def GlobalAnalysisGPCR (pr_data, pr_result, dist_thresold = 5.0, chemical_search = 0, option_stat = 0, option_model = 0):
# search chemical substructures in docked ligand
if chemical_search == 1 :
SearchChemicalSubstruct(pr_data, pr_result, control = 1)
# build structure
struct_neighbor = SearchNeighbor (pr_data, pr_result, dist_thresold = dist_thresold, debug = 1)
for drug in struct_neighbor.keys () :
pr_drug = pathManage.CreatePathDir(pr_result + str(drug) + "/")
if option_stat == 1:
# statistic -> same statistic as global database
statistic.globalRunStatistic(struct_neighbor[drug], dist_thresold, pr_drug)
if option_model == 1 :
SabilizationBySB(struct_neighbor[drug], pr_drug)
def main (name_database, max_distance = 5.0, RX = 3.00, RFree = 0.25, option_superimpose = 0, option_on_complexes_by_ligand = 0, option_bond = 0, option_stat = 0, option_stat_dataset = 0, option_merge = 0, verbose = 1):
#format input
max_distance = float (max_distance)
# run one database
pr_result = pathManage.result (name_database)
# search ligand in PDB
searchPDB.ligands(name_database, pr_result)
# dataset with resolution
l_p_dataset = datasetFinal.Builder(name_database, RX, RFree, option_on_complexes_by_ligand)
# ########################
# # Parsing dataset #
# ########################
# #
if option_stat_dataset == 1 :
for p_dataset in l_p_dataset :
statistic.ParseDataSet(p_dataset)
# ####################
# # result directory #
# ####################
#
#
# run for every dataset -> with diffrent resolution
# short cut
# l_p_dataset = ["/home/borrel/saltBridgesProject/result/PDB/3.0_0.25_uniquePDB/dataset_3.00.txt" ]
# # #
for p_dataset in l_p_dataset :
pr_result = pathManage.CreatePathDir(p_dataset[:-4] + "/")
pr_hetion = pathManage.CreatePathDir(p_dataset[:-4] + "/HET/")
if verbose == 1 :
print "== control path Main =="
print pr_result
print pr_hetion
print "======================="
# # stat -> build structure, not filter is !!!
d_sub_neighbor = searchPDB.globalSearch(max_distance, p_dataset, pr_result)
# remove iron close -> statistic before
# Becarful because the dictionnary change
print "control-1", len(d_sub_neighbor["I"])
d_close_het = hetCloseAnalysis.removeNeighborIron (d_sub_neighbor, pr_hetion + "ionSummarySubstruct.txt")
print "control-2", len(d_sub_neighbor["I"])
if option_superimpose == 1 :
# superimpose neighbors -> refaire a Helsinki car MAJ de de la PDB
superimpose.globalNeighbor (d_sub_neighbor, "I", pr_result)
superimpose.globalNeighbor (d_sub_neighbor, "II", pr_result)
superimpose.globalNeighbor (d_sub_neighbor, "III", pr_result)
superimpose.globalNeighbor (d_sub_neighbor, "IMD", pr_result)
superimpose.globalNeighbor (d_sub_neighbor, "GAI", pr_result)
superimpose.globalNeighbor (d_sub_neighbor, "COO", pr_result)
# superimpose neighbors -> with het first stabilization
# superimpose.globalNeighbor (d_close_het, "I", pr_hetion)
# superimpose.globalNeighbor (d_close_het, "II", pr_hetion)
# superimpose.globalNeighbor (d_close_het, "III", pr_hetion)
# superimpose.globalNeighbor (d_close_het, "IMD", pr_hetion)
# superimpose.globalNeighbor (d_close_het, "GAI", pr_hetion)
if option_bond == 1 :
# check planarity imidazole + guanidium
statistic.planarityImidazole (d_sub_neighbor, pr_result)
statistic.planarityGuanidium (d_sub_neighbor, pr_result)
statistic.lenBondAnalysis(d_sub_neighbor, "I", pr_result)
statistic.lenBondAnalysis(d_sub_neighbor, "II", pr_result)
statistic.lenBondAnalysis(d_sub_neighbor, "III", pr_result)
if option_stat == 1:
# statistic
statistic.globalRunStatistic(d_sub_neighbor, max_distance, pr_result)
# statistic.globalRunStatistic(d_close_het, max_distance, pr_hetion)
if option_merge == 1:
if option_on_complexes_by_ligand == 1:
statistic.MergeDataSet(pathManage.result (name_database + "/" + str (RX) + "_" + str (RFree) + "_uniquePDB"), "dataset_1.50", "dataset_3.00")
statistic.MergeDataSet(pathManage.result (name_database + "/" + str (RX) + "_" + str (RFree) + "_uniquePDB"), "dataset_1.50", "dataset_3.00", arom = 1)
else :
statistic.MergeDataSet(pathManage.result (name_database + "/" + str (RX) + "_" + str (RFree)), "dataset_1.50", "dataset_3.00")
