def gene_pre_frcmod_file(ionids, naamol2f, stpdbf, stfpf, scresf, prefcdf,
ffchoice, gaff, frcmodfs, watermodel):
print "******************************************************************"
print "* *"
print "*===================Generate the Initial frcmod file=============*"
print "* *"
print "******************************************************************"
libdict = {}
chargedict = {}
for mol2f in naamol2f:
libdict1, chargedict1 = get_lib_dict(mol2f)
libdict.update(libdict1)
chargedict.update(chargedict1)
#get the parameter dicts
Params = get_parm_dict(ffchoice, gaff, frcmodfs)
massparms = Params.mass
bondparms = Params.bond
angparms = Params.ang
dihparms = Params.dih
impparms = Params.imp
nbparms = Params.nb
#--------------------------------------------------------------------------
#############Get the metal center information####################
#--------------------------------------------------------------------------
mol, atids, resids = get_atominfo_fpdb(stpdbf)
#get the blist
blist = get_mc_blist(mol, atids, ionids, stfpf)
#get_all_the_lists from standard model
all_list = get_all_list(mol, blist, atids, 10.0)
#atom type dictionary, key is the atom id, value is atom type
attypdict = {}
#atom ids which has been transfered to another atom type
atidtrans = []
#get the information for the three from finger print
fp = open(stfpf, 'r')
for line in fp:
if line[0:4] != "LINK":
atinfo, atid, attyp1st, symbol, attyp2nd = line.split()
atid = int(atid)
attyp1st = addspace(attyp1st)
attyp2nd = addspace(attyp2nd)
attypdict[atid] = (attyp1st, attyp2nd)
if attyp1st != attyp2nd:
atidtrans.append(atid)
fp.close()
print "Atoms which has changed the atom types:", atidtrans
for atid in atidtrans:
resid = mol.atoms[atid].resid
resname = mol.residues[resid].resname
attyp1 = attypdict[atid][0]
attyp2 = attypdict[atid][1]
print str(resid) + '-' + resname + '@' + str(atid) + '-' + \
mol.atoms[atid].atname + ' : ' + attyp1, '-->', attyp2
#-------------------------------------------------------------------------
########Print the pre-generated frcmod files##############
#-------------------------------------------------------------------------
fmf = open(prefcdf, 'w')
#for atoms which changed atom types
print >> fmf, 'REMARK GOES HERE, THIS FILE IS GENERATED BY MCPB.PY'
print >> fmf, 'MASS'
for atid in atidtrans:
if atid not in ionids: #not include metal ion
atyp1 = attypdict[atid][0]
atyp2 = attypdict[atid][1]
print >> fmf, 'YES', atyp2 + massparms[atyp1]
#for metal ions
for i in ionids:
attyp = attypdict[i][1]
atname = mol.atoms[i].atname
if len(atname) > 1:
atname = atname[0] + atname[1:].lower()
massi = Mass[atname]
print >> fmf, 'YES', attyp + ' ' + str(round(massi, 2)) + \
' ' + atname + ' ion'
#--------------------------------------------------------------------------
bondparamsdict1 = {} #For metal ions
bondparamsdict2 = {} #For the others
print >> fmf, ' '
print >> fmf, 'BOND'
#for bond
for bonds in all_list.bondlist:
i = bonds[0]
j = bonds[1]
if list(set(ionids) & set(bonds)) != []:
#The bonds which related to the ions
bondtyp2 = (attypdict[i][1], attypdict[j][1])
if (bondtyp2 not in bondparamsdict1.keys()) and (bondtyp2[::-1] \
not in bondparamsdict1.keys()):
bondparamsdict1[bondtyp2] = ' '
elif list(set(atidtrans) & set(bonds)) != []:
#The bonds related to the atoms which changed their atom types
bondtyp1 = (attypdict[i][0], attypdict[j][0])
bondtyp2 = (attypdict[i][1], attypdict[j][1])
if (bondtyp2 not in bondparamsdict2.keys()) and (bondtyp2[::-1] \
not in bondparamsdict2.keys()):
if bondtyp1 in bondparms.keys():
bondparamsdict2[bondtyp2] = bondparms[bondtyp1]
elif bondtyp1[::-1] in bondparms.keys():
bondparamsdict2[bondtyp2] = bondparms[bondtyp1[::-1]]
for i in bondparamsdict1.keys():
print >> fmf, 'NON', i[0] + '-' + i[1] + bondparamsdict1[i]
for i in bondparamsdict2.keys():
print >> fmf, 'YES', i[0] + '-' + i[1] + bondparamsdict2[i]
#--------------------------------------------------------------------------
coparas = []
r_scresf = open(scresf, 'r')
for line in r_scresf:
line = line.strip('\n')
line = line.split('-')
resid = int(line[1])
if ('GLY' in line) or ('KCO' in line) or ('ACE' in line):
if resid+1 not in resids:
coparas.append(resid)
r_scresf.close()
angparamsdict1 = {} #For metal ions
angparamsdict2 = {} #For the others
print >> fmf, ' '
print >> fmf, 'ANGL'
#for angle
for angs in all_list.anglist:
i = angs[0]
j = angs[1]
k = angs[2]
if list(set(ionids) & set(angs)) != []:
#The angles which related to the ions
angtyp2 = (attypdict[i][1], attypdict[j][1], attypdict[k][1])
if (angtyp2 not in angparamsdict1.keys()) and (angtyp2[::-1] \
not in angparamsdict1.keys()):
angparamsdict1[angtyp2] = ' '
#print >> fmf, 'NON', attypdict[i][1] + '-' + attypdict[j][1] + \
#'-' + attypdict[k][1]
elif list(set(atidtrans) & set(angs)) != []:
#The angles related to the atoms
#which changed their atom types
angtyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0])
angtyp2 = (attypdict[i][1], attypdict[j][1], attypdict[k][1])
if (angtyp2 not in angparamsdict2.keys()) and (angtyp2[::-1] \
not in angparamsdict2.keys()):
if angtyp1 in angparms.keys():
angparamsdict2[angtyp2] = angparms[angtyp1]
elif angtyp1[::-1] in angparms.keys():
angparamsdict2[angtyp2] = angparms[angtyp1[::-1]]
#Add for a specific situation
for i in coparas:
for atid in atidtrans:
if mol.atoms[atid].atname == 'O' and mol.atoms[atid].resid == i:
angtyp1 = (attypdict[atid][0], 'C ', 'N ')
angtyp2 = (attypdict[atid][1], 'C ', 'N ')
if (angtyp2 not in angparamsdict2.keys()) and (angtyp2[::-1] \
not in angparamsdict2.keys()):
if angtyp1 in angparms.keys():
angparamsdict2[angtyp2] = angparms[angtyp1]
elif angtyp1[::-1] in angparms.keys():
angparamsdict2[angtyp2] = angparms[angtyp1[::-1]]
for i in angparamsdict1.keys():
print >> fmf, 'NON', i[0] + '-' + i[1] + '-' + i[2] + angparamsdict1[i]
for i in angparamsdict2.keys():
print >> fmf, 'YES', i[0] + '-' + i[1] + '-' + i[2] + angparamsdict2[i]
#--------------------------------------------------------------------------
dihparamsdict = {}
#for dihedral
for dihs in all_list.dihlist:
i = dihs[0]
j = dihs[1]
k = dihs[2]
l = dihs[3]
if list(set(ionids) & set(dihs)) != []:
#The dihedral related to the metal ions
dihtyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0], \
attypdict[l][0])
dihtyp1n = (attypdict[i][1], attypdict[j][1], attypdict[k][1], \
attypdict[l][1])
if (dihtyp1 not in dihparamsdict.keys()) and (dihtyp1[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = [' 3 0.00 0.0 ', \
' 3. ', ' ']
elif list(set(atidtrans) & set(dihs)) != []:
if list(set(atidtrans) & set(dihs[0::3])) == []:
#Neither the 1st and 4th atom change atom types
#There is 2nd or 3rd or both changed atom type(s)
dihtyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0], \
attypdict[l][0])
dihtyp1n = (attypdict[i][1], attypdict[j][1], attypdict[k][1], \
attypdict[l][1])
dihtyp2 = ('X ', attypdict[j][0], attypdict[k][0], 'X ')
dihtyp2n = ('X ', attypdict[j][1], attypdict[k][1], 'X ')
if dihtyp1 in dihparms.keys():
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = dihparms[dihtyp1]
elif dihtyp1[::-1] in dihparms.keys():
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = dihparms[dihtyp1[::-1]]
elif dihtyp2 in dihparms.keys():
if (dihtyp2n not in dihparamsdict.keys()) and (dihtyp2n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp2n] = dihparms[dihtyp2]
elif dihtyp2[::-1] in dihparms.keys():
if (dihtyp2n not in dihparamsdict.keys()) and (dihtyp2n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp2n] = dihparms[dihtyp2[::-1]]
else:
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = [' 3 0.00 0.0 ', \
' 3. ', ' ']
else:
#There is 1st or 4th atoms or both changed the atom type(s)
dihtyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0], \
attypdict[l][0])
dihtyp1n = (attypdict[i][1], attypdict[j][1], attypdict[k][1], \
attypdict[l][1])
dihtyp2 = ('X ', attypdict[j][1], attypdict[k][1], 'X ')
if dihtyp1 in dihparms.keys():
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = dihparms[dihtyp1]
elif dihtyp1[::-1] in dihparms.keys():
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = dihparms[dihtyp1[::-1]]
else:
if (dihtyp2 in dihparms.keys()) or (dihtyp2[::-1] \
in dihparms.keys()):
continue
elif (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = [' 3 0.00 0.0 ', \
' 3. ', ' ']
#Add for a specfic situation
for i in coparas:
for atid in atidtrans:
if mol.atoms[atid].atname == 'O' and mol.atoms[atid].resid == i:
for ionid in ionids:
if ((atid, ionid, 1) in all_list.bondlist) or \
((ionid, atid, 1) in all_list.bondlist):
dihtyp1 = (attypdict[ionid][0], attypdict[atid][0], 'C ', 'N ')
dihtyp2 = (attypdict[ionid][1], attypdict[atid][1], 'C ', 'N ')
if (dihtyp2 not in dihparamsdict) and (dihtyp2[::-1] not in dihparamsdict):
if dihtyp1 in dihparms.keys():
dihparamsdict[dihtyp2] = dihparms[dihtyp1]
elif dihtyp1[::-1] in dihparms.keys():
dihparamsdict[dihtyp2] = dihparms[dihtyp1[::-1]]
else:
dihparamsdict[dihtyp2] = [' 3 0.00 0.0 ', \
' 3. ', ' ']
print >> fmf, ' '
print >> fmf, 'DIHE'
for keyv in dihparamsdict.keys():
if 'X ' not in keyv: #For types don't contain X
valv = dihparamsdict[keyv]
keyv = keyv[0] + '-' + keyv[1] + '-' + keyv[2] + '-' + keyv[3]
temp = len(valv)/3
for i in range(0, temp):
temp1 = i * 3
print >> fmf, 'YES', keyv, valv[temp1] + valv[temp1+1] + \
valv[temp1+2]
for keyv in dihparamsdict.keys():
if 'X ' in keyv: #For types contain X
valv = dihparamsdict[keyv]
keyv = keyv[0] + '-' + keyv[1] + '-' + keyv[2] + '-' + keyv[3]
temp = len(valv)/3
for i in range(0, temp):
temp1 = i * 3
print >> fmf, 'YES', keyv, valv[temp1] + valv[temp1+1] + \
valv[temp1+2]
#--------------------------------------------------------------------------
impparamsdict = {}
#For improper torsion
for imps in all_list.implist:
i = imps[0]
j = imps[1]
k = imps[2]
l = imps[3]
if list(set(ionids) & set(imps)) != []:
continue
elif list(set(atidtrans) & set(imps)) != []:
imptyps = {}
#1 situation
imptyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0], \
attypdict[l][0])
imptyp1n = (attypdict[i][1], attypdict[j][1], attypdict[k][1], \
attypdict[l][1])
#3 situations
imptyp2 = ('X ', 'X ', attypdict[k][0], attypdict[i][0])
imptyp2n = ('X ', 'X ', attypdict[k][1], attypdict[i][1])
imptyp3 = ('X ', 'X ', attypdict[k][0], attypdict[j][0])
imptyp3n = ('X ', 'X ', attypdict[k][1], attypdict[j][1])
imptyp4 = ('X ', 'X ', attypdict[k][0], attypdict[l][0])
imptyp4n = ('X ', 'X ', attypdict[k][1], attypdict[l][1])
#6 situations
imptyp5 = ('X ', attypdict[i][0], attypdict[k][0], attypdict[j][0])
imptyp5n = ('X ', attypdict[i][1], attypdict[k][1], attypdict[j][1])
imptyp6 = ('X ', attypdict[j][0], attypdict[k][0], attypdict[i][0])
imptyp6n = ('X ', attypdict[j][1], attypdict[k][1], attypdict[i][1])
imptyp7 = ('X ', attypdict[i][0], attypdict[k][0], attypdict[l][0])
imptyp7n = ('X ', attypdict[i][0], attypdict[k][1], attypdict[l][1])
imptyp8 = ('X ', attypdict[l][0], attypdict[k][0], attypdict[i][0])
imptyp8n = ('X ', attypdict[l][1], attypdict[k][1], attypdict[i][1])
imptyp9 = ('X ', attypdict[j][0], attypdict[k][0], attypdict[l][0])
imptyp9n = ('X ', attypdict[j][1], attypdict[k][1], attypdict[l][1])
imptyp10 = ('X ', attypdict[l][0], attypdict[k][0], attypdict[j][0])
imptyp10n = ('X ', attypdict[l][1], attypdict[k][1], attypdict[j][1])
imptyps[imptyp1] = imptyp1n
imptyps[imptyp2] = imptyp2n
imptyps[imptyp3] = imptyp3n
imptyps[imptyp4] = imptyp4n
imptyps[imptyp5] = imptyp5n
imptyps[imptyp6] = imptyp6n
imptyps[imptyp7] = imptyp7n
imptyps[imptyp8] = imptyp8n
imptyps[imptyp9] = imptyp9n
imptyps[imptyp10] = imptyp10n
for imptypkey in imptyps.keys():
if imptypkey in impparms.keys():
impparamsdict[imptyps[imptypkey]] = impparms[imptypkey]
print >> fmf, ' '
print >> fmf, 'IMPR'
#for improper torsion
for i in impparamsdict.keys():
if i not in impparms.keys():
imptypkey = i[0] + '-' + i[1] + '-' + i[2] + '-' + i[3]
print >> fmf, 'YES', imptypkey, impparamsdict[i]
#--------------------------------------------------------------------------
#for nb
print >> fmf, ' '
print >> fmf, 'NONB'
for atid in atidtrans: #For the others
if atid not in ionids:
attyp1 = attypdict[atid][0]
attyp2 = attypdict[atid][1]
print >> fmf, 'YES ', attyp2 + nbparms[attyp1]
IonLJParaDict = get_ionljparadict(watermodel)
for i in ionids: #For metal ions
element = mol.atoms[i].element
chg = str(int(chargedict[mol.atoms[i].resname]))
attyp2 = attypdict[i][1]
rmin = IonLJParaDict[element + chg][0]
ep = IonLJParaDict[element + chg][1]
annot = IonLJParaDict[element + chg][2]
print >> fmf, 'YES %s %11.3f %13.10f %-s' %(attyp2, rmin, \
ep, annot)
print >> fmf, ' '
print >> fmf, ' '
fmf.close()
#--------------------------------------------------------------------------
#Move the file, delete the repeat parts
os.system("mv %s temp" %prefcdf)
os.system("uniq temp > %s" %prefcdf)
os.system("rm temp")
def gene_pre_frcmod_file(ionids, naamol2f, stpdbf, stfpf, scresf, prefcdf,
ffchoice, gaff, frcmodfs, watermodel):
print "******************************************************************"
print "* *"
print "*===================Generate the Initial frcmod file=============*"
print "* *"
print "******************************************************************"
libdict = {}
chargedict = {}
for mol2f in naamol2f:
libdict1, chargedict1 = get_lib_dict(mol2f)
libdict.update(libdict1)
chargedict.update(chargedict1)
#get the parameter dicts
Params = get_parm_dict(ffchoice, gaff, frcmodfs)
massparms = Params.mass
bondparms = Params.bond
angparms = Params.ang
dihparms = Params.dih
impparms = Params.imp
nbparms = Params.nb
#--------------------------------------------------------------------------
#############Get the metal center information####################
#--------------------------------------------------------------------------
mol, atids, resids = get_atominfo_fpdb(stpdbf)
#get the blist
blist = get_mc_blist(mol, atids, ionids, stfpf)
#get_all_the_lists from standard model
all_list = get_all_list(mol, blist, atids, 10.0)
#atom type dictionary, key is the atom id, value is atom type
attypdict = {}
#atom ids which has been transfered to another atom type
atidtrans = []
#get the information for the three from finger print
fp = open(stfpf, 'r')
for line in fp:
if line[0:4] != "LINK":
atinfo, atid, attyp1st, symbol, attyp2nd = line.split()
atid = int(atid)
attyp1st = addspace(attyp1st)
attyp2nd = addspace(attyp2nd)
attypdict[atid] = (attyp1st, attyp2nd)
if attyp1st != attyp2nd:
atidtrans.append(atid)
fp.close()
print "Atoms which has changed the atom types:", atidtrans
for atid in atidtrans:
resid = mol.atoms[atid].resid
resname = mol.residues[resid].resname
attyp1 = attypdict[atid][0]
attyp2 = attypdict[atid][1]
print str(resid) + '-' + resname + '@' + str(atid) + '-' + \
mol.atoms[atid].atname + ' : ' + attyp1, '-->', attyp2
#-------------------------------------------------------------------------
########Print the pre-generated frcmod files##############
#-------------------------------------------------------------------------
fmf = open(prefcdf, 'w')
#for atoms which changed atom types
print >> fmf, 'REMARK GOES HERE, THIS FILE IS GENERATED BY MCPB.PY'
print >> fmf, 'MASS'
for atid in atidtrans:
if atid not in ionids: #not include metal ion
atyp1 = attypdict[atid][0]
atyp2 = attypdict[atid][1]
print >> fmf, 'YES', atyp2 + massparms[atyp1]
#for metal ions
for i in ionids:
attyp = attypdict[i][1]
atname = mol.atoms[i].atname
if len(atname) > 1:
atname = atname[0] + atname[1:].lower()
massi = Mass[atname]
print >> fmf, 'YES', attyp + ' ' + str(round(massi, 2)) + \
' ' + atname + ' ion'
#--------------------------------------------------------------------------
bondparamsdict1 = {} #For metal ions
bondparamsdict2 = {} #For the others
print >> fmf, ' '
print >> fmf, 'BOND'
#for bond
for bonds in all_list.bondlist:
i = bonds[0]
j = bonds[1]
if list(set(ionids) & set(bonds)) != []:
#The bonds which related to the ions
bondtyp2 = (attypdict[i][1], attypdict[j][1])
if (bondtyp2 not in bondparamsdict1.keys()) and (bondtyp2[::-1] \
not in bondparamsdict1.keys()):
bondparamsdict1[bondtyp2] = ' '
elif list(set(atidtrans) & set(bonds)) != []:
#The bonds related to the atoms which changed their atom types
bondtyp1 = (attypdict[i][0], attypdict[j][0])
bondtyp2 = (attypdict[i][1], attypdict[j][1])
if (bondtyp2 not in bondparamsdict2.keys()) and (bondtyp2[::-1] \
not in bondparamsdict2.keys()):
if bondtyp1 in bondparms.keys():
bondparamsdict2[bondtyp2] = bondparms[bondtyp1]
elif bondtyp1[::-1] in bondparms.keys():
bondparamsdict2[bondtyp2] = bondparms[bondtyp1[::-1]]
for i in bondparamsdict1.keys():
print >> fmf, 'NON', i[0] + '-' + i[1] + bondparamsdict1[i]
for i in bondparamsdict2.keys():
print >> fmf, 'YES', i[0] + '-' + i[1] + bondparamsdict2[i]
#--------------------------------------------------------------------------
coparas = []
r_scresf = open(scresf, 'r')
for line in r_scresf:
line = line.strip('\n')
line = line.split('-')
resid = int(line[1])
if ('GLY' in line) or ('KCO' in line) or ('ACE' in line):
if resid + 1 not in resids:
coparas.append(resid)
r_scresf.close()
angparamsdict1 = {} #For metal ions
angparamsdict2 = {} #For the others
print >> fmf, ' '
print >> fmf, 'ANGL'
#for angle
for angs in all_list.anglist:
i = angs[0]
j = angs[1]
k = angs[2]
if list(set(ionids) & set(angs)) != []:
#The angles which related to the ions
angtyp2 = (attypdict[i][1], attypdict[j][1], attypdict[k][1])
if (angtyp2 not in angparamsdict1.keys()) and (angtyp2[::-1] \
not in angparamsdict1.keys()):
angparamsdict1[angtyp2] = ' '
#print >> fmf, 'NON', attypdict[i][1] + '-' + attypdict[j][1] + \
#'-' + attypdict[k][1]
elif list(set(atidtrans) & set(angs)) != []:
#The angles related to the atoms
#which changed their atom types
angtyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0])
angtyp2 = (attypdict[i][1], attypdict[j][1], attypdict[k][1])
if (angtyp2 not in angparamsdict2.keys()) and (angtyp2[::-1] \
not in angparamsdict2.keys()):
if angtyp1 in angparms.keys():
angparamsdict2[angtyp2] = angparms[angtyp1]
elif angtyp1[::-1] in angparms.keys():
angparamsdict2[angtyp2] = angparms[angtyp1[::-1]]
#Add for a specific situation
for i in coparas:
for atid in atidtrans:
if mol.atoms[atid].atname == 'O' and mol.atoms[atid].resid == i:
angtyp1 = (attypdict[atid][0], 'C ', 'N ')
angtyp2 = (attypdict[atid][1], 'C ', 'N ')
if (angtyp2 not in angparamsdict2.keys()) and (angtyp2[::-1] \
not in angparamsdict2.keys()):
if angtyp1 in angparms.keys():
angparamsdict2[angtyp2] = angparms[angtyp1]
elif angtyp1[::-1] in angparms.keys():
angparamsdict2[angtyp2] = angparms[angtyp1[::-1]]
for i in angparamsdict1.keys():
print >> fmf, 'NON', i[0] + '-' + i[1] + '-' + i[2] + angparamsdict1[i]
for i in angparamsdict2.keys():
print >> fmf, 'YES', i[0] + '-' + i[1] + '-' + i[2] + angparamsdict2[i]
#--------------------------------------------------------------------------
dihparamsdict = {}
#for dihedral
for dihs in all_list.dihlist:
i = dihs[0]
j = dihs[1]
k = dihs[2]
l = dihs[3]
if list(set(ionids) & set(dihs)) != []:
#The dihedral related to the metal ions
dihtyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0], \
attypdict[l][0])
dihtyp1n = (attypdict[i][1], attypdict[j][1], attypdict[k][1], \
attypdict[l][1])
if (dihtyp1 not in dihparamsdict.keys()) and (dihtyp1[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = [' 3 0.00 0.0 ', \
' 3. ', ' ']
elif list(set(atidtrans) & set(dihs)) != []:
if list(set(atidtrans) & set(dihs[0::3])) == []:
#Neither the 1st and 4th atom change atom types
#There is 2nd or 3rd or both changed atom type(s)
dihtyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0], \
attypdict[l][0])
dihtyp1n = (attypdict[i][1], attypdict[j][1], attypdict[k][1], \
attypdict[l][1])
dihtyp2 = ('X ', attypdict[j][0], attypdict[k][0], 'X ')
dihtyp2n = ('X ', attypdict[j][1], attypdict[k][1], 'X ')
if dihtyp1 in dihparms.keys():
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = dihparms[dihtyp1]
elif dihtyp1[::-1] in dihparms.keys():
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = dihparms[dihtyp1[::-1]]
elif dihtyp2 in dihparms.keys():
if (dihtyp2n not in dihparamsdict.keys()) and (dihtyp2n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp2n] = dihparms[dihtyp2]
elif dihtyp2[::-1] in dihparms.keys():
if (dihtyp2n not in dihparamsdict.keys()) and (dihtyp2n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp2n] = dihparms[dihtyp2[::-1]]
else:
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = [' 3 0.00 0.0 ', \
' 3. ', ' ']
else:
#There is 1st or 4th atoms or both changed the atom type(s)
dihtyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0], \
attypdict[l][0])
dihtyp1n = (attypdict[i][1], attypdict[j][1], attypdict[k][1], \
attypdict[l][1])
dihtyp2 = ('X ', attypdict[j][1], attypdict[k][1], 'X ')
if dihtyp1 in dihparms.keys():
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = dihparms[dihtyp1]
elif dihtyp1[::-1] in dihparms.keys():
if (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = dihparms[dihtyp1[::-1]]
else:
if (dihtyp2 in dihparms.keys()) or (dihtyp2[::-1] \
in dihparms.keys()):
continue
elif (dihtyp1n not in dihparamsdict.keys()) and (dihtyp1n[::-1] \
not in dihparamsdict.keys()):
dihparamsdict[dihtyp1n] = [' 3 0.00 0.0 ', \
' 3. ', ' ']
#Add for a specfic situation
for i in coparas:
for atid in atidtrans:
if mol.atoms[atid].atname == 'O' and mol.atoms[atid].resid == i:
for ionid in ionids:
if ((atid, ionid, 1) in all_list.bondlist) or \
((ionid, atid, 1) in all_list.bondlist):
dihtyp1 = (attypdict[ionid][0], attypdict[atid][0],
'C ', 'N ')
dihtyp2 = (attypdict[ionid][1], attypdict[atid][1],
'C ', 'N ')
if (dihtyp2 not in dihparamsdict) and (
dihtyp2[::-1] not in dihparamsdict):
if dihtyp1 in dihparms.keys():
dihparamsdict[dihtyp2] = dihparms[dihtyp1]
elif dihtyp1[::-1] in dihparms.keys():
dihparamsdict[dihtyp2] = dihparms[
dihtyp1[::-1]]
else:
dihparamsdict[dihtyp2] = [' 3 0.00 0.0 ', \
' 3. ', ' ']
print >> fmf, ' '
print >> fmf, 'DIHE'
for keyv in dihparamsdict.keys():
if 'X ' not in keyv: #For types don't contain X
valv = dihparamsdict[keyv]
keyv = keyv[0] + '-' + keyv[1] + '-' + keyv[2] + '-' + keyv[3]
temp = len(valv) / 3
for i in range(0, temp):
temp1 = i * 3
print >> fmf, 'YES', keyv, valv[temp1] + valv[temp1+1] + \
valv[temp1+2]
for keyv in dihparamsdict.keys():
if 'X ' in keyv: #For types contain X
valv = dihparamsdict[keyv]
keyv = keyv[0] + '-' + keyv[1] + '-' + keyv[2] + '-' + keyv[3]
temp = len(valv) / 3
for i in range(0, temp):
temp1 = i * 3
print >> fmf, 'YES', keyv, valv[temp1] + valv[temp1+1] + \
valv[temp1+2]
#--------------------------------------------------------------------------
impparamsdict = {}
#For improper torsion
for imps in all_list.implist:
i = imps[0]
j = imps[1]
k = imps[2]
l = imps[3]
if list(set(ionids) & set(imps)) != []:
continue
elif list(set(atidtrans) & set(imps)) != []:
imptyps = {}
#1 situation
imptyp1 = (attypdict[i][0], attypdict[j][0], attypdict[k][0], \
attypdict[l][0])
imptyp1n = (attypdict[i][1], attypdict[j][1], attypdict[k][1], \
attypdict[l][1])
#3 situations
imptyp2 = ('X ', 'X ', attypdict[k][0], attypdict[i][0])
imptyp2n = ('X ', 'X ', attypdict[k][1], attypdict[i][1])
imptyp3 = ('X ', 'X ', attypdict[k][0], attypdict[j][0])
imptyp3n = ('X ', 'X ', attypdict[k][1], attypdict[j][1])
imptyp4 = ('X ', 'X ', attypdict[k][0], attypdict[l][0])
imptyp4n = ('X ', 'X ', attypdict[k][1], attypdict[l][1])
#6 situations
imptyp5 = ('X ', attypdict[i][0], attypdict[k][0], attypdict[j][0])
imptyp5n = ('X ', attypdict[i][1], attypdict[k][1],
attypdict[j][1])
imptyp6 = ('X ', attypdict[j][0], attypdict[k][0], attypdict[i][0])
imptyp6n = ('X ', attypdict[j][1], attypdict[k][1],
attypdict[i][1])
imptyp7 = ('X ', attypdict[i][0], attypdict[k][0], attypdict[l][0])
imptyp7n = ('X ', attypdict[i][0], attypdict[k][1],
attypdict[l][1])
imptyp8 = ('X ', attypdict[l][0], attypdict[k][0], attypdict[i][0])
imptyp8n = ('X ', attypdict[l][1], attypdict[k][1],
attypdict[i][1])
imptyp9 = ('X ', attypdict[j][0], attypdict[k][0], attypdict[l][0])
imptyp9n = ('X ', attypdict[j][1], attypdict[k][1],
attypdict[l][1])
imptyp10 = ('X ', attypdict[l][0], attypdict[k][0],
attypdict[j][0])
imptyp10n = ('X ', attypdict[l][1], attypdict[k][1],
attypdict[j][1])
imptyps[imptyp1] = imptyp1n
imptyps[imptyp2] = imptyp2n
imptyps[imptyp3] = imptyp3n
imptyps[imptyp4] = imptyp4n
imptyps[imptyp5] = imptyp5n
imptyps[imptyp6] = imptyp6n
imptyps[imptyp7] = imptyp7n
imptyps[imptyp8] = imptyp8n
imptyps[imptyp9] = imptyp9n
imptyps[imptyp10] = imptyp10n
for imptypkey in imptyps.keys():
if imptypkey in impparms.keys():
impparamsdict[imptyps[imptypkey]] = impparms[imptypkey]
print >> fmf, ' '
print >> fmf, 'IMPR'
#for improper torsion
for i in impparamsdict.keys():
if i not in impparms.keys():
imptypkey = i[0] + '-' + i[1] + '-' + i[2] + '-' + i[3]
print >> fmf, 'YES', imptypkey, impparamsdict[i]
#--------------------------------------------------------------------------
#for nb
print >> fmf, ' '
print >> fmf, 'NONB'
for atid in atidtrans: #For the others
if atid not in ionids:
attyp1 = attypdict[atid][0]
attyp2 = attypdict[atid][1]
print >> fmf, 'YES ', attyp2 + nbparms[attyp1]
IonLJParaDict = get_ionljparadict(watermodel)
for i in ionids: #For metal ions
element = mol.atoms[i].element
chg = str(int(chargedict[mol.atoms[i].resname]))
attyp2 = attypdict[i][1]
rmin = IonLJParaDict[element + chg][0]
ep = IonLJParaDict[element + chg][1]
annot = IonLJParaDict[element + chg][2]
print >> fmf, 'YES %s %11.3f %13.10f %-s' %(attyp2, rmin, \
ep, annot)
print >> fmf, ' '
print >> fmf, ' '
fmf.close()
#--------------------------------------------------------------------------
#Move the file, delete the repeat parts
os.system("mv %s temp" % prefcdf)
os.system("uniq temp > %s" % prefcdf)
os.system("rm temp")
" other option are, g09 (means Gaussian09), \n"
" and gms (means GAMESS-US)]")
(options, args) = parser.parse_args()
mol, atids, resids = get_atominfo_fpdb(options.inputfile)
if options.nstdpdb is True:
for i in atids:
atname = mol.atoms[i].atname
if atname[1] in ['0', '1', '2', '3', '4', '5', '6', '7', '8', '9']:
mol.atoms[i].element = atname[0]
else:
mol.atoms[i].element = atname[0:2]
blist = get_blist(mol, atids)
all_list = get_all_list(mol, blist, atids, 8.0)
natids = {}
for i in range(0, len(atids)):
natids[atids[i]] = i + 1
#crds after optimization
if options.softversion in ['g03', 'g09']:
crds = get_crds_from_fchk(options.hessfile, len(atids))
elif options.softversion == 'gms':
crds = get_crds_from_gms(options.hessfile)
#Whole Hessian Matrix
if options.softversion in ['g03', 'g09']:
fcmatrix = get_matrix_from_fchk(options.hessfile, 3*len(atids))
elif options.softversion == 'gms':
