/usr/lib/python2.7/dist-packages/chempy/tinker/amber.py is in pymol 1.8.4.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#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:
#-* Scott Dixon, Metaphorics, LLC
#-*
#-*
#Z* -------------------------------------------------------------------
from __future__ import print_function
from chempy import feedback
import string
import copy
default_extra = { # atomic number, and normal valency (for tinker)
# NOTE: THIS SET IS ONLY USED IF THERE ARE NO TINKER RECORDS
# IN THE PARAMETER FILE
# bromine
'BR' : [ 35 , 1 ],
# carbon
'C' : [ 6 , 3 ],
'CA' : [ 6 , 3 ],
'CB' : [ 6 , 3 ],
'CC' : [ 6 , 3 ],
'CF' : [ 6 , 3 ],
'CK' : [ 6 , 3 ],
'CM' : [ 6 , 3 ],
'CN' : [ 6 , 3 ],
'CQ' : [ 6 , 3 ],
'CR' : [ 6 , 3 ],
'CT' : [ 6 , 4 ],
'CV' : [ 6 , 3 ],
'CW' : [ 6 , 3 ],
'CY' : [ 6 , 2 ],
'CX' : [ 6 , 2 ],
'C5' : [ 6 , 3 ],
'C*' : [ 6 , 3 ],
# calcium
'C0' : [ 20 , 3 ],
# chloride
'Cl' : [ 17 , 1 ],
# fluorine
'F' : [ 9 , 1 ],
# hydrogen
'H' : [ 1 , 1 ],
'H1' : [ 1 , 1 ],
'H2' : [ 1 , 1 ],
'H3' : [ 1 , 1 ],
'H4' : [ 1 , 1 ],
'H5' : [ 1 , 1 ],
'HA' : [ 1 , 1 ],
'HC' : [ 1 , 1 ],
'HO' : [ 1 , 1 ],
'HP' : [ 1 , 1 ],
'HS' : [ 1 , 1 ],
'HW' : [ 1 , 2 ],
# iodine
'I' : [ 53 , 1 ],
# chloride anion
'IM' : [ 17 , 0 ],
# sodium cation
'IP' : [ 11 , 0 ],
# magnesium
'MG' : [ 12 , 0 ],
# nitrogen
'N' : [ 7 , 3 ],
'N*' : [ 7 , 2 ],
'N2' : [ 7 , 3 ],
'N3' : [ 7 , 4 ],
'NA' : [ 7 , 3 ],
'NB' : [ 7 , 2 ],
'NC' : [ 7 , 2 ],
'NX' : [ 7 , 2 ],
'NZ' : [ 7 , 3 ],
#
'OW' : [ 8 , 2 ],
'OH' : [ 8 , 2 ],
'OS' : [ 8 , 2 ],
'O' : [ 8 , 1 ],
'O2' : [ 8 , 1 ],
'OM' : [ 8 , 1 ],
'OZ' : [ 8 , 1 ],
'P' : [ 15 , 4 ],
'S' : [ 16 , 2 ],
'SO' : [ 16 , 4 ],
'SX' : [ 16 , 2 ],
'SH' : [ 16 , 2 ],
# copper
'CU' : [ 29 , 0 ],
# iron
'FE' : [ 26 , 0 ],
# lithium
'Li' : [ 3 , 0 ],
# potassium
'K' : [ 19 , 0 ],
# rubidium
'Rb' : [ 37 , 0 ],
# cesium
'Cs' : [ 55 , 0 ],
# calcium (alternate)
'Ca' : [ 20 , 0 ],
# dummy
'X ' : [ 6 , 1 ],
# zinc
'Z0' : [ 30 , 0 ],
'Z4' : [ 30 , 4 ],
'Z5' : [ 30 , 5 ],
}
class Parameters:
def __init__(self,fname):
if feedback['actions']:
print(' '+str(self.__class__)+': loading from "%s"...' % fname)
f = open(fname)
# skip
l = f.readline()
# read names & molecular weights
self.type = []
self.mw = {}
while 1:
l = string.strip(f.readline())
if not len(l): break
a2 = string.strip(l[0:2])
self.type.append(a2)
self.mw[a2] = [float(l[3:13]),string.strip(l[34:])]
# skip 1
l = f.readline()
# read bonds
self.bond = {}
while 1:
l = string.strip(f.readline())
if not len(l): break
a5 = l[0:5]
self.bond[a5] = [float(l[5:12]),float(l[12:22]),
string.strip(l[22:])]
# read angles
self.angle = {}
while 1:
l = string.strip(f.readline())
if not len(l): break
a5 = l[0:8]
self.angle[a5] = [float(l[8:16]),float(l[16:28]),
string.strip(l[28:])]
# read torsion
self.torsion = {}
while 1:
l = string.strip(f.readline())
if not len(l): break
a5 = l[0:11]
if a5 in self.torsion:
self.torsion[a5].extend(
[int(l[11:15]),
float(l[15:27]),
float(l[27:36]),
abs(int(float(l[40:52]))),
string.strip(l[52:])])
else:
self.torsion[a5] = [int(l[11:15]),
float(l[15:27]),
float(l[27:36]),
abs(int(float(l[40:52]))),
string.strip(l[52:])]
# read impropers
self.improper = {}
while 1:
l = string.strip(f.readline())
if not len(l): break
a5 = l[0:11]
self.improper[a5] = [float(l[15:27]),
float(l[27:40]),
abs(int(float(l[40:51]))),
string.strip(l[51:])]
# skip
while 1:
l = string.strip(f.readline())
if not len(l): break
# read vdw equivalents
self.vdw_eq = {}
while 1:
l = string.strip(f.readline())
if not len(l): break
a4 = string.strip(l[0:4])
l = l[4:]
while len(l):
self.vdw_eq[string.strip(l[0:4])] = a4
l = l[4:]
# skip
l = string.strip(f.readline())
# read vdw parameters
self.vdw = {}
while 1:
l = string.strip(f.readline())
if not len(l): break
l = ' ' + l
a4 = string.strip(l[0:4])
self.vdw[a4] = [float(l[4:20]),
float(l[20:37]),
string.strip(l[37:])]
# read extra tinker information if present
self.extra = {}
while 1:
l = f.readline()
if not l: break
if l[0:6] == 'TINKER':
self.extra[string.strip(l[6:12])] = [
int(l[12:18]),
int(l[18:24])]
if not self.extra:
self.extra = default_extra
# now generate redundant equivalents
for a in self.vdw_eq.keys():
self.vdw[a] = self.vdw[self.vdw_eq[a]]
for a in list(self.bond.keys()):
k = a[3:5]+'-'+a[0:2]
self.bond[k] = self.bond[a]
for a in list(self.angle.keys()):
k = a[6:8]+'-'+a[3:5]+'-'+a[0:2]
self.angle[k] = self.angle[a]
def dump(self):
for b in self.type:
print(b)
kees = list(self.mw.keys())
kees.sort()
for b in kees:
print(b,self.mw[b])
kees = list(self.vdw_eq.keys())
kees.sort()
for b in kees:
print(b,self.vdw_eq[b])
kees = list(self.vdw.keys())
kees.sort()
for b in kees:
print(b,self.vdw[b])
kees = list(self.bond.keys())
kees.sort()
for b in kees:
print(b,self.bond[b])
kees = list(self.angle.keys())
kees.sort()
for b in kees:
print(b,self.angle[b])
kees = list(self.torsion.keys())
kees.sort()
for b in kees:
print(b,self.torsion[b])
kees = list(self.improper.keys())
kees.sort()
for b in kees:
print(b,self.improper[b])
kees = list(self.vdw.keys())
kees.sort()
for b in kees:
print(b,self.vdw[b])
class Topology:
def __init__(self,model):
self.model = model
if feedback['actions']:
print(' '+str(self.__class__)+': searching...')
# get a connected version too
cmodel = copy.deepcopy(model).convert_to_connected()
# find atom types in molecule
self.present = {}
for a in model.atom:
self.present[a.text_type] = 1
# copy bonds
self.bond = {}
for b in model.bond:
a0 = b.index[0]
a1 = b.index[1]
if a0 < a1:
self.bond[(a0,a1)] = 1
else:
self.bond[(a1,a0)] = 1
# find angles
self.angle = {}
ang = self.angle
for b in model.bond:
a0 = b.index[0]
a1 = b.index[1]
for c in cmodel.bond[a0]: # a0 in center
a2 = c.index[0]
if a2 not in (a0,a1): # outside atom
if a1 < a2:
an = (a1,a0,a2)
else:
an = (a2,a0,a1)
ang[an] = 1
a2 = c.index[1]
if a2 not in (a0,a1): # outside atom
if a1 < a2:
an = (a1,a0,a2)
else:
an = (a2,a0,a1)
ang[an] = 1
for c in cmodel.bond[a1]: # a1 in center
a2 = c.index[0]
if a2 not in (a0,a1): # outside atom
if a0 < a2:
an = (a0,a1,a2)
else:
an = (a2,a1,a0)
ang[an] = 1
a2 = c.index[1]
if a2 not in (a0,a1): # outside atom
if a0 < a2:
an = (a0,a1,a2)
else:
an = (a2,a1,a0)
ang[an] = 1
# find torsions
self.torsion = {}
tors = self.torsion
for b in model.bond: # use bond as center of torsion
a1 = b.index[0]
a2 = b.index[1]
for c in cmodel.bond[a1]:
a0 = c.index[0]
if a0 not in (a1,a2): # outside atom
for d in cmodel.bond[a2]:
a3 = d.index[0]
if a3 not in (a0,a1,a2): # outside atom
if a0 < a3:
to = (a0,a1,a2,a3)
else:
to = (a3,a2,a1,a0)
tors[to] = 1
a3 = d.index[1]
if a3 not in (a0,a1,a2): # outside atom
if a0 < a3:
to = (a0,a1,a2,a3)
else:
to = (a3,a2,a1,a0)
tors[to] = 1
a0 = c.index[1]
if a0 not in (a1,a2): # outside atom
for d in cmodel.bond[a2]:
a3 = d.index[0]
if a3 not in (a0,a1,a2): # outside atom
if a0 < a3:
to = (a0,a1,a2,a3)
else:
to = (a3,a2,a1,a0)
tors[to] = 1
a3 = d.index[1]
if a3 not in (a0,a1,a2): # outside atom
if a0 < a3:
to = (a0,a1,a2,a3)
else:
to = (a3,a2,a1,a0)
tors[to] = 1
# find impropers (only autogenerates for atoms with 3 bonds)
self.improper = {}
impr = self.improper
a2 = 0
for a in model.atom: # a2 is the center atom
bnd = cmodel.bond[a2]
if len(bnd) == 3:
lst = []
for b in bnd:
at = b.index[0]
if at == a2:
at = b.index[1]
lst.append(at)
lst.sort()
impr[(lst[0],lst[1],a2,lst[2])] = 1
a2 = a2 + 1
if feedback['actions']:
print(' '+str(self.__class__)+': found:')
print(' '+str(self.__class__)+': types %6d' % (
len(list(self.present.keys()))))
print(' '+str(self.__class__)+': bonds %6d' % (
len(list(self.bond.keys()))))
print(' '+str(self.__class__)+': angles %6d' % (
len(list(self.angle.keys()))))
print(' '+str(self.__class__)+': torsions %6d' % (
len(list(self.torsion.keys()))))
print(' '+str(self.__class__)+': impropers %6d' % (
len(list(self.improper.keys()))))
def dump(self):
kees = list(self.present.keys())
kees.sort()
for b in kees:
print(b)
kees = list(self.bond.keys())
kees.sort()
for b in kees:
print(b)
kees = list(self.angle.keys())
kees.sort()
for b in kees:
print(b)
kees = list(self.torsion.keys())
kees.sort()
for b in kees:
print(b)
kees = list(self.improper.keys())
kees.sort()
for b in kees:
print(b)
def get_list(self):
return [list(self.bond.keys()),
list(self.angle.keys()),
list(self.torsion.keys()),
list(self.improper.keys())]
class Subset:
def __init__(self,par,top):
if feedback['actions']:
print(' '+str(self.__class__)+': applying parameter set to topology...')
self.model = top.model
self.present = copy.deepcopy(top.present)
atype = []
for a in self.model.atom:
atype.append(a.text_type)
# extra tinker info (atomic number, valency)
self.miss_extra = []
self.extra = {}
s_extra = self.extra
present = top.present
p_extra = par.extra
for kee in present.keys():
if kee in p_extra:
s_extra[kee] = p_extra[kee]
else:
self.miss_extra.append(kee)
# molecular weight
self.miss_mw = []
self.mw = {}
s_mw = self.mw
present = top.present
p_mw = par.mw
for kee in present.keys():
if kee in p_mw:
s_mw[kee] = p_mw[kee]
else:
self.miss_mw.append(kee)
# van der waals
self.miss_vdw = []
self.vdw = {}
s_vdw = self.vdw
present = top.present
p_vdw = par.vdw
for kee in present.keys():
if kee in p_vdw:
s_vdw[kee] = p_vdw[kee]
else:
self.miss_vdw.append(kee)
# bonds
self.miss_bond = []
self.bond = {}
s_bond = self.bond
bond = top.bond
p_bond = par.bond
for a in list(bond.keys()):
kee = "%-2s-%-2s" % (atype[a[0]],atype[a[1]])
if kee in p_bond:
s_bond[kee] = p_bond[kee]
else:
self.miss_bond.append((a,kee))
# angles
self.miss_angle = []
self.angle = {}
s_angle = self.angle
angle = top.angle
p_angle = par.angle
for a in angle.keys():
kee = "%-2s-%-2s-%-2s" % (atype[a[0]],atype[a[1]],atype[a[2]])
if kee in p_angle:
s_angle[kee] = p_angle[kee]
else:
self.miss_angle.append((a,kee))
# torsions
self.miss_torsion = []
self.torsion = {}
s_torsion = self.torsion
torsion = top.torsion
p_torsion = par.torsion
for a in list(torsion.keys()):
at0=atype[a[0]]
at1=atype[a[1]]
at2=atype[a[2]] # center atom
at3=atype[a[3]]
while 1: # not a real loop, just "else" avoidance
kee1 = "%-2s-%-2s-%-2s-%-2s" % (at0,at1,at2,at3)
if kee1 in p_torsion:
s_torsion[kee1] = p_torsion[kee1]
break
kee2 = "%-2s-%-2s-%-2s-%-2s" % (at3,at2,at1,at0)
if kee2 in p_torsion:
s_torsion[kee2] = p_torsion[kee2]
break
kee = "X -%-2s-%-2s-X " % (at1,at2)
if kee in p_torsion:
s_torsion[kee1] = p_torsion[kee]
break
kee = "X -%-2s-%-2s-X " % (at2,at1)
if kee in p_torsion:
s_torsion[kee2] = p_torsion[kee]
break
self.miss_torsion.append((a,kee1))
break
# impropers
self.miss_improper = []
self.improper = {}
s_improper = self.improper
improper = top.improper
p_improper = par.improper
for a in improper.keys():
at0=atype[a[0]]
at1=atype[a[1]]
at2=atype[a[2]] # center atom
at3=atype[a[3]]
while 1: # not a real loop, just "else" avoidance
kee1 = "%-2s-%-2s-%-2s-%-2s" % (at1,at3,at2,at0)
if kee1 in p_improper:
s_improper[kee1] = p_improper[kee1]
break
kee2 = "%-2s-%-2s-%-2s-%-2s" % (at3,at1,at2,at0)
if kee2 in p_improper:
s_improper[kee2] = p_improper[kee2]
break
kee3 = "%-2s-%-2s-%-2s-%-2s" % (at0,at3,at2,at1)
if kee3 in p_improper:
s_improper[kee3] = p_improper[kee3]
break
kee4 = "%-2s-%-2s-%-2s-%-2s" % (at3,at0,at2,at1)
if kee4 in p_improper:
s_improper[kee4] = p_improper[kee4]
break
kee5 = "%-2s-%-2s-%-2s-%-2s" % (at0,at1,at2,at3)
if kee5 in p_improper:
s_improper[kee5] = p_improper[kee5]
break
kee6 = "%-2s-%-2s-%-2s-%-2s" % (at1,at0,at2,at3)
if kee6 in p_improper:
s_improper[kee6] = p_improper[kee6]
break
kee = "X -%-2s-%-2s-%-2s" % (at3,at2,at0)
if kee in p_improper:
s_improper[kee1] = p_improper[kee]
break
kee = "X -%-2s-%-2s-%-2s" % (at1,at2,at0)
if kee in p_improper:
s_improper[kee2] = p_improper[kee]
break
kee = "X -%-2s-%-2s-%-2s" % (at3,at2,at1)
if kee in p_improper:
s_improper[kee3] = p_improper[kee]
break
kee = "X -%-2s-%-2s-%-2s" % (at0,at2,at1)
if kee in p_improper:
s_improper[kee4] = p_improper[kee]
break
kee = "X -%-2s-%-2s-%-2s" % (at1,at2,at3)
if kee in p_improper:
s_improper[kee5] = p_improper[kee]
break
kee = "X -%-2s-%-2s-%-2s" % (at0,at2,at3)
if kee in p_improper:
s_improper[kee6] = p_improper[kee]
break
kee = "X -X -%-2s-%-2s" % (at2,at0)
if kee in p_improper:
s_improper[kee1] = p_improper[kee]
break
kee = "X -X -%-2s-%-2s" % (at2,at1)
if kee in p_improper:
s_improper[kee3] = p_improper[kee]
break
kee = "X -X -%-2s-%-2s" % (at2,at3)
if kee in p_improper:
s_improper[kee5] = p_improper[kee]
break
self.miss_improper.append((a,kee1))
break
if feedback['actions']:
print(' '+str(self.__class__)+': missing:')
print(' '+str(self.__class__)+': mol. wts. %6d' % (
len(self.miss_mw)))
print(' '+str(self.__class__)+': vdw %6d' % (
len(self.miss_vdw)))
print(' '+str(self.__class__)+': bonds %6d' % (
len(self.miss_bond)))
print(' '+str(self.__class__)+': angles %6d' % (
len(self.miss_angle)))
print(' '+str(self.__class__)+': torsions %6d' % (
len(self.miss_torsion)))
print(' '+str(self.__class__)+': impropers %6d (usually okay)' % (
len(self.miss_improper)))
print(' '+str(self.__class__)+': extra tinker info %6d' % (
len(self.miss_extra)))
def dump(self):
kees = list(self.mw.keys())
kees.sort()
for b in kees:
print(b,self.mw[b])
kees = list(self.bond.keys())
kees.sort()
for b in kees:
print(b,self.bond[b])
kees = list(self.angle.keys())
kees.sort()
for b in kees:
print(b,self.angle[b])
kees = list(self.torsion.keys())
kees.sort()
for b in kees:
print(b,self.torsion[b])
kees = list(self.improper.keys())
kees.sort()
for b in kees:
print(b,self.improper[b])
kees = list(self.vdw.keys())
kees.sort()
for b in kees:
print(b,self.vdw[b])
def dump_missing(self,impropers=0):
if len(self.miss_mw):
print(' '+str(self.__class__)+': missing molecular weights...')
for b in self.miss_mw:
print(" ",b)
if len(self.miss_vdw):
print(' '+str(self.__class__)+': missing van der Waalss...')
for b in self.miss_vdw:
print(" ",b)
if len(self.miss_bond):
print(' '+str(self.__class__)+': missing bonds...')
for b in self.miss_bond:
print(" ",b)
if len(self.miss_angle):
print(' '+str(self.__class__)+': missing angless...')
for b in self.miss_angle:
print(" ",b)
if len(self.miss_torsion):
print(' '+str(self.__class__)+': missing torsions...')
for b in self.miss_torsion:
print(" ",b)
if impropers:
if len(self.miss_improper):
print(' '+str(self.__class__)+': missing impropers...')
for b in self.miss_improper:
print(" ",b)
def complete(self):
if not ( len(self.miss_mw) or
len(self.miss_vdw) or
len(self.miss_bond) or
len(self.miss_angle) or
len(self.miss_torsion) ):
return 1
else:
return 0
def assign_types(self):
c = 0
self.mapping = {}
map = self.mapping
kees = list(self.present.keys())
label = []
type = []
kees.sort()
for a in kees:
c = c + 1
st = str(c)
label.append(st)
type.append(a)
map[a] = st
# assign numeric types
for a in self.model.atom:
a.numeric_type = map[a.text_type]
def write_tinker_prm(self,fname,proofread=None,smooth=None):
c = 0
self.mapping = {}
map = self.mapping
kees = list(self.present.keys())
label = []
type = []
kees.sort()
if proofread:
for a in kees:
label.append(a)
type.append(a)
map[a] = a
else:
for a in kees:
c = c + 1
st = str(c)
label.append(st)
type.append(a)
map[a] = st
# assign numeric types as per the parameter we're writing
for a in self.model.atom:
a.numeric_type = map[a.text_type]
f = open(fname,'w')
if smooth:
f.write('''
forcefield SMOOTH AMBER
vdwtype GAUSSIAN
gausstype LJ-2
''')
else:
f.write('''
forcefield AMBER95
vdwtype LENNARD-JONES
''')
f.write('''
radiusrule ARITHMETIC
radiustype R-MIN
radiussize RADIUS
epsilonrule GEOMETRIC
vdw-14-use
vdw-scale 2.0
chg-14-use
chg-scale 1.2
dielectric 1.0
''')
# types
for c in range(len(self.present)):
at = type[c]
f.write("atom %6s %6s %-2s %-25s %3d %10.3f%6d\n" % (
label[c],label[c],at,'"'+self.mw[at][1][0:23]+'"',
self.extra[at][0],
self.mw[at][0],self.extra[at][1]))
# van der waals
for c in range(len(self.present)):
at = type[c]
f.write("vdw %8s %10.4f %10.4f\n" % (
map[at],self.vdw[at][0],self.vdw[at][1]))
# bonds
bond = {}
for a in list(self.bond.keys()):
kee = (map[string.strip(a[0:2])],map[string.strip(a[3:5])])
bond[kee] = a
kees = list(bond.keys())
kees.sort()
for a in kees:
kee = bond[a]
f.write("bond %6s%5s %10.1f %10.4f\n" % (
a[0],a[1],self.bond[kee][0],self.bond[kee][1]))
# angles
angle = {}
for a in list(self.angle.keys()):
kee = (map[string.strip(a[0:2])],
map[string.strip(a[3:5])],
map[string.strip(a[6:8])],
)
angle[kee] = a
kees = list(angle.keys())
kees.sort()
for a in kees:
kee = angle[a]
f.write("angle %5s%5s%5s%9.2f %8.2f\n" % (
a[0],a[1],a[2],self.angle[kee][0],self.angle[kee][1]))
# impropers
if not smooth:
improper = {}
for a in self.improper.keys():
kee = (map[string.strip(a[0:2])],
map[string.strip(a[3:5])],
map[string.strip(a[6:8])],
map[string.strip(a[9:11])],
)
improper[kee] = a
kees = list(improper.keys())
kees.sort()
for a in kees:
kee = improper[a]
f.write("imptors %5s%5s%5s%5s %10.3f%7.1f%3d\n" % (
a[0],a[1],a[2],a[3],self.improper[kee][0],
self.improper[kee][1],self.improper[kee][2]))
else:
improper = {}
for a in self.improper.keys():
kee = (map[string.strip(a[0:2])],
map[string.strip(a[3:5])],
map[string.strip(a[6:8])],
map[string.strip(a[9:11])],
)
improper[kee] = a
kees = list(improper.keys())
kees.sort()
for a in kees:
kee = improper[a]
f.write("improper %5s%5s%5s%5s %10.2f 0.00\n" % (
a[2],a[0],a[1],a[3],self.improper[kee][0]*3.5))
# torsions
torsion = {}
for a in self.torsion.keys():
kee = (map[string.strip(a[0:2])],
map[string.strip(a[3:5])],
map[string.strip(a[6:8])],
map[string.strip(a[9:11])],
)
torsion[kee] = a
kees = list(torsion.keys())
kees.sort()
for a in kees:
kee = torsion[a]
st = "torsion %5s%5s%5s%5s " % (
a[0],a[1],a[2],a[3])
lst = self.torsion[kee]
div = lst[0]
lst = lst[1:]
while len(lst):
st = st + "%10.3f%7.1f%3d " % (
lst[0]/div,lst[1],lst[2])
lst = lst[5:]
while len(st)>79:
st = string.replace(st,' ',' ')
f.write(st+"\n")
# null charge records
for c in range(len(self.present)):
a = label[c]
f.write("charge %6s %10.4f\n" % (a,0.0))
f.close()
def get_list(self):
list = []
c = 0
self.mapping = {}
map = self.mapping
kees = list(self.present.keys())
label = []
type = []
kees.sort()
for a in kees:
c = c + 1
st = str(c)
type.append(a)
map[a] = c
# assign numeric types as per the parameter we're writing
for a in self.model.atom:
a.numeric_type = map[a.text_type]
# types
typ_list = []
for c in range(len(self.present)):
at = type[c]
typ_list.append((map[at],self.extra[at][0],self.mw[at][0],self.extra[at][1]))
list.append(typ_list)
# van der waals
vdw_list = []
for c in range(len(self.present)):
at = type[c]
vdw_list.append((map[at],self.vdw[at][0],self.vdw[at][1]))
list.append(vdw_list)
# bonds
bnd_list = []
bond = {}
for a in list(self.bond.keys()):
kee = (map[string.strip(a[0:2])],map[string.strip(a[3:5])])
bond[kee] = a
kees = list(bond.keys())
kees.sort()
for a in kees:
kee = bond[a]
bnd_list.append((a[0],a[1],self.bond[kee][0],self.bond[kee][1]))
list.append(bnd_list)
# angles
ang_list = []
angle = {}
for a in self.angle.keys():
kee = (map[string.strip(a[0:2])],
map[string.strip(a[3:5])],
map[string.strip(a[6:8])],
)
angle[kee] = a
kees = list(angle.keys())
kees.sort()
for a in kees:
kee = angle[a]
ang_list.append((a[0],a[1],a[2],self.angle[kee][0],self.angle[kee][1]))
list.append(ang_list)
# impropers
imp_list = []
improper = {}
for a in self.improper.keys():
kee = (map[string.strip(a[0:2])],
map[string.strip(a[3:5])],
map[string.strip(a[6:8])],
map[string.strip(a[9:11])],
)
improper[kee] = a
kees = list(improper.keys())
kees.sort()
for a in kees:
kee = improper[a]
imp_list.append((a[0],a[1],a[2],a[3],self.improper[kee][0],
self.improper[kee][1],self.improper[kee][2]))
list.append(imp_list)
# torsions
tor_list = []
torsion = {}
for a in self.torsion.keys():
kee = (map[string.strip(a[0:2])],
map[string.strip(a[3:5])],
map[string.strip(a[6:8])],
map[string.strip(a[9:11])],
)
torsion[kee] = a
kees = list(torsion.keys())
kees.sort()
for a in kees:
kee = torsion[a]
tor = [ a[0],a[1],a[2],a[3] ]
lst = self.torsion[kee]
div = lst[0]
lst = lst[1:]
while len(lst):
tor.extend([lst[0]/div,lst[1],lst[2]])
lst = lst[5:]
tor_list.append(tor)
list.append(tor_list)
return list
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