Write GhostFragments as an MultiModel trajectory where each successive Model has one more Fragment
Parameters:
-
ghost_frags
(list[GhostFragment])
–
An iterable of GhostFragments
-
file_name
(AnyStr, default:
getcwd()
)
–
The path that the file should be written to
Returns:
The file_name
Source code in symdesign/structure/fragment/visuals.py
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69 | def write_fragment_pairs_as_accumulating_states(
ghost_frags: list[GhostFragment], file_name: AnyStr = os.getcwd()) -> AnyStr:
"""Write GhostFragments as an MultiModel trajectory where each successive Model has one more Fragment
Args:
ghost_frags: An iterable of GhostFragments
file_name: The path that the file should be written to
Returns:
The file_name
"""
if '.pdb' not in file_name:
file_name += '.pdb'
with open(file_name, 'w') as f:
atom_iterator = 0
residue_iterator = 1
chain_generator = chain_id_generator()
mapped_chain_id = next(chain_generator)
model_number = 1
# Write the monofrag that ghost frags are paired against
f.write(f'MODEL {model_number:>4d}\n')
ghost_frag_init = ghost_frags[0]
frag_model, frag_paired_chain = ghost_frag_init.fragment_db.paired_frags[ghost_frag_init.ijk]
trnsfmd_fragment = frag_model.get_transformed_copy(*ghost_frag_init.transformation)
# Set mapped_chain to A
mapped_chain = trnsfmd_fragment.chain(
tuple(set(frag_model.chain_ids).difference({frag_paired_chain, '9'}))[0])
mapped_chain.chain_id = mapped_chain_id
# Renumber residues
trnsfmd_fragment.renumber_residues(at=residue_iterator)
# Write
f.write('%s\n' % mapped_chain.get_atom_record(atom_offset=atom_iterator))
# Iterate atom/residue numbers
atom_iterator += mapped_chain.number_of_atoms
residue_iterator += mapped_chain.number_of_residues
f.write('ENDMDL\n')
# Write all subsequent models, stacking each subsequent model on the previous
fragment_lines = []
for model_number, ghost_frag in enumerate(ghost_frags, model_number + 1):
f.write(f'MODEL {model_number:>4d}\n')
frag_model, frag_paired_chain = ghost_frag.fragment_db.paired_frags[ghost_frag.ijk]
trnsfmd_fragment = frag_model.get_transformed_copy(*ghost_frag.transformation)
# Iterate only the paired chain with new chainID
trnsfmd_fragment.chain(frag_paired_chain).chain_id = next(chain_generator)
# Set the mapped chain to the single mapped_chain_id
trnsfmd_fragment.chain(tuple(
set(frag_model.chain_ids).difference({frag_paired_chain, '9'})
)[0]).chain_id = mapped_chain_id
trnsfmd_fragment.renumber_residues(at=residue_iterator)
fragment_lines.append(trnsfmd_fragment.get_atom_record(atom_offset=atom_iterator))
# trnsfmd_fragment.write(file_handle=f)
f.write('%s\n' % '\n'.join(fragment_lines))
atom_iterator += frag_model.number_of_atoms
residue_iterator += frag_model.number_of_residues
f.write('ENDMDL\n')
return file_name
|