Exemplo n.º 1
0
Arquivo: main.py Projeto: ABorrel/LSRs
def analysisBS (name_lig, ID_seq = '0.0', debug = 1):
    
    pr_result = pathManage.result(name_lig)
    pr_out = pathManage.result(name_lig + "/sameBS")
    
    # log files
    p_log_file = pr_out + "log.txt"
    filout_log = open (p_log_file, "w")

    # dictionnar with files
    d_file_BS = {}
    d_file_BS["global"] = open (pr_out + name_lig + "_", "w")
    d_file_BS["global"].write ("name_bs\tRMSD_prot\tRMSD_BS_ca\tRMSD_BS_all\tD_max\tl_at_BS\tidentic\n")
    d_file_BS["summary"] = open (pr_out + "summary.txt", "w")
    pr_dataset = pathManage.dataset(name_lig)
     
     
    l_folder_ref = listdir(pr_result)
    nb_BS = 0
    nb_BS_filtered = 0
    nb_same_BS = 0  
    for PDB_ref in l_folder_ref  :
        if debug : print PDB_ref
        if len (PDB_ref) != 4 : 
            continue
         
        p_pdb_ref = pathManage.findPDBRef(pr_dataset + PDB_ref + "/")
        l_p_query = pathManage.findPDBQueryTransloc (pathManage.result(name_lig) + PDB_ref + "/")
        
        if debug : print l_p_query
        for p_query in l_p_query : 
            
            # read TM Align
            if debug : print p_query.split ("/")[-1][7:-4]
            
            p_TMalign =  pathManage.alignmentOutput(name_lig) + p_pdb_ref.split ("/")[-1][0:-4] + "__" + p_query.split ("/")[-1][7:-4] + "/RMSD"
            try : score_align = parseTMalign.parseOutputTMalign(p_TMalign)
            except : 
                filout_log.write ("ERROR TM align " + p_TMalign + "\n")
                continue
            nb_BS = nb_BS + 1
            
            if score_align["IDseq"] >= ID_seq : 
                nb_BS_filtered = nb_BS_filtered + 1
                
                l_p_substruct_ref = pathManage.findSubstructRef (pr_dataset + PDB_ref + "/", name_lig)
                
                # sub BS
                for p_substruct_ref in l_p_substruct_ref : 
                    struct_substitued = p_substruct_ref.split ("_")[-2]
                    
                    # write header
                    if not struct_substitued in d_file_BS.keys () : 
                        d_file_BS[struct_substitued] = open (pr_out + name_lig + "_" + struct_substitued + "_", "w")
                        d_file_BS[struct_substitued].write ("name_bs\tRMSD_prot\tRMSD_BS_ca\tRMSD_BS_all\tD_max\tl_at_BS\tidentic\n")
                        
                    RMSD_bs = analysis.computeRMSDBS (p_pdb_ref, p_query, p_substruct_ref, pr_out)
                    if RMSD_bs != [] : 
                        d_file_BS[struct_substitued].write (p_substruct_ref.split("/")[-1][0:-4] +  "_*_" + p_query.split ("/")[-1][0:-4] + "\t" + str(score_align["RMSD"]) + "\t" + str(RMSD_bs[1]) + "\t" + str(RMSD_bs[0]) + "\t" + str(RMSD_bs[2]) + "\t" + str(RMSD_bs[-2]) + "\t" + str(RMSD_bs[-1]) + "\n")
                      
  

                p_ligand_ref = pathManage.findligandRef(pr_dataset + PDB_ref + "/", name_lig)
                RMSD_bs_lig = analysis.computeRMSDBS (p_pdb_ref, p_query, p_ligand_ref, pr_out)
                if RMSD_bs_lig != [] : 
                    d_file_BS["global"].write (p_ligand_ref.split("/")[-1][0:-4] +  "_*_" + p_query.split ("/")[-1][0:-4] + "\t" + str(score_align["RMSD"]) + "\t" + str(RMSD_bs_lig[1]) + "\t" + str(RMSD_bs_lig[0]) + "\t" + str(RMSD_bs_lig[2]) + "\t" + str(RMSD_bs_lig[-2]) + "\t" + str(RMSD_bs_lig[-1]) + "\n")
                    if RMSD_bs_lig [-1] == 1 : 
                        nb_same_BS = nb_same_BS + 1


    # write summary
    d_file_BS["summary"].write ("BS global: " + str (nb_BS) + "\n")
    d_file_BS["summary"].write ("BS - IDseq " + str (ID_seq) + "%: " +  str (nb_BS_filtered) + "\n")
    d_file_BS["summary"].write ("BS - same atom number: " + str (nb_same_BS) + "\n")
    
    filout_log.close ()
                    
    
    # close files and run histograms                
    for k_dico in d_file_BS.keys () : 
        p_file = d_file_BS[k_dico].name
        d_file_BS[k_dico].close ()
        if name_lig == "ATP" : 
            runOtherSoft.RhistogramRMSD(p_file, max_RMSD = 5.0)
        elif name_lig == "ADP" : 
            runOtherSoft.RhistogramRMSD(p_file, max_RMSD = 4.0)
        elif name_lig == "AMP" : 
            runOtherSoft.RhistogramRMSD(p_file, max_RMSD = 4.0)
        else : 
            runOtherSoft.RhistogramRMSD(p_file, max_RMSD = 3.5)
             

        
    return 1
Exemplo n.º 2
0
Arquivo: main.py Projeto: ABorrel/LSRs
def retrieveSubstructSuperimposed (name_lig, thresold_BS = 4.5, thresold_superimposed_ribose = 2.5, thresold_superimposed_pi = 3, thresold_shaep = 0.4):

    # ouput
    p_dir_dataset = pathManage.dataset(name_lig)
    p_dir_result = pathManage.result(name_lig )
    l_folder_ref = listdir(p_dir_dataset)

    # log control
    p_log = open(p_dir_result + "log_superimposed.txt", "w")

    # control extraction
    d_control = {}
    d_control["pr ref"] = 0
    d_control["lig query"] = 0
    d_control["subref"] = {}
    d_control["subref empty"] = {}
    d_control["out sheap"] = {}
    filout_control = open (p_dir_result + "quality_extraction.txt", "w")

    # stock smile code
    d_smile = {}

    # sheap control
    d_filout_sheap = {}
    d_filout_sheap ["list"] = [p_dir_result + "shaep_global.txt"]
    d_filout_sheap["global"] = open (p_dir_result + "shaep_global.txt", "w") 
    d_filout_sheap["global"].write ("name\tbest_similarity\tshape_similarity\tESP_similarity\n")

    for ref_folder in l_folder_ref :
        # control folder reference name
        if len (ref_folder) != 4 : 
            p_log.write ("[ERROR folder] -> " + ref_folder + "\n")
            continue

        # reference
        p_lig_ref = pathManage.findligandRef(p_dir_dataset + ref_folder + "/", name_lig)
        try:
            lig_ref_parsed = parsePDB.loadCoordSectionPDB(p_lig_ref, "HETATM")
#             print len (lig_ref_parsed)
        except:
            p_log.write ("[ERROR ligand ref] -> " + p_lig_ref + "\n")
            continue

        #control
        d_control["pr ref"] = d_control["pr ref"] + 1

        # output by reference
        p_dir_result_ref = pathManage.result(name_lig + "/" + ref_folder)
        d_filout_superimposed = {}
        d_filout_superimposed["global"] = open (p_dir_result_ref + "all_ligand_aligned.pdb", "w")
        d_filout_superimposed["sheap"] = open (p_dir_result_ref + "all_ligand_aligned_" + str (thresold_shaep)  + ".pdb", "w")
        
        
        
        # write lig ref -> connect matrix corrrect in all reference and all sheap
        writePDBfile.coordinateSection(d_filout_superimposed["global"], lig_ref_parsed, "HETATM", connect_matrix = 1)
        writePDBfile.coordinateSection(d_filout_superimposed["sheap"], lig_ref_parsed, "HETATM", connect_matrix = 1)
        
        # inspect folder dataset
        l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
        for pdbfile in l_pdbfile : 
            # no ligand file
            if len (pdbfile.split ("_")) == 1 : 
                continue
            pdbfile = pdbfile[:-4] # remove extention
            
            if len(pdbfile.split ("_")[0]) == 3  and len(pdbfile.split ("_")[1]) == 4 and pdbfile.split ("_")[1] != ref_folder:
                p_lig = p_dir_dataset + ref_folder + "/" + pdbfile  + ".pdb"
                if p_lig_ref != p_lig : 
                    # pass case where ligand replace same ligand -> does not need run
                    if pdbfile.split ("_")[0] == name_lig : 
                        p_log.write ("[REMOVE] -> same ligand substituate")
                        continue
                    
                    # parsed ligand query
                    lig_parsed = parsePDB.loadCoordSectionPDB(p_lig, "HETATM")

                    # find matrix of rotation
                    p_matrix = pathManage.findMatrix(p_lig_ref, p_lig, name_lig)
                    # control file matrix exist
                    if not path.exists(p_matrix) : 
                        p_log.write ("[ERROR] -> Matrix transloc " + p_lig_ref + " " + p_lig + " " + name_lig + "\n")
                        continue
                    
                    # control
                    d_control["lig query"] = d_control["lig query"] + 1
                    
                    # find the path of complex used
                    p_complex = p_dir_dataset + ref_folder + "/" + p_lig.split ("/")[-1][4:]
                    
                    # ligand rotated -> change the referentiel
                    superposeStructure.applyMatrixLigand(lig_parsed, p_matrix)
                    
                    
                    # use substruct
                    l_p_substruct_ref = pathManage.findSubstructRef (pathManage.dataset(name_lig) + ref_folder + "/" , name_lig)
                    for p_substruct_ref in l_p_substruct_ref : 
                        # ribose or phosphate
                        struct_type = p_substruct_ref.split ("_")[-2]
                        substruct_parsed = parsePDB.loadCoordSectionPDB(p_substruct_ref, "HETATM")
                        
                        l_atom_substituate = neighborSearch.searchNeighborAtom(substruct_parsed, lig_parsed, struct_type, p_log, thresold_superimposed_ribose = thresold_superimposed_ribose, thresold_superimposed_pi = thresold_superimposed_pi)    
                        # control find 
                        if len (l_atom_substituate) == 0 :  
                            if not struct_type in d_control["subref empty"].keys () : 
                                d_control["subref empty"][struct_type] = 1
                            else : 
                                d_control["subref empty"][struct_type] = d_control["subref empty"][struct_type] + 1
                            continue
                        
                        else : 
                            if not struct_type in d_control["subref"].keys () : 
                                d_control["subref"][struct_type] = 1
                            else : 
                                d_control["subref"][struct_type] = d_control["subref"][struct_type] + 1
                            
                            # write PDB file, convert smile
                            p_substituate_pdb = p_dir_result_ref + "substituent_" + pdbfile.split ("_")[0] + "_" + pdbfile.split ("_")[1] + "_" + struct_type + ".pdb"
                            writePDBfile.coordinateSection(p_substituate_pdb, l_atom_substituate, recorder="HETATM", header=0, connect_matrix = 1)
    
                            # sheap reference on part of ligand
                            p_sheap = runOtherSoft.runShaep (p_substruct_ref, p_substituate_pdb, p_substituate_pdb[0:-4] + ".hit", clean = 0)
                            val_sheap = parseShaep.parseOutputShaep (p_sheap)
                            if val_sheap == {} : 
                                p_log.write ("[ERROR] -> ShaEP " + p_substituate_pdb + " " + p_substruct_ref + "\n")
                                
                                if not struct_type in d_control["out sheap"].keys () :
                                    d_control["out sheap"][struct_type] = 1
                                else : 
                                    d_control["out sheap"][struct_type] = d_control["out sheap"][struct_type] + 1
                                continue
                            
                            # control thresold sheap
                            if not struct_type in d_filout_sheap.keys () : 
                                d_filout_sheap[struct_type] = {}
                                d_filout_sheap[struct_type] = open (p_dir_result + "shaep_global_" + struct_type + ".txt", "w")
                                d_filout_sheap[struct_type].write ("name\tbest_similarity\tshape_similarity\tESP_similarity\n")
                                d_filout_sheap["list"].append (p_dir_result + "shaep_global_" + struct_type + ".txt") # to improve with python function
                            
                            # write value in ShaEP control
                            d_filout_sheap[struct_type].write (ref_folder + "_" +  str(pdbfile.split ("_")[1]) + "_" + struct_type + "_" + str (pdbfile.split ("_")[0]) + "\t" + str(val_sheap["best_similarity"]) + "\t" + str(val_sheap["shape_similarity"]) + "\t" + str(val_sheap["ESP_similarity"]) + "\n")
                            d_filout_sheap["global"].write (ref_folder + "_" +  str(pdbfile.split ("_")[1]) + "_" + struct_type + "_" + str (pdbfile.split ("_")[0]) + "\t" + str(val_sheap["best_similarity"]) + "\t" + str(val_sheap["shape_similarity"]) + "\t" + str(val_sheap["ESP_similarity"]) + "\n")
                            
                            # rename file substituent with shaEP value
                            rename(p_substituate_pdb, p_substituate_pdb[:-4] + "_" + str (val_sheap["best_similarity"]) + ".pdb")
                            # rename and change the file name
                            p_substituate_pdb = p_substituate_pdb[:-4] + "_" + str (val_sheap["best_similarity"]) + ".pdb"
                            
                            # write all substruct in global file
                            writePDBfile.coordinateSection(d_filout_superimposed["global"], lig_parsed, recorder= "HETATM", header = str(p_lig.split ("/")[-1]) + "_" + str (val_sheap["best_similarity"]) ,  connect_matrix = 1)
                            
                            # control sheap thresold    
                            if float(val_sheap["best_similarity"]) >= thresold_shaep  : 
                                
                                # write subligand superimposed selected in global files
                                writePDBfile.coordinateSection(d_filout_superimposed["sheap"], lig_parsed, recorder= "HETATM", header = str(p_lig.split ("/")[-1]) + "_" + str (val_sheap["best_similarity"]) ,  connect_matrix = 1)
                                
                                ############
                                # write BS #
                                ############
                                # not only protein superimposed -> also ion and water
                                l_atom_complex = parsePDB.loadCoordSectionPDB(p_complex)
                                superposeStructure.applyMatrixProt(l_atom_complex, p_matrix)
                                p_file_cx = p_dir_result_ref +  "CX_" + p_lig.split ("/")[-1]
                                # write CX
                                writePDBfile.coordinateSection(p_file_cx, l_atom_complex, recorder="ATOM", header= p_lig.split ("/")[-1], connect_matrix = 0)
    
                                # search atom in BS
                                l_atom_binding_site = []
                                for atom_complex in l_atom_complex : 
                                    for atom_substruct in lig_parsed : 
                                        if parsePDB.distanceTwoatoms (atom_substruct, atom_complex) <= thresold_BS :
                                            if not atom_complex in l_atom_binding_site : 
                                                l_atom_binding_site.append (deepcopy(atom_complex))
                                
                                # 3. retrieve complet residue
                                l_atom_BS_res = parsePDB.getResidues(l_atom_binding_site, l_atom_complex)
                                                
                                # 4. write binding site
                                p_binding = p_dir_result_ref +  "BS_" + p_lig.split ("/")[-1]
                                writePDBfile.coordinateSection(p_binding, l_atom_BS_res, "ATOM", p_binding, connect_matrix = 0)
                                
                                # smile code substituate analysis                    
                                # Step smile -> not conversion if shaep not validate 
                                smile_find = runOtherSoft.babelConvertPDBtoSMILE(p_substituate_pdb)
                                if not struct_type in d_smile.keys ()  :
                                    d_smile[struct_type] = {}
                                    d_smile[struct_type][smile_find] = {}
                                    d_smile[struct_type][smile_find]["count"] = 1
                                    d_smile[struct_type][smile_find]["PDB"] = [pdbfile.split ("_")[1]]
                                    d_smile[struct_type][smile_find]["ligand"] = [pdbfile.split ("_")[0]]
                                    d_smile[struct_type][smile_find]["ref"] = [ref_folder]
                                else : 
                                    if not smile_find in d_smile[struct_type].keys () : 
                                        d_smile[struct_type][smile_find] = {}
                                        d_smile[struct_type][smile_find]["count"] = 1
                                        d_smile[struct_type][smile_find]["PDB"] = [pdbfile.split ("_")[1]]
                                        d_smile[struct_type][smile_find]["ligand"] = [pdbfile.split ("_")[0]] 
                                        d_smile[struct_type][smile_find]["ref"] = [ref_folder]
                                    else : 
                                        d_smile[struct_type][smile_find]["count"] = d_smile[struct_type][smile_find]["count"] + 1
                                        d_smile[struct_type][smile_find]["PDB"].append (pdbfile.split ("_")[1])
                                        d_smile[struct_type][smile_find]["ligand"].append (pdbfile.split ("_")[0])
                                        d_smile[struct_type][smile_find]["ref"].append (ref_folder)

                            else : 
                                if not struct_type in d_control["out sheap"].keys () : 
                                    d_control["out sheap"][struct_type] = 1
                                else : 
                                    d_control["out sheap"][struct_type] = d_control["out sheap"][struct_type] + 1

        tool.closeDicoFile (d_filout_superimposed)

    # sheap control    
    tool.closeDicoFile (d_filout_sheap)
    for p_file_sheap in d_filout_sheap["list"] : 
        runOtherSoft.RhistogramMultiple (p_file_sheap)    
        
            
    # write list of smile
    for substruct in d_smile.keys () : 
        p_list_smile = pathManage.result(name_lig) + "list_" + substruct + "_" + str (thresold_shaep) + "_smile.txt"
        filout_smile = open (p_list_smile, "w")
        for smile_code in d_smile[substruct].keys () : 
            l_lig = d_smile[substruct][smile_code]["ligand"]
            l_PDB = d_smile[substruct][smile_code]["PDB"]
            l_ref = d_smile[substruct][smile_code]["ref"]
            filout_smile.write (str (smile_code) + "\t" + str (d_smile[substruct][smile_code]["count"]) + "\t" + " ".join (l_PDB) + "\t" + " ".join (l_ref) + "\t" + " ".join(l_lig) + "\n")
        filout_smile.close ()
    p_log.close ()
    
    # control
    filout_control.write ("NB ref: " + str(d_control["pr ref"]) + "\n")
    filout_control.write ("Ligand query: " + str(d_control["lig query"]) + "\n")
    for k in d_control["subref"].keys () :
        filout_control.write ("LSR " + str (k) + ": " + str(d_control["subref"][k]) + "\n")
    for k in d_control["subref empty"].keys () :
        filout_control.write ("NB LSR empty " + str (k) + ": " + str(d_control["subref empty"][k]) + "\n")
    for k in d_control["out sheap"].keys () :
        filout_control.write ("LSR out by sheap " + str (k) + ": " + str(d_control["out sheap"][k]) + "\n")
    
    filout_control.write ("**********************\n\n")
    for k in d_control["subref"].keys () :
        filout_control.write ("LSR keep" + str (k) + ": " + str(d_control["subref"][k] - d_control["out sheap"][k]) + "\n")
    
    filout_control.close ()
    
    return 1
Exemplo n.º 3
0
def analysisBS(name_lig, ID_seq='0.0', debug=1):

    pr_result = pathManage.result(name_lig)
    pr_out = pathManage.result(name_lig + "/sameBS")

    # log files
    p_log_file = pr_out + "log.txt"
    filout_log = open(p_log_file, "w")

    # dictionnar with files
    d_file_BS = {}
    d_file_BS["global"] = open(pr_out + name_lig + "_", "w")
    d_file_BS["global"].write(
        "name_bs\tRMSD_prot\tRMSD_BS_ca\tRMSD_BS_all\tD_max\tl_at_BS\tidentic\n"
    )
    d_file_BS["summary"] = open(pr_out + "summary.txt", "w")
    pr_dataset = pathManage.dataset(name_lig)

    l_folder_ref = listdir(pr_result)
    nb_BS = 0
    nb_BS_filtered = 0
    nb_same_BS = 0
    for PDB_ref in l_folder_ref:
        if debug: print PDB_ref
        if len(PDB_ref) != 4:
            continue

        p_pdb_ref = pathManage.findPDBRef(pr_dataset + PDB_ref + "/")
        l_p_query = pathManage.findPDBQueryTransloc(
            pathManage.result(name_lig) + PDB_ref + "/")

        if debug: print l_p_query
        for p_query in l_p_query:

            # read TM Align
            if debug: print p_query.split("/")[-1][7:-4]

            p_TMalign = pathManage.alignmentOutput(name_lig) + p_pdb_ref.split(
                "/")[-1][0:-4] + "__" + p_query.split("/")[-1][7:-4] + "/RMSD"
            try:
                score_align = parseTMalign.parseOutputTMalign(p_TMalign)
            except:
                filout_log.write("ERROR TM align " + p_TMalign + "\n")
                continue
            nb_BS = nb_BS + 1

            if score_align["IDseq"] >= ID_seq:
                nb_BS_filtered = nb_BS_filtered + 1

                l_p_substruct_ref = pathManage.findSubstructRef(
                    pr_dataset + PDB_ref + "/", name_lig)

                # sub BS
                for p_substruct_ref in l_p_substruct_ref:
                    struct_substitued = p_substruct_ref.split("_")[-2]

                    # write header
                    if not struct_substitued in d_file_BS.keys():
                        d_file_BS[struct_substitued] = open(
                            pr_out + name_lig + "_" + struct_substitued + "_",
                            "w")
                        d_file_BS[struct_substitued].write(
                            "name_bs\tRMSD_prot\tRMSD_BS_ca\tRMSD_BS_all\tD_max\tl_at_BS\tidentic\n"
                        )

                    RMSD_bs = analysis.computeRMSDBS(p_pdb_ref, p_query,
                                                     p_substruct_ref, pr_out)
                    if RMSD_bs != []:
                        d_file_BS[struct_substitued].write(
                            p_substruct_ref.split("/")[-1][0:-4] + "_*_" +
                            p_query.split("/")[-1][0:-4] + "\t" +
                            str(score_align["RMSD"]) + "\t" + str(RMSD_bs[1]) +
                            "\t" + str(RMSD_bs[0]) + "\t" + str(RMSD_bs[2]) +
                            "\t" + str(RMSD_bs[-2]) + "\t" + str(RMSD_bs[-1]) +
                            "\n")

                p_ligand_ref = pathManage.findligandRef(
                    pr_dataset + PDB_ref + "/", name_lig)
                RMSD_bs_lig = analysis.computeRMSDBS(p_pdb_ref, p_query,
                                                     p_ligand_ref, pr_out)
                if RMSD_bs_lig != []:
                    d_file_BS["global"].write(
                        p_ligand_ref.split("/")[-1][0:-4] + "_*_" +
                        p_query.split("/")[-1][0:-4] + "\t" +
                        str(score_align["RMSD"]) + "\t" + str(RMSD_bs_lig[1]) +
                        "\t" + str(RMSD_bs_lig[0]) + "\t" +
                        str(RMSD_bs_lig[2]) + "\t" + str(RMSD_bs_lig[-2]) +
                        "\t" + str(RMSD_bs_lig[-1]) + "\n")
                    if RMSD_bs_lig[-1] == 1:
                        nb_same_BS = nb_same_BS + 1

    # write summary
    d_file_BS["summary"].write("BS global: " + str(nb_BS) + "\n")
    d_file_BS["summary"].write("BS - IDseq " + str(ID_seq) + "%: " +
                               str(nb_BS_filtered) + "\n")
    d_file_BS["summary"].write("BS - same atom number: " + str(nb_same_BS) +
                               "\n")

    filout_log.close()

    # close files and run histograms
    for k_dico in d_file_BS.keys():
        p_file = d_file_BS[k_dico].name
        d_file_BS[k_dico].close()
        if name_lig == "ATP":
            runOtherSoft.RhistogramRMSD(p_file, max_RMSD=5.0)
        elif name_lig == "ADP":
            runOtherSoft.RhistogramRMSD(p_file, max_RMSD=4.0)
        elif name_lig == "AMP":
            runOtherSoft.RhistogramRMSD(p_file, max_RMSD=4.0)
        else:
            runOtherSoft.RhistogramRMSD(p_file, max_RMSD=3.5)

    return 1
Exemplo n.º 4
0
def globalArrangement (pr_orgin, p_smile, p_family, name_ligand, l_ligand_out):
    
#     print "--------"
#     print pr_orgin
#     print p_smile
#     print p_family
#     print name_ligand
#     print "--------"
    
    
    subst = p_smile.split ("_")[-3]
    
    filin = open (p_smile, "r")
    l_line_smile = filin.readlines ()
    filin.close()
    
    for line_smile in l_line_smile : 
        
        # search substructure
#         print line_smile
        l_PDB_query = line_smile.split ("\t")[-3].split (" ")
#         print l_PDB_query
        l_PDB_ref = line_smile.split ("\t")[-2].split (" ")
        l_ligand = line_smile.strip().split ("\t")[-1].split (" ")
        
        # search replacement
        smile = line_smile.split ("\t")[0]
        
        # search if LSR is small -> thresold < 3
        small_LSR = smileAnalysis.smallLSR (smile) 
        if subst == "ribose" :  
            if small_LSR == 1 : 
                first_folder = "ribose_small"
            else : 
                first_folder = "ribose"
        else : 
            if small_LSR == 1 : 
                first_folder = "Pi_small"
            else : 
                first_folder = "Pi"
        
        
        print smile, l_PDB_query, l_PDB_ref, l_ligand, subst, small_LSR
        replacement, metal = smileAnalysis.searchReplacement (smile, l_PDB_query[0], l_PDB_ref[0], name_ligand)
        
        # case with cycle -> search replacement 2
        if replacement == "cycle" : 
            replacement2, metal = smileAnalysis.searchReplacement (smile, l_PDB_query[0], l_PDB_ref[0], name_ligand, in_cycle = 1)
            replacement = replacement + "/" + replacement2 # new folder

        # case metal
        if replacement == "metal" : 
            print metal, l_PDB_query, l_PDB_ref, name_ligand
        
        len_find = len (l_PDB_ref)
        i = 0
        while i < len_find : 
            
            # exclusion of ligand out
            if l_ligand[i] in l_ligand_out : 
                i = i + 1
                continue
            
            
            group, family = analysis.findFamilyAndGroup(l_PDB_ref[i])
            
            # folder reference
            pr_dataset = pathManage.dataset(name_ligand + "/" + l_PDB_ref[i])
            
            PDB_ref = pathManage.findPDBRef(pr_dataset)
            p_ligand_ref = pathManage.findligandRef(pr_dataset , name_ligand)
            l_frag_ref = pathManage.findSubstructRef(pr_dataset, name_ligand)
            for f_ref in l_frag_ref :
                if search (subst, f_ref) : 
                    p_frag_ref = f_ref
                    break
            
            # folder_query
            pr_result = pathManage.result(name_ligand + "/" + l_PDB_ref[i])
            l_protein_tranloc = pathManage.findPDBQueryTransloc(pr_result)
            for p_t in l_protein_tranloc : 
                if search (l_ligand[i], p_t) and search (l_PDB_query[i], p_t) : 
                    p_protein_query = p_t
                    break
                
            if replacement != "metal" : 
                p_lig_query = pathManage.findligandQuery(pr_dataset , l_ligand[i], l_PDB_query[i])
            else : 
                p_lig_query = pathManage.findligandQuery(pr_dataset ,metal, l_PDB_query[i])
            # need apply transloc matrix
            matrix_transloc = pathManage.findMatrix(p_ligand_ref, p_lig_query, name_ligand)
            lig_query_parsed = parsePDB.loadCoordSectionPDB(p_lig_query)
            try : superposeStructure.applyMatrixLigand(lig_query_parsed, matrix_transloc)
            except : 
                i = i + 1
                continue
            
            
            p_lig_substituate = pathManage.findSubstructFind(pr_result, l_ligand[i], l_PDB_query[i], subst)
            l_p_BS = pathManage.findFileBS(pr_result, l_PDB_query[i])
            for BS in l_p_BS : 
                if search (l_ligand[i], BS) : 
                    p_BS = BS
                    break
            
            
#             print pr_final
#             print "***************"
#             print PDB_ref
#             print p_ligand_ref
#             print p_frag_ref
#             print "----"
#             print p_protein_query
#             print p_lig_query
#             print p_lig_substituate
#             print p_BS
#             print "**************"
            # ajouter group + family 2 lettre
            pr_final = pr_orgin + first_folder + "/" + replacement + "/" + str (family) + "-"  + str (group) + "_" + l_PDB_ref[i] +  "/" 
            pr_ligand = pr_orgin + first_folder + "/" + replacement + "/" + str (family) + "-" +  str (group) + "_" + l_PDB_ref[i] + "/LGD/"
            pr_BS = pr_orgin + first_folder + "/" + replacement + "/" + str (family) + "-" + str (group) + "_" + l_PDB_ref[i] + "/BS/"
            pr_sust = pr_orgin + first_folder + "/" + replacement + "/" + str (family) + "-"  + str (group) + "_" + l_PDB_ref[i] + "/LSR/"
            
            if not path.isdir(pr_final):
                makedirs (pr_final)
            
            if not path.isdir(pr_ligand):
                makedirs (pr_ligand)
            
            if not path.isdir(pr_BS):
                makedirs (pr_BS)
                
            if not path.isdir(pr_sust):
                makedirs (pr_sust)   
            
            # list file
            p_list_smile_queries = pr_sust + "list.smile"
            if not path.exists(p_list_smile_queries) : 
                file_smile_queries = open (p_list_smile_queries, "w")
            else : 
                file_smile_queries = open (p_list_smile_queries, "a")
            file_smile_queries.write (str(smile) + "\n")
            file_smile_queries.close ()
            
            # lig de la query
            writePDBfile.coordinateSection(pr_ligand + "LGD_" + p_lig_query.split ("/")[-1], lig_query_parsed, recorder = "HETATM", header = "LCG_" + p_lig_query.split ("/")[-1], connect_matrix = 1)
            runOtherSoft.babelConvertPDBtoSMILE(pr_ligand + "LGD_" + p_lig_query.split ("/")[-1], clean_smi = 1)
            # lig de reference + smile
            copy2(p_ligand_ref, pr_ligand + "LGD_REF_" + p_ligand_ref.split ("/")[-1])
            runOtherSoft.babelConvertPDBtoSMILE(pr_ligand + "LGD_REF_" + p_ligand_ref.split ("/")[-1])
            # LSR de ref
            copy2(p_frag_ref, pr_sust + "LSR_REF_" + name_ligand + "_" + l_PDB_ref[i] + ".pdb")
            # protein query
            #copy2(p_protein_query, pr_final)
            # LSR query -> p_lig_ref only for the name
            copy2(p_lig_substituate, pr_sust + "LSR_" + subst + "_"  + p_lig_query.split ("/")[-1])
            # BS query
            copy2(p_BS, pr_BS)   
            
            # BS from reference
            l_atom_BS = parsePDB.computeBS (PDB_ref, p_ligand_ref, thresold = 4.50, option_onlyATOM = 0)
            writePDBfile.coordinateSection(pr_BS + "BS_REF_" + name_ligand + "_" + PDB_ref.split ("/")[-1], l_atom_BS, recorder = "ATOM", header = "BS_REF_" + name_ligand + "_" + PDB_ref, connect_matrix = 0)
            
            i = i + 1
    
    return 1
Exemplo n.º 5
0
def retrieveSubstructSuperimposed(name_lig,
                                  thresold_BS=4.5,
                                  thresold_superimposed_ribose=2.5,
                                  thresold_superimposed_pi=3,
                                  thresold_shaep=0.4):

    # ouput
    p_dir_dataset = pathManage.dataset(name_lig)
    p_dir_result = pathManage.result(name_lig)
    l_folder_ref = listdir(p_dir_dataset)

    # log control
    p_log = open(p_dir_result + "log_superimposed.txt", "w")

    # control extraction
    d_control = {}
    d_control["pr ref"] = 0
    d_control["lig query"] = 0
    d_control["subref"] = {}
    d_control["subref empty"] = {}
    d_control["out sheap"] = {}
    filout_control = open(p_dir_result + "quality_extraction.txt", "w")

    # stock smile code
    d_smile = {}

    # sheap control
    d_filout_sheap = {}
    d_filout_sheap["list"] = [p_dir_result + "shaep_global.txt"]
    d_filout_sheap["global"] = open(p_dir_result + "shaep_global.txt", "w")
    d_filout_sheap["global"].write(
        "name\tbest_similarity\tshape_similarity\tESP_similarity\n")

    for ref_folder in l_folder_ref:
        # control folder reference name
        if len(ref_folder) != 4:
            p_log.write("[ERROR folder] -> " + ref_folder + "\n")
            continue

        # reference
        p_lig_ref = pathManage.findligandRef(p_dir_dataset + ref_folder + "/",
                                             name_lig)
        try:
            lig_ref_parsed = parsePDB.loadCoordSectionPDB(p_lig_ref, "HETATM")
#             print len (lig_ref_parsed)
        except:
            p_log.write("[ERROR ligand ref] -> " + p_lig_ref + "\n")
            continue

        #control
        d_control["pr ref"] = d_control["pr ref"] + 1

        # output by reference
        p_dir_result_ref = pathManage.result(name_lig + "/" + ref_folder)
        d_filout_superimposed = {}
        d_filout_superimposed["global"] = open(
            p_dir_result_ref + "all_ligand_aligned.pdb", "w")
        d_filout_superimposed["sheap"] = open(
            p_dir_result_ref + "all_ligand_aligned_" + str(thresold_shaep) +
            ".pdb", "w")

        # write lig ref -> connect matrix corrrect in all reference and all sheap
        writePDBfile.coordinateSection(d_filout_superimposed["global"],
                                       lig_ref_parsed,
                                       "HETATM",
                                       connect_matrix=1)
        writePDBfile.coordinateSection(d_filout_superimposed["sheap"],
                                       lig_ref_parsed,
                                       "HETATM",
                                       connect_matrix=1)

        # inspect folder dataset
        l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
        for pdbfile in l_pdbfile:
            # no ligand file
            if len(pdbfile.split("_")) == 1:
                continue
            pdbfile = pdbfile[:-4]  # remove extention

            if len(pdbfile.split("_")[0]) == 3 and len(pdbfile.split(
                    "_")[1]) == 4 and pdbfile.split("_")[1] != ref_folder:
                p_lig = p_dir_dataset + ref_folder + "/" + pdbfile + ".pdb"
                if p_lig_ref != p_lig:
                    # pass case where ligand replace same ligand -> does not need run
                    if pdbfile.split("_")[0] == name_lig:
                        p_log.write("[REMOVE] -> same ligand substituate")
                        continue

                    # parsed ligand query
                    lig_parsed = parsePDB.loadCoordSectionPDB(p_lig, "HETATM")

                    # find matrix of rotation
                    p_matrix = pathManage.findMatrix(p_lig_ref, p_lig,
                                                     name_lig)
                    # control file matrix exist
                    if not path.exists(p_matrix):
                        p_log.write("[ERROR] -> Matrix transloc " + p_lig_ref +
                                    " " + p_lig + " " + name_lig + "\n")
                        continue

                    # control
                    d_control["lig query"] = d_control["lig query"] + 1

                    # find the path of complex used
                    p_complex = p_dir_dataset + ref_folder + "/" + p_lig.split(
                        "/")[-1][4:]

                    # ligand rotated -> change the referentiel
                    superposeStructure.applyMatrixLigand(lig_parsed, p_matrix)

                    # use substruct
                    l_p_substruct_ref = pathManage.findSubstructRef(
                        pathManage.dataset(name_lig) + ref_folder + "/",
                        name_lig)
                    for p_substruct_ref in l_p_substruct_ref:
                        # ribose or phosphate
                        struct_type = p_substruct_ref.split("_")[-2]
                        substruct_parsed = parsePDB.loadCoordSectionPDB(
                            p_substruct_ref, "HETATM")

                        l_atom_substituate = neighborSearch.searchNeighborAtom(
                            substruct_parsed,
                            lig_parsed,
                            struct_type,
                            p_log,
                            thresold_superimposed_ribose=
                            thresold_superimposed_ribose,
                            thresold_superimposed_pi=thresold_superimposed_pi)
                        # control find
                        if len(l_atom_substituate) == 0:
                            if not struct_type in d_control[
                                    "subref empty"].keys():
                                d_control["subref empty"][struct_type] = 1
                            else:
                                d_control["subref empty"][
                                    struct_type] = d_control["subref empty"][
                                        struct_type] + 1
                            continue

                        else:
                            if not struct_type in d_control["subref"].keys():
                                d_control["subref"][struct_type] = 1
                            else:
                                d_control["subref"][struct_type] = d_control[
                                    "subref"][struct_type] + 1

                            # write PDB file, convert smile
                            p_substituate_pdb = p_dir_result_ref + "substituent_" + pdbfile.split(
                                "_")[0] + "_" + pdbfile.split(
                                    "_")[1] + "_" + struct_type + ".pdb"
                            writePDBfile.coordinateSection(p_substituate_pdb,
                                                           l_atom_substituate,
                                                           recorder="HETATM",
                                                           header=0,
                                                           connect_matrix=1)

                            # sheap reference on part of ligand
                            p_sheap = runOtherSoft.runShaep(
                                p_substruct_ref,
                                p_substituate_pdb,
                                p_substituate_pdb[0:-4] + ".hit",
                                clean=0)
                            val_sheap = parseShaep.parseOutputShaep(p_sheap)
                            if val_sheap == {}:
                                p_log.write("[ERROR] -> ShaEP " +
                                            p_substituate_pdb + " " +
                                            p_substruct_ref + "\n")

                                if not struct_type in d_control[
                                        "out sheap"].keys():
                                    d_control["out sheap"][struct_type] = 1
                                else:
                                    d_control["out sheap"][
                                        struct_type] = d_control["out sheap"][
                                            struct_type] + 1
                                continue

                            # control thresold sheap
                            if not struct_type in d_filout_sheap.keys():
                                d_filout_sheap[struct_type] = {}
                                d_filout_sheap[struct_type] = open(
                                    p_dir_result + "shaep_global_" +
                                    struct_type + ".txt", "w")
                                d_filout_sheap[struct_type].write(
                                    "name\tbest_similarity\tshape_similarity\tESP_similarity\n"
                                )
                                d_filout_sheap["list"].append(
                                    p_dir_result + "shaep_global_" +
                                    struct_type +
                                    ".txt")  # to improve with python function

                            # write value in ShaEP control
                            d_filout_sheap[struct_type].write(
                                ref_folder + "_" + str(pdbfile.split("_")[1]) +
                                "_" + struct_type + "_" +
                                str(pdbfile.split("_")[0]) + "\t" +
                                str(val_sheap["best_similarity"]) + "\t" +
                                str(val_sheap["shape_similarity"]) + "\t" +
                                str(val_sheap["ESP_similarity"]) + "\n")
                            d_filout_sheap["global"].write(
                                ref_folder + "_" + str(pdbfile.split("_")[1]) +
                                "_" + struct_type + "_" +
                                str(pdbfile.split("_")[0]) + "\t" +
                                str(val_sheap["best_similarity"]) + "\t" +
                                str(val_sheap["shape_similarity"]) + "\t" +
                                str(val_sheap["ESP_similarity"]) + "\n")

                            # rename file substituent with shaEP value
                            rename(
                                p_substituate_pdb,
                                p_substituate_pdb[:-4] + "_" +
                                str(val_sheap["best_similarity"]) + ".pdb")
                            # rename and change the file name
                            p_substituate_pdb = p_substituate_pdb[:-4] + "_" + str(
                                val_sheap["best_similarity"]) + ".pdb"

                            # write all substruct in global file
                            writePDBfile.coordinateSection(
                                d_filout_superimposed["global"],
                                lig_parsed,
                                recorder="HETATM",
                                header=str(p_lig.split("/")[-1]) + "_" +
                                str(val_sheap["best_similarity"]),
                                connect_matrix=1)

                            # control sheap thresold
                            if float(val_sheap["best_similarity"]
                                     ) >= thresold_shaep:

                                # write subligand superimposed selected in global files
                                writePDBfile.coordinateSection(
                                    d_filout_superimposed["sheap"],
                                    lig_parsed,
                                    recorder="HETATM",
                                    header=str(p_lig.split("/")[-1]) + "_" +
                                    str(val_sheap["best_similarity"]),
                                    connect_matrix=1)

                                ############
                                # write BS #
                                ############
                                # not only protein superimposed -> also ion and water
                                l_atom_complex = parsePDB.loadCoordSectionPDB(
                                    p_complex)
                                superposeStructure.applyMatrixProt(
                                    l_atom_complex, p_matrix)
                                p_file_cx = p_dir_result_ref + "CX_" + p_lig.split(
                                    "/")[-1]
                                # write CX
                                writePDBfile.coordinateSection(
                                    p_file_cx,
                                    l_atom_complex,
                                    recorder="ATOM",
                                    header=p_lig.split("/")[-1],
                                    connect_matrix=0)

                                # search atom in BS
                                l_atom_binding_site = []
                                for atom_complex in l_atom_complex:
                                    for atom_substruct in lig_parsed:
                                        if parsePDB.distanceTwoatoms(
                                                atom_substruct,
                                                atom_complex) <= thresold_BS:
                                            if not atom_complex in l_atom_binding_site:
                                                l_atom_binding_site.append(
                                                    deepcopy(atom_complex))

                                # 3. retrieve complet residue
                                l_atom_BS_res = parsePDB.getResidues(
                                    l_atom_binding_site, l_atom_complex)

                                # 4. write binding site
                                p_binding = p_dir_result_ref + "BS_" + p_lig.split(
                                    "/")[-1]
                                writePDBfile.coordinateSection(
                                    p_binding,
                                    l_atom_BS_res,
                                    "ATOM",
                                    p_binding,
                                    connect_matrix=0)

                                # smile code substituate analysis
                                # Step smile -> not conversion if shaep not validate
                                smile_find = runOtherSoft.babelConvertPDBtoSMILE(
                                    p_substituate_pdb)
                                if not struct_type in d_smile.keys():
                                    d_smile[struct_type] = {}
                                    d_smile[struct_type][smile_find] = {}
                                    d_smile[struct_type][smile_find][
                                        "count"] = 1
                                    d_smile[struct_type][smile_find]["PDB"] = [
                                        pdbfile.split("_")[1]
                                    ]
                                    d_smile[struct_type][smile_find][
                                        "ligand"] = [pdbfile.split("_")[0]]
                                    d_smile[struct_type][smile_find]["ref"] = [
                                        ref_folder
                                    ]
                                else:
                                    if not smile_find in d_smile[
                                            struct_type].keys():
                                        d_smile[struct_type][smile_find] = {}
                                        d_smile[struct_type][smile_find][
                                            "count"] = 1
                                        d_smile[struct_type][smile_find][
                                            "PDB"] = [pdbfile.split("_")[1]]
                                        d_smile[struct_type][smile_find][
                                            "ligand"] = [
                                                pdbfile.split("_")[0]
                                            ]
                                        d_smile[struct_type][smile_find][
                                            "ref"] = [ref_folder]
                                    else:
                                        d_smile[struct_type][smile_find][
                                            "count"] = d_smile[struct_type][
                                                smile_find]["count"] + 1
                                        d_smile[struct_type][smile_find][
                                            "PDB"].append(
                                                pdbfile.split("_")[1])
                                        d_smile[struct_type][smile_find][
                                            "ligand"].append(
                                                pdbfile.split("_")[0])
                                        d_smile[struct_type][smile_find][
                                            "ref"].append(ref_folder)

                            else:
                                if not struct_type in d_control[
                                        "out sheap"].keys():
                                    d_control["out sheap"][struct_type] = 1
                                else:
                                    d_control["out sheap"][
                                        struct_type] = d_control["out sheap"][
                                            struct_type] + 1

        tool.closeDicoFile(d_filout_superimposed)

    # sheap control
    tool.closeDicoFile(d_filout_sheap)
    for p_file_sheap in d_filout_sheap["list"]:
        runOtherSoft.RhistogramMultiple(p_file_sheap)

    # write list of smile
    for substruct in d_smile.keys():
        p_list_smile = pathManage.result(
            name_lig) + "list_" + substruct + "_" + str(
                thresold_shaep) + "_smile.txt"
        filout_smile = open(p_list_smile, "w")
        for smile_code in d_smile[substruct].keys():
            l_lig = d_smile[substruct][smile_code]["ligand"]
            l_PDB = d_smile[substruct][smile_code]["PDB"]
            l_ref = d_smile[substruct][smile_code]["ref"]
            filout_smile.write(
                str(smile_code) + "\t" +
                str(d_smile[substruct][smile_code]["count"]) + "\t" +
                " ".join(l_PDB) + "\t" + " ".join(l_ref) + "\t" +
                " ".join(l_lig) + "\n")
        filout_smile.close()
    p_log.close()

    # control
    filout_control.write("NB ref: " + str(d_control["pr ref"]) + "\n")
    filout_control.write("Ligand query: " + str(d_control["lig query"]) + "\n")
    for k in d_control["subref"].keys():
        filout_control.write("LSR " + str(k) + ": " +
                             str(d_control["subref"][k]) + "\n")
    for k in d_control["subref empty"].keys():
        filout_control.write("NB LSR empty " + str(k) + ": " +
                             str(d_control["subref empty"][k]) + "\n")
    for k in d_control["out sheap"].keys():
        filout_control.write("LSR out by sheap " + str(k) + ": " +
                             str(d_control["out sheap"][k]) + "\n")

    filout_control.write("**********************\n\n")
    for k in d_control["subref"].keys():
        filout_control.write("LSR keep" + str(k) + ": " +
                             str(d_control["subref"][k] -
                                 d_control["out sheap"][k]) + "\n")

    filout_control.close()

    return 1