1# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- 2# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 3# 4# MDAnalysis --- https://www.mdanalysis.org 5# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors 6# (see the file AUTHORS for the full list of names) 7# 8# Released under the GNU Public Licence, v2 or any higher version 9# 10# Please cite your use of MDAnalysis in published work: 11# 12# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, 13# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. 14# MDAnalysis: A Python package for the rapid analysis of molecular dynamics 15# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th 16# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. 17# 18# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. 19# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. 20# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 21# 22 23""" 24PDBQT topology parser 25===================== 26 27Use a PDBQT_ file to build a minimum internal structure representation (list of 28atoms), including AutoDock_ atom types (stored as :attr:`Atom.type`) and 29partial charges (:attr:`Atom.charge`). 30 31* Reads a PDBQT file line by line and does not require sequential atom numbering. 32* Multi-model PDBQT files are not supported. 33 34Notes 35----- 36Only reads atoms and their names; connectivity is not 37deduced. Masses are guessed and set to 0 if unknown. 38 39 40See Also 41-------- 42`MDAnalysis.coordinates.PDBQT` 43 44 45Classes 46------- 47.. autoclass:: PDBQTParser 48 :members: 49 :inherited-members: 50 51 52.. _PDBQT: 53 http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file 54.. _AutoDock: 55 http://autodock.scripps.edu/ 56""" 57from __future__ import absolute_import 58 59import numpy as np 60 61from . import guessers 62from ..lib import util 63from .base import TopologyReaderBase, change_squash 64from ..core.topology import Topology 65from ..core.topologyattrs import ( 66 Atomids, 67 Atomnames, 68 AltLocs, 69 Atomtypes, 70 Charges, 71 Masses, 72 Occupancies, 73 RecordTypes, 74 Resids, 75 Resnums, 76 Resnames, 77 Segids, 78 Tempfactors, 79) 80 81 82class PDBQTParser(TopologyReaderBase): 83 """Read topology from a PDBQT file. 84 85 Creates the following Attributes: 86 - atom ids (serial) 87 - atom types 88 - atom names 89 - altLocs 90 - resnames 91 - chainIDs (becomes segid) 92 - resids 93 - record_types (ATOM/HETATM) 94 - icodes 95 - occupancies 96 - tempfactors 97 - charges 98 99 Guesses the following: 100 - elements 101 - masses 102 103 .. versionchanged:: 0.18.0 104 Added parsing of Record types 105 """ 106 format = 'PDBQT' 107 108 def parse(self, **kwargs): 109 """Parse atom information from PDBQT file *filename*. 110 111 Returns 112 ------- 113 MDAnalysis Topology object 114 """ 115 record_types = [] 116 serials = [] 117 names = [] 118 altlocs = [] 119 resnames = [] 120 chainids = [] 121 resids = [] 122 icodes = [] 123 occupancies = [] 124 tempfactors = [] 125 charges = [] 126 atomtypes = [] 127 128 with util.openany(self.filename) as f: 129 for line in f: 130 line = line.strip() 131 if not line.startswith(('ATOM', 'HETATM')): 132 continue 133 record_types.append(line[:6].strip()) 134 serials.append(int(line[6:11])) 135 names.append(line[12:16].strip()) 136 altlocs.append(line[16:17].strip()) 137 resnames.append(line[17:21].strip()) 138 chainids.append(line[21:22].strip()) 139 resids.append(int(line[22:26])) 140 icodes.append(line[26:27].strip()) 141 occupancies.append(float(line[54:60])) 142 tempfactors.append(float(line[60:66])) 143 charges.append(float(line[66:76])) 144 atomtypes.append(line[77:80].strip()) 145 146 n_atoms = len(serials) 147 148 masses = guessers.guess_masses(atomtypes) 149 150 attrs = [] 151 for attrlist, Attr, dtype in ( 152 (record_types, RecordTypes, object), 153 (serials, Atomids, np.int32), 154 (names, Atomnames, object), 155 (altlocs, AltLocs, object), 156 (occupancies, Occupancies, np.float32), 157 (tempfactors, Tempfactors, np.float32), 158 (charges, Charges, np.float32), 159 (atomtypes, Atomtypes, object), 160 ): 161 attrs.append(Attr(np.array(attrlist, dtype=dtype))) 162 attrs.append(Masses(masses, guessed=True)) 163 164 resids = np.array(resids, dtype=np.int32) 165 icodes = np.array(icodes, dtype=object) 166 resnames = np.array(resnames, dtype=object) 167 chainids = np.array(chainids, dtype=object) 168 169 residx, (resids, icodes, resnames, chainids) = change_squash( 170 (resids, icodes), (resids, icodes, resnames, chainids)) 171 n_residues = len(resids) 172 attrs.append(Resids(resids)) 173 attrs.append(Resnums(resids.copy())) 174 attrs.append(Resnames(resnames)) 175 176 segidx, (segids,) = change_squash((chainids,), (chainids,)) 177 n_segments = len(segids) 178 attrs.append(Segids(segids)) 179 180 top = Topology(n_atoms, n_residues, n_segments, 181 attrs=attrs, 182 atom_resindex=residx, 183 residue_segindex=segidx) 184 185 return top 186