def ligands(name_database, pr_init):
'''search ligands in PDB database
out : list of ligands with PDB files associated'''
print "Start Search Ligand In PDB file"
# control file exist
if path.exists(pr_init + "resultLigandInPDB") and path.getsize(pr_init + "resultLigandInPDB") != 0:
return pr_init + "resultLigandInPDB"
# import list PBD from file .dat
# http://www.rcsb.org/pdb/rest/representatives?cluster=50
l_PDB = managePDB.retriveListPDB(name_database)
l_d_lig = []
for PDB_ID in l_PDB:
d_lig_PDB = structure.ligandPDB()
d_lig_PDB["name"] = PDB_ID
l_lig_in = parsing.retrieveListLigand(pathManage.pathDitrectoryPDB() + PDB_ID.lower() + ".pdb")
d_lig_PDB["ligands"] = l_lig_in
l_d_lig.append(d_lig_PDB)
# write result file
p_out = writeFile.resultLigandInPDB(l_d_lig, pr_init)
print "END Search Ligand In PDB file"
return p_out
def ControlHETATOMModelFile (pr_data, pr_result, l_lig_control = []):
# Write file ligand
l_ligand = listdir(pr_data)
for ligand in l_ligand :
# control if file exist and size
p_file_lig = pathManage.CreatePathDir(pr_result + str (ligand) + "/" ) + "ligInModel"
if path.exists(p_file_lig) :
return
else :
file_lig = open (p_file_lig, "w")
print "ligand", ligand
l_file = listdir(pr_data + ligand + "/")
d_temp = {}
for model_file in l_file :
l_lig_PDB = parsing.retrieveListLigand(pr_data + ligand + "/" + model_file)
print "***", l_lig_PDB
if len (l_lig_PDB) == 0 :
continue
else :
for lig in l_lig_PDB :
if not l_lig_control == [] and lig in l_lig_control :
if not lig in d_temp.keys () :
d_temp[lig] = []
d_temp[lig].append (pr_data + ligand + "/" + model_file)
else :
continue
# write temp control
for lig in d_temp.keys () :
file_lig.write (str (lig) + "\t" + " ".join(d_temp[lig]) + "\n")
file_lig.close ()
return
