def SearchChemicalSubstruct (pr_data, pr_result, control = 0):
# substructure search
p_filout = pr_result + "findSruct"
filout = open (p_filout, "w")
l_ligand = listdir(pr_data)
print l_ligand
for ligand in l_ligand :
print ligand
l_file = listdir(pr_data + ligand + "/")
for f in l_file :
if ligand == "ZM241385" or ligand == "source":
group = f
else :
group = f.split ("_")[-2]
p_file_PDB = pr_data + ligand + "/" + f
print p_file_PDB
if control == 1 :
ControlPDBFormat(p_file_PDB)
l_atom = parsing.loadCoordSectionPDB(p_file_PDB, remove_H = 1)
if ligand == "ZM241385" :
ll_atom_lig = parsing.retrieveLigand(l_atom, "ZMA")
else :
ll_atom_lig = parsing.retrieveLigand(l_atom, "RES")
for l_atom_lig in ll_atom_lig :
l_subs = searchPDB.interestStructure(l_atom_lig, more_flex = 1)
filout.write (str (ligand) + "\t" + str (f) + "\t" + str (group) + "\t" + " ".join(l_subs) + "\n")
filout.close ()
# best group ergomine -> 2128 (2013) && 6882 (2013)
# best group taladegid -> 7527 (2013) Vanderblit
# best group eticlopride -> 1285 (2010)
# ZM241385 => mod7msp
def ControlPDBFormat (p_PDB):
"""
Rewrite model PDB file
"""
l_res = ["ILE", "LEU", "LYS", "PHE", "TYR", "VAL", "SER", "MET", "ARG", "TRP", "PRO", "GLY", "GLU", "ASN", "HIS", "ALA", "ASP", "GLN", "THR", "CYS"]
l_atom_PDB = parsing.loadCoordSectionPDB(p_PDB)
filout = open (p_PDB, "w")
l_atom_het = []
for atom_PDB in l_atom_PDB :
if atom_PDB["resName"] in l_res :
writePDBfile.coordinateSection(filout, [atom_PDB], "ATOM", header = 0)
else :
l_atom_het.append (deepcopy(atom_PDB))
writePDBfile.coordinateSection(filout, l_atom_het, recorder = "HETATM", header = 0, connect_matrix = 1)
filout.close ()