def boss2opmTorsion(bnd_df, num2opls, st_no, molecule_data, itpf):
dhd = []
for line in molecule_data.MolData['TORSIONS']:
# dt = np.genfromtxt(line, dtype='f8')
dt = [float(f) for f in line]
dhd.append(dt)
dhd = np.array(dhd)
dhd = dhd * 4.184 # kcal to kj conversion
dhd = dhd # Komm = Vopls/2
dhd_df = pd.DataFrame(dhd, columns=['V1', 'V2', 'V3', 'V4'])
ats = []
for line in molecule_data.MolData['ATOMS'][3:]:
dt = [
line.split()[0],
line.split()[4],
line.split()[6],
line.split()[8]
]
# dt = map(int, dt)
dt = [int(d) for d in dt]
ats.append(dt)
for line in molecule_data.MolData['ADD_DIHED']:
# dt = map(int, line)
dt = [int(l) for l in line]
ats.append(dt)
assert len(ats) == len(
dhd), 'Number of Dihedral angles in Zmatrix and Out file dont match'
ats = np.array(ats) - st_no
for i in range(len(ats)):
for j in range(len(ats[0])):
if ats[i][j] < 0:
ats[i][j] = 0
at_df = pd.DataFrame(ats, columns=['I', 'J', 'K', 'L'])
final_df = pd.concat([dhd_df, at_df], axis=1, join_axes=[at_df.index])
bndlist = list(bnd_df.UR) + (list(bnd_df.UR))
final_df['TY'] = [
'Proper' if ucomb(
list([final_df.I[n], final_df.J[n], final_df.K[n], final_df.L[n]]),
bndlist) == 3 else 'Improper' for n in range(len(final_df.I))
]
final_df['SumV'] = np.abs(final_df.V1) + np.abs(final_df.V2) + np.abs(
final_df.V3) + np.abs(final_df.V4)
# final_df = final_df[final_df['SumV'] != 0.00]
final_df['TI'] = [num2opls[j] for j in final_df.I]
final_df['TJ'] = [num2opls[j] for j in final_df.J]
final_df['TK'] = [num2opls[j] for j in final_df.K]
final_df['TL'] = [num2opls[j] for j in final_df.L]
if len(final_df.index) > 0:
final_df['NAME'] = final_df.TI + '-' + final_df.TJ + \
'-' + final_df.TK + '-' + final_df.TL
final_df = final_df.sort_values(['NAME'])
# final_df.to_csv('bos_torsions.csv', index=False)
tor_bos = final_df.drop(['I', 'J', 'K', 'L', 'TI', 'TJ', 'TK', 'TL'],
1)
tor_bos = tor_bos.drop_duplicates()
df = final_df.ix[tor_bos.index]
return final_df, df
else:
return final_df, final_df
def Boss2CharmmTorsion(bnd_df, num2opls, st_no, molecule_data, num2typ2symb):
# print num2opls
dhd = []
for line in molecule_data.MolData['TORSIONS']:
dt = [float(l) for l in line]
dhd.append(dt)
dhd = np.array(dhd)
dhd = dhd # kcal to kj conversion
dhd = dhd / 2.0 # Komm = Vopls/2
dhd_df = pd.DataFrame(dhd, columns=['V1', 'V2', 'V3', 'V4'])
ats = []
for line in molecule_data.MolData['ATOMS'][3:]:
dt = [
line.split()[0],
line.split()[4],
line.split()[6],
line.split()[8]
]
dt = [int(d) for d in dt]
ats.append(dt)
for line in molecule_data.MolData['ADD_DIHED']:
dt = [int(l) for l in line]
ats.append(dt)
assert len(ats) == len(
dhd), 'Number of Dihedral angles in Zmatrix and Out file dont match'
ats = np.array(ats) - st_no
for i in range(len(ats)):
for j in range(len(ats[0])):
if ats[i][j] < 0:
ats[i][j] = 0
at_df = pd.DataFrame(ats, columns=['I', 'J', 'K', 'L'])
final_df = pd.concat([dhd_df, at_df], axis=1, join_axes=[at_df.index])
bndlist = list(bnd_df.UR) + (list(bnd_df.UR))
final_df['TY'] = [
'Proper' if ucomb(
list([final_df.I[n], final_df.J[n], final_df.K[n], final_df.L[n]]),
bndlist) == 3 else 'Improper' for n in range(len(final_df.I))
]
# final_df['SumV'] = np.abs(
# final_df.V1) + np.abs(final_df.V2) + np.abs(final_df.V3) + np.abs(final_df.V4)
# final_df = final_df[final_df['SumV'] != 0.00]
final_df['TI'] = [num2typ2symb[j][2] for j in final_df.I]
final_df['TJ'] = [num2typ2symb[j][2] for j in final_df.J]
final_df['TK'] = [num2typ2symb[j][2] for j in final_df.K]
final_df['TL'] = [num2typ2symb[j][2] for j in final_df.L]
final_df['SYMB'] = [
' '.join([
num2typ2symb[final_df.I[i]][0], num2typ2symb[final_df.J[i]][0],
num2typ2symb[final_df.K[i]][0], num2typ2symb[final_df.L[i]][0]
]) for i in final_df.index
]
if len(final_df.index) > 0:
final_df['NAME'] = final_df.TI + '-' + final_df.TJ + \
'-' + final_df.TK + '-' + final_df.TL
return final_df
def boss2opmTorsion(bnd_df, num2opls, st_no, molecule_data, xmlf):
dhd = []
for line in molecule_data.MolData['TORSIONS']:
dt = [float(l) for l in line]
dhd.append(dt)
dhd = np.array(dhd)
dhd = dhd * 4.184 # kcal to kj conversion
dhd = dhd / 2.0 # Komm = Vopls/2
dhd_df = pd.DataFrame(dhd, columns=['V1', 'V2', 'V3', 'V4'])
ats = []
for line in molecule_data.MolData['ATOMS'][3:]:
dt = [
line.split()[0],
line.split()[4],
line.split()[6],
line.split()[8]
]
dt = [int(d) for d in dt]
ats.append(dt)
for line in molecule_data.MolData['ADD_DIHED']:
dt = [int(l) for l in line]
ats.append(dt)
assert len(ats) == len(
dhd), 'Number of Dihedral angles in Zmatrix and Out file dont match'
ats = np.array(ats) - st_no
for i in range(len(ats)):
for j in range(len(ats[0])):
if ats[i][j] < 0:
ats[i][j] = 0
at_df = pd.DataFrame(ats, columns=['I', 'J', 'K', 'L'])
final_df = pd.concat([dhd_df, at_df], axis=1, join_axes=[at_df.index])
bndlist = list(bnd_df.UR) + (list(bnd_df.UR))
final_df['TY'] = [
'Proper' if ucomb(
list([final_df.I[n], final_df.J[n], final_df.K[n], final_df.L[n]]),
bndlist) == 3 else 'Improper' for n in range(len(final_df.I))
]
final_df['SumV'] = np.abs(final_df.V1) + np.abs(final_df.V2) + np.abs(
final_df.V3) + np.abs(final_df.V4)
if len(final_df.index) >= 1:
final_df['TI'] = [num2opls[j] for j in final_df.I]
final_df['TJ'] = [num2opls[j] for j in final_df.J]
final_df['TK'] = [num2opls[j] for j in final_df.K]
final_df['TL'] = [num2opls[j] for j in final_df.L]
final_df['NAME'] = final_df.TI + '-' + final_df.TJ + \
'-' + final_df.TK + '-' + final_df.TL
final_df = final_df.sort_values(['NAME'])
final_df.to_csv('bos_torsions.csv', index=False)
tor_bos = final_df.drop(['I', 'J', 'K', 'L', 'TI', 'TJ', 'TK', 'TL'],
1)
tor_bos = tor_bos.drop_duplicates()
df = final_df.ix[tor_bos.index][[
'TI', 'TJ', 'TK', 'TL', 'V1', 'V2', 'V3', 'V4', 'TY', 'I', 'J',
'K', 'L'
]]
torlist = []
for row in df[df.TY == 'Proper'].iterrows():
index, dat = row
data = dat.tolist()
torlist.append(printDihed(data[0:-4]))
for row in df[df.TY == 'Improper'].iterrows():
index, dat = row
ndata = tor_cent([dat.I, dat.J, dat.K, dat.L], bndlist)
sdata = [num2opls[j] for j in ndata]
vdata = [dat.V1, dat.V2, dat.V3, dat.V4, dat.TY]
if len(set([dat.TI, dat.TJ, dat.TK, dat.TL])) > 3:
torlist.append(printDihed(sdata + vdata))
# fin_list = list(set(torlist))
xmlf.write('<PeriodicTorsionForce>\n')
for npt in torlist:
xmlf.write("%s\n" % npt)
xmlf.write('</PeriodicTorsionForce>\n')
return None
