def gene_by_QM_fitting_zmatrix(smpdbf, 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(smpdbf)
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(smpdbf, 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(smpdbf)
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(smpdbf, ionids, stfpf, pref, finf):
print("******************************************************************")
print("* *")
print("*===========Using the empirical way to solve the problem=========*")
print("* *")
print("******************************************************************")
#Read from small pdb
mol, atids, resids = get_atominfo_fpdb(smpdbf)
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_by_QM_fitting_zmatrix(smpdbf, 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(smpdbf)
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(smpdbf, 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(smpdbf)
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(smpdbf, ionids, stfpf, pref, finf):
print("******************************************************************")
print("* *")
print("*===========Using the empirical way to solve the problem=========*")
print("* *")
print("******************************************************************")
#Read from small pdb
mol, atids, resids = get_atominfo_fpdb(smpdbf)
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')
