Source code for pycgtool.parsers.itp

"""Module containing classes used to parse ITP/TOP file format."""

import collections
import logging
import pathlib

from .cfg import CFG, NoSectionError, DuplicateSectionError

logger = logging.getLogger(__name__)

[docs]class ITP(CFG): """Class representing an .itp file. Contains a dictionary of sections for every molecule definition. """
[docs] def _read_file(self, filepath: pathlib.Path) -> None: mol_sections = ["atoms", "bonds", "angles", "dihedrals"] with open(filepath) as itp_file: curr_section = None curr_mol = None for line in itp_file: line = self._read_line(line, filepath) if not line: continue if line.startswith("["): curr_section = line.strip("[ ]") if curr_section in mol_sections: # pragma: no cover # This allows a section to appear twice within a single molecule definition # It is not clear whether this is allowed by GROMACS but does no harm self[curr_mol].setdefault(curr_section, []) continue # cannot detect this branch due to the peephole optimizer toks = tuple(line.split()) if curr_section == "moleculetype": curr_mol = toks[0] if curr_mol in self: raise DuplicateSectionError(curr_mol, filepath) self[curr_mol] = collections.OrderedDict() elif curr_section in mol_sections: self[curr_mol][curr_section].append(toks) elif curr_section is None: raise NoSectionError(filepath) else: "File '%s' contains unexpected section '%s'", filepath, curr_section, )