def get_lib_dict(ff_choice):
if ff_choice in list(FF_DICT.keys()):
mol, atids, resids = get_atominfo(FF_DICT[ff_choice].mol2f)
else:
mol, atids, resids = get_atominfo(ff_choice)
libdict = {} #resname + atname : atom type, atom charge
chargedict = {} #resname : charge
for i in resids:
charge = 0.0
for j in mol.residues[i].resconter:
#key is residue name and atom name
key = mol.residues[i].resname + '-' + mol.atoms[j].atname
if len(mol.atoms[j].atomtype) == 1:
mol.atoms[j].atomtype = mol.atoms[j].atomtype + ' '
#value is atom type and atom charge
val = (mol.atoms[j].atomtype, mol.atoms[j].charge)
libdict[key] = val
#cummulative charge of the residue
charge = charge + mol.atoms[j].charge
chargedict[mol.residues[i].resname] = charge
#Alias HN as H
#atnames = [mol.atoms[k].atname for k in mol.residues[i].resconter]
#if set(['H', 'N', 'C', 'O']) < set(atnames):
# libdict[mol.residues[i].resname + '-HN'] = \
# libdict[mol.residues[i].resname + '-H']
return libdict, chargedict
def get_lib_dict(parms):
global add
if parms in ['ff94', 'ff99', 'ff99SB']:
mol, atids, resids = get_atominfo(add + 'parm94.mol2')
elif (parms == 'ff03'):
mol, atids, resids = get_atominfo(add + 'parm03.mol2')
elif (parms == 'ff03.r1'):
mol, atids, resids = get_atominfo(add + 'parm03_r1.mol2')
elif (parms == 'ff10'):
mol, atids, resids = get_atominfo(add + 'parm10.mol2')
elif parms in ['ff12SB', 'ff14SB']:
mol, atids, resids = get_atominfo(add + 'parm12.mol2')
else:
mol, atids, resids = get_atominfo(parms)
libdict = {} #resname + atname : atom type, atom charge
chargedict = {} #resname : charge
for i in resids:
charge = 0.0
for j in mol.residues[i].resconter:
#key is residue name and atom name
key = mol.residues[i].resname + '-' + mol.atoms[j].atname
if len(mol.atoms[j].atomtype) == 1:
mol.atoms[j].atomtype = mol.atoms[j].atomtype + ' '
#value is atom type and atom charge
val = (mol.atoms[j].atomtype, mol.atoms[j].charge)
libdict[key] = val
#cummulative charge of the residue
charge = charge + mol.atoms[j].charge
chargedict[mol.residues[i].resname] = charge
#Alias HN as H
#atnames = [mol.atoms[k].atname for k in mol.residues[i].resconter]
#if set(['H', 'N', 'C', 'O']) < set(atnames):
# libdict[mol.residues[i].resname + '-HN'] = \
# libdict[mol.residues[i].resname + '-H']
return libdict, chargedict
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('source oldff/leaprc.%s' %ff_choice, file=lp)
elif ff_choice in ['ff03.r1', 'ff12SB', 'ff14SB']:
print('source leaprc.%s' %ff_choice, file=lp)
print('source leaprc.gaff', file=lp)
#Add atom types, for bonded model
if model in [1, 2]:
if atomdefs.keys() != []:
print('addAtomTypes {', file=lp)
for i in sorted(list(atomdefs.keys())):
print(' { "%s" "%s" "sp3" }' %(i, atomdefs[i]), file=lp)
print('}', file=lp)
#load lib and frcmod files for monovalent ions (for salt)
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff03.r1']:
print('loadoff atomic_ions.lib', file=lp)
print('loadamberparams frcmod.ions1lsm_hfe_%s' %watermodel, file=lp)
#Load mol2 file for the refitting charge residues
if model in [1, 2]:
for i in resns:
print('%s = loadmol2 %s.mol2' %(i, i), file=lp)
elif model == 3:
for i in naamol2fs:
print('%s = loadmol2 %s.mol2' %(i, i), file=lp)
#Load frcmod files for non-standard residues and metal site
for i in frcmodfs:
print('loadamberparams %s' %i, file=lp)
if model == 1:
print('loadamberparams %s' %finfcdf, file=lp)
elif model == 2:
for frcmodf in frcmodfs:
print('loadamberparams %s' %frcmodf, file=lp)
elif model == 3:
for metresn in metresns:
print('loadoff %s.lib' %metresn, file=lp)
for frcmodf in frcmodfs:
print('loadamberparams %s' %frcmodf, file=lp)
#load pdb file
print('mol = loadpdb %s' %fipdbf, file=lp)
##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('bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2, file=lp)
##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('bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2, file=lp)
##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(j, file=lp)
#Save dry structure
print('savepdb mol %s_dry.pdb' %gname, file=lp)
print('saveamberparm mol %s_dry.prmtop %s_dry.inpcrd' \
%(gname, gname), file=lp)
#Solvatebox
if watermodel == 'tip3p':
print('solvatebox mol TIP3PBOX 10.0', file=lp)
elif watermodel == 'spce':
print('solvatebox mol SPCBOX 10.0', file=lp)
print('loadamberparams frcmod.spce', file=lp)
elif watermodel == 'tip4pew':
print('solvatebox mol TIP4PEWBOX 10.0', file=lp)
print('loadamberparams frcmod.tip4pew', file=lp)
#Add counter ions
print('addions mol Na+ 0', file=lp)
print('addions mol Cl- 0', file=lp)
#Save solvated structure
print('savepdb mol %s_solv.pdb' %gname, file=lp)
print('saveamberparm mol %s_solv.prmtop %s_solv.inpcrd' \
%(gname, gname), file=lp)
print('quit', file=lp)
print(' ', file=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('source oldff/leaprc.%s' % ff_choice, file=lp)
elif ff_choice in ['ff03.r1', 'ff12SB', 'ff14SB']:
print('source leaprc.%s' % ff_choice, file=lp)
print('source leaprc.gaff', file=lp)
#Add atom types, for bonded model
if model in [1, 2]:
if atomdefs.keys() != []:
print('addAtomTypes {', file=lp)
for i in sorted(list(atomdefs.keys())):
print(' { "%s" "%s" "sp3" }' % (i, atomdefs[i]),
file=lp)
print('}', file=lp)
#load lib and frcmod files for monovalent ions (for salt)
if ff_choice in ['ff94', 'ff99', 'ff99SB', 'ff03', 'ff03.r1']:
print('loadoff atomic_ions.lib', file=lp)
print('loadamberparams frcmod.ions1lsm_hfe_%s' % watermodel, file=lp)
#Load mol2 file for the refitting charge residues
if model in [1, 2]:
for i in resns:
print('%s = loadmol2 %s.mol2' % (i, i), file=lp)
elif model == 3:
for i in naamol2fs:
print('%s = loadmol2 %s.mol2' % (i, i), file=lp)
#Load frcmod files for non-standard residues and metal site
for i in frcmodfs:
print('loadamberparams %s' % i, file=lp)
if model == 1:
print('loadamberparams %s' % finfcdf, file=lp)
elif model == 2:
for frcmodf in frcmodfs:
print('loadamberparams %s' % frcmodf, file=lp)
elif model == 3:
for metresn in metresns:
print('loadoff %s.lib' % metresn, file=lp)
for frcmodf in frcmodfs:
print('loadamberparams %s' % frcmodf, file=lp)
#load pdb file
print('mol = loadpdb %s' % fipdbf, file=lp)
##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('bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2, file=lp)
##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('bond', 'mol.' + str(resid1) + '.' + atname1, 'mol.' + \
str(resid2) + '.' + atname2, file=lp)
##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(j, file=lp)
#Save dry structure
print('savepdb mol %s_dry.pdb' % gname, file=lp)
print('saveamberparm mol %s_dry.prmtop %s_dry.inpcrd' \
%(gname, gname), file=lp)
#Solvatebox
if watermodel == 'tip3p':
print('solvatebox mol TIP3PBOX 10.0', file=lp)
elif watermodel == 'spce':
print('solvatebox mol SPCBOX 10.0', file=lp)
print('loadamberparams frcmod.spce', file=lp)
elif watermodel == 'tip4pew':
print('solvatebox mol TIP4PEWBOX 10.0', file=lp)
print('loadamberparams frcmod.tip4pew', file=lp)
#Add counter ions
print('addions mol Na+ 0', file=lp)
print('addions mol Cl- 0', file=lp)
#Save solvated structure
print('savepdb mol %s_solv.pdb' % gname, file=lp)
print('saveamberparm mol %s_solv.prmtop %s_solv.inpcrd' \
%(gname, gname), file=lp)
print('quit', file=lp)
print(' ', file=lp)
lp.close()
print('Finish generating the leap input file.')