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

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
from .tables import SYBYL2SYMB

import warnings

[docs]class MOL2Parser(TopologyReaderBase): """Reads topology from a Tripos_ MOL2_ file. Creates the following Attributes: - Atomids - Atomnames - Atomtypes - Charges - Resids - Resnames - Bonds - Elements Guesses the following: - masses Notes ----- Elements are obtained directly from the SYBYL atom types. If some atoms have unknown atom types, they will be assigned an empty element record. If all atoms have unknown atom types, the elements attribute will not be set. .. versionchanged:: 0.9 Now subclasses TopologyReaderBase .. versionchanged:: 0.20.0 Allows for comments at the top of the file Ignores status bit strings .. versionchanged:: 2.0.0 Bonds attribute is not added if no bonds are present in MOL2 file .. versionchanged: 2.0.0 Parse elements from atom types. """ 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.get("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"])) 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) validated_elements = np.empty(n_atoms, dtype="U3") invalid_elements = set() for i, at in enumerate(types): if at in SYBYL2SYMB: validated_elements[i] = SYBYL2SYMB[at] else: invalid_elements.add(at) validated_elements[i] = '' # Print single warning for all unknown elements, if any if invalid_elements: warnings.warn("Unknown elements found for some " f"atoms: {invalid_elements}. " "These have been given an empty element record.") masses = guessers.guess_masses(validated_elements) 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)) if not np.all(validated_elements == ''): attrs.append(Elements(validated_elements)) 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))) # don't add Bonds if there are none (Issue #3057) if bond_lines: 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