print >> sys.stderr, ' residues in the topology file ' + prmtop
sys.exit()
if not (" %s " % prmtop_residues[resnums[x]-1]) in titrate_residues:
print >> sys.stderr, 'Error: Residue ' + str(resnums[x]) + ' is a ' + prmtop_residues[resnums[x]-1] + \
'. This is not in the list of titratable residues!'
sys.exit()
else:
titrated_residue_nums.append(resnums[x])
# otherwise, add in all matching residues
else:
for x in range(len(prmtop_residues)-1):
if " %s " % prmtop_residues[x] in titrate_residues:
check_data = cpin_data.getData(prmtop_residues[x], igb, has_water)
# make sure we aren't adding termini
if len(check_data[0])-2 == prmtop_object.parm_data['RESIDUE_POINTER'][x+1] - prmtop_object.parm_data['RESIDUE_POINTER'][x]:
titrated_residue_nums.append(x+1)
# Check to make sure that at least one residue is going to be titrated
if len(titrated_residue_nums) == 0:
print >> sys.stderr, 'Error: No titratable residues conform to your criteria!'
sys.exit()
# Now filter out the notresnums
for x in range(len(notresnums)):
for y in range(len(titrated_residue_nums)):
if notresnums[x] == titrated_residue_nums[y]:
def printusage():
""" Prints the usage statement and quits """
print "ChangeState.py <prmtop> <residue> <state> <new_prmtop>"
sys.exit(0)
if len(sys.argv) != 5 or sys.argv[1] in ['--help', '-help', '-h', '--h']:
printusage()
prmtop = amberParm(sys.argv[1])
if not prmtop.valid:
print >> sys.stderr, 'Error: %s is not a valid prmtop!' % sys.argv[1]
printusage()
res = int(sys.argv[2]) - 1
data = getData(prmtop.parm_data['RESIDUE_LABEL'][res], 5)
starting_point = prmtop.parm_data['RESIDUE_POINTER'][res] - 1
state = int(sys.argv[3])
for i in range(2, len(data[state])):
atnum = starting_point + i - 2
print "Changing %-4s from charge %8.4f to %8.4f" % \
( prmtop.parm_data['ATOM_NAME'][atnum], prmtop.parm_data['CHARGE'][atnum],
data[state][i] )
prmtop.parm_data['CHARGE'][atnum] = data[state][i]
prmtop.writeParm(sys.argv[4])
print 'Done!'
def printusage():
""" Prints the usage statement and quits """
print "ChangeState.py <prmtop> <residue> <state> <new_prmtop>"
sys.exit(0)
if len(sys.argv) != 5 or sys.argv[1] in ['--help','-help','-h','--h']:
printusage()
prmtop = amberParm(sys.argv[1])
if not prmtop.valid:
print >> sys.stderr, 'Error: %s is not a valid prmtop!' % sys.argv[1]
printusage()
res = int(sys.argv[2]) - 1
data = getData(prmtop.parm_data['RESIDUE_LABEL'][res],5)
starting_point = prmtop.parm_data['RESIDUE_POINTER'][res] - 1
state = int(sys.argv[3])
for i in range(2,len(data[state])):
atnum = starting_point + i - 2
print "Changing %-4s from charge %8.4f to %8.4f" % \
( prmtop.parm_data['ATOM_NAME'][atnum], prmtop.parm_data['CHARGE'][atnum],
data[state][i] )
prmtop.parm_data['CHARGE'][atnum] = data[state][i]
prmtop.writeParm(sys.argv[4])
print 'Done!'
