def write_solvent(atomistic_fragments, residue_type):
merge_coord = [line['coord'] for line in atomistic_fragments]
coord, index_conversion = at_mod.index_conversion_generate(
atomistic_fragments, merge_coord)
at_mod.write_pdb(
atomistic_fragments, coord, index_conversion,
g_var.working_dir + residue_type + '/' + residue_type + '_all.pdb')
def align_user_chains(final_coordinates_atomistic):
atomistic_protein_centered, cg_com = center_atomistic(
) ## centers each chain by center of mass
at_com_group, cg_com_group = rotate_protein_monomers(
atomistic_protein_centered, final_coordinates_atomistic, cg_com)
atomistic_protein_rotated = apply_rotations_to_chains(
final_coordinates_atomistic, atomistic_protein_centered, at_com_group,
cg_com_group, cg_com
) ## apply rotation matrix to atoms and build in missing residues
final_user_supplied_coord = correct_disulphide_bonds(
atomistic_protein_rotated
) ## fixes sulphur distances in user structure
for chain, protein in final_user_supplied_coord.items():
at_id = 0
coord = []
final_atom = []
for resid, residue in protein.items():
for atom in residue.values():
coord.append(atom['coord'])
final_atom.append({'atom_name':atom['atom'], 'residue_name':atom['res_type'], 'chain':chain, 'residue_id':resid,\
'x':atom['coord'][0],'y':atom['coord'][1],'z':atom['coord'][2]})
at_id += 1
corrected_coords, index_conversion = at_mod.index_conversion_generate(
final_atom, coord)
at_mod.write_pdb(
final_atom, corrected_coords, index_conversion, g_var.working_dir +
'PROTEIN/PROTEIN_aligned_' + str(chain) + '.pdb')