def Boss2CharmmRTF(num2typ2symb, Qs, resid, bnd_df, angs,props,imps):
charges = [float(Qs[i][1]) for i in range(len(Qs))]
rtf = open(resid + '.top', 'w+')
rtf.write('Remarks LigParGen generated XPLOR-TOP file for Bonvin group (by Leela Dodda)\n')
rtf.write('\nset echo=false end\n')
rtf.write('\nautogenerate angles=True dihedrals=True end\n')
rtf.write('{ atomType mass }\n')
Mass = ['MASS %s %3.4f \n' % (num2typ2symb[i][2], bossElement2Mass(bossPdbAtom2Element(num2typ2symb[i][0]))) for i in range(len(Qs))]
for i in range(len(Mass)):
rtf.write('%s' % Mass[i])
rtf.write('\nRESIdue %5s\n' % (resid))
rtf.write('\nGROUP\n')
rtf.write('\n{ atomName atomType Charge } \n')
for i in range(len(Qs)):
rtf.write('ATOM %6s TYPE= %6s CHARGE= %8s END\n' % (num2typ2symb[i][0], bossPdbAtom2Element(
num2typ2symb[i][0]) + num2typ2symb[i][1][-3:], Qs[i][1]))
rtf.write('\n{ Bonds: atomName1 atomName2 } \n')
for (x, y) in zip(bnd_df.cl1, bnd_df.cl2):
rtf.write('BOND %s %s \n' % (num2typ2symb[x][0], num2typ2symb[y][0]))
rtf.write('\n{ Angles: atomName1 atomName2 atomName3} \n')
for a in angs: rtf.write('ANGLe %s \n'%a)
rtf.write('\n{ Proper Dihedrals: aName1 aName2 aName3 aName4 } \n')
for i in props:
rtf.write('DIHEdral %s \n' % (i.replace("-", " ")))
rtf.write('\n{ Improper Dihedrals: aName1 aName2 aName3 aName4 }\n')
for i in imps:
rtf.write('IMPRoper %s \n' % (i.replace("-", " ")))
rtf.write('\nEND {RESIdue UNK}\n')
rtf.write('\nset echo=true end\n')
rtf.close()
return None
def Boss2CharmmRTF(num2typ2symb, Qs, resid, bnd_df, imps):
charges = [float(Qs[i][1]) for i in range(len(Qs))]
rtf = open(resid + '.rtf', 'w+')
rtf.write(
'! generated RTF file for NAMD/CHARMM \n! Written by Leela S. Dodda ([email protected])\n'
)
Mass = [
'MASS %d %s %3.4f %s \n' %
((i + 1), num2typ2symb[i][2],
bossElement2Mass(bossPdbAtom2Element(
num2typ2symb[i][0])), bossPdbAtom2Element(num2typ2symb[i][0]))
for i in range(len(Qs))
]
for i in range(len(Mass)):
rtf.write('%s' % Mass[i])
rtf.write('AUTO ANGLES DIHE \n')
rtf.write('RESI %5s %3.3f \n' % (resid, sum(charges)))
for i in range(len(Qs)):
rtf.write(
'ATOM %s %s %s \n' %
(num2typ2symb[i][0], bossPdbAtom2Element(num2typ2symb[i][0]) +
num2typ2symb[i][1][-3:], Qs[i][1]))
for (x, y) in zip(bnd_df.cl1, bnd_df.cl2):
rtf.write('BOND %s %s \n' % (num2typ2symb[x][0], num2typ2symb[y][0]))
for i in imps:
rtf.write('IMPR %s \n' % (i.replace("-", " ")))
rtf.write('PATCH FIRST NONE LAST NONE \n')
rtf.write('END \n')
rtf.close()
return None
def bossData(molecule_data):
ats_file = molecule_data.MolData['ATOMS']
types = []
for i in enumerate(ats_file):
types.append([i[1].split()[1], 'opls_' + i[1].split()[2]])
st_no = 3
Qs = molecule_data.MolData['Q_LJ']
assert len(Qs) == len(types), 'Please check the at_info and Q_LJ_dat files'
# num2opls = {}
# for i in range(0, len(types)):
# num2opls[i] = Qs[i][0]
num2typ2symb = {i: types[i] for i in range(len(Qs))}
for i in range(len(Qs)):
num2typ2symb[i].append(
bossPdbAtom2Element(num2typ2symb[i][0]) + num2typ2symb[i][1][-3:])
# print(num2typ2symb[i],bossElement2Mass(num2typ2symb[i][0]))
num2typ2symb[i].append(bossPdbAtom2Element(num2typ2symb[i][0]))
num2typ2symb[i].append(bossElement2Mass(num2typ2symb[i][3]))
num2typ2symb[i].append(Qs[i][0])
num2opls = {}
for i in num2typ2symb.keys():
num2opls[i] = num2typ2symb[i][2]
# return (types, Qs, num2opls, st_no, num2typ2symb)
num2pqrtype = OrderedDict(num2typ2symb)
for i in range(len(Qs)):
num2pqrtype[i].append(Qs[i][1])
num2pqrtype[i].append(Qs[i][2])
return (types, Qs, num2opls, st_no, num2typ2symb, num2pqrtype)
def Boss2CharmmRTF(num2typ2symb, Qs, resid, bnd_df, angs, props, imps):
charges = [float(Qs[i][1]) for i in range(len(Qs))]
rtf = open(resid + '.lib', 'w+')
rtf.write('#Remarks LigParGen generated for Q (by Leela Dodda)\n')
rtf.write('\n{%s}\n' % resid)
rtf.write('[ atoms ]\n')
for i in range(len(Qs)):
rtf.write(
'%8d %6s %6s %8s \n' %
(i + 1, num2typ2symb[i][0], bossPdbAtom2Element(num2typ2symb[i][0])
+ num2typ2symb[i][1][-3:], Qs[i][1]))
rtf.write('[bonds]')
for (x, y) in zip(bnd_df.cl1, bnd_df.cl2):
rtf.write('\n%8s %8s' % (num2typ2symb[x][0], num2typ2symb[y][0]))
rtf.write('\n[impropers]\n')
for i in imps:
rtf.write('%s \n' % (i.replace("-", " ")))
rtf.write('[charge_groups]\n')
for i in range(len(Qs)):
rtf.write('%4s' % num2typ2symb[i][0])
rtf.write(
'\n*------------------------------------------------------------------\n'
)
rtf.close()
return None
def bossData(molecule_data):
ats_file = molecule_data.MolData['ATOMS']
types = []
for i in enumerate(ats_file):
types.append([i[1].split()[1], 'opls_' + i[1].split()[2]])
st_no = 3
Qs = molecule_data.MolData['Q_LJ']
assert len(Qs) == len(types), 'Please check the at_info and Q_LJ_dat files'
num2opls = {}
for i in range(0, len(types)):
num2opls[i] = Qs[i][0]
num2typ2symb = {i: types[i] for i in range(len(Qs))}
for i in range(len(Qs)):
trm = bossPdbAtom2Element(num2typ2symb[i][0]) + num2typ2symb[i][1][-3:]
num2typ2symb[i].append(trm[0:4])
num2typ2symb[i].append(bossPdbAtom2Element(num2typ2symb[i][0]))
num2typ2symb[i].append(bossElement2Mass(num2typ2symb[i][3]))
num2typ2symb[i].append(Qs[i][0])
return (types, Qs, num2opls, st_no, num2typ2symb)
def Boss2CharmmPRM(resid, num2typ2symb, Qs, bnd_df, ang_df, tor_df):
#### COLLECTING NONBONDING PART #######
prm = open(resid + '.Q.prm', 'w+')
prm.write(
'# LigParGen generated Q-PARAM file for Aqvist group (by Leela Dodda)\n'
)
prm.write('\n[options]\n')
prm.write('\n[atom_types]\n')
for i in range(len(Qs)):
eps = float(Qs[i][3])
sig = float(Qs[i][2])
ALJ = 2 * sig**6 * np.sqrt(eps)
BLJ = 2 * sig**3 * np.sqrt(eps)
prm.write('%4s %10.4f %10.4f %10.4f %10.4f %10.4f %10.4f\n' %
(num2typ2symb[i][2], ALJ, ALJ, 0.000, BLJ, BLJ,
bossElement2Mass(bossPdbAtom2Element(num2typ2symb[i][0]))))
prm.write('\n[bonds]\n')
for i in bnd_df.index:
prm.write(
'%s %6s %8.1f %8.4f \n' %
(num2typ2symb[bnd_df.cl1[i]][2], num2typ2symb[bnd_df.cl2[i]][2],
bnd_df.KIJ[i], bnd_df.RIJ[i]))
prm.write('\n[angles]\n')
for i in ang_df.index:
prm.write(
'%s %5s %5s %8.1f %8.2f \n' %
(num2typ2symb[ang_df.cl1[i]][2], num2typ2symb[ang_df.cl2[i]][2],
num2typ2symb[ang_df.cl3[i]][2], ang_df.K[i], ang_df.R[i]))
prm.write('\n[torsions]\n')
if len(tor_df.index) > 0:
tor_df = tor_df.drop_duplicates(['NAME', 'TY'])
pro_df = tor_df[tor_df.TY == 'Proper']
for i in list(pro_df.index):
ndf = pro_df.ix[i]
pro_out = retDihed(ndf.to_dict())
for i in range(4):
prm.write('%s' % pro_out[i])
prm.write(
' X X X X 0.00000 1 0.000000 ! WILD CARD FOR MISSING TORSION PARAMETERS\n'
)
prm.write('\n[impropers]\n')
imp_df = tor_df[tor_df.TY == 'Improper']
for i in list(imp_df.index):
ndf = tor_df.ix[i]
imp_out = retDihedImp(ndf.to_dict())
for i in range(len(imp_out)):
prm.write('%s' % imp_out[i])
prm.write(
' X X X X 0.00000 2 0.000000 ! WILD CARD FOR MISSING IMPROPER PARAMETERS \n'
)
prm.close()
return None
def Boss2CharmmRTF(num2typ2symb, Qs, resid, bnd_df, angs, props, imps):
charges = [float(Qs[i][1]) for i in range(len(Qs))]
rtf = open(resid + '.top', 'w+')
rtf.write(
'Remarks generated XPLOR-TOP file for Bonvin group (by Leela Dodda)\n')
rtf.write('\nset echo=false end\n')
rtf.write('\nautogenerate angles=True dihedrals=True end\n')
rtf.write('{ atomType mass }\n')
Mass = [
'MASS %s %3.4f \n' %
(num2typ2symb[i][2],
bossElement2Mass(bossPdbAtom2Element(num2typ2symb[i][0])))
for i in range(len(Qs))
]
for i in range(len(Mass)):
rtf.write('%s' % Mass[i])
rtf.write('\nRESIdue %5s\n' % (resid))
rtf.write('\nGROUP\n')
rtf.write('\n{ atomName atomType Charge } \n')
for i in range(len(Qs)):
rtf.write('ATOM %6s TYPE= %6s CHARGE= %8s END\n' %
(num2typ2symb[i][0], num2typ2symb[i][2], Qs[i][1]))
rtf.write('\n{ Bonds: atomName1 atomName2 } \n')
for (x, y) in zip(bnd_df.cl1, bnd_df.cl2):
rtf.write('BOND %s %s \n' % (num2typ2symb[x][0], num2typ2symb[y][0]))
bndlist = list(bnd_df.UR) + list(bnd_df.UR)
imp_list = []
for i, dat in imps.iterrows():
ndata = tor_cent([dat.I, dat.J, dat.K, dat.L], bndlist)
sdata = [num2typ2symb[j][0] for j in ndata]
imp_list.append('-'.join(sdata))
rtf.write('\n{ Improper Dihedrals: aName1 aName2 aName3 aName4 }\n')
for i in imp_list:
rtf.write('IMPRoper %s \n' % (i.replace("-", " ")))
rtf.write('\nEND {RESIdue UNK}\n')
rtf.write('\nset echo=true end\n')
rtf.close()
return None
