def searchNeighborAtom(substruct_parsed,
lig_query_parsed,
struct_type,
log_file,
thresold_superimposed_ribose=2.5,
thresold_superimposed_pi=3):
l_atom_substituate = []
if struct_type == "ribose":
for atom_substruct in substruct_parsed:
for atom_query in lig_query_parsed:
if parsePDB.distanceTwoatoms(
atom_substruct,
atom_query) <= thresold_superimposed_ribose:
out = copy(atom_query)
if not out in l_atom_substituate:
l_atom_substituate.append(out)
else:
l_atom_interest = retrievePi(substruct_parsed)
for atom_interest in l_atom_interest:
for atom_query in lig_query_parsed:
if parsePDB.distanceTwoatoms(
atom_interest, atom_query) <= thresold_superimposed_pi:
out = copy(atom_query)
if not out in l_atom_substituate:
l_atom_substituate.append(out)
# control out empty
if l_atom_substituate == []:
log_file.write("[Not substituate] -> " +
substruct_parsed[0]["resName"] + struct_type + "\n")
return []
else:
return l_atom_substituate
def searchNeighborAtom(substruct_parsed, lig_query_parsed, struct_type, log_file, thresold_superimposed_ribose = 2.5, thresold_superimposed_pi = 3 ) :
l_atom_substituate = []
if struct_type == "ribose" :
for atom_substruct in substruct_parsed :
for atom_query in lig_query_parsed :
if parsePDB.distanceTwoatoms(atom_substruct, atom_query) <= thresold_superimposed_ribose :
out = copy(atom_query)
if not out in l_atom_substituate :
l_atom_substituate.append (out)
else :
l_atom_interest = retrievePi (substruct_parsed)
for atom_interest in l_atom_interest :
for atom_query in lig_query_parsed :
if parsePDB.distanceTwoatoms(atom_interest, atom_query) <= thresold_superimposed_pi :
out = copy(atom_query)
if not out in l_atom_substituate :
l_atom_substituate.append (out)
# control out empty
if l_atom_substituate == [] :
log_file.write ("[Not substituate] -> " + substruct_parsed[0] ["resName"]+ struct_type + "\n")
return []
else :
return l_atom_substituate
def RMSDTwoList (l_atom1, l_atom2) :
nb_ca = 0.0
d_max = {"value": 0.0}
diff_position_all = 0.0
diff_position_ca = 0.0
if len (l_atom1) != len (l_atom2) or len (l_atom2) == 0 :
print "ERROR - RMSD: list length different or null"
return []
else :
i = 0
while i < len (l_atom1):
if l_atom1[i]["name"] != l_atom2[i]["name"] and l_atom1[i]["resName"] != l_atom2[i]["resName"]:
print l_atom1[i]["name"] , l_atom2[i]["name"]
print "ERROR"
return []
else :
d_atom = parsePDB.distanceTwoatoms(l_atom1[i], l_atom2[i])
diff_position_all = diff_position_all + d_atom
if l_atom1[i]["name"] == "CA" :
diff_position_ca = diff_position_ca + d_atom
nb_ca = nb_ca + 1
if d_atom > d_max["value"] :
d_max["value"] = d_atom
d_max["atom"] = l_atom1[i]["name"] + "-" + l_atom2[i]["name"] + "_" + l_atom1[i]["resName"] + "-" + l_atom2[i]["resName"]
i = i + 1
# print d_max
return [sqrt(diff_position_all / len (l_atom1)), sqrt (diff_position_ca / nb_ca), d_max["value"], len (l_atom1)]
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 enantiomer(l_ligand, name_folder_final, debug = 1) :
"to do file output"
pr_final = pathManage.result("final_" + name_folder_final)
pr_enantiomer = pathManage.generatePath(pr_final + "enantiomer/")
l_ref = []
d_filout = {}
for ligand in l_ligand :
d_filout[ligand] = {}
d_filout[ligand]["O3OP"]= open (pr_enantiomer + ligand + "_" + "O3OP" , "w")
d_filout[ligand]["O4O5"]= open (pr_enantiomer + ligand + "_" + "O4O5" , "w")
d_filout[ligand]["OPOP"]= open (pr_enantiomer + ligand + "_" + "OPOP" , "w")
l_pr_type_ref = listdir(pr_final)
for pr_type_ref in l_pr_type_ref :
if debug : print "1", pr_type_ref
# case where pr_substruct is a file not a folder
try : l_pr_sub = listdir(pr_final + pr_type_ref + "/")
except : continue
for pr_sub in l_pr_sub :
print "2", pr_sub
# case cycle -> append in list respertory with new folder
if pr_sub == "cycle" :
l_pr_sub.remove ("cycle")
l_pr_sub_cycle = listdir (pr_final + pr_type_ref + "/cycle")
for pr_sub_cycle in l_pr_sub_cycle :
l_pr_sub.append ("cycle/" + pr_sub_cycle)
break
for pr_sub in l_pr_sub :
try : l_pr_ref = listdir (pr_final + pr_type_ref + "/" + pr_sub)
except : pass
if debug : print "3", pr_sub
for pr_ref in l_pr_ref :
if debug : print "4", pr_ref
# case no folder
try : l_file = listdir(pr_final + pr_type_ref + "/" + pr_sub + "/" + pr_ref + "/LGD/")
except : continue
for name_file in l_file :
if search("LGD_REF_A",name_file) and search(".pdb",name_file):
#print "2222", l_ref
if name_file.split("_")[3][:4] in l_ref :
print "!!!!!", "IN"
break
else : l_ref.append (name_file.split ("_")[3][:4])
ligand = name_file.split ("_")[2]
l_atom_ligand = parsePDB.loadCoordSectionPDB(pr_final + pr_type_ref + "/" + pr_sub + "/" + pr_ref + "/LGD/" + name_file, "HETATM")
d_minO3OP = 100
for atom_ligand in l_atom_ligand :
if atom_ligand["name"] == "O4'" :
atom_O4 = atom_ligand
elif atom_ligand["name"] == "O5'" :
atom_O5 = atom_ligand
elif atom_ligand["name"] == "O3'" :
atom_O3 = atom_ligand
elif atom_ligand["name"] == "O1A" :
atom_O1A = atom_ligand
elif atom_ligand["name"] == "O2A" :
atom_O2A = atom_ligand
elif atom_ligand["name"] == "O1B" :
atom_O1B = atom_ligand
elif atom_ligand["name"] == "O2B" :
atom_O2B = atom_ligand
#elif atom_ligand["name"] == "O3B" :
# atom_O3B = atom_ligand
# d O4 - O5
try : d_O4O5 = parsePDB.distanceTwoatoms(atom_O4, atom_O5)
except : continue
d_filout[ligand]["O4O5"].write (pr_ref + "_" + pr_type_ref + "\t" + str (d_O4O5) + "\n")
# d O3 - OP
for atom_ligand in l_atom_ligand :
if ligand == "AMP" :
if atom_ligand["name"] == "O1P" or atom_ligand["name"] == "O2P" or atom_ligand["name"] == "O3P" :
d_tempO3OP = parsePDB.distanceTwoatoms(atom_O3, atom_ligand)
if d_tempO3OP < d_minO3OP :
d_minO3OP = d_tempO3OP
atom_tempO3OP = deepcopy(atom_ligand)
else :
if atom_ligand["name"] == "O1A" or atom_ligand["name"] == "O2A" or atom_ligand["name"] == "O3A" :
d_tempO3OP = parsePDB.distanceTwoatoms(atom_O4, atom_ligand)
if d_tempO3OP < d_minO3OP :
d_minO3OP = d_tempO3OP
atom_tempO3OP = deepcopy(atom_ligand)
d_filout[ligand]["O3OP"].write (pr_ref + "_" + pr_type_ref +"_" + str(atom_tempO3OP["name"]) + "\t" + str (d_minO3OP) + "\n")
# d OP OP
d_OP = {}
if ligand == "ATP" or ligand == "ADP" :
d_OP ["O1AO1B"] = parsePDB.distanceTwoatoms(atom_O1A, atom_O1B)
d_OP ["O1AO2B"] = parsePDB.distanceTwoatoms(atom_O1A, atom_O2B)
#d_OP ["O1AO3B"] = parsePDB.distanceTwoatoms(atom_O1A, atom_O3B)
d_OP ["O2AO1B"] = parsePDB.distanceTwoatoms(atom_O2A, atom_O1B)
d_OP ["O2AO2B"] = parsePDB.distanceTwoatoms(atom_O2A, atom_O2B)
#d_OP ["O2AO3B"] = parsePDB.distanceTwoatoms(atom_O2A, atom_O3B)
d_minOPOP = min (d_OP.values())
#print d_minOPOP
k_min = [name for name, age in d_OP.items() if age == min (d_OP.values())][0]
#print k_min
d_filout[ligand]["OPOP"].write (pr_ref + "_" + pr_type_ref + "_" + str(k_min) + "\t" + str (d_minOPOP) + "\n")
try :
del d_OP
del atom_O1A
del atom_O1B
del atom_O2A
del atom_O2B
except :
pass
try :
del atom_O3
del atom_O4
del atom_O5
except :
pass
# close files
for lig in l_ligand :
for type_dist in d_filout[lig].keys () :
p_file = d_filout[lig][type_dist].name
d_filout[lig][type_dist].close ()
runOtherSoft.Rhistogram(p_file, type_dist, brk = 20)
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 analyseIons (pr_dataset, name_ligand, p_filout, thresold_max_interaction = 4.0) :
l_folder_ref = listdir(pr_dataset)
filout = open (p_filout, "w")
if name_ligand == "ATP" :
filout.write ("PDB\tIon\tD1\tD2\tD3\tAngle1\tAngle2\tAt1\tAt2\tA3\n")
else :
filout.write ("PDB\tIon\tD1\tD2\tAngle\tAt1\tAt2\n")
# dictionnary of counting
d_count = {}
d_count["CX"] = 0
d_count["CX + ions"] = 0
d_count["BS + ions"] = 0
d_count["BS + 1-ion"] = 0
d_count["BS + 2-ions"] = 0
d_count["BS + more-ions"] = 0
d_count["Interact-1"] = 0
d_count["Interact-2"] = 0
# dictionnary by ions
d_ions = {}
for ref_folder in l_folder_ref :
only_one = 0
if len (ref_folder) != 4 :
continue
d_count["CX"] = d_count["CX"] + 1
l_temp = []
# path and complex
p_lig_ref = pathManage.findligandRef(pr_dataset + ref_folder + "/", name_ligand)
p_complex = pathManage.findPDBRef(pr_dataset + ref_folder + "/")
# parsing
lig_ref_parsed = parsePDB.loadCoordSectionPDB(p_lig_ref, "HETATM")
l_het_parsed = parsePDB.loadCoordSectionPDB(p_complex, "HETATM")
# retrieve phosphate
l_pi = retrieveTwoAtomForAngle (lig_ref_parsed, name_ligand)
if l_pi == [] : # case ligand without phosphate
continue
flag_interact = 0
flag_between_1 = 0
flag_between_2 = 0
for het_parsed in l_het_parsed :
if het_parsed["resName"] in l_ions :
d_count["CX + ions"] = d_count["CX + ions"] + 1
if not het_parsed ["resName"] in d_ions.keys () :
d_ions[het_parsed["resName"]] = 0
if not het_parsed["resName"] in l_temp :
d_ions[het_parsed["resName"]] = d_ions[het_parsed["resName"]] + 1
l_temp.append (het_parsed["resName"])
PDB_id = ref_folder
d1 = parsePDB.distanceTwoatoms(l_pi[0], het_parsed)
d2 = parsePDB.distanceTwoatoms(l_pi[1], het_parsed)
if name_ligand == "ATP" :
# print len(l_pi), ref_folder, p_lig_ref
d3 = parsePDB.distanceTwoatoms(l_pi[2], het_parsed)
angle_bis = parsePDB.angleVector(l_pi[1], het_parsed, l_pi[2])
angle = parsePDB.angleVector(l_pi[0], het_parsed, l_pi[1])
if d1 < 10 and d2 < 10 :
if not het_parsed["resName"] in d_count.keys () :
d_count[het_parsed["resName"]] = 0
if only_one == 0 :
d_count[het_parsed["resName"]] = d_count[het_parsed["resName"]] + 1
only_one = 1
d_count["BS + ions"] = d_count["BS + ions"] + 1
flag_interact = flag_interact + 1
if d1 < thresold_max_interaction and d2 < thresold_max_interaction :
flag_between_1 = flag_between_1 + 1
if name_ligand == "ATP" :
if d3 < thresold_max_interaction and d2 < thresold_max_interaction :
flag_between_2 = flag_between_2 + 1
filout.write (str (PDB_id) + "\t" + str(het_parsed["resName"]) + "\t" + str(d1) + "\t" + str(d2) + "\t" + str (d3) + "\t" + str(angle) + "\t" + str(angle_bis) + "\t" + str(l_pi[0]["serial"]) + "\t" + str(l_pi[1]["serial"]) + "\t" + str(l_pi[2]["serial"]) + "\n")
else :
filout.write (str (PDB_id) + "\t" + str(het_parsed["resName"]) + "\t" + str(d1) + "\t" + str(d2) + "\t" + str(angle) + "\t" + str(l_pi[0]["serial"]) + "\t" + str(l_pi[1]["serial"]) + "\n")
if flag_interact == 1 :
d_count["BS + 1-ion"] = d_count["BS + 1-ion"] + 1
elif flag_interact == 2 :
d_count["BS + 2-ions"] = d_count["BS + 2-ions"] + 1
elif flag_interact > 2 :
d_count["BS + more-ions"] = d_count["BS + more-ions"] + 1
if flag_between_1 >= 1 :
d_count["Interact-1"] = d_count["Interact-1"] + flag_between_1
if flag_between_2 >= 1 :
d_count["Interact-2"] = d_count["Interact-2"] + flag_between_2
filout.close ()
filout_count = open (p_filout[0:-4] + "count.txt", "w")
filout_count.write ("CX: " + str (d_count["CX"]) + "\n")
filout_count.write ("CX + ions: " + str (d_count["CX + ions"]) + "\n")
filout_count.write ("BS + ions: " + str(d_count["BS + ions"]) + "\n")
filout_count.write ("BS + 1-ion: " + str(d_count["BS + 1-ion"]) + "\n")
filout_count.write ("BS + 2-ions: " + str(d_count["BS + 2-ions"]) + "\n")
filout_count.write ("BS + more-ions: " + str(d_count["BS + more-ions"]) + "\n")
filout_count.write ("Interact Pi-alpha + Pi-beta: " + str(d_count["Interact-1"]) + "\n")
filout_count.write ("Interact Pi-beta + Pi-gama: " + str(d_count["Interact-2"]) + "\n")
filout_count.close ()
filout_by_ion = open(p_filout[0:-4] + "byIons_" + name_ligand, "w")
l_k = d_ions.keys ()
for k in l_k :
filout_by_ion.write (str (k.capitalize()) + "\t" + str (d_ions[k]) + "\n")
filout_by_ion.close ()
runOtherSoft.barplot (p_filout[0:-4] + "byIons_" + name_ligand)
def computeRMSDBS (p_ref, p_query, p_substruct, pr_result, thresold_BS = 6) :
l_atom_query_parsed = parsePDB.loadCoordSectionPDB(p_query, "ATOM")
l_atom_ref_parsed = parsePDB.loadCoordSectionPDB(p_ref, "ATOM")
l_atom_substruct = parsePDB.loadCoordSectionPDB(p_substruct)
l_BS_ref = []
for atom_substruct in l_atom_substruct :
for atom_ref in l_atom_ref_parsed :
d_atom = parsePDB.distanceTwoatoms(atom_substruct, atom_ref)
if d_atom <= thresold_BS :
l_BS_ref.append (atom_ref)
# retrieve residue full
l_BS_ref = parsePDB.getResidues(l_BS_ref, l_atom_ref_parsed)
# print len (l_BS_ref)
# print len (l_atom_query_parsed)
l_BS_query = []
flag_identic_crystal = 1
for atomBS_ref in l_BS_ref :
# print atomBS_parsed
d_max = 100.0
for atom_query in l_atom_query_parsed :
if atom_query["resName"] == atomBS_ref["resName"] and atom_query["name"] == atomBS_ref["name"] :
d = parsePDB.distanceTwoatoms(atom_query, atomBS_ref)
if d < d_max :
d_max = d
res_temp = atom_query
#if d_max < thresold_BS :
if "res_temp" in locals () :
l_BS_query.append (deepcopy(res_temp))
# identic check number
if res_temp["resSeq"] != atomBS_ref["resSeq"] :
flag_identic_crystal = 0
#else :
# case structure not found
# return []
# print len (l_BS_query), len (l_BS_ref)
l_RMSD = RMSDTwoList (l_BS_query, l_BS_ref)
# write PDB
#p_filout_pdb = pr_result + p_query.split ("/")[-1][0:-4] + "_" + str (flag_identic_crystal) + "_" + p_substruct.split ("_")[-2] + "_" + p_ref.split ("/")[-1]
#filout_pdb = open (p_filout_pdb, "w")
#writePDBfile.coordinateSection(filout_pdb, l_BS_ref, recorder = "ATOM")
#writePDBfile.coordinateSection(filout_pdb, l_BS_query, recorder = "ATOM", header = 0 )
#filout_pdb.close ()
if l_RMSD == [] :
return []
else :
return l_RMSD + [flag_identic_crystal]