def applyTMAlign(substruct):
p_dir_dataset = pathManage.dataset(substruct)
l_folder = listdir(p_dir_dataset)
for ref_folder in l_folder:
if len(ref_folder) != 4:
continue
l_pdbfile = listdir(p_dir_dataset + ref_folder + "/")
p_pdb_ref = pathManage.findPDBRef(p_dir_dataset + ref_folder + "/")
for pdbfile in l_pdbfile:
# try if PDB not ligand
if len(pdbfile.split("_")[0]) != 4 or not search(".pdb", pdbfile):
continue
# same alignment
elif p_dir_dataset + ref_folder + "/" + pdbfile == p_pdb_ref:
continue
else:
p_file_pdb = p_dir_dataset + ref_folder + "/" + pdbfile
p_dir_align = pathManage.alignmentOutput(
substruct + "/" + p_pdb_ref.split("/")[-1][:-4] + "__" +
p_file_pdb.split("/")[-1][:-4])
# superimpose
runOtherSoft.runTMalign(p_file_pdb, p_pdb_ref, p_dir_align)
return 1
def analysisBS(name_lig, ID_seq='0.0', debug=1):
pr_result = pathManage.result(name_lig)
pr_out = pathManage.result(name_lig + "/sameBS")
# log files
p_log_file = pr_out + "log.txt"
filout_log = open(p_log_file, "w")
# dictionnar with files
d_file_BS = {}
d_file_BS["global"] = open(pr_out + name_lig + "_", "w")
d_file_BS["global"].write(
"name_bs\tRMSD_prot\tRMSD_BS_ca\tRMSD_BS_all\tD_max\tl_at_BS\tidentic\n"
)
d_file_BS["summary"] = open(pr_out + "summary.txt", "w")
pr_dataset = pathManage.dataset(name_lig)
l_folder_ref = listdir(pr_result)
nb_BS = 0
nb_BS_filtered = 0
nb_same_BS = 0
for PDB_ref in l_folder_ref:
if debug: print PDB_ref
if len(PDB_ref) != 4:
continue
p_pdb_ref = pathManage.findPDBRef(pr_dataset + PDB_ref + "/")
l_p_query = pathManage.findPDBQueryTransloc(
pathManage.result(name_lig) + PDB_ref + "/")
if debug: print l_p_query
for p_query in l_p_query:
# read TM Align
if debug: print p_query.split("/")[-1][7:-4]
p_TMalign = pathManage.alignmentOutput(name_lig) + p_pdb_ref.split(
"/")[-1][0:-4] + "__" + p_query.split("/")[-1][7:-4] + "/RMSD"
try:
score_align = parseTMalign.parseOutputTMalign(p_TMalign)
except:
filout_log.write("ERROR TM align " + p_TMalign + "\n")
continue
nb_BS = nb_BS + 1
if score_align["IDseq"] >= ID_seq:
nb_BS_filtered = nb_BS_filtered + 1
l_p_substruct_ref = pathManage.findSubstructRef(
pr_dataset + PDB_ref + "/", name_lig)
# sub BS
for p_substruct_ref in l_p_substruct_ref:
struct_substitued = p_substruct_ref.split("_")[-2]
# write header
if not struct_substitued in d_file_BS.keys():
d_file_BS[struct_substitued] = open(
pr_out + name_lig + "_" + struct_substitued + "_",
"w")
d_file_BS[struct_substitued].write(
"name_bs\tRMSD_prot\tRMSD_BS_ca\tRMSD_BS_all\tD_max\tl_at_BS\tidentic\n"
)
RMSD_bs = analysis.computeRMSDBS(p_pdb_ref, p_query,
p_substruct_ref, pr_out)
if RMSD_bs != []:
d_file_BS[struct_substitued].write(
p_substruct_ref.split("/")[-1][0:-4] + "_*_" +
p_query.split("/")[-1][0:-4] + "\t" +
str(score_align["RMSD"]) + "\t" + str(RMSD_bs[1]) +
"\t" + str(RMSD_bs[0]) + "\t" + str(RMSD_bs[2]) +
"\t" + str(RMSD_bs[-2]) + "\t" + str(RMSD_bs[-1]) +
"\n")
p_ligand_ref = pathManage.findligandRef(
pr_dataset + PDB_ref + "/", name_lig)
RMSD_bs_lig = analysis.computeRMSDBS(p_pdb_ref, p_query,
p_ligand_ref, pr_out)
if RMSD_bs_lig != []:
d_file_BS["global"].write(
p_ligand_ref.split("/")[-1][0:-4] + "_*_" +
p_query.split("/")[-1][0:-4] + "\t" +
str(score_align["RMSD"]) + "\t" + str(RMSD_bs_lig[1]) +
"\t" + str(RMSD_bs_lig[0]) + "\t" +
str(RMSD_bs_lig[2]) + "\t" + str(RMSD_bs_lig[-2]) +
"\t" + str(RMSD_bs_lig[-1]) + "\n")
if RMSD_bs_lig[-1] == 1:
nb_same_BS = nb_same_BS + 1
# write summary
d_file_BS["summary"].write("BS global: " + str(nb_BS) + "\n")
d_file_BS["summary"].write("BS - IDseq " + str(ID_seq) + "%: " +
str(nb_BS_filtered) + "\n")
d_file_BS["summary"].write("BS - same atom number: " + str(nb_same_BS) +
"\n")
filout_log.close()
# close files and run histograms
for k_dico in d_file_BS.keys():
p_file = d_file_BS[k_dico].name
d_file_BS[k_dico].close()
if name_lig == "ATP":
runOtherSoft.RhistogramRMSD(p_file, max_RMSD=5.0)
elif name_lig == "ADP":
runOtherSoft.RhistogramRMSD(p_file, max_RMSD=4.0)
elif name_lig == "AMP":
runOtherSoft.RhistogramRMSD(p_file, max_RMSD=4.0)
else:
runOtherSoft.RhistogramRMSD(p_file, max_RMSD=3.5)
return 1
