-
Notifications
You must be signed in to change notification settings - Fork 670
/
Copy pathPDBQT.py
356 lines (311 loc) · 15.3 KB
/
PDBQT.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
# -*- 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
#
"""
PDBQT structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.PDBQT`
===========================================================================
MDAnalysis reads coordinates from PDBQT_ files and additional optional
data such as B-factors, partial charge and AutoDock_ atom types. It
is also possible to substitute a PDBQT file for a PSF file in order to
define the list of atoms (but no connectivity information will be
available in this case).
.. _PDBQT:
http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
.. _AutoDock:
http://autodock.scripps.edu/
"""
import os
import errno
import itertools
import numpy as np
import warnings
from ..lib import util
from . import base
class PDBQTReader(base.SingleFrameReaderBase):
"""PDBQTReader that reads a PDBQT-formatted file, no frills.
Records read:
- CRYST1 for unitcell A,B,C, alpha,beta,gamm
- ATOM. HETATM for x,y,z
Original `PDB format documentation`_ with `AutoDOCK extensions`_
.. _PDB format documentation:
http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
.. _AutoDOCK extensions:
http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
============= ============ =========== =============================================
COLUMNS DATA TYPE FIELD DEFINITION
============= ============ =========== =============================================
1 - 6 Record name "CRYST1"
7 - 15 Real(9.3) a a (Angstroms).
16 - 24 Real(9.3) b b (Angstroms).
25 - 33 Real(9.3) c c (Angstroms).
34 - 40 Real(7.2) alpha alpha (degrees).
41 - 47 Real(7.2) beta beta (degrees).
48 - 54 Real(7.2) gamma gamma (degrees).
1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator. IGNORED
18 - 21 Residue name resName Residue name.
22 Character chainID Chain identifier.
23 - 26 Integer resSeq Residue sequence number.
27 AChar iCode Code for insertion of residues. IGNORED
31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms.
39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms.
47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms.
55 - 60 Real(6.2) occupancy Occupancy.
61 - 66 Real(6.2) tempFactor Temperature factor.
67 - 70 LString(4) footnote Usually blank. IGNORED.
71 - 76 Real(6.4) partialChrg Gasteiger PEOE partial charge *q*.
79 - 80 LString(2) atomType AutoDOCK atom type *t*.
============= ============ =========== =============================================
We ignore torsion notation and just pull the partial charge and atom type columns::
COMPND NSC7810
REMARK 3 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: A7_7 and C22_23
REMARK 2 A between atoms: A9_9 and A11_11
REMARK 3 A between atoms: A17_17 and C21_21
ROOT
123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference)
ATOM 1 A1 INH I 1.054 3.021 1.101 0.00 0.00 0.002 A
ATOM 2 A2 INH I 1.150 1.704 0.764 0.00 0.00 0.012 A
ATOM 3 A3 INH I -0.006 0.975 0.431 0.00 0.00 -0.024 A
ATOM 4 A4 INH I 0.070 -0.385 0.081 0.00 0.00 0.012 A
ATOM 5 A5 INH I -1.062 -1.073 -0.238 0.00 0.00 0.002 A
ATOM 6 A6 INH I -2.306 -0.456 -0.226 0.00 0.00 0.019 A
ATOM 7 A7 INH I -2.426 0.885 0.114 0.00 0.00 0.052 A
ATOM 8 A8 INH I -1.265 1.621 0.449 0.00 0.00 0.002 A
ATOM 9 A9 INH I -1.339 2.986 0.801 0.00 0.00 -0.013 A
ATOM 10 A10 INH I -0.176 3.667 1.128 0.00 0.00 0.013 A
ENDROOT
BRANCH 9 11
ATOM 11 A11 INH I -2.644 3.682 0.827 0.00 0.00 -0.013 A
ATOM 12 A16 INH I -3.007 4.557 -0.220 0.00 0.00 0.002 A
ATOM 13 A12 INH I -3.522 3.485 1.882 0.00 0.00 0.013 A
ATOM 14 A15 INH I -4.262 5.209 -0.177 0.00 0.00 -0.024 A
ATOM 15 A17 INH I -2.144 4.784 -1.319 0.00 0.00 0.052 A
ATOM 16 A14 INH I -5.122 4.981 0.910 0.00 0.00 0.012 A
ATOM 17 A20 INH I -4.627 6.077 -1.222 0.00 0.00 0.012 A
ATOM 18 A13 INH I -4.749 4.135 1.912 0.00 0.00 0.002 A
ATOM 19 A19 INH I -3.777 6.285 -2.267 0.00 0.00 0.002 A
ATOM 20 A18 INH I -2.543 5.650 -2.328 0.00 0.00 0.019 A
BRANCH 15 21
ATOM 21 C21 INH I -0.834 4.113 -1.388 0.00 0.00 0.210 C
ATOM 22 O1 INH I -0.774 2.915 -1.581 0.00 0.00 -0.644 OA
ATOM 23 O3 INH I 0.298 4.828 -1.237 0.00 0.00 -0.644 OA
ENDBRANCH 15 21
ENDBRANCH 9 11
BRANCH 7 24
ATOM 24 C22 INH I -3.749 1.535 0.125 0.00 0.00 0.210 C
ATOM 25 O2 INH I -4.019 2.378 -0.708 0.00 0.00 -0.644 OA
ATOM 26 O4 INH I -4.659 1.196 1.059 0.00 0.00 -0.644 OA
ENDBRANCH 7 24
TORSDOF 3
123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference)
.. versionchanged:: 0.11.0
Frames now 0-based instead of 1-based
"""
format = 'PDBQT'
units = {'time': None, 'length': 'Angstrom'}
def _read_first_frame(self):
coords = []
unitcell = np.zeros(6, dtype=np.float32)
with util.openany(self.filename) as pdbfile:
for line in pdbfile:
# Should only break at the 'END' of a model definition
# and prevent premature exit for a torsion termination
# , eg, ENDBRANCH
if line.startswith('END\n'):
break
if line.startswith('CRYST1'):
# lengths
x, y, z = np.float32((line[6:15], line[15:24], line[24:33]))
# angles
A, B, G = np.float32((line[33:40], line[40:47], line[47:54]))
unitcell[:] = x, y, z, A, B, G
if line.startswith(('ATOM', 'HETATM')):
# convert all entries at the end once for optimal speed
coords.append([line[30:38], line[38:46], line[46:54]])
self.n_atoms = len(coords)
self.ts = self._Timestep.from_coordinates(
coords,
**self._ts_kwargs)
self.ts.dimensions = unitcell
self.ts.frame = 0 # 0-based frame number
if self.convert_units:
# in-place !
self.convert_pos_from_native(self.ts._pos)
if self.ts.dimensions is not None:
self.convert_pos_from_native(self.ts.dimensions[:3])
def Writer(self, filename, **kwargs):
"""Returns a permissive (simple) PDBQTWriter for *filename*.
Parameters
----------
filename : str
filename of the output PDBQT file
Returns
-------
:class:`PDBQTWriter`
"""
return PDBQTWriter(filename, **kwargs)
class PDBQTWriter(base.WriterBase):
"""PDBQT writer that implements a subset of the PDB_ 3.2 standard and the PDBQT_ spec.
.. _PDB: http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
.. _PDBQT: http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
.. versionchanged:: 2.6.0
Files are now written in `wt` mode, and keep extensions, allowing
for files to be written under compressed formats
"""
fmt = {
'ATOM': ("ATOM {serial:5d} {name:<4.4s} {resName:<4.4s}"
"{chainID:1.1s}{resSeq:4d}{iCode:1.1s}"
" {pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{occupancy:6.2f}"
"{tempFactor:6.2f} {charge:< 1.3f} {element:<2.2s}\n"),
'REMARK': "REMARK {0}\n",
'TITLE': "TITLE {0}\n",
'CRYST1': ("CRYST1{box[0]:9.3f}{box[1]:9.3f}{box[2]:9.3f}"
"{ang[0]:7.2f}{ang[1]:7.2f}{ang[2]:7.2f} "
"{spacegroup:<11s}{zvalue:4d}\n"),
}
format = 'PDBQT'
units = {'time': None, 'length': 'Angstrom'}
pdb_coor_limits = {"min": -999.9995, "max": 9999.9995}
def __init__(self, filename, **kwargs):
self.filename = util.filename(filename, ext='pdbqt', keep=True)
self.pdb = util.anyopen(self.filename, 'wt')
def close(self):
self.pdb.close()
def write(self, selection, frame=None):
"""Write selection at current trajectory frame to file.
Parameters
----------
selection : AtomGroup
The selection to be written
frame : int (optional)
optionally move to frame index `frame` before writing; the default
is to write the current trajectory frame
Note
----
The last letter of the
:attr:`~MDAnalysis.core.groups.Atom.segid` is used as the PDB
chainID.
.. versionchanged:: 0.11.0
Frames now 0-based instead of 1-based
"""
try:
u = selection.universe
except AttributeError:
errmsg = "Input obj is neither an AtomGroup or Universe"
raise TypeError(errmsg) from None
if frame is not None:
u.trajectory[frame] # advance to frame
else:
try:
frame = u.trajectory.ts.frame
except AttributeError:
frame = 0 # should catch cases when we are analyzing a single PDB (?)
atoms = selection.atoms # make sure to use atoms (Issue 46)
coor = atoms.positions # can write from selection == Universe (Issue 49)
# Check attributes
attrs = {}
missing_topology = []
for attr, dflt in (
('altLocs', ' '),
('charges', 0.0),
('icodes', ' '),
('names', 'X'),
('occupancies', 1.0),
('resids', 1),
('resnames', 'UNK'),
('tempfactors', 0.0),
('types', ' '),
):
try:
attrs[attr] = getattr(atoms, attr)
except AttributeError:
attrs[attr] = itertools.cycle((dflt,))
missing_topology.append(attr)
# Order of preference: chainids -> segids -> blank string
try:
attrs['chainids'] = atoms.chainids
except AttributeError:
try:
attrs['chainids'] = atoms.segids
except AttributeError:
attrs['chainids'] = itertools.cycle((' ',))
missing_topology.append('chainids')
if missing_topology:
warnings.warn(
"Supplied AtomGroup was missing the following attributes: "
"{miss}. These will be written with default values. "
"".format(miss=', '.join(missing_topology)))
# check if any coordinates are illegal (coordinates are already
# in Angstroem per package default)
if not self.has_valid_coordinates(self.pdb_coor_limits, coor):
self.close()
try:
os.remove(self.filename)
except OSError as err:
if err.errno == errno.ENOENT:
pass
raise ValueError(
"PDB files must have coordinate values between {0:.3f}"
" and {1:.3f} Angstroem: No file was written."
"".format(self.pdb_coor_limits["min"],
self.pdb_coor_limits["max"]))
# Write title record
# http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html
line = "FRAME " + str(frame) + " FROM " + str(u.trajectory.filename)
self.pdb.write(self.fmt['TITLE'].format(line))
# Write CRYST1 record
# http://www.wwpdb.org/documentation/file-format-content/format32/sect8.html
box = self.convert_dimensions_to_unitcell(u.trajectory.ts)
self.pdb.write(self.fmt['CRYST1'].format(box=box[:3], ang=box[3:],
spacegroup='P 1', zvalue=1))
# Write atom records
# http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html
for serial, (pos, name, resname, chainid, resid, icode,
occupancy, tempfactor, charge, element) in enumerate(
zip(coor, attrs['names'], attrs['resnames'], attrs['chainids'],
attrs['resids'], attrs['icodes'], attrs['occupancies'],
attrs['tempfactors'], attrs['charges'], attrs['types']),
start=1):
serial = util.ltruncate_int(serial, 5) # check for overflow here?
resid = util.ltruncate_int(resid, 4)
name = name[:4]
if len(name) < 4:
name = " " + name # customary to start in column 14
chainid = chainid.strip()[-1:] # take the last character
self.pdb.write(self.fmt['ATOM'].format(
serial=serial,
name=name,
resName=resname,
chainID=chainid,
resSeq=resid,
iCode=icode,
pos=pos,
occupancy=occupancy,
tempFactor=tempfactor,
charge=charge,
element=element,
))
self.close()