def applyTMAlign (substruct):
p_dir_dataset = pathManage.dataset(substruct)
l_folder = listdir(p_dir_dataset)
for ref_folder in l_folder:
if len (ref_folder) != 4:
continue
l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
p_pdb_ref = pathManage.findPDBRef(p_dir_dataset + ref_folder + "/")
for pdbfile in l_pdbfile:
# try if PDB not ligand
if len(pdbfile.split ("_")[0]) != 4 or not search (".pdb", pdbfile):
continue
# same alignment
elif p_dir_dataset + ref_folder + "/" + pdbfile == p_pdb_ref:
continue
else:
p_file_pdb = p_dir_dataset + ref_folder + "/" + pdbfile
p_dir_align = pathManage.alignmentOutput(substruct + "/" + p_pdb_ref.split ("/")[-1][:-4] + "__" + p_file_pdb.split ("/")[-1][:-4])
# superimpose
runOtherSoft.runTMalign(p_file_pdb, p_pdb_ref, p_dir_align)
return 1
def applyTMAlign(substruct):
p_dir_dataset = pathManage.dataset(substruct)
l_folder = listdir(p_dir_dataset)
for ref_folder in l_folder:
if len(ref_folder) != 4:
continue
l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
p_pdb_ref = pathManage.findPDBRef(p_dir_dataset + ref_folder + "/")
for pdbfile in l_pdbfile:
# try if PDB not ligand
if len(pdbfile.split("_")[0]) != 4 or not search(".pdb", pdbfile):
continue
# same alignment
elif p_dir_dataset + ref_folder + "/" + pdbfile == p_pdb_ref:
continue
else:
p_file_pdb = p_dir_dataset + ref_folder + "/" + pdbfile
p_dir_align = pathManage.alignmentOutput(
substruct + "/" + p_pdb_ref.split("/")[-1][:-4] + "__" +
p_file_pdb.split("/")[-1][:-4])
# superimpose
runOtherSoft.runTMalign(p_file_pdb, p_pdb_ref, p_dir_align)
return 1
def searchReplacement (smile, PDB_query, PDB_ref, name_ligand, in_cycle = 0) :
metal_find = searchMetal (smile)
if metal_find != 0 :
p_dir_dataset = pathManage.dataset(name_ligand + "/" + PDB_ref)
l_PDB_query = pathManage.findPDBQueryDataset(p_dir_dataset)
for p_query in l_PDB_query :
if search (PDB_query, p_query):
p_PDB_query = p_query
break
if "p_PDB_query" in locals() :
l_atom_parsed = parsePDB.loadCoordSectionPDB(p_query)
l_ions_PDB = parsePDB.retrieveListIon(l_atom_parsed)
if metal_find in l_ions_PDB :
l_atom_ion = parsePDB.retrieveLigand(l_atom_parsed, metal_find)
filout = open (p_dir_dataset + str(metal_find) + "_" + p_query.split("/")[-1], "w")
for atom_ion in l_atom_ion :
writePDBfile.coordinateSection(filout, atom_ion, recorder = "HETATM", header = str(metal_find), connect_matrix = 0)
filout.close ()
return "metal", metal_find
if in_cycle == 0:
if searchRing(smile) == 1 :
return "cycle",""
if searchP(smile) == 1 :
return "P", ""
elif searchB(smile) == 1 :
return "B",""
elif searchF (smile) == 1 :
return "F", ""
elif searchCl (smile) == 1 :
return "Cl", ""
elif searchBr (smile) == 1 :
return "Br", ""
elif searchBe (smile) == 1 :
return "Be", ""
elif searchNO2 (smile) == 1 :
return "NO2", ""
elif searchSulfonyl(smile) == 1:
return "SO2",""
elif searchS (smile) == 1 :
return "S", ""
elif searchCON (smile) == 1 :
return "CON",""
elif searchCarboxy (smile) == 1 :
return "COO",""
elif searchConly(smile) == 1 :
return "onlyC", ""
elif searchCandO (smile) == 1 :
return "C+O", ""
elif searchCandN (smile) == 1 :
return "C+N", ""
elif searchCandOandN (smile) == 1 :
return "C+O+N", ""
return "other" ,""
def datasetPreparation (ligand_ID, clean = 1):
p_dir_dataset = pathManage.dataset(ligand_ID)
l_folder = listdir(p_dir_dataset)
indent = 0
for ref_folder in l_folder :
# file include in dataset folder
if len (ref_folder) != 4:
continue
l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
indent = indent + 1
print ref_folder, indent
# clean repertory -> only PDB ref and PDB
l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
if clean == 1 :
for pdbfile in l_pdbfile :
p_file_pdb = p_dir_dataset + ref_folder + "/" + pdbfile
if not search (".pdb", pdbfile ) or search ("subref", pdbfile) or len (pdbfile.split("_")[0]) == 3:
remove (p_file_pdb)
l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
for pdbfile in l_pdbfile :
p_file_pdb = p_dir_dataset + ref_folder + "/" + pdbfile
# extract ligand in PDB
l_ligand = parsePDB.retrieveListLigand(p_file_pdb)
# print l_ligand
if l_ligand == []:
continue
else:
l_atom_pdb_parsed = parsePDB.loadCoordSectionPDB(p_file_pdb)
for name_ligand in l_ligand :
l_lig_parsed = parsePDB.retrieveLigand(l_atom_pdb_parsed, name_ligand)
if l_lig_parsed == [] :
continue
p_filout_ligand = p_dir_dataset + ref_folder + "/" + name_ligand + "_" + path.split(p_file_pdb)[1]
writePDBfile.coordinateSection(p_filout_ligand , l_lig_parsed[0], "HETATM", header=0 , connect_matrix = 1)
# ligand_ID write for shaep
# print p_dir_dataset + ref_folder + "/"
p_lig_ref = pathManage.findligandRef(p_dir_dataset + ref_folder + "/", ligand_ID)
if p_lig_ref == 0:
continue
# print p_lig_ref
lig_ref_parsed = parsePDB.loadCoordSectionPDB(p_lig_ref)
d_l_atom_substruct = substructTools.retrieveSubstruct(lig_ref_parsed, ligand_ID)
# case with AMP without phosphate
if d_l_atom_substruct == {}:
continue
# write ligand_ID
for subs in d_l_atom_substruct.keys ():
p_filout_substruct = p_dir_dataset + ref_folder + "/subref_" + subs + "_" + ref_folder + ".pdb"
writePDBfile.coordinateSection(p_filout_substruct , d_l_atom_substruct [subs], "HETATM", header=0 , connect_matrix = 1)
return 1
def ionIdentification(name_ligand):
"""
step 4
search in the close environment if metal is here
compute distance and angles
"""
# in folder
p_dir_dataset = pathManage.dataset(name_ligand)
p_filout = pathManage.result(name_ligand) + "ionsAnalysis.txt"
ionSearch.analyseIons(p_dir_dataset, name_ligand, p_filout)
def classifRefProtein(pr_dataset,
l_lig,
thresold_identity=30.0,
thresold_similarity=30.0):
pr_out = pathManage.result("clasifRef")
# case fasta file
pr_align_seq = pathManage.generatePath(pr_out + "alignSeq/")
l_p_fasta = []
for lig in l_lig:
pr_dataset = pathManage.dataset(lig)
l_file_by_lig = listdir(pr_dataset)
l_pr_ref_by_lig = [pr_dataset + x for x in l_file_by_lig]
for pr_ref_by_lig in l_pr_ref_by_lig:
PDB_folder = pr_ref_by_lig.split("/")[-1]
try:
l_file = listdir(pr_ref_by_lig)
except:
continue
for file_ref in l_file:
if search("^" + PDB_folder, file_ref):
PDB_ID = file_ref[0:-4]
PDB_ID = PDB_ID[0:4].lower() + PDB_ID[4:]
# PDB ID with chain associated
p_fasta = downloadFile.importFasta(
PDB_ID,
pr_align_seq,
dir_by_PDB=0,
debug=1,
fastaGlobal="/home/borrel/Yue_project/pdb_seqres.txt")
l_p_fasta.append(p_fasta)
break
d_outNeedle = applyNeedleList(l_p_fasta, pr_align_seq)
# writeMatrix
writeMatrixFromDico(d_outNeedle, pr_out + "matrixSimilarSeq", "similarity")
writeMatrixFromDico(d_outNeedle, pr_out + "matrixIDSeq", "identity")
#Group reference -> l 209
p_group_id = GroupRef(
d_outNeedle, "identity",
pr_out + "groupIdentity" + "_" + str(thresold_identity) + ".txt",
thresold_identity, l_lig)
p_group_sim = GroupRef(
d_outNeedle, "similarity",
pr_out + "groupSimilarity" + "_" + str(thresold_similarity) + ".txt",
thresold_similarity, l_lig)
# merge not alone prot
MergeGroup(p_group_id)
MergeGroup(p_group_sim)
def ionIdentification (name_ligand):
"""
step 4
search in the close environment if metal is here
compute distance and angles
"""
# in folder
p_dir_dataset = pathManage.dataset(name_ligand)
p_filout = pathManage.result(name_ligand) + "ionsAnalysis.txt"
ionSearch.analyseIons (p_dir_dataset, name_ligand, p_filout)
def builtDatasetGlobal(p_list_ligand,
ligand_ID,
thresold_RX=2.5,
thresold_blast=1e-4,
verbose=1):
# directory with dataset
p_dir_dataset = pathManage.dataset(ligand_ID)
# directory with result
p_dir_result = pathManage.result(ligand_ID + "/datasetBuilding")
# first extract reference
d_dataset = extractReference(p_list_ligand, p_dir_dataset, p_dir_result,
ligand_ID)
# file with name and family
analysis.familyPDBRef(d_dataset, p_dir_dataset + "family_PDB.txt")
if verbose: toolViewStructDataset(d_dataset)
# select reference
# remove RX and same chain
p_dir_align = pathManage.result(ligand_ID + "/datasetBuilding/aligmentRef")
filterReferenceByOne(d_dataset,
p_dir_align,
ligand_ID,
thresold_RX=thresold_RX)
if verbose: toolViewStructDataset(d_dataset)
# conserve only unique protein
filterGlobalDataset(d_dataset, p_dir_align)
if verbose: toolViewStructDataset(d_dataset)
# run blast by sequence conserved
p_dir_blast = pathManage.result(ligand_ID + "/datasetBuilding/blast")
RunBlast.globalRun(d_dataset, p_dir_blast)
if verbose: toolViewStructDataset(d_dataset)
# filter by e-value and RX
filterBlastResult(d_dataset,
p_dir_dataset,
ligand_ID,
thresold_RX=thresold_RX,
thresold_blast=thresold_blast)
if verbose: toolViewStructDataset(d_dataset)
# clean folder dataset
cleanFolderDataset(d_dataset, p_dir_dataset)
def builtDatasetGlobal (p_list_ligand, ligand_ID, thresold_RX = 2.5, thresold_blast = 1e-4, verbose = 1 ):
# directory with dataset
p_dir_dataset = pathManage.dataset(ligand_ID)
# directory with result
p_dir_result = pathManage.result(ligand_ID + "/datasetBuilding")
# first extract reference
d_dataset = extractReference (p_list_ligand, p_dir_dataset, p_dir_result, ligand_ID)
# file with name and family
analysis.familyPDBRef (d_dataset, p_dir_dataset + "family_PDB.txt")
if verbose : toolViewStructDataset (d_dataset)
# select reference
# remove RX and same chain
p_dir_align = pathManage.result(ligand_ID + "/datasetBuilding/aligmentRef")
filterReferenceByOne (d_dataset, p_dir_align, ligand_ID, thresold_RX = thresold_RX)
if verbose : toolViewStructDataset (d_dataset)
# conserve only unique protein
filterGlobalDataset (d_dataset, p_dir_align)
if verbose : toolViewStructDataset (d_dataset)
# run blast by sequence conserved
p_dir_blast = pathManage.result(ligand_ID + "/datasetBuilding/blast")
RunBlast.globalRun (d_dataset, p_dir_blast)
if verbose : toolViewStructDataset (d_dataset)
# filter by e-value and RX
filterBlastResult (d_dataset, p_dir_dataset,ligand_ID, thresold_RX = thresold_RX, thresold_blast = thresold_blast)
if verbose : toolViewStructDataset (d_dataset)
# clean folder dataset
cleanFolderDataset (d_dataset, p_dir_dataset)
def classifRefProtein (pr_dataset, l_lig, thresold_identity = 30.0, thresold_similarity = 30.0):
pr_out = pathManage.result("clasifRef")
# case fasta file
pr_align_seq = pathManage.generatePath(pr_out + "alignSeq/")
l_p_fasta = []
for lig in l_lig :
pr_dataset = pathManage.dataset(lig)
l_file_by_lig = listdir(pr_dataset)
l_pr_ref_by_lig =[pr_dataset + x for x in l_file_by_lig]
for pr_ref_by_lig in l_pr_ref_by_lig :
PDB_folder = pr_ref_by_lig.split ("/")[-1]
try : l_file = listdir(pr_ref_by_lig)
except : continue
for file_ref in l_file :
if search("^" + PDB_folder, file_ref) :
PDB_ID = file_ref[0:-4]
PDB_ID = PDB_ID[0:4].lower () + PDB_ID[4:]
# PDB ID with chain associated
p_fasta = downloadFile.importFasta(PDB_ID, pr_align_seq, dir_by_PDB = 0, debug = 1, fastaGlobal = "/home/borrel/Yue_project/pdb_seqres.txt")
l_p_fasta.append (p_fasta)
break
d_outNeedle = applyNeedleList (l_p_fasta, pr_align_seq)
# writeMatrix
writeMatrixFromDico (d_outNeedle, pr_out + "matrixSimilarSeq", "similarity" )
writeMatrixFromDico (d_outNeedle, pr_out + "matrixIDSeq", "identity" )
#Group reference -> l 209
p_group_id = GroupRef (d_outNeedle, "identity", pr_out + "groupIdentity" +"_" + str (thresold_identity) + ".txt", thresold_identity, l_lig)
p_group_sim = GroupRef (d_outNeedle, "similarity", pr_out + "groupSimilarity" +"_" + str (thresold_similarity) + ".txt", thresold_similarity, l_lig)
# merge not alone prot
MergeGroup (p_group_id)
MergeGroup (p_group_sim)
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
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
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
def datasetPreparation(ligand_ID, clean=1):
p_dir_dataset = pathManage.dataset(ligand_ID)
l_folder = listdir(p_dir_dataset)
indent = 0
for ref_folder in l_folder:
# file include in dataset folder
if len(ref_folder) != 4:
continue
l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
indent = indent + 1
print ref_folder, indent
# clean repertory -> only PDB ref and PDB
l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
if clean == 1:
for pdbfile in l_pdbfile:
p_file_pdb = p_dir_dataset + ref_folder + "/" + pdbfile
if not search(".pdb", pdbfile) or search(
"subref", pdbfile) or len(pdbfile.split("_")[0]) == 3:
remove(p_file_pdb)
l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
for pdbfile in l_pdbfile:
p_file_pdb = p_dir_dataset + ref_folder + "/" + pdbfile
# extract ligand in PDB
l_ligand = parsePDB.retrieveListLigand(p_file_pdb)
# print l_ligand
if l_ligand == []:
continue
else:
l_atom_pdb_parsed = parsePDB.loadCoordSectionPDB(p_file_pdb)
for name_ligand in l_ligand:
l_lig_parsed = parsePDB.retrieveLigand(
l_atom_pdb_parsed, name_ligand)
if l_lig_parsed == []:
continue
p_filout_ligand = p_dir_dataset + ref_folder + "/" + name_ligand + "_" + path.split(
p_file_pdb)[1]
writePDBfile.coordinateSection(p_filout_ligand,
l_lig_parsed[0],
"HETATM",
header=0,
connect_matrix=1)
# ligand_ID write for shaep
# print p_dir_dataset + ref_folder + "/"
p_lig_ref = pathManage.findligandRef(p_dir_dataset + ref_folder + "/",
ligand_ID)
if p_lig_ref == 0:
continue
# print p_lig_ref
lig_ref_parsed = parsePDB.loadCoordSectionPDB(p_lig_ref)
d_l_atom_substruct = substructTools.retrieveSubstruct(
lig_ref_parsed, ligand_ID)
# case with AMP without phosphate
if d_l_atom_substruct == {}:
continue
# write ligand_ID
for subs in d_l_atom_substruct.keys():
p_filout_substruct = p_dir_dataset + ref_folder + "/subref_" + subs + "_" + ref_folder + ".pdb"
writePDBfile.coordinateSection(p_filout_substruct,
d_l_atom_substruct[subs],
"HETATM",
header=0,
connect_matrix=1)
return 1
def countingSubstituent (name_final, debug = 1):
pr_final_folder = pathManage.result("final_" + name_final)
d_count = {}
d_lig = {}
d_by_ref = {}
d_count_pr = {}
l_file_final = listdir(pr_final_folder)
if debug : print "1", pr_final_folder
for pr_type_subref in l_file_final :
# case where pr type is a file not a folder
try : l_pr_sub = listdir(pr_final_folder + pr_type_subref + "/")
except : continue
if debug: print "2",pr_final_folder + pr_type_subref + "/"
# case cycle append one directory
if "cycle" in l_pr_sub :
l_pr_sub.remove ("cycle")
l_second_sub = listdir (pr_final_folder + pr_type_subref + "/cycle/")
for second_sub in l_second_sub :
l_pr_sub.append ("cycle/" + second_sub)
for pr_sub in l_pr_sub :
# case where pr_type_substituent is a folder
try : l_pr_PDBref = listdir(pr_final_folder + pr_type_subref + "/" + pr_sub + "/")
except : continue
if debug : print "3", pr_final_folder + pr_type_subref, pr_sub
for pr_PDBref in l_pr_PDBref :
PDB_ref = pr_PDBref.split ("_")[-1]
family_ref = pr_PDBref.split ("-")[0]
group_ref = pr_PDBref.split ("_")[0].split ("-")[-1]
pr_LGD = pr_final_folder + pr_type_subref + "/" + pr_sub + "/" + pr_PDBref + "/LGD/"
pr_LSR = pr_final_folder + pr_type_subref + "/" + pr_sub + "/" + pr_PDBref + "/LSR/"
pr_BS = pr_final_folder + pr_type_subref + "/" + pr_sub + "/" + pr_PDBref + "/BS/"
if debug :
print "4",pr_LGD
print "4", pr_BS
print "4", pr_LSR
################
# folder LSR #
################
l_file_LSR = listdir (pr_LSR)
for file_LSR in l_file_LSR :
# -> count by type sub reference
if search ("LSR_", file_LSR) and file_LSR.split ("_")[1] != "REF" :
ligand_sub = file_LSR.split ("_")[1]
if debug : print "5", file_LSR
if not ligand_sub in d_count.keys () :
d_count[ligand_sub] = {}
if not pr_sub in d_count[ligand_sub].keys () :
d_count[ligand_sub][pr_sub] = 0
d_count[ligand_sub][pr_sub] = d_count[ligand_sub][pr_sub] + 1
################
# complet LSR #
################
elif search ("LSR", file_LSR):
# case LSR reference #
######################
if search ("REF_", file_LSR) :
lig_ref = file_LSR.split ("_")[2][:3]
if not lig_ref in d_by_ref.keys () :
d_by_ref[lig_ref] = {}
type_ref = pr_type_subref.split ("_")[0]
if not type_ref in d_by_ref[lig_ref].keys () :
d_by_ref[lig_ref][type_ref] = 0
d_by_ref[lig_ref][type_ref] = d_by_ref[lig_ref][type_ref] + 1
#################
# folder LGD #
#################
l_file_LGD = listdir(pr_LGD)
for file_LGD in l_file_LGD :
# print file_ref
if search ("LGD", file_LGD):
ligand = file_LGD.split ("_")[1]
if ligand == "REF" :
continue
if not ligand in d_lig.keys () :
d_lig[ligand] = {}
d_lig[ligand]["count"] = 0
d_lig[ligand]["group"] = []
d_lig[ligand]["family"] = []
d_lig[ligand]["count"] = d_lig[ligand]["count"] + 1
d_lig[ligand]["family"].append (str(family_ref))
d_lig[ligand]["group"].append (str(group_ref))
###############
# folder BS #
###############
l_file_BS = listdir(pr_BS)
for file_BS in l_file_BS :
if search ("BS_REF", file_BS):
lig_ref = file_BS.split ("_")[2]
pr_ref = file_BS.split ("_")[3].split (".")[0]
print lig_ref, pr_ref, "*****"
if not lig_ref in d_count_pr.keys () :
d_count_pr[lig_ref] = {}
d_count_pr[lig_ref]["pr ref"] = []
d_count_pr[lig_ref]["pr queries"] = []
d_count_pr[lig_ref]["lig queries"] = []
if not pr_ref in d_count_pr[lig_ref]["pr ref"] :
d_count_pr[lig_ref]["pr ref"].append (pr_ref)
try:
family = analysis.findFamily (pr_ref, pathManage.dataset (lig_ref) + "family_PDB.txt")
if not family in d_count_pr[lig_ref].keys () :
d_count_pr[lig_ref][family] = 0
d_count_pr[lig_ref][family] = d_count_pr[lig_ref][family] + 1
except: pass
# BS -> query
for file_BS in l_file_BS :
# for not reference BS
if not search ("BS_REF", file_BS) :
lig_querie = file_BS.split ("_")[1]
prot_querie = file_BS.split ("_")[2][0:4]
print prot_querie, lig_querie, "*******"
# find ligand reference
# lig ref define in previous step
d_count_pr[lig_ref]["pr queries"].append (prot_querie)
d_count_pr[lig_ref]["lig queries"].append (lig_querie)
# write and plot #
##################
pr_result = pathManage.generatePath(pr_final_folder + "counting/")
for ligand_sub in d_count.keys () :
p_filout = pr_result + ligand_sub
filout = open (p_filout, "w")
filout.write ("\t".join(d_count[ligand_sub].keys ()) + "\n")
l_value = [str(x) for x in d_count[ligand_sub].values ()]
filout.write ("\t".join(l_value) + "\n")
filout.close ()
runOtherSoft.piePlot(p_filout)
filout_lig = open (pr_result + "count_ligand", "w")
filout_lig.write ("Ligand ID\tNumber of occurences in the dataset\tNumber of different clusters\tList of clusters\tList of protein families\n")
for lig in d_lig.keys () :
if d_lig[lig] > 1 :
filout_lig.write (str (lig) + "\t" + str (d_lig[lig]["count"]) + "\t" + str(len (list (set(d_lig[lig]["group"])))) + "\t" + " ".join (d_lig[lig]["group"]) + "\t" + " ".join (d_lig[lig]["family"]) + "\n")
filout_lig.close ()
filout_LSR_lig = open (pr_result + "CountByLigandRef", "w")
for lig_ref in d_by_ref.keys () :
filout_LSR_lig.write ("====" + str (lig_ref) + "====\n")
for sub_ref in d_by_ref[lig_ref].keys () :
filout_LSR_lig.write (str (sub_ref) + ": " + str (d_by_ref[lig_ref][sub_ref]) + "\n")
filout_LSR_lig.close ()
filout_pr_count = open (pr_result + "count_pr", "w")
for lig in d_count_pr.keys () :
filout_pr_count.write ("====" + str (lig) + "====\n")
filout_pr_count.write ("nb ref pr: " + str (len (d_count_pr[lig]["pr ref"])) + "\n")
filout_pr_count.write ("nb querie pr: " + str (len (d_count_pr[lig]["pr queries"])) + "\n")
filout_pr_count.write ("nb ligand queries: " + str (len (d_count_pr[lig]["lig queries"])) + "\n")
for family in d_count_pr[lig].keys () :
if family != "pr ref" and family != "pr queries" and family != "lig queries" :
filout_pr_count.write ("Ref " + str (family) + ": " + str (d_count_pr[lig][family]) + "\n")
filout_pr_count.close ()
runOtherSoft.barplot(pr_result + "count_ligand")
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
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
