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 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 applyTMAlignList(l_pr_ref, pr_out):
pathManage.generatePath(pr_out)
nb_pr_ref = len(l_pr_ref)
d_out = {}
i = 0
while i < nb_pr_ref:
j = i + 1
PDB1 = l_pr_ref[i].split("/")[-1][0:4]
# print PDB1
while j < nb_pr_ref:
PDB2 = l_pr_ref[j].split("/")[-1][0:4]
# folder TM align
pr_alignement = pr_out + PDB1 + "__" + PDB2 + "/"
#print pr_alignement
#print PDB1,i, PDB2,j
#print l_pr_ref[i]
# RUN
out_file = runOtherSoft.runTMalign(l_pr_ref[i], l_pr_ref[j],
pr_alignement)
# clean folders -> pb with several run -> clean too fast -> try / except
try:
CleanResultTMalign(pr_alignement)
except:
pass
# parse result
if not PDB1 in d_out.keys():
if not PDB2 in d_out.keys():
d_out[PDB1] = {}
d_out[PDB1][PDB2] = parseTMalign.parseOutputTMalign(
out_file[-1])
else:
d_out[PDB2][PDB1] = {}
d_out[PDB2][PDB1] = parseTMalign.parseOutputTMalign(
out_file[-1])
else:
d_out[PDB1][PDB2] = {}
d_out[PDB1][PDB2] = parseTMalign.parseOutputTMalign(
out_file[-1])
j = j + 1
i = i + 1
return d_out
def applyTMAlignList (l_pr_ref, pr_out):
pathManage.generatePath(pr_out)
nb_pr_ref = len (l_pr_ref)
d_out = {}
i = 0
while i < nb_pr_ref :
j = i + 1
PDB1 = l_pr_ref[i].split ("/")[-1][0:4]
# print PDB1
while j < nb_pr_ref :
PDB2 = l_pr_ref[j].split ("/")[-1][0:4]
# folder TM align
pr_alignement = pr_out + PDB1 + "__" + PDB2 + "/"
#print pr_alignement
#print PDB1,i, PDB2,j
#print l_pr_ref[i]
# RUN
out_file = runOtherSoft.runTMalign(l_pr_ref[i], l_pr_ref[j], pr_alignement)
# clean folders -> pb with several run -> clean too fast -> try / except
try : CleanResultTMalign (pr_alignement)
except : pass
# parse result
if not PDB1 in d_out.keys () :
if not PDB2 in d_out.keys () :
d_out[PDB1] = {}
d_out[PDB1][PDB2] = parseTMalign.parseOutputTMalign(out_file[-1])
else :
d_out[PDB2][PDB1] = {}
d_out[PDB2][PDB1] = parseTMalign.parseOutputTMalign(out_file[-1])
else :
d_out[PDB1][PDB2] = {}
d_out[PDB1][PDB2] = parseTMalign.parseOutputTMalign(out_file[-1])
j = j + 1
i = i + 1
return d_out