Source code for MDAnalysis.topology.MOL2Parser

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MOL2 file format --- :mod:`MDAnalysis.coordinates.MOL2`

Classes to read Tripos_ molecule structure format (MOL2_) coordinate
and topology files. Used by the DOCK_ docking code.

.. _MOL2:
.. _Tripos:
.. _DOCK:


.. autoclass:: MOL2Parser

from __future__ import absolute_import

import os
import numpy as np

from . import guessers
from ..lib.util import openany
from .base import TopologyReaderBase, squash_by
from ..core.topologyattrs import (
from ..core.topology import Topology

[docs]class MOL2Parser(TopologyReaderBase): """Read topology from a Tripos_ MOL2_ file. Create the following Attributes: - Atomids - Atomnames - Atomtypes - Charges - Resids, - Resnames - Bonds Guesses the following: - masses .. versionchanged:: 0.9 Now subclasses TopologyReaderBase .. versionchanged:: 0.20.0 Allows for comments at the top of the file Ignores status bit strings """ format = 'MOL2'
[docs] def parse(self, **kwargs): """Parse MOL2 file *filename* and return the dict `structure`. Returns ------- A MDAnalysis Topology object """ blocks = [] with openany(self.filename) as f: for i, line in enumerate(f): # found new molecules if "@<TRIPOS>MOLECULE" in line: if len(blocks): break blocks.append({"start_line": i, "lines": []}) if len(blocks): blocks[-1]["lines"].append(line) if not len(blocks): raise ValueError("The mol2 file '{0}' needs to have at least one" " @<TRIPOS>MOLECULE block".format(self.filename)) block = blocks[0] sections = {} cursor = None for line in block["lines"]: if "@<TRIPOS>" in line: cursor = line.split("@<TRIPOS>")[1].strip().lower() sections[cursor] = [] continue elif line.startswith("#") or line == "\n": continue sections[cursor].append(line) atom_lines, bond_lines = sections["atom"], sections["bond"] if not len(atom_lines): raise ValueError("The mol2 block ({0}:{1}) has no atoms".format( os.path.basename(self.filename), block["start_line"])) if not len(bond_lines): raise ValueError("The mol2 block ({0}:{1}) has no bonds".format( os.path.basename(self.filename), block["start_line"])) ids = [] names = [] types = [] resids = [] resnames = [] charges = [] for a in atom_lines: aid, name, x, y, z, atom_type, resid, resname, charge = a.split()[:9] ids.append(aid) names.append(name) types.append(atom_type) resids.append(resid) resnames.append(resname) charges.append(charge) n_atoms = len(ids) masses = guessers.guess_masses(types) attrs = [] attrs.append(Atomids(np.array(ids, dtype=np.int32))) attrs.append(Atomnames(np.array(names, dtype=object))) attrs.append(Atomtypes(np.array(types, dtype=object))) attrs.append(Charges(np.array(charges, dtype=np.float32))) attrs.append(Masses(masses, guessed=True)) resids = np.array(resids, dtype=np.int32) resnames = np.array(resnames, dtype=object) residx, resids, (resnames,) = squash_by( resids, resnames) n_residues = len(resids) attrs.append(Resids(resids)) attrs.append(Resnums(resids.copy())) attrs.append(Resnames(resnames)) attrs.append(Segids(np.array(['SYSTEM'], dtype=object))) bonds = [] bondorder = [] for b in bond_lines: # bond_type can be: 1, 2, am, ar bid, a0, a1, bond_type = b.split()[:4] a0, a1 = int(a0) - 1, int(a1) - 1 bond = tuple(sorted([a0, a1])) bondorder.append(bond_type) bonds.append(bond) attrs.append(Bonds(bonds, order=bondorder)) top = Topology(n_atoms, n_residues, 1, attrs=attrs, atom_resindex=residx) return top