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 waterGlobal (name_database, limit_acc = 00.0):
"""
Number of water molecules in PDB
arg: -> Path folder database
-> name folder result
-> limit acc
return: NONE
"""
pr_result = pathManage.result (name_database + "/water")
# retrieve list PDB file
l_PDBID = managePDB.retriveListPDB(name_database)
# calcul acc with NACESS
if limit_acc != 0.0 :
for PDB_ID in l_PDBID :
p_PDB = pathManage.pathDitrectoryPDB () + PDB_ID + ".pdb"
runOtherSoft.runNACESS(p_PDB, pathManage.pathDitrectoryPDB (), multi_run = 0)
p_filout = waterAnalysis.resolutionWater(l_PDBID, pr_result, limit_acc)
runScriptR.waterPlotResolution (p_filout)