pycgtool.forcefield
¶
This module contains a single class ForceField used to output a GROMACS .ff forcefield.
Module Contents¶
Classes¶
Class used to output a GROMACS .ff forcefield |
Functions¶
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Copy files from one directory to another. |
Attributes¶
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pycgtool.forcefield.
PathLike
¶
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pycgtool.forcefield.
copy_files
(src_dir: pathlib.Path, dest_dir: pathlib.Path, files: Iterable[str]) → None[source]¶ Copy files from one directory to another.
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class
pycgtool.forcefield.
ForceField
(name: str, dir_path: PathLike = pathlib.Path('.'))[source]¶ Class used to output a GROMACS .ff forcefield
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static
bond_section
(bonds, section_header, multiplicity=None)[source]¶ Populate an RTP bond/angle/dihedral section.
- Parameters
bonds (iterable[Bond]) – Iterable of bonds to add to RTP
section_header (str) – RTP section header i.e. “bonds”/”angles”/”dihedrals”
multiplicity (int) – Multiplicity of dihedral, default is None
- Return List[str]
Lines to add to RTP file
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static
write_rtp
(mapping, bonds)[source]¶ Return lines of a GROMACS RTP file.
This file defines the residues present in the forcefield and allows pdb2gmx to be used.
- Parameters
- Return (list[str], set[str], set[str], set[str])
List of lines for RTP file, Set of residues requiring N terminal records, Set of residues requiring C terminal records,
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static
write_r2b
(n_terms, c_terms)[source]¶ Return lines of a GROMACS R2B file.
This file defines names used for chain terminal records for PDB2GMX.
- Parameters
n_terms (Iterable[str]) – Set of molecule names requiring N terminal records
c_terms (Iterable[str]) – Set of molecule names requiring C terminal records
- Return List[str]
Lines of R2B file
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static