def check_for_multiple_molecule_entries(self):
tp = Topology('topol.top', assign_types = False)
mol_dic = OrderedDict()
for m in tp.molecules:
if mol_dic.has_key(m[0]):
mol_dic[m[0]]+=m[1]
else:
mol_dic[m[0]] = m[1]
tp.molecules = []
for key, val in mol_dic.items():
tp.molecules.append( [key, val] )
tp.write('topol.top')
def main(argv):
options = [
Option( "-split", "bool", False, "Write splitted topologies for vdw and q morphes"),
Option( "-scale_mass", "bool", True, "scale_mass"),
]
files = [
FileOption("-p", "r",["top"],"topol.top", "Input Topology File"),
FileOption("-itp", "r",["itp"],"topol.itp", "Optional Input ITP File"),
FileOption("-o", "w",["top","itp"],"newtop.top", "Topology or ITP output file "),
FileOption("-ff", "dir",["ff"],"amber99sbmut", "Mutation force field "),
FileOption("-log", "w",["log"],"bstate.log", "Log file"),
]
help_text = ('This script adds a B state to an .itp or .top file for a hybrid residue.',
'Hybrid residues in the topology file are recognized automatically.',
'-scale_mass flag sets dummy masses to 1.0, this option is set to True by default.',
'Currently available force fields:',
' - amber99sbmut (Hornak et al, 2006)',
' - amber99sb-star-ildn-mut (Best & Hummer, 2009; Lindorff-Larsen et al, 2010)',
' - charmm22starmut.ff (Piana et al, 2011)',
' - charmm36mut (Best et al, 2012)',
' - oplsaamut (Jorgensen et al, 1996; Kaminski et al, 2001)',
'',
'',
'Please cite:',
'Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger and Bert L. de Groot.',
'Automated Protein Structure and Topology Generation for Alchemical Perturbations.',
'J. Comput. Chem. 2015, 36, 348-354. DOI: 10.1002/jcc.23804',
'',
'Old pmx (pymacs) version:',
'Daniel Seeliger and Bert L. de Groot. Protein Thermostability Calculations Using',
'Alchemical Free Energy Simulations, Biophysical Journal, 98(10):2309-2316 (2010)',
'',
'',
'',
)
cmdl = Commandline( argv, options = options,
fileoptions = files,
program_desc = help_text,
check_for_existing_files = False )
do_scale_mass = cmdl['-scale_mass']
top_file = cmdl['-p']
out_file = cmdl['-o']
log_file = cmdl['-log']
mtp_file = os.path.join( get_ff_path(cmdl['-ff']), 'mutres.mtp')
ffbonded_file = os.path.join( get_ff_path(cmdl['-ff']), 'ffbonded.itp')
do_split = cmdl['-split']
if cmdl.opt['-itp'].is_set:
input_itp = cmdl['-itp']
else:
input_itp = None
if input_itp and out_file.split('.')[-1] != 'itp':
out_file = change_outfile_format(out_file, 'itp')
print 'log_> Setting outfile name to %s' % out_file
if input_itp:
print 'log_> Reading input files "%s" and "%s"' % (top_file, input_itp)
topol = Topology( input_itp, topfile = top_file, version = 'new', ff = cmdl['-ff'] )
else:
print 'log_> Reading input file "%s"' % (top_file)
topol = Topology( top_file, version = 'new', ff = cmdl['-ff'] )
# for i in topol.dihedrals:
# print i[0].id,i[1].id,i[2].id,i[3].id
m = Model( atoms = topol.atoms ) # create model with residue list
topol.residues = m.residues # use model residue list
rlist, rdic = get_hybrid_residues( m, mtp_file, version = 'new')
topol.assign_fftypes() # correct b-states
# for atom in m.atoms:
# print atom.type
# if atom.atomtypeB is not None:
# print "typeB"
# print atom.typeB
for r in rlist:
print 'log_> Hybrid Residue -> %d | %s ' % (r.id, r.resname )
find_bonded_entries( topol )
find_angle_entries( topol )
dih_predef_default = []
find_predefined_dihedrals(topol,rlist,rdic,ffbonded_file,dih_predef_default, cmdl['-ff'])
find_dihedral_entries( topol, rlist, rdic, dih_predef_default )
__add_extra_DNA_impropers(topol, rlist, 1, [180,40,2],[180,40,2])
qA, qB = sum_charge_of_states( rlist )
qA_mem = copy.deepcopy( qA )
qB_mem = copy.deepcopy( qB )
print 'log_> Total charge of state A = ', topol.get_qA()
print 'log_> Total charge of state B = ', topol.get_qB()
topol.write( out_file, scale_mass = do_scale_mass, target_qB = qB )
# topol.check_special_dihedrals( )
# done normal topology for full switch
if cmdl['-split']: # write splitted topology
root, ext = os.path.splitext(out_file)
out_file_qoff = root+'_qoff'+ext
out_file_vdw = root+'_vdw'+ext
out_file_qon = root+'_qon'+ext
print '------------------------------------------------------'
print 'log_> Creating splitted topologies............'
print 'log_> Making "qoff" topology : "%s"' % out_file_qoff
contQ = copy.deepcopy(qA_mem)
topol.write( out_file_qoff, stateQ = 'AB', stateTypes = 'AA', dummy_qB='off',
scale_mass = do_scale_mass, target_qB = qA, stateBonded = 'AA', full_morphe = False )
print 'log_> Charge of state A: %g' % topol.qA
print 'log_> Charge of state B: %g' % topol.qB
print '------------------------------------------------------'
print 'log_> Making "vdw" topology : "%s"' % out_file_vdw
contQ = copy.deepcopy(qA_mem)
topol.write( out_file_vdw, stateQ = 'BB', stateTypes = 'AB', dummy_qA='off', dummy_qB = 'off',
scale_mass = do_scale_mass, target_qB = contQ, stateBonded = 'AB' , full_morphe = False)
print 'log_> Charge of state A: %g' % topol.qA
print 'log_> Charge of state B: %g' % topol.qB
print '------------------------------------------------------'
print 'log_> Making "qon" topology : "%s"' % out_file_qon
topol.write( out_file_qon, stateQ = 'BB', stateTypes = 'BB', dummy_qA='off', dummy_qB = 'on',
scale_mass = do_scale_mass, target_qB = qB_mem, stateBonded = 'BB' , full_morphe = False)
print 'log_> Charge of state A: %g' % topol.qA
print 'log_> Charge of state B: %g' % topol.qB
print '------------------------------------------------------'
print
print 'making b-states done...........'
print
def main(argv):
options = [
Option("-split", "bool", False,
"Write splitted topologies for vdw and q morphes"),
Option("-scale_mass", "bool", True, "scale_mass"),
Option("-dna", "bool", False,
"generate hybrid residue for the DNA nucleotides"),
Option("-rna", "bool", False,
"generate hybrid residue for the RNA nucleotides"),
]
files = [
FileOption("-p", "r", ["top"], "topol.top", "Input Topology File"),
FileOption("-itp", "r", ["itp"], "topol.itp",
"Optional Input ITP File"),
FileOption("-o", "w", ["top", "itp"], "newtop.top",
"Topology or ITP output file "),
FileOption("-ff", "dir", ["ff"], "amber99sbmut",
"Mutation force field "),
FileOption("-log", "w", ["log"], "bstate.log", "Log file"),
]
help_text = (
'This script adds a B state to an .itp or .top file for a hybrid residue.',
'Hybrid residues in the topology file are recognized automatically.',
'-scale_mass flag sets dummy masses to 1.0, this option is set to True by default.',
'Currently available force fields:',
' - amber99sbmut (Hornak et al, 2006)',
' - amber99sb-star-ildn-mut (Best & Hummer, 2009; Lindorff-Larsen et al, 2010)',
' - charmm22starmut.ff (Piana et al, 2011)',
' - charmm36mut (Best et al, 2012)',
' - oplsaamut (Jorgensen et al, 1996; Kaminski et al, 2001)',
'',
'',
'Please cite:',
'Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger and Bert L. de Groot.',
'Automated Protein Structure and Topology Generation for Alchemical Perturbations.',
'J. Comput. Chem. 2015, 36, 348-354. DOI: 10.1002/jcc.23804',
'',
'Old pmx (pymacs) version:',
'Daniel Seeliger and Bert L. de Groot. Protein Thermostability Calculations Using',
'Alchemical Free Energy Simulations, Biophysical Journal, 98(10):2309-2316 (2010)',
'',
'',
'',
)
cmdl = Commandline(argv,
options=options,
fileoptions=files,
program_desc=help_text,
check_for_existing_files=False)
do_scale_mass = cmdl['-scale_mass']
top_file = cmdl['-p']
out_file = cmdl['-o']
log_file = cmdl['-log']
bDNA = cmdl['-dna']
bRNA = cmdl['-rna']
if bDNA:
mtp_file = os.path.join(get_ff_path(cmdl['-ff']), 'mutres_dna.mtp')
elif bRNA:
mtp_file = os.path.join(get_ff_path(cmdl['-ff']), 'mutres_rna.mtp')
else:
mtp_file = os.path.join(get_ff_path(cmdl['-ff']), 'mutres.mtp')
ffbonded_file = os.path.join(get_ff_path(cmdl['-ff']), 'ffbonded.itp')
do_split = cmdl['-split']
if cmdl.opt['-itp'].is_set:
input_itp = cmdl['-itp']
else:
input_itp = None
if input_itp and out_file.split('.')[-1] != 'itp':
out_file = change_outfile_format(out_file, 'itp')
print 'log_> Setting outfile name to %s' % out_file
if input_itp:
# print 'log_> Reading input files "%s" and "%s"' % (top_file, input_itp)
# topol = Topology( input_itp, topfile = top_file, version = 'new', ff = cmdl['-ff'] )
print 'log_> Reading input .itp file "%s""' % (input_itp)
topol = Topology(input_itp,
topfile=None,
version='new',
ff=cmdl['-ff'],
ffpath=get_ff_path(cmdl['-ff']))
else:
print 'log_> Reading input .top file "%s"' % (top_file)
topol = Topology(top_file,
topfile=top_file,
version='new',
ff=cmdl['-ff'])
# for i in topol.dihedrals:
# print i[0].id,i[1].id,i[2].id,i[3].id
m = Model(atoms=topol.atoms) # create model with residue list
topol.residues = m.residues # use model residue list
rlist, rdic = get_hybrid_residues(m, mtp_file, version='new')
topol.assign_fftypes() # correct b-states
# for atom in m.atoms:
# print atom.type
# if atom.atomtypeB is not None:
# print "typeB"
# print atom.typeB
for r in rlist:
print 'log_> Hybrid Residue -> %d | %s ' % (r.id, r.resname)
find_bonded_entries(topol)
find_angle_entries(topol)
dih_predef_default = []
find_predefined_dihedrals(topol, rlist, rdic, ffbonded_file,
dih_predef_default, cmdl['-ff'])
find_dihedral_entries(topol, rlist, rdic, dih_predef_default)
__add_extra_DNA_RNA_impropers(topol, rlist, 1, [180, 40, 2], [180, 40, 2])
qA, qB = sum_charge_of_states(rlist)
qA_mem = copy.deepcopy(qA)
qB_mem = copy.deepcopy(qB)
print 'log_> Total charge of state A = ', topol.get_qA()
print 'log_> Total charge of state B = ', topol.get_qB()
topol.write(out_file, scale_mass=do_scale_mass, target_qB=qB)
# topol.check_special_dihedrals( )
# done normal topology for full switch
if cmdl['-split']: # write splitted topology
root, ext = os.path.splitext(out_file)
out_file_qoff = root + '_qoff' + ext
out_file_vdw = root + '_vdw' + ext
out_file_qon = root + '_qon' + ext
print '------------------------------------------------------'
print 'log_> Creating splitted topologies............'
print 'log_> Making "qoff" topology : "%s"' % out_file_qoff
contQ = copy.deepcopy(qA_mem)
topol.write(out_file_qoff,
stateQ='AB',
stateTypes='AA',
dummy_qB='off',
scale_mass=do_scale_mass,
target_qB=qA,
stateBonded='AA',
full_morphe=False)
print 'log_> Charge of state A: %g' % topol.qA
print 'log_> Charge of state B: %g' % topol.qB
print '------------------------------------------------------'
print 'log_> Making "vdw" topology : "%s"' % out_file_vdw
contQ = copy.deepcopy(qA_mem)
topol.write(out_file_vdw,
stateQ='BB',
stateTypes='AB',
dummy_qA='off',
dummy_qB='off',
scale_mass=do_scale_mass,
target_qB=contQ,
stateBonded='AB',
full_morphe=False)
print 'log_> Charge of state A: %g' % topol.qA
print 'log_> Charge of state B: %g' % topol.qB
print '------------------------------------------------------'
print 'log_> Making "qon" topology : "%s"' % out_file_qon
topol.write(out_file_qon,
stateQ='BB',
stateTypes='BB',
dummy_qA='off',
dummy_qB='on',
scale_mass=do_scale_mass,
target_qB=qB_mem,
stateBonded='BB',
full_morphe=False)
print 'log_> Charge of state A: %g' % topol.qA
print 'log_> Charge of state B: %g' % topol.qB
print '------------------------------------------------------'
print
print 'making b-states done...........'
print
def main(argv):
options = [
Option( "-split", "bool", False, "Write splitted topologies for vdw and q morphes"),
Option( "-scale_mass", "bool", True, "scale_mass"),
]
files = [
FileOption("-p", "r",["top"],"topol.top", "Input Topology File"),
FileOption("-itp", "r",["itp"],"topol.top", "Optional Input ITP File"),
FileOption("-o", "w",["top","itp"],"newtop.top", "Topology or ITP output file "),
FileOption("-log", "w",["log"],"bstate.log", "Log file"),
]
help_text = ['']
cmdl = Commandline( argv, options = options,
fileoptions = files,
program_desc = help_text,
check_for_existing_files = False )
do_scale_mass = cmdl['-scale_mass']
top_file = cmdl['-p']
out_file = cmdl['-o']
log_file = cmdl['-log']
do_split = cmdl['-split']
if cmdl.opt['-itp'].is_set:
input_itp = cmdl['-itp']
else:
input_itp = None
if input_itp and out_file.split('.')[-1] != 'itp':
out_file = change_outfile_format(out_file, 'itp')
print 'log_> Setting outfile name to %s' % out_file
if input_itp:
print 'log_> Reading input files "%s" and "%s"' % (top_file, input_itp)
topol = Topology( input_itp, topfile = top_file)
else:
print 'log_> Reading input file "%s"' % (top_file)
topol = Topology( top_file )
m = Model( atoms = topol.atoms ) # create model with residue list
topol.residues = m.residues # use model residue list
rlist, rdic = get_hybrid_residues( m, 'ffamber99sb.mtp')
topol.assign_fftypes() # correct b-states
for r in rlist:
print 'log_> Hybrid Residue -> %d | %s ' % (r.id, r.resname )
find_bonded_entries( topol )
find_angle_entries( topol )
find_predefined_dihedrals(topol,rlist,rdic)
find_dihedral_entries( topol )
__add_extra_DNA_impropers(topol, rlist, 1, [180,40,2],[180,40,2])
qA, qB = sum_charge_of_states( rlist )
qA_mem = copy.deepcopy( qA )
qB_mem = copy.deepcopy( qB )
print 'log_> Total charge of state A = ', topol.get_qA()
print 'log_> Total charge of state B = ', topol.get_qB()
topol.write( out_file, scale_mass = do_scale_mass, target_qB = qB )
# topol.check_special_dihedrals( )
# done normal topology for full switch
if cmdl['-split']: # write splitted topology
root, ext = os.path.splitext(out_file)
out_file_qoff = root+'_qoff'+ext
out_file_vdw = root+'_vdw'+ext
out_file_qon = root+'_qon'+ext
print '------------------------------------------------------'
print 'log_> Creating splitted topologies............'
print 'log_> Making "qoff" topology : "%s"' % out_file_qoff
contQ = copy.deepcopy(qA_mem)
topol.write( out_file_qoff, stateQ = 'AB', stateTypes = 'AA', dummy_qB='off',
scale_mass = do_scale_mass, target_qB = qA, stateBonded = 'AA', full_morphe = False )
print 'log_> Charge of state A: %g' % topol.qA
print 'log_> Charge of state B: %g' % topol.qB
print '------------------------------------------------------'
print 'log_> Making "vdw" topology : "%s"' % out_file_vdw
contQ = copy.deepcopy(qA_mem)
topol.write( out_file_vdw, stateQ = 'BB', stateTypes = 'AB', dummy_qA='off', dummy_qB = 'off',
scale_mass = do_scale_mass, target_qB = contQ, stateBonded = 'AB' , full_morphe = False)
print 'log_> Charge of state A: %g' % topol.qA
print 'log_> Charge of state B: %g' % topol.qB
print '------------------------------------------------------'
print 'log_> Making "qon" topology : "%s"' % out_file_qon
topol.write( out_file_qon, stateQ = 'BB', stateTypes = 'BB', dummy_qA='off', dummy_qB = 'on',
scale_mass = do_scale_mass, target_qB = qB_mem, stateBonded = 'BB' , full_morphe = False)
print 'log_> Charge of state A: %g' % topol.qA
print 'log_> Charge of state B: %g' % topol.qB
print '------------------------------------------------------'
