def SuperimposeFirstNeighbors (st_atom, pr_result): d_nb_neighbor = structure.nbNeighbor () for subs in st_atom.keys () : if subs == "global" : continue l_at_ref = structure.substructureCoord(subs) d_atom_superiposed = {} pr_superimpose = pr_result + subs + "/" pathManage.CreatePathDir(pr_superimpose) nb_ind = d_nb_neighbor[subs] # number of considered neighbors for at_central in st_atom[subs] : PDB_ID = at_central["PDB"] name_ligand = at_central["resName"] # all atom ligand l_at_lig = loadFile.ExtractInfoPDBID(PDB_ID)[name_ligand][0] # change not tested l_at_subs = retrieveAtom.substructure (subs, at_central, l_at_lig) v_atom_ref = mat(array(groupAtomCoord(l_at_ref[0:3]))) v_atom_central = mat(array(groupAtomCoord(l_at_subs[0:3]))) rotation, translocation = rigid_transform_3D(v_atom_central, v_atom_ref) if rotation == None or translocation == None : continue v_atom_rotated = applyTranformation(rotation, translocation, v_atom_central) l_atom_rotated = applyTranformation(rotation, translocation, l_atom_in=l_at_subs) print rmse(v_atom_central, v_atom_ref), "RMSE 1" print rmse(v_atom_ref, v_atom_rotated), "RMSE 2" # print v_atom_rotated # print "************compare**********" # print l_at_subs # print l_atom_rotated l_neighbor = deepcopy(at_central["neighbors"]) if len (l_neighbor) < nb_ind : continue else : l_combination = [] l_atom_neighbors = [] for i_neighbors in range (1, nb_ind + 1) : atom_class, d_atom = statistic.searchMoreClose (l_neighbor) l_combination.append (atom_class) l_atom_neighbors.append (d_atom) l_combination.sort () k = "_".join (l_combination) if not k in d_atom_superiposed.keys () : d_atom_superiposed[k] = [] l_atom_neighbor_rotated = applyTranformation(rotation, translocation, l_atom_in = l_atom_neighbors) d_atom_superiposed[k] = d_atom_superiposed[k] + l_atom_rotated + l_atom_neighbor_rotated for k in d_atom_superiposed.keys () : # write gif pr_init_gif = pr_superimpose + "gif/" pathManage.CreatePathDir(pr_init_gif) p_file_coord = writeFile.coordinates3D (d_atom_superiposed[k], pr_init_gif + k + ".coord", subs) runScriptR.plot3D (p_file_coord, option = "global") # write one PDB by atom close type pr_init_PDB = pr_superimpose + "/PDB/" pathManage.CreatePathDir(pr_init_PDB) writeFile.coordinates3DPDB (d_atom_superiposed[k], subs, pr_init_PDB + k + ".pdb" )
def globalNeighbor (atom_interest_close, subs, p_dir_result, option_filter = 1) : p_dir_result = pathManage.imposeNeighbors (p_dir_result) # extract from ideal position l_at_ref = structure.substructureCoord(subs) l_superimpose_neighbor = [] l_superimpose_subs = [] l_RMSE = [] for at_central in atom_interest_close[subs] : PDB_ID = at_central["PDB"] serial_at_central = at_central["serial"] name_ligand = at_central["resName"] # all atom ligand l_at_lig = loadFile.ExtractInfoPDBID(PDB_ID)[name_ligand][0] # change not tested # for at_ligand in l_at_lig : # print at_ligand l_at_subs = retrieveAtom.substructure (subs, at_central, l_at_lig) if subs == "GAI" : v_atom_central = mat(array(groupAtomCoord(l_at_subs))) v_atom_ref = mat(array(groupAtomCoord(l_at_ref))) elif subs == "COO" : v_atom_central = mat(array(groupAtomCoord(l_at_subs))) v_atom_ref = mat(array(groupAtomCoord(l_at_ref[1:]))) else : v_atom_central = mat(array(groupAtomCoord(l_at_subs))) v_atom_ref = mat(array(groupAtomCoord(l_at_ref))) rotation, translocation = rigid_transform_3D(v_atom_central, v_atom_ref) if rotation == None or translocation == None : continue v_atom_rotated = applyTranformation(rotation, translocation, v_atom_central) l_subs_rotated = applyTranformation(rotation, translocation, l_atom_in = l_at_subs) RMSE_rot = rmse(v_atom_ref, v_atom_rotated) print rmse(v_atom_central, v_atom_ref), "RMSE 1" print rmse(v_atom_ref, v_atom_rotated), "RMSE 2" l_RMSE.append (str(RMSE_rot)) # print v_atom_rotated # print "************compare**********" # print l_at_subs # print l_subs_rotated # print "/////////////////////////////" l_atom_neighbors = deepcopy(at_central["neighbors"]) if option_filter == 1 : # reduce the list of neighbor criteria = structure.criteraAngle(subs) d_min = criteria["distance"][0] d_max = criteria["distance"][1] n_neighbor = len (l_atom_neighbors) i = 0 while i < n_neighbor : if l_atom_neighbors[i]["distance"] < d_min or l_atom_neighbors[i]["distance"] > d_max : del l_atom_neighbors[i] n_neighbor = n_neighbor - 1 else : i = i +1 try : l_atom_neighbor_rotated = applyTranformation(rotation, translocation, l_atom_in=l_atom_neighbors) l_superimpose_neighbor = l_superimpose_neighbor + l_atom_neighbor_rotated l_superimpose_subs.append (l_subs_rotated) except : continue # color with b factor tool.colorAtomType (l_superimpose_neighbor) # write gif # pr_init_gif = p_dir_result + "/gif/" + subs + "/" # pathManage.CreatePathDir(pr_init_gif) # p_file_coord = writeFile.coordinates3D (l_superimpose_neighbor + l_superimpose_subs, pr_init_gif + subs + "_neigbor.coord", subs) # runScriptR.plot3D (p_file_coord) # write one PDB by atom close type pr_init_PDB = p_dir_result + "/PDB/" + subs + "/" pathManage.CreatePathDir(pr_init_PDB) file_RMSE = open (pr_init_PDB + "RMSE", "w") file_RMSE.write ("\n".join(l_RMSE) + "\n") file_RMSE.close () writeFile.coordinates3DPDBbyNeighborType (l_superimpose_neighbor, l_superimpose_subs, subs, pr_init_PDB)