from cpin_data import getData
from chemistry.amber.readparm import amberParm
import sys, os
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] )
output = sys.argv[x+1]
elif sys.argv[x] == '-fraction':
fraction = float(sys.argv[x+1])
elif sys.argv[x] == '-y':
x += 1
while x < len(sys.argv) and not sys.argv[x].startswith('-'):
mdcrds.append(sys.argv[x])
x += 1
except IndexError:
print 'Error: Improper command!'
printusage()
except ValueError:
print 'Error: "percent" must be a floating point decimal!'
printusage()
parm = amberParm(prmtop)
if len(mdcrds) == 0: # if no mdcrd supplied, give default
mdcrds.append('mdcrd')
ptraj = utilities.which('cpptraj') # look for ptraj
if ptraj is None:
print 'Error: cpptraj needed for FindSaltbridge.py!'
sys.exit() # quit if not found
if not parm.valid:
printusage()
for x in range(len(mdcrds)): # check for mdcrd existences
if utilities.fileexists(mdcrds[x]) == -1:
printusage()
output = sys.argv[x + 1]
elif sys.argv[x] == '-fraction':
fraction = float(sys.argv[x + 1])
elif sys.argv[x] == '-y':
x += 1
while x < len(sys.argv) and not sys.argv[x].startswith('-'):
mdcrds.append(sys.argv[x])
x += 1
except IndexError:
print 'Error: Improper command!'
printusage()
except ValueError:
print 'Error: "percent" must be a floating point decimal!'
printusage()
parm = amberParm(prmtop)
if len(mdcrds) == 0: # if no mdcrd supplied, give default
mdcrds.append('mdcrd')
ptraj = utilities.which('cpptraj') # look for ptraj
if ptraj is None:
print 'Error: cpptraj needed for FindSaltbridge.py!'
sys.exit() # quit if not found
if not parm.valid:
printusage()
for x in range(len(mdcrds)): # check for mdcrd existences
if utilities.fileexists(mdcrds[x]) == -1:
printusage()
parser.addOption('-debug',
'debug',
help='0: Suppress tracebacks, ' + '1: print tracebacks',
default=0)
opt = parser.Parse()
debug_printlevel = opt.debug
opt.number = int(opt.number)
if not opt.prmtop1 or not opt.prmtop2:
parser.print_help()
# Set up the prmtop objects
print >> sys.stdout, 'Reading topology files'
parm1 = amberParm(opt.prmtop1)
parm2 = amberParm(opt.prmtop2)
print >> sys.stdout, 'Validating topology files'
if not (parm1.valid and parm2.valid):
print >> sys.stderr, 'Error: Problems with input prmtop files!'
parser.print_help()
if parm1.parm_data['RESIDUE_LABEL'] != parm2.parm_data['RESIDUE_LABEL']:
print >> sys.stderr, 'Error: You must have the same number of residues ' + \
' in each prmtop!'
sys.exit(1)
if parm1.parm_data['ATOM_NAME'] != parm2.parm_data['ATOM_NAME']:
print >> sys.stderr, 'Error: Atom sequences must be the same in each prmtop!'
sys.exit(1)
#!/usr/bin/env python
# Find the number of residues in a given prmtop
from sys import stderr, stdout, exit, argv
from chemistry.amber.readparm import amberParm
from os import path
def usage():
print >> stderr, "{0} <prmtop>".format(path.split(argv[0])[1])
exit()
if len(argv) != 2:
usage()
x = amberParm(argv[1])
if x.exists:
print x.ptr(path.split(argv[0])[1].strip('.py'))
else:
print >> stderr, '{0} does not exist!'.format(argv[1])
#!/usr/bin/env python
# Find the number of residues in a given prmtop
from sys import stderr, stdout, exit, argv
from chemistry.amber.readparm import amberParm
from os import path
def usage():
print >> stderr, "{0} <prmtop>".format(path.split(argv[0])[1])
exit()
if len(argv) != 2:
usage()
x = amberParm(argv[1])
if x.exists:
print x.ptr(path.split(argv[0])[1].strip('.py'))
else:
print >> stderr, '{0} does not exist!'.format(argv[1])
# Get arbitrary num of resnames to remove from the list
elif sys.argv[x] == '-states': # states flag
x += 1
while x < len(sys.argv) and not sys.argv[x].startswith("-"):
dataholder = sys.argv[x].split(",")
for y in range(len(dataholder)):
if len(dataholder[y].strip()) != 0:
residue_states.append(dataholder[y].strip())
x += 1
# while loop may have been triggered by a flag; rewind to read flag
x -= 1
except IndexError:
print >> sys.stderr, 'Error: Command line error!'
printusage()
prmtop_object = amberParm(prmtop)
has_water = 'WAT' in prmtop_object.parm_data['RESIDUE_LABEL']
if not prmtop_object.exists:
sys.exit()
if igb == ' ':
if not ignore_warn:
print >> sys.stderr, 'Warning: igb value not specified. igb = 5 used as default. ' + \
'Be sure to use this value for your constant pH simulations!'
igb = '5'
try:
prmtop_residues = prmtop_object.parm_data["RESIDUE_LABEL"]
prmtop_indices = prmtop_object.parm_data['RESIDUE_POINTER']
except KeyError:
'Error: Could not find RESIDUE_LABEL or RESIDUE_POINTER in %s!' % prmtop
""" Changes the protonation state of a given residue in a given prmtop """
from cpin_data import getData
from chemistry.amber.readparm import amberParm
import sys, os
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] )
