def globalSearch (dist_thresold, p_file_dataset, pr_result, debug = 1):
pr_summary = pr_result + "Sum/"
if debug : print "Directory summary", pr_summary
# load structure in summary ---> if use need place option one PDB by ligand
d_neighbor = loadFile.loadCloseStruct (pr_summary)
if d_neighbor != None :
if debug :
print "Type of structure stock", type (d_neighbor["global"])
return d_neighbor
#start, logFile = log.initAction("search neighbors in " +path.basename(p_file_dataset))
l_lig = loadFile.resultFilterPDBLigand(p_file_dataset)
nb_lig = len(l_lig)
# ##Count Structure
d_neighbor = {}
l_neighbor_global = []
# ##Write summary file
d_files_summary = writeFile.openFileSummary(pr_summary)# sumary result
# inialization !!!!!!!
i = 0
while i < nb_lig :
if debug: print "Ligand: " + str(l_lig[i]["name"]) + " " + str(i) + " " + str(nb_lig)
nb_PDB = len(l_lig[i]["PDB"])
# take only one PDB by ligand
j = 0
while j < nb_PDB :
name_PDB = l_lig[i]["PDB"][j]
l_atom_ligand = loadFile.ExtractInfoPDBID(l_lig[i]["PDB"][j])[l_lig[i]["name"]][0] # change not tested
# search neighbor for every atom in ligand selected
globalNeighbors(dist_thresold, l_atom_ligand, name_PDB, l_neighbor_global)
# search neighbor for interest
interestGroup(dist_thresold, l_atom_ligand, name_PDB, d_neighbor)
j = j + 1
i = i + 1
writeFile.neighborStruct(d_neighbor, l_neighbor_global, d_files_summary)
writeFile.closeFileSummary(d_files_summary)
# case where load directly substructure => why do not load directly in dictionnary
d_neighbor["global"] = l_neighbor_global
return d_neighbor
def searchLigandInDataSetFile (datasetFile, nameLigand):
"""Search ligand in dataset file (out dataset construction)
in: dataset file, name of ligand
out: index of ligand or 0"""
listLigandsInPDB = loadFile.resultFilterPDBLigand(datasetFile)
nbLigand = len(listLigandsInPDB)
i = 0
while i < nbLigand :
if listLigandsInPDB[i]["name"] == nameLigand :
return i
i = i + 1
return 0
def retrievePDBFile(fileDataset, dir_PDB):
ligandWithPDB = loadFile.resultFilterPDBLigand(fileDataset)
for ligandPDB in ligandWithPDB :
for pdbName in ligandPDB["PDB"] :
pdbFilePath = dir_PDB + pdbName + ".pdb"
if not isfile(pdbFilePath) :
adressePDB = "http://www.pdb.org/pdb/files/" + pdbName + ".pdb"
try:
pathFilePDB = urlretrieve(adressePDB)
print pathFilePDB
cmd = "mv " + pathFilePDB[0] + " " + pdbFilePath
print cmd
system (cmd)
except:
print "Impossible retrieve PDB file"
def SearchNeighbor (pr_data, pr_result, dist_thresold = 5.0, debug = 1):
# write file with HETATM in PDB -> to used same function
l_lig_model = ["ZMA", "UNK", "RES", "CAU", "P0G", "CY8", "1KS"] # goal of this list is to remove the modified amino acid
ControlHETATOMModelFile (pr_data, pr_result, l_lig_control = l_lig_model)
l_drug = listdir(pr_data)
d_out = {}
for drug in l_drug :
# pr result
pr_drug = pathManage.CreatePathDir(pr_result + str(drug) + "/")
l_lig = loadFile.resultFilterPDBLigand(pr_drug + "ligInModel")
if debug == 1 :
print "List ligand for drug->"
print drug
print len (l_lig)
print l_lig
if l_lig == [] :
print "ERROR: find HET in model -> l68 GPCRDockAnalysis"
return {}
else :
#file summary
pr_summary = pr_drug + "Sum/"
# load structure in summary ---> if use need place option one PDB by ligand
d_neighbor = loadFile.loadCloseStruct (pr_summary, control_empty_file = 0)
if d_neighbor == None :
print "Write Sum File"
#write summary file
d_files_summary = writeFile.openFileSummary(pr_summary)
# structure of stock
d_neighbor = {}
l_neighbor_global = []
# search neighbor
nb_lig = len (l_lig)
i = 0
while i < nb_lig :
j = 0
nb_model = len (l_lig[i]["PDB"])
print nb_model
while j < nb_model :
l_atom_ligand = loadFile.ExtractInfoPDBID(l_lig[i]["PDB"][j])[l_lig[i]["name"]][0] # change not tested
# search neighbor for every atom in ligand selected
searchPDB.globalNeighbors(dist_thresold, l_atom_ligand, l_lig[i]["PDB"][j], l_neighbor_global)
# search neighbor for interest
searchPDB.interestGroup(dist_thresold, l_atom_ligand, l_lig[i]["PDB"][j], d_neighbor, more_flex = 1)
j = j + 1
i = i + 1
writeFile.neighborStruct(d_neighbor, l_neighbor_global, d_files_summary)
writeFile.closeFileSummary(d_files_summary)
# case where load directly substructure => why do not load directly in dictionnary
d_neighbor["global"] = l_neighbor_global
#stock
print "Stock neighbor l164:", d_neighbor.keys()
if not drug in d_out.keys () :
d_out[drug] = deepcopy(d_neighbor)
return d_out
