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")
def gene_resp_input_file(lgpdbf, ionids, stfpf, ffchoice, mol2fs,
chgmod, fixchg_resids, lgchg):
libdict, chargedict = get_lib_dict(ffchoice)
for mol2f in mol2fs:
libdict1, chargedict1 = get_lib_dict(mol2f)
libdict.update(libdict1)
chargedict.update(chargedict1)
mol, atids, resids = get_atominfo_fpdb(lgpdbf)
reslist = get_reslist(mol, resids)
blist = get_mc_blist(mol, atids, ionids, stfpf)
bnoatids = [] #Binding backbone N and C Atom IDs
mcresids = [] #Metal site residues
stfpff = open(stfpf, 'r')
for line in stfpff:
if line[0:4] != 'LINK':
line = line.split()
line = line[0].split('-')
mcresids.append(int(line[0]))
else:
line = line.strip('\n')
line = line.split()
if (line[-1][-1] in ['N3', 'N', 'O', 'OXT']):
atid, atom = line[-1].split('-')
bnoatids.append(int(atid))
stfpff.close()
bnoresids = [] #Binding Backbone N and C Residue IDs, which are not fitted
#with backbone restriction in the charge fitting
for i in bnoatids:
resid = mol.atoms[i].resid
if resid not in bnoresids:
bnoresids.append(resid)
angresids = [] #ACE, NME, GLY residues
for i in resids:
if i not in mcresids:
angresids.append(i)
#Get the total charge of the system-------------------------------------
totchg = 0.0
for i in resids:
resname = mol.residues[i].resname
if i in reslist.nterm:
reschg = chargedict['N' + resname]
elif i in reslist.cterm:
reschg = chargedict['C' + resname]
else:
reschg = chargedict[resname]
totchg = totchg + reschg
totchg = int(round(totchg, 0))
if lgchg == -99:
lgchg = totchg
#-------------------------------------------------------------------------
##############RESP1.IN file###############################################
#-------------------------------------------------------------------------
print "***Generating the 1st stage resp charge fitting input file..."
#print the 1st part, the title
fresp1 = open('resp1.in', 'w')
print >> fresp1, "Resp charges for organic molecule"
print >> fresp1, " "
print >> fresp1, " &cntrl"
print >> fresp1, " "
print >> fresp1, " nmol = 1,"
print >> fresp1, " ihfree = 1,"
print >> fresp1, " ioutopt = 1,"
print >> fresp1, " "
print >> fresp1, " &end"
print >> fresp1, " 1.0"
print >> fresp1, "Resp charges for organic molecule"
print >> fresp1, "%5d" %lgchg,
print >> fresp1, "%4d" %len(atids)
#2. print the 2nd part, the free and fozen atoms---------------------------
natids = [i for i in range(1, len(atids)+1)] #new atids
iddict = {} #First number in iddict is new atom id, second is atomic number
for i in range(0, len(atids)):
iddict[atids[i]] = natids[i]
for i in atids:
element = mol.atoms[i].element
elenum = Atnum[element]
iddict[i] = (iddict[i], elenum)
for i in resids:
get_equal_atoms(mol, i, blist, iddict)
#other atoms (except the CH2 and CH3 groups) are frozen
for i in atids:
if (len(iddict[i]) == 2):
iddict[i] = (iddict[i][0], iddict[i][1], -99)
for i in atids:
#if iddict[i][2] == -99:
print >> fresp1, "%5d" %iddict[i][1],
print >> fresp1, "%4s" %'0'
#else:
# print >> fresp1, "%5d" %iddict[i][1],
# print >> fresp1, "%4s" %iddict[i][2]
fresp1.close()
add_restriction('resp1.in', libdict, mol, resids, reslist, mcresids,
bnoresids, angresids, iddict, chgmod, fixchg_resids)
#-------------------------------------------------------------------------
####################RESP2.IN file#########################################
#-------------------------------------------------------------------------
print "***Generating the 2nd stage resp charge fitting input file..."
#1. print the 1st part, the title------------------------------------------
fresp2 = open('resp2.in', 'w')
print >> fresp2, "Resp charges for organic molecule"
print >> fresp2, " "
print >> fresp2, " &cntrl"
print >> fresp2, " "
print >> fresp2, " nmol = 1,"
print >> fresp2, " ihfree = 1,"
print >> fresp2, " ioutopt = 1,"
print >> fresp2, " iqopt = 2,"
print >> fresp2, " qwt = 0.001,"
print >> fresp2, " "
print >> fresp2, " &end"
print >> fresp2, " 1.0"
print >> fresp2, "Resp charges for organic molecule"
print >> fresp2, "%5d" %lgchg,
print >> fresp2, "%4d" %len(atids)
#2. print the 2nd part, the free or frozen information---------------------
for i in atids:
print >> fresp2, "%5d" %iddict[i][1],
print >> fresp2, "%4s" %iddict[i][2]
fresp2.close()
add_restriction('resp2.in', libdict, mol, resids, reslist, mcresids,
bnoresids, angresids, iddict, chgmod, fixchg_resids)
def resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids,\
ffchoice, mol2fs, metcenres2, chgmod, fixchg_resids, g0x, lgchg):
print "******************************************************************"
print "* *"
print "*======================RESP Charge fitting=======================*"
print "* *"
print "******************************************************************"
gene_resp_input_file(lgpdbf, ionids, stfpf, ffchoice, mol2fs,
chgmod, fixchg_resids, lgchg)
#-------------------------------------------------------------------------
####################RESP charge fitting###################################
#-------------------------------------------------------------------------
print '***Doing the RESP charge fiting...'
espf = mklogf.strip('.log') + '.esp'
if g0x in ['g03', 'g09']:
get_esp_from_gau(mklogf, espf)
elif g0x == 'gms':
get_esp_from_gms(mklogf, espf)
os.system("resp -O -i resp1.in -o resp1.out -p resp1.pch -t resp1.chg \
-e %s -s resp1_calc.esp" %espf)
os.system("resp -O -i resp2.in -o resp2.out -p resp2.pch -q resp1.chg \
-t resp2.chg -e %s -s resp2_calc.esp" %espf)
#-------------------------------------------------------------------------
####################Collecting the atom type and charge data##############
#-------------------------------------------------------------------------
#------------Atom type----------
sddict = {} #get the atom type information from standard model
scf = open(stfpf, 'r')
for line in scf:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split(' ')
line = [i for i in line if i != '']
if len(line[-1]) == 1:
line[-1] = line[-1] + ' '
sddict[line[0]] = line[-1]
scf.close()
#------------Charge-------------
chgs = read_resp_file('resp2.chg')
metcenres1 = [] #original name of the metal center residue
stlist = [] #get the atom name list from the standard model
stf = open(stfpf, 'r')
for line in stf:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split()
stlist.append(line[0])
line = line[0].split('-')
lresname = line[0] + '-' + line[1]
if lresname not in metcenres1:
metcenres1.append(lresname)
stf.close()
llist = [] #get the atom name list from the large model
lf = open(lgfpf, 'r')
for line in lf:
line = line.strip('\n')
llist.append(line)
lf.close()
ldict = {} #get charge of the large model, one-to-one relationship
for i in range(0, len(llist)):
ldict[llist[i]] = chgs[i]
stdict = {} #get the charge of the standard model
for i in ldict.keys():
if i in stlist:
stdict[i] = ldict[i]
#-------------------------------------------------------------------------
####################Checking Models#########################
#-------------------------------------------------------------------------
print "=========================Checking models=========================="
print '***Check the large model...'
if len(chgs) != len(llist):
raise pymsmtError('Error: the charges and atom numbers are mismatch '
'for the large model!')
else:
print 'Good. The charges and atom numbers are match for the ' + \
'large model.'
print 'Good. There are ' + str(len(llist)) + ' atoms in the ' + \
'large model.'
print '***Check the standard model...'
if len(stlist) != len(stdict):
raise pymsmtError('Error: the charges and atom numbers are mismatch '
'for the standard model!')
else:
print 'Good. The charges and atom numbers are match for the ' + \
'standard model.'
print 'Good. There are ' + str(len(stlist)) + ' atoms in the ' + \
'standard model.'
print '***Check the residue names provided...'
if len(metcenres1) != len(metcenres2):
print 'You gave the residue names: ', str(metcenres2)
print 'Database had them: ', str(metcenres1)
raise pymsmtError('Error: The number of the residue names given is '
'mismatch the database!')
else:
print 'Good. The number of the residue names given matches ' + \
'the database.'
#-------------------------------------------------------------------------
####################Building mol2 files for modeling######################
#-------------------------------------------------------------------------
#Load the force field
libdict, chargedict = get_lib_dict(ffchoice)
for mol2f in mol2fs:
libdict1, chargedict1 = get_lib_dict(mol2f)
libdict.update(libdict1)
chargedict.update(chargedict1)
##get the bondlist
mol, atids, resids = get_atominfo_fpdb(stpdbf) #from standard pdb
blist = get_mc_blist(mol, atids, ionids, stfpf)
blist2 = [(i[0], i[1]) for i in blist]
print "=======================Building mol2 files========================"
#for each residue, print out the mol2 file
for i in range(0, len(resids)):
resconter = mol.residues[resids[i]].resconter #atom ids in the residue
resname1 = mol.residues[resids[i]].resname #load residue name
resname2 = metcenres2[i] #new residue name
#Backbone atoms use AMBER backbone atom types
#if resname1 in resnamel:
# for bbatm in ['N', 'H', 'CA', 'HA','C', 'O']:
# key1 = str(resids[i]) + '-' + resname1 + '-' + bbatm
# key2 = resname1 + '-' + bbatm
# sddict[key1] = libdict[key2][0]
#New id dict
iddict1 = {}
for j in range(0, len(resconter)):
iddict1[resconter[j]] = j + 1
#Bond list for each residue with new atom ids
blist_each = []
for k in blist2:
if set(resconter) & set(k) == set(k):
blist_each.append((iddict1[k[0]], iddict1[k[1]]))
print_mol2f(resids[i], resname1, resname2, resconter, mol, iddict1, \
sddict, stdict, blist_each)
def gene_by_QM_fitting_zmatrix(scpdbf, ionids, stfpf, pref, finf, logfname,
scalef):
print "=============Using the Z-matrix method to generate the parameters."
sturefs, vals, fcs = get_fc_from_log(logfname)
#pdb file
mol, atids, resids = get_atominfo_fpdb(scpdbf)
blist = get_mc_blist(mol, atids, ionids, stfpf)
alist = get_alist(mol, blist)
#reverse new id dict
rvnatids = {}
for i in range(0, len(atids)):
rvnatids[i+1] = atids[i]
attypdict = get_attypdict(stfpf, atids)
missbondtyps, missangtyps = get_misstyps(pref)
#final parameter dicts
finalparmdict = {}
#for bond
print "=======================Generate the bond parameters==============="
for misbond in missbondtyps:
bondlen = []
bfconst = []
for i in range(0, len(sturefs)):
if len(sturefs[i]) == 2:
at1 = sturefs[i][0]
at2 = sturefs[i][1]
bondtyp = (attypdict[rvnatids[at1]], attypdict[rvnatids[at2]])
"The unit in log file is Angs."
if bondtyp == misbond or bondtyp[::-1] == misbond:
dis = vals[i]
fcfinal = fcs[i] * HB2_TO_KCAL_MOL_A2 * 0.5
fcfinal = fcfinal * scalef * scalef
#Hatree/(Bohr^2) to kcal/(mol*angstrom^2)
#Times 0.5 factor since AMBER use k(r-r0)^2 but not 1/2*k*(r-r0)^2
bondlen.append(dis)
bfconst.append(fcfinal)
#Get average bond parameters
misbondat12 = misbond[0] + '-' + misbond[1]
bond_para = avg_bond_para(misbondat12, bondlen, bfconst)
#get the force constant
finalparmdict[misbondat12] = bond_para
#for angle
print "=======================Generate the angle parameters=============="
for misang in missangtyps:
angvals = []
afconst = []
for i in range(0, len(sturefs)):
if len(sturefs[i]) == 3:
at1 = sturefs[i][0]
at2 = sturefs[i][1]
at3 = sturefs[i][2]
angtyp = (attypdict[rvnatids[at1]], attypdict[rvnatids[at2]], attypdict[rvnatids[at3]])
if angtyp == misang or angtyp[::-1] == misang:
angval = vals[i]
fcfinal = fcs[i] * H_TO_KCAL_MOL * 0.5
fcfinal = fcfinal * scalef * scalef
#Hatree to kcal/mol
#Times 0.5 factor since AMBER use k(r-r0)^2 but not 1/2*k*(r-r0)^2
angvals.append(angval)
afconst.append(fcfinal)
#Get average angle parameters
misangat123 = misang[0] + '-' + misang[1] + '-' + misang[2]
ang_para = avg_angle_para(misangat123, angvals, afconst)
finalparmdict[misangat123] = ang_para
#Print out the final frcmod file
print_frcmod_file(pref, finf, finalparmdict, 'Z-matrix')
def gene_by_QM_fitting_sem(scpdbf, ionids, stfpf, pref, finf, chkfname,
logfile, g0x, scalef, bondavg, angavg):
print "==================Using the Seminario method to solve the problem."
mol, atids, resids = get_atominfo_fpdb(scpdbf)
blist = get_mc_blist(mol, atids, ionids, stfpf)
alist = get_alist(mol, blist)
#crds after optimization
if g0x in ['g03', 'g09']:
crds = get_crds_from_fchk(chkfname, len(atids))
elif g0x == 'gms':
crds = get_crds_from_gms(logfile)
#Whole Hessian Matrix
if g0x in ['g03', 'g09']:
fcmatrix = get_matrix_from_fchk(chkfname, 3*len(atids))
elif g0x == 'gms':
fcmatrix = get_matrix_from_gms(logfile, 3*len(atids))
natids = {}
for i in range(0, len(atids)):
natids[atids[i]] = i + 1
attypdict = get_attypdict(stfpf, atids)
missbondtyps, missangtyps = get_misstyps(pref)
finalparmdict = {}
#for bond
print "=======================Generate the bond parameters==============="
for misbond in missbondtyps:
bondlen = []
bfconst = []
for bond in blist:
at1 = bond[0]
at2 = bond[1]
bondtyp = (attypdict[at1], attypdict[at2])
"The unit in fchk file is a.u. so the distance is in Bohr."
if bondtyp == misbond or bondtyp[::-1] == misbond:
nat1 = natids[at1]
nat2 = natids[at2]
if bondavg == 1:
dis, fcfinal, stdv = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat2, scalef, bondavg)
print '### Bond force constant between ' + \
mol.atoms[at1].resname + str(mol.atoms[at1].resid) + '@' + mol.atoms[at1].atname + ' and ' + \
mol.atoms[at2].resname + str(mol.atoms[at2].resid) + '@' + mol.atoms[at2].atname + ' : ' + \
str(round(fcfinal, 1)) + ' with StdDev ' + str(round(stdv, 1))
elif bondavg == 0:
dis, fcfinal = get_bond_fc_with_sem(crds, fcmatrix, nat1, nat2, scalef, bondavg)
bondlen.append(dis)
bfconst.append(fcfinal)
#Get average bond parameters
misbondat12 = misbond[0] + '-' + misbond[1]
bond_para = avg_bond_para(misbondat12, bondlen, bfconst)
#get the force constant
finalparmdict[misbondat12] = bond_para
#for angle
print "=======================Generate the angle parameters=============="
for misang in missangtyps:
angvals = []
afconst = []
for ang in alist:
at1 = ang[0]
at2 = ang[1]
at3 = ang[2]
angtyp = (attypdict[at1], attypdict[at2], attypdict[at3])
if angtyp == misang or angtyp[::-1] == misang:
nat1 = natids[at1]
nat2 = natids[at2]
nat3 = natids[at3]
if angavg == 1:
angval, fcfinal, stdv = get_ang_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, scalef, angavg)
print '### Angle force constant between ' + \
mol.atoms[at1].resname + str(mol.atoms[at1].resid) + '@' + mol.atoms[at1].atname + ', ' + \
mol.atoms[at2].resname + str(mol.atoms[at2].resid) + '@' + mol.atoms[at2].atname + ' and ' + \
mol.atoms[at3].resname + str(mol.atoms[at3].resid) + '@' + mol.atoms[at3].atname + ' : ' + \
str(round(fcfinal, 2)) + ' with StdDev ' + str(round(stdv, 2))
elif angavg == 0:
angval, fcfinal = get_ang_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, scalef, angavg)
angvals.append(angval)
afconst.append(fcfinal)
#Get average angle parameters
misangat123 = misang[0] + '-' + misang[1] + '-' + misang[2]
ang_para = avg_angle_para(misangat123, angvals, afconst)
finalparmdict[misangat123] = ang_para
#Print out the final frcmod file
print_frcmod_file(pref, finf, finalparmdict, 'Seminario')
def gene_by_empirical_way(scpdbf, ionids, stfpf, pref, finf):
print "******************************************************************"
print "* *"
print "*===========Using the empirical way to solve the problem=========*"
print "* *"
print "******************************************************************"
#Read from sidechain pdb
mol, atids, resids = get_atominfo_fpdb(scpdbf)
blist = get_mc_blist(mol, atids, ionids, stfpf)
alist = get_alist(mol, blist)
attypdict = get_attypdict(stfpf, atids)
missbondtyps, missangtyps = get_misstyps(pref)
finalparmdict = {}
#for bond
print "=======================Generate the bond parameters==============="
for misbond in missbondtyps:
bondlen = []
bfconst = []
for bond in blist:
at1 = bond[0]
at2 = bond[1]
bondtyp = (attypdict[at1], attypdict[at2])
if bondtyp == misbond or bondtyp[::-1] == misbond:
crd1 = mol.atoms[at1].crd
crd2 = mol.atoms[at2].crd
dis = calc_bond(crd1, crd2)
dis = round(dis, 4)
bondlen.append(dis)
#get the atom number
elmt1 = mol.atoms[at1].element
elmt2 = mol.atoms[at2].element
elmts = [elmt1, elmt2]
elmts = sorted(elmts)
fcfinal = fcfit_ep_bond(dis, elmts)
bfconst.append(fcfinal)
#Get average bond parameters
misbondat12 = misbond[0] + '-' + misbond[1]
bond_para = avg_bond_para(misbondat12, bondlen, bfconst)
#get the force constant
finalparmdict[misbondat12] = bond_para
#for angle
print "=======================Generate the angle parameters=============="
for misang in missangtyps:
angvals = []
afconst = []
for ang in alist:
at1 = ang[0]
at2 = ang[1]
at3 = ang[2]
angtyp = (attypdict[at1], attypdict[at2], attypdict[at3])
if angtyp == misang or angtyp[::-1] == misang:
crd1 = mol.atoms[at1].crd
crd2 = mol.atoms[at2].crd
crd3 = mol.atoms[at3].crd
angval = calc_angle(crd1, crd2, crd3)
angvals.append(angval)
elmt1 = mol.atoms[at1].element
elmt2 = mol.atoms[at2].element
elmt3 = mol.atoms[at3].element
elmts = [elmt1, elmt2, elmt3]
fcfinal = fcfit_ep_angle(elmts)
afconst.append(fcfinal)
#Get average angle parameters
misangat123 = misang[0] + '-' + misang[1] + '-' + misang[2]
ang_para = avg_angle_para(misangat123, angvals, afconst)
finalparmdict[misangat123] = ang_para
#Print out the final frcmod file
print_frcmod_file(pref, finf, finalparmdict, 'empirical')
def gene_leaprc(gname, orpdbf, fipdbf, stpdbf, stfpf, ionids,\
ionmol2fs, ioninf, mcresname, naamol2fs, ff_choice, frcmodfs,
finfcdf, ileapf, model, watermodel='tip3p', paraset='cm'):
print "******************************************************************"
print "* *"
print "*=================Generating input file for leap=================*"
print "* *"
print "******************************************************************"
#---------------------Generate the new pdb file--------------------------
#mol0 is the old mol while mol is new mol file with new names
mol0, atids0, resids0 = get_atominfo_fpdb(orpdbf)
reslist0 = get_reslist(mol0, resids0)
mol, atids, resids = get_atominfo_fpdb(orpdbf)
#rename the residue names into AMBER style, e.g. HIS --> HID, HIP, HIE
mol = rename_res(mol, atids)
#get the disulfur bond information
disul = get_diS_bond(mol, atids)
#resname the old residue names to new ones if it is not metal ion
if model in [1, 2]:
metcenres1 = [] #Old residue ids
fp = open(stfpf, 'r')
for line in fp:
if line[0:4] != "LINK":
line = line.split('-')
if int(line[0]) not in metcenres1:
metcenres1.append(int(line[0]))
fp.close()
metcenres2 = mcresname #New residue names
resndict = {}
resns = []
for i in range(0, len(metcenres1)):
resndict[metcenres1[i]] = metcenres2[i]
resns.append(metcenres2[i])
for i in resndict.keys():
mol.residues[i].resname = resndict[i]
writepdb(mol, atids, fipdbf)
#----------------------------get the atom names which changed atom type
if model in [1, 2]:
atomdefs = {}
fp0 = open(stfpf, 'r')
for line in fp0:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split()
if line[2] != line[4]:
atnewtype = line[4]
element = mol.atoms[int(line[1])].element
if atnewtype not in atomdefs.keys():
atomdefs[atnewtype] = element
else:
if element != atomdefs[atnewtype]:
raise pymsmtError('There are atoms in fingerprint file '
'of standard model with same atom type '
'but different element.')
fp0.close()
#---------------------Get the bond information, mol2 is the standard model
if model == 1:
mol2, atids2, resids2 = get_atominfo_fpdb(stpdbf)
blist = get_mc_blist(mol2, atids2, ionids, stfpf)
blist1 = [(i[0], i[1]) for i in blist]
#----------------------Generate the lib file and get the frcmod file name
if model == 2:
frcmodfs = []
for ionmol2f in ionmol2fs:
ionmol, ionatids, ionresids = get_atominfo(ionmol2f)
for i in ionatids:
element = ionmol.atoms[i].element
chg = int(ionmol.atoms[i].charge)
frcmodf = get_frcmod_fname(element, chg, watermodel, paraset)
if frcmodf not in frcmodfs:
frcmodfs.append(frcmodf)
elif model == 3 and ioninf != []:
#get the metal information
metresns = ioninf[0::4]
metatns = ioninf[1::4]
metelmts = ioninf[2::4]
metelmts = [i[0] + i[1:].lower() for i in metelmts]
metchgs = ioninf[3::4]
metchgs = [int(i) for i in metchgs]
#check the charge of the metal ions
for metchg in metchgs:
if metchg < -1 or metchg > 4:
raise pymsmtError('Could not deal with atomic ion which has charge '
'less than -1 or bigger than +4.')
frcmodfs = []
for i in range(0, len(metresns)):
if metchgs[i] > 1: #if it is -1 or +1 ions, no need to create the lib file
gene_ion_libfile(metresns[i], metatns[i], metelmts[i], metchgs[i])
frcmodf = get_frcmod_fname(metelmts[i], metchgs[i], watermodel, paraset)
if frcmodf not in frcmodfs:
frcmodfs.append(frcmodf)
#-----------------------Generate the leap input file-----------------------
print 'Generating the leap input file...'
##Generate the tleap.in file
lp = open(ileapf, 'w')
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff10']:
print >> lp, 'source oldff/leaprc.%s' %ff_choice
elif ff_choice in ['ff03.r1', 'ff12SB', 'ff14SB']:
print >> lp, 'source leaprc.%s' %ff_choice
print >> lp, 'source leaprc.gaff'
#Add atom types, for bonded model
if model in [1, 2]:
if atomdefs.keys() != []:
print >> lp, 'addAtomTypes {'
for i in atomdefs.keys():
print >> lp, ' { "%s" "%s" "sp3" }' %(i, atomdefs[i])
print >> lp, '}'
#load lib and frcmod files for monovalent ions (for salt)
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff03.r1']:
print >> lp, 'loadoff atomic_ions.lib'
print >> lp, 'loadamberparams frcmod.ions1lsm_hfe_%s' %watermodel
#Load mol2 file for the refitting charge residues
if model in [1, 2]:
for i in resns:
print >> lp, '%s = loadmol2 %s.mol2' %(i, i)
elif model == 3:
for i in naamol2fs:
print >> lp, '%s = loadmol2 %s.mol2' %(i, i)
#Load frcmod files for non-standard residues and metal site
for i in frcmodfs:
print >> lp, 'loadamberparams %s' %i
if model == 1:
print >> lp, 'loadamberparams %s' %finfcdf
elif model == 2:
for frcmodf in frcmodfs:
print >> lp, 'loadamberparams %s' %frcmodf
elif model == 3:
for metresn in metresns:
print >> lp, 'loadoff %s.lib' %metresn
for frcmodf in frcmodfs:
print >> lp, 'loadamberparams %s' %frcmodf
#load pdb file
print >> lp, 'mol = loadpdb %s' %fipdbf
##The Disulfur Bond information
if disul != []:
for i in disul:
at1 = i[0]
at2 = i[1]
resid1 = mol.atoms[at1].resid
resid2 = mol.atoms[at2].resid
atname1 = mol.atoms[at1].atname
atname2 = mol.atoms[at2].atname
print >> lp, 'bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2
##Bond including the metal ions
if model == 1:
for bond in blist1:
if list(set(bond) & set(ionids)) != []:
at1 = bond[0]
at2 = bond[1]
resid1 = mol.atoms[at1].resid
resid2 = mol.atoms[at2].resid
atname1 = mol.atoms[at1].atname
atname2 = mol.atoms[at2].atname
print >> lp, 'bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2
##Nonstandard residues with nearby residues
if model in [1, 2]:
bondcmds = []
for i in metcenres1:
resname = mol0.residues[i].resname
print 'Renamed residues includes: ' + str(i) + '-' + resname
if i in reslist0.nterm:
cmdi = 'bond mol.' + str(i) + '.C' + ' mol.' + str(i+i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
elif i in reslist0.cterm:
cmdi = 'bond mol.' + str(i-1) + '.C' + ' mol.' + str(i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
elif i in reslist0.std:
cmdi = 'bond mol.' + str(i-1) + '.C' + ' mol.' + str(i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
cmdi = 'bond mol.' + str(i) + '.C' + ' mol.' + str(i+1) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
for j in bondcmds:
print >> lp, j
#Save dry structure
print >> lp, 'savepdb mol %s_dry.pdb' %gname
print >> lp, 'saveamberparm mol %s_dry.prmtop %s_dry.inpcrd' \
%(gname, gname)
#Solvatebox
if watermodel == 'tip3p':
print >> lp, 'solvatebox mol TIP3PBOX 10.0'
elif watermodel == 'spce':
print >> lp, 'solvatebox mol SPCBOX 10.0'
print >> lp, 'loadamberparams frcmod.spce'
elif watermodel == 'tip4pew':
print >> lp, 'solvatebox mol TIP4PEWBOX 10.0'
print >> lp, 'loadamberparams frcmod.tip4pew'
#Add counter ions
print >> lp, 'addions mol Na+ 0'
print >> lp, 'addions mol Cl- 0'
#Save solvated structure
print >> lp, 'savepdb mol %s_solv.pdb' %gname
print >> lp, 'saveamberparm mol %s_solv.prmtop %s_solv.inpcrd' \
%(gname, gname)
print >> lp, 'quit'
print >> lp, ' '
lp.close()
print 'Finish generating the leap input file.'
def gene_leaprc(gname, orpdbf, fipdbf, stpdbf, stfpf, ionids,\
ionmol2fs, ioninf, mcresname, naamol2fs, ff_choice, frcmodfs,
finfcdf, ileapf, model, watermodel='tip3p', paraset='cm'):
print "******************************************************************"
print "* *"
print "*=================Generating input file for leap=================*"
print "* *"
print "******************************************************************"
#---------------------Generate the new pdb file--------------------------
#mol0 is the old mol while mol is new mol file with new names
mol0, atids0, resids0 = get_atominfo_fpdb(orpdbf)
reslist0 = get_reslist(mol0, resids0)
mol, atids, resids = get_atominfo_fpdb(orpdbf)
#rename the residue names into AMBER style, e.g. HIS --> HID, HIP, HIE
mol = rename_res(mol, atids)
#get the disulfur bond information
disul = get_diS_bond(mol, atids)
#resname the old residue names to new ones if it is not metal ion
if model in [1, 2]:
metcenres1 = [] #Old residue ids
fp = open(stfpf, 'r')
for line in fp:
if line[0:4] != "LINK":
line = line.split('-')
if int(line[0]) not in metcenres1:
metcenres1.append(int(line[0]))
fp.close()
metcenres2 = mcresname #New residue names
resndict = {}
resns = []
for i in range(0, len(metcenres1)):
resndict[metcenres1[i]] = metcenres2[i]
resns.append(metcenres2[i])
for i in resndict.keys():
mol.residues[i].resname = resndict[i]
writepdb(mol, atids, fipdbf)
#----------------------------get the atom names which changed atom type
if model in [1, 2]:
atomdefs = {}
fp0 = open(stfpf, 'r')
for line in fp0:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split()
if line[2] != line[4]:
atnewtype = line[4]
element = mol.atoms[int(line[1])].element
if atnewtype not in atomdefs.keys():
atomdefs[atnewtype] = element
else:
if element != atomdefs[atnewtype]:
raise pymsmtError(
'There are atoms in fingerprint file '
'of standard model with same atom type '
'but different element.')
fp0.close()
#---------------------Get the bond information, mol2 is the standard model
if model == 1:
mol2, atids2, resids2 = get_atominfo_fpdb(stpdbf)
blist = get_mc_blist(mol2, atids2, ionids, stfpf)
blist1 = [(i[0], i[1]) for i in blist]
#----------------------Generate the lib file and get the frcmod file name
if model == 2:
frcmodfs = []
for ionmol2f in ionmol2fs:
ionmol, ionatids, ionresids = get_atominfo(ionmol2f)
for i in ionatids:
element = ionmol.atoms[i].element
chg = int(ionmol.atoms[i].charge)
frcmodf = get_frcmod_fname(element, chg, watermodel, paraset)
if frcmodf not in frcmodfs:
frcmodfs.append(frcmodf)
elif model == 3 and ioninf != []:
#get the metal information
metresns = ioninf[0::4]
metatns = ioninf[1::4]
metelmts = ioninf[2::4]
metelmts = [i[0] + i[1:].lower() for i in metelmts]
metchgs = ioninf[3::4]
metchgs = [int(i) for i in metchgs]
#check the charge of the metal ions
for metchg in metchgs:
if metchg < -1 or metchg > 4:
raise pymsmtError(
'Could not deal with atomic ion which has charge '
'less than -1 or bigger than +4.')
frcmodfs = []
for i in range(0, len(metresns)):
if metchgs[
i] > 1: #if it is -1 or +1 ions, no need to create the lib file
gene_ion_libfile(metresns[i], metatns[i], metelmts[i],
metchgs[i])
frcmodf = get_frcmod_fname(metelmts[i], metchgs[i], watermodel,
paraset)
if frcmodf not in frcmodfs:
frcmodfs.append(frcmodf)
#-----------------------Generate the leap input file-----------------------
print 'Generating the leap input file...'
##Generate the tleap.in file
lp = open(ileapf, 'w')
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff10']:
print >> lp, 'source oldff/leaprc.%s' % ff_choice
elif ff_choice in ['ff03.r1', 'ff12SB', 'ff14SB']:
print >> lp, 'source leaprc.%s' % ff_choice
print >> lp, 'source leaprc.gaff'
#Add atom types, for bonded model
if model in [1, 2]:
if atomdefs.keys() != []:
print >> lp, 'addAtomTypes {'
for i in atomdefs.keys():
print >> lp, ' { "%s" "%s" "sp3" }' % (i, atomdefs[i])
print >> lp, '}'
#load lib and frcmod files for monovalent ions (for salt)
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff03.r1']:
print >> lp, 'loadoff atomic_ions.lib'
print >> lp, 'loadamberparams frcmod.ions1lsm_hfe_%s' % watermodel
#Load mol2 file for the refitting charge residues
if model in [1, 2]:
for i in resns:
print >> lp, '%s = loadmol2 %s.mol2' % (i, i)
elif model == 3:
for i in naamol2fs:
print >> lp, '%s = loadmol2 %s.mol2' % (i, i)
#Load frcmod files for non-standard residues and metal site
for i in frcmodfs:
print >> lp, 'loadamberparams %s' % i
if model == 1:
print >> lp, 'loadamberparams %s' % finfcdf
elif model == 2:
for frcmodf in frcmodfs:
print >> lp, 'loadamberparams %s' % frcmodf
elif model == 3:
for metresn in metresns:
print >> lp, 'loadoff %s.lib' % metresn
for frcmodf in frcmodfs:
print >> lp, 'loadamberparams %s' % frcmodf
#load pdb file
print >> lp, 'mol = loadpdb %s' % fipdbf
##The Disulfur Bond information
if disul != []:
for i in disul:
at1 = i[0]
at2 = i[1]
resid1 = mol.atoms[at1].resid
resid2 = mol.atoms[at2].resid
atname1 = mol.atoms[at1].atname
atname2 = mol.atoms[at2].atname
print >> lp, 'bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2
##Bond including the metal ions
if model == 1:
for bond in blist1:
if list(set(bond) & set(ionids)) != []:
at1 = bond[0]
at2 = bond[1]
resid1 = mol.atoms[at1].resid
resid2 = mol.atoms[at2].resid
atname1 = mol.atoms[at1].atname
atname2 = mol.atoms[at2].atname
print >> lp, 'bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2
##Nonstandard residues with nearby residues
if model in [1, 2]:
bondcmds = []
for i in metcenres1:
resname = mol0.residues[i].resname
print 'Renamed residues includes: ' + str(i) + '-' + resname
if i in reslist0.nterm:
cmdi = 'bond mol.' + str(i) + '.C' + ' mol.' + str(i +
i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
elif i in reslist0.cterm:
cmdi = 'bond mol.' + str(i -
1) + '.C' + ' mol.' + str(i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
elif i in reslist0.std:
cmdi = 'bond mol.' + str(i -
1) + '.C' + ' mol.' + str(i) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
cmdi = 'bond mol.' + str(i) + '.C' + ' mol.' + str(i +
1) + '.N'
if cmdi not in bondcmds:
bondcmds.append(cmdi)
for j in bondcmds:
print >> lp, j
#Save dry structure
print >> lp, 'savepdb mol %s_dry.pdb' % gname
print >> lp, 'saveamberparm mol %s_dry.prmtop %s_dry.inpcrd' \
%(gname, gname)
#Solvatebox
if watermodel == 'tip3p':
print >> lp, 'solvatebox mol TIP3PBOX 10.0'
elif watermodel == 'spce':
print >> lp, 'solvatebox mol SPCBOX 10.0'
print >> lp, 'loadamberparams frcmod.spce'
elif watermodel == 'tip4pew':
print >> lp, 'solvatebox mol TIP4PEWBOX 10.0'
print >> lp, 'loadamberparams frcmod.tip4pew'
#Add counter ions
print >> lp, 'addions mol Na+ 0'
print >> lp, 'addions mol Cl- 0'
#Save solvated structure
print >> lp, 'savepdb mol %s_solv.pdb' % gname
print >> lp, 'saveamberparm mol %s_solv.prmtop %s_solv.inpcrd' \
%(gname, gname)
print >> lp, 'quit'
print >> lp, ' '
lp.close()
print 'Finish generating the leap input file.'