Source code for MDAnalysis.coordinates.MOL2

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#

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

Classes to work with Tripos_ molecule structure format (MOL2_) coordinate and
topology files. Used, for instance, by the DOCK_ docking code.


Example for working with mol2 files
-----------------------------------

To open a mol2, remove all hydrogens and save as a new file, use the following::

  u = Universe("Molecule.mol2")
  gr = u.select_atoms("not name H*")
  print(len(u.atoms), len(gr))
  gr.write("Molecule_noh.mol2")

.. _MOL2: http://www.tripos.com/data/support/mol2.pdf
.. _Tripos: http://www.tripos.com/
.. _DOCK: http://dock.compbio.ucsf.edu/


See Also
--------
rdkit: rdkit_ is an open source cheminformatics toolkit with more mol2
       functionality

.. _rdkit: http://www.rdkit.org/docs/GettingStartedInPython.html


Classes
-------

.. autoclass:: MOL2Reader
   :members:

.. autoclass:: MOL2Writer
   :members:


MOL2 format notes
-----------------

* MOL2 Format Specification:  (http://www.tripos.com/data/support/mol2.pdf)
* Example file (http://www.tripos.com/mol2/mol2_format3.html)::

    #    Name: benzene
    #    Creating user name: tom
    #    Creation time: Wed Dec 28 00:18:30 1988

    #    Modifying user name: tom
    #    Modification time: Wed Dec 28 00:18:30 1988

    @<TRIPOS>MOLECULE
    benzene
    12 12 1  0   0
    SMALL
    NO_CHARGES


    @<TRIPOS>ATOM
    1   C1  1.207   2.091   0.000   C.ar    1   BENZENE 0.000
    2   C2  2.414   1.394   0.000   C.ar    1   BENZENE 0.000
    3   C3  2.414   0.000   0.000   C.ar    1   BENZENE 0.000
    4   C4  1.207   -0.697  0.000   C.ar    1   BENZENE 0.000
    5   C5  0.000   0.000   0.000   C.ar    1   BENZENE 0.000
    6   C6  0.000   1.394   0.000   C.ar    1   BENZENE 0.000
    7   H1  1.207   3.175   0.000   H   1   BENZENE 0.000
    8   H2  3.353   1.936   0.000   H   1   BENZENE 0.000
    9   H3  3.353   -0.542  0.000   H   1   BENZENE 0.000
    10  H4  1.207   -1.781  0.000   H   1   BENZENE 0.000
    11  H5  -0.939  -0.542  0.000   H   1   BENZENE 0.000
    12  H6  -0.939  1.936   0.000   H   1   BENZENE 0.000
    @<TRIPOS>BOND
    1   1   2   ar
    2   1   6   ar
    3   2   3   ar
    4   3   4   ar
    5   4   5   ar
    6   5   6   ar
    7   1   7   1
    8   2   8   1
    9   3   9   1
    10  4   10  1
    11  5   11  1
    12  6   12  1
   @<TRIPOS>SUBSTRUCTURE
    1   BENZENE 1   PERM    0   ****    ****    0   ROOT

"""
from __future__ import absolute_import
from six import raise_from

import numpy as np

from . import base
from ..lib import util


[docs]class MOL2Reader(base.ReaderBase): """Reader for MOL2 structure format. .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based. MOL2 now reuses the same Timestep object for every frame, previously created a new instance of Timestep each frame. .. versionchanged:: 0.20.0 Allows for comments at top of file. Ignores status bit strings """ format = 'MOL2' units = {'time': None, 'length': 'Angstrom'} def __init__(self, filename, **kwargs): """Read coordinates from `filename`. Parameters ---------- filename : str or NamedStream name of the mol2 file or stream """ super(MOL2Reader, self).__init__(filename, **kwargs) self.n_atoms = None blocks = [] with util.openany(filename) as f: for i, line in enumerate(f): # found new molecules if "@<TRIPOS>MOLECULE" in line: blocks.append({"start_line": i, "lines": []}) if len(blocks): blocks[-1]["lines"].append(line) self.n_frames = len(blocks) self.frames = blocks sections, coords = self.parse_block(blocks[0]) self.n_atoms = len(coords) self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs) self.ts = self._read_frame(0) def parse_block(self, block): 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 Exception("The mol2 (starting at line {0}) block has no atoms" "".format(block["start_line"])) elif self.n_atoms is None: # First time round, remember the number of atoms self.n_atoms = len(atom_lines) elif len(atom_lines) != self.n_atoms: raise ValueError( "MOL2Reader assumes that the number of atoms remains unchanged" " between frames; the current " "frame has {0}, the next frame has {1} atoms" "".format(self.n_atoms, len(atom_lines))) if not len(bond_lines): raise Exception("The mol2 (starting at line {0}) block has no bonds" "".format(block["start_line"])) coords = np.zeros((self.n_atoms, 3), dtype=np.float32) for i, a in enumerate(atom_lines): aid, name, x, y, z, atom_type, resid, resname, charge = a.split()[:9] #x, y, z = float(x), float(y), float(z) coords[i, :] = x, y, z return sections, coords def _read_next_timestep(self, ts=None): if ts is None: ts = self.ts else: # TODO: cleanup _read_frame() to use a "free" Timestep raise NotImplementedError("MOL2Reader cannot assign to a timestep") frame = self.frame + 1 return self._read_frame(frame) def _read_frame(self, frame): unitcell = np.zeros(6, dtype=np.float32) try: block = self.frames[frame] except IndexError: raise_from(IOError("Invalid frame {0} for trajectory with length {1}" "".format(frame, len(self))), None) sections, coords = self.parse_block(block) for sect in ['molecule', 'substructure']: try: self.ts.data[sect] = sections[sect] except KeyError: pass self.ts.positions = np.array(coords, dtype=np.float32) self.ts.unitcell = unitcell if self.convert_units: # in-place ! self.convert_pos_from_native(self.ts._pos) self.convert_pos_from_native(self.ts._unitcell[:3]) self.ts.frame = frame return self.ts def _reopen(self): # Make frame think it's before start, so calling next # reads first frame self.ts.frame = -1
[docs]class MOL2Writer(base.WriterBase): """mol2 format writer Write a file in the Tripos_ molecule structure format (MOL2_). Note ---- :class:`MOL2Writer` can only be used to write out previously loaded MOL2 files. If you're trying to convert, for example, a PDB file to MOL you should use other tools, like rdkit_. Here is an example how to use rdkit_ to convert a PDB to MOL:: from rdkit import Chem mol = Chem.MolFromPDBFile("molecule.pdb", removeHs=False) Chem.MolToMolFile(mol, "molecule.mol" ) MOL2 writer is currently not available for rdkit master. It requires SYBYL atomtype generation. See page 7 for list of SYBYL atomtypes (http://tripos.com/tripos_resources/fileroot/pdfs/mol2_format2.pdf). .. _rdkit: http://www.rdkit.org/docs/GettingStartedInPython.html .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based """ format = 'MOL2' multiframe = True units = {'time': None, 'length': 'Angstrom'} def __init__(self, filename, n_atoms=None, convert_units=True): """Create a new MOL2Writer Parameters ---------- filename: str name of output file convert_units: bool (optional) units are converted to the MDAnalysis base format; [``True``] """ self.filename = filename self.convert_units = convert_units # convert length and time to base units self.frames_written = 0 self.file = util.anyopen(self.filename, 'w') # open file on init
[docs] def close(self): self.file.close()
[docs] def encode_block(self, obj): """ Parameters ---------- obj : AtomGroup or Universe """ traj = obj.universe.trajectory ts = traj.ts try: molecule = ts.data['molecule'] except KeyError: raise_from(NotImplementedError( "MOL2Writer cannot currently write non MOL2 data"), None) # Need to remap atom indices to 1 based in this selection mapping = {a: i for i, a in enumerate(obj.atoms, start=1)} # Grab only bonds between atoms in the obj # ie none that extend out of it bondgroup = obj.bonds.atomgroup_intersection(obj, strict=True) bonds = sorted((b[0], b[1], b.order) for b in bondgroup) bond_lines = ["@<TRIPOS>BOND"] bond_lines.extend("{0:>5} {1:>5} {2:>5} {3:>2}" "".format(bid, mapping[atom1], mapping[atom2], order) for bid, (atom1, atom2, order)in enumerate( bonds, start=1)) bond_lines.append("\n") bond_lines = "\n".join(bond_lines) atom_lines = ["@<TRIPOS>ATOM"] atom_lines.extend("{0:>4} {1:>4} {2:>13.4f} {3:>9.4f} {4:>9.4f}" " {5:>4} {6} {7} {8:>7.4f}" "".format(mapping[a], a.name, a.position[0], a.position[1], a.position[2], a.type, a.resid, a.resname, a.charge) for a in obj.atoms) atom_lines.append("\n") atom_lines = "\n".join(atom_lines) try: substructure = ["@<TRIPOS>SUBSTRUCTURE\n"] + ts.data['substructure'] except KeyError: substructure = "" check_sums = molecule[1].split() check_sums[0], check_sums[1] = str(len(obj.atoms)), str(len(bondgroup)) # prevent behavior change between repeated calls # see gh-2678 molecule_0_store = molecule[0] molecule_1_store = molecule[1] molecule[1] = "{0}\n".format(" ".join(check_sums)) molecule.insert(0, "@<TRIPOS>MOLECULE\n") return_val = ("".join(molecule) + atom_lines + bond_lines + "".join(substructure)) molecule[0] = molecule_0_store molecule[1] = molecule_1_store return return_val
[docs] def write(self, obj): """Write a new frame to the MOL2 file. Parameters ---------- obj : AtomGroup or Universe """ self.write_next_timestep(obj)
[docs] def write_next_timestep(self, obj): """Write a new frame to the MOL2 file. Parameters ---------- obj : AtomGroup or Universe """ block = self.encode_block(obj) self.file.writelines(block)