-
Notifications
You must be signed in to change notification settings - Fork 2
/
prepare_receptor4.py
190 lines (168 loc) · 7.66 KB
/
prepare_receptor4.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
#!/usr/bin/env python
#
#
#
# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/Utilities24/prepare_receptor4.py,v 1.13 2010/01/25 23:37:14 rhuey Exp $
#
import os
from MolKit import Read
import MolKit.molecule
import MolKit.protein
from AutoDockTools.MoleculePreparation import AD4ReceptorPreparation
if __name__ == '__main__':
import sys
import getopt
def usage():
"Print helpful, accurate usage statement to stdout."
print "Usage: prepare_receptor4.py -r filename"
print
print " Description of command..."
print " -r receptor_filename "
print " supported file types include pdb,mol2,pdbq,pdbqs,pdbqt, possibly pqr,cif"
print " Optional parameters:"
print " [-v] verbose output (default is minimal output)"
print " [-o pdbqt_filename] (default is 'molecule_name.pdbqt')"
print " [-A] type(s) of repairs to make: "
print " 'bonds_hydrogens': build bonds and add hydrogens "
print " 'bonds': build a single bond from each atom with no bonds to its closest neighbor"
print " 'hydrogens': add hydrogens"
print " 'checkhydrogens': add hydrogens only if there are none already"
print " 'None': do not make any repairs "
print " (default is 'None')"
print " [-C] preserve all input charges ie do not add new charges "
print " (default is addition of gasteiger charges)"
print " [-p] preserve input charges on specific atom types, eg -p Zn -p Fe"
print " [-U] cleanup type:"
print " 'nphs': merge charges and remove non-polar hydrogens"
print " 'lps': merge charges and remove lone pairs"
print " 'waters': remove water residues"
print " 'nonstdres': remove chains composed entirely of residues of"
print " types other than the standard 20 amino acids"
print " 'deleteAltB': remove XX@B atoms and rename XX@A atoms->XX"
print " (default is 'nphs_lps_waters_nonstdres') "
print " [-e] delete every nonstd residue from any chain"
print " 'True': any residue whose name is not in this list:"
print " ['CYS','ILE','SER','VAL','GLN','LYS','ASN', "
print " 'PRO','THR','PHE','ALA','HIS','GLY','ASP', "
print " 'LEU', 'ARG', 'TRP', 'GLU', 'TYR','MET', "
print " 'HID', 'HSP', 'HIE', 'HIP', 'CYX', 'CSS']"
print " will be deleted from any chain. "
print " NB: there are no nucleic acid residue names at all "
print " in the list and no metals. "
print " (default is False which means not to do this)"
print " [-M] interactive "
print " (default is 'automatic': outputfile is written with no further user input)"
print " [-d dictionary_filename] file to contain receptor summary information"
# process command arguments
try:
opt_list, args = getopt.getopt(sys.argv[1:], 'r:vo:A:Cp:U:eM:d:')
except getopt.GetoptError, msg:
print 'prepare_receptor4.py: %s' %msg
usage()
sys.exit(2)
# initialize required parameters
#-s: receptor
receptor_filename = None
# optional parameters
verbose = None
#-A: repairs to make: add bonds and/or hydrogens or checkhydrogens
repairs = ''
#-C default: add gasteiger charges
charges_to_add = 'gasteiger'
#-p preserve charges on specific atom types
preserve_charge_types=None
#-U: cleanup by merging nphs_lps, nphs, lps, waters, nonstdres
cleanup = "nphs_lps_waters_nonstdres"
#-o outputfilename
outputfilename = None
#-m mode
mode = 'automatic'
#-e delete every nonstd residue from each chain
delete_single_nonstd_residues = None
#-d dictionary
dictionary = None
#'r:vo:A:Cp:U:eMh'
for o, a in opt_list:
if o in ('-r', '--r'):
receptor_filename = a
if verbose: print 'set receptor_filename to ', a
if o in ('-v', '--v'):
verbose = True
if verbose: print 'set verbose to ', True
if o in ('-o', '--o'):
outputfilename = a
if verbose: print 'set outputfilename to ', a
if o in ('-A', '--A'):
repairs = a
if verbose: print 'set repairs to ', a
if o in ('-C', '--C'):
charges_to_add = None
if verbose: print 'do not add charges'
if o in ('-p', '--p'):
if not preserve_charge_types:
preserve_charge_types = a
else:
preserve_charge_types = preserve_charge_types + ','+ a
if verbose: print 'preserve initial charges on ', preserve_charge_types
if o in ('-U', '--U'):
cleanup = a
if verbose: print 'set cleanup to ', a
if o in ('-e', '--e'):
delete_single_nonstd_residues = True
if verbose: print 'set delete_single_nonstd_residues to True'
if o in ('-M', '--M'):
mode = a
if verbose: print 'set mode to ', a
if o in ('-d', '--d'):
dictionary = a
if verbose: print 'set dictionary to ', dictionary
if o in ('-h', '--'):
usage()
sys.exit()
if not receptor_filename:
print 'prepare_receptor4: receptor filename must be specified.'
usage()
sys.exit()
#what about nucleic acids???
mols = Read(receptor_filename)
if verbose: print 'read ', receptor_filename
mol = mols[0]
preserved = {}
if charges_to_add is not None and preserve_charge_types is not None:
preserved_types = preserve_charge_types.split(',')
if verbose: print "preserved_types=", preserved_types
for t in preserved_types:
if verbose: print 'preserving charges on type->', t
if not len(t): continue
ats = mol.allAtoms.get(lambda x: x.autodock_element==t)
if verbose: print "preserving charges on ", ats.name
for a in ats:
if a.chargeSet is not None:
preserved[a] = [a.chargeSet, a.charge]
if len(mols)>1:
if verbose: print "more than one molecule in file"
#use the molecule with the most atoms
ctr = 1
for m in mols[1:]:
ctr += 1
if len(m.allAtoms)>len(mol.allAtoms):
mol = m
if verbose: print "mol set to ", ctr, "th molecule with", len(mol.allAtoms), "atoms"
mol.buildBondsByDistance()
if verbose:
print "setting up RPO with mode=", mode,
print "and outputfilename= ", outputfilename
print "charges_to_add=", charges_to_add
print "delete_single_nonstd_residues=", delete_single_nonstd_residues
RPO = AD4ReceptorPreparation(mol, mode, repairs, charges_to_add,
cleanup, outputfilename=outputfilename,
preserved=preserved,
delete_single_nonstd_residues=delete_single_nonstd_residues,
dict=dictionary)
if charges_to_add is not None:
#restore any previous charges
for atom, chargeList in preserved.items():
atom._charges[chargeList[0]] = chargeList[1]
atom.chargeSet = chargeList[0]
# To execute this command type:
# prepare_receptor4.py -r pdb_file -o outputfilename -A checkhydrogens