def GMX_pairs(tors, ang, bond):
atom_list = np.array(list(bond.cl1) + list(bond.cl2))
atom_list = np.sort(atom_list)
atom_list = np.unique(atom_list)
dict_bond = {
ano:
list(bond[bond.cl1 == ano]['cl2']) + list(bond[bond.cl2 == ano]['cl1'])
for ano in atom_list
}
dict_ang = {}
for ano in atom_list:
tr_1 = []
for bno in dict_bond[ano]:
tr_1 += dict_bond[bno]
tr_1 = list(set(tr_1))
tr_1.remove(ano)
dict_ang[ano] = tr_1
NP_dat = []
for a in dict_bond.keys():
for b in dict_bond[a]:
NP_dat.append([
a, b, 1,
pairing_func(a + 1, b + 1)[0],
pairing_func(a + 1, b + 1)[1]
])
for c in dict_ang[b]:
NP_dat.append([
a, c, 3,
pairing_func(a + 1, c + 1)[0],
pairing_func(a + 1, c + 1)[1]
])
for a in dict_ang.keys():
for b in dict_ang[a]:
NP_dat.append([
a, b, 2,
pairing_func(a + 1, b + 1)[0],
pairing_func(a + 1, b + 1)[1]
])
for c in dict_bond[b]:
NP_dat.append([
a, c, 3,
pairing_func(a + 1, c + 1)[0],
pairing_func(a + 1, c + 1)[1]
])
NP_df = pd.DataFrame(NP_dat, columns=['I', 'J', 'BSEP', 'UNQ', 'TY'])
NP_df = NP_df[NP_df.I != NP_df.J] # CASES WITH 3 MEMBERED RINGS
NP_df = NP_df.sort_values(['UNQ'])
NP_B = NP_df[NP_df.BSEP == 1]
NP_A = NP_df[NP_df.BSEP == 2]
NP_T = NP_df[NP_df.BSEP == 3]
NP_T = NP_T.drop_duplicates(['UNQ'])
NP_T = NP_T[~NP_T.UNQ.isin(NP_B.UNQ)]
NP_T = NP_T[~NP_T.UNQ.isin(NP_A.UNQ)]
# NP_T.to_csv('BOND_ANGS.csv', index=False)
return list(NP_T.TY)
def boss2gmxBond(molecule_data, st_no, itpf):
bdat = molecule_data.MolData['BONDS']
bdat['cl1'] = [x - st_no if not x - st_no < 0 else 0 for x in bdat['cl1']]
bdat['cl2'] = [x - st_no if not x - st_no < 0 else 0 for x in bdat['cl2']]
bnd_df = pd.DataFrame(bdat)
bnd_df['KIJ'] = bnd_df['KIJ']
bnd_df['RIJ'] = bnd_df['RIJ']
bnd_df['UNQ'] = [
pairing_func(i + 1, j + 1)[0] for i, j in zip(bnd_df.cl1, bnd_df.cl2)
]
bnd_df['UNQ'] = [
pairing_func(i, j)[0] for i, j in zip(bnd_df.cl1, bnd_df.cl2)
]
bnd_df['UF'] = ((bnd_df.cl1 + bnd_df.cl2) *
(bnd_df.cl1 + bnd_df.cl2 + 1) * 0.5) + bnd_df.cl2
bnd_df['UR'] = ((bnd_df.cl1 + bnd_df.cl2) *
(bnd_df.cl1 + bnd_df.cl2 + 1) * 0.5) + bnd_df.cl1
connects = []
for (ai, aj) in zip(bnd_df.cl1, bnd_df.cl2):
connects.append("{:>5}{:>5} 1".format(aj + 1, ai + 1))
full_bnd = bnd_df.copy()
bnd_df = bnd_df.drop_duplicates(['TIJ'])
return full_bnd, connects
def boss2desmond(resid, molecule_data, pdb_file):
types, Qs, num2opls, st_no, num2typ2symb = bossData(molecule_data)
itpf = open(resid + '.cms', 'w+')
itpf.write("""{
s_m_m2io_version
:::
2.0.0
}
f_m_ct {
s_m_title
r_chorus_box_ax
r_chorus_box_ay
r_chorus_box_az
r_chorus_box_bx
r_chorus_box_by
r_chorus_box_bz
r_chorus_box_cx
r_chorus_box_cy
r_chorus_box_cz
s_ffio_ct_type
:::
"Desmond file created by (written by Leela S Dodda)"
70.0
0.0
0.0
0.0
70.0
0.0
0.0
0.0
70.0
full_system
m_atom[%d] {
# First column is atom index #
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_residue_number
s_m_pdb_residue_name
i_m_atomic_number
s_m_atom_name
r_ffio_x_vel
r_ffio_y_vel
r_ffio_z_vel
:::
""" % (len(Qs)))
#print(molecule_data.MolData['XYZ'])
xyz = molecule_data.MolData['XYZ']
for i, r in xyz.iterrows():
itpf.write(
' %d %d %10.8f %10.8f %10.8f 1 \"MOL\" %d \"%s\" 0.00000000 0.00000000 0.00000000\n'
% (i + 1, 1, r.X, r.Y, r.Z, r.at_num, r.at_symb))
bnd_df, connects = boss2gmxBond(molecule_data, st_no, itpf)
itpf.write(''' :::
}
m_bond[%d] {
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
''' % (len(bnd_df.index)))
for rb in bnd_df.iterrows():
i, r = rb
itpf.write(' %d %d %d %d %d %d\n' %
(i + 1, r.cl2 + 1, r.cl1 + 1, 1, 1, 1))
itpf.write(''' :::
}
}
f_m_ct {
s_m_title
r_chorus_box_ax
r_chorus_box_ay
r_chorus_box_az
r_chorus_box_bx
r_chorus_box_by
r_chorus_box_bz
r_chorus_box_cx
r_chorus_box_cy
r_chorus_box_cz
s_ffio_ct_type
:::
"MOL"
70.0
0.0
0.0
0.0
70.0
0.0
0.0
0.0
70.0
solute
m_atom[%d] {
# First column is atom index #
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_residue_number
s_m_pdb_residue_name
i_m_atomic_number
s_m_atom_name
r_ffio_x_vel
r_ffio_y_vel
r_ffio_z_vel
:::
''' % (len(Qs)))
xyz = molecule_data.MolData['XYZ']
for i, r in xyz.iterrows():
itpf.write(
' %d %d %10.8f %10.8f %10.8f 1 \"MOL\" %d \"%s\" 0.00000000 0.00000000 0.00000000\n'
% (i + 1, 1, r.X, r.Y, r.Z, r.at_num, r.at_symb))
# bnd_df, connects = boss2gmxBond(molecule_data, st_no, itpf)
itpf.write(''' :::
}
m_bond[%d] {
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
''' % (len(bnd_df.index)))
for rb in bnd_df.iterrows():
i, r = rb
itpf.write(' %d %d %d %d %d %d\n' %
(i + 1, r.cl2 + 1, r.cl1 + 1, 1, 1, 1))
# for i,r in bnd_df.iterrows():itpf.write(' %d %d %d %d %d %d\n'%(i+1,r.cl2+1,r.cl1+1,1,1,1))
itpf.write(''' :::
}
ffio_ff {
s_ffio_name
s_ffio_comb_rule
i_ffio_version
:::
"MOL"
GEOMETRIC
1.0.0
ffio_vdwtypes[%d] {
s_ffio_name
s_ffio_funct
r_ffio_c1
r_ffio_c2
:::
''' % (len(Qs)))
for i in range(len(Qs)):
itpf.write(
' %d %s LJ12_6_sig_epsilon %10.8f %10.8f\n' %
(i + 1, num2typ2symb[i][1], float(Qs[i][2]), float(Qs[i][3])))
itpf.write(''' :::
}
ffio_sites[%d] {
s_ffio_type
r_ffio_charge
r_ffio_mass
s_ffio_vdwtype
i_ffio_resnr
s_ffio_residue
:::
''' % (len(Qs)))
for i in range(len(Qs)):
itpf.write(
' %d atom %10.8f %10.8f %s 1 MOL\n' %
(i + 1, float(Qs[i][1]), num2typ2symb[i][4], num2typ2symb[i][1]))
itpf.write(''' :::
}''')
itpf.write(''' ffio_bonds[%d] {
i_ffio_ai
i_ffio_aj
s_ffio_funct
r_ffio_c1
r_ffio_c2
:::
''' % (len(bnd_df.index)))
EXCLUSIONS_12_13 = {'BI': [], 'BJ': [], 'UID': []}
for rb in bnd_df.iterrows():
i, r = rb
itpf.write(' %d %d %d HARM %10.8f %10.8f\n' %
(i + 1, r.cl2 + 1, r.cl1 + 1, r.RIJ, r.KIJ))
EXCLUSIONS_12_13['BI'].append(int(r.cl1 + 1))
EXCLUSIONS_12_13['BJ'].append(int(r.cl2 + 1))
EXCLUSIONS_12_13['UID'].append(pairing_func(r.cl2 + 1, r.cl1 + 1)[0])
full_ang = boss2gmxAngle(molecule_data.MolData['ANGLES'], num2opls, st_no,
itpf)
itpf.write(''' :::
}
ffio_angles[%d] {
i_ffio_ai
i_ffio_aj
i_ffio_ak
s_ffio_funct
r_ffio_c1
r_ffio_c2
:::
''' % (len(full_ang.index)))
for rb in full_ang.iterrows():
i, r = rb
itpf.write(' %d %d %d %d HARM %10.8f %10.8f\n' %
(i + 1, r.cl1 + 1, r.cl2 + 1, r.cl3 + 1, r.R, r.K))
EXCLUSIONS_12_13['BI'].append(int(r.cl1 + 1))
EXCLUSIONS_12_13['BJ'].append(int(r.cl3 + 1))
EXCLUSIONS_12_13['UID'].append(pairing_func(r.cl3 + 1, r.cl1 + 1)[0])
full_tor, tor_df = boss2opmTorsion(bnd_df, num2opls, st_no, molecule_data,
itpf)
itpf.write(''' :::
}
ffio_dihedrals[%d] {
i_ffio_ai
i_ffio_aj
i_ffio_ak
i_ffio_al
s_ffio_funct
r_ffio_c0
r_ffio_c1
r_ffio_c2
r_ffio_c3
r_ffio_c4
:::
''' % (len(full_tor.index)))
full_tor.index = range(0, len(full_tor.index))
EXCEPTION_14 = {'BI': [], 'BJ': [], 'UID': []}
for rb in full_tor.iterrows():
i, r = rb
if r.TY == 'Proper':
itpf.write(
' %d %d %d %d %d Opls_proper 0 %10.8f %10.8f %10.8f %10.8f\n'
% (i + 1, r.I + 1, r.J + 1, r.K + 1, r.L + 1, r.V1, r.V2, r.V3,
r.V4))
EXCLUSIONS_12_13['BI'].append(int(r.I + 1))
EXCLUSIONS_12_13['BJ'].append(int(r.L + 1))
EXCLUSIONS_12_13['UID'].append(pairing_func(r.I + 1, r.L + 1)[0])
EXCEPTION_14['BI'].append(int(r.I + 1))
EXCEPTION_14['BJ'].append(int(r.L + 1))
EXCEPTION_14['UID'].append(pairing_func(r.I + 1, r.L + 1)[0])
elif r.TY == 'Improper':
itpf.write(
' %d %d %d %d %d Opls_improper 0 %10.8f %10.8f %10.8f %10.8f\n'
% (i + 1, r.I + 1, r.J + 1, r.K + 1, r.L + 1, r.V1, r.V2, r.V3,
r.V4))
excl = (pd.DataFrame(EXCLUSIONS_12_13))
excl = excl.drop_duplicates(['UID'])
excp = (pd.DataFrame(EXCEPTION_14))
excp = excp.drop_duplicates(['UID'])
itpf.write(''' :::
}
ffio_torsion_torsion[0] {
:::
:::
}
''')
itpf.write(''' ffio_exclusions[%d] {
i_ffio_ai
i_ffio_aj
:::
''' % (len(excl.index)))
excl.index = range(len(excl.index))
for rb in excl.iterrows():
i, r = rb
itpf.write(' %d %d %d\n' % (i + 1, r.BI, r.BJ))
itpf.write(''' :::
}
ffio_pairs[%d] {
i_ffio_ai
i_ffio_aj
s_ffio_funct
r_ffio_c1
r_ffio_c2
:::
''' % (len(excp.index) * 2))
# prop_tor = full_tor[full_tor.TY=='Proper']
excp.index = range(len(excp.index))
for rb in excp.iterrows():
i, r = rb
itpf.write(' %d %d %d Coulomb 0.5 <>\n' % (2 * i + 1, r.BI, r.BJ))
itpf.write(' %d %d %d LJ 0.5 <>\n' % (2 * (i + 1), r.BI, r.BJ))
itpf.write(''' :::
}
ffio_constraints[0] {
:::
:::
}
}
}
''')
itpf.close()
return None