def WriteDataset (d_lig_PDB, pr_init, debug = 1) :
"""
Write folder with dataset
-> run quality criteria analysis
"""
pr_quality = pathManage.parsingDataset(pr_init)
l_RX = []
l_RFree = []
d_dataset = structure.resolutionFilter()
for lig in d_lig_PDB.keys () :
if debug == 1 :
print "===Write dataset-1==="
print lig, "ligand"
print d_lig_PDB[lig], "list of PDB"
for PDB in d_lig_PDB[lig]:
if debug == 1 :
print "===Write dataset-2==="
print PDB, lig, "PDB + lig"
print d_dataset, "append struct"
quality = parsing.Quality(PDB)
RX = quality[0]
RFree = quality[1]
BuilderDatasetDict(PDB, lig, RX, d_dataset)
l_RX.append (RX)
l_RFree.append (RFree)
# quality
p_rx = writeFile.listFloat(l_RX, pr_quality + "RX")
p_rf = writeFile.listFloat(l_RFree, pr_quality + "RFree")
runScriptR.histDistance(p_rx, "RX")
runScriptR.histDistance(p_rf, "RFree")
return writeFile.resultFilterLigandPDB(d_dataset, pr_init )
def GlobalBondLength (name_database, RX_thresold = 1.5):
# directory
pr_result = pathManage.result(name_database + "/CXbound" + str (RX_thresold))
pr_database = pathManage.result(name_database)
# filout with distance
p_CN = pr_result + "distanceCN"
p_CO = pr_result + "distanceCO"
p_CC = pr_result + "distanceCC"
p_coplar = pr_result + "distanceCoplar"
filout_CN = open (p_CN, "w")
filout_CO = open (p_CO, "w")
filout_CC = open (p_CC, "w")
filout_coplar = open (p_coplar, "w")
# load PDB with logand
if not path.exists(pr_database + "resultLigandInPDB") :
print "ERROR => file with ligand and PDB does not exist"
return
else :
d_lig_PDB = loadFile.LigandInPDB(pr_database + "resultLigandInPDB")
nb_lig = len(d_lig_PDB.keys())
print d_lig_PDB.keys()
i = 0
while (i < nb_lig):
name_lig = d_lig_PDB.keys()[i]
l_PDB = d_lig_PDB[name_lig]
for PDB in l_PDB :
# controle RX
RX = parsing.Quality(PDB)[0]
# print RX
if RX <= RX_thresold :
l_atom_lig = loadFile.ligandInPDBConnectMatrixLigand(PDB, name_lig)
l_distCN = BondLengthCandX (l_atom_lig, "N")
l_distCO = BondLengthCandX (l_atom_lig, "O")
l_distCC = BondLengthCandX (l_atom_lig, "C")
l_coplarIII = CoplanarityIII(l_atom_lig)
if l_distCN != [] :
filout_CN.write ("\n".join (l_distCN) + "\n")
if l_distCO != [] :
filout_CO.write ("\n".join (l_distCO) + "\n")
if l_distCC != [] :
filout_CC.write ("\n".join (l_distCC) + "\n")
if l_coplarIII != [] :
filout_coplar.write ("\n".join (l_coplarIII) + "\n")
# take only one PDB by ligand not more
i = i + 1
continue
i = i + 1
filout_CO.close ()
filout_CN.close ()
filout_CC.close ()
filout_coplar.close ()
runScriptR.histDistance(p_CN, "CN")
runScriptR.histDistance(p_CO, "CO")
runScriptR.histDistance(p_CC, "CC")
runScriptR.histDistance(p_coplar, "coplar")