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. Dealing with optional fields: 1. ``resid`` will set to 1 when not provided. 2. If no atoms have ``resname`` field, resnames attribute will not be set; If some atoms have ``resname`` while some do not, :exc:`ValueError` will occur. 3. If "NO_CHARGES" shows up in "@<TRIPOS>MOLECULE" section and no atoms have the ``charge`` field, charges attribute will not be set; If "NO_CHARGES" shows up while ``charge`` field appears, :exc:`ValueError` will occur; If a charge model is specified while some atoms don't have ``charge``, :exc:`ValueError` will occur as well. Raises ------ ValueError If some atoms have the optional field ``resname`` (aka ``subst_name``) while some do not. ValueError If "NO_CHARGES" shows up in "@<TRIPOS>MOLECULE" section while some atoms have the optional field ``charge``. ValueError If a charge model is specified in "@<TRIPOS>MOLECULE" section while some atoms do not have the optional field ``charge``. .. 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. .. versionchanged:: 2.2.0 Read MOL2 files with optional columns omitted. """ 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 = [] has_charges = sections['molecule'][3].strip() != 'NO_CHARGES' for a in atom_lines: columns = a.split() if len(columns) >= 9: aid, name, x, y, z, atom_type, \ resid, resname, charge = columns[:9] elif len(columns) < 6: raise ValueError(f"The @<TRIPOS>ATOM block in mol2 file" f" {os.path.basename(self.filename)}" f" should have at least 6 fields to be" f" unpacked: atom_id atom_name x y z" f" atom_type [subst_id[subst_name" f" [charge [status_bit]]]]") else: aid, name, x, y, z, atom_type = columns[:6] id_name_charge = [1, None, None] for i in range(6, len(columns)): id_name_charge[i-6] = columns[i] resid, resname, charge = id_name_charge if has_charges: if charge is None: raise ValueError(f"The mol2 file {self.filename}" f" indicates a charge model" f"{sections['molecule'][3]}, but" f" no charge provided in line: {a}") else: if charge is not None: raise ValueError(f"The mol2 file {self.filename}" f" indicates no charges, but charge" f" {charge} provided in line: {a}.") 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))) if has_charges: 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) if np.all(resnames): residx, resids, (resnames,) = squash_by( resids, resnames) n_residues = len(resids) attrs.append(Resids(resids)) attrs.append(Resnums(resids.copy())) attrs.append(Resnames(resnames)) elif not np.any(resnames): residx, resids, _ = squash_by(resids,) n_residues = len(resids) attrs.append(Resids(resids)) attrs.append(Resnums(resids.copy())) else: raise ValueError(f"Some atoms in the mol2 file {self.filename}" f" have subst_name while some do not.") 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