/usr/lib/python2.7/dist-packages/chempy/mmd.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 | #A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#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,Connected
from chempy import Storage,Atom,Bond
import string
import copy
class MMD(Storage):
#---------------------------------------------------------------------------------
def fromList(self,MMODList):
model = Connected()
# get header information
nAtom = int(MMODList[0][1:6])
model.molecule.title = string.strip(MMODList[0][8:])
irec = 1
# loop through atoms
cnt = 0
for a in range(nAtom):
model.bond.append([])
for a in range(nAtom):
at = Atom()
at.numeric_type = int(MMODList[irec][1:4])
# extract connectivity information
tokens = string.splitfields(MMODList[irec][5:52])
at.neighbor = []
at.bondorder = []
for i in range(6):
if tokens[2*i] != "0":
a2 = int(tokens[2*i])-1
if (a2>cnt):
b = Bond()
b.index = [cnt,a2]
b.order = int(tokens[2*i+1])
model.bond[b.index[0]].append(b) # note two refs to same object
model.bond[b.index[1]].append(b) # note two refs to same object
else:
break
# extract other information
at.coord = [float(MMODList[irec][53:64]),
float(MMODList[irec][65:76]), float(MMODList[irec][77:88])]
at.resi = string.strip(MMODList[irec][89:94])
at.resi_number = int(at.resi)
resn_code = string.strip(MMODList[irec][94:95])
if len(resn_code): at.resn_code = resn_code
color_code = string.strip(MMODList[irec][96:100])
if color_code!='':
at.color_code = int(color_code)
else:
at.color_code = 0
chain = string.strip(MMODList[irec][95:96])
if len(chain): at.chain = chain
at.partial_charge = float(MMODList[irec][100:109])
at.resn = MMODList[irec][119:123]
name = string.strip(MMODList[irec][124:128])
if len(name): at.name = name
model.atom.append(at)
irec = irec + 1
cnt = cnt + 1
# fill in remaining datatypes
cnt = 1
for a in model.atom:
a.text_type = MMOD_atom_data[a.numeric_type][0]
a.symbol = MMOD_atom_data[a.numeric_type][1]
a.formal_charge = MMOD_atom_data[a.numeric_type][4]
cnt = cnt + 1
return(model.convert_to_indexed())
#---------------------------------------------------------------------------------
def updateFromList(self,model,list): # updates charges and coordinates
nAtom = int(list[0][1:6])
try:
model.molecule.energy = float(list[0][58:68])/4.184 # convert to kcal
except:
if hasattr(model.molecule,'energy'):
del model.molecule.energy
if nAtom!=model.nAtom:
raise RuntimeError(" mmd: atom count mismatch")
c = 0
for a in list[1:]:
mac = model.atom[c]
mac.coord = [float(a[53:64]),
float(a[65:76]), float(a[77:88])]
mac.partial_charge = float(a[100:109])
c = c + 1
#---------------------------------------------------------------------------------
def toList(self,model,no_blank_names=1):
conn = copy.deepcopy(model)
conn = conn.convert_to_connected()
MMODList = []
MMODList.append(" %5d %-70s\n" %(conn.nAtom,conn.molecule.title))
c = 0
for i in conn.atom:
# construct neighbor list
neighbors = len(conn.bond[c])*[0]
bondorders = len(conn.bond[c])*[0]
j = 0
for b in conn.bond[c]:
n = b.index[0]
if n == c:
n = b.index[1]
neighbors[j] = n + 1
bondorders[j] = b.order
j = j + 1
# assemble output line
if i.numeric_type>0:
tline = " %3d" % (i.numeric_type)
else:
tline = " %3d" % 64
for j in range(len(conn.bond[c])):
tline = tline + " %5d %1d" % (neighbors[j], bondorders[j])
tline = tline + " %11.6f %11.6f %11.6f " % (i.coord[0],
i.coord[1], i.coord[2])
name = i.name
if not len(name):
if no_blank_names:
name = "%s%d" % (i.symbol,c+1)
name = name[0:4]
tline = tline + "%5d%1s%1s%4d%9.5f%9.5f %-4s %4s\n" % \
(i.resi_number,i.resn_code, i.chain, i.color_code,
i.partial_charge, i.partial_charge, i.resn, name)
MMODList.append(tline)
c = c + 1
return(MMODList)
#---------------------------------------------------------------------------------
'#Ntype Atype Elem Hybr Att Chg\n',
MMOD_atom_data = {
1: ['C1','C' ,'sp' , 2, 0],
2: ['C2','C' ,'sp2', 3, 0],
3: ['C3','C' ,'sp3', 4, 0],
4: ['CA','C' ,'sp3', 3, 0],
5: ['CB','C' ,'sp3', 2, 0],
6: ['CC','C' ,'sp3', 1, 0],
7: ['CD','C' ,'sp2', 2, 0],
8: ['CE','C' ,'sp2', 1, 0],
9: ['CF','C' ,'sp' , 1, 0],
10: ['CM','C' ,'unk',-1,-1],
11: ['CP','C' ,'unk',-1, 1],
12: ['CR','C' ,'unk',-1, 0],
14: ['C0','C' ,'unk',-1, 0],
15: ['O2','O' ,'sp2', 1, 0],
16: ['O3','O' ,'sp3', 2, 0],
17: ['OA','O' ,'sp3', 1, 0],
18: ['OM','O' ,'sp3', 1,-1],
19: ['OW','O' ,'sp3', 0, 0],
20: ['OP','O' ,'sp2', 2, 1],
21: ['OQ','O' ,'sp3', 3, 1],
23: ['O0','O' ,'unk',-1, 0],
24: ['N1','N' ,'sp' , 1, 0],
25: ['N2','N' ,'sp2', 2, 0],
26: ['N3','N' ,'sp3', 3, 0],
27: ['NA','N' ,'sp3', 2, 0],
28: ['NB','N' ,'sp3', 1, 0],
29: ['NC','N' ,'sp3', 0, 0],
30: ['ND','N' ,'sp2', 1, 0],
31: ['N4','N' ,'sp2', 3, 1],
32: ['N5','N' ,'sp3', 4, 1],
33: ['NE','N' ,'sp3', 3, 1],
34: ['NF','N' ,'sp3', 2, 1],
35: ['NG','N' ,'sp3', 1, 1],
36: ['NH','N' ,'sp2', 2, 1],
37: ['NI','N' ,'sp2', 1, 1],
40: ['N0','N' ,'unk',-1, 0],
41: ['H1','H' ,'s' , 1, 0],
42: ['H2','H' ,'s' , 1, 0],
43: ['H3','H' ,'s' , 1, 0],
44: ['H4','H' ,'s' , 0, 0],
45: ['H5','H' ,'s' , 0, 0],
48: ['H0','H' ,'s' ,-1, 0],
49: ['S1','S' ,'sp3', 2, 0],
50: ['SA','S' ,'sp3', 1, 0],
51: ['SM','S' ,'sp3', 0,-1],
52: ['S0','S' ,'unk',-1, 0],
53: ['P0','P' ,'unk',-1, 0],
54: ['B2','B' ,'sp2', 2, 0],
55: ['B3','B' ,'sp3', 3, 0],
56: ['F0','F' ,'sp3', 1, 0],
57: ['Cl','Cl','sp3', 1, 0],
58: ['Br','Br','sp3', 1, 0],
59: ['I0','I' ,'sp3', 1, 0],
60: ['Si','Si','unk',-1, 0],
61: ['Du','Du','unk',-1, 0],
62: ['Du','Du','unk',-1, 0],
63: ['Lp','Lp','unk', 1, 0],
64: ['Du','Du','unk',-1, 0]};
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