A', 13, ' ', 27.68, 39.674, 32.761, 1.0, 0.0, 'C', ''), Atom(62, 63, 'C', ' ', 'ALA', 'A', 13, ' ', 26.504, 40.634, 32.645, 1.0, 0.0, 'C', ''), Atom(63, 64, 'O', ' ', 'ALA', 'A', 13, ' ', 26.69, 41.815, 32.36, 1.0, 0.0, 'O', ''), Atom(64, 65, 'CB', ' ', 'ALA', 'A', 13, ' ', 27.69, 38.779, 31.527, 1.0, 0.0, 'C', ''), Atom(65, 66, 'N', ' ', 'ALA', 'A', 14, ' ', 25.291, 40.121, 32.868, 1.0, 0.0, 'N', ''), Atom(66, 67, 'CA', ' ', 'ALA', 'A', 14, ' ', 24.093, 40.932, 32.789, 1.0, 0.0, 'C', ''), Atom(67, 68, 'C', ' ', 'ALA', 'A', 14, ' ', 24.193, 42.112, 33.745, 1.0, 0.0, 'C', ''), Atom(68, 69, 'O', ' ', 'ALA', 'A', 14, ' ', 23.905, 43.245, 33.367, 1.0, 0.0, 'O', ''), Atom(69, 70, 'CB', ' ', 'ALA', 'A', 14, ' ', 22.856, 40.12, 33.158, 1.0, 0.0, 'C', ''), Atom(70, 71, 'N', ' ', 'ALA', 'A', 15, ' ', 24.604, 41.841, 34.986, 1.0, 0.0, 'N', ''), Atom(71, 72, 'CA', ' ', 'ALA', 'A', 15, ' ', 24.742, 42.878, 35.989, 1.0, 0.0, 'C', ''), Atom(72, 73, 'C', ' ', 'ALA', 'A', 15, ' ', 25.691, 43.96, 35.497, 1.0, 0.0, 'C', ''), Atom(73, 74, 'O', ' ', 'ALA', 'A', 15, ' ', 25.39, 45.147, 35.602, 1.0, 0.0, 'O', ''), Atom(74, 75, 'CB', ' ', 'ALA', 'A', 15, ' ', 24.418, 41.969, 34.808, 1.0, 0.0, 'C', '')])

Caution. After the first time this helix is created as a Structure, the alpha_helix_15_atoms Atom instances will have their .coords set to the alpha_helix_15 'parent' Structure instance. Transformation of this Structure causes the starting coordinates in each Atom instance in alpha_helix_15_atoms to be transformed as well. Making new structures from this Atoms container is sufficient to detach them, but the coordinates are moved from program start after usage the first time. This behavior isn't ideal, but a consequence of construction of Atom instances from the singular attribute basis with the intention to be reused

ArrayIndexer module-attribute 

ArrayIndexer = Type[Union[Sequence[int], Sequence[bool], slice, None]]

Where integers, slices :, ellipsis ..., None and integer or boolean arrays are valid indices

Log 

Log(log: Logger | None = logging.getLogger('null'))

Responsible for StructureBase logging operations

Parameters:

  • log (Logger | None, default: getLogger('null') ) –

    The logging.Logger to handle StructureBase logging. If None is passed a Logger with NullHandler is used

Source code in symdesign/structure/base.py 
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def __init__(self, log: Logger | None = logging.getLogger('null')):
    """Construct the instance

    Args:
        log: The logging.Logger to handle StructureBase logging. If None is passed a Logger with NullHandler is used
    """
    self.log = log

SymmetryBase 

SymmetryBase(rotation_matrices: ndarray = None, translation_matrices: ndarray = None, **kwargs)

Bases: ABC

Adds functionality for symmetric manipulation of Structure instances

Collects known keyword arguments for all derived classes to protect object. Should always be the last class in the method resolution order of derived classes.

Source code in symdesign/structure/base.py 
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def __init__(self, rotation_matrices: np.ndarray = None, translation_matrices: np.ndarray = None, **kwargs):
    self._symmetry = self._symmetric_dependents = None
    try:
        super().__init__(**kwargs)  # SymmetryBase
    except TypeError:
        raise TypeError(
            f"The argument(s) passed to the {self.__class__.__name__} instance weren't recognized and aren't "
            f"accepted by the object class: {', '.join(kwargs.keys())}\n\nIt's likely that your class MRO is "
            "insufficient for your passed arguments or you have passed invalid arguments")

symmetry property writable 

symmetry: str | None

The symmetry of the Structure described by its Schönflies notation

symmetric_dependents property writable 

symmetric_dependents: list[StructureBase] | list

Access the symmetrically dependent Structure instances

reset_symmetry_state 

reset_symmetry_state() -> None

Remove any state variable associated with the instance

Source code in symdesign/structure/base.py 
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def reset_symmetry_state(self) -> None:
    """Remove any state variable associated with the instance"""
    # self.log.debug(f"Removing symmetric attributes from {repr(self)}")
    for attribute in self.symmetry_state_attributes:
        try:
            delattr(self, attribute)
        except AttributeError:
            continue

is_symmetric 

is_symmetric() -> bool

Query whether the Structure is symmetric. Returns True if self.symmetry is not None

Source code in symdesign/structure/base.py 
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def is_symmetric(self) -> bool:
    """Query whether the Structure is symmetric. Returns True if self.symmetry is not None"""
    return self._symmetry is not None

has_symmetric_dependents 

has_symmetric_dependents() -> bool

Evaluates to True if the Structure has symmetrically dependent children

Source code in symdesign/structure/base.py 
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def has_symmetric_dependents(self) -> bool:
    """Evaluates to True if the Structure has symmetrically dependent children"""
    return True if self._symmetric_dependents else False

StructureMetadata 

StructureMetadata(biological_assembly: str | int = None, cryst_record: str = None, entity_info: dict[str, dict[dict | list | str]] = None, file_path: AnyStr = None, reference_sequence: str | dict[str, str] = None, resolution: float = None, **kwargs)

Contains all metadata available from structure file parsing

Parameters:

  • biological_assembly (str | int, default: None ) –

    The integer of the biological assembly (as indicated by PDB AssemblyID format)

  • cryst_record (str, default: None ) –

    The string specifying how the molecule is situated in a lattice

  • entity_info (dict[str, dict[dict | list | str]], default: None ) –

    A mapping of the metadata to their distinct molecular identifiers

  • file_path (AnyStr, default: None ) –

    The location on disk where the file was accessed

  • reference_sequence (str | dict[str, str], default: None ) –

    The reference sequence (according to expression sequence or reference database)

  • resolution (float, default: None ) –

    The level of detail available from an experimental dataset contributing to the sharpness with which structural data can contribute towards building a model

Source code in symdesign/structure/base.py 
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def __init__(self, biological_assembly: str | int = None, cryst_record: str = None,
             entity_info: dict[str, dict[dict | list | str]] = None, file_path: AnyStr = None,
             reference_sequence: str | dict[str, str] = None, resolution: float = None, **kwargs):
    """Construct the instance

    Args:
        biological_assembly: The integer of the biological assembly (as indicated by PDB AssemblyID format)
        cryst_record: The string specifying how the molecule is situated in a lattice
        entity_info: A mapping of the metadata to their distinct molecular identifiers
        file_path: The location on disk where the file was accessed
        reference_sequence: The reference sequence (according to expression sequence or reference database)
        resolution: The level of detail available from an experimental dataset contributing to the sharpness with
            which structural data can contribute towards building a model
    """
    if biological_assembly is None:
        self.biological_assembly = biological_assembly
    else:
        self.biological_assembly = str(biological_assembly)
    self.cryst_record = cryst_record
    self.entity_info = entity_info
    self.file_path = file_path
    self.reference_sequence = reference_sequence
    self.resolution = resolution

CoordinateOpsMixin

Bases: ABC

coords abstractmethod property writable 

coords

distance_from_reference 

distance_from_reference(reference: ndarray = utils.symmetry.origin, measure: str = 'mean', **kwargs) -> float

From a Structure, find the furthest coordinate from the origin (default) or from a reference.

Parameters:

  • reference (ndarray, default: origin ) –

    The reference where the point should be measured from. Default is origin

  • measure (str, default: 'mean' ) –

    The measurement to take with respect to the reference. Could be 'mean', 'min', 'max', or any numpy function to describe computed distance scalars

Returns:

  • float –

    The distance from the reference point to the furthest point

Source code in symdesign/structure/base.py 
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def distance_from_reference(
    self, reference: np.ndarray = utils.symmetry.origin, measure: str = 'mean', **kwargs
) -> float:
    """From a Structure, find the furthest coordinate from the origin (default) or from a reference.

    Args:
        reference: The reference where the point should be measured from. Default is origin
        measure: The measurement to take with respect to the reference. Could be 'mean', 'min', 'max', or any
            numpy function to describe computed distance scalars

    Returns:
        The distance from the reference point to the furthest point
    """
    if reference is None:
        reference = utils.symmetry.origin

    return getattr(np, measure)(np.linalg.norm(self.coords - reference, axis=1))

translate 

translate(translation: list[float] | ndarray, **kwargs) -> None

Perform a translation to the Structure ensuring only the Structure container of interest is translated ensuring the underlying coords are not modified

Parameters:

  • translation (list[float] | ndarray) –

    The first translation to apply, expected array shape (3,)

Source code in symdesign/structure/base.py 
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def translate(self, translation: list[float] | np.ndarray, **kwargs) -> None:
    """Perform a translation to the Structure ensuring only the Structure container of interest is translated
    ensuring the underlying coords are not modified

    Args:
        translation: The first translation to apply, expected array shape (3,)
    """
    self._transforming = True
    self.coords += translation
    self._transforming = False

rotate 

rotate(rotation: list[list[float]] | ndarray, **kwargs) -> None

Perform a rotation to the Structure ensuring only the Structure container of interest is rotated ensuring the underlying coords are not modified

Parameters:

  • rotation (list[list[float]] | ndarray) –

    The first rotation to apply, expected array shape (3, 3)

Source code in symdesign/structure/base.py 
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def rotate(self, rotation: list[list[float]] | np.ndarray, **kwargs) -> None:
    """Perform a rotation to the Structure ensuring only the Structure container of interest is rotated ensuring the
    underlying coords are not modified

    Args:
        rotation: The first rotation to apply, expected array shape (3, 3)
    """
    self._transforming = True
    self.coords = np.matmul(self.coords, np.transpose(rotation))  # Allows a list to be passed
    # self.coords = np.matmul(self.coords, rotation.swapaxes(-2, -1))  # Essentially a transpose
    self._transforming = False

transform 

transform(rotation: list[list[float]] | ndarray = None, translation: list[float] | ndarray = None, rotation2: list[list[float]] | ndarray = None, translation2: list[float] | ndarray = None, **kwargs) -> None

Perform a specific transformation to the Structure ensuring only the Structure container of interest is transformed ensuring the underlying coords are not modified

Transformation proceeds by matrix multiplication and vector addition with the order of operations as: rotation, translation, rotation2, translation2

Parameters:

  • rotation (list[list[float]] | ndarray, default: None ) –

    The first rotation to apply, expected array shape (3, 3)

  • translation (list[float] | ndarray, default: None ) –

    The first translation to apply, expected array shape (3,)

  • rotation2 (list[list[float]] | ndarray, default: None ) –

    The second rotation to apply, expected array shape (3, 3)

  • translation2 (list[float] | ndarray, default: None ) –

    The second translation to apply, expected array shape (3,)

Source code in symdesign/structure/base.py 
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def transform(
    self, rotation: list[list[float]] | np.ndarray = None, translation: list[float] | np.ndarray = None,
    rotation2: list[list[float]] | np.ndarray = None, translation2: list[float] | np.ndarray = None, **kwargs
) -> None:
    """Perform a specific transformation to the Structure ensuring only the Structure container of interest is
    transformed ensuring the underlying coords are not modified

    Transformation proceeds by matrix multiplication and vector addition with the order of operations as:
    rotation, translation, rotation2, translation2

    Args:
        rotation: The first rotation to apply, expected array shape (3, 3)
        translation: The first translation to apply, expected array shape (3,)
        rotation2: The second rotation to apply, expected array shape (3, 3)
        translation2: The second translation to apply, expected array shape (3,)
    """
    if rotation is not None:  # Required for np.ndarray or None checks
        new_coords = np.matmul(self.coords, np.transpose(rotation))  # Allows list to be passed...
        # new_coords = np.matmul(self.coords, rotation.swapaxes(-2, -1))  # Essentially a transpose
    else:
        new_coords = self.coords  # No need to copy as this is a view

    if translation is not None:  # Required for np.ndarray or None checks
        new_coords += translation

    if rotation2 is not None:  # Required for np.ndarray or None checks
        np.matmul(new_coords, np.transpose(rotation2), out=new_coords)  # Allows list to be passed...
        # np.matmul(new_coords, rotation2.swapaxes(-2, -1), out=new_coords)  # Essentially a transpose

    if translation2 is not None:  # Required for np.ndarray or None checks
        new_coords += translation2

    self._transforming = True
    self.coords = new_coords
    self._transforming = False

copy abstractmethod 

copy()
Source code in symdesign/structure/base.py 
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@abc.abstractmethod
def copy(self):
    """"""

get_transformed_copy 

get_transformed_copy(rotation: list[list[float]] | ndarray = None, translation: list[float] | ndarray = None, rotation2: list[list[float]] | ndarray = None, translation2: list[float] | ndarray = None) -> StructureBase

Make a semi-deep copy of the Structure object with the coordinates transformed in cartesian space

Transformation proceeds by matrix multiplication and vector addition with the order of operations as: rotation, translation, rotation2, translation2

Parameters:

  • rotation (list[list[float]] | ndarray, default: None ) –

    The first rotation to apply, expected array shape (3, 3)

  • translation (list[float] | ndarray, default: None ) –

    The first translation to apply, expected array shape (3,)

  • rotation2 (list[list[float]] | ndarray, default: None ) –

    The second rotation to apply, expected array shape (3, 3)

  • translation2 (list[float] | ndarray, default: None ) –

    The second translation to apply, expected array shape (3,)

Returns:

Source code in symdesign/structure/base.py 
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def get_transformed_copy(
    self, rotation: list[list[float]] | np.ndarray = None, translation: list[float] | np.ndarray = None,
    rotation2: list[list[float]] | np.ndarray = None, translation2: list[float] | np.ndarray = None
) -> StructureBase:  # Todo -> Self in python 3.11
    """Make a semi-deep copy of the Structure object with the coordinates transformed in cartesian space

    Transformation proceeds by matrix multiplication and vector addition with the order of operations as:
    rotation, translation, rotation2, translation2

    Args:
        rotation: The first rotation to apply, expected array shape (3, 3)
        translation: The first translation to apply, expected array shape (3,)
        rotation2: The second rotation to apply, expected array shape (3, 3)
        translation2: The second translation to apply, expected array shape (3,)

    Returns:
        A transformed copy of the original object
    """
    if rotation is not None:  # Required for np.ndarray or None checks
        new_coords = np.matmul(self.coords, np.transpose(rotation))  # Allows list to be passed...
        # new_coords = np.matmul(self.coords, rotation.swapaxes(-2, -1))  # Essentially a transpose
    else:
        new_coords = self.coords  # No need to copy as this is a view

    if translation is not None:  # Required for np.ndarray or None checks
        new_coords += translation

    if rotation2 is not None:  # Required for np.ndarray or None checks
        np.matmul(new_coords, np.transpose(rotation2), out=new_coords)  # Allows list to be passed...
        # np.matmul(new_coords, rotation2.swapaxes(-2, -1), out=new_coords)  # Essentially a transpose

    if translation2 is not None:  # Required for np.ndarray or None checks
        new_coords += translation2

    new_structure = self.copy()
    new_structure._transforming = True
    new_structure.coords = new_coords
    new_structure._transforming = False

    return new_structure

StructureBase 

StructureBase(parent: StructureBase = None, log: Log | Logger | bool = True, coords: ndarray | Coordinates | list[list[float]] = None, name: str = None, file_path: AnyStr = None, biological_assembly: str | int = None, cryst_record: str = None, resolution: float = None, entity_info: dict[str, dict[dict | list | str]] = None, reference_sequence: str | dict[str, str] = None, **kwargs)

Bases: SymmetryBase, CoordinateOpsMixin, ABC

Manipulates Coordinates and Log instances as well as the .atom_indices.

Additionally. sorts through parent Structure and dependent Structure hierarchies during Structure subclass creation.

Parameters:

  • parent (StructureBase, default: None ) –

    If another Structure object created this Structure instance, pass the 'parent' instance. Will take ownership over Structure containers (coords, atoms, residues) for dependent Structures

  • log (Log | Logger | bool, default: True ) –

    The Log or Logger instance, or the name for the logger to handle parent Structure logging. None or False prevents logging while any True assignment enables it

  • coords (ndarray | Coordinates | list[list[float]], default: None ) –

    When setting up a parent Structure instance, the coordinates of that Structure

  • name (str, default: None ) –

    The identifier for the Structure instance

Source code in symdesign/structure/base.py 
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def __init__(self, parent: StructureBase = None, log: Log | Logger | bool = True,
             coords: np.ndarray | Coordinates | list[list[float]] = None, name: str = None,
             # metadata: StructureMetadata = None,
             file_path: AnyStr = None, biological_assembly: str | int = None,
             cryst_record: str = None, resolution: float = None,
             entity_info: dict[str, dict[dict | list | str]] = None,
             reference_sequence: str | dict[str, str] = None,
             # entity_info=None,
             **kwargs):
    # These shouldn't be passed as they should be stripped by prior constructors...
    # entity_names=None, rotation_matrices=None, translation_matrices=None,
    # metadata=None, pose_format=None, query_by_sequence=True, rename_chains=None
    """Construct the instance

    Args:
        parent: If another Structure object created this Structure instance, pass the 'parent' instance. Will take
            ownership over Structure containers (coords, atoms, residues) for dependent Structures
        log: The Log or Logger instance, or the name for the logger to handle parent Structure logging.
            None or False prevents logging while any True assignment enables it
        coords: When setting up a parent Structure instance, the coordinates of that Structure
        name: The identifier for the Structure instance
    """
    self.name = name if name not in [None, False] else f'Unnamed_{self.__class__.__name__}'
    if parent is not None:  # Initialize StructureBase from parent
        self._parent = parent
    else:  # This is the parent
        self._parent_ = None
        self.metadata = StructureMetadata(
            biological_assembly=biological_assembly, cryst_record=cryst_record, entity_info=entity_info,
            file_path=file_path, reference_sequence=reference_sequence, resolution=resolution
        )
        # Initialize Log
        if log:
            if isinstance(log, Log):  # Initialized Log
                self._log = log
            elif isinstance(log, Logger):  # logging.Logger object
                self._log = Log(log)
            elif isinstance(log, str):
                self._log = Log(utils.start_log(name=f'{__name__}.{self.name}', level=log))
            else:  # log is True or some other type:  # Use the module logger
                self._log = Log(logger)
        else:  # When explicitly passed as None or False, uses the null logger
            self._log = null_struct_log  # Log()

        # Initialize Coordinates
        if coords is None:  # Check this first
            # Most init occurs from Atom instances that are their own parent until another StructureBase adopts them
            self._coords = Coordinates()
        elif isinstance(coords, Coordinates):
            self._coords = coords
        else:  # Create a Coordinates instance. This assumes the dimensions are correct. Coordinates() handles if not
            self._coords = Coordinates(coords)

    # try:
    super().__init__(**kwargs)  # StructureBase

parent property 

parent: StructureBase | None

Return the instance's 'parent' StructureBase which is responsible for manipulation of Structure containers

log property writable 

log: Logger

The StructureBase Logger

coords property writable 

coords: ndarray

The coordinates for the Atoms in the StructureBase object

is_dependent 

is_dependent() -> bool

Is this instance a dependent on a parent StructureBase?

Source code in symdesign/structure/base.py 
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def is_dependent(self) -> bool:
    """Is this instance a dependent on a parent StructureBase?"""
    return self._parent_ is not None

is_parent 

is_parent() -> bool

Is this instance a parent?

Source code in symdesign/structure/base.py 
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def is_parent(self) -> bool:
    """Is this instance a parent?"""
    return self._parent_ is None

make_parent 

make_parent()

Remove this instance from its parent, making it a parent in the process

Source code in symdesign/structure/base.py 
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def make_parent(self):
    """Remove this instance from its parent, making it a parent in the process"""
    # Set parent explicitly as None
    self.__setattr__(_parent_variable, None)
    # Create a new, Coords instance detached from the parent
    self._coords = Coordinates(self.coords)

reset_state 

reset_state()

Removes attributes that are valid for the current state. Additionally, resets the symmetry state if symmetric

This is useful for transfer of ownership, or changes in the state that should be overwritten

Source code in symdesign/structure/base.py 
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def reset_state(self):
    """Removes attributes that are valid for the current state. Additionally, resets the symmetry state if symmetric

    This is useful for transfer of ownership, or changes in the state that should be overwritten
    """
    # self.log.debug(f'Resetting {repr(self)} state_attributes')
    for attr in self.state_attributes:
        try:
            self.__delattr__(attr)
        except AttributeError:
            continue

    self.reset_symmetry_state()

Atom 

Atom(index: int = None, number: int = None, atom_type: str = None, alt_location: str = ' ', residue_type: str = None, chain_id: str = None, residue_number: int = None, code_for_insertion: str = ' ', x: float = None, y: float = None, z: float = None, occupancy: float = None, b_factor: float = None, element: str = None, charge: str = None, coords: list[float] = None, **kwargs)

Bases: CoordinateOpsMixin

Contains Atom metadata and a single coordinate position

Parameters:

  • index (int, default: None ) –

    The zero-indexed number to describe this Atom instance's position in a StructureBaseContainer

  • number (int, default: None ) –

    The integer number describing this Atom instances position in comparison to others instances

  • atom_type (str, default: None ) –

    The characters describing the classification of atom via membership to a molecule

  • alt_location (str, default: ' ' ) –

    Whether the observation of the Atom has alternative evidences

  • residue_type (str, default: None ) –

    The characters describing the molecular unit to which this Atom belongs

  • chain_id (str, default: None ) –

    The identifier which signifies this Atom instances membership to a larger polymer

  • residue_number (int, default: None ) –

    The integer of the polymer that this Atom belongs too

  • code_for_insertion (str, default: ' ' ) –

    Whether the Atom is included in a residue which is inserted according to a common numbering scheme

  • x (float, default: None ) –

    The x axis value of the instances coordinate position, i.e., it's x coordinate

  • y (float, default: None ) –

    The y axis value of the instances coordinate position, i.e., it's y coordinate

  • z (float, default: None ) –

    The z axis value of the instances coordinate position, i.e., it's z coordinate

  • occupancy (float, default: None ) –

    The fraction of the time this Atom is observed in the experiment

  • b_factor (float, default: None ) –

    The thermal fluctuation for the Atom OR a value for which structural representation should account

  • element (str, default: None ) –

    The atomic symbol for the Atom

  • charge (str, default: None ) –

    The numeric value for the electronic charge of the Atom

  • coords (list[float], default: None ) –

    The set of values of the x, y, and z coordinate position

  • **kwargs –
Source code in symdesign/structure/base.py 
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def __init__(self, index: int = None, number: int = None, atom_type: str = None, alt_location: str = ' ',
             residue_type: str = None, chain_id: str = None, residue_number: int = None,
             code_for_insertion: str = ' ', x: float = None, y: float = None, z: float = None,
             occupancy: float = None, b_factor: float = None, element: str = None, charge: str = None,
             coords: list[float] = None, **kwargs):
    """Construct the instance

    Args:
        index: The zero-indexed number to describe this Atom instance's position in a StructureBaseContainer
        number: The integer number describing this Atom instances position in comparison to others instances
        atom_type: The characters describing the classification of atom via membership to a molecule
        alt_location: Whether the observation of the Atom has alternative evidences
        residue_type: The characters describing the molecular unit to which this Atom belongs
        chain_id: The identifier which signifies this Atom instances membership to a larger polymer
        residue_number: The integer of the polymer that this Atom belongs too
        code_for_insertion: Whether the Atom is included in a residue which is inserted according to a common
            numbering scheme
        x: The x axis value of the instances coordinate position, i.e., it's x coordinate
        y: The y axis value of the instances coordinate position, i.e., it's y coordinate
        z: The z axis value of the instances coordinate position, i.e., it's z coordinate
        occupancy: The fraction of the time this Atom is observed in the experiment
        b_factor: The thermal fluctuation for the Atom OR a value for which structural representation should account
        element: The atomic symbol for the Atom
        charge: The numeric value for the electronic charge of the Atom
        coords: The set of values of the x, y, and z coordinate position
        **kwargs:
    """
    # super().__init__(**kwargs)  # Atom
    self.index = index
    # self._atom_indices = [index]
    self.number = number
    self._type = atom_type
    # Comply with special .pdb formatting syntax by padding type with a space if len(atom_type) == 4
    self._type_str = f'{"" if atom_type[3:] else " "}{atom_type:<3s}'
    self.alt_location = alt_location
    self.residue_type = residue_type
    self.chain_id = chain_id
    self.residue_number = residue_number
    self.code_for_insertion = code_for_insertion
    if coords is not None:
        self._coords_ = coords
    elif x is not None and y is not None and z is not None:
        self._coords_ = [x, y, z]
    else:
        self._coords_ = []
    self.occupancy = occupancy
    self.b_factor = b_factor
    self.element = element
    self.charge = charge
    self.sasa = None

type property 

type: str

This can't currently be set

atom_indices property 

atom_indices: list[int]

The index of the Atom in the Atoms/Coords container

coords property writable 

coords: ndarray

The coordinates for the Atom. Array is 1 dimensional in contrast to other .coords properties

center_of_mass property 

center_of_mass: ndarray

The center of mass (the Atom coordinates). Provided for compatibility with StructureBase API

radius property 

radius: float

The width of the Atom

x property writable 

x: float

Access the value for the x coordinate

y property writable 

y: float

Access the value for the y coordinate

z property writable 

z: float

Access the value for the z coordinate

without_coordinates classmethod 

without_coordinates(idx, number, atom_type, alt_location, residue_type, chain_id, residue_number, code_for_insertion, occupancy, b_factor, element, charge)

Initialize Atom record data without coordinates. Performs all type casting

Source code in symdesign/structure/base.py 
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@classmethod
def without_coordinates(cls, idx, number, atom_type, alt_location, residue_type, chain_id, residue_number,
                        code_for_insertion, occupancy, b_factor, element, charge):
    """Initialize Atom record data without coordinates. Performs all type casting"""
    return cls(index=idx, number=int(number), atom_type=atom_type, alt_location=alt_location,
               residue_type=residue_type, chain_id=chain_id, residue_number=int(residue_number),
               code_for_insertion=code_for_insertion, occupancy=float(occupancy), b_factor=float(b_factor),
               element=element, charge=charge, coords=[])  # Use a list for speed

is_dependent 

is_dependent() -> bool

Is this instance a dependent on a parent StructureBase?

Source code in symdesign/structure/base.py 
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def is_dependent(self) -> bool:
    """Is this instance a dependent on a parent StructureBase?"""
    return True

is_parent 

is_parent() -> bool

Is this instance a parent?

Source code in symdesign/structure/base.py 
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def is_parent(self) -> bool:
    """Is this instance a parent?"""
    return False

make_parent 

make_parent()

Remove this instance from its parent, making it a parent in the process

Source code in symdesign/structure/base.py 
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def make_parent(self):
    """Remove this instance from its parent, making it a parent in the process"""
    # super().make_parent()  # When subclassing StructureBase
    # Create a new, Coords instance detached from the parent
    self._coords = Coordinates(self.coords)
    self.index = 0
    self.reset_state()

reset_state 

reset_state()

Remove attributes that are valid for the current state

This is useful for transfer of ownership, or changes in the state that should be overwritten

Source code in symdesign/structure/base.py 
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def reset_state(self):
    """Remove attributes that are valid for the current state

    This is useful for transfer of ownership, or changes in the state that should be overwritten
    """
    for attr in self.state_attributes:
        try:
            self.__delattr__(attr)
        except AttributeError:
            continue

is_backbone_and_cb 

is_backbone_and_cb() -> bool

Is the Atom is a backbone or CB Atom? Includes N, CA, C, O, and CB

Source code in symdesign/structure/base.py 
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def is_backbone_and_cb(self) -> bool:
    """Is the Atom is a backbone or CB Atom? Includes N, CA, C, O, and CB"""
    return self._type in protein_backbone_and_cb_atom_types

is_backbone 

is_backbone() -> bool

Is the Atom is a backbone Atom? These include N, CA, C, and O

Source code in symdesign/structure/base.py 
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def is_backbone(self) -> bool:
    """Is the Atom is a backbone Atom? These include N, CA, C, and O"""
    return self._type in protein_backbone_atom_types

is_cb 

is_cb(gly_ca: bool = True) -> bool

Is the Atom a CB atom? Default returns True if Glycine and Atom is CA

Parameters:

  • gly_ca (bool, default: True ) –

    Whether to include Glycine CA in the boolean evaluation

Source code in symdesign/structure/base.py 
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def is_cb(self, gly_ca: bool = True) -> bool:
    """Is the Atom a CB atom? Default returns True if Glycine and Atom is CA

    Args:
        gly_ca: Whether to include Glycine CA in the boolean evaluation
    """
    if gly_ca:
        return self._type == 'CB' or (self.residue_type == 'GLY' and self._type == 'CA')
    else:
        #                                         When Rosetta assigns, it is this   v, but PDB assigns this v
        return self._type == 'CB' or (self.residue_type == 'GLY' and (self._type == '2HA' or self._type == 'HA3'))

is_ca 

is_ca() -> bool

Is the Atom a CA atom?

Source code in symdesign/structure/base.py 
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def is_ca(self) -> bool:
    """Is the Atom a CA atom?"""
    return self._type == 'CA'

is_heavy 

is_heavy() -> bool

Is the Atom a heavy atom?

Source code in symdesign/structure/base.py 
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def is_heavy(self) -> bool:
    """Is the Atom a heavy atom?"""
    return 'H' not in self._type

get_atom_record 

get_atom_record() -> str

Provide the Atom as an Atom record string

Returns:

  • str –

    The archived .pdb formatted ATOM records for the Structure

Source code in symdesign/structure/base.py 
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def get_atom_record(self) -> str:
    """Provide the Atom as an Atom record string

    Returns:
        The archived .pdb formatted ATOM records for the Structure
    """
    x, y, z = list(self.coords)
    # Add 1 to the self.index since this is 0 indexed
    return f'ATOM  {self.index + 1:5d} {self._type_str}{self.alt_location:1s}{self.residue_type:3s}' \
           f'{self.chain_id:>2s}{self.residue_number:4d}{self.code_for_insertion:1s}   ' \
           f'{x:8.3f}{y:8.3f}{z:8.3f}{self.occupancy:6.2f}{self.b_factor:6.2f}          ' \
           f'{self.element:>2s}{self.charge:2s}'

__str__ 

__str__() -> str

Represent Atom in PDB format

Source code in symdesign/structure/base.py 
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def __str__(self) -> str:
    """Represent Atom in PDB format"""
    # Use self.type_str to comply with the PDB format specifications because of the atom type field
    # ATOM     32  CG2 VAL A 132       9.902  -5.550   0.695  1.00 17.48           C  <-- PDB format
    # Checks if len(atom.type)=4 with slice v. If not insert a space
    return f'ATOM  {"{}"} {self._type_str}{self.alt_location:1s}{"{}"}{"{}"}{"{}"}' \
           f'{self.code_for_insertion:1s}   {"{}"}{self.occupancy:6.2f}{self.b_factor:6.2f}          ' \
           f'{self.element:>2s}{self.charge:2s}'

StructureBaseContainer 

StructureBaseContainer(structs: Sequence[StructureBase] | ndarray = None)

Bases: Generic[_StructType]

Container for a StructureBase instances

Parameters:

  • structs (Sequence[StructureBase] | ndarray, default: None ) –

    The StructureBase instances to store. Should be a homogeneous Sequence

Source code in symdesign/structure/base.py 
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def __init__(self, structs: Sequence[StructureBase] | np.ndarray = None):
    """Construct the instance

    Args:
        structs: The StructureBase instances to store. Should be a homogeneous Sequence
    """
    if structs is None:
        structs = []
    elif not isinstance(structs, (np.ndarray, list)):
        structs = list(structs)
        # raise TypeError(
        #     f"Can't initialize {self.__class__.__name__} with {type(structs).__name__}. Type must be a "
        #     f'numpy.ndarray or list[{StructureBase.__name__}]')

    self.structs = np.array(structs, dtype=np.object_)

reindex abstractmethod property 

reindex

are_dependents 

are_dependents() -> bool

Check if any of the StructureBase instances are dependents of another StructureBase

Source code in symdesign/structure/base.py 
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def are_dependents(self) -> bool:
    """Check if any of the StructureBase instances are dependents of another StructureBase"""
    for struct in self:
        if struct.is_dependent():
            return True
    return False

append 

append(new_structures: list[_StructType] | ndarray)

Append additional StructureBase instances to the StructureBaseContainer

Parameters:

  • new_structures (list[_StructType] | ndarray) –

    The Structure instances to append

Source code in symdesign/structure/base.py 
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def append(self, new_structures: list[_StructType] | np.ndarray):
    """Append additional StructureBase instances to the StructureBaseContainer

    Args:
        new_structures: The Structure instances to append
    """
    self.structs = np.concatenate((self.structs, new_structures))

delete 

delete(indices: Sequence[int])

Delete StructureBase instances from the StructureBaseContainer

Parameters:

  • indices (Sequence[int]) –

    The indices to delete

Source code in symdesign/structure/base.py 
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def delete(self, indices: Sequence[int]):
    """Delete StructureBase instances from the StructureBaseContainer

    Args:
        indices: The indices to delete
    """
    self.structs = np.delete(self.structs, indices)

insert 

insert(at: int, new_structures: list[_StructType] | ndarray)

Insert StructureBase instances into the StructureBaseContainer

Parameters:

  • at (int) –

    The index to perform the insert at

  • new_structures (list[_StructType] | ndarray) –

    The Structure instances to insert

Source code in symdesign/structure/base.py 
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def insert(self, at: int, new_structures: list[_StructType] | np.ndarray):
    """Insert StructureBase instances into the StructureBaseContainer

    Args:
        at: The index to perform the insert at
        new_structures: The Structure instances to insert
    """
    self.structs = np.concatenate((
        self.structs[:at],
        new_structures if isinstance(new_structures, Iterable) else [new_structures],
        self.structs[at:]
    ))

set 

set(new_structures: list[_StructType] | ndarray)

Set the StructureBaseContainer with new StructureBase instances

Parameters:

  • new_structures (list[_StructType] | ndarray) –

    The new instances which should make up the container

Source code in symdesign/structure/base.py 
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def set(self, new_structures: list[_StructType] | np.ndarray):
    """Set the StructureBaseContainer with new StructureBase instances

    Args:
        new_structures: The new instances which should make up the container
    """
    self.structs = np.array(new_structures)
    self.reindex()

reset_state 

reset_state()

Remove any attributes from the Structure instances that are part of the current state

This is useful for transfer of ownership, or changes in the state that need to be overwritten

Source code in symdesign/structure/base.py 
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def reset_state(self):
    """Remove any attributes from the Structure instances that are part of the current state

    This is useful for transfer of ownership, or changes in the state that need to be overwritten
    """
    for struct in self:
        struct.reset_state()

set_attributes 

set_attributes(**kwargs)

Set Structure attributes passed by keyword to their corresponding value

Source code in symdesign/structure/base.py 
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def set_attributes(self, **kwargs):
    """Set Structure attributes passed by keyword to their corresponding value"""
    for struct in self:
        for key, value in kwargs.items():
            setattr(struct, key, value)

Atoms 

Atoms(structs: Sequence[StructureBase] | ndarray = None)

Bases: StructureBaseContainer

Parameters:

  • structs (Sequence[StructureBase] | ndarray, default: None ) –

    The StructureBase instances to store. Should be a homogeneous Sequence

Source code in symdesign/structure/base.py 
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def __init__(self, structs: Sequence[StructureBase] | np.ndarray = None):
    """Construct the instance

    Args:
        structs: The StructureBase instances to store. Should be a homogeneous Sequence
    """
    if structs is None:
        structs = []
    elif not isinstance(structs, (np.ndarray, list)):
        structs = list(structs)
        # raise TypeError(
        #     f"Can't initialize {self.__class__.__name__} with {type(structs).__name__}. Type must be a "
        #     f'numpy.ndarray or list[{StructureBase.__name__}]')

    self.structs = np.array(structs, dtype=np.object_)

reindex 

reindex(start_at: int = 0)

Set each Atom instance index according to incremental Atoms/Coords index

Parameters:

  • start_at (int, default: 0 ) –

    The index to start reindexing at. Must be [0, 'inf']

Source code in symdesign/structure/base.py 
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def reindex(self, start_at: int = 0):
    """Set each Atom instance index according to incremental Atoms/Coords index

    Args:
        start_at: The index to start reindexing at. Must be [0, 'inf']
    """
    if start_at == 0:
        _start_at = start_at
    else:
        _start_at = start_at - 1
        if start_at < 0:
            _start_at += len(self)
    try:
        prior_struct, *other_structs = self.structs[_start_at:]
    except ValueError:  # Not enough values to unpack as the index didn't slice anything
        raise IndexError(
            f'{self.reindex.__name__}: {start_at=} is outside of the {self.__class__.__name__} indices with '
            f'size {len(self)}')
    else:
        if start_at == 0:
            prior_struct.index = 0

        for idx, struct in enumerate(other_structs, prior_struct.index + 1):
            struct.index = idx

ContainsAtoms 

ContainsAtoms(atoms: list[Atom] | Atoms = None, atom_indices: list[int] = None, **kwargs)

Bases: StructureBase, ABC

Parameters:

  • atoms (list[Atom] | Atoms, default: None ) –

    Atom instances to initialize the instance

Source code in symdesign/structure/base.py 
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def __init__(self, atoms: list[Atom] | Atoms = None, atom_indices: list[int] = None, **kwargs):
    """Construct the instance

    Args:
        atoms: Atom instances to initialize the instance
    """
    super().__init__(**kwargs)  # ContainsAtoms
    if self.is_parent():
        if atoms is not None:
            self._assign_atoms(atoms)
        else:  # Create an empty container
            # try:
            #     self._atoms
            # except AttributeError:
            self._atoms = Atoms()
    elif atom_indices is not None:
        try:
            atom_indices[0]
        except (TypeError, IndexError):
            raise ValueError(
                f"The {self.__class__.__name__} wasn't passed 'atom_indices' which are required for initialization")

        if not isinstance(atom_indices, list):
            atom_indices = list(atom_indices)
        self._atom_indices = atom_indices

atoms property 

atoms: list[Atom] | None

Return the Atom instances in the StructureBase

atom_indices property 

atom_indices: list[int]

The Atoms/Coords indices which the StructureBase has access to

number_of_atoms property 

number_of_atoms: int

The number of atoms/coordinates in the StructureBase

backbone_and_cb_indices abstractmethod property 

backbone_and_cb_indices: list[int]

The indices that index the StructureBase backbone and CB Atoms/Coords

backbone_indices abstractmethod property 

backbone_indices: list[int]

The indices that index the StructureBase backbone and CB Atoms/Coords

ca_indices abstractmethod property 

ca_indices: list[int]

The indices that index the StructureBase CA Atoms/Coords

cb_indices abstractmethod property 

cb_indices: list[int]

The indices that index the StructureBase CB Atoms/Coords

heavy_indices abstractmethod property 

heavy_indices: list[int]

The indices that index the StructureBase heavy (non-hydrogen) Atoms/Coords

side_chain_indices abstractmethod property 

side_chain_indices: list[int]

The indices that index the StructureBase side-chain Atoms/Coords

backbone_atoms property 

backbone_atoms: list[Atom]

Returns backbone Atom instances from the StructureBase

backbone_and_cb_atoms property 

backbone_and_cb_atoms: list[Atom]

Returns backbone and CB Atom instances from the StructureBase

ca_atoms property 

ca_atoms: list[Atom]

Returns CA Atom instances from the StructureBase

cb_atoms property 

cb_atoms: list[Atom]

Returns CB Atom instances from the StructureBase

heavy_atoms property 

heavy_atoms: list[Atom]

Returns heavy Atom instances from the StructureBase

side_chain_atoms property 

side_chain_atoms: list[Atom]

Returns side chain Atom instances from the StructureBase

center_of_mass property 

center_of_mass: ndarray

The center of mass for the Atom coordinates

radius property 

radius: float

The furthest point from the center of mass of the StructureBase

radius_of_gyration property 

radius_of_gyration: float

The measurement of the implied radius (Angstroms) affecting how the StructureBase diffuses through solution

Satisfies the equation

Rg = SQRT(SUM|i->N(Ri**2)/N)

Where: - Ri is the radius of the point i from the center of mass point - N is the total number of points

backbone_coords property 

backbone_coords: ndarray

Return a view of the Coords from the StructureBase with backbone atom coordinates

backbone_and_cb_coords property 

backbone_and_cb_coords: ndarray

Return a view of the Coords from the StructureBase with backbone and CB atom coordinates. Includes glycine CA

ca_coords property 

ca_coords: ndarray

Return a view of the Coords from the Structure with CA atom coordinates

cb_coords property 

cb_coords: ndarray

Return a view of the Coords from the Structure with CB atom coordinates

heavy_coords property 

heavy_coords: ndarray

Return a view of the Coords from the StructureBase with heavy atom coordinates

side_chain_coords property 

side_chain_coords: ndarray

Return a view of the Coords from the StructureBase with side chain atom coordinates

start_index property 

start_index: int

The first atomic index of the StructureBase

end_index property 

end_index: int

The last atomic index of the StructureBase

make_parent 

make_parent()

Remove this instance from its parent, making it a parent in the process

Source code in symdesign/structure/base.py 
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def make_parent(self):
    """Remove this instance from its parent, making it a parent in the process"""
    super().make_parent()
    # Populate the Structure with its existing instances removed of any indexing
    self._assign_atoms(self.atoms)
    self.reset_state()

get_base_containers 

get_base_containers() -> dict[str, Any]

Access each of the constituent structure container attributes

Returns:

  • dict[str, Any] –

    The instance structural containers as a dictionary with attribute as key and container as value

Source code in symdesign/structure/base.py 
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def get_base_containers(self) -> dict[str, Any]:
    """Access each of the constituent structure container attributes

    Returns:
        The instance structural containers as a dictionary with attribute as key and container as value
    """
    return dict(coords=self._coords, atoms=self._atoms)

neighboring_atom_indices 

neighboring_atom_indices(distance: float = 8.0, **kwargs) -> list[int]

Returns the Atom instances in the Structure

Parameters:

  • distance (float, default: 8.0 ) –

    The distance to measure neighbors by

Returns:

  • list[int] –

    The sorted atom_indices which are in contact with this instance, however, do not belong to the instance

Source code in symdesign/structure/base.py 
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def neighboring_atom_indices(self, distance: float = 8., **kwargs) -> list[int]:  # np.ndarray:
    """Returns the Atom instances in the Structure

    Args:
        distance: The distance to measure neighbors by

    Returns:
        The sorted atom_indices which are in contact with this instance, however, do not belong to the instance
    """
    parent_coords = self._coords.coords
    atom_indices = self.atom_indices

    # Create a "self.coords" and modify only coordinates in the ContainsAtoms instance
    modified_self_coords = parent_coords.copy()
    # Translate each self coordinate
    modified_self_coords[atom_indices] = parent_coords.max(axis=0) + [1000, 1000, 1000]
    modified_coords_balltree = BallTree(modified_self_coords)

    # Query for neighbors of the self coordinates but excluding the self indices
    coords = parent_coords[atom_indices]
    query = modified_coords_balltree.query_radius(coords, distance)

    return sorted({idx for contacts in query.tolist() for idx in contacts.tolist()})

atom 

atom(atom_number: int) -> Atom | None

Returns the Atom specified by atom number if a matching Atom is found, otherwise None

Source code in symdesign/structure/base.py 
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def atom(self, atom_number: int) -> Atom | None:
    """Returns the Atom specified by atom number if a matching Atom is found, otherwise None"""
    for atom in self.atoms:
        if atom.number == atom_number:
            return atom
    return None

renumber_atoms 

renumber_atoms(at: int = 1)

Renumber all Atom objects sequentially starting with 1

Parameters:

  • at (int, default: 1 ) –

    The number to start renumbering at

Source code in symdesign/structure/base.py 
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def renumber_atoms(self, at: int = 1):
    """Renumber all Atom objects sequentially starting with 1

    Args:
        at: The number to start renumbering at
    """
    for idx, atom in enumerate(self.atoms, at):
        atom.number = idx

reset_indices 

reset_indices()

Reset the indices attached to the instance

Source code in symdesign/structure/base.py 
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def reset_indices(self):
    """Reset the indices attached to the instance"""
    for attr in self._indices_attributes:
        try:
            delattr(self, attr)
        except AttributeError:
            continue

format_header 

format_header(**kwargs) -> str

Returns the base .pdb formatted header

Returns:

  • str –

    The .pdb file header string

Source code in symdesign/structure/base.py 
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def format_header(self, **kwargs) -> str:
    """Returns the base .pdb formatted header

    Returns:
        The .pdb file header string
    """
    # XXXX should be substituted for the PDB code. Ex:
    # f'HEADER    VIRAL PROTEIN                           28-MAY-21   7OP2              \n'
    # f'HEADER    VIRAL PROTEIN/DE NOVO PROTEIN           11-MAY-12   4ATZ              \n'
    return \
        f'HEADER    {self.name[:40]:<40s}{utils.short_start_date.upper():<12s}{"XXXX":<18s}\n' \
        'EXPDTA    THEORETICAL MODEL                                                     \n' \
        'REMARK 220                                                                      \n' \
        'REMARK 220 EXPERIMENTAL DETAILS                                                 \n' \
        'REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING              \n' \
        f'REMARK 220  DATE OF DATA COLLECTION        : {utils.long_start_date:<35s}\n' \
        f'REMARK 220 REMARK: MODEL GENERATED BY {putils.program_name.upper():<50s}\n' \
        f'REMARK 220         VERSION {putils.commit_short:<61s}\n'

get_atom_record abstractmethod 

get_atom_record(**kwargs) -> str

Provide the Structure Atom instances as a .pdb file string

Other Parameters:

  • chain_id –

    str = None - The chain ID to use

  • atom_offset –

    int = 0 - How much to offset the atom number by. Default returns one-indexed

Returns:

  • str –

    The archived .pdb formatted ATOM records for the Structure

Source code in symdesign/structure/base.py 
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@abc.abstractmethod
def get_atom_record(self, **kwargs) -> str:
    """Provide the Structure Atom instances as a .pdb file string

    Keyword Args:
        chain_id: str = None - The chain ID to use
        atom_offset: int = 0 - How much to offset the atom number by. Default returns one-indexed

    Returns:
        The archived .pdb formatted ATOM records for the Structure
    """

write 

write(out_path: bytes | str = os.getcwd(), file_handle: IO = None, header: str = None, **kwargs) -> AnyStr | None

Write Atom instances to a file specified by out_path or with a passed file_handle

If a file_handle is passed, no header information will be written. Arguments are mutually exclusive

Parameters:

  • out_path (bytes | str, default: getcwd() ) –

    The location where the Structure object should be written to disk

  • file_handle (IO, default: None ) –

    Used to write Structure details to an open FileObject

  • header (str, default: None ) –

    A string that is desired at the top of the file

Keyword Args chain_id: str = None - The chain ID to use atom_offset: int = 0 - How much to offset the atom index by. Default uses one-indexed atom numbers

Returns:

  • AnyStr | None –

    The name of the written file if out_path is used

Source code in symdesign/structure/base.py 
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def write(
    self, out_path: bytes | str = os.getcwd(), file_handle: IO = None, header: str = None, **kwargs
) -> AnyStr | None:
    """Write Atom instances to a file specified by out_path or with a passed file_handle

    If a file_handle is passed, no header information will be written. Arguments are mutually exclusive

    Args:
        out_path: The location where the Structure object should be written to disk
        file_handle: Used to write Structure details to an open FileObject
        header: A string that is desired at the top of the file

    Keyword Args
        chain_id: str = None - The chain ID to use
        atom_offset: int = 0 - How much to offset the atom index by. Default uses one-indexed atom numbers

    Returns:
        The name of the written file if out_path is used
    """
    if file_handle:
        file_handle.write(f'{self.get_atom_record(**kwargs)}\n')
        return None
    else:  # out_path always has default argument current working directory
        _header = self.format_header()
        if header is not None:
            if not isinstance(header, str):
                header = str(header)
            _header += (header if header[-2:] == '\n' else f'{header}\n')

        with open(out_path, 'w') as outfile:
            outfile.write(_header)
            outfile.write(f'{self.get_atom_record(**kwargs)}\n')
        return out_path

get_atoms 

get_atoms(numbers: Container = None, **kwargs) -> list[Atom]

Retrieves Atom instances. Returns all by default unless a list of numbers is specified

Parameters:

  • numbers (Container, default: None ) –

    The Atom numbers of interest

Returns:

  • list[Atom] –

    The requested Atom objects

Source code in symdesign/structure/base.py 
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def get_atoms(self, numbers: Container = None, **kwargs) -> list[Atom]:
    """Retrieves Atom instances. Returns all by default unless a list of numbers is specified

    Args:
        numbers: The Atom numbers of interest

    Returns:
        The requested Atom objects
    """
    if numbers is not None:
        if isinstance(numbers, Container):
            return [atom for atom in self.atoms if atom.number in numbers]
        else:
            self.log.error(f'The passed numbers type "{type(numbers).__name__}" must be a Container. Returning'
                           f' all Atom instances instead')
    return self.atoms

set_atoms_attributes 

set_atoms_attributes(**kwargs)

Set attributes specified by key, value pairs for Atoms in the Structure

Other Parameters:

  • numbers –

    Container[int] = None - The Atom numbers of interest

  • pdb –

    bool = False - Whether to search for numbers as they were parsed (if True)

Source code in symdesign/structure/base.py 
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def set_atoms_attributes(self, **kwargs):
    """Set attributes specified by key, value pairs for Atoms in the Structure

    Keyword Args:
        numbers: Container[int] = None - The Atom numbers of interest
        pdb: bool = False - Whether to search for numbers as they were parsed (if True)
    """
    for atom in self.get_atoms(**kwargs):
        for kwarg, value in kwargs.items():
            setattr(atom, kwarg, value)

Residue 

Residue(**kwargs)

Bases: ContainsAtoms, ResidueFragment

Parameters:

  • **kwargs –
Source code in symdesign/structure/base.py 
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def __init__(self, **kwargs):
    """Construct the instance

    Args:
        **kwargs:
    """
    super().__init__(**kwargs)  # Residue
    if self.is_parent():
        # Setting up a parent (independent) Residue
        self._ensure_valid_residue()
        self.start_index = 0

    self.delegate_atoms()

index property 

index

The Residue index in a Residues container

range property 

range: list[int]

The range of indices corresponding to the Residue atoms

type1 property 

type1: str

Access the one character representation of the amino acid type

backbone_indices property writable 

backbone_indices: list[int]

The indices that index the Residue backbone Atoms/Coords

backbone_and_cb_indices property writable 

backbone_and_cb_indices: list[int]

The indices that index the Residue backbone and CB Atoms/Coords

ca_indices property 

ca_indices: list[int]

Return the index of the CA Atom as a list in the Residue Atoms/Coords

cb_indices property 

cb_indices: list[int]

Return the index of the CB Atom as a list in the Residue Atoms/Coords. Will return CA index if Glycine

side_chain_indices property writable 

side_chain_indices: list[int]

The indices that index the Residue side chain Atoms/Coords

heavy_indices property writable 

heavy_indices: list[int]

The indices that index the Residue heavy (non-hydrogen) Atoms/Coords

n property 

n: Atom | None

Return the amide N Atom object

n_coords property 

n_coords: ndarray | None

Return the amide N Atom coordinate

n_atom_index property 

n_atom_index: int | None

Return the index of the amide N Atom in the Structure Atoms/Coords

n_index property 

n_index: int | None

Return the index of the amide N Atom in the Residue Atoms/Coords

h property 

h: Atom | None

Return the amide H Atom object

h_coords property 

h_coords: ndarray | None

Return the amide H Atom coordinate

h_atom_index property 

h_atom_index: int | None

Return the index of the amide H Atom in the Structure Atoms/Coords

h_index property 

h_index: int | None

Return the index of the amide H Atom in the Residue Atoms/Coords

ca property 

ca: Atom | None

Return the CA Atom object

ca_coords property 

ca_coords: ndarray | None

Return the CA Atom coordinate

ca_atom_index property 

ca_atom_index: int | None

Return the index of the CA Atom in the Structure Atoms/Coords

ca_index property 

ca_index: int | None

Return the index of the CA Atom in the Residue Atoms/Coords

cb property 

cb: Atom | None

Return the CB Atom object

cb_coords property 

cb_coords: ndarray | None

Return the CB Atom coordinate

cb_atom_index property 

cb_atom_index: int | None

Return the index of the CB Atom in the Structure Atoms/Coords

cb_index property 

cb_index: int | None

Return the index of the CB Atom in the Residue Atoms/Coords

c property 

c: Atom | None

Return the carbonyl C Atom object

c_coords property 

c_coords: ndarray | None

Return the carbonyl C Atom coordinate

c_atom_index property 

c_atom_index: int | None

Return the index of the carbonyl C Atom in the Structure Atoms/Coords

c_index property 

c_index: int | None

Return the index of the carbonyl C Atom in the Residue Atoms/Coords

o property 

o: Atom | None

Return the carbonyl O Atom object

o_coords property 

o_coords: ndarray | None

Return the carbonyl O Atom coords

o_atom_index property 

o_atom_index: int | None

Return the index of the carbonyl C Atom in the Structure Atoms/Coords

o_index property 

o_index: int | None

Return the index of the carbonyl O Atom in the Residue Atoms/Coords

prev_residue property 

prev_residue: Residue | None

The previous Residue in the Structure if this Residue is part of a polymer

next_residue property 

next_residue: Residue | None

The next Residue in the Structure if this Residue is part of a polymer

local_density property writable 

local_density: float

Describes how many heavy Atoms are within a distance (default = 12 Angstroms) of Residue heavy Atoms

secondary_structure property writable 

secondary_structure: str

Return the secondary structure designation as defined by a secondary structure calculation

sasa property writable 

sasa: float

Return the solvent accessible surface area as calculated by a solvent accessible surface area calculator

sasa_apolar property writable 

sasa_apolar: float

Return apolar solvent accessible surface area as calculated by a solvent accessible surface area calculator

sasa_polar property writable 

sasa_polar: float

Return polar solvent accessible surface area as calculated by a solvent accessible surface area calculator

relative_sasa property 

relative_sasa: float

The solvent accessible surface area relative to the standard surface accessibility of the Residue type

spatial_aggregation_propensity property writable 

spatial_aggregation_propensity: float

The Residue contact order, which describes how far away each Residue makes contacts in the polymer chain

contact_order property writable 

contact_order: float

The Residue contact order, which describes how far away each Residue makes contacts in the polymer chain

start_index 

start_index(index: int)

Set Residue atom_indices starting with atom_indices[0] as start_index. Creates remainder incrementally and updates individual Atom instance .index accordingly

Source code in symdesign/structure/base.py 
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@ContainsAtoms.start_index.setter
def start_index(self, index: int):
    """Set Residue atom_indices starting with atom_indices[0] as start_index. Creates remainder incrementally and
    updates individual Atom instance .index accordingly
    """
    self._atom_indices = list(range(index, index + self.number_of_atoms))
    for atom, index in zip(self._atoms[self._atom_indices], self._atom_indices):
        atom.index = index
    # Clear all the indices attributes for this Residue
    self.reset_indices()

delegate_atoms 

delegate_atoms()

Set the Residue atoms from a parent StructureBase

Source code in symdesign/structure/base.py 
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def delegate_atoms(self):
    """Set the Residue atoms from a parent StructureBase"""
    side_chain_indices, heavy_indices = [], []
    # try:
    #     for idx, atom in enumerate(self.atoms):
    #         match atom.type:  # Todo python 3.10
    #             case 'N':
    #                 self._n_index = idx
    #                 if self.number is None:
    #                     self.chain_id = atom.chain_id
    #                     self.number = atom.residue_number
    #                     self.type = atom.residue_type
    #                else:
    #                    raise stutils.ConstructionError(
    #                        f"Couldn't create a {self.__class__.__name__} with multiple 'N' Atom instances"
    #                    )
    #             case 'CA':
    #                 self._ca_index = idx
    #             case 'CB':
    #                 self._cb_index = idx
    #             case 'C':
    #                 self._c_index = idx
    #             case 'O':
    #                 self._o_index = idx
    #             case 'H':
    #                 self._h_index = idx
    #             case _:
    #                 side_chain_indices.append(idx)
    #                 if 'H' not in atom.type:
    #                     heavy_indices.append(idx)
    # except SyntaxError:  # python version not 3.10
    for idx, atom in enumerate(self.atoms):
        atom_type = atom.type
        if atom_type == 'N':
            self._n_index = idx
            if self.number is None:
                self.chain_id = atom.chain_id
                self.number = atom.residue_number
                self.type = atom.residue_type
            else:
                raise stutils.ConstructionError(
                    f"Couldn't create a {self.__class__.__name__} with multiple 'N' Atom instances"
                )
        elif atom_type == 'CA':
            self._ca_index = idx
        elif atom_type == 'CB':
            self._cb_index = idx
        elif atom_type == 'C':
            self._c_index = idx
        elif atom_type == 'O':
            self._o_index = idx
        elif atom_type == 'H':  # 1H or H1
            self._h_index = idx
        # elif atom_type == 'OXT':
        #     self._oxt_index = idx
        # elif atom_type == 'H2':
        #     self._h2_index = idx
        # elif atom_type == 'H3':
        #     self._h3_index = idx
        else:
            side_chain_indices.append(idx)
            if 'H' not in atom_type:
                heavy_indices.append(idx)

    # Construction ensures proper order for _bb_indices even if out of order
    # Important this order is correct for ProteinMPNN
    self.backbone_indices = [getattr(self, f'_{index}_index', None) for index in ['n', 'ca', 'c', 'o']]
    cb_index = getattr(self, '_cb_index', None)
    if cb_index:
        cb_indices = [cb_index]
    else:
        if self.type == 'GLY':  # Set _cb_index, but don't include in backbone_and_cb_indices
            self._cb_index = getattr(self, '_ca_index')
        cb_indices = []

    # By using private backbone_indices variable v, None is removed
    self.backbone_and_cb_indices = self._bb_indices + cb_indices
    self.heavy_indices = self._bb_and_cb_indices + heavy_indices
    self.side_chain_indices = side_chain_indices

contains_hydrogen 

contains_hydrogen() -> bool

Returns whether the Residue contains hydrogen atoms

Source code in symdesign/structure/base.py 
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def contains_hydrogen(self) -> bool:  # in Structure too
    """Returns whether the Residue contains hydrogen atoms"""
    return self.heavy_indices != self._atom_indices

is_n_termini 

is_n_termini() -> bool

Returns whether the Residue is the n-termini of the parent Structure

Source code in symdesign/structure/base.py 
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def is_n_termini(self) -> bool:
    """Returns whether the Residue is the n-termini of the parent Structure"""
    return self.prev_residue is None

is_c_termini 

is_c_termini() -> bool

Returns whether the Residue is the c-termini of the parent Structure

Source code in symdesign/structure/base.py 
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def is_c_termini(self) -> bool:
    """Returns whether the Residue is the c-termini of the parent Structure"""
    return self.next_residue is None

get_upstream 

get_upstream(number: int = None) -> list[Residue]

Get the Residues upstream of (n-terminal to) the current Residue

Parameters:

  • number (int, default: None ) –

    The number of residues to retrieve. If not provided gets all

Returns:

  • list[Residue] –

    The Residue instances in n- to c-terminal order

Source code in symdesign/structure/base.py 
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def get_upstream(self, number: int = None) -> list[Residue]:
    """Get the Residues upstream of (n-terminal to) the current Residue

    Args:
        number: The number of residues to retrieve. If not provided gets all

    Returns:
        The Residue instances in n- to c-terminal order
    """
    if number is None:
        number = sys.maxsize
    elif number == 0:
        raise ValueError("Can't get 0 upstream residues. 1 or more must be specified")

    last_prev_residue = self.prev_residue
    prev_residues = [last_prev_residue]
    idx = 0
    try:
        for idx in range(abs(number) - 1):
            prev_residue = last_prev_residue.prev_residue
            prev_residues.append(prev_residue)
            last_prev_residue = prev_residue
    except AttributeError:  # Hit a termini, where prev_residue is None
        # logger.debug(f'Stopped at {idx=} with {repr(prev_residues)}. Popping the last')
        prev_residues.pop(idx)
    else:  # For the edge case where the last added residue is a termini, strip from results
        if last_prev_residue is None:
            prev_residues.pop()

    return prev_residues[::-1]

get_downstream 

get_downstream(number: int = None) -> list[Residue]

Get the Residues downstream of (c-terminal to) the current Residue

Parameters:

  • number (int, default: None ) –

    The number of residues to retrieve. If not provided gets all

Returns:

  • list[Residue] –

    The Residue instances in n- to c-terminal order

Source code in symdesign/structure/base.py 
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def get_downstream(self, number: int = None) -> list[Residue]:
    """Get the Residues downstream of (c-terminal to) the current Residue

    Args:
        number: The number of residues to retrieve. If not provided gets all

    Returns:
        The Residue instances in n- to c-terminal order
    """
    if number is None:
        number = sys.maxsize
    elif number == 0:
        raise ValueError("Can't get 0 downstream residues. 1 or more must be specified")

    last_next_residue = self.next_residue
    next_residues = [last_next_residue]
    idx = 0
    try:
        for idx in range(abs(number) - 1):
            next_residue = last_next_residue.next_residue
            next_residues.append(next_residue)
            last_next_residue = next_residue
    except AttributeError:  # Hit a termini, where next_residue is None
        # logger.debug(f'Stopped at {idx=} with {repr(next_residues)}. Popping the last')
        next_residues.pop(idx)
    else:  # For the edge case where the last added residue is a termini, strip from results
        if last_next_residue is None:
            next_residues.pop()

    return next_residues

get_neighbors 

get_neighbors(distance: float = 8.0, **kwargs) -> list[Residue]

If this Residue instance is part of a polymer, find neighboring Residue instances defined by a distance

Parameters:

  • distance (float, default: 8.0 ) –

    The distance to measure neighbors by

Returns:

  • list[Residue] –

    The Residue instances that are within the distance to this Residue

Source code in symdesign/structure/base.py 
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def get_neighbors(self, distance: float = 8., **kwargs) -> list[Residue]:
    """If this Residue instance is part of a polymer, find neighboring Residue instances defined by a distance

    Args:
        distance: The distance to measure neighbors by

    Returns:
        The Residue instances that are within the distance to this Residue
    """
    try:
        return self.parent.get_residues_by_atom_indices(self.neighboring_atom_indices(distance=distance, **kwargs))
    except AttributeError:  # This Residue is the parent
        return [self]

mutation_possibilities_from_directive 

mutation_possibilities_from_directive(directive: directives = None, background: set[str] = None, special: bool = False, **kwargs) -> set[protein_letters3_alph1_literal] | set

Select mutational possibilities for each Residue based on the Residue and a directive

Parameters:

  • directive (directives, default: None ) –

    Where the choice is one of 'special', 'same', 'different', 'charged', 'polar', 'apolar', 'hydrophobic', 'aromatic', 'hbonding', 'branched'

  • background (set[str], default: None ) –

    The background amino acids to compare possibilities against

  • special (bool, default: False ) –

    Whether to include special residues

Returns:

  • set[protein_letters3_alph1_literal] | set –

    The possible amino acid types available given the mutational directive

Source code in symdesign/structure/base.py 
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def mutation_possibilities_from_directive(
    self, directive: directives = None, background: set[str] = None, special: bool = False, **kwargs
) -> set[protein_letters3_alph1_literal] | set:
    """Select mutational possibilities for each Residue based on the Residue and a directive

    Args:
        directive: Where the choice is one of 'special', 'same', 'different', 'charged', 'polar', 'apolar',
            'hydrophobic', 'aromatic', 'hbonding', 'branched'
        background: The background amino acids to compare possibilities against
        special: Whether to include special residues

    Returns:
        The possible amino acid types available given the mutational directive
    """
    if not directive or directive not in mutation_directives:
        self.log.debug(f'{self.mutation_possibilities_from_directive.__name__}: The mutation directive {directive} '
                       f'is not a valid directive yet. Possible directives are: {", ".join(mutation_directives)}')
        return set()
        # raise TypeError('%s: The mutation directive %s is not a valid directive yet. Possible directives are: %s'
        #                 % (self.mutation_possibilities_from_directive.__name__, directive,
        #                    ', '.join(mutation_directives)))

    current_properties = residue_properties[self.type]
    if directive == 'same':
        properties = current_properties
    elif directive == 'different':  # hmm not right -> .difference({hbonding, branched}) <- for ex. polar if apolar
        properties = set(aa_by_property.keys()).difference(current_properties)
    else:
        properties = [directive]
    available_aas = set(aa for prop in properties for aa in aa_by_property[prop])

    if directive != 'special' and not special:
        available_aas = available_aas.difference(aa_by_property['special'])
    if background:
        available_aas = background.intersection(available_aas)

    return available_aas

distance 

distance(other: Residue, dtype: str = 'ca') -> float

Return the distance from this Residue to another specified by atom type "dtype"

Parameters:

  • other (Residue) –

    The other Residue to measure against

  • dtype (str, default: 'ca' ) –

    The Atom type to perform the measurement with

Returns:

  • float –

    The Euclidean distance between the specified Atom type

Source code in symdesign/structure/base.py 
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def distance(self, other: Residue, dtype: str = 'ca') -> float:
    """Return the distance from this Residue to another specified by atom type "dtype"

    Args:
        other: The other Residue to measure against
        dtype: The Atom type to perform the measurement with

    Returns:
        The Euclidean distance between the specified Atom type
    """
    return np.linalg.norm(getattr(self, f'.{dtype}_coords') - getattr(other, f'.{dtype}_coords'))

get_atom_record 

get_atom_record(chain_id: str = None, atom_offset: int = 0, **kwargs) -> str

Provide the Structure Atoms as a PDB file string

Parameters:

  • chain_id (str, default: None ) –

    The chain ID to use

  • atom_offset (int, default: 0 ) –

    How much to offset the atom number by. Default returns one-indexed

Returns:

  • str –

    The archived .pdb formatted ATOM records for the Structure

Source code in symdesign/structure/base.py 
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def get_atom_record(self, chain_id: str = None, atom_offset: int = 0, **kwargs) -> str:
    """Provide the Structure Atoms as a PDB file string

    Args:
        chain_id: The chain ID to use
        atom_offset: How much to offset the atom number by. Default returns one-indexed

    Returns:
        The archived .pdb formatted ATOM records for the Structure
    """
    return f'{self.__str__(chain_id=chain_id, atom_offset=atom_offset, **kwargs)}\n'

__str__ 

__str__(chain_id: str = None, atom_offset: int = 0, **kwargs) -> str

Format the Residue into the contained Atoms. The Atom number is truncated at 5 digits for PDB compliant formatting

Parameters:

  • chain_id (str, default: None ) –

    The chain ID to use

  • atom_offset (int, default: 0 ) –

    How much to offset the atom number by. Default returns one-indexed

Returns:

  • str –

    The archived .pdb formatted ATOM records for the Residue

Source code in symdesign/structure/base.py 
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def __str__(self, chain_id: str = None, atom_offset: int = 0, **kwargs) -> str:
    #         type=None, number=None
    """Format the Residue into the contained Atoms. The Atom number is truncated at 5 digits for PDB compliant
    formatting

    Args:
        chain_id: The chain ID to use
        atom_offset: How much to offset the atom number by. Default returns one-indexed

    Returns:
        The archived .pdb formatted ATOM records for the Residue
    """
    #     pdb: Whether the Residue representation should use the number at file parsing
    # format the string returned from each Atom, such as
    #  'ATOM  %s  CG2 %s %s%s    %s  1.00 17.48           C  0'
    #       AtomIdx  TypeChNumberCoords
    # To
    #  'ATOM     32  CG2 VAL A 132       9.902  -5.550   0.695  1.00 17.48           C  0'
    # self.type, self.alt_location, self.code_for_insertion, self.occupancy, self.b_factor,
    #                     self.element, self.charge)
    # res_str = self.residue_string(**kwargs)
    res_str = format(self.type, '3s'), format(chain_id or self.chain_id, '>2s'), format(self.number, '4d')
    # Add 1 to make index one-indexed
    offset = 1 + atom_offset
    # Limit atom_index with atom_index_slice to keep ATOM record correct length v
    return '\n'.join(atom.__str__().format(format(atom_idx + offset, '5d')[atom_index_slice],
                                           *res_str, '{:8.3f}{:8.3f}{:8.3f}'.format(*coord))
                     for atom, atom_idx, coord in zip(self.atoms, self._atom_indices, self.coords.tolist()))

Residues 

Residues(structs: Sequence[StructureBase] | ndarray = None)

Bases: StructureBaseContainer

Parameters:

  • structs (Sequence[StructureBase] | ndarray, default: None ) –

    The StructureBase instances to store. Should be a homogeneous Sequence

Source code in symdesign/structure/base.py 
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def __init__(self, structs: Sequence[StructureBase] | np.ndarray = None):
    """Construct the instance

    Args:
        structs: The StructureBase instances to store. Should be a homogeneous Sequence
    """
    if structs is None:
        structs = []
    elif not isinstance(structs, (np.ndarray, list)):
        structs = list(structs)
        # raise TypeError(
        #     f"Can't initialize {self.__class__.__name__} with {type(structs).__name__}. Type must be a "
        #     f'numpy.ndarray or list[{StructureBase.__name__}]')

    self.structs = np.array(structs, dtype=np.object_)

reindex 

reindex(start_at: int = 0)

Index the Residue instances and their corresponding Atom/Coords indices according to their position

Parameters:

  • start_at (int, default: 0 ) –

    The index to start reindexing at. Must be [0, 'inf']

Source code in symdesign/structure/base.py 
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def reindex(self, start_at: int = 0):
    """Index the Residue instances and their corresponding Atom/Coords indices according to their position

    Args:
        start_at: The index to start reindexing at. Must be [0, 'inf']
    """
    self.set_index(start_at=start_at)
    self.reindex_atoms(start_at=start_at)

set_index 

set_index(start_at: int = 0)

Index the Residue instances according to their position in the Residues container

Parameters:

  • start_at (int, default: 0 ) –

    The Residue index to start reindexing at

Source code in symdesign/structure/base.py 
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def set_index(self, start_at: int = 0):
    """Index the Residue instances according to their position in the Residues container

    Args:
        start_at: The Residue index to start reindexing at
    """
    for idx, struct in enumerate(self.structs[start_at:].tolist(), start_at):
        struct._index = idx

reindex_atoms 

reindex_atoms(start_at: int = 0)

Index the Residue instances Atoms/Coords indices according to incremental Atoms/Coords index. Responsible for updating member Atom.index attributes as well

Parameters:

  • start_at (int, default: 0 ) –

    The index to start reindexing at. Must be [0, 'inf']

Source code in symdesign/structure/base.py 
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def reindex_atoms(self, start_at: int = 0):
    """Index the Residue instances Atoms/Coords indices according to incremental Atoms/Coords index. Responsible
    for updating member Atom.index attributes as well

    Args:
        start_at: The index to start reindexing at. Must be [0, 'inf']
    """
    if start_at == 0:
        _start_at = start_at
    else:
        _start_at = start_at - 1
        if start_at < 0:
            _start_at += len(self)

    struct: Residue
    prior_struct: Residue
    try:
        # prior_struct, *other_structs = self.structs[start_at - 1:]
        prior_struct, *other_structs = self[_start_at:]
    except ValueError:  # Not enough values to unpack as the index didn't slice anything
        raise IndexError(
            f'{self.reindex_atoms.__name__}: {start_at=} is outside of the allowed {self.__class__.__name__} '
            f'indices with size {len(self)}')
    else:
        if start_at == 0:
            prior_struct.start_index = start_at

        for struct in other_structs:
            struct.start_index = prior_struct.end_index + 1
            prior_struct = struct

StructureIndexMixin

Bases: ABC

is_parent abstractmethod 

is_parent() -> bool
Source code in symdesign/structure/base.py 
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@abc.abstractmethod
def is_parent(self) -> bool:
    """"""

ContainsResidues 

ContainsResidues(structure: ContainsResidues = None, residues: list[Residue] | Residues = None, residue_indices: list[int] = None, pose_format: bool = False, fragment_db: FragmentDatabase = None, **kwargs)

Bases: ContainsAtoms, StructureIndexMixin

Structure object handles Atom/Residue/Coords manipulation of all Structure containers. Must pass parent and residue_indices, atoms and coords, or residues to initialize

Polymer/Chain designation. This designation essentially means it contains Residue instances in a Residues object

Parameters:

  • structure (ContainsResidues, default: None ) –

    Create the instance based on an existing Structure instance

  • residues (list[Residue] | Residues, default: None ) –

    The Residue instances which should constitute a new Structure instance

  • residue_indices (list[int], default: None ) –

    The indices which specify the particular Residue instances to make this Structure instance. Used with a parent to specify a subdivision of a larger Structure

  • pose_format (bool, default: False ) –

    Whether to initialize with continuous Residue numbering from 1 to N

Other Parameters:

  • atoms –

    list[Atom] | Atoms = None - The Atom instances which should constitute a new Structure instance

  • parent –

    StructureBase = None - If another Structure object created this Structure instance, pass the 'parent' instance. Will take ownership over Structure containers (coords, atoms, residues) for dependent Structures

  • log –

    Log | Logger | bool = True - The Log or Logger instance, or the name for the logger to handle parent Structure logging. None or False prevents logging while any True assignment enables it

  • coords –

    Coords | np.ndarray | list[list[float]] = None - When setting up a parent Structure instance, the coordinates of that Structure

  • name –

    str = None - The identifier for the Structure instance

Source code in symdesign/structure/base.py 
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def __init__(self, structure: ContainsResidues = None,
             residues: list[Residue] | Residues = None, residue_indices: list[int] = None,
             pose_format: bool = False, fragment_db: fragment.db.FragmentDatabase = None, **kwargs):
    """Construct the instance

    Args:
        structure: Create the instance based on an existing Structure instance
        residues: The Residue instances which should constitute a new Structure instance
        residue_indices: The indices which specify the particular Residue instances to make this Structure instance.
            Used with a parent to specify a subdivision of a larger Structure
        pose_format: Whether to initialize with continuous Residue numbering from 1 to N

    Keyword Args:
        atoms: list[Atom] | Atoms = None - The Atom instances which should constitute a new Structure instance
        parent: StructureBase = None - If another Structure object created this Structure instance, pass the
            'parent' instance. Will take ownership over Structure containers (coords, atoms, residues) for
            dependent Structures
        log: Log | Logger | bool = True - The Log or Logger instance, or the name for the logger to handle parent
            Structure logging. None or False prevents logging while any True assignment enables it
        coords: Coords | np.ndarray | list[list[float]] = None - When setting up a parent Structure instance, the
            coordinates of that Structure
        name: str = None - The identifier for the Structure instance
    """
    if structure:
        if isinstance(structure, ContainsResidues):
            model_kwargs = structure.get_base_containers()
            for key, value in model_kwargs.items():
                if key in kwargs:
                    logger.warning(f"Passing an argument for '{key}' while providing the 'model' argument "
                                   f"overwrites the '{key}' argument from the 'model'")
            new_model_kwargs = {**model_kwargs, **kwargs}
            super().__init__(**new_model_kwargs)
        else:
            raise NotImplementedError(
                f"Setting {self.__class__.__name__} with model={type(structure).__name__} isn't supported")
    else:
        super().__init__(**kwargs)  # ContainsResidues

    # self._coords_indexed_residues_ = None
    # self._residue_indices = None
    # self.secondary_structure = None
    # self.nucleotides_present = False
    self._fragment_db = fragment_db
    self.sasa = None
    self.ss_sequence_indices = []
    self.ss_type_sequence = []

    if self.is_dependent():
        try:
            residue_indices[0]
        except TypeError:
            if isinstance(self, Structures):  # Structures handles this itself
                return
            raise stutils.ConstructionError(
                f"The {self.__class__.__name__} wasn't passed 'residue_indices' which are required for "
                f"initialization"
            )

        if not isinstance(residue_indices, list):
            residue_indices = list(residue_indices)
        # Must set this before setting _atom_indices
        self._residue_indices = residue_indices
        # Get the atom_indices from the provided residues
        self._atom_indices = [idx for residue in self.residues for idx in residue.atom_indices]
    # Setting up a parent Structure
    elif residues:  # Assume the passed residues aren't bound to an existing Structure
        self._assign_residues(residues)
    elif self.atoms:
        # Assume ContainsAtoms initialized .atoms. Make Residue instances, Residues
        self._create_residues()
    else:  # Set up an empty Structure or let subclass handle population
        return

    if pose_format:
        self.pose_numbering()

ss_sequence_indices instance-attribute 

ss_sequence_indices: list[int] = []

Index which indicates the Residue membership to the secondary structure type element sequence

ss_type_sequence instance-attribute 

ss_type_sequence: list[str] = []

The ordered secondary structure type sequence which contains one character/secondary structure element

fragment_db property writable 

fragment_db: FragmentDatabase

The FragmentDatabase used to create Fragment instances

sequence property writable 

sequence: str

Holds the Structure amino acid sequence

residue_indices property 

residue_indices: list[int] | None

Return the residue indices which belong to the Structure

residues property 

residues: list[Residue] | None

Return the Residue instances in the Structure

alphafold_atom_mask property 

alphafold_atom_mask: ndarray

Return an Alphafold mask describing which Atom positions have Coord data

alphafold_coords property 

alphafold_coords: ndarray

Return a view of the Coords from the StructureBase in Alphafold coordinate format

coords_indexed_residues property 

coords_indexed_residues: list[Residue]

Returns the Residue associated with each Coord in the Structure

Returns:

  • list[Residue] –

    Each Residue which owns the corresponding index in the .atoms/.coords attribute

backbone_coords_indexed_residues property 

backbone_coords_indexed_residues: list[Residue]

Returns the Residue associated with each backbone Atom/Coord in the Structure

Returns:

  • list[Residue] –

    Each Residue which owns the corresponding index in the .atoms/.coords attribute

backbone_and_cb_coords_indexed_residues property 

backbone_and_cb_coords_indexed_residues: list[Residue]

Returns the Residue associated with each backbone and CB Atom/Coord in the Structure

Returns:

  • list[Residue] –

    Each Residue which owns the corresponding index in the .atoms/.coords attribute

heavy_coords_indexed_residues property 

heavy_coords_indexed_residues: list[Residue]

Returns the Residue associated with each heavy Atom/Coord in the Structure

Returns:

  • list[Residue] –

    Each Residue which owns the corresponding index in the .atoms/.coords attribute

side_chain_coords_indexed_residues property 

side_chain_coords_indexed_residues: list[Residue]

Returns the Residue associated with each side chain Atom/Coord in the Structure

Returns:

  • list[Residue] –

    Each Residue which owns the corresponding index in the .atoms/.coords attribute

number_of_residues property 

number_of_residues: int

Access the number of Residues in the Structure

backbone_indices property 

backbone_indices: list[int]

The indices that index the Structure backbone Atoms/Coords

backbone_and_cb_indices property 

backbone_and_cb_indices: list[int]

The indices that index the Structure backbone and CB Atoms. Inherently gets CA of Residue instances missing CB

cb_indices property 

cb_indices: list[int]

The indices that index the Structure CB Atoms. Inherently gets CA of Residue instances missing CB

ca_indices property 

ca_indices: list[int]

The indices that index the Structure CA Atoms/Coords

heavy_indices property 

heavy_indices: list[int]

The indices that index the Structure heavy Atoms/Coords

side_chain_indices property 

side_chain_indices: list[int]

The indices that index the Structure side chain Atoms/Coords

helix_cb_indices property 

helix_cb_indices: list[int]

The indices that index the Structure helical CB Atoms/Coords

n_terminal_residue property 

n_terminal_residue: Residue

Retrieve the Residue from the n-termini

c_terminal_residue property 

c_terminal_residue: Residue

Retrieve the Residue from the c-termini

relative_sasa property 

relative_sasa: list[float]

Return a per-residue array of the relative solvent accessible area for the Structure

sasa_apolar property 

sasa_apolar: list[float]

Return a per-residue array of the polar (hydrophilic) solvent accessible area for the Structure

sasa_polar property 

sasa_polar: list[float]

Return a per-residue array of the apolar (hydrophobic) solvent accessible area for the Structure

surface_residues property 

surface_residues: list[Residue]

Get the Residue instances that reside on the surface of the molecule

Parameters:

  • relative_sasa_thresh –

    The relative area threshold that the Residue should have before it is considered 'surface'. Default cutoff is based on Levy, E. 2010

Other Parameters:

  • atom –

    bool = True - Whether the output should be generated for each atom. If False, will be generated for each Residue

  • probe_radius –

    float = 1.4 - The radius which surface area should be generated

Returns:

  • list[Residue] –

    The surface Residue instances

interior_residues property 

interior_residues: list[Residue]

Get the Residue instances that reside in the interior of the molecule

Parameters:

  • relative_sasa_thresh –

    The relative area threshold that the Residue should fall below before it is considered 'interior'. Default cutoff is based on Levy, E. 2010

Other Parameters:

  • atom –

    bool = True - Whether the output should be generated for each atom. If False, will be generated for each Residue

  • probe_radius –

    float = 1.4 - The radius which surface area should be generated

Returns:

  • list[Residue] –

    The interior Residue instances

secondary_structure property writable 

secondary_structure: str

The Structure secondary structure assignment as provided by the DEFAULT_SS_PROGRAM

spatial_aggregation_propensity property 

spatial_aggregation_propensity: ndarray

Return the spatial aggregation propensity on a per-residue basis

Returns:

  • ndarray –

    The array of floats representing the spatial aggregation propensity for each Residue in the Structure

contact_order property writable 

contact_order: ndarray

Return the contact order on a per-Residue basis

Returns:

  • ndarray –

    The array of floats representing the contact order for each Residue in the Structure

from_residues classmethod 

from_residues(residues: list[Residue] | Residues, **kwargs)

Initialize from existing Residue instances

Source code in symdesign/structure/base.py 
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@classmethod
def from_residues(cls, residues: list[Residue] | Residues, **kwargs):
    """Initialize from existing Residue instances"""
    return cls(residues=residues, **kwargs)

from_structure classmethod 

from_structure(structure: ContainsResidues, **kwargs)

Initialize from an existing Structure

Source code in symdesign/structure/base.py 
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@classmethod
def from_structure(cls, structure: ContainsResidues, **kwargs):
    """Initialize from an existing Structure"""
    return cls(structure=structure, **kwargs)

assign_residues_from_structures 

assign_residues_from_structures(structures: Iterable[ContainsResidues])

Initialize the instance from existing structure instance attributes, .coords, and .atoms, and .residues

Source code in symdesign/structure/base.py 
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def assign_residues_from_structures(self, structures: Iterable[ContainsResidues]):
    """Initialize the instance from existing structure instance attributes, .coords, and .atoms, and .residues"""
    atoms, residues, coords = [], [], []
    for structure in structures:
        atoms.extend(structure.atoms)
        residues.extend(structure.residues)
        coords.append(structure.coords)

    self._assign_residues(residues, atoms=atoms, coords=coords)

make_parent 

make_parent()

Remove this instance from its parent, making it a parent in the process

Source code in symdesign/structure/base.py 
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def make_parent(self):
    """Remove this instance from its parent, making it a parent in the process"""
    super(ContainsAtoms, ContainsAtoms).make_parent(self)
    # Populate the Structure with its existing instances removed of any indexing
    self._assign_residues(self.residues, atoms=self.atoms)
    self.reset_state()

get_base_containers 

get_base_containers() -> dict[str, Any]

Returns the instance structural containers as a dictionary with attribute as key and container as value

Source code in symdesign/structure/base.py 
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def get_base_containers(self) -> dict[str, Any]:
    """Returns the instance structural containers as a dictionary with attribute as key and container as value"""
    return dict(coords=self._coords, atoms=self._atoms, residues=self._residues)

contains_hydrogen 

contains_hydrogen() -> bool

Returns whether the Structure contains hydrogen atoms

Source code in symdesign/structure/base.py 
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def contains_hydrogen(self) -> bool:  # in Residue too
    """Returns whether the Structure contains hydrogen atoms"""
    try:
        return self._contains_hydrogen
    except AttributeError:
        # Sample 20 residues from various "locations".
        # If H is still present but not found, there is an anomaly in the Structure
        slice_amount = max(int(self.number_of_residues / 20), 1)
        for residue in self.residues[::slice_amount]:
            if residue.contains_hydrogen():
                self._contains_hydrogen = True
                break
        else:
            self._contains_hydrogen = False

    return self._contains_hydrogen

get_coords_subset 

get_coords_subset(residue_numbers: Container[int] = None, indices: Iterable[int] = None, start: int = None, end: int = None, dtype: coords_type_literal = 'ca') -> ndarray

Return a view of a subset of the Coords from the Structure specified by a range of Residue numbers

Parameters:

  • residue_numbers (Container[int], default: None ) –

    The Residue numbers to return

  • indices (Iterable[int], default: None ) –

    Residue indices of interest

  • start (int, default: None ) –

    The Residue number to start at. Inclusive

  • end (int, default: None ) –

    The Residue number to end at. Inclusive

  • dtype (coords_type_literal, default: 'ca' ) –

    The type of coordinates to get

Returns:

  • ndarray –

    The specific coordinates from the Residue instances with the specified dtype

Source code in symdesign/structure/base.py 
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def get_coords_subset(self, residue_numbers: Container[int] = None, indices: Iterable[int] = None,
                      start: int = None, end: int = None, dtype: stutils.coords_type_literal = 'ca') -> np.ndarray:
    """Return a view of a subset of the Coords from the Structure specified by a range of Residue numbers

    Args:
        residue_numbers: The Residue numbers to return
        indices: Residue indices of interest
        start: The Residue number to start at. Inclusive
        end: The Residue number to end at. Inclusive
        dtype: The type of coordinates to get

    Returns:
        The specific coordinates from the Residue instances with the specified dtype
    """
    if indices is None:
        if residue_numbers is None:
            if start is not None and end is not None:
                residue_numbers = list(range(start, end + 1))
            else:
                raise ValueError(
                    f"{self.get_coords_subset.__name__}: Must provide either 'indices', 'residue_numbers' or "
                    f"'start' and 'end'")
        residues = self.get_residues(residue_numbers)
    else:
        residues = self.get_residues(indices=indices)

    coords_type = 'coords' if dtype == 'all' else f'{dtype}_coords'
    return np.concatenate([getattr(residue, coords_type) for residue in residues])

set_residues_attributes 

set_residues_attributes(**kwargs)

Set attributes specified by key, value pairs for Residues in the Structure

Other Parameters:

  • numbers –

    Container[int] = None - The Atom numbers of interest

  • pdb –

    bool = False - Whether to search for numbers as they were parsed (if True)

Source code in symdesign/structure/base.py 
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def set_residues_attributes(self, **kwargs):
    """Set attributes specified by key, value pairs for Residues in the Structure

    Keyword Args:
        numbers: Container[int] = None - The Atom numbers of interest
        pdb: bool = False - Whether to search for numbers as they were parsed (if True)
    """
    for residue in self.get_residues(**kwargs):
        for kwarg, value in kwargs.items():
            setattr(residue, kwarg, value)

get_residue_atom_indices 

get_residue_atom_indices(**kwargs) -> list[int]

Returns Atom indices for Residue instances. Returns all by default unless numbers are specified, returns only those Residue instance selected by number.

Other Parameters:

  • numbers –

    Container[int] = None - The Residue numbers of interest

Source code in symdesign/structure/base.py 
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def get_residue_atom_indices(self, **kwargs) -> list[int]:
    """Returns Atom indices for Residue instances. Returns all by default unless numbers are specified, returns only
    those Residue instance selected by number.

    Keyword Args:
        numbers: Container[int] = None - The Residue numbers of interest
    """
    atom_indices = []
    for residue in self.get_residues(**kwargs):
        atom_indices.extend(residue.atom_indices)
    return atom_indices

get_residues_by_atom_indices 

get_residues_by_atom_indices(atom_indices: ArrayIndexer) -> list[Residue]

Retrieve Residues in the Structure specified by Atom indices

Parameters:

  • atom_indices (ArrayIndexer) –

    The atom indices to retrieve Residue objects by

Returns:

  • list[Residue] –

    The sorted, unique Residue instances corresponding to the provided atom_indices

Source code in symdesign/structure/base.py 
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def get_residues_by_atom_indices(self, atom_indices: ArrayIndexer) -> list[Residue]:
    """Retrieve Residues in the Structure specified by Atom indices

    Args:
        atom_indices: The atom indices to retrieve Residue objects by

    Returns:
        The sorted, unique Residue instances corresponding to the provided atom_indices
    """
    if self.is_parent():
        _struct = self
    else:
        _struct = self.parent

    all_residues = _struct._coords_indexed_residues[atom_indices].tolist()
    return sorted(set(all_residues), key=lambda residue: residue.index)

renumber 

renumber()

Change the Atom and Residue numbering. Access the readtime Residue number in Residue.pdb_number attribute

Source code in symdesign/structure/base.py 
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def renumber(self):
    """Change the Atom and Residue numbering. Access the readtime Residue number in Residue.pdb_number attribute"""
    self.renumber_atoms()
    self.pose_numbering()

pose_numbering 

pose_numbering()

Change the Residue numbering to start at 1. Access the readtime Residue number in .pdb_number attribute

Source code in symdesign/structure/base.py 
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def pose_numbering(self):
    """Change the Residue numbering to start at 1. Access the readtime Residue number in .pdb_number attribute"""
    for idx, residue in enumerate(self.residues, 1):
        residue.number = idx
    self.log.debug(f'{self.name} was formatted in Pose numbering (residues now 1 to {self.number_of_residues})')

renumber_residues 

renumber_residues(index: int = 0, at: int = 1)

Renumber Residue objects sequentially starting with "at"

Parameters:

  • index (int, default: 0 ) –

    The index to start the renumbering process

  • at (int, default: 1 ) –

    The number to start renumbering at

Source code in symdesign/structure/base.py 
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def renumber_residues(self, index: int = 0, at: int = 1):
    """Renumber Residue objects sequentially starting with "at"

    Args:
        index: The index to start the renumbering process
        at: The number to start renumbering at
    """
    for idx, residue in enumerate(self.residues[index:], at):
        residue.number = idx

get_residues 

get_residues(numbers: Container[int] = None, indices: Iterable[int] = None, **kwargs) -> list[Residue]

Returns Residue instances as specified. Returns all by default

Parameters:

  • numbers (Container[int], default: None ) –

    Residue numbers of interest

  • indices (Iterable[int], default: None ) –

    Residue indices of interest for the Structure

Returns:

  • list[Residue] –

    The requested Residue instances, sorted in the order they appear in the Structure

Source code in symdesign/structure/base.py 
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def get_residues(self, numbers: Container[int] = None, indices: Iterable[int] = None, **kwargs) -> list[Residue]:
    """Returns Residue instances as specified. Returns all by default

    Args:
        numbers: Residue numbers of interest
        indices: Residue indices of interest for the Structure

    Returns:
        The requested Residue instances, sorted in the order they appear in the Structure
    """
    residues = self.residues
    if numbers is not None:
        if isinstance(numbers, Container):
            residues = [residue for residue in residues if residue.number in numbers]
        else:
            self.log.warning(f'The passed numbers type "{type(numbers).__name__}" must be a Container. Returning '
                             f'all Residue instances instead')
    elif indices is not None:
        try:
            residues = [residues[idx] for idx in indices]
        except IndexError:
            number_of_residues = self.number_of_residues
            for idx in indices:
                if idx < 0 or idx >= number_of_residues:
                    raise IndexError(
                        f'The residue index {idx} is out of bounds for the {self.__class__.__name__} {self.name} '
                        f'with size of {number_of_residues} residues')
    return residues

residue 

residue(residue_number: int) -> Residue | None

Retrieve the specified Residue

Parameters:

  • residue_number (int) –

    The number of the Residue to search for

Source code in symdesign/structure/base.py 
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def residue(self, residue_number: int) -> Residue | None:
    """Retrieve the specified Residue

    Args:
        residue_number: The number of the Residue to search for
    """
    for residue in self.residues:
        if residue.number == residue_number:
            return residue
    return None

add_ideal_helix 

add_ideal_helix(termini: termini_literal = 'n', length: int = 5, alignment_length: int = 5)

Add an ideal helix to a termini given by a certain length

Parameters:

  • termini (termini_literal, default: 'n' ) –

    The termini to add the ideal helix to

  • length (int, default: 5 ) –

    The length of the addition, where viable values are [1-10] residues additions

  • alignment_length (int, default: 5 ) –

    The number of residues used to calculation overlap of the target to the ideal helix

Source code in symdesign/structure/base.py 
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def add_ideal_helix(self, termini: stutils.termini_literal = 'n', length: int = 5, alignment_length: int = 5):
    """Add an ideal helix to a termini given by a certain length

    Args:
        termini: The termini to add the ideal helix to
        length: The length of the addition, where viable values are [1-10] residues additions
        alignment_length: The number of residues used to calculation overlap of the target to the ideal helix
    """
    maximum_extension_length = 15 - alignment_length
    if length > maximum_extension_length:
        number_of_iterations, length = divmod(length, maximum_extension_length)
        # First add the remainder 'length' with the specified alignment length,
        self.add_ideal_helix(termini=termini, length=length, alignment_length=alignment_length)
        # Then perform 10 residue extensions until complete
        # Using the default 10 and 5 alignment to prevent any errors from alignment of shorter amount from
        # propagating to the ideal addition and creating ideal "kinks"
        addition_count = count()
        while next(addition_count) != number_of_iterations:
            self.add_ideal_helix(termini=termini, length=10)

        return
    elif length < 1:
        return
    else:
        self.log.debug(f'Adding {length} residue ideal helix to {termini}-terminus of {self.name}')

    alpha_helix_15_struct = ContainsResidues.from_atoms(alpha_helix_15_atoms)

    if termini == 'n':
        residue = self.n_terminal_residue
        residue_index = residue.index
        fixed_coords = self.get_coords_subset(
            indices=list(range(residue_index, residue_index + alignment_length)), dtype='backbone')

        ideal_end_index = alpha_helix_15_struct.c_terminal_residue.index + 1
        ideal_start_index = ideal_end_index - alignment_length
        moving_coords = alpha_helix_15_struct.get_coords_subset(
            indices=list(range(ideal_start_index, ideal_end_index)), dtype='backbone')
        rmsd, rot, tx = superposition3d(fixed_coords, moving_coords)
        alpha_helix_15_struct.transform(rotation=rot, translation=tx)

        # Add residues
        helix_add_start = ideal_start_index - length
        # Exclude ideal_start_index from residue selection
        add_residues = alpha_helix_15_struct.get_residues(indices=list(range(helix_add_start, ideal_start_index)))
    elif termini == 'c':
        residue = self.c_terminal_residue
        residue_index = residue.index + 1
        fixed_coords = self.get_coords_subset(
            indices=list(range(residue_index - alignment_length, residue_index)), dtype='backbone')

        ideal_start_index = alpha_helix_15_struct.n_terminal_residue.index
        ideal_end_index = ideal_start_index + alignment_length
        moving_coords = alpha_helix_15_struct.get_coords_subset(
            indices=list(range(ideal_start_index, ideal_end_index)), dtype='backbone')
        rmsd, rot, tx = superposition3d(fixed_coords, moving_coords)
        alpha_helix_15_struct.transform(rotation=rot, translation=tx)

        # Add residues
        helix_add_end = ideal_end_index + length
        # Leave out the residue with ideal_end_index, and include the helix_add_end number
        add_residues = alpha_helix_15_struct.get_residues(indices=list(range(ideal_end_index, helix_add_end)))
    else:
        raise ValueError(
            f"'termini' must be either 'n' or 'c', not {termini}")

    self.insert_residues(residue_index, add_residues, chain_id=residue.chain_id)

get_residue_atoms 

get_residue_atoms(**kwargs) -> list[Atom]

Return the Atoms contained in the Residue objects matching a set of residue numbers

Other Parameters:

  • numbers –

    Container[int] = None – Residue numbers of interest

  • indices –

    Iterable[int] = None – Residue indices of interest for the Structure

Returns:

  • list[Atom] –

    The Atom instances belonging to the Residue instances

Source code in symdesign/structure/base.py 
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def get_residue_atoms(self, **kwargs) -> list[Atom]:
    """Return the Atoms contained in the Residue objects matching a set of residue numbers

    Keyword Args:
        numbers: Container[int] = None – Residue numbers of interest
        indices: Iterable[int] = None – Residue indices of interest for the Structure

    Returns:
        The Atom instances belonging to the Residue instances
    """
    atoms = []
    for residue in self.get_residues(**kwargs):
        atoms.extend(residue.atoms)
    return atoms

mutate_residue 

mutate_residue(residue: Residue = None, index: int = None, number: int = None, to: str = 'A', **kwargs) -> list[int] | list

Mutate a specific Residue to a new residue type. Type can be 1 or 3 letter format

Parameters:

  • residue (Residue, default: None ) –

    A Residue instance to mutate

  • index (int, default: None ) –

    A Residue index to select the Residue instance of interest

  • number (int, default: None ) –

    A Residue number to select the Residue instance of interest

  • to (str, default: 'A' ) –

    The type of amino acid to mutate to

Returns:

  • list[int] | list –

    The indices of the Atoms being removed from the Structure

Source code in symdesign/structure/base.py 
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def mutate_residue(self, residue: Residue = None, index: int = None, number: int = None, to: str = 'A', **kwargs) \
        -> list[int] | list:
    """Mutate a specific Residue to a new residue type. Type can be 1 or 3 letter format

    Args:
        residue: A Residue instance to mutate
        index: A Residue index to select the Residue instance of interest
        number: A Residue number to select the Residue instance of interest
        to: The type of amino acid to mutate to

    Returns:
        The indices of the Atoms being removed from the Structure
    """
    if index is not None:
        try:
            residue = self.residues[index]
        except IndexError:
            raise IndexError(
                f'The residue index {index} is out of bounds for the {self.__class__.__name__} '
                f'{self.name} with size of {self.number_of_residues} residues')
    elif number is not None:
        residue = self.residue(number)

    if residue is None:
        raise ValueError(
            f"Can't {self.mutate_residue.__name__} without Residue instance, index, or number")
    elif self.is_dependent():
        _parent = self.parent
        self.log.debug(f"{self.mutate_residue.__name__} can't be performed on a dependent StructureBase. "
                       f"Calling on the {self.__class__.__name__}.parent {repr(_parent)}")
        # Ensure the deletion is done by the Structure parent to account for everything correctly
        return _parent.mutate_residue(residue, to=to)

    to = protein_letters_1to3.get(to.upper(), to.upper())
    if residue.type == to:  # No mutation necessary
        return []
    else:
        try:
            protein_letters_3to1_extended[to]
        except KeyError:
            raise KeyError(
                f"The mutation type '{to}' isn't a viable Residue type")
    self.log.debug(f'Mutating {residue.type}{residue.number}{to}')
    residue.type = to
    for atom in residue.atoms:
        atom.residue_type = to

    # Find the corresponding Residue Atom indices to delete
    delete_indices = residue.side_chain_indices
    if not delete_indices:  # There are no indices
        return []
    else:  # Clear all state variables for all Residue instances
        self._residues.reset_state()
        # residue.side_chain_indices = []

    # Remove indices from the Residue, and Structure atom_indices
    residue_atom_indices = residue.atom_indices
    residue_atom_delete_index = residue_atom_indices.index(delete_indices[0])
    _atom_indices = self._atom_indices
    structure_atom_delete_index = _atom_indices.index(delete_indices[0])
    for _ in iter(delete_indices):
        residue_atom_indices.pop(residue_atom_delete_index)
        _atom_indices.pop(structure_atom_delete_index)

    self._offset_indices(start_at=structure_atom_delete_index, offset=-len(delete_indices), dtype='atom')

    # Re-index all succeeding Atom and Residue instance indices
    self._coords.delete(delete_indices)
    self._atoms.delete(delete_indices)
    # self._atoms.reindex(start_at=structure_atom_delete_index)
    self._residues.reindex_atoms(start_at=residue.index)

    # Reissue the atom assignments for the Residue
    residue.delegate_atoms()
    self.reset_state()

    return delete_indices

delete_residues 

delete_residues(residues: Iterable[Residue] = None, indices: Iterable[int] = None, numbers: Container[int] = None, **kwargs) -> list[Residue] | list

Deletes Residue instances from the Structure

Parameters:

  • residues (Iterable[Residue], default: None ) –

    Residue instances to delete

  • indices (Iterable[int], default: None ) –

    Residue indices to select the Residue instances of interest

  • numbers (Container[int], default: None ) –

    Residue numbers to select the Residue instances of interest

Returns:

  • list[Residue] | list –

    Each deleted Residue

Source code in symdesign/structure/base.py 
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def delete_residues(self, residues: Iterable[Residue] = None, indices: Iterable[int] = None,
                    numbers: Container[int] = None, **kwargs) -> list[Residue] | list:
    """Deletes Residue instances from the Structure

    Args:
        residues: Residue instances to delete
        indices: Residue indices to select the Residue instances of interest
        numbers: Residue numbers to select the Residue instances of interest

    Returns:
        Each deleted Residue
    """
    if indices is not None:
        residues = self.get_residues(indices=indices)
    elif numbers is not None:
        residues = self.get_residues(numbers=numbers)

    if residues is None:
        raise ValueError(
            f"Can't {self.delete_residues.__name__} without Residue instances. Provide with indices, numbers, or "
            "residues")
    elif not residues:
        self.log.debug(f'{self.delete_residues.__name__}: No residues found')
        return []
    elif self.is_dependent():  # Call on the parent
        _parent = self.parent
        self.log.debug(f"{self.delete_residues.__name__} can't be performed on a dependent StructureBase. "
                       f"Calling on the {self.__class__.__name__}.parent {repr(_parent)}")
        # Ensure the deletion is done by the Structure parent to account for everything correctly
        return _parent.delete_residues(residues=residues)

    # Find the Residue, Atom indices to delete
    atom_indices = []
    for residue in residues:
        self.log.debug(f'Deleting {residue.type}{residue.number}')
        atom_indices.extend(residue.atom_indices)

    if not atom_indices:
        return []  # There are no indices for the Residue instances
    else:  # Find the Residue indices to delete
        residue_indices = []
        for residue in residues:
            residue_indices.append(residue.index)

    # Remove indices from the Residue, and Structure atom_indices
    self._delete_indices(atom_indices, dtype='atom')
    self._delete_indices(residue_indices, dtype='residue')
    # Re-index all succeeding Atom and Residue instance indices
    self._coords.delete(atom_indices)
    self._atoms.delete(atom_indices)
    self._residues.delete(residue_indices)
    self._residues.reindex(start_at=residue_indices[0])

    # Clear state variables for remaining Residue instances. Residue deletion affected remaining attrs and indices
    self._residues.reset_state()
    # Reindex the coords/residues map
    self.reset_state()

    return residues

insert_residue_type 

insert_residue_type(index: int, residue_type: str, chain_id: str = None) -> Residue

Insert a standard Residue type into the Structure at the origin. No structural alignment is performed!

Parameters:

  • index (int) –

    The residue index where a new Residue should be inserted into the Structure

  • residue_type (str) –

    Either the 1 or 3 letter amino acid code for the residue in question

  • chain_id (str, default: None ) –

    The chain identifier to associate the new Residue with

Returns:

  • Residue –

    The newly inserted Residue object

Source code in symdesign/structure/base.py 
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def insert_residue_type(self, index: int, residue_type: str, chain_id: str = None) -> Residue:
    """Insert a standard Residue type into the Structure at the origin. No structural alignment is performed!

    Args:
        index: The residue index where a new Residue should be inserted into the Structure
        residue_type: Either the 1 or 3 letter amino acid code for the residue in question
        chain_id: The chain identifier to associate the new Residue with

    Returns:
        The newly inserted Residue object
    """
    if self.is_dependent():  # Call on the parent
        _parent = self.parent
        self.log.debug(f"{self.insert_residue_type.__name__} can't be performed on a dependent StructureBase. "
                       f"Calling on the {self.__class__.__name__}.parent {repr(_parent)}")
        # Ensure the deletion is done by the Structure parent to account for everything correctly
        if chain_id is None:
            chain_id = getattr(self, 'chain_id', None)
        return _parent.insert_residue_type(index, residue_type, chain_id=chain_id)

    self.log.debug(f'Inserting {residue_type} into index {index} of {self.name}')

    # Convert incoming amino acid to an index to select the stutils.reference_residue.
    # protein_letters_alph1 has a matching index
    reference_index = \
        protein_letters_alph1.find(protein_letters_3to1_extended.get(residue_type, residue_type.upper()))
    if reference_index == -1:
        raise IndexError(
            f"{self.insert_residue_type.__name__} of residue_type '{residue_type}' isn't allowed")
    if index < 0:
        raise IndexError(
            f"{self.insert_residue_type.__name__} at index {index} < 0 isn't allowed")

    # Grab the reference atom coordinates and push into the atom list
    new_residue = reference_residues[reference_index].copy()

    # Find the prior and next Residue, atom_start_index (starting atom in new Residue index)
    residues = self.residues
    if index == 0:  # n-termini = True
        prev_residue = None
        atom_start_index = 0
    else:
        prev_residue = residues[index - 1]
        atom_start_index = prev_residue.end_index + 1

    try:
        next_residue = residues[index]
    except IndexError:  # c_termini = True
        next_residue = None
        if not prev_residue:  # Insertion on an empty Structure? block for now to simplify chain identification
            raise stutils.DesignError(
                f"Can't {self.insert_residue_type.__name__} for an empty {self.__class__.__name__} class")

    # Set found attributes
    new_residue._insert = True

    # Insert the new_residue coords, atoms, and residues into the Structure
    self._coords.insert(atom_start_index, new_residue.coords)
    self._atoms.insert(atom_start_index, new_residue.atoms)
    self._residues.insert(index, [new_residue])
    # After coords, atoms, residues insertion into "_" containers, set parent to self
    new_residue._parent = self

    # Reformat indices
    # new_residue.start_index = atom_start_index
    # self._atoms.reindex(start_at=atom_start_index)  # Called in self._residues.reindex
    self._residues.reindex(start_at=index)  # .set_index()
    # Insert new_residue index and atom_indices into Structure indices
    self._insert_indices(index, [index], dtype='residue')
    self._insert_indices(atom_start_index, new_residue.atom_indices, dtype='atom')

    # Set the new chain_id. Must occur after self._residue_indices update if chain isn't provided
    if chain_id is None:  # Try to solve without it...
        if prev_residue and next_residue:
            if prev_residue.chain_id == next_residue.chain_id:
                chain_id = prev_residue.chain_id
            else:  # There is a discrepancy which means this is an internal termini
                raise stutils.DesignError(chain_assignment_error)
        # This can be solved as it represents an absolute termini case
        elif prev_residue:
            chain_id = prev_residue.chain_id
        else:
            chain_id = next_residue.chain_id
    new_residue.chain_id = chain_id

    # Solve the Residue number and renumber Structure if there is overlap
    if prev_residue and next_residue:
        tentative_number = prev_residue.number + 1
        if tentative_number == next_residue.number:
            # There is a conflicting insertion
            # The prev_residue could also be inserted and needed to be numbered lower
            try:  # Check residue._insert
                prev_residue._insert
            except AttributeError:  # Not inserted. Renumber all subsequent
                # self.renumber_residues()
                residues_renumber = residues[index:]
                for residue in residues_renumber:
                    residue.number = residue.number + 1
            else:
                for residue in prev_residue.get_upstream() + [prev_residue]:
                    residue.number = residue.number - 1

        new_residue.number = tentative_number
    elif prev_residue:
        new_residue.number = prev_residue.number + 1
    else:  # next_residue
        # This cautionary note may not apply anymore
        #  Subtracting one may not be enough if this insert_residue_type() is part of a set of inserts and all
        #  n-terminal insertions are being conducted before this next_residue. Clean this in the first check of
        #  this logic block
        new_residue.number = next_residue.number - 1

    try:
        secondary_structure = self._secondary_structure
    except AttributeError:  # When not set yet
        self.calculate_secondary_structure()  # The new_residue will be included
    else:  # Insert the new ss with a coiled assumption
        # ASSUME the insertion is disordered and coiled segment
        new_residue.secondary_structure = DEFAULT_SS_COIL_IDENTIFIER
        self._secondary_structure = \
            secondary_structure[:index] + DEFAULT_SS_COIL_IDENTIFIER + secondary_structure[index:]

    # Reindex the coords/residues map
    self.reset_state()

    return new_residue

insert_residues 

insert_residues(index: int, new_residues: Iterable[Residue], chain_id: str = None) -> list[Residue]

Insert Residue instances into the Structure at the origin. No structural alignment is performed!

Parameters:

  • index (int) –

    The index to perform the insertion at

  • new_residues (Iterable[Residue]) –

    The Residue instances to insert

  • chain_id (str, default: None ) –

    The chain identifier to associate the new Residue instances with

Returns:

  • list[Residue] –

    The inserted Residue instances

Source code in symdesign/structure/base.py 
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def insert_residues(self, index: int, new_residues: Iterable[Residue], chain_id: str = None) -> list[Residue]:
    """Insert Residue instances into the Structure at the origin. No structural alignment is performed!

    Args:
        index: The index to perform the insertion at
        new_residues: The Residue instances to insert
        chain_id: The chain identifier to associate the new Residue instances with

    Returns:
        The inserted Residue instances
    """
    if not new_residues:
        return []

    if self.is_dependent():  # Call on the parent
        _parent = self.parent
        self.log.debug(f"{self.insert_residues.__name__} can't be performed on a dependent StructureBase. "
                       f"Calling on the {self.__class__.__name__}.parent {repr(_parent)}")
        # Ensure the deletion is done by the Structure parent to account for everything correctly
        if chain_id is None:
            chain_id = getattr(self, 'chain_id', None)
        return _parent.insert_residues(index, new_residues, chain_id=chain_id)

    # Make a copy of the Residue instances
    new_residues = [residue.copy() for residue in new_residues]
    number_new_residues = len(new_residues)

    # Find the prior and next Residue, atom_start_index (starting atom in new Residue index)
    residues = self.residues
    if index == 0:  # n-termini = True
        prev_residue = _prev_residue = None
        atom_start_index = 0
    else:
        prev_residue = _prev_residue = residues[index - 1]
        atom_start_index = prev_residue.end_index + 1

    try:
        next_residue = residues[index]
    except IndexError:  # c_termini = True
        next_residue = None
        if not prev_residue:  # Insertion on an empty Structure? block for now to simplify chain identification
            raise stutils.DesignError(
                f"Can't {self.insert_residue_type.__name__} for an empty {self.__class__.__name__} class")

    # Set found attributes
    # prev_residue, *other_residues = new_residues
    for residue in new_residues:
        residue._insert = True

    # Insert the new_residue coords, atoms, and residues into the Structure
    self._coords.insert(atom_start_index, np.concatenate([residue.coords for residue in new_residues]))
    self._atoms.insert(atom_start_index, [atom for residue in new_residues for atom in residue.atoms])
    self._residues.insert(index, new_residues)
    # After coords, atoms, residues insertion into "_" containers, set parent to self
    for residue in new_residues:
        residue._parent = self

    # Reformat indices
    # new_residue.start_index = atom_start_index
    # self._atoms.reindex(start_at=atom_start_index)  # Called in self._residues.reindex
    self._residues.reindex(start_at=index)  # .set_index()
    # Insert new_residue index and atom_indices into Structure indices
    new_residue_atom_indices = list(range(atom_start_index, new_residues[-1].end_index + 1))
    self._insert_indices(atom_start_index, new_residue_atom_indices, dtype='atom')
    new_residue_indices = list(range(index, index + number_new_residues))
    self._insert_indices(index, new_residue_indices, dtype='residue')

    # Set the new chain_id. Must occur after self._residue_indices update if chain isn't provided
    if chain_id is None:  # Try to solve without it...
        if prev_residue and next_residue:
            if prev_residue.chain_id == next_residue.chain_id:
                chain_id = prev_residue.chain_id
            else:  # There is a discrepancy which means this is an internal termini
                raise stutils.DesignError(chain_assignment_error)
        # This can be solved as it represents an absolute termini case
        elif prev_residue:
            chain_id = prev_residue.chain_id
        else:
            chain_id = next_residue.chain_id
    for residue in new_residues:
        residue.chain_id = chain_id

    # Solve the Residue number and renumber Structure if there is overlap
    if prev_residue and next_residue:
        first_number = prev_residue.number + 1
        tentative_residue_numbers = list(range(first_number, first_number + number_new_residues))
        if next_residue.number in tentative_residue_numbers:
            # There is a conflicting insertion. Correct existing residue numbers
            # The prev_residue could also be inserted and needed to be numbered lower
            try:  # Check residue._insert
                prev_residue._insert
            except AttributeError:  # Not inserted. Renumber all subsequent
                # self.renumber_residues()
                residues_renumber = residues[index:]
                for residue in residues_renumber:
                    residue.number = residue.number + number_new_residues
            else:
                for residue in prev_residue.get_upstream() + [prev_residue]:
                    residue.number = residue.number - number_new_residues
        # Set the new numbers
        for residue, new_number in zip(new_residues, tentative_residue_numbers):
            residue.number = new_number
    elif prev_residue:
        _prev_residue = prev_residue
        for residue in new_residues:
            residue.number = _prev_residue.number + 1
            _prev_residue = residue
    else:  # next_residue
        # This cautionary note may not apply to insert_residues(
        #  Subtracting one may not be enough if insert_residues() is part of a set of inserts and all
        #  n-terminal insertions are being conducted before this next_residue. Clean this in the first check of
        #  this logic block
        _prev_residue = next_residue
        for residue in reversed(new_residues):
            residue.number = _prev_residue.number - 1
            _prev_residue = residue

    # Reindex the coords/residues map
    self.reset_state()

    return new_residues

delete_termini 

delete_termini(how: str = 'unstructured', termini: termini_literal = None)

Remove Residue instances from the Structure termini that are not helices

Uses the default secondary structure prediction program's SS_HELIX_IDENTIFIERS (typically 'H') to search for non-conforming secondary structure

Parameters:

  • how (str, default: 'unstructured' ) –

    How should termini be trimmed? Either 'unstructured' (default) or 'to_helices' can be used. If 'unstructured', will use 'SS_DISORDER_IDENTIFIERS' (typically coil) to detect disorder. Function will then remove any disordered segments, as well as turns ('T') that exist between disordered segments If 'to_helices', will use 'SS_HELIX_IDENTIFIERS' (typically 'H') to remove any non-conforming secondary structure elements until a helix is reached

  • termini (termini_literal, default: None ) –

    If a specific termini should be targeted, which one?

Source code in symdesign/structure/base.py 
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def delete_termini(self, how: str = 'unstructured', termini: stutils.termini_literal = None):
    """Remove Residue instances from the Structure termini that are not helices

    Uses the default secondary structure prediction program's SS_HELIX_IDENTIFIERS (typically 'H') to search for
    non-conforming secondary structure

    Args:
        how: How should termini be trimmed? Either 'unstructured' (default) or 'to_helices' can be used.
            If 'unstructured',
                will use 'SS_DISORDER_IDENTIFIERS' (typically coil) to detect disorder. Function will then remove any
                disordered segments, as well as turns ('T') that exist between disordered segments
            If 'to_helices',
                will use 'SS_HELIX_IDENTIFIERS' (typically 'H') to remove any non-conforming secondary structure
                elements until a helix is reached
        termini: If a specific termini should be targeted, which one?
    """
    if termini is None or termini.lower() == 'nc':
        termini_ = 'nc'
    elif termini in 'NnCc':  # Only one of the two
        termini_ = termini.lower()
    else:
        raise ValueError(
            f"'termini' must be one of 'n' or 'c', not '{termini}")

    secondary_structure = working_secondary_structure = self.secondary_structure
    number_of_residues = self.number_of_residues
    # no_nterm_disorder_ss = secondary_structure.lstrip(SS_DISORDER_IDENTIFIERS)
    # n_removed_nterm_res = number_of_residues - len(no_nterm_disorder_ss)
    # no_cterm_disorder_ss = secondary_structure.rstrip(SS_DISORDER_IDENTIFIERS)
    # n_removed_cterm_res = number_of_residues - len(no_cterm_disorder_ss)
    # sasa = self.relative_sasa
    # self.log.debug(f'Found n-term relative sasa {sasa[:n_removed_nterm_res + 10]}')
    # self.log.debug(f'Found c-term relative sasa {sasa[-(n_removed_cterm_res + 10):]}')

    n_removed_nterm_res = 0
    # Remove coils. Find the next coil. If only ss present is (T)urn, then remove that as well and start again
    for idx, termini in enumerate('NC'):
        if idx == 0:  # n-termini
            self.log.debug(f'Starting N-term is: {working_secondary_structure[:15]}')
            possible_secondary_structure = working_secondary_structure
        else:  # c-termini
            self.log.debug(f'N-term is: {working_secondary_structure[:15]}')
            # Get the number of n-termini removed
            n_removed_nterm_res = number_of_residues - len(working_secondary_structure)
            # Reverse the sequence to get the c-termini first
            possible_secondary_structure = working_secondary_structure[::-1]
            self.log.debug(f'Starting C-term (reversed) is: {possible_secondary_structure[:15]}')

        if how == 'to_helices':
            ss_helix_index = possible_secondary_structure.find(SS_HELIX_IDENTIFIERS)
            working_secondary_structure = working_secondary_structure[ss_helix_index:]
        else:  # how == 'unstructured'
            ss_disorder_index = possible_secondary_structure.find(SS_DISORDER_IDENTIFIERS)
            while ss_disorder_index == 0:  # Go again
                # Remove DISORDER ss
                working_secondary_structure = possible_secondary_structure.lstrip(SS_DISORDER_IDENTIFIERS)
                # Next try to remove TURN ss. Only remove if it is between DISORDER segments
                possible_secondary_structure = working_secondary_structure.lstrip(SS_TURN_IDENTIFIERS)
                ss_disorder_index = possible_secondary_structure.find(SS_DISORDER_IDENTIFIERS)

    self.log.debug(f'C-term (reversed) is: {working_secondary_structure[:15]}')

    residues = self.residues
    _delete_residues = []
    context_length = 10
    if 'n' in termini_ and n_removed_nterm_res:
        old_ss = secondary_structure[:n_removed_nterm_res + context_length]
        self.log.debug(f'Found N-term secondary_structure {secondary_structure[:n_removed_nterm_res + 5]}')
        self.log.info(f"Removing {n_removed_nterm_res} N-terminal residues. Resulting secondary structure:\n"
                      f"\told : {old_ss}...\n"
                      f"\tnew : {'-' * n_removed_nterm_res}{old_ss[n_removed_nterm_res:]}...")
        _delete_residues += residues[:n_removed_nterm_res]

    # Get the number of c-termini removed
    n_removed_cterm_res = number_of_residues - len(working_secondary_structure) - n_removed_nterm_res
    if 'c' in termini_ and n_removed_cterm_res:
        c_term_index = number_of_residues - n_removed_cterm_res
        old_ss = secondary_structure[c_term_index - context_length:]
        self.log.debug(f'Found C-term secondary_structure {secondary_structure[-(n_removed_cterm_res + 5):]}')
        self.log.info(f"Removing {n_removed_cterm_res} C-terminal residues. Resulting secondary structure:\n"
                      f"\told :...{old_ss}\n"
                      f"\tnew :...{old_ss[:-n_removed_cterm_res]}{'-' * n_removed_cterm_res}")
        _delete_residues += residues[c_term_index:]

    self.delete_residues(_delete_residues)

local_density 

local_density(residues: list[Residue] = None, residue_numbers: list[int] = None, distance: float = 12.0) -> list[float]

Return the number of Atoms within 'distance' Angstroms of each Atom in the requested Residues

Parameters:

  • residues (list[Residue], default: None ) –

    The Residues to include in the calculation

  • residue_numbers (list[int], default: None ) –

    The numbers of the Residues to include in the calculation

  • distance (float, default: 12.0 ) –

    The cutoff distance with which Atoms should be included in local density

Returns:

  • list[float] –

    An array like containing the local density around each requested Residue

Source code in symdesign/structure/base.py 
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def local_density(self, residues: list[Residue] = None, residue_numbers: list[int] = None, distance: float = 12.) \
        -> list[float]:
    """Return the number of Atoms within 'distance' Angstroms of each Atom in the requested Residues

    Args:
        residues: The Residues to include in the calculation
        residue_numbers: The numbers of the Residues to include in the calculation
        distance: The cutoff distance with which Atoms should be included in local density

    Returns:
        An array like containing the local density around each requested Residue
    """
    if residues:
        coords = []
        for residue in residues:
            coords.extend(residue.heavy_coords)
        coords_indexed_residues = [residue for residue in residues for _ in residue.heavy_indices]
    elif residue_numbers:
        coords = []
        residues = self.get_residues(numbers=residue_numbers)
        for residue in residues:
            coords.extend(residue.heavy_coords)
        coords_indexed_residues = [residue for residue in residues for _ in residue.heavy_indices]
    else:  # use all Residue instances
        residues = self.residues
        coords = self.heavy_coords
        coords_indexed_residues = self.heavy_coords_indexed_residues

    # in case this was already called, we should set all to 0.
    if residues[0].local_density > 0:
        for residue in residues:
            residue.local_density = 0.

    all_atom_tree = BallTree(coords)
    all_atom_counts_query = all_atom_tree.query_radius(coords, distance, count_only=True)
    # residue_neighbor_counts, current_residue = 0, coords_indexed_residues[0]
    current_residue = coords_indexed_residues[0]
    for residue, atom_neighbor_counts in zip(coords_indexed_residues, all_atom_counts_query.tolist()):
        if residue == current_residue:
            current_residue.local_density += atom_neighbor_counts
        else:  # We have a new residue, find the average
            current_residue.local_density /= current_residue.number_of_heavy_atoms
            current_residue = residue
            current_residue.local_density += atom_neighbor_counts
    # Ensure the last residue is calculated
    current_residue.local_density /= current_residue.number_of_heavy_atoms  # Find the average

    return [residue.local_density for residue in self.residues]

is_clash 

is_clash(measure: coords_type_literal = stutils.default_clash_criteria, distance: float = stutils.default_clash_distance, warn: bool = False, silence_exceptions: bool = False, report_hydrogen: bool = False) -> bool

Check if the Structure contains any self clashes. If clashes occur with the Backbone, return True. Reports the Residue where the clash occurred and the clashing Atoms

Parameters:

  • measure (coords_type_literal, default: default_clash_criteria ) –

    The atom type to measure clashing by

  • distance (float, default: default_clash_distance ) –

    The distance which clashes should be checked

  • warn (bool, default: False ) –

    Whether to emit warnings about identified clashes. Output grouped into measure vs non-measure

  • silence_exceptions (bool, default: False ) –

    Whether to silence the raised ClashError and Return True instead

  • report_hydrogen (bool, default: False ) –

    Whether to report clashing hydrogen atoms

Returns:

  • bool –

    True if the Structure clashes, False if not

Source code in symdesign/structure/base.py 
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def is_clash(self, measure: stutils.coords_type_literal = stutils.default_clash_criteria,
             distance: float = stutils.default_clash_distance,
             warn: bool = False, silence_exceptions: bool = False,
             report_hydrogen: bool = False) -> bool:
    """Check if the Structure contains any self clashes. If clashes occur with the Backbone, return True. Reports
    the Residue where the clash occurred and the clashing Atoms

    Args:
        measure: The atom type to measure clashing by
        distance: The distance which clashes should be checked
        warn: Whether to emit warnings about identified clashes. Output grouped into measure vs non-measure
        silence_exceptions: Whether to silence the raised ClashError and Return True instead
        report_hydrogen: Whether to report clashing hydrogen atoms

    Raises:
        ClashError if the Structure has an identified clash

    Returns:
        True if the Structure clashes, False if not
    """
    if measure == 'backbone_and_cb':
        other = 'non-cb sidechain'
    elif measure == 'heavy':
        other = 'hydrogen'
        report_hydrogen = True
    elif measure == 'backbone':
        other = 'sidechain'
    elif measure == 'cb':
        other = 'non-cb'
    elif measure == 'ca':
        other = 'non-ca'
    else:  # measure == 'all'
        other = 'solvent'  # this should never appear unless someone added solvent parsing

    coords_type = 'coords' if measure == 'all' else f'{measure}_coords'
    # cant use heavy_coords as the Residue.atom_indices aren't offset for the BallTree made from them...
    # another option is to only care about heavy atoms on the residues...
    # if self.contains_hydrogen():
    #     atom_tree = BallTree(self.heavy_coords)
    #     coords_indexed_residues = self.heavy_coords_indexed_residues
    #     atoms = self.heavy_atoms
    # else:

    # Set up the query indices. BallTree is faster upon timeit with 131 msec/loop
    atom_tree = BallTree(self.coords)
    atoms = self.atoms
    measured_clashes, other_clashes = [], []

    def return_true(): return True

    clashes = False
    _any_clashes: Callable[[Iterable[int]], bool]
    """Local helper to separate clash reporting from clash generation"""
    clash_msg = f'{self.name} contains Residue {measure} atom clashes at a {distance} A distance'
    if warn:

        def _any_clashes(_clash_indices: Iterable[int]) -> bool:
            new_clashes = any(_clash_indices)
            if new_clashes:
                for clashing_idx in _clash_indices:
                    atom = atoms[clashing_idx]
                    if getattr(atom, f'is_{measure}', return_true)():
                        measured_clashes.append((residue, atom))
                    elif report_hydrogen:  # Report all clashes, no need to check
                        other_clashes.append((residue, atom))
                    elif atom.is_heavy():  # Check if atom is a heavy atom then report if it is
                        other_clashes.append((residue, atom))

            return clashes or new_clashes

        # Using _any_clashes to set the global clashes
        #     clashes = _any_clashes(): ... return clashes
        # While checking global clashes against new_clashes
    else:  # Raise a ClashError to defer to caller
        def _any_clashes(_clash_indices: Iterable[int]) -> bool:
            for clashing_idx in _clash_indices:
                if getattr(atoms[clashing_idx], f'is_{measure}', return_true)():
                    raise stutils.ClashError(clash_msg)

            return clashes

    residues = self.residues
    # Check first and last residue with different considerations given covalent bonding
    try:
        residue, next_residue = residues[:2]
        # residue, next_residue, *other_residues = self.residues
    except ValueError:  # Can't unpack
        # residues < 2. Insufficient to check clashing
        return False

    # Query each residue with requested coords_type against the atom_tree
    residue_atom_contacts = atom_tree.query_radius(getattr(residue, coords_type), distance)
    # residue_atom_contacts returns as ragged nested array, (array of different sized array)
    # Reduce the dimensions to all contacts
    all_contacts = {atom_contact for residue_contacts in residue_atom_contacts.tolist()
                    for atom_contact in residue_contacts.tolist()}
    try:
        # Subtract the N and C atoms from the adjacent residues for each residue as these are within a bond
        clashes = _any_clashes(
            all_contacts.difference(residue.atom_indices + [next_residue.n_atom_index]))
        prev_residue = residue
        residue = next_residue

        # Perform routine for all middle residues
        for next_residue in residues[2:]:
            residue_atom_contacts = atom_tree.query_radius(getattr(residue, coords_type), distance)
            all_contacts = {atom_contact for residue_contacts in residue_atom_contacts.tolist()
                            for atom_contact in residue_contacts.tolist()}
            clashes = _any_clashes(
                all_contacts.difference(
                    [prev_residue.o_atom_index, prev_residue.c_atom_index, next_residue.n_atom_index]
                    + residue.atom_indices
                ))
            prev_residue = residue
            residue = next_residue

        residue_atom_contacts = atom_tree.query_radius(getattr(residue, coords_type), distance)
        all_contacts = {atom_contact for residue_contacts in residue_atom_contacts.tolist()
                        for atom_contact in residue_contacts.tolist()}
        clashes = _any_clashes(
            all_contacts.difference([prev_residue.o_atom_index, prev_residue.c_atom_index]
                                    + residue.atom_indices)
        )
    except stutils.ClashError as error:  # Raised by _any_clashes()
        if silence_exceptions:
            return True
        else:
            raise error
    else:
        if clashes:
            if measured_clashes:
                bb_info = '\n\t'.join(f'Chain {residue.chain_id} {residue.number:5d}: {atom.get_atom_record()}'
                                      for residue, atom in measured_clashes)
                self.log.error(f'{self.name} contains {len(measured_clashes)} {measure} clashes from the following '
                               f'Residues to the corresponding Atom:\n\t{bb_info}')
                raise stutils.ClashError(clash_msg)
            if other_clashes:
                sc_info = '\n\t'.join(f'Chain {residue.chain_id} {residue.number:5d}: {atom.get_atom_record()}'
                                      for residue, atom in other_clashes)
                self.log.warning(f'{self.name} contains {len(other_clashes)} {other} clashes between the '
                                 f'following Residues:\n\t{sc_info}')
    return False

get_sasa 

get_sasa(probe_radius: float = 1.4, atom: bool = True, **kwargs)

Use FreeSASA to calculate the surface area of residues in the Structure object.

Parameters:

  • probe_radius (float, default: 1.4 ) –

    The radius which surface area should be generated

  • atom (bool, default: True ) –

    Whether the output should be generated for each atom. If False, will be generated for each Residue

Sets

self.sasa, self.residue(s).sasa

Source code in symdesign/structure/base.py 
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def get_sasa(self, probe_radius: float = 1.4, atom: bool = True, **kwargs):
    """Use FreeSASA to calculate the surface area of residues in the Structure object.

    Args:
        probe_radius: The radius which surface area should be generated
        atom: Whether the output should be generated for each atom. If False, will be generated for each Residue

    Sets:
        self.sasa, self.residue(s).sasa
    """
    if atom:
        out_format = 'pdb'
    # --format=pdb --depth=atom
    # REMARK 999 This PDB file was generated by FreeSASA 2.0.
    # REMARK 999 In the ATOM records temperature factors have been
    # REMARK 999 replaced by the SASA of the atom, and the occupancy
    # REMARK 999 by the radius used in the calculation.
    # MODEL        1                                        [radii][sasa]
    # ATOM   2557  C   PHE C 113      -2.627 -17.654  13.108  1.61  1.39
    # ATOM   2558  O   PHE C 113      -2.767 -18.772  13.648  1.42 39.95
    # ATOM   2559  CB  PHE C 113      -1.255 -16.970  11.143  1.88 13.46
    # ATOM   2560  CG  PHE C 113      -0.886 -17.270   9.721  1.61  1.98
    # ATOM   2563 CE1  PHE C 113      -0.041 -18.799   8.042  1.76 28.76
    # ATOM   2564 CE2  PHE C 113      -0.694 -16.569   7.413  1.76  2.92
    # ATOM   2565  CZ  PHE C 113      -0.196 -17.820   7.063  1.76  4.24
    # ATOM   2566 OXT  PHE C 113      -2.515 -16.590  13.750  1.46 15.09
    # ...
    # TER    7913      GLU A 264
    # ENDMDL EOF
    # if residue:
    else:
        out_format = 'seq'
    # --format=seq
    # Residues in ...
    # SEQ A    1 MET :   74.46
    # SEQ A    2 LYS :   96.30
    # SEQ A    3 VAL :    0.00
    # SEQ A    4 VAL :    0.00
    # SEQ A    5 VAL :    0.00
    # SEQ A    6 GLN :    0.00
    # SEQ A    7 ILE :    0.00
    # SEQ A    8 LYS :    0.87
    # SEQ A    9 ASP :    1.30
    # SEQ A   10 PHE :   64.55
    # ...
    # \n EOF
    if self.contains_hydrogen():
        include_hydrogen = ['--hydrogen']  # the addition of hydrogen changes results quite a bit
    else:
        include_hydrogen = []
    cmd = [putils.freesasa_exe_path, f'--format={out_format}', '--probe-radius', str(probe_radius),
           '-c', putils.freesasa_config_path, '--n-threads=2'] + include_hydrogen
    self.log.debug(f'FreeSASA:\n{subprocess.list2cmdline(cmd)}')
    p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
    out, err = p.communicate(input=self.get_atom_record().encode('utf-8'))
    # if err:  # usually results from Hydrogen atoms, silencing
    #     self.log.warning('\n%s' % err.decode('utf-8'))
    sasa_output = out.decode('utf-8').split('\n')
    if_idx = 0
    if atom:
        # slice removes first REMARK, MODEL and final TER, MODEL regardless of # of chains, TER inclusion
        # since return_atom_record doesn't have models, these won't be present and no option to freesasa about model
        # would be provided with above subprocess call
        atoms = self.atoms
        for line_split in map(str.split, sasa_output[5:-2]):  # Does slice remove need for if line[0] == 'ATOM'?
            if line_split[0] == 'ATOM':  # This line appears necessary as MODEL can be added if MODEL is written
                atoms[if_idx].sasa = float(line_split[-1])
                if_idx += 1
    else:
        seq_slice = slice(3)
        sasa_slice = slice(16, None)
        residues = self.residues
        for idx, line in enumerate(sasa_output[1:-1]):  # Does slice remove the need for if line[:3] == 'SEQ'?
            if line[seq_slice] == 'SEQ':  # Doesn't seem that this equality is sufficient ^
                residues[if_idx].sasa = float(line[sasa_slice])
                if_idx += 1
    try:
        self.sasa = sum([residue.sasa for residue in self.residues])
    except RecursionError:
        self.log.error('RecursionError measuring SASA')
        os.makedirs(putils.sasa_debug_dir, exist_ok=True)
        self.write(out_path=os.path.join(putils.sasa_debug_dir, f'SASA-INPUT-{self.name}.pdb'))
        with open(os.path.join(putils.sasa_debug_dir, f'SASA-OUTPUT-{self.name}.pdb'), 'w') as f:
            f.write('%s\n' % '\n'.join(sasa_output))

        raise stutils.DesignError(
            "Measurement of SASA isn't working, probably due to a missing Atom. Debug files written to "
            f'{putils.sasa_debug_dir}')

get_surface_area_residues 

get_surface_area_residues(residues: list[Residue] = None, dtype: sasa_types_literal = 'polar', **kwargs) -> float

Get the surface area for specified residues

Parameters:

  • residues (list[Residue], default: None ) –

    The Residues to sum. If not provided, will be retrieved by .get_residues()

  • dtype (sasa_types_literal, default: 'polar' ) –

    The type of area classification to query.

Other Parameters:

  • atom –

    bool = True - Whether the output should be generated for each atom. If False, will be generated for each Residue

  • probe_radius –

    float = 1.4 - The radius which surface area should be generated

  • numbers –

    Container[int] = None – Residue numbers of interest

  • indices –

    Iterable[int] = None – Residue indices of interest for the Structure

Returns:

  • float –

    Angstrom^2 of surface area

Source code in symdesign/structure/base.py 
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def get_surface_area_residues(
    self, residues: list[Residue] = None, dtype: sasa_types_literal = 'polar', **kwargs
) -> float:
    """Get the surface area for specified residues

    Args:
        residues: The Residues to sum. If not provided, will be retrieved by `.get_residues()`
        dtype: The type of area classification to query.

    Keyword Args:
        atom: bool = True - Whether the output should be generated for each atom.
            If False, will be generated for each Residue
        probe_radius: float = 1.4 - The radius which surface area should be generated
        numbers: Container[int] = None – Residue numbers of interest
        indices: Iterable[int] = None – Residue indices of interest for the Structure

    Returns:
        Angstrom^2 of surface area
    """
    if not self.sasa:
        self.get_sasa(**kwargs)

    if not residues:
        residues = self.get_residues(**kwargs)

    sasa_dtype = f'sasa_{dtype}'
    try:
        return sum([getattr(residue, sasa_dtype) for residue in residues])
    except AttributeError:
        raise ValueError(
            f" {dtype=} is an invalid 'sasa_dtype'. Viable types are {', '.join(sasa_types)}"
        )

errat 

errat(out_path: AnyStr = os.getcwd()) -> tuple[float, ndarray]

Find the overall and per residue Errat accuracy for the given Structure

Parameters:

  • out_path (AnyStr, default: getcwd() ) –

    The path where Errat files should be written

Returns:

  • tuple[float, ndarray] –

    Overall Errat score, Errat value/residue array

Source code in symdesign/structure/base.py 
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def errat(self, out_path: AnyStr = os.getcwd()) -> tuple[float, np.ndarray]:
    """Find the overall and per residue Errat accuracy for the given Structure

    Args:
        out_path: The path where Errat files should be written

    Returns:
        Overall Errat score, Errat value/residue array
    """
    # name = 'errat_input-%s-%d.pdb' % (self.name, random() * 100000)
    # current_struc_file = self.write(out_path=os.path.join(out_path, name))
    # errat_cmd = [putils.errat_exe_path, os.path.splitext(name)[0], out_path]  # for writing file first
    # os.system('rm %s' % current_struc_file)
    out_path = out_path if out_path[-1] == os.sep else out_path + os.sep  # errat needs trailing "/"
    errat_cmd = [putils.errat_exe_path, out_path]  # for passing atoms by stdin
    # p = subprocess.Popen(errat_cmd, stdin=subprocess.PIPE, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
    # out, err = p.communicate(input=self.get_atom_record().encode('utf-8'))
    # logger.info(self.get_atom_record()[:120])
    iteration = 1
    all_residue_scores = []
    number_of_residues = self.number_of_residues
    while iteration < 5:
        p = subprocess.run(errat_cmd, input=self.get_atom_record(), encoding='utf-8', capture_output=True)
        all_residue_scores = p.stdout.strip().split('\n')
        # Subtract one due to the addition of overall score
        if len(all_residue_scores) - 1 == number_of_residues:
            break
        iteration += 1

    if iteration == 5:
        error = p.stderr.strip().split('\n')
        self.log.debug(f"{self.errat.__name__} couldn't generate the correct output length. "
                       f'({len(all_residue_scores) - 1}) != number_of_residues ({number_of_residues}). Got stderr:'
                       f'\n{error}')
    # errat_output_file = os.path.join(out_path, '%s.ps' % name)
    # errat_output_file = os.path.join(out_path, 'errat.ps')
    # else:
    # print(subprocess.list2cmdline(['grep', 'Overall quality factor**: ', errat_output_file]))
    # p = subprocess.Popen(['grep', 'Overall quality factor', errat_output_file],
    #                      stdout=subprocess.PIPE, stderr=subprocess.DEVNULL)
    # errat_out, errat_err = p.communicate()
    try:
        # overall_score = set(errat_out.decode().split('\n'))
        # all_residue_scores = list(map(str.strip, errat_out.split('\n'), 'Residue '))
        # all_residue_scores = errat_out.split('\n')
        overall_score = all_residue_scores.pop(-1)
        return float(overall_score.split()[-1]), \
            np.array([float(score[-1]) for score in map(str.split, all_residue_scores)])
    except (IndexError, AttributeError, ValueError):  # ValueError when returning text instead of float
        self.log.warning(f'{self.name}: Failed to generate ERRAT measurement. Errat returned: {all_residue_scores}')
        return 0., np.array([0. for _ in range(number_of_residues)])

stride 

stride(to_file: AnyStr = None, **kwargs)

Calculates the secondary structure using the program Stride

Args to_file: The location of a file to save the Stride output

Sets

Each contained Residue instance .secondary_structure attribute

Source code in symdesign/structure/base.py 
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def stride(self, to_file: AnyStr = None, **kwargs):
    """Calculates the secondary structure using the program Stride

    Args
        to_file: The location of a file to save the Stride output

    Sets:
        Each contained Residue instance `.secondary_structure` attribute
    """
    # REM  -------------------- Secondary structure summary -------------------  XXXX
    # REM                .         .         .         .         .               XXXX
    # SEQ  1    IVQQQNNLLRAIEAQQHLLQLTVWGIKQLQAGGWMEWDREINNYTSLIHS   50          XXXX
    # STR       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH  HHHHHHHHHHHHHHHHH               XXXX
    # REM                                                                        XXXX
    # SEQ  51   LIEESQN                                              57          XXXX
    # STR       HHHHHH                                                           XXXX
    # REM                                                                        XXXX
    # LOC  AlphaHelix   ILE     3 A      ALA     33 A                            XXXX
    # LOC  AlphaHelix   TRP    41 A      GLN     63 A                            XXXX
    # REM                                                                        XXXX
    # REM  --------------- Detailed secondary structure assignment-------------  XXXX
    # REM                                                                        XXXX
    # REM  |---Residue---|    |--Structure--|   |-Phi-|   |-Psi-|  |-Area-|      XXXX
    # ASG  ILE A    3    1    H    AlphaHelix    360.00    -29.07     180.4      XXXX
    # ASG  VAL A    4    2    H    AlphaHelix    -64.02    -45.93      99.8      XXXX
    # ASG  GLN A    5    3    H    AlphaHelix    -61.99    -39.37      82.2      XXXX

    # ASG    Detailed secondary structure assignment
    # Format:
    #  5-8  Residue type
    #  9-10 Protein chain identifier
    #  11-15 PDB residue number
    #  16-20 Ordinal residue number
    #  24-25 One letter secondary structure code **)
    #  26-39 Full secondary structure name
    #  42-49 Phi angle
    #  52-59 Psi angle
    #  61-69 Residue solvent accessible area
    #
    # -rId1Id2..  Read only Chains Id1, Id2 ...
    # -cId1Id2..  Process only Chains Id1, Id2 ...

    # The Stride based secondary structure names of each unique element where possible values are
    #  H:Alpha helix,
    #  G:3-10 helix,
    #  I:PI-helix,
    #  E:Extended conformation,
    #  B/b:Isolated bridge,
    #  T:Turn,
    #  C:Coil (none of the above)'
    current_struc_file = self.write(out_path=f'stride_input-{self.name}-{random() * 100000}.pdb')
    p = subprocess.Popen([putils.stride_exe_path, current_struc_file],
                         stdout=subprocess.PIPE, stderr=subprocess.DEVNULL)
    out, err = p.communicate()
    struct_file = Path(current_struc_file)
    struct_file.unlink(missing_ok=True)
    # self.log.debug(f'Stride file is at: {current_struc_file}')

    if out:
        if to_file:
            with open(to_file, 'wb') as f:
                f.write(out)
        stride_output = out.decode('utf-8').split('\n')
    else:
        self.log.warning(f'{self.name}: No secondary structure assignment found with Stride')
        return

    residue_idx = count()
    residues = self.residues
    for line in stride_output:
        # residue_idx = int(line[10:15])
        if line[0:3] == 'ASG':
            # residue_idx = int(line[15:20])  # one-indexed, use in Structure version...
            # line[10:15].strip().isdigit():  # residue number -> line[10:15].strip().isdigit():
            # self.chain(line[9:10]).residue(int(line[10:15].strip())).secondary_structure = line[24:25]
            residues[next(residue_idx)].secondary_structure = line[24:25]

    self.secondary_structure = ''.join(residue.secondary_structure for residue in residues)

is_termini_helical 

is_termini_helical(termini: termini_literal = 'n', window: int = 5) -> bool

Using assigned secondary structure, probe for helical termini using a segment of 'window' residues. Will remove any disordered residues from the specified termini before checking, with the assumption that the disordered terminal residues are not integral to the structure

Parameters:

  • termini (termini_literal, default: 'n' ) –

    Either 'n' or 'c' should be specified

  • window (int, default: 5 ) –

    The segment size to search

Returns:

  • bool –

    True if the specified terminus has a stretch of helical residues the length of the window

Source code in symdesign/structure/base.py 
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def is_termini_helical(self, termini: stutils.termini_literal = 'n', window: int = 5) -> bool:
    """Using assigned secondary structure, probe for helical termini using a segment of 'window' residues. Will
    remove any disordered residues from the specified termini before checking, with the assumption that the
    disordered terminal residues are not integral to the structure

    Args:
        termini: Either 'n' or 'c' should be specified
        window: The segment size to search

    Returns:
        True if the specified terminus has a stretch of helical residues the length of the window
    """
    # Strip "disorder" from the termini, then use the window to compare against the secondary structure
    search_window = window * 2
    if termini in 'Nn':
        term_window = self.secondary_structure.lstrip(SS_DISORDER_IDENTIFIERS)[:search_window]
    elif termini in 'Cc':
        term_window = self.secondary_structure.rstrip(SS_DISORDER_IDENTIFIERS)[-search_window:]
    else:
        raise ValueError(
            f"The termini value {termini} isn't allowed. Must indicate one of {get_args(stutils.termini_literal)}")

    if 'H' * window in term_window:
        return True
    else:
        return False

calculate_secondary_structure 

calculate_secondary_structure(**kwargs)

Perform the secondary structure calculation for the Structure using the DEFAULT_SS_PROGRAM

Other Parameters:

  • to_file –

    AnyStr = None - The location of a file to save secondary structure calculations

Source code in symdesign/structure/base.py 
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def calculate_secondary_structure(self, **kwargs):
    """Perform the secondary structure calculation for the Structure using the DEFAULT_SS_PROGRAM

    Keyword Args:
        to_file: AnyStr = None - The location of a file to save secondary structure calculations
    """
    self.__getattribute__(DEFAULT_SS_PROGRAM)(**kwargs)  # self.stride()

termini_proximity_from_reference 

termini_proximity_from_reference(termini: termini_literal = 'n', reference: ndarray = utils.symmetry.origin, **kwargs) -> float

Finds the orientation of the termini from the origin (default) or from a reference point

Parameters:

  • termini (termini_literal, default: 'n' ) –

    Either 'n' or 'c' should be specified

  • reference (ndarray, default: origin ) –

    The reference where the point should be measured from

Returns:

  • float –

    When compared to the reference, 1 if the termini is more than halfway from the center of the Structure and -1 if the termini is less than halfway from the center of the Structure

Source code in symdesign/structure/base.py 
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def termini_proximity_from_reference(self, termini: stutils.termini_literal = 'n',
                                     reference: np.ndarray = utils.symmetry.origin, **kwargs) -> float:
    """Finds the orientation of the termini from the origin (default) or from a reference point

    Args:
        termini: Either 'n' or 'c' should be specified
        reference: The reference where the point should be measured from

    Returns:
        When compared to the reference, 1 if the termini is more than halfway from the center of the Structure and
            -1 if the termini is less than halfway from the center of the Structure
    """
    if termini == 'n':
        residue_coords = self.residues[0].n_coords
    elif termini == 'c':
        residue_coords = self.residues[-1].c_coords
    else:
        raise ValueError(
            f"'termini' must be either 'n' or 'c', not {termini}")

    if reference is None:
        reference = utils.symmetry.origin

    max_distance = self.distance_from_reference(reference=reference, measure='max')
    min_distance = self.distance_from_reference(reference=reference, measure='min')
    coord_distance = np.linalg.norm(residue_coords - reference)
    if abs(coord_distance - max_distance) < abs(coord_distance - min_distance):
        return 1  # Termini further from the reference
    else:
        return -1  # Termini closer to the reference

get_atom_record 

get_atom_record(**kwargs) -> str

Provides the Structure as a 'PDB' formatted string of Atom records

Other Parameters:

  • chain_id –

    str = None - The chain ID to use

  • atom_offset –

    int = 0 - How much to offset the atom number by. Default returns one-indexed

Returns:

  • str –

    The archived .pdb formatted ATOM records for the Structure

Source code in symdesign/structure/base.py 
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def get_atom_record(self, **kwargs) -> str:
    """Provides the Structure as a 'PDB' formatted string of Atom records

    Keyword Args:
        chain_id: str = None - The chain ID to use
        atom_offset: int = 0 - How much to offset the atom number by. Default returns one-indexed

    Returns:
        The archived .pdb formatted ATOM records for the Structure
    """
    return '\n'.join(residue.__str__(**kwargs) for residue in self.residues)

get_fragments 

get_fragments(residues: list[Residue] = None, residue_numbers: list[int] = None, fragment_db: FragmentDatabase = None, **kwargs) -> list[MonoFragment]

From the Structure, find Residues with a matching fragment type as identified in a fragment library

Parameters:

  • residues (list[Residue], default: None ) –

    The specific Residues to search for

  • residue_numbers (list[int], default: None ) –

    The specific residue numbers to search for

  • fragment_db (FragmentDatabase, default: None ) –

    The FragmentDatabase with representative fragment types to query against

Returns:

  • list[MonoFragment] –

    The MonoFragments found on the Structure

Source code in symdesign/structure/base.py 
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def get_fragments(self, residues: list[Residue] = None, residue_numbers: list[int] = None,
                  fragment_db: fragment.db.FragmentDatabase = None, **kwargs) -> list[fragment.MonoFragment]:
    """From the Structure, find Residues with a matching fragment type as identified in a fragment library

    Args:
        residues: The specific Residues to search for
        residue_numbers: The specific residue numbers to search for
        fragment_db: The FragmentDatabase with representative fragment types  to query against

    Returns:
        The MonoFragments found on the Structure
    """
    if not residues and not residue_numbers:
        return []

    if fragment_db is None:
        fragment_db = self.fragment_db
        if fragment_db is None:
            raise ValueError("Can't assign fragments without passing 'fragment_db' or setting .fragment_db")
        self.log.warning(f"Without passing 'fragment_db', using the existing .fragment_db={repr(fragment_db)}")

    try:
        fragment_db.representatives
    except AttributeError:
        raise TypeError(
            f"The passed fragment_db is not of the required type "
            f"'{fragment.db.FragmentDatabase.__class__.__name__}'")

    fragment_length = fragment_db.fragment_length
    fragment_range = range(*fragment_db.fragment_range)
    fragments = []
    for residue_number in residue_numbers:
        frag_residues = self.get_residues(numbers=[residue_number + i for i in fragment_range])

        if len(frag_residues) == fragment_length:
            new_fragment = fragment.MonoFragment(residues=frag_residues, fragment_db=fragment_db, **kwargs)
            if new_fragment.i_type:
                fragments.append(new_fragment)

    return fragments

get_fragment_residues 

get_fragment_residues(residues: list[Residue] = None, residue_numbers: list[int] = None, fragment_db: FragmentDatabase = None, rmsd_thresh: float = fragment.Fragment.rmsd_thresh, **kwargs) -> list | list[Residue]

Assigns a Fragment type to Residue instances identified from a FragmentDatabase, and returns them

Parameters:

  • residues (list[Residue], default: None ) –

    The specific Residues to search for

  • residue_numbers (list[int], default: None ) –

    The specific residue numbers to search for

  • fragment_db (FragmentDatabase, default: None ) –

    The FragmentDatabase with representative fragment types to query the Residue against

  • rmsd_thresh (float, default: rmsd_thresh ) –

    The threshold for which a rmsd should fail to produce a fragment match

Sets

Each Fragment Residue instance self.guide_coords, self.i_type

Returns:

  • list | list[Residue] –

    The Residue instances that match Fragment representatives from the Structure

Source code in symdesign/structure/base.py 
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def get_fragment_residues(self, residues: list[Residue] = None, residue_numbers: list[int] = None,
                          fragment_db: fragment.db.FragmentDatabase = None,
                          rmsd_thresh: float = fragment.Fragment.rmsd_thresh, **kwargs) -> list | list[Residue]:
    """Assigns a Fragment type to Residue instances identified from a FragmentDatabase, and returns them

    Args:
        residues: The specific Residues to search for
        residue_numbers: The specific residue numbers to search for
        fragment_db: The FragmentDatabase with representative fragment types to query the Residue against
        rmsd_thresh: The threshold for which a rmsd should fail to produce a fragment match

    Sets:
        Each Fragment Residue instance self.guide_coords, self.i_type

    Returns:
        The Residue instances that match Fragment representatives from the Structure
    """
    if fragment_db is None:
        fragment_db = self.fragment_db
        if fragment_db is None:
            raise ValueError("Can't assign fragments without passing 'fragment_db' or setting .fragment_db")
        self.log.warning(f"Without passing 'fragment_db', using the existing .fragment_db={repr(fragment_db)}")

    try:
        fragment_db.representatives
    except AttributeError:
        raise TypeError(
            f"The passed fragment_db is not of the required type "
            f"'{fragment.db.FragmentDatabase.__class__.__name__}'")

    if residue_numbers is not None:
        residues = self.get_residues(numbers=residue_numbers)

    # Get iterable of residues
    residues = self.residues if residues is None else residues

    # Get neighboring ca coords on each side by retrieving flanking residues. If not fragment_length, remove
    fragment_length = fragment_db.fragment_length
    frag_lower_range, frag_upper_range = fragment_db.fragment_range

    # Iterate over the residues in reverse to remove any indices that are missing and convert to coordinates
    viable_residues = []
    residues_ca_coords = []
    for residue in residues:
        residue_set = \
            residue.get_upstream(frag_lower_range) + [residue] + residue.get_downstream(frag_upper_range-1)
        if len(residue_set) == fragment_length:
            residues_ca_coords.append([residue.ca_coords for residue in residue_set])
            viable_residues.append(residue)

    residue_ca_coords = np.array(residues_ca_coords)

    # Solve for fragment type (secondary structure classification could be used too)
    found_fragments = []
    for idx, residue in enumerate(viable_residues):
        min_rmsd = float('inf')
        residue_ca_coord_set = residue_ca_coords[idx]
        for fragment_type, representative in fragment_db.representatives.items():
            rmsd, rot, tx = superposition3d(residue_ca_coord_set, representative.ca_coords)
            if rmsd <= rmsd_thresh and rmsd <= min_rmsd:
                residue.frag_type = fragment_type
                min_rmsd = rmsd

        if residue.frag_type:
            residue.fragment_db = fragment_db
            residue._fragment_coords = fragment_db.representatives[residue.frag_type].backbone_coords
            found_fragments.append(residue)

    return found_fragments

find_fragments 

find_fragments(fragment_db: FragmentDatabase = None, **kwargs) -> list[tuple[GhostFragment, Fragment, float]]

Search Residue instances to find Fragment instances that are neighbors, returning all Fragment pairs. By default, returns all Residue instances neighboring FragmentResidue instances

Parameters:

  • fragment_db (FragmentDatabase, default: None ) –

    The FragmentDatabase with representative fragment types to query the Residue against

Other Parameters:

  • residues –

    list[Residue] = None - The specific Residues to search for

  • residue_numbers –

    list[int] = None - The specific residue numbers to search for

  • rmsd_thresh –

    float = fragment.Fragment.rmsd_thresh - The threshold for which a rmsd should fail to produce a fragment match

  • distance –

    float = 8.0 - The distance to query for neighboring fragments

  • min_match_value –

    float = 2 - The minimum value which constitutes an acceptable fragment z_score

  • clash_coords –

    np.ndarray = None – The coordinates to use for checking for GhostFragment clashes

Returns:

  • list[tuple[GhostFragment, Fragment, float]] –

    The GhostFragment, Fragment pairs, along with their match score

Source code in symdesign/structure/base.py 
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def find_fragments(self, fragment_db: fragment.db.FragmentDatabase = None, **kwargs) \
        -> list[tuple[fragment.GhostFragment, fragment.Fragment, float]]:
    """Search Residue instances to find Fragment instances that are neighbors, returning all Fragment pairs.
    By default, returns all Residue instances neighboring FragmentResidue instances

    Args:
        fragment_db: The FragmentDatabase with representative fragment types to query the Residue against

    Keyword Args:
        residues: list[Residue] = None - The specific Residues to search for
        residue_numbers: list[int] = None - The specific residue numbers to search for
        rmsd_thresh: float = fragment.Fragment.rmsd_thresh - The threshold for which a rmsd should fail to produce
            a fragment match
        distance: float = 8.0 - The distance to query for neighboring fragments
        min_match_value: float = 2 - The minimum value which constitutes an acceptable fragment z_score
        clash_coords: np.ndarray = None – The coordinates to use for checking for GhostFragment clashes

    Returns:
        The GhostFragment, Fragment pairs, along with their match score
    """
    if fragment_db is None:
        fragment_db = self.fragment_db
        if fragment_db is None:
            raise ValueError("Can't assign fragments without passing 'fragment_db' or setting .fragment_db")
        self.log.warning(f"Without passing 'fragment_db', using the existing .fragment_db={repr(fragment_db)}")

    fragment_time_start = time.time()
    frag_residues = self.get_fragment_residues(fragment_db=fragment_db, **kwargs)
    self.log.info(f'Found {len(frag_residues)} fragments on {self.name}')

    frag_residue_indices = [residue.index for residue in frag_residues]
    all_fragment_pairs = []
    for frag_residue in frag_residues:
        # frag_neighbors = frag_residue.get_residue_neighbors(**kwargs)
        neighbors = self.get_residues_by_atom_indices(frag_residue.neighboring_atom_indices(**kwargs))
        # THIS GETS NON-SELF FRAGMENTS TOO
        # frag_neighbors = [residue for residue in neighbors if residue.frag_type]
        # if not frag_neighbors:
        #     continue
        frag_neighbors = [residue for residue in neighbors if residue.index in frag_residue_indices]
        if not frag_neighbors:
            continue
        all_fragment_pairs.extend(fragment.find_fragment_overlap([frag_residue], frag_neighbors, **kwargs))

    self.log.debug(f'Took {time.time() - fragment_time_start:.8f}s')
    return all_fragment_pairs

spatial_aggregation_propensity_per_residue 

spatial_aggregation_propensity_per_residue(distance: float = 5.0, **kwargs) -> list[float]

Calculate the spatial aggregation propensity on a per-residue basis using calculated heavy atom contacts to define which Residue instances are in contact.

Caution: Contrasts with published method due to use of relative sasa for each Residue instance instead of relative sasa for each Atom instance

Parameters:

  • distance (float, default: 5.0 ) –

    The distance in angstroms to measure Atom instances in contact

Other Parameters:

  • probe_radius –

    float = 1.4 - The radius which surface area should be generated

Returns:

  • list[float] –

    The floats representing the spatial aggregation propensity for each Residue in the Structure

Source code in symdesign/structure/base.py 
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def spatial_aggregation_propensity_per_residue(self, distance: float = 5., **kwargs) -> list[float]:
    """Calculate the spatial aggregation propensity on a per-residue basis using calculated heavy atom contacts to
    define which Residue instances are in contact.

    Caution: Contrasts with published method due to use of relative sasa for each Residue instance instead of
    relative sasa for each Atom instance

    Args:
        distance: The distance in angstroms to measure Atom instances in contact

    Keyword Args:
        probe_radius: float = 1.4 - The radius which surface area should be generated

    Returns:
        The floats representing the spatial aggregation propensity for each Residue in the Structure
    """
    # SASA Keyword args that are not reported as available
    # atom: bool = True - Whether the output should be generated for each atom.
    #     If False, will be generated for each Residue
    if not self.sasa:
        self.get_sasa(**kwargs)
    # Set up the hydrophobicity parameters
    hydrophobicity_ = hydrophobicity_values_glycine_centered['black_and_mould']
    # Get heavy Atom coordinates
    heavy_coords = self.heavy_coords
    # Make and query a tree
    tree = BallTree(heavy_coords)
    query = tree.query_radius(heavy_coords, distance)

    residues = self.residues
    # In case this was already called, all should be set to 0.0
    for residue in residues:
        residue.spatial_aggregation_propensity = 0.
        # Set the hydrophobicity_ attribute in a first pass to reduce repetitive lookups
        residue.hydrophobicity_ = hydrophobicity_[residue.type]

    heavy_atom_coords_indexed_residues = self.heavy_coords_indexed_residues
    contacting_pairs = set((heavy_atom_coords_indexed_residues[idx1], heavy_atom_coords_indexed_residues[idx2])
                           for idx2, contacts in enumerate(query.tolist()) for idx1 in contacts.tolist())
    # Residue.spatial_aggregation_propensity starts as 0., so we are adding any observation to that attribute
    for residue1, residue2 in contacting_pairs:
        # Multiply suggested hydrophobicity value by the Residue.relative_sasa
        # Only set on residue1 as this is the "center" of the calculation
        residue1.spatial_aggregation_propensity = residue2.hydrophobicity_ * residue2.relative_sasa

    return [residue.spatial_aggregation_propensity for residue in residues]

contact_order_per_residue 

contact_order_per_residue(sequence_distance_cutoff: int = 2, distance: float = 6.0) -> list[float]

Calculate the contact order on a per-residue basis using calculated heavy atom contacts

Parameters:

  • sequence_distance_cutoff (int, default: 2 ) –

    The residue spacing required to count a contact as a true contact

  • distance (float, default: 6.0 ) –

    The distance in angstroms to measure Atom instances in contact

Returns:

  • list[float] –

    The floats representing the contact order for each Residue in the Structure

Source code in symdesign/structure/base.py 
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def contact_order_per_residue(self, sequence_distance_cutoff: int = 2, distance: float = 6.) -> list[float]:
    """Calculate the contact order on a per-residue basis using calculated heavy atom contacts

    Args:
        sequence_distance_cutoff: The residue spacing required to count a contact as a true contact
        distance: The distance in angstroms to measure Atom instances in contact

    Returns:
        The floats representing the contact order for each Residue in the Structure
    """
    # Get heavy Atom coordinates
    heavy_coords = self.heavy_coords
    # Make and query a tree
    tree = BallTree(heavy_coords)
    query = tree.query_radius(heavy_coords, distance)

    residues = self.residues
    # In case this was already called, we should set all to 0.0
    for residue in residues:
        residue.contact_order = 0.

    heavy_atom_coords_indexed_residues = self.heavy_coords_indexed_residues
    contacting_pairs = set((heavy_atom_coords_indexed_residues[idx1], heavy_atom_coords_indexed_residues[idx2])
                           for idx2, contacts in enumerate(query.tolist()) for idx1 in contacts.tolist())
    # Residue.contact_order starts as 0., so we are adding any observation to that attribute
    for residue1, residue2 in contacting_pairs:
        # Calculate using number since index might not actually specify the intended distance
        residue_sequence_distance = abs(residue1.number - residue2.number)
        if residue_sequence_distance >= sequence_distance_cutoff:
            # Only set on residue1 so that we don't overcount
            residue1.contact_order += residue_sequence_distance

    number_residues = len(residues)
    for residue in residues:
        residue.contact_order /= number_residues

    return [residue.contact_order for residue in residues]

format_resfile_from_directives 

format_resfile_from_directives(residue_directives: dict[int | Residue, str], include: dict[int | Residue, set[str]] = None, background: dict[int | Residue, set[str]] = None, **kwargs) -> list[str]

Format Residue mutational potentials given Residues/residue numbers and corresponding mutation directive. Optionally, include specific amino acids and limit to a specific background. Both dictionaries accessed by same keys as residue_directives

Parameters:

  • residue_directives (dict[int | Residue, str]) –

    {Residue object: 'mutational_directive', ...}

  • include (dict[int | Residue, set[str]], default: None ) –

    Include a set of specific amino acids for each residue

  • background (dict[int | Residue, set[str]], default: None ) –

    The background amino acids to compare possibilities against

Other Parameters:

  • special –

    bool = False - Whether to include special residues

Returns:

  • list[str] –

    For each Residue, returns the string formatted for a resfile with a 'PIKAA' and amino acid type string

Source code in symdesign/structure/base.py 
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def format_resfile_from_directives(self, residue_directives: dict[int | Residue, str],
                                   include: dict[int | Residue, set[str]] = None,
                                   background: dict[int | Residue, set[str]] = None, **kwargs) -> list[str]:
    """Format Residue mutational potentials given Residues/residue numbers and corresponding mutation directive.
    Optionally, include specific amino acids and limit to a specific background. Both dictionaries accessed by same
    keys as residue_directives

    Args:
        residue_directives: {Residue object: 'mutational_directive', ...}
        include: Include a set of specific amino acids for each residue
        background: The background amino acids to compare possibilities against

    Keyword Args:
        special: bool = False - Whether to include special residues

    Returns:
        For each Residue, returns the string formatted for a resfile with a 'PIKAA' and amino acid type string
    """
    if background is None:
        background = {}
    if include is None:
        include = {}

    res_file_lines = []
    residues = self.residues
    for residue_index, directive in residue_directives.items():
        if isinstance(residue_index, Residue):
            residue = residue_index
            residue_index = residue.index
        else:
            residue = residues[residue_index]

        allowed_aas = residue.mutation_possibilities_from_directive(
            directive, background=background.get(residue_index), **kwargs)
        allowed_aas = {protein_letters_3to1_extended[aa] for aa in allowed_aas}
        allowed_aas = allowed_aas.union(include.get(residue_index, {}))
        res_file_lines.append(f'{residue.number} {residue.chain_id} PIKAA {"".join(sorted(allowed_aas))}')

    return res_file_lines

make_resfile 

make_resfile(residue_directives: dict[Residue | int, str], out_path: AnyStr = os.getcwd(), header: list[str] = None, **kwargs) -> AnyStr

Format a resfile for the Rosetta Packer from Residue mutational directives

Parameters:

  • residue_directives (dict[Residue | int, str]) –

    {Residue/int: 'mutational_directive', ...}

  • out_path (AnyStr, default: getcwd() ) –

    Directory to write the file

  • header (list[str], default: None ) –

    A header to constrain all Residues for packing

Other Parameters:

  • include –

    dict[Residue | int, set[str]] = None - Include a set of specific amino acids for each residue

  • background –

    dict[Residue | int, set[str]] = None - The background amino acids to compare possibilities

  • special –

    bool = False - Whether to include special residues

Returns:

  • AnyStr –

    The path to the resfile

Source code in symdesign/structure/base.py 
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def make_resfile(self, residue_directives: dict[Residue | int, str], out_path: AnyStr = os.getcwd(),
                 header: list[str] = None, **kwargs) -> AnyStr:
    """Format a resfile for the Rosetta Packer from Residue mutational directives

    Args:
        residue_directives: {Residue/int: 'mutational_directive', ...}
        out_path: Directory to write the file
        header: A header to constrain all Residues for packing

    Keyword Args:
        include: dict[Residue | int, set[str]] = None - Include a set of specific amino acids for each residue
        background: dict[Residue | int, set[str]] = None - The background amino acids to compare possibilities
        special: bool = False - Whether to include special residues

    Returns:
        The path to the resfile
    """
    residue_lines = self.format_resfile_from_directives(residue_directives, **kwargs)
    res_file = os.path.join(out_path, f'{self.name}.resfile')
    with open(res_file, 'w') as f:
        # Format the header
        f.write('%s\n' % ('\n'.join(header + ['start']) if header else 'start'))
        # Start the body
        f.write('%s\n' % '\n'.join(residue_lines))

    return res_file

set_b_factor_by_attribute 

set_b_factor_by_attribute(dtype: residue_attributes_literal)

Set the b-factor entry for every Residue to a Residue attribute

Parameters:

  • dtype (residue_attributes_literal) –

    The attribute of interest

Source code in symdesign/structure/base.py 
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def set_b_factor_by_attribute(self, dtype: residue_attributes_literal):
    """Set the b-factor entry for every Residue to a Residue attribute

    Args:
        dtype: The attribute of interest
    """
    if isinstance(dtype, str):
        # self.set_residues_attributes(b_factor=dtype)
        for residue in self.residues:
            residue.b_factor = getattr(residue, dtype)
    else:
        raise TypeError(
            f"The type '{dtype.__class__.__name__}' isn't a string. To {self.set_b_factor_by_attribute.__name__}, "
            "you must provide 'dtype' as a string specifying a Residue attribute")

set_b_factor_data 

set_b_factor_data(values: Iterable[float])

Set the b-factor entry for every Residue to a value from an array-like

Parameters:

  • values (Iterable[float]) –

    Array-like of integer types to set each Residue instance 'b_factor' attribute to

Source code in symdesign/structure/base.py 
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def set_b_factor_data(self, values: Iterable[float]):
    """Set the b-factor entry for every Residue to a value from an array-like

    Args:
        values: Array-like of integer types to set each Residue instance 'b_factor' attribute to
    """
    if isinstance(values, Iterable):
        values = list(values)
        if len(values) != self.number_of_residues:
            raise ValueError(
                f"Can't provide a array-like of values with length {len(values)} != {self.number_of_residues}, the "
                "number of residues")
        for residue, value in zip(self.residues, values):
            residue.b_factor = value
    else:
        raise TypeError(
            f"The type '{values.__class__.__name__}' isn't an Iterable. To {self.set_b_factor_data.__name__}, you "
            "must provide the 'values' as an Iterable of integer type with length = number_of_residues")

Structures 

Structures(structures: Iterable[ContainsResidues], dtype: str = None, **kwargs)

Bases: ContainsResidues, UserList

A view of a set of Structure instances. This isn't used at the moment

Parameters:

  • structures (Iterable[ContainsResidues]) –

    The Iterable of Structure to set the Structures with

  • dtype (str, default: None ) –

    If an empty Structures, the specific subclass of Structure that Structures contains

Source code in symdesign/structure/base.py 
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def __init__(self, structures: Iterable[ContainsResidues], dtype: str = None, **kwargs):
    """Pass the parent Structure with parent= to initialize .log, .coords, .atoms, and .residues

    Args:
        structures: The Iterable of Structure to set the Structures with
        dtype: If an empty Structures, the specific subclass of Structure that Structures contains
    """
    super().__init__(initlist=structures, **kwargs)  # initlist sets UserList.data to Iterable[Structure]
    raise NotImplementedError("This class isn't functional yet")
    if self.is_parent():
        raise stutils.ConstructionError(
            f"Couldn't create {Structures.__name__} without passing 'parent' argument"
        )

    if not self.data:  # Set up an empty Structures
        self.dtype = dtype if dtype else 'Structure'
    elif all([True if isinstance(structure, ContainsResidues) else False for structure in self]):
        # self.data = [structure for structure in structures]
        self._atom_indices = []
        for structure in self:
            self._atom_indices.extend(structure.atom_indices)
        self._residue_indices = []
        for structure in self:
            self._residue_indices.extend(structure.residue_indices)

        self.dtype = dtype if dtype else type(self.data[0]).__name__
    else:
        raise ValueError(
            f"Can't set {self.__class__.__name__} by passing '{', '.join(type(structure) for structure in self)}, "
            f'must set with type [Structure, ...] or an empty constructor. Ex: Structures()')

    # Overwrite attributes in Structure
    self.name = f'{self.parent.name}-{dtype}Selection'

dtype instance-attribute 

dtype: str

The type of Structure in instance

structures property 

structures: list[ContainsResidues]

Returns the underlying data in Structures

parse_seqres 

parse_seqres(seqres_lines: list[str]) -> dict[str, str]

Convert SEQRES information to single amino acid dictionary format

Parameters:

  • seqres_lines (list[str]) –

    The list of lines containing SEQRES information

Returns:

  • dict[str, str] –

    The mapping of each chain to its reference sequence

Source code in symdesign/structure/base.py 
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def parse_seqres(seqres_lines: list[str]) -> dict[str, str]:  # list[str]:
    """Convert SEQRES information to single amino acid dictionary format

    Args:
        seqres_lines: The list of lines containing SEQRES information

    Returns:
        The mapping of each chain to its reference sequence
    """
    # SEQRES   1 A  182  THR THR ALA SER THR SER GLN VAL ARG GLN ASN TYR HIS
    # SEQRES   2 A  182  GLN ASP SER GLU ALA ALA ILE ASN ARG GLN ILE ASN LEU
    # SEQRES   3 A  182  GLU LEU TYR ALA SER TYR VAL TYR LEU SER MET SER TYR
    # SEQRES ...
    # SEQRES  16 C  201  SER TYR ILE ALA GLN GLU
    # In order to account for MultiModel files where the chain names are all the same, using the parsed order
    # instead of a dictionary as later entries would overwrite earlier ones making them inaccurate
    # If the file is screwed up in that it has chains in a different order than the seqres, then this wouldn't work
    # I am opting for the standard .pdb file format and if it is messed up this is the users problem
    reference_sequence = {}
    for line in seqres_lines:
        chain, length, *sequence = line.split()
        if chain in reference_sequence:
            reference_sequence[chain].extend(list(sequence))
        else:
            reference_sequence[chain] = list(sequence)

    # Format the sequences as a one AA letter list
    reference_sequences = {}  # []
    for chain, sequence in reference_sequence.items():
        # Ensure we parse selenomethionine correctly
        one_letter_sequence = [protein_letters_3to1_extended_mse.get(aa, '-')
                               for aa in sequence]
        reference_sequences[chain] = ''.join(one_letter_sequence)
        # reference_sequences.append(''.join(one_letter_sequence))

    return reference_sequences

read_pdb_file 

read_pdb_file(file: AnyStr = None, pdb_lines: Iterable[str] = None, separate_coords: bool = True, **kwargs) -> dict[str, Any]

Reads .pdb file and returns structural information pertaining to parsed file

By default, returns the coordinates as a separate numpy.ndarray which is parsed directly by StructureBase. This will be associated with each Atom however, separate parsing is done for efficiency. To include coordinate info with the individual Atom instances, pass separate_coords=False. (Not recommended)

Parameters:

  • file (AnyStr, default: None ) –

    The path to the file to parse

  • pdb_lines (Iterable[str], default: None ) –

    If lines are already read, provide the lines instead

  • separate_coords (bool, default: True ) –

    Whether to separate parsed coordinates from Atom instances. Will be returned as two separate entries in the parsed dictionary, otherwise returned with coords=None

Returns:

  • dict[str, Any] –

    The dictionary containing all the parsed structural information

Source code in symdesign/structure/base.py 
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def read_pdb_file(file: AnyStr = None, pdb_lines: Iterable[str] = None, separate_coords: bool = True, **kwargs) -> \
        dict[str, Any]:
    """Reads .pdb file and returns structural information pertaining to parsed file

    By default, returns the coordinates as a separate numpy.ndarray which is parsed directly by StructureBase. This will
    be associated with each Atom however, separate parsing is done for efficiency. To include coordinate info with the
    individual Atom instances, pass separate_coords=False. (Not recommended)

    Args:
        file: The path to the file to parse
        pdb_lines: If lines are already read, provide the lines instead
        separate_coords: Whether to separate parsed coordinates from Atom instances. Will be returned as two separate
            entries in the parsed dictionary, otherwise returned with coords=None

    Returns:
        The dictionary containing all the parsed structural information
    """
    if pdb_lines:
        # path, extension = None, None
        assembly: str | None = None
        name = None
    elif file is not None:
        with open(file, 'r') as f:
            pdb_lines = f.readlines()
        path, extension = os.path.splitext(file)
        name = os.path.basename(path)

        if extension[-1].isdigit():
            # If last character is not a letter, then the file is an assembly, or the extension was provided weird
            assembly: str | None = extension.translate(utils.keep_digit_table)
        else:
            assembly = None
    else:
        raise ValueError(
            f"{read_pdb_file.__name__}: Must provide the argument 'file' or 'pdb_lines'")

    # type to info index:   1    2    3    4    5    6    7     11     12   13   14
    # eventual type:      int, str, str, str, str, int, str, float, float, str, str]] = []
    temp_info: list[tuple[str, str, str, str, str, str, str, str, str, str, str]] = []
    # type to info index:   1    2    3    4    5    6    7 8,9,10     11     12   13   14
    # fields w/ coords   [int, str, str, str, str, int, str, float, float, float, str, str]
    coords: list[list[float]] = []
    cryst_record: str = None
    dbref: dict[str, dict[str, str]] = {}
    entity_info: dict[str, dict[str, dict | list | str]] = {}
    header: list = []
    resolution: float | None = None
    seq_res_lines: list[str] = []
    biomt = []

    entity = None
    current_operation = -1
    alt_loc_str = ' '
    # for line_tokens in map(str.split, pdb_lines):
    #     # 0       1       2          3             4             5      6               7                   8  9
    #     # remark, number, atom_type, alt_location, residue_type, chain, residue_number, code_for_insertion, x, y,
    #     #     10 11   12         13       14
    #     #     z, occ, temp_fact, element, charge = \
    #     #     line[6:11].strip(), int(line[6:11]), line[12:16].strip(), line[16:17].strip(), line[17:20].strip(),
    #     #     line[21:22], int(line[22:26]), line[26:27].strip(), float(line[30:38]), float(line[38:46]), \
    #     #     float(line[46:54]), float(line[54:60]), float(line[60:66]), line[76:78].strip(), line[78:80].strip()
    for line in pdb_lines:
        remark = line[slice_remark]
        if remark == 'ATOM  ' or line[slice_residue_type] == 'MSE' and remark == 'HETATM':
            # if remove_alt_location and alt_location not in ['', 'A']:
            if line[slice_alt_location] not in [alt_loc_str, 'A']:
                continue
            # number = int(line[slice_number])
            residue_type = line[slice_residue_type].strip()
            if residue_type == 'MSE':
                residue_type = 'MET'
                atom_type = line[slice_atom_type].strip()
                if atom_type == 'SE':
                    atom_type = 'SD'  # change type from Selenium to Sulfur delta
            else:
                atom_type = line[slice_atom_type].strip()
            # prepare line information for population of Atom objects
            temp_info.append((line[slice_number], atom_type, alt_loc_str, residue_type, line[slice_chain],
                              line[slice_residue_number], line[slice_code_for_insertion].strip(),
                              line[slice_occ], line[slice_temp_fact],
                              line[slice_element].strip(), line[slice_charge].strip()))
            # temp_info.append((int(line[slice_number]), atom_type, alt_loc_str, residue_type, line[slice_chain],
            #                   int(line[slice_residue_number]), line[slice_code_for_insertion].strip(),
            #                   float(line[slice_occ]), float(line[slice_temp_fact]),
            #                   line[slice_element].strip(), line[slice_charge].strip()))
            # Prepare the atomic coordinates for addition to numpy array
            coords.append([float(line[slice_x]), float(line[slice_y]), float(line[slice_z])])
        elif remark == 'SEQRES':
            seq_res_lines.append(line[11:])
        elif remark == 'REMARK':
            header.append(line.strip())
            remark_number = line[slice_number]
            # elif line[:18] == 'REMARK 350   BIOMT':
            if remark_number == ' 350 ':  # 6:11  '   BIOMT'
                # integration of the REMARK 350 BIOMT
                # REMARK 350
                # REMARK 350 BIOMOLECULE: 1
                # REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC
                # REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
                # REMARK 350 SOFTWARE USED: PISA
                # REMARK 350 TOTAL BURIED SURFACE AREA: 6220 ANGSTROM**2
                # REMARK 350 SURFACE AREA OF THE COMPLEX: 28790 ANGSTROM**2
                # REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL
                # REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
                # REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
                # REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
                # REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
                try:
                    _, _, biomt_indicator, operation_number, x, y, z, tx = line.split()
                except ValueError:  # Not enough values to unpack
                    continue
                if biomt_indicator == 'BIOMT':
                    if operation_number != current_operation:  # Reached a new transformation matrix
                        current_operation = operation_number
                        biomt.append([])
                    # Add the transformation to the current matrix
                    biomt[-1].append(list(map(float, (x, y, z, tx))))
            elif remark_number == '   2 ':  # 6:11 ' RESOLUTION'
                try:
                    resolution = float(line[22:30].strip().split()[0])
                except (IndexError, ValueError):
                    resolution = None
        elif 'DBREF' in remark:
            header.append(line.strip())
            chain = line[12:14].strip().upper()
            if line[5:6] == '2':
                db_accession_id = line[18:40].strip()
            else:
                db = line[26:33].strip()
                if line[5:6] == '1':  # skip grabbing db_accession_id until DBREF2
                    continue
                db_accession_id = line[33:42].strip()
            dbref[chain] = {'db': db, 'accession': db_accession_id}  # implies each chain has only one id
        elif remark == 'COMPND' and 'MOL_ID' in line:
            header.append(line.strip())
            entity = line[line.rfind(':') + 1: line.rfind(';')].strip()
        elif remark == 'COMPND' and 'CHAIN' in line and entity:  # retrieve from standard .pdb file notation
            header.append(line.strip())
            # entity number (starting from 1) = {'chains' : {A, B, C}}
            entity_info[f'{name}_{entity}'] = \
                {'chains': list(map(str.strip, line[line.rfind(':') + 1:].strip().rstrip(';').split(',')))}
            entity = None
        elif remark == 'SCALE ':
            header.append(line.strip())
        elif remark == 'CRYST1':
            header.append(line.strip())
            cryst_record = line  # Don't .strip() so '\n' is attached for output
            # uc_dimensions, space_group = parse_cryst_record(cryst_record)
            # cryst = {'space': space_group, 'a_b_c': tuple(uc_dimensions[:3]), 'ang_a_b_c': tuple(uc_dimensions[3:])}

    if not temp_info:
        if file:
            raise ValueError(
                f'The file {file} has no ATOM records')
        else:
            raise ValueError("The provided 'pdb_lines' have no ATOM records")

    # Combine entity_info with the reference_sequence info and dbref info
    if seq_res_lines:
        reference_sequence = parse_seqres(seq_res_lines)
    else:
        reference_sequence = None

    for entity_name, info in entity_info.items():
        # Grab the first chain from the identified chains, and use it to grab the reference sequence
        chain = info['chains'][0]
        try:
            info['reference_sequence'] = reference_sequence[chain]  # Used when parse_seqres returns dict[str, str]
        except TypeError:  # This is None
            pass
        try:
            info['dbref'] = dbref[chain]
        except KeyError:  # Keys are missing
            pass

    # # Convert the incrementing reference sequence to a list of the sequences
    # reference_sequence = list(reference_sequence.values())

    if biomt:
        biomt = np.array(biomt, dtype=float)
        rotation_matrices = biomt[:, :, :3]
        translation_matrices = biomt[:, :, 3:].squeeze()
    else:
        rotation_matrices = translation_matrices = None

    parsed_info = \
        dict(atoms=[Atom.without_coordinates(idx, *info) for idx, info in enumerate(temp_info)]
             if separate_coords else
             # Initialize with individual coords. Not sure why anyone would do this, but include for compatibility
             [Atom(number=int(number), atom_type=atom_type, alt_location=alt_location, residue_type=residue_type,
                   chain_id=chain_id, residue_number=int(residue_number), code_for_insertion=code_for_insertion,
                   coords=coords[idx], occupancy=float(occupancy), b_factor=float(b_factor), element=element,
                   charge=charge)
              for idx, (number, atom_type, alt_location, residue_type, chain_id, residue_number, code_for_insertion,
                        occupancy, b_factor, element, charge)
              in enumerate(temp_info)],
             biological_assembly=assembly,
             rotation_matrices=rotation_matrices,
             translation_matrices=translation_matrices,
             coords=coords if separate_coords else None,
             cryst_record=cryst_record,
             entity_info=entity_info,
             name=name,
             resolution=resolution,
             reference_sequence=reference_sequence,
             )
    # Explicitly overwrite any parsing if argument was passed to caller
    parsed_info.update(**kwargs)
    return parsed_info

read_mmcif_file 

read_mmcif_file(file: AnyStr = None, **kwargs) -> dict[str, Any]

Reads .cif file and returns structural information pertaining to parsed file

By default, returns the coordinates as a separate numpy.ndarray which is parsed directly by StructureBase. This will be associated with each Atom however, separate parsing is done for efficiency. To include coordinate info with the individual Atom instances, pass separate_coords=False. (Not recommended)

Parameters:

  • file (AnyStr, default: None ) –

    The path to the file to parse

Returns:

  • dict[str, Any] –

    The dictionary containing all the parsed structural information

Source code in symdesign/structure/base.py 
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def read_mmcif_file(file: AnyStr = None, **kwargs) -> dict[str, Any]:
    """Reads .cif file and returns structural information pertaining to parsed file

    By default, returns the coordinates as a separate numpy.ndarray which is parsed directly by StructureBase. This will
    be associated with each Atom however, separate parsing is done for efficiency. To include coordinate info with the
    individual Atom instances, pass separate_coords=False. (Not recommended)

    Args:
        file: The path to the file to parse

    Returns:
        The dictionary containing all the parsed structural information
    """
    # if lines:
    #     # path, extension = None, None
    #     assembly: str | None = None
    #     name = None
    # el
    if file is not None:
        path, extension = os.path.splitext(file)
        name = os.path.basename(path)
        ignore_fields = []
        data: dict[str, dict[str, Any]] = cif_reader.read(file, ignore=ignore_fields)
        if extension[-1].isdigit():
            # If last character is not a letter, then the file is an assembly, or the extension was provided weird
            assembly: str | None = extension.translate(utils.keep_digit_table)
        elif 'assembly' in name:
            assembly = name[name.find('assembly'):].translate(utils.keep_digit_table)
        else:
            assembly = None
    else:
        raise ValueError(
            f"{read_mmcif_file.__name__}: Must provide the argument 'file'"
        )

    #  name = kwargs.pop('name', None)
    #  if not name:
    #      name = os.path.basename(os.path.splitext(file)[0])
    #
    #  input(data.keys())
    #  for k, v_ in data.items():
    #      # input(f'{list(v_.keys())}')
    #      # ['_entry', '_audit_conform', '_database_2', '_pdbx_database_PDB_obs_spr', '_pdbx_database_related',
    #      #  '_pdbx_database_status', '_audit_author', '_citation', '_citation_author', '_cell', '_symmetry',
    #      #  '_entity', '_entity_poly', '_entity_poly_seq', '_entity_src_gen', '_struct_ref', '_struct_ref_seq',
    #      #  '_struct_ref_seq_dif', '_chem_comp', '_exptl', '_exptl_crystal', '_exptl_crystal_grow', '_diffrn',
    #      #  '_diffrn_detector', '_diffrn_radiation', '_diffrn_radiation_wavelength', '_diffrn_source', '_reflns',
    #      #  '_reflns_shell', '_refine', '_refine_hist', '_refine_ls_restr', '_refine_ls_shell', '_pdbx_refine',
    #      #  '_struct', '_struct_keywords', '_struct_asym', '_struct_biol', '_struct_conf', '_struct_conf_type',
    #      #  '_struct_mon_prot_cis', '_struct_sheet', '_struct_sheet_order', '_struct_sheet_range',
    #      #  '_pdbx_struct_sheet_hbond', '_atom_sites', '_atom_type', '_atom_site', '_atom_site_anisotrop',
    #      #  '_pdbx_poly_seq_scheme', '_pdbx_struct_assembly', '_pdbx_struct_assembly_gen',
    #      #  '_pdbx_struct_assembly_prop', '_pdbx_struct_oper_list', '_pdbx_audit_revision_history',
    #      #  '_pdbx_audit_revision_details', '_pdbx_audit_revision_group', '_pdbx_refine_tls',
    #      #  '_pdbx_refine_tls_group', '_pdbx_phasing_MR', '_phasing', '_software', '_pdbx_validate_torsion',
    #      #  '_pdbx_unobs_or_zero_occ_atoms', '_pdbx_unobs_or_zero_occ_residues', '_space_group_symop']
    #      for idx, (k, v) in enumerate(v_.items()):
    #          # if k == '_atom_sites':
    #          #     input(v.keys())
    #          # if k in ['_database_2', '_pdbx_database_PDB_obs_spr', '_pdbx_database_related', '_pdbx_database_status']:
    #          #     print('Database key', k)
    #          #     input(v)
    #          # if k in ['_entity', '_entity_poly', '_entity_poly_seq', '_struct_ref']:  # '_entity_src_gen', '_struct_ref_seq'
    #          #     print('Sequence key', k)
    #          #     input(v)
    #          # if k in ['_cell', '_symmetry',
    #          #          # '_space_group_symop'
    #          #          ]:
    #          #     print('Symmetry key', k)
    #          #     input(v)
    #          # if k in ['_reflns', '_reflns_shell', '_refine', '_refine_hist', '_refine_ls_restr', '_refine_ls_shell', '_pdbx_refine',]:
    #          #     print('Diffraction key', k)
    #          #     input(v)
    #          # if k in [
    #          #     # '_struct', '_struct_keywords', '_struct_asym', '_struct_biol',
    #          #     '_pdbx_struct_assembly', '_pdbx_struct_assembly_gen',
    #          #     # '_pdbx_struct_assembly_prop',
    #          #     '_pdbx_struct_oper_list',
    #          # ]:
    #          #     print('struct key', k)
    #          #     input(v)
    #          # if k == '_atom_site':
    #          #     """
    #          #     key group_PDB
    #          #     values ['ATOM', 'ATOM', 'ATOM', 'ATOM', 'ATOM', 'ATOM', 'ATOM', 'ATOM', 'ATOM', 'ATOM']
    #          #     key id
    #          #     values ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10']
    #          #     key type_symbol
    #          #     values ['N', 'C', 'C', 'O', 'C', 'O', 'N', 'C', 'C', 'O']
    #          #     key label_atom_id
    #          #     values ['N', 'CA', 'C', 'O', 'CB', 'OG', 'N', 'CA', 'C', 'O']
    #          #     key label_alt_id
    #          #     values ['.', '.', '.', '.', '.', '.', '.', '.', '.', '.']
    #          #     key label_comp_id
    #          #     values ['SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'VAL', 'VAL', 'VAL', 'VAL']
    #          #     key label_asym_id
    #          #     values ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A']
    #          #     key label_entity_id
    #          #     values ['1', '1', '1', '1', '1', '1', '1', '1', '1', '1']
    #          #     key label_seq_id
    #          #     values ['3', '3', '3', '3', '3', '3', '4', '4', '4', '4']
    #          #     key pdbx_PDB_ins_code
    #          #     values ['?', '?', '?', '?', '?', '?', '?', '?', '?', '?']
    #          #     key Cartn_x
    #          #     values ['25.947', '25.499', '24.208', '23.310', '26.585', '27.819', '24.126', '22.943', '22.353', '23.081']
    #          #     key Cartn_y
    #          #     values ['8.892', '10.149', '9.959', '10.800', '10.734', '10.839', '8.851', '8.533', '7.200', '6.224']
    #          #     key Cartn_z
    #          #     values ['43.416', '42.828', '42.038', '42.084', '41.925', '42.615', '41.310', '40.519', '40.967', '41.152']
    #          #     key occupancy
    #          #     values ['1.00', '1.00', '1.00', '1.00', '1.00', '1.00', '1.00', '1.00', '1.00', '1.00']
    #          #     key B_iso_or_equiv
    #          #     values ['67.99', '79.33', '61.67', '60.15', '81.39', '86.58', '62.97', '56.54', '56.17', '85.78']
    #          #     key pdbx_formal_charge
    #          #     values ['?', '?', '?', '?', '?', '?', '?', '?', '?', '?']
    #          #     key auth_seq_id
    #          #     values ['3', '3', '3', '3', '3', '3', '4', '4', '4', '4']
    #          #     key auth_comp_id
    #          #     values ['SER', 'SER', 'SER', 'SER', 'SER', 'SER', 'VAL', 'VAL', 'VAL', 'VAL']
    #          #     key auth_asym_id
    #          #     values ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A']
    #          #     key auth_atom_id
    #          #     values ['N', 'CA', 'C', 'O', 'CB', 'OG', 'N', 'CA', 'C', 'O']
    #          #     key pdbx_PDB_model_num
    #          #     values ['1', '1', '1', '1', '1', '1', '1', '1', '1', '1']
    #          #     """
    #          #     for k__, v__ in v.items():
    #          #         # ['group_PDB', 'id', 'type_symbol', 'label_atom_id', 'label_alt_id', 'label_comp_id', 'label_asym_id', 'label_entity_id', 'label_seq_id', 'pdbx_PDB_ins_code', 'Cartn_x', 'Cartn_y', 'Cartn_z', 'occupancy', 'B_iso_or_equiv', 'pdbx_formal_charge', 'auth_seq_id', 'auth_comp_id', 'auth_asym_id', 'auth_atom_id', 'pdbx_PDB_model_num']
    #          #         print('key', k__)
    #          #         input(f'values {v__[:10]}')
    #          #     input('DONE')
    #          pass

    provided_dataname, *_ = data.keys()
    if _:
        raise ValueError(
            f"Found multiple values for the cif 'provided_dataname'={_}")

    # Extract the data of interest as saved by the provided_dataname
    data = data[provided_dataname]

    # def format_mmcif_dict(data: dict[str, Any], name: str = None, **kwargs) -> dict:
    atom_data = data.get('_atom_site')
    atom_numbers = atom_data.get('id')
    number_of_atoms = len(atom_numbers)
    atom_types = atom_data.get('label_atom_id')
    alt_locations = atom_data.get('label_alt_id', repeat(' ', number_of_atoms))
    residue_types = atom_data.get('label_comp_id')
    chains = atom_data.get('label_asym_id')
    residue_numbers = atom_data.get('label_seq_id')
    occupancies = atom_data.get('occupancy')
    code_for_insertion = atom_data.get('', repeat(' ', number_of_atoms))
    b_factors = atom_data.get('B_iso_or_equiv')
    element = atom_data.get('type_symbol', repeat(None, number_of_atoms))
    charge = atom_data.get('pdbx_formal_charge', repeat(None, number_of_atoms))
    alt_locations = ''.join(alt_locations).replace('.', ' ')
    code_for_insertion = ''.join(code_for_insertion).replace('.', ' ')
    charge = ''.join(charge).replace('?', ' ')

    atoms = [Atom.without_coordinates(idx, *info) for idx, info in enumerate(
        zip(atom_numbers, atom_types, alt_locations, residue_types, chains, residue_numbers, code_for_insertion,
            occupancies, b_factors, element, charge))]

    coords = np.array([atom_data.get('Cartn_x'),
                       atom_data.get('Cartn_y'),
                       atom_data.get('Cartn_z')], dtype=float).T
    cell_data = data.get('_cell')
    if cell_data:
        # 'length_a': '124.910', 'length_b': '189.250', 'length_c': '376.830',
        # 'angle_alpha': '90.00', 'angle_beta': '90.02', 'angle_gamma': '90.00'
        # Formatted in Hermann-Mauguin notation
        space_group = data.get('_symmetry', {}).get('space_group_name_H-M')
        cryst_record = utils.symmetry.generate_cryst1_record(
            list(map(float, (cell_data['length_a'], cell_data['length_b'], cell_data['length_c'],
                             cell_data['angle_alpha'], cell_data['angle_beta'], cell_data['angle_gamma']))),
            space_group)
    else:
        cryst_record = None

    reflections_data = data.get('_reflns')
    if reflections_data:
        resolution = reflections_data['d_resolution_high']
    else:
        resolution = None

    # _struct_ref
    # Get the cannonical sequence
    entity_data = data.get('_entity_poly')
    db_data = data.get('_struct_ref')
    if db_data:
        # 'db_name': ['UNP', 'UNP'], 'db_code': ['B0BGB0_9BACT', 'Q4Q413_LEIMA'],
        # 'pdbx_db_accession': ['B0BGB0', 'Q4Q413'], 'entity_id': ['1', '2'],
        # 'pdbx_seq_one_letter_code': ['MESVNTSFLSPSLVTIRDFDNGQFAVLRIGRTGFPADKGDIDLCLDKMKGVRDAQQSIGDDTEFGFKGPHIRIRCVDIDD\nKHTYNAMVYVDLIVGTGASEVERETAEELAKEKLRAALQVDIADEHSCVTQFEMKLREELLSSDSFHPDKDEYYKDFL', 'MPVIQTFVSTPLDHHKRENLAQVYRAVTRDVLGKPEDLVMMTFHDSTPMHFFGSTDPVACVRVEALGGYGPSEPEKVTSI\nVTAAITKECGIVADRIFVLYFSPLHCGWNGTNF']
        entity_info = {f'{name}_{entity_id}': {'chains': [],
                                               'reference_sequence': reference_sequence.replace('\n', ''),
                                               'dbref': {'db': db_name, 'accession': db_accession}}
                       for entity_id, reference_sequence, db_name, db_accession in zip(
                db_data.get('entity_id'),
                entity_data.get('pdbx_seq_one_letter_code_can'),  # db_data.get('pdbx_seq_one_letter_code'),
                db_data.get('db_name'), db_data.get('pdbx_db_accession'))
                       }
    else:
        entity_info = {}
    operations = data.get('_pdbx_struct_oper_list')
    if operations:
        biomt = np.array(
            [operations['matrix[1][1]'], operations['matrix[1][2]'], operations['matrix[1][3]'],
             operations['vector[1]'],
             operations['matrix[2][1]'], operations['matrix[2][2]'], operations['matrix[2][3]'],
             operations['vector[2]'],
             operations['matrix[3][1]'], operations['matrix[3][2]'], operations['matrix[3][3]'],
             operations['vector[3]']], dtype=float)
        # print('biomt', biomt)

        if isinstance(operations['id'], list):
            biomt = biomt.T
        biomt = biomt.reshape(-1, 3, 4).tolist()
        # print('biomt', biomt)
    else:
        biomt = None

    # # Separated...
    # rotations = np.array(
    #     [operations['matrix[1][1]'], operations['matrix[1][2]'], operations['matrix[1][3]'],
    #      operations['matrix[2][1]'], operations['matrix[2][2]'], operations['matrix[2][3]'],
    #      operations['matrix[3][1]'], operations['matrix[3][2]'], operations['matrix[3][3]']], dtype=float)
    # translations = np.array([operations['vector[1]'], operations['vector[2]'], operations['vector[3]']],
    #                         dtype=float)
    # print('rotations', rotations)
    # print('translations', translations)
    # if isinstance(operations['id'], list):
    #     # number_of_operations = len(operations['id'])
    #     rotations = rotations.T  # .reshape(-1, 3, 3)
    #     # rotations = rotations.reshape(-1, number_of_operations)
    #     translations = translations.T
    # # else:
    # #     pass
    # translations = translations.reshape(-1, 3)
    # rotations = rotations.reshape(-1, 3, 3)
    #
    # print('rotations', rotations)
    # print('translations', translations)
    # # biomt = rotations, translations

    # reference_sequence = {chain: reference_sequence}
    formatted_info = dict(
        atoms=atoms,
        biological_assembly=assembly,
        biomt=biomt,
        coords=coords,
        # coords=coords if separate_coords else None,
        cryst_record=cryst_record,
        entity_info=entity_info,
        name=name,
        resolution=resolution,
        # reference_sequence=reference_sequence,
    )
    # Explicitly overwrite any parsing if argument was passed to caller
    formatted_info.update(**kwargs)

    return formatted_info