def get_bad(mol, gaff_atoms, amber_atoms, non_std_atom_indexes):
"""Computes the atoms involved in bonds, angles and dihedrals spanning both
the non standard residue specified and and the rest of the protein.
Returns mixed amber-gaff, gaff-gaff and amber-amber combinations"""
from cc_notebook import unwind
std_nn_ind = unwind([[n for n in mol.graph.neighbors[i] if n not in non_std_atom_indexes] for i in non_std_atom_indexes])
nstd_nn_ind = [[n for n in mol.graph.neighbors[i] if n in non_std_atom_indexes] for i in std_nn_ind]
std_nnn_ind = [[n for n in mol.graph.neighbors[i] if n not in non_std_atom_indexes] for i in std_nn_ind]
nstd_nnn_ind = [[n for n in mol.graph.neighbors[i] if n in non_std_atom_indexes] for i in unwind(nstd_nn_ind)]
amb_std_nn = [amber_atoms[i] for i in std_nn_ind]
amb_std_nnn = [[amber_atoms[i] for i in nnn_ind] for nnn_ind in std_nnn_ind]
gaff_std_nn = [gaff_atoms[i] for i in std_nn_ind]
gaff_std_nnn = [[gaff_atoms[i] for i in nnn_ind] for nnn_ind in std_nnn_ind]
amb_nstd_nn = [[amber_atoms[i] for i in nn_ind] for nn_ind in nstd_nn_ind]
amb_nstd_nnn = [[amber_atoms[i] for i in nnn_ind] for nnn_ind in nstd_nnn_ind]
gaff_nstd_nn = [[gaff_atoms[i] for i in nn_ind] for nn_ind in nstd_nn_ind]
gaff_nstd_nnn = [[gaff_atoms[i] for i in nnn_ind] for nnn_ind in nstd_nnn_ind]
bonds, gbonds, abonds = [], [], []
for i in range(len(amb_std_nn)):
for k in range(len(gaff_nstd_nn[i])):
bonds.append([amb_std_nn[i], gaff_nstd_nn[i][k]])
gbonds.append([gaff_std_nn[i], gaff_nstd_nn[i][k]])
abonds.append([amb_std_nn[i], amb_nstd_nn[i][k]])
dihedrals, gdihedrals, adihedrals = [], [], []
for i in range(len(amb_std_nn)):
for j in range(len(amb_std_nnn[i])):
for k in range(len(gaff_nstd_nn[i])):
for l in range(len(gaff_nstd_nnn[i])):
dihedrals.append([amb_std_nnn[i][j], amb_std_nn[i], gaff_nstd_nn[i][k], gaff_nstd_nnn[i][l]])
gdihedrals.append([gaff_std_nnn[i][j], gaff_std_nn[i], gaff_nstd_nn[i][k], gaff_nstd_nnn[i][l]])
adihedrals.append([amb_std_nnn[i][j], amb_std_nn[i], amb_nstd_nn[i][k], amb_nstd_nnn[i][l]])
angles, gangles, aangles = [], [], []
for i in range(len(dihedrals)):
ang1, ang2 = dihedrals[i][0:-1], dihedrals[i][1:]
if ang1 not in angles:
angles.append(ang1)
gangles.append(gdihedrals[i][0:-1])
aangles.append(adihedrals[i][0:-1])
if ang2 not in angles:
angles.append(ang2)
gangles.append(gdihedrals[i][1:])
aangles.append(adihedrals[i][1:])
return {'mixed':[bonds, angles, dihedrals], 'gaff': [gbonds, gangles, gdihedrals] , 'amber': [abonds, aangles, adihedrals]}
def get_ht_ind(mol, non_std_atom_indexes):
"""returns the head and the tail index of the nonstandard residue specified"""
from cc_notebook import unwind
std_nn_ind = unwind([[n for n in mol.graph.neighbors[i] if n not in non_std_atom_indexes] for i in non_std_atom_indexes])
nstd_nn_ind = [[n for n in mol.graph.neighbors[i] if n in non_std_atom_indexes] for i in std_nn_ind]
return unwind(nstd_nn_ind) - non_std_atom_indexes[0]