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#!/usr/bin/python
#*******************************************************************************
# *
# Viewmol *
# *
# U F F . P Y *
# *
# Copyright (c) Joerg-R. Hill, October 2003 *
# *
#*******************************************************************************
#
# $Id: uff.py,v 1.1 2003/11/07 13:20:17 jrh Exp $
# $Log: uff.py,v $
# Revision 1.1 2003/11/07 13:20:17 jrh
# Initial revision
#
#
import os
import string
import viewmol
import molecule
import atom
import label
class uff:
def writeFiles(self, dir, mol):
self.writeCoordinateFile(dir, mol)
self.writeTopologyFile(dir, mol)
self.writeControlFile(dir)
def writeCoordinateFile(self, dir, mol):
coordFile=open(dir+"/coord", "w")
coordFile.write("$coord\n")
for i in mol.getAtoms():
coords=i.coordinates()
name=i.getElement().getSymbol()
line="%22.14f%22.14f%22.14f %s\n" % (coords[0]/0.52917706, coords[1]/0.52917706, coords[2]/0.52917706, name)
coordFile.write(line)
coordFile.write("$end\n")
coordFile.close()
def writeTopologyFile(self, dir, mol):
# Build connectivity from bonds
connectivity={}
for i in mol.getBonds():
if not connectivity.has_key(i[0]):
connectivity[i[0]]=[]
connectivity[i[0]].append(i[1])
if not connectivity.has_key(i[1]):
connectivity[i[1]]=[]
connectivity[i[1]].append(i[0])
# Write topology file
topologyFile=open(dir+"/ufftopology", "w")
topologyFile.write("$ufftopology\nnxtnei12\n")
# Only the nxtnei12 data group is necessary, Turbomole's
# UFF module can determine the other ones automatically
for i in connectivity.keys():
self.writeList(topologyFile, i, connectivity[i])
def writeList(self, topologyFile, which, list):
line=" %5d %5d\n" % (which+1, len(list))
topologyFile.write(line)
line=" "
for i in list:
word=" %5d" % (i+1)
line=line + word
line=line + "\n"
topologyFile.write(line)
def writeControlFile(self, dir):
controlFile=open(dir+"/control", "w")
controlFile.write("$title\n")
controlFile.write("Test\n")
controlFile.write("$operating system unix\n")
controlFile.write("$symmetry c1\n")
controlFile.write("$coord file=coord\n")
controlFile.write("$uff\n")
controlFile.write(" 500 1 1 ! maxcycle,modus,nqeq\n")
controlFile.write(" 111111 ! iterm\n")
controlFile.write(" 0.10D-07 0.10D-04 ! econv,gconv\n")
controlFile.write(" 0.00 1.10 ! qtot,dfac\n")
controlFile.write(" 0.10D+03 0.10D-04 0.30 ! epssteep,epssearch,dqmax\n")
controlFile.write(" 25 0.10 0.00 ! mxls,dhls,ahls\n")
controlFile.write(" 1.00 0.00 0.00 ! alpha,beta,gamma\n")
controlFile.write(" F F F ! transform,lnumhess,lmd\n")
controlFile.write("$ufftopology file=ufftopology\n")
controlFile.write("$end\n")
controlFile.close()
def runUFF(self, dir):
size=viewmol.getWindowSize()
energy=label.label()
energy.translate(20, size[1]-20, 0)
energy.text("UFF energy")
for line in os.popen("cd "+dir+"; uff").readlines():
if line[0:10] == "UFF energy":
energy.text(line)
os.remove(dir+"/control")
os.remove(dir+"/ufftopology")
os.remove(dir+"/uffgradient")
os.remove(dir+"/uffgradx")
try:
os.remove(dir+"/uffconverged")
os.remove(dir+"/uffhessian0-0")
except OSError:
viewmol.write("uff did not converge")
energy.delete()
def readResults(self, dir, mol):
coordFile=open(dir+"/coord", "r")
line=coordFile.readline()
for i in mol.getAtoms():
line=coordFile.readline()
if line[0:4] != "$end":
words=string.split(line)
i.coordinates(float(words[0])*0.52917706, float(words[1])*0.52917706, float(words[2])*0.52917706)
coordFile.close()
os.remove(dir+"/coord")
def run(self):
dir="/tmp"
for i in viewmol.getMolecules():
self.writeFiles(dir, i)
self.runUFF(dir)
self.readResults(dir, i)
def register(self, language):
viewmol.registerMenuItem("UFF optimization")
#-------------------------
if __name__ == '__main__':
optimization=uff()
uff.run(optimization)
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