def changeradii(root, amber_prmtop, messages):
""" Allows users to change the GB Radius set """
title = 'Choose a Radius Set'
desc = ('Select a radius set for implicit solvent\n' +
'calculations. This has the same effect as\n' +
'"set default PBRadii <value>" in tleap')
radius_selection = StringVar()
namelist = ['bondi', 'mbondi', 'mbondi2', 'mbondi3', 'amber6']
cmd_window = _guiwidgets.RadioButtonWindow(
amber_prmtop, title, desc, radius_selection, namelist)
# Wait until the window is destroyed, then get the variable and pass it
# over to the class
cmd_window.wait_window()
sel = str(radius_selection.get())
if sel:
action = actions.changeRadii(amber_prmtop, ArgumentList(sel))
messages.write('%s\n' % action)
action.execute()
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('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 (1, 2, 5, 7, 8):
raise AmberError('-igb must be 1, 2, 5, 7, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-intdiel must be either 1 or 2 currently')
# Print warning about old format
if opt.oldfmt:
sys.stderr.write(
'Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0!\n'
' You should use the new format for simulations with temperatures other than 300.0 Kelvins\n'
)
# 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 AmberError('%s is not a titratable residue!' % resname)
elif not getattr(residues, resname).typ == "ph":
raise AmberError('%s is not a pH titratable residue!' %
resname)
titratable_residues.append(resname)
else:
for resname in residues.titratable_residues:
if getattr(residues, resname).typ == "ph":
titratable_residues.append(resname)
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 AmberError('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 AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum - 1]
if not resname in titratable_residues:
raise AmberError('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') + 1 -
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')
main_reslist.write_cpin(output, opt.igb, opt.intdiel, opt.oldfmt, "ph")
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 or res is residues.PRN:
has_carboxylate = True
break
if has_carboxylate:
sys.stderr.write(
'Warning: Carboxylate residues in explicit solvent '
'simulations require a modified topology file!\n'
'Use the -op flag to print one.\n')
else:
changeRadii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4,PRN@OD=,OE=,O1=,O2=',
1.3).execute()
parm.overwrite = True
parm.write_parm(opt.outparm)
else:
if opt.outparm is not None:
sys.stderr.write(
'A new prmtop is only necessary for explicit solvent '
'CpHMD/pH-REMD simulations.\n')
sys.stderr.write('CPIN generation complete!\n')
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('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 (1, 2, 5, 7, 8):
raise AmberError('-igb must be 1, 2, 5, 7, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-intdiel must be either 1 or 2 currently')
# Print warning about old format
if opt.oldfmt:
sys.stderr.write('Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0!\n'
' You should use the new format for simulations with temperatures other than 300.0 Kelvins\n')
# 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 AmberError('%s is not a titratable residue!' % resname)
elif not getattr(residues, resname).typ == "ph":
raise AmberError('%s is not a pH-active titratable residue!' % resname)
titratable_residues.append(resname)
else:
for resname in residues.titratable_residues:
if getattr(residues, resname).typ == "ph":
titratable_residues.append(resname)
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:
# @jaimergp: If None values are not filtered out, comparisons
# will fail in Py3k. This patch was discussed and approved in
# GitLab issue 122 (@vwcruzeiro, @swails)
# Error obtained in serial tests in conda-forge builds:
# Traceback (most recent call last):
# File "/home/conda/amber/bin/cpinutil.py", line 325, in <module>
# main(opt)
# File "/home/conda/amber/bin/cpinutil.py", line 191, in main
# if getattr(residues, res).pKa < minpka: continue
# TypeError: '<' not supported between instances of 'NoneType' and 'int'
# ./Run.cpin: Program error
# make[1]: *** [test.cpinutil] Error 1
if getattr(residues, res).pKa is None: continue
# /@jaimergp
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 AmberError('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 AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
raise AmberError('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)
trescnt = 0
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') + 1 -
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])
trescnt += 1
# Prints a warning if the number of titratable residues is larger than 50
if trescnt > 50: sys.stderr.write('Warning: Your CPIN file has more than 50 titratable residues! pmemd and sander have a\n'
' default limit of 50 titrable residues, thus this CPIN file can only be used\n'
' if the definitions for this limit are modified at the top of\n'
' $AMBERHOME/src/pmemd/src/constantph.F90 or $AMBERHOME/AmberTools/src/sander/constantph.F90.\n'
' AMBER needs to be recompilied after these files are modified.\n')
# 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')
main_reslist.write_cpin(output, opt.igb, opt.intdiel, opt.oldfmt, "ph")
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 or res is residues.PRN:
has_carboxylate = True
break
if has_carboxylate:
sys.stderr.write(
'Warning: Carboxylate residues in explicit solvent '
'simulations require a modified topology file!\n'
' Use the -op flag to print one.\n'
)
else:
changeRadii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4,PRN@OD=,OE=,O1=,O2=', 1.3).execute()
parm.overwrite = True
parm.write_parm(opt.outparm)
else:
if opt.outparm is not None:
sys.stderr.write(
'A new prmtop is only necessary for explicit solvent '
'CpHMD/pH-REMD simulations.\n'
)
sys.stderr.write('CPIN generation complete!\n')
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('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 (1, 2, 5, 7, 8):
raise AmberError('-igb must be 1, 2, 5, 7, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-intdiel must be either 1 or 2 currently')
# Print warning about old format
if opt.oldfmt:
sys.stderr.write('Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0!\n'
' You should use the new format for simulations with temperatures other than 300.0 Kelvins\n')
# 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 AmberError('%s is not a titratable residue!' % resname)
elif not getattr(residues, resname).typ == "ph":
raise AmberError('%s is not a pH-active titratable residue!' % resname)
titratable_residues.append(resname)
else:
for resname in residues.titratable_residues:
if getattr(residues, resname).typ == "ph":
titratable_residues.append(resname)
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 AmberError('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 AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
raise AmberError('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)
trescnt = 0
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') + 1 -
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])
trescnt += 1
# Prints a warning if the number of titratable residues is larger than 50
if trescnt > 50: sys.stderr.write('Warning: Your CPIN file has more than 50 titratable residues! pmemd and sander have a\n'
' default limit of 50 titrable residues, thus this CPIN file can only be used\n'
' if the definitions for this limit are modified at the top of\n'
' $AMBERHOME/src/pmemd/src/constantph.F90 or $AMBERHOME/AmberTools/src/sander/constantph.F90.\n'
' AMBER needs to be recompilied after these files are modified.\n')
# 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')
main_reslist.write_cpin(output, opt.igb, opt.intdiel, opt.oldfmt, "ph")
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 or res is residues.PRN:
has_carboxylate = True
break
if has_carboxylate:
sys.stderr.write(
'Warning: Carboxylate residues in explicit solvent '
'simulations require a modified topology file!\n'
' Use the -op flag to print one.\n'
)
else:
changeRadii(parm, 'mbondi2').execute()
change(parm, 'RADII', ':AS4,GL4,PRN@OD=,OE=,O1=,O2=', 1.3).execute()
parm.overwrite = True
parm.write_parm(opt.outparm)
else:
if opt.outparm is not None:
sys.stderr.write(
'A new prmtop is only necessary for explicit solvent '
'CpHMD/pH-REMD simulations.\n'
)
sys.stderr.write('CPIN generation complete!\n')
def main(opt):
# Check all of the arguments
if not os.path.exists(opt.prmtop):
raise AmberError('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 AmberError('-igb must be 2, 5, or 8!')
if resnums is not None and notresnums is not None:
raise AmberError('Cannot specify -resnums and -notresnums together')
if resnames is not None and notresnames is not None:
raise AmberError('Cannot specify -resnames and -notresnames together')
if opt.intdiel != 1 and opt.intdiel != 2:
raise AmberError('-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 AmberError('%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 AmberError('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 AmberError('%s only has %d residues. (%d chosen)' %
(parm, parm.ptr('nres'), resnum))
if resnum <= 0:
raise AmberError('Cannot select negative residue numbers.')
resname = parm.parm_data['RESIDUE_LABEL'][resnum-1]
if not resname in titratable_residues:
raise AmberError('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') + 1 -
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')
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:
sys.stderr.write(
'Warning: Carboxylate residues in explicit solvent '
'simulations require a modified topology file!\n'
'Use the -op flag to print one.\n'
)
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:
sys.stderr.write(
'A new prmtop is only necessary for explicit solvent '
'CpHMD/pH-REMD simulations.\n'
)
