iphasimulator.docking_inputs

Polymer-only PDB for docking, from a GROMACS .gro and its topology (notebook 11).

Only the polymer is written: the atoms with one residue name, PHA for systems built with 06A (and the polymer benchmark) or LIG for CHARMM-GUI systems. Before writing, the polymer must be whole: a molecule split across the periodic box would give the docking program a broken structure.

Attributes

`MAX_BOND_NM`
`HYDROGEN_MAX_MASS`
`WHOLE_MOLECULE_ADVICE`

Classes

`PolymerWholeCheck`	Bonded heavy-atom distances of the polymer (nm).
`PolymerPdbExport`

Functions

`check_polymer_whole`(→ PolymerWholeCheck)	Measure every bonded heavy-atom pair of the polymer; whole if all are < `max_bond_nm`.
`export_polymer_pdb`(→ PolymerPdbExport)	Write the polymer only (`residue_name`) as a PDB, after checking it is whole.

Module Contents

iphasimulator.docking_inputs.MAX_BOND_NM = 0.3

iphasimulator.docking_inputs.HYDROGEN_MAX_MASS = 4.0

iphasimulator.docking_inputs.WHOLE_MOLECULE_ADVICE = 'Use a whole-molecule frame instead, e.g. the representative frame from notebook 08 or a frame...

class iphasimulator.docking_inputs.PolymerWholeCheck

Bonded heavy-atom distances of the polymer (nm).

residue_name: str

atoms: int

heavy_bonds: int

longest_bond: tuple[str, str, float]

broken_bonds: tuple[tuple[str, str, float], ...]

max_bond_nm: float = 0.3

property is_whole: bool

class iphasimulator.docking_inputs.PolymerPdbExport

pdb_path: pathlib.Path

atoms: int

check: PolymerWholeCheck

iphasimulator.docking_inputs.check_polymer_whole(gro_path: str | pathlib.Path, topology_path: str | pathlib.Path, residue_name: str = 'PHA', max_bond_nm: float = MAX_BOND_NM) → PolymerWholeCheck

Measure every bonded heavy-atom pair of the polymer; whole if all are < max_bond_nm.

Bonds come from the polymer’s [ moleculetype ] (named like its residue) in the topology or its #include files; coordinates come from the .gro file.

iphasimulator.docking_inputs.export_polymer_pdb(gro_path: str | pathlib.Path, topology_path: str | pathlib.Path, pdb_path: str | pathlib.Path, *, residue_name: str = 'PHA', max_bond_nm: float = MAX_BOND_NM) → PolymerPdbExport

Write the polymer only (residue_name) as a PDB, after checking it is whole.

Raises ValueError without writing anything when a bonded heavy-atom pair is max_bond_nm or longer. Atoms and residues are renumbered from 1, in chain A; coordinates are converted from nm to Å; no box (CRYST1) record is written.