structure

Provide objects for manipulation and modeling of protein structures

This module allows you to load protein structural files, manipulate their coordinates, and measure aspects of their position, relationships, and shape properties. Additionally, identify structural symmetry and inherently model symmetric relationships, including their interfaces.

structure

• An Atom has a Coordinate.

|Atom|                                                         <- Structure
 |xyz|                                                         <- Coordinate

• A Residue ContainsAtoms and ContainsCoordinates.

|Residue - - - - - - |                                         <- Structure
 [Atom|Atom|Atom|Atom]                                         <- Structure

• A Structure ContainsResidues.

|Structure - - - - - - - - - - - - - - - - - - - - - - - - - | <- Structure
 [Residue|Residue|Residue|Residue|Residue|Residue|Residue|...] <- Structure

• A Structure also ContainsAtoms and ContainsCoordinates.

|Structure - - - - - - - - - - - - - - - - - - - - - - - - - | <- Structure
 [Atom|Atom|Atom|Atom|Atom|Atom|Atom|Atom|Atom|Atom|Atom|Atom] <- Structure
 [xyz|xyz|xyz|xyz|xyz|xyz|xyz|xyz|xyz|xyz|xyz|xyz|xyz|xyz|xyz] <- Coordinate

• A Chain is an instance of a Structure.

|Chain - - - - - - - - - - - - - - - - - - - - - - - - - - - | <- Structure

• A [Complex][structure.model.Complex] is a Structure that ContainsChains.

|Complex - - - - - - - - - - - - - - - - - - - - - - - - - - | <- Structure
/Structure * - * - * - * - * - * - * - * - * - * - * - * - * \ <- Structure
 [Chain- - - - - - - - - - - - |Chain- - - - - - - - - - - - ] <- Structure

Loading a Structure

sequence

• Every Structure is a GeneProduct.

|Structure - - - - - - - - - - - - - - - - - - - - - - - - - | <- Structure
/GeneProduct-> MPEAIRELNGHILFNCKALVDTGSSYPKQCDAKTGMIALQRPESA \ <- Sequence(Protein)

• Each GeneProduct represents a Gene.

|GeneProduct - - - - - - - - - - - - - - - - - - - - - - - - | <- Sequence
/Gene-> ATGCCTGAAGCTATTCGTGAATTAAATGGTCATATTTTATTTAATTGTAAAG \ <- Sequence(DNA)
/ CTTTAGTTGATACTGGTTCTTCTTATCCTAAACAATGTGATGCTAAAACTGGTATGAT \
/ TGCTTTACAACGTCCTGAATCTGCT - - - -  - - - - - - - - - - - - \

• An Entity maps a biological instance of a Structure which ContainsChains(1-N) and is a [Complex][structure.model.Complex], to a single GeneProduct.

|Entity- - - - - - - - - - - - - - - - - - - - - - - - - - - | <- Structure
/GeneProduct * - * - * - * - * - * - * - * - * - * - * - * - \ <- Seq
 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
 [Chain- - - - - - - - - - - - - - - - - - - - - - - - - - - ] <- Structure
 /GeneProduct- - - - - - - - - - - - - - - - - - - - - - - - \ <- Seq
 [Chain- - - - - - - - - - - - |Chain- - - - - - - - - - - - ] <- Structure
 /GeneProduct- - - - - - - - - |GeneProduct- - - - - - - - - \ <- Seq
 [Chain- - - - - - - |Chain- - - - - - - |Chain- - - - - - - ] <- Structure
 /GeneProduct- - - - |GeneProduct- - - - |GeneProduct- - - - \ <- Seq
 [Chain- - - - -|Chain - - - - |Chain- - - - -|Chain - - - - ] <- Structure
 /GeneProduct- -|GeneProduct - |GeneProduct- -|GeneProduct - \ <- Seq
 [Chain- - |Chain- - |Chain- - |Chain- - |Chain- - |Chain- - | <- Structure
 /GeneProd.|GeneProd.|GeneProd.|GeneProd.|GeneProd.|GeneProd.\ <- Seq

• As a result of GeneProduct duplication, an Entity can be a SymmetricModel.

Working with interfaces

• A Complex ContainsGeneProducts.

|Complex- - - - - - - - - - - - - - - - - - - - - - - - - - -| <- Structure
 [Entity- - - - - - - - - - - - - - - - - - - - - - - - - - -] <- Seq
 [Entity- - - - - - - - -||Entity- - - - - - - - - - - - - - ] <- Seq

Working with pieces of Structure

• A Fragment ContainsResidues, but only a few and thus is a small Structure representation.

|Fragment - - - - - - - - - - - - - - - -|                     <- Structure
 [Residue|Residue|Residue|Residue|Residue]                     <- Structure

Each Fragment can map to other Fragment instances so that larger Structure can be broken down into pairs of Fragment. Such Fragment overlap with neighboring Fragment such as those that aare mapped to a separate "sliding window" register.

|Structure - - - - - - - - - - - - - - - - - - - - - - - - - | <- Structure
 Fragment- - - |Fragment - - -|Fragment- - - |Fragment - - - | <- Structure
    |Fragment- - - |Fragment - - -|Fragment- - - |             <- Structure
        |Fragment- - - |Fragment - - -|Fragment- - - |         <- Structure
            |Fragment- - - |Fragment - - -|Fragment- - - |     <- Structure

The module contains the following classes:

• Pose() - Create a symmetry-aware object to manipulate a collection of Entity instances
• Model() - Create an object to manipulate a collection of Chain instances
• Entity() - Create a symmetry-aware object to manipulate structurally homologous Chain instances

The module contains the following functions:

• () - Returns

Examples:

>>> from pathlib import Path
>>> from symdesign import structure
>>>
>>> structure_file = Path(Path.cwd(), 'tests', '1xyz.pdb1')
>>> # structure_file = Path(Path.cwd(), 'tests', '1xyz-assembly1.cif')
>>> pose_1xyz = structure.model.Pose.from_file(structure_file)
>>> # Transform the pose to the coordinate origin
>>> pose_1xyz.transform(translation=-pose_1xyz.center_of_mass)
>>> chain_a_1xyz = pose_1xyz.get_chain('A')
>>> for residue in chain_a_1xyz.residues:
...     print(f'Residue {residue.type}{residue.number} has a B-factor of {residue.b_factor} and {residue.sasa} '
...           '$\AA$² of solvent accessible surface area')
Residue M1 has a B-factor of 47.08 and 34.02 A2 of solvent accessible surface area
Residue V2 has a B-factor of 54.11 and 12.83 A2 of solvent accessible surface area
...
>>>
>>> chain_a_1xyz_per_residue_sasa = sum([residue.sasa for residue in chain_a_1xyz.residues])
>>> chain_a_1xyz_per_residue_sasa == chain_a_1xyz.sasa
True
>>> for entity_idx, entity in enumerate(pose_1xyz.entities, 1):
...     print(f'The Entity #{entity_idx} is {entity.name}')
...     print(entity == chain_a_1xyz)

Structure initialization arguments Process various types of Structure containers to update the Model with the corresponding information

Parameters:

• entities –

  bool | list[Entity] | Structures = True - Whether to create Entity instances from passed Structure container instances, or existing Entity instances to create the Model with

• entity_names –

  Sequence = None - Names explicitly passed for the Entity instances. Length must equal number of entities. Names will take precedence over query_by_sequence if passed

• chains –

  bool | list[Chain] | Structures = True - Whether to create Chain instances from passed Structure container instances, or existing Chain instances to create the Model with

• query_by_sequence –

  bool = True - Whether the PDB API should be queried for an Entity name by matching sequence. Only used if entity_names not provided

• structure –

  ContainsResidues = None - Create the instance based on an existing Structure instance

• fragment_db –

  FragmentDatabase = None - The identity of the FragmentDatabase to use for Fragment based operations

• residues –

  list[Residue] | Residues = None - The Residue instances which should constitute a new instance

• residue_indices –

  list[int] = None - The indices which specify the particular Residue instances to make this ContainsResidues instance. Used with a parent to specify a subdivision of a larger structure

• 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

• biological_assembly –

  str | None = None - The integer of the biological assembly (as indicated by PDB AssemblyID format)

• cryst_record –

  str | None - The string specifying how the molecule is situated in a lattice

• entity_info –

  dict[str, dict[dict | list | str]] - A mapping of the metadata to their distinct molecular identifiers

• file_path –

  AnyStr | None - The location on disk where the file was accessed

• reference_sequence –

  str | dict[str, str] = None - The reference sequence according to expression sequence or reference database

• resolution –

  float | None = None: The level of detail available from an experimental dataset contributing to the sharpness with which structural data can contribute towards building a model