pygen_structures.mol_containers.molecule module

Module containing the Molecule class.

This class is used to create CHARMM structures from a list of RESI names, a CHARMMResidueTopologyFile and a dict mapping PRES names to indices of the residues they are to be applied to (or “FIRST”/”LAST”).

Manipulation of 3D coordinates is performed in the Structure class so that 3D functionality can be applied to residue objects.

class pygen_structures.mol_containers.molecule.Molecule(name: str = 'Unset', residues: (<class 'list'>, None) = None, topology: (<class 'pygen_structures.charmm_containers.CHARMMResidueTopologyFile'>, None) = None, patches: (typing.Dict[str, typing.List[int]], None) = None, segment: (<class 'str'>, None) = None, fixed_atoms: (typing.Dict[typing.Tuple[int, str], typing.Tuple[float, float, float]], None) = None, use_etkdg: bool = True)

Bases: object

A complete CHARMM molecule. This can be written to PSF and/or PDB

Parameters

• name – The name of the molecule, used in the PSF and PDB.

• residues – a list of CHARMMResidue

• topology – the CHARMMResidueTopologyFile to provide the patches.

• patches – a dict of patch names to a list of the residue indices the patch is to be applied to (or “FIRST”/”LAST”) magic strings.

• segment – the segment ID to be used when the Atom records are created. This must be less than four characters.

• fixed_atoms – a mapping of atom_id to the fixed coords

• use_etkdg – In the structure, when generating coords, use empirical distance generation (if True) or a traditional distance generation approach.

The following attributes are set during finalization:

Parameters

• atoms – a list of Atom

• impropers – a list of tuples with Atom indices for the PSF

• cross_maps – a list of tuples with Atom indices for the PSF

• topology_files – a set of paths to the .rtf/.str files

These are private attributes:

Parameters

• _structure – the underlying Structure object

• _id_to_index – a mapping of atom_id to index.

• _finalized – True if Molecule.finalize() has been called.

check_parameters(parameter_set: pygen_structures.charmm_containers.CHARMMParameterFile) → bool

Check if parameters needed by the molecule are present in a parameter set. Returns True if all parameters are present, otherwise false.

Parameters

parameter_set – CHARMMParameterFile

Returns

True if all parameters are matched

finalize() → None

Finalize the molecule, getting it to a state where it can be represented directly as a PDB file or PSF file.

classmethod from_sequence(sequence: List[str], topology: pygen_structures.charmm_containers.CHARMMResidueTopologyFile, patches: (typing.Dict[str, typing.List[int]], None) = None, name: (<class 'str'>, None) = None, segid: (<class 'str'>, None) = None)

Create the Molecule instance from a list of residues, a CHARMM topology file and a list containing patches to be applied.

Parameters

• sequence – a list of CHARMM residues

• topology – a CHARMMResidueTopologyFile

• patches – a dict of CHARMMPatchResidueDefinition names from topology to the indices of the residue the patch is to be applied to.

• name – the name of the Molecule

• segid – the segment for the PDB/PDB. Must contain four characters or fewer.

get_adjacency_matrix() → numpy.ndarray

get_conect_records() → List[str]

Build the PDB CONECT records from the adjacency matrix.

to_mol()

to_pdb_block() → str

Build the PDB records and return the PDB as a string.

Returns

PDB block as string

to_pdb_file(pdb_path: str) → None

Write the molecule to a PDB file.

Parameters

pdb_path – path to PDB file.

to_psf_block() → str

Build the PSF records and return the PSF as a string.

Returns

PSF block as string

to_psf_file(psf_path) → None

Write the molecule to a PSF file.

Parameters

psf_path – Path to PSF file.

to_structure() → pygen_structures.mol_containers.structure.Structure

Create a Structure using information from atoms and bonds

Returns

the generated Structure