"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "data/chempy/tinker/make_simple.py" between
pymol-v1.8.6.0.tar.bz2 and pymol-v2.1.0.tar.bz2

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

[ To the main PyMOL source changes report ]

make_simple.py  (pymol-v1.8.6.0.tar.bz2):make_simple.py  (pymol-v2.1.0.tar.bz2)
from __future__ import print_function
import string import string
import os import os
import sys import sys
# ChemPy Simple Forcefield (CSFF) Generator Script # ChemPy Simple Forcefield (CSFF) Generator Script
# #
# A simplified force field based on Amber Parm99 # A simplified force field based on Amber Parm99
# =================================================== # ===================================================
# This force field is designed to be used to answer # This force field is designed to be used to answer
# general questions about shape and size of small # general questions about shape and size of small
skipping to change at line 58 skipping to change at line 60
# skip # skip
l = f.readline() l = f.readline()
# read names & molecular weights # read names & molecular weights
self.type = [] self.type = []
self.mw = {} self.mw = {}
while 1: while 1:
l = string.strip(f.readline()) l = string.strip(f.readline())
if not len(l): break if not len(l): break
a2 = string.strip(l[0:2]) a2 = string.strip(l[0:2])
self.type.append(a2) self.type.append(a2)
if not self.mw.has_key(a2): if a2 not in self.mw:
self.mw[a2] = [] self.mw[a2] = []
self.mw[a2].append([l[3:]]) self.mw[a2].append([l[3:]])
# skip 1 # skip 1
l = f.readline() l = f.readline()
# read bonds # read bonds
self.bond = {} self.bond = {}
while 1: while 1:
l = string.strip(f.readline()) l = string.strip(f.readline())
if not len(l): break if not len(l): break
a5 = l[0:5] a5 = l[0:5]
if a5[0:2]>a5[3:5]: if a5[0:2]>a5[3:5]:
a5 = a5[3:5]+'-'+a5[0:2] a5 = a5[3:5]+'-'+a5[0:2]
if not self.bond.has_key(a5): if a5 not in self.bond:
self.bond[a5] = [] self.bond[a5] = []
self.bond[a5].append([l[5:]]) self.bond[a5].append([l[5:]])
# read angles # read angles
self.angle = {} self.angle = {}
while 1: while 1:
l = string.strip(f.readline()) l = string.strip(f.readline())
if not len(l): break if not len(l): break
a5 = l[0:8] a5 = l[0:8]
if a5[0:2]>a5[6:8]: if a5[0:2]>a5[6:8]:
a5 = a5[6:8]+'-'+a5[3:5]+'-'+a5[0:2] a5 = a5[6:8]+'-'+a5[3:5]+'-'+a5[0:2]
if not self.angle.has_key(a5): if a5 not in self.angle:
self.angle[a5] = [] self.angle[a5] = []
self.angle[a5].append([l[8:]]) self.angle[a5].append([l[8:]])
# read torsion # read torsion
self.torsion = {} self.torsion = {}
while 1: while 1:
l = string.strip(f.readline()) l = string.strip(f.readline())
if not len(l): break if not len(l): break
a5 = l[0:11] a5 = l[0:11]
if not self.torsion.has_key(a5): if a5 not in self.torsion:
self.torsion[a5] = [] self.torsion[a5] = []
self.torsion[a5].append([l[11:]]) self.torsion[a5].append([l[11:]])
# read impropers # read impropers
self.improper = {} self.improper = {}
while 1: while 1:
l = string.strip(f.readline()) l = string.strip(f.readline())
if not len(l): break if not len(l): break
a5 = l[0:11] a5 = l[0:11]
if not self.improper.has_key(a5): if a5 not in self.improper:
self.improper[a5] = [] self.improper[a5] = []
self.improper[a5].append([l[11:]]) self.improper[a5].append([l[11:]])
# skip # skip
while 1: while 1:
l = string.strip(f.readline()) l = string.strip(f.readline())
if not len(l): break if not len(l): break
# read vdw equivalents # read vdw equivalents
self.vdw_eq = {} self.vdw_eq = {}
while 1: while 1:
l = string.strip(f.readline()) l = string.strip(f.readline())
skipping to change at line 165 skipping to change at line 167
"tmp3.dat > tmp4.dat") "tmp3.dat > tmp4.dat")
os.system("sed 's/SO/T4/g;s/SX/TA/g;s/SH/T2/g;s/-S /-T2/g;s/S -/T2-/g;' "+ os.system("sed 's/SO/T4/g;s/SX/TA/g;s/SH/T2/g;s/-S /-T2/g;s/S -/T2-/g;' "+
"tmp4.dat > tmp5.dat") "tmp4.dat > tmp5.dat")
os.system("sed 's/-F /-R1/g;s/F -/R1-/g;s/-I /-R4/g;s/I -/R4-/g;"+ os.system("sed 's/-F /-R1/g;s/F -/R1-/g;s/-I /-R4/g;s/I -/R4-/g;"+
"s/Cl/R2/g;s/Br/R3/g;' tmp5.dat > tmp6.dat") "s/Cl/R2/g;s/Br/R3/g;' tmp5.dat > tmp6.dat")
tmp = BlankObject() tmp = BlankObject()
print "CSFF: Chemical Python Simplified Force Field by Warren L. DeLano" print("CSFF: Chemical Python Simplified Force Field by Warren L. DeLano")
load(tmp,'tmp6.dat') load(tmp,'tmp6.dat')
kees = tmp.mw.keys() kees = list(tmp.mw.keys())
kees.sort() kees.sort()
for a in kees: for a in kees:
c = '' c = ''
lst = '' lst = ''
for b in tmp.mw[a]: for b in tmp.mw[a]:
if lst!=b[0][0:8]: if lst!=b[0][0:8]:
print "%s%-2s %s" %(c,a,b[0]) print("%s%-2s %s" %(c,a,b[0]))
c = ' ' c = ' '
lst = b[0][0:8] lst = b[0][0:8]
l = [ l = [
'QA 16.00 0.434 delocalized, cationic oxygen', 'QA 16.00 0.434 delocalized, cationic oxygen',
'T1 32.06 2.900 Thiocarbonyl', 'T1 32.06 2.900 Thiocarbonyl',
] ]
for a in l: for a in l:
print a print(a)
print print()
print "A J1 J2 J3 J4 JN Q1 Q2 QN" print("A J1 J2 J3 J4 JN Q1 Q2 QN")
kees = tmp.bond.keys() kees = list(tmp.bond.keys())
kees.sort() kees.sort()
for a in kees: for a in kees:
if len(tmp.bond[a])==1: if len(tmp.bond[a])==1:
print "%-1s%s" %(a,tmp.bond[a][0][0]) print("%-1s%s" %(a,tmp.bond[a][0][0]))
else: else:
f1 = 0.0 f1 = 0.0
f2 = 0.0 f2 = 0.0
c = 0 c = 0
for b in tmp.bond[a]: for b in tmp.bond[a]:
f1 = f1 + float(b[0][0:9]) f1 = f1 + float(b[0][0:9])
f2 = f2 + float(b[0][9:18]) f2 = f2 + float(b[0][9:18])
c = c + 1 c = c + 1
f1 = f1 / c f1 = f1 / c
f2 = f2 / c f2 = f2 / c
print "%-1s%7.1f%9.3f combination of %d"%(a,f1,f2,c) print("%-1s%7.1f%9.3f combination of %d"%(a,f1,f2,c))
# missing bond terms # missing bond terms
l = [ l = [
'A -QN 434.0 1.010 INCORRECT HYDROGEN', 'A -QN 434.0 1.010 INCORRECT HYDROGEN',
'A -JN 434.0 1.010 INCORRECT HYDROGEN', 'A -JN 434.0 1.010 INCORRECT HYDROGEN',
'A -JA 434.0 1.010 WLD from A -J3', 'A -JA 434.0 1.010 WLD from A -J3',
'D2-DJ 428.0 1.425 WLD from CA-D2', 'D2-DJ 428.0 1.425 WLD from CA-D2',
'D2-D3 450.0 1.331 WLD gross estimate', 'D2-D3 450.0 1.331 WLD gross estimate',
'D2-Q2 480.0 1.240 WLD from D3-Q2', 'D2-Q2 480.0 1.240 WLD from D3-Q2',
skipping to change at line 287 skipping to change at line 289
'Q2-Q2 453.7 1.370 WLD gross estimate', 'Q2-Q2 453.7 1.370 WLD gross estimate',
'Q2-T4 525.0 1.500 WLD gross estimate', 'Q2-T4 525.0 1.500 WLD gross estimate',
'TA-TA 166.0 2.038 WLD from T2-T2', 'TA-TA 166.0 2.038 WLD from T2-T2',
'TA-T4 166.0 2.038 WLD from T2-T2', 'TA-T4 166.0 2.038 WLD from T2-T2',
'T2-T4 166.0 2.038 WLD from T2-T2', 'T2-T4 166.0 2.038 WLD from T2-T2',
] ]
for a in l: for a in l:
if tmp.bond.has_key(a[0:5]): if a[0:5] in tmp.bond:
sys.stderr.write("Duplicate bond: %s\n"%a) sys.stderr.write("Duplicate bond: %s\n"%a)
print a print(a)
print print()
kees = tmp.angle.keys() kees = list(tmp.angle.keys())
kees.sort() kees.sort()
for a in kees: for a in kees:
if len(tmp.angle[a])==1: if len(tmp.angle[a])==1:
print "%-1s%s" %(a,tmp.angle[a][0][0]) print("%-1s%s" %(a,tmp.angle[a][0][0]))
else: else:
f1 = 0.0 f1 = 0.0
f2 = 0.0 f2 = 0.0
c = 0 c = 0
for b in tmp.angle[a]: for b in tmp.angle[a]:
f1 = f1 + float(b[0][0:10]) f1 = f1 + float(b[0][0:10])
f2 = f2 + float(b[0][10:22]) f2 = f2 + float(b[0][10:22])
c = c + 1 c = c + 1
f1 = f1 / c f1 = f1 / c
f2 = f2 / c f2 = f2 / c
print "%-1s%8.1f%12.2f combination of %d"%(a,f1,f2,c) print("%-1s%8.1f%12.2f combination of %d"%(a,f1,f2,c))
# missing angle terms # missing angle terms
l = [ l = [
'A -QN-J3 50.0 109.50 INCORRECT HYDROGEN', 'A -QN-J3 50.0 109.50 INCORRECT HYDROGEN',
'A -JN-J3 50.0 109.50 INCORRECT HYDROGEN', 'A -JN-J3 50.0 109.50 INCORRECT HYDROGEN',
'A -D3-D2 50.0 119.10 WLD from A -D3-J3', 'A -D3-D2 50.0 119.10 WLD from A -D3-J3',
'A -D3-J1 50.0 119.10 WLD from A -D3-J3', 'A -D3-J1 50.0 119.10 WLD from A -D3-J3',
'A -D3-JA 50.0 119.10 WLD from A -D3-J3', 'A -D3-JA 50.0 119.10 WLD from A -D3-J3',
'A -D3-R1 50.0 119.10 WLD from A -D3-J3', 'A -D3-R1 50.0 119.10 WLD from A -D3-J3',
'A -D3-R2 50.0 119.10 WLD from A -D3-J3', 'A -D3-R2 50.0 119.10 WLD from A -D3-J3',
'A -D3-R3 50.0 119.10 WLD from A -D3-J3', 'A -D3-R3 50.0 119.10 WLD from A -D3-J3',
skipping to change at line 979 skipping to change at line 981
'TA-D3-TA 70.0 118.00 WLD gross estimate', 'TA-D3-TA 70.0 118.00 WLD gross estimate',
'TA-DA-TA 70.0 120.00 WLD from DA-DA-TA', 'TA-DA-TA 70.0 120.00 WLD from DA-DA-TA',
'TA-D4-TA 70.0 109.00 WLD gross estimate', 'TA-D4-TA 70.0 109.00 WLD gross estimate',
'TA-DJ-TA 70.0 120.00 WLD from DA-DA-TA', 'TA-DJ-TA 70.0 120.00 WLD from DA-DA-TA',
] ]
for a in l: for a in l:
if tmp.angle.has_key(a[0:8]): if a[0:8] in tmp.angle:
sys.stderr.write("Duplicate angle: %s\n"%a) sys.stderr.write("Duplicate angle: %s\n"%a)
print a print(a)
print print()
# missing generalized torsions (divisors/forces need to be checked...) # missing generalized torsions (divisors/forces need to be checked...)
l = [ l = [
'X -D2-DJ-X 2 0.00 0.0 2. WLD null', 'X -D2-DJ-X 2 0.00 0.0 2. WLD null',
'X -D2-D3-X 2 0.00 0.0 2. WLD null', 'X -D2-D3-X 2 0.00 0.0 2. WLD null',
'X -D2-J3-X 2 0.00 0.0 2. WLD null', 'X -D2-J3-X 2 0.00 0.0 2. WLD null',
'X -D2-JA-X 2 0.00 0.0 2. WLD null', 'X -D2-JA-X 2 0.00 0.0 2. WLD null',
'X -D2-T2-X 2 0.00 0.0 2. WLD null', 'X -D2-T2-X 2 0.00 0.0 2. WLD null',
'X -D2-Q2-X 2 0.00 0.0 2. WLD null', 'X -D2-Q2-X 2 0.00 0.0 2. WLD null',
'X -D3-JA-X 4 8.70 180.0 2. WLD from X -DJ-D3-X ', 'X -D3-JA-X 4 8.70 180.0 2. WLD from X -DJ-D3-X ',
'X -D3-J1-X 1 0.0 0.0 2. WLD null', 'X -D3-J1-X 1 0.0 0.0 2. WLD null',
skipping to change at line 1033 skipping to change at line 1035
'X -Q2-T4-X 4 2.40 0.0 3. WLD from X -J4-T4-X ', 'X -Q2-T4-X 4 2.40 0.0 3. WLD from X -J4-T4-X ',
'X -Q2-Q2-X 9 1.40 0.0 3. WLD from X -D4-D4-X ', 'X -Q2-Q2-X 9 1.40 0.0 3. WLD from X -D4-D4-X ',
'X -T2-T2-X 1 3.50 0.0 -2. WLD from D4-T2-T2-D 4', 'X -T2-T2-X 1 3.50 0.0 -2. WLD from D4-T2-T2-D 4',
'X -T2-T2-X 1 0.60 0.0 3. WLD from D4-T2-T2-D 4', 'X -T2-T2-X 1 0.60 0.0 3. WLD from D4-T2-T2-D 4',
'X -T2-T4-X 1 0.0 0.0 2. WLD null', 'X -T2-T4-X 1 0.0 0.0 2. WLD null',
'X -TA-TA-X 1 0.0 0.0 2. WLD null', 'X -TA-TA-X 1 0.0 0.0 2. WLD null',
'X -TA-T4-X 1 0.0 0.0 2. WLD null', 'X -TA-T4-X 1 0.0 0.0 2. WLD null',
] ]
for a in l: for a in l:
if tmp.torsion.has_key(a[0:11]): if a[0:11] in tmp.torsion:
sys.stderr.write("Duplicate torsion: %s\n"%a) sys.stderr.write("Duplicate torsion: %s\n"%a)
print a print(a)
kees = tmp.torsion.keys() kees = list(tmp.torsion.keys())
kees.sort() kees.sort()
kees.reverse() kees.reverse()
for a in kees: for a in kees:
if len(tmp.torsion[a])==1: if len(tmp.torsion[a])==1:
print "%-1s%s" %(a,tmp.torsion[a][0][0]) print("%-1s%s" %(a,tmp.torsion[a][0][0]))
else: else:
b = tmp.torsion[a][0] b = tmp.torsion[a][0]
f1 = float(b[0][0:6]) f1 = float(b[0][0:6])
f2 = float(b[0][6:14]) f2 = float(b[0][6:14])
f3 = float(b[0][14:27]) f3 = float(b[0][14:27])
f4 = float(b[0][27:42]) f4 = float(b[0][27:42])
c = 1 c = 1
flag = 0 flag = 0
for b in tmp.torsion[a][1:]: for b in tmp.torsion[a][1:]:
if ((f1 != float(b[0][0:6])) or if ((f1 != float(b[0][0:6])) or
(f3 != float(b[0][14:27])) or (f3 != float(b[0][14:27])) or
(f4 != float(b[0][27:42]))): (f4 != float(b[0][27:42]))):
flag=1 flag=1
break break
f2 = f2 + float(b[0][6:14]) f2 = f2 + float(b[0][6:14])
c = c + 1 c = c + 1
if not flag: if not flag:
f2 = f2 / c f2 = f2 / c
print "%-1s%4d%8.2f%13.1f%14d. combination of %d"%(a,f1,f2,f3,f 4,c) print("%-1s%4d%8.2f%13.1f%14d. combination of %d"%(a,f1,f2,f3,f 4,c))
else: else:
flag = 0 flag = 0
ck = {} ck = {}
for b in tmp.torsion[a]: for b in tmp.torsion[a]:
f4 = float(b[0][27:42]) f4 = float(b[0][27:42])
if ck.has_key(f4): if f4 in ck:
flag=1 flag=1
break break
ck[f4] = 1 ck[f4] = 1
if not flag: if not flag:
for b in tmp.torsion[a]: for b in tmp.torsion[a]:
print "%-1s%s" %(a,b[0]) print("%-1s%s" %(a,b[0]))
else: # known special cases else: # known special cases
if a == 'X -D4-J4-X ': if a == 'X -D4-J4-X ':
print "%-1s%s" %(a,tmp.torsion[a][1][0]) print("%-1s%s" %(a,tmp.torsion[a][1][0]))
elif a == 'X -D4-J3-X ': elif a == 'X -D4-J3-X ':
print "%-1s%s" %(a,tmp.torsion[a][1][0]) print("%-1s%s" %(a,tmp.torsion[a][1][0]))
elif a == 'Q2-D4-D4-Q2': elif a == 'Q2-D4-D4-Q2':
print "%-1s%s" %(a,tmp.torsion[a][1][0]) print("%-1s%s" %(a,tmp.torsion[a][1][0]))
print "%-1s%s" %(a,tmp.torsion[a][2][0]) print("%-1s%s" %(a,tmp.torsion[a][2][0]))
elif a == 'A -D4-DJ-Q1': elif a == 'A -D4-DJ-Q1':
print "%-1s%s" %(a,tmp.torsion[a][1][0]) print("%-1s%s" %(a,tmp.torsion[a][1][0]))
print "%-1s%s" %(a,tmp.torsion[a][2][0]) print("%-1s%s" %(a,tmp.torsion[a][2][0]))
else: else:
for b in tmp.torsion[a]: for b in tmp.torsion[a]:
print " %-1s%s" %(a,b[0]) print(" %-1s%s" %(a,b[0]))
# missing specific torsions # missing specific torsions
l = [ l = [
'A -T2-T2-D4 1 3.50 0.0 -2. WLD from D4-T2-T2-D 4', 'A -T2-T2-D4 1 3.50 0.0 -2. WLD from D4-T2-T2-D 4',
'A -T2-T2-D4 1 0.60 0.0 3. WLD from D4-T2-T2-D 4', 'A -T2-T2-D4 1 0.60 0.0 3. WLD from D4-T2-T2-D 4',
] ]
for a in l: for a in l:
if tmp.torsion.has_key(a[0:11]): if a[0:11] in tmp.torsion:
sys.stderr.write("Duplicate torsion: %s\n"%a) sys.stderr.write("Duplicate torsion: %s\n"%a)
print a print(a)
print print()
# missing general impropers # missing general impropers
l = [ l = [
'X -X -DJ-JA 10.5 180. 2. WLD from X -X -DJ-Q 1', 'X -X -DJ-JA 10.5 180. 2. WLD from X -X -DJ-Q 1',
'X -X -DJ-QN 10.5 180. 2. WLD from X -X -DJ-Q 1', 'X -X -DJ-QN 10.5 180. 2. WLD from X -X -DJ-Q 1',
] ]
for a in l: for a in l:
if tmp.improper.has_key(a[0:11]): if a[0:11] in tmp.improper:
sys.stderr.write("Duplicate improper: %s\n"%a) sys.stderr.write("Duplicate improper: %s\n"%a)
print a print(a)
print print()
kees = tmp.improper.keys() kees = list(tmp.improper.keys())
kees.sort() kees.sort()
kees.reverse() kees.reverse()
for a in kees: # no major redundancy, just print the first record for a in kees: # no major redundancy, just print the first record
print "%-1s%s" %(a,tmp.improper[a][0][0]) print("%-1s%s" %(a,tmp.improper[a][0][0]))
print ''' print('''
A Q2 0000. 0000. 4. flag for fast water A Q2 0000. 0000. 4. flag for fast water
J1 J1 J2 J3 J4 J1 J1 J2 J3 J4
D2 D2 D3 D4 D2 D2 D3 D4
MOD4 RE MOD4 RE
A 1.3870 0.0157 A Venstra et al JCC,8,(1992),963 A 1.3870 0.0157 A Venstra et al JCC,8,(1992),963
QN 1.6612 0.2100 O OPLS QN 1.6612 0.2100 O OPLS
QA 1.6612 0.2100 O OPLS QA 1.6612 0.2100 O OPLS
Q2 1.6612 0.2100 O OPLS Q2 1.6612 0.2100 O OPLS
skipping to change at line 1182 skipping to change at line 1184
# oxygen # oxygen
TINKER QA 8 3 TINKER QA 8 3
TINKER Q2 8 2 TINKER Q2 8 2
TINKER Q1 8 1 TINKER Q1 8 1
TINKER QN 8 1 TINKER QN 8 1
# sulfer # sulfer
TINKER T4 16 4 TINKER T4 16 4
TINKER TA 16 2 TINKER TA 16 2
TINKER T2 16 2 TINKER T2 16 2
TINKER T1 16 1 TINKER T1 16 1
''' ''')
os.unlink('tmp1.dat') os.unlink('tmp1.dat')
os.unlink('tmp2.dat') os.unlink('tmp2.dat')
os.unlink('tmp3.dat') os.unlink('tmp3.dat')
os.unlink('tmp4.dat') os.unlink('tmp4.dat')
os.unlink('tmp5.dat') os.unlink('tmp5.dat')
os.unlink('tmp6.dat') os.unlink('tmp6.dat')
 End of changes. 37 change blocks. 
47 lines changed or deleted 49 lines changed or added
To the Python Programs section of the PyMOL source changes report or the top of this page
Mainly generated by pkgdiff using rfcdiff
Home  |  About  |  Features  |  All  |  Newest  |  Dox  |  Diffs  |  RSS Feeds  |  Screenshots  |  Comments  |  Imprint  |  Privacy  |  HTTP(S)