def main(mmpInputFile, xyzInputFile=None, outf=None,
referenceInputFile=None, generateFlag=False):
bondLengthTerms = { }
bondAngleTerms = { }
def addBondLength(atm1, atm2):
assert atm1 != atm2
if atm2 < atm1:
atm1, atm2 = atm2, atm1
if bondLengthTerms.has_key(atm1):
if atm2 not in bondLengthTerms[atm1]:
bondLengthTerms[atm1].append(atm2)
else:
bondLengthTerms[atm1] = [ atm2 ]
def getBonds(atm1):
lst = [ ]
if bondLengthTerms.has_key(atm1):
for x in bondLengthTerms[atm1]:
lst.append(x)
for key in bondLengthTerms.keys():
if atm1 in bondLengthTerms[key]:
if key not in lst:
lst.append(key)
lst.sort()
return lst
def addBondAngle(atm1, atm2, atm3):
if atm3 < atm1:
atm1, atm3 = atm3, atm1
value = (atm2, atm3)
if bondAngleTerms.has_key(atm1):
if value not in bondAngleTerms[atm1]:
bondAngleTerms[atm1].append(value)
else:
bondAngleTerms[atm1] = [ value ]
if outf != None:
ss, sys.stdout = sys.stdout, outf
mmp = MmpFile()
mmp.read(mmpInputFile)
xyz = XyzFile()
if xyzInputFile != None:
xyz.read(xyzInputFile)
else:
# copy xyz file from mmp file
import Atom
for i in range(len(mmp)):
ma = mmp.atoms[i]
element = Atom._PeriodicTable[ma.elem]
x, y, z = ma.x, ma.y, ma.z
a = Atom.Atom()
a.fromXyz(element, x, y, z)
xyz.atoms.append(a)
assert len(xyz) != 0
assert len(xyz) == len(mmp)
# store all the bonds in bondLengthTerms
for i in range(len(mmp)):
a = mmp.atoms[i]
for b in a.bonds:
addBondLength(i, b - 1)
# generate angles from chains of two bonds
for first in range(len(mmp)):
for second in getBonds(first):
for third in getBonds(second):
if first != third:
addBondAngle(first, second, third)
lengthList = [ ]
for first in bondLengthTerms.keys():
for second in bondLengthTerms[first]:
lengthList.append((first, second,
measureLength(xyz, first, second)))
angleList = [ ]
for first in bondAngleTerms.keys():
for second, third in bondAngleTerms[first]:
angleList.append((first, second, third,
measureAngle(xyz, first, second, third)))
if generateFlag:
for a1, a2, L in lengthList:
print "LENGTH", a1, a2, L
for a1, a2, a3, A in angleList:
print "ANGLE", a1, a2, a3, A
if referenceInputFile != None:
badness = False
# read in LENGTH lines, compare them to this guy
inf = open(referenceInputFile)
lp = ap = 0
for line in inf.readlines():
if line.startswith("LENGTH "):
fields = line[7:].split()
a1, a2, L = (string.atoi(fields[0]),
string.atoi(fields[1]),
string.atof(fields[2]))
a11, a22, LL = lengthList[lp]
lp += 1
if a1 != a11 or a2 != a22:
print ("Wrong length term (%d, %d), should be (%d, %d)"
% (a11, a22, a1, a2))
badness = True
break
if abs(L - LL) > LENGTH_TOLERANCE:
print ("Wrong bond length at (%d, %d), it's %f, should be %f"
% (a1, a2, LL, L))
badness = True
break
elif line.startswith("ANGLE "):
fields = line[6:].split()
a1, a2, a3, A = (string.atoi(fields[0]),
string.atoi(fields[1]),
string.atoi(fields[2]),
string.atof(fields[3]))
a11, a22, a33, AA = angleList[ap]
ap += 1
if a1 != a11 or a2 != a22 or a3 != a33:
print ("Wrong angle term (%d, %d, %d), should be (%d, %d, %d)"
% (a11, a22, a33, a1, a2, a3))
badness = True
break
if abs(L - LL) > ANGLE_TOLERANCE:
print ("Wrong bond angle at (%d, %d, %d), it's %f, should be %f"
% (a1, a2, a3, AA, A))
badness = True
break
else:
print "Unknown line in reference file:", line
badness = True
break
if not badness:
print "OK"
if outf != None:
outf.close()
sys.stdout = ss
$Id$
"""
__author__ = "Will"
import sys
from MmpFile import MmpFile
from XyzFile import XyzFile
import Atom
try:
mmpInputFile = sys.argv[1]
xyz = XyzFile()
mmp = MmpFile()
mmp.read(mmpInputFile)
for i in range(len(mmp)):
ma = mmp.atoms[i]
element = Atom._PeriodicTable[ma.elem]
x, y, z = ma.x, ma.y, ma.z
a = Atom.Atom()
a.fromXyz(element, x, y, z)
xyz.atoms.append(a)
xyz.write(mmpInputFile)
except Exception, e:
if e:
sys.stderr.write(sys.argv[0] + ": " + e.args[0] + "\n")
$Id: xyzmerge.py 8124 2005-11-21 16:43:17Z wware $
"""
__author__ = "Will"
import sys
from MmpFile import MmpFile
from XyzFile import XyzFile
try:
mmpInputFile = sys.argv[1]
xyzInputFile = sys.argv[2]
xyz = XyzFile()
xyz.read(xyzInputFile)
mmp = MmpFile()
mmp.read(mmpInputFile)
assert len(xyz) != 0
assert len(xyz) == len(mmp)
for i in range(len(xyz)):
xa = xyz.atoms[i]
ma = mmp.atoms[i]
assert xa.elem == ma.elem
ma.x, ma.y, ma.z = xa.x, xa.y, xa.z
mmp.write()
except Exception, e:
if e:
$Id$
"""
__author__ = "Will"
import sys
from MmpFile import MmpFile
from XyzFile import XyzFile
try:
mmpInputFile = sys.argv[1]
xyzInputFile = sys.argv[2]
xyz = XyzFile()
xyz.read(xyzInputFile)
mmp = MmpFile()
mmp.read(mmpInputFile)
assert len(xyz) != 0
assert len(xyz) == len(mmp)
for i in range(len(xyz)):
xa = xyz.atoms[i]
ma = mmp.atoms[i]
assert xa.elem == ma.elem
ma.x, ma.y, ma.z = xa.x, xa.y, xa.z
mmp.write()
except Exception, e:
if e:
