/usr/lib/python2.7/dist-packages/chempy/mol2.py is in pymol 1.7.0.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright Schrodinger LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information.
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-*
#-*
#-*
#Z* -------------------------------------------------------------------
from chempy.models import Indexed
from chempy import Storage,Atom,Bond,feedback
import string
class MOL2(Storage):
def __init__(self,**kwargs):
if 'cmd' in kwargs:
self.cmd = kwargs['cmd']
else:
self.cmd = None
# RTIs
_fields = { "alt_type" : "@<TRIPOS>ALT_TYPE\n",
"anchor_atom" : "@<TRIPOS>ANCHOR_ATOM\n",
"associated_annotation" : "@<TRIPOS>ASSOCIATED_ANNOTATION\n",
"atom" : "@<TRIPOS>ATOM\n",
"bond" : "@<TRIPOS>BOND\n",
"center_of_mass" : "@<TRIPOS>CENTER_OF_MASS\n",
"centroid" : "@<TRIPOS>CENTROID\n",
"comment" : "@<TRIPOS>COMMENT\n",
"crysin" : "@<TRIPOS>CRYSIN\n",
"dict" : "@<TRIPOS>DICT\n",
"data_file" : "@<TRIPOS>DATA_FILE\n",
"extension_point" : "@<TRIPOS>EXTENSION_POINT\n",
"ff_pbc" : "@<TRIPOS>FF_PBC\n",
"ffcon_angle" : "@<TRIPOS>FFCON_ANGLE\n",
"ffcon_dist" : "@<TRIPOS>FFCON_DIST\n",
"ffcon_multi" : "@<TRIPOS>FFCON_MULTI\n",
"ffcon_range" : "@<TRIPOS>FFCON_RANGE\n",
"ffcon_torsion" : "@<TRIPOS>FFCON_TORSION\n",
"line" : "@<TRIPOS>LINE\n",
"lsplane" : "@<TRIPOS>LSPLANE\n",
"molecule" : "@<TRIPOS>MOLECULE\n",
"normal" : "@<TRIPOS>NORMAL\n",
"qsar_align_rule" : "@<TRIPOS>QSAR_ALIGN_RULE\n",
"ring_closure" : "@<TRIPOS>RING_CLOSURE\n",
"rotatable_bond" : "@<TRIPOS>ROTATABLE_BOND\n",
"search_dist" : "@<TRIPOS>SEARCH_DIST\n",
"search_options" : "@<TRIPOS>SEARCH_OPTIONS\n",
"set" : "@<TRIPOS>SET\n",
"substructure" : "@<TRIPOS>SUBSTRUCTURE\n",
"u_feat" : "@<TRIPOS>U_FEAT\n",
"unity_atom_attr" : "@<TRIPOS>UNITY_ATOM_ATTR\n",
"unity_bond_attr" : "@<TRIPOS>UNITY_BOND_ATTR\n" }
_molType = { "small" : "SMALL\n",
"bio" : "BIOPOLYMER\n",
"prot" : "PROTEIN\n",
"nuc" : "NUCLEIC_ACID\n",
"sacc" : "SACCHARIDE\n" }
_chargeType = { "none" : "NO_CHARGES\n",
"del" : "DEL_RE\n",
"gast" : "GASTEIGER\n",
"gast_h" : "GAST_HUCK\n",
"huck" : "HUCKEL\n",
"pull" : "PULLMAN\n",
"gauss80" : "GAUSS80_CHARGES\n",
"ampac" : "AMPAC_CHARGES\n",
"mull" : "MULLIKEN_CHARGES\n",
"dict" : "DICT_ CHARGES\n",
"mmff94" : "MMFF94_CHARGES\n",
"user" : "USER_CHARGES\n" }
_bondTypes = { 1 : "1",
2 : "2",
3 : "3",
"amide" : "am",
4 : "ar",
"dummy" : "du",
"unknown" : "un",
0 : "nc",
"not_connected" : "nc" }
def fromList(self,molList):
pass
def toList(self,model,**kwargs):
molList = []
if 'state' in kwargs:
state = kwargs['state']
else:
state = None
if 'selection' in kwargs:
sel = kwargs['selection']
else:
sel = None
f = MOL2._fields
c = MOL2._chargeType
m = MOL2._molType
n = "\n"
molList.append("# created with PyMOL")
if model.molecule.comments!='':
molList.append("# COMMENTS:"+n)
molList.append("# " + model.molecule.comments)
# RTI MOLECULE
molList.append(n+f["molecule"])
molList.append(model.molecule.title+n)
subst=feat=sets=0
molList.append("%d\t%d\t%d\t%d\t%d\n" % (model.nAtom,model.nBond,subst,feat,sets))
# TODO: Guess this from the user's selection
mKey="prot"
## if self.cmd!=None and state!=None and sel!=None:
## nPoly = self.cmd.count_atoms("poly and (%s and state %s)" % (sel,state))
## nOrg = self.cmd.count_atoms("org and (%s and state %s)" % (sel,state))
## nIno = self.cmd.count_atoms("inorganic and (%s and state %s)" % (sel,state))
## nNuc = self.cmd.count_atoms("(resn DA+DG+DC+DT+A+C+G+U) and (%s and state %s)" (sel,state))
## # not too happy w/this
## # - poly
## if nPoly==0:
## # - nuc
## if nNuc==0:
## # - org
## if nOrg==0:
## # - ino
## if nIno==0:
## # what are you?!
## # you have no polymer, no organic, no nucleic, no inorganic
## # default, is wrong, but so are the others
## mKey = "prot"
## # ino - all
## else:
## mKey = "small"
## # org
## else:
## mKey = "small"
## # nuc
## else:
## if nIno==0 and nOrg==0:
## mKey = "nuc"
## else:
## mKey = "bio"
## # poly
## else:
## mKey="prot"
molList.append(m[mKey])
# TODO: Guess this
molList.append(c["user"])
# RTI ATOM
molList.append(f["atom"])
for a in range(len(model.atom)):
at = model.atom[a]
molList.append("%d\t%4s\t%.3f\t%.3f\t%.3f\t%2s\t%.3f\n" %
(at.index,
at.name or at.symbol or "X",
at.coord[0],at.coord[1],at.coord[2],
at.text_type, at.q))
# RTI BOND
molList.append(f["bond"])
for b in range(len(model.bond)):
bo = model.bond[b]
bOrder = MOL2._bondTypes[bo.order]
molList.append("%d %d %d %s\n" % (b,1+bo.index[0],1+bo.index[1],str(bOrder)))
molList.append("\n")
return molList
def strToFile(self,dat,fname,**params):
if feedback['io']:
print ' chempy: writing mol2 to file "%s".' % fname
fp = open(fname,'w')
result = fp.writelines(dat)
fp.close()
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