class AmberSystem(object):
""" An Amber system with a topology file and input coordinate file """
# ==============================
def __init__(self, prmtop, inpcrd):
# Only load the inpcrd file if it actually exists.
# if os.path.exists(inpcrd): self.prmtop = AmberParm(prmtop, inpcrd)
# else: self.prmtop = AmberParm(prmtop)
self.prmtop = AmberParm(prmtop)
self.inpcrd = inpcrd
# ==============================
def periodic(self):
""" Returns whether or not a topology file is set up for PBC """
# PBCs are indicated by a non-zero IFBOX pointer
return bool(self.prmtop.ptr('ifbox'))
# ==============================
def query_radii(self):
""" Returns the radii set in the topology file """
return self.prmtop.parm_data['RADIUS_SET'][0]
# ==============================
def set_radii(self, igb=0, radius_set='mbondi'):
""" Sets the radius set to a new one using parmed """
# If someone sets an igb, change to the appropriate radius set
if igb:
if igb == 1: radius_set = 'mbondi'
elif igb == 2: radius_set = 'mbondi2'
elif igb == 5: radius_set = 'mbondi2'
elif igb == 7: radius_set = 'bondi'
elif igb == 8: radius_set = 'mbondi3'
if not radius_set in ['mbondi', 'mbondi2', 'mbondi3', 'bondi', 'amber6']:
raise InputError('Bad radius set! Choose from ' +
'mbondi, mbondi2, mbondi3, bondi, and amber6')
parmed = which('parmed.py')
change_str = ("setOverwrite True\n" +
"changeRadii %s\n" % radius_set +
"parmout %s\n" % self.prmtop +
"go\n")
process = Popen([parmed, '-q', '-n', str(self.prmtop)], stdin=PIPE,
stderr=PIPE, stdout=PIPE)
(output, error) = process.communicate(change_str)
if process.wait():
raise ProgramError('parmed.py failed to change radii!')
# Reload our topology file now that we've changed radius sets
self.prmtop = AmberParm(str(self.prmtop))
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise CpinInputError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
minpka = opt.minpka
maxpka = opt.maxpka
if not opt.igb in (2, 5, 8):
raise CpinInputError('-igb must be 2, 5, or 8!')
if resnums is not None and notresnums is not None:
raise CpinInputError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise CpinInputError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise CpinInputError('-intdiel must be either 1 or 2 currently')
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise CpinInputError('%s is not a titratable residue!' % resname)
titratable_residues.append(resname)
else:
titratable_residues = residues.titratable_residues[:]
print str(titratable_residues)
solvent_ions = ['WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+',
'Mg+', 'Rb+', 'CIO', 'IB', 'MG2']
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
if getattr(residues, res).pKa < minpka: continue
if getattr(residues, res).pKa > maxpka: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise CpinInputError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise CpinInputError('%s only has %d residues. (%d chosen)' % (parm,
parm.ptr('nres'), resnum))
if resnum <= 0:
raise CpinInputError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
raise CpinInputError('Residue number %s [%s] is not titratable' %
(resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated, first_solvent=first_solvent)
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
print resname
continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = parm.ptr('natom')-parm.parm_data['RESIDUE_POINTER'][resnum-1]
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum-1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum-1])
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w', 0)
main_reslist.write_cpin(output, opt.igb, opt.intdiel)
if opt.output is not None:
output.close()
if solvated:
if opt.outparm is None:
has_carboxylate = False
for res in main_reslist:
if res is residues.AS4 or res is residues.GL4:
has_carboxylate = True
break
if has_carboxylate:
print >> sys.stderr, "Warning: Carboxylate residues in explicit ",
print >> sys.stderr, "solvent simulations require a modified"
print >> sys.stderr, "topology file! Use the -op flag to print one."
else:
changeradii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4@OD=,OE=', 1.3).execute()
parm.overwrite = True
parm.writeParm(opt.outparm)
else:
if opt.outparm is not None:
print >> sys.stderr, "A new prmtop is only necessary for explicit ",
print >> sys.stderr, "solvent CpHMD simulations."
sys.stderr.write('CPIN generation complete!\n')
class AmberSystem(object):
""" An Amber system with a topology file and input coordinate file """
# ==============================
def __init__(self, prmtop, inpcrd):
# Only load the inpcrd file if it actually exists.
# if os.path.exists(inpcrd): self.prmtop = AmberParm(prmtop, inpcrd)
# else: self.prmtop = AmberParm(prmtop)
self.prmtop = AmberParm(prmtop)
self.inpcrd = inpcrd
# ==============================
def periodic(self):
""" Returns whether or not a topology file is set up for PBC """
# PBCs are indicated by a non-zero IFBOX pointer
return bool(self.prmtop.ptr('ifbox'))
# ==============================
def query_radii(self):
""" Returns the radii set in the topology file """
return self.prmtop.parm_data['RADIUS_SET'][0]
# ==============================
def set_radii(self, igb=0, radius_set='mbondi'):
""" Sets the radius set to a new one using parmed """
# If someone sets an igb, change to the appropriate radius set
if igb:
if igb == 1: radius_set = 'mbondi'
elif igb == 2: radius_set = 'mbondi2'
elif igb == 5: radius_set = 'mbondi2'
elif igb == 7: radius_set = 'bondi'
elif igb == 8: radius_set = 'mbondi3'
if not radius_set in [
'mbondi', 'mbondi2', 'mbondi3', 'bondi', 'amber6'
]:
raise InputError('Bad radius set! Choose from ' +
'mbondi, mbondi2, mbondi3, bondi, and amber6')
parmed = which('parmed.py')
change_str = ("setOverwrite True\n" + "changeRadii %s\n" % radius_set +
"parmout %s\n" % self.prmtop + "go\n")
process = Popen(
[parmed, '-q', '-n', str(self.prmtop)],
stdin=PIPE,
stderr=PIPE,
stdout=PIPE)
(output, error) = process.communicate(change_str)
if process.wait():
raise ProgramError('parmed.py failed to change radii!')
# Reload our topology file now that we've changed radius sets
self.prmtop = AmberParm(str(self.prmtop))
def natom(topfile):
parm = AmberParm(topfile)
return parm.ptr("NATOM")
def resnum(topfile):
parm = AmberParm(topfile)
return parm.ptr("NRES")
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise CpinInputError('prmtop file (%s) is missing' % opt.prmtop)
# Process the arguments that take multiple args
resstates = process_arglist(opt.resstates, int)
resnums = process_arglist(opt.resnums, int)
notresnums = process_arglist(opt.notresnums, int)
resnames = process_arglist(opt.resnames, str)
notresnames = process_arglist(opt.notresnames, str)
minpka = opt.minpka
maxpka = opt.maxpka
if not opt.igb in (2, 5, 8):
raise CpinInputError('-igb must be 2, 5, or 8!')
if resnums is not None and notresnums is not None:
raise CpinInputError(
'Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise CpinInputError(
'Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise CpinInputError('-intdiel must be either 1 or 2 currently')
# Set the list of residue names we will be willing to titrate
titratable_residues = []
if notresnames is not None:
for resname in residues.titratable_residues:
if resname in notresnames: continue
titratable_residues.append(resname)
elif resnames is not None:
for resname in resnames:
if not resname in residues.titratable_residues:
raise CpinInputError('%s is not a titratable residue!' %
resname)
titratable_residues.append(resname)
else:
titratable_residues = residues.titratable_residues[:]
solvent_ions = [
'WAT', 'Na+', 'Br-', 'Cl-', 'Cs+', 'F-', 'I-', 'K+', 'Li+', 'Mg+',
'Rb+', 'CIO', 'IB', 'MG2'
]
# Filter titratable residues based on min and max pKa
new_reslist = []
for res in titratable_residues:
if getattr(residues, res).pKa < minpka: continue
if getattr(residues, res).pKa > maxpka: continue
new_reslist.append(res)
titratable_residues = new_reslist
del new_reslist
# Make sure we still have a couple residues
if len(titratable_residues) == 0:
raise CpinInputError('No titratable residues fit your criteria!')
# Load the topology file
parm = AmberParm(opt.prmtop)
# Replace an un-set notresnums with an empty list so we get __contains__()
if notresnums is None:
notresnums = []
# If we have a list of residue numbers, check that they're all titratable
if resnums is not None:
for resnum in resnums:
if resnum > parm.ptr('nres'):
raise CpinInputError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise CpinInputError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum - 1]
if not resname in titratable_residues:
raise CpinInputError(
'Residue number %s [%s] is not titratable' %
(resnum, resname))
else:
# Select every residue except those in notresnums
resnums = []
for resnum in range(1, parm.ptr('nres') + 1):
if resnum in notresnums: continue
resnums.append(resnum)
solvated = False
first_solvent = 0
if 'WAT' in parm.parm_data['RESIDUE_LABEL']:
solvated = True
for i, res in enumerate(parm.parm_data['RESIDUE_LABEL']):
if res in solvent_ions:
first_solvent = parm.parm_data['RESIDUE_POINTER'][i]
break
main_reslist = TitratableResidueList(system_name=opt.system,
solvated=solvated,
first_solvent=first_solvent)
for resnum in resnums:
resname = parm.parm_data['RESIDUE_LABEL'][resnum - 1]
if not resname in titratable_residues: continue
res = getattr(residues, resname)
# Filter out termini (make sure the residue in the prmtop has as many
# atoms as the titratable residue defined in residues.py)
if resnum == parm.ptr('nres'):
natoms = parm.ptr('natom') - parm.parm_data['RESIDUE_POINTER'][
resnum - 1]
else:
natoms = (parm.parm_data['RESIDUE_POINTER'][resnum] -
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
if natoms != len(res.atom_list): continue
# If we have gotten this far, add it to the list.
main_reslist.add_residue(res, resnum,
parm.parm_data['RESIDUE_POINTER'][resnum - 1])
# Set the states if requested
if resstates is not None:
main_reslist.set_states(resstates)
# Open the output file
if opt.output is None:
output = sys.stdout
else:
output = open(opt.output, 'w', 0)
main_reslist.write_cpin(output, opt.igb, opt.intdiel)
if opt.output is not None:
output.close()
if solvated:
if opt.outparm is None:
has_carboxylate = False
for res in main_reslist:
if res is residues.AS4 or res is residues.GL4:
has_carboxylate = True
break
if has_carboxylate:
print >> sys.stderr, "Warning: Carboxylate residues in explicit ",
print >> sys.stderr, "solvent simulations require a modified"
print >> sys.stderr, "topology file! Use the -op flag to print one."
else:
changeradii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4@OD=,OE=', 1.3).execute()
parm.overwrite = True
parm.writeParm(opt.outparm)
else:
if opt.outparm is not None:
print >> sys.stderr, "A new prmtop is only necessary for explicit ",
print >> sys.stderr, "solvent CpHMD simulations."
sys.stderr.write('CPIN generation complete!\n')
