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 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 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 extractLGDfile(prclassif, prresult):
"""Extract from folder classification """
# test if file in folder result
if len(listdir(prresult)) > 1:
return prresult
lprref = []
lfoldergroups = listdir(prclassif)
for foldergroup in lfoldergroups:
if foldergroup == "cycle":
lsubtypes = listdir(prclassif + "/cycle/")
for subtype in lsubtypes:
lrefprot = listdir(prclassif + "/cycle/" + subtype)
for refprot in lrefprot:
lprref.append(prclassif + "/cycle/" + subtype + "/" + refprot)
else:
lrefprot = listdir(prclassif + "/" + foldergroup + "/")
for refprot in lrefprot:
lprref.append(prclassif + "/" + foldergroup + "/" + refprot)
lout = []
for prefprot in lprref:#########################################to reduce
refprot = prefprot.split("/")[-1]
if not refprot in lout:
pathManage.generatePath(prresult + refprot)
lout.append(refprot)
# copy file LGD
lfileLGD = listdir(prefprot + "/LGD/")
for fileLGD in lfileLGD:
ligid = fileLGD.split("_")[1]
if ligid == "REF":
ligid = fileLGD.split("_")[2]
pdbid = refprot.split("_")[-1]
LSR = "REF"
else:
pdbid = fileLGD.split("_")[2]
LSR = prefprot.split("/")[-2].replace("_", "")
if prefprot.split("/")[-3] == "cycle":
LSR = "cycle-" + str(LSR)
nameout = str(LSR) + "_" + str(ligid) + "_" + str(pdbid) + str(fileLGD[-4:])
copyfile(prefprot + "/LGD/" + fileLGD, prresult + refprot + "/" + nameout)
# extract SMILES LSR
dLSR = {}
pfileLSR = prresult + refprot + "/listLSRsmiles"
filoutLSR = open(pfileLSR, "w")
# header
ltypeLSR = ["pi1", "pi2", "pi3"]
filoutLSR.write("\t".join(ltypeLSR) + "\n")
prLSRin = prefprot + "/LSR/"
lfileLSR = listdir(prLSRin)
for fileLSR in lfileLSR:
if search("^LSR", fileLSR) and search("pdb", fileLSR):
lelemname = fileLSR.split("_")
nameLSR = lelemname[1]
if nameLSR == "REF":
continue
else:
lig = lelemname[2]
PDBid = lelemname[3]
smiles = runOtherSoft.babelConvertPDBtoSMILE (prLSRin + fileLSR, rm_smi = 1)
#print(smiles, "l101 - ligandSimilarity")
kin = str(lig) + "-" + PDBid
if not kin in dLSR.keys():
dLSR[kin] = {}
for typeLSR in ltypeLSR:
dLSR[kin][typeLSR] = "-"
dLSR[kin][nameLSR] = smiles
# write filout
for kin in dLSR.keys():
lsmiles = [dLSR[kin][i] for i in ltypeLSR]
filoutLSR.write(kin + "\t" + "\t".join(lsmiles) + "\n")
filoutLSR.close()
return prresult
def extractLGDfile(prclassif, prresult):
"""Extract from folder classification """
# test if file in folder result
#if len(listdir(prresult)) > 1:
# return prresult
lprref = []
lfoldergroups = listdir(prclassif)
for foldergroup in lfoldergroups:
if foldergroup == "cycle":
lsubtypes = listdir(prclassif + "/cycle/")
for subtype in lsubtypes:
lrefprot = listdir(prclassif + "/cycle/" + subtype)
for refprot in lrefprot:
lprref.append(prclassif + "/cycle/" + subtype + "/" + refprot)
else:
lrefprot = listdir(prclassif + "/" + foldergroup + "/")
for refprot in lrefprot:
lprref.append(prclassif + "/" + foldergroup + "/" + refprot)
lout = []
dLSR = {}
ltypeLSR = ["pi1", "pi2", "pi3"]
for prefprot in lprref:#########################################to reduce
refprot = prefprot.split("/")[-1]
if not refprot in lout:
pathManage.generatePath(prresult + refprot)
lout.append(refprot)
# copy file LGD
lfileLGD = listdir(prefprot + "/LGD/")
for fileLGD in lfileLGD:
ligid = fileLGD.split("_")[1]
if ligid == "REF":
ligid = fileLGD.split("_")[2]
pdbid = refprot.split("_")[-1]
LSR = "REF"
else:
pdbid = fileLGD.split("_")[2]
LSR = prefprot.split("/")[-2].replace("_", "")
if prefprot.split("/")[-3] == "cycle":
LSR = "cycle-" + str(LSR)
nameout = str(LSR) + "_" + str(ligid) + "_" + str(pdbid) + str(fileLGD[-4:])
copyfile(prefprot + "/LGD/" + fileLGD, prresult + refprot + "/" + nameout)
# extract SMILES LSR
folderresult = prresult + refprot + "/"
if not folderresult in dLSR.keys():
dLSR[folderresult] = {}
prLSRin = prefprot + "/LSR/"
lfileLSR = listdir(prLSRin)
for fileLSR in lfileLSR:
#print prefprot + "/LSR/" + fileLSR,"l93===ligandSimilarity"
if search("^LSR", fileLSR) and search("pdb", fileLSR):
lelemname = fileLSR.split("_")
nameLSR = lelemname[1]
if nameLSR == "REF":
continue
else:
lig = lelemname[2]
PDBid = lelemname[3]
smiles = runOtherSoft.babelConvertPDBtoSMILE (prLSRin + fileLSR, rm_smi = 1)
#print(smiles, "l101 - ligandSimilarity")
kin = str(lig) + "-" + PDBid
if not kin in dLSR[folderresult].keys():
dLSR[folderresult][kin] = {}
for typeLSR in ltypeLSR:
dLSR[folderresult][kin][typeLSR] = "-"
dLSR[folderresult][kin][nameLSR] = smiles
#print dLSR
# write filout
for folderresult in dLSR.keys():
pfileLSR = folderresult + "listLSRsmiles"
if path.exists(pfileLSR):
filoutLSR = open(pfileLSR, "a")
else:
filoutLSR = open(pfileLSR, "w")
filoutLSR.write("\t".join(ltypeLSR) + "\n")
for kin in dLSR[folderresult].keys():
lsmiles = [dLSR[folderresult][kin][i] for i in ltypeLSR]
print lsmiles, "l.122 ligandSimilarity.py"
filoutLSR.write(kin + "\t" + "\t".join(lsmiles) + "\n")
filoutLSR.close()
return prresult
