def __exit__(self, exc_type, exc_value, traceback):
relaxed_name = "relaxed"
relaxed_molecule = molecules.Molecule(relaxed_name, self.relaxed_file,
self.experiment)
relaxed_molecule.assemble_from_CHARMM(self.chain_ids,
self.output_molecule_files,
self.resnums)
CharmmProc.__exit__(self, exc_type, exc_value, traceback)
def main():
in_file = gaussian.GaussianCom(IN_GAUCOM)
system = molecules.Molecule('system',in_file.atoms_list)
charge = system.get_charge()
charge_line = '{0} 1 {0} 1 {0} 1\n'.format(int(charge))
in_file.multiplicity_line = charge_line
route_section = """%nproc=8
%mem=1gb
# oniom(b3lyp/6-31g(d):amber=softonly)=embed geom(notest,connectivity)\n"""
in_file.route_section = route_section
for no, atom in enumerate(in_file.atoms_list):
if atom.resinfo.resname != 'WAT':
in_file.atoms_list[no].oniom.layer = 'H'
in_file.redo_connectivity_list()
in_file.write_to_file(OUT_GAUCOM)
def load_molecules(self):
""" Create text to load Molecules in a CHARMM script. """
# Merge all of the molecules.
merged_structure = molecules.merge(self.molecules)
# Save the merged structure in charmm_format_file.
charmm_format_name = "charmm_format"
handle, charmm_format_file = tempfile.mkstemp(suffix=".pdb",
dir=self.directory)
merged_molecule = molecules.Molecule(charmm_format_name,
charmm_format_file,
self.experiment)
# CHARMM needs all of the molecules to be in separate PDB files, so disassemble the merged molecule into separate files.
chains, files = merged_molecule.disassemble_for_CHARMM(
structure=merged_structure, directory=self.directory)
# Remove the file of the merged structure, which is no longer needed.
try:
os.remove(charmm_format_file)
except OSError:
pass
# Write the part of the script that loads the chains.
self.chain_ids = list()
for chain, _file in zip(chains, files):
_id = chain.get_id()
self.chain_ids.append(_id)
segment = make_segment_name(_id)
base_name = os.path.basename(_file)
self.lines.extend([
"! Load Chain {}".format(_id),
"open read unit 10 form name {}".format(base_name),
"read sequ pdb offi unit 10", "close unit 10",
"gene {} setup".format(segment),
"open read unit 10 form name {}".format(base_name),
"read coor pdb unit 10", "close unit 10"
])
# Add any missing atoms to the chain.
self.lines.extend(ic_fill())
def iteration(stdgeom, currentfile, opt, loopid, convthreshold):
os.system('cp ' + currentfile.comname + ' MM0.com')
with open('MM0.com', 'r') as f:
dihds = ''
for line in f:
if line.find('AmbTrs') >= 0:
dihds += line
while True:
currentfile = rxccfile.File('MM' + str(loopid))
if opt == 'opt':
os.system('sed -i "s/#p opt=(nomicro,cartesian) /#p /g" ' +
currentfile.comname)
os.system('sed -i "s/#p/#p opt=(nomicro,cartesian)/g" ' +
currentfile.comname)
os.system('sed -i "/freq/d" ' + currentfile.comname)
os.system('sed -i "/chk/d" ' + currentfile.comname)
elif opt == 'calcall':
os.system(
'sed -i "s/#p opt=(nomicro,cartesian,tight,calcall) /#p /g" '
+ currentfile.comname)
os.system(
'sed -i "s/#p opt=(nomicro,cartesian,tight,calcall) /#p /g" '
+ currentfile.comname)
os.system(
'sed -i "s/#p/#p opt=(nomicro,cartesian,tight,calcall)/g" '
+ currentfile.comname)
os.system('sed -i "/freq/d" ' + currentfile.comname)
os.system('sed -i "/chk/d" ' + currentfile.comname)
# if loopid>1000:
# raise StopIteration
currentfile.com.read()
try:
currentfile.com.rung09()
currentfile.com.isover()
currentfile.runformchk()
ifstop = True
os.system('rm ' + currentfile.chkname + ' ' +
currentfile.logname)
except:
logging.error("Calculation failed, try again.")
try:
currentfile.com.rung09()
currentfile.com.isover()
currentfile.runformchk()
ifstop = True
os.system('rm ' + currentfile.chkname + ' ' +
currentfile.logname)
except:
logging.critical('Calculation still failed, continue...')
currentfile.runformchk()
os.system('rm ' + currentfile.chkname + ' ' +
currentfile.logname)
ifstop = False
# logging.info('minimum max2 is chosen from loop'+str(minmax2loop))
# os.system('cp MM'+str(minmax2loop)+'.com ../'+mmresult[0:3]+'amd'+mmresult[3:]+'.com')
# os.system('sed -i "s/#p opt=(verytight,z-matrix,calcall)/#p /g" ../*.com')
# os.system('sed -i "/chk/d" ../*.com')
# return
currentfile.fchk.read()
currentgeom = rxmol.Molecule('currentgeom')
currentgeom.readfromxyz(io.StringIO(currentfile.fchk.xyz))
currentgeom.readchargefromlist(currentfile.com.atomchargelist)
currentgeom.readtypefromlist(currentfile.com.atomtypelist)
currentgeom.readconnectivity(currentfile.com.connectivity)
for angle in currentgeom.anglelist.values():
for anglefunc in currentfile.com.nozomuanglefunc:
if matchangle(angle, anglefunc):
angle.nozomufunc = anglefunc
for bond in currentgeom.bondlist.values():
for bondfunc in currentfile.com.nozomubondfunc:
if matchbond(bond, bondfunc):
bond.nozomufunc = bondfunc
# reassign current eqvalue
for nozomufunc in currentfile.com.nozomuanglefunc:
eq = 0
i = 0
for angle in currentgeom.anglelist.values():
if angle.nozomufunc == nozomufunc:
eq += angle.anglevalue
i += 1
nozomufunc.eqvalue = eq / i
for nozomufunc in currentfile.com.nozomubondfunc:
eq = 0
i = 0
for bond in currentgeom.bondlist.values():
if bond.nozomufunc == nozomufunc:
eq += bond.length
i += 1
nozomufunc.eqvalue = eq / i
currentL = []
currentL.extend(currentfile.com.nozomuanglefunc)
currentL.extend(currentfile.com.nozomubondfunc)
for item1 in currentL:
for item2 in currentL:
if item1.value == item2.value and item1.repr != item2.repr:
item1.eqvalue = (item1.eqvalue + item2.eqvalue) / 2
item2.eqvalue = item1.eqvalue
logging.debug('Averaged old eqvalue ' + item1.repr +
' and ' + item2.repr + ' ' +
str(item2.eqvalue))
delta1 = [
x.eqvalue - y.eqvalue for x, y in zip(stdL, currentL)
if x.type == 'bond'
]
delta2 = [
x.eqvalue - y.eqvalue for x, y in zip(stdL, currentL)
if x.type == 'angle'
]
max1 = sorted(delta1, key=abs, reverse=True)[0]
max2 = sorted(delta2, key=abs, reverse=True)[0]
try:
if abs(max2) < abs(minmax2):
minmax2 = abs(max2)
minmax2loop = loopid
except:
minmax2 = abs(max2)
minmax2loop = loopid
if loopid - minmax2loop > convthreshold:
logging.info(
'Stopped for convergence: max Delta2 do not decrease in ' +
str(convthreshold) + ' cycles')
if opt == 'calcall':
logging.info('minimum max2 is chosen from loop' +
str(minmax2loop))
os.system('cp MM' + str(minmax2loop) + '.com ../katachi_' +
mmresult + '.com')
os.system(
'sed -i "s/#p opt=(nomicro,cartesian,tight,calcall)/#p freq/g" ../*.com'
)
os.system('sed -i "/chk/d" ../*.com')
return loopid
else:
opt = 'calcall'
minmax2 = 100
minmax2loop = loopid
logging.info('------------------------------')
logging.info('Loop ' + str(loopid) + ' keyword ' + opt +
': max bond delta: ' + str(max1) +
' max angle delta: ' + str(max2))
logging.info('MinMax2 is ' + str(minmax2) + ' at loop ' +
str(minmax2loop))
logging.info('------------------------------')
if abs(max1) < 0.0001 and abs(max2) < 0.01:
if opt == 'opt':
opt = 'calcall'
logging.info('-------------------------------------------')
logging.info('opt converged at ' + str(max1) + ' ' +
str(max2) + ' ' + str(loopid))
logging.info('-------------------------------------------')
minmax2 = 100
minmax2loop = loopid + 1
elif opt == 'calcall':
logging.info('-------------------------------------------')
logging.info('calcall converged at ' + str(max1) + ' ' +
str(max2) + ' ' + str(loopid))
logging.info('-------------------------------------------')
os.system('cp ' + currentfile.comname + ' ../katachi_' +
mmresult + '.com')
os.system(
'sed -i "s/#p opt=(nomicro,cartesian,tight,calcall)/#p freq/g" ../*.com'
)
os.system('sed -i "/chk/d" ../*.com')
if ifstop:
return loopid
delta = [x.eqvalue - y.eqvalue for x, y in zip(stdL, currentL)]
try:
type(last)
except UnboundLocalError:
if loopid != 0:
lastfile = rxccfile.File('MM' + str(loopid - 1))
lastfile.com.read()
lastL = []
lastL.extend(lastfile.com.nozomuanglefunc)
lastL.extend(lastfile.com.nozomubondfunc)
last = lastL
else:
last = copy.deepcopy(stdL)
for now, std, former, delt in zip(currentL, stdL, last, delta):
if former.eqvalue + delt > 0 and former.eqvalue + delt < 180:
now.eqvalue = former.eqvalue + delt
if now.type == 'bond' and abs(delt) > 0.0001:
logging.warning(now.repr + ' ' + str(delt))
if now.type == 'angle' and abs(delt) > 0.01:
logging.warning(now.repr + ' ' + str(delt))
for item1 in currentL:
for item2 in currentL:
if item1.value == item2.value and item1.repr != item2.repr:
item1.eqvalue = (item1.eqvalue + item2.eqvalue) / 2
item2.eqvalue = item1.eqvalue
logging.debug('Averaged new eqvalue ' + item1.repr +
' and ' + item2.repr + ' ' +
str(item2.eqvalue))
last = copy.deepcopy(currentL)
finalxyz = ''
for atom in stdgeom:
finalxyz += atom.atomsym + '-' + atom.atomtype + '-' + '{:<9.6f}'.format(
float(atom.atomcharge)) + ' ' + ' '.join(
["{: .12f}".format(x) for x in atom.coords]) + '\n'
finalhead = currentfile.com.commandline + '\nfinal\n\n' + str(
currentfile.fchk.totalcharge
) + ' ' + str(
currentfile.fchk.multiplicity
) + '\n' + finalxyz + '\n' + currentfile.com.connectivity + '\n'
finaltail = ''
finaltail += dihds
for item in currentfile.com.nozomuanglefunc:
finaltail += 'HrmBnd1 ' + item.repr + ' '
parm = "{: .3f}".format(item.value)
finaltail += ' ' + parm + ' {: .4f}'.format(
item.eqvalue) + '\n'
for item in currentfile.com.nozomubondfunc:
finaltail += 'HrmStr1 ' + item.repr + ' '
parm = "{: .3f}".format(item.value)
finaltail += ' ' + parm + ' {: .5f}'.format(
item.eqvalue) + '\n'
for addfunc in currentfile.com.additionfunc:
finaltail += addfunc.content
for nozovdw in currentfile.com.nozomuvdw:
finaltail += nozovdw.content
finaltail += '\n\n'
loopid += 1
with open('MM' + str(loopid) + '.com', 'w') as f:
f.write(finalhead + finaltail)
del currentgeom
del currentfile