Louis BECQUEY

renamed renumbered_rna_only to rna_only

......@@ -321,8 +321,7 @@ class Chain:
self.file = path_to_3D_data+"rna_mapped_to_Rfam/"+self.chain_label+".cif"
else:
status = f"Extract {self.pdb_id}-{self.pdb_chain_id}"
self.file = path_to_3D_data+"renumbered_rna_only/"+self.chain_label+".cif"
#self.file = path_to_3D_data+"rna_only/"+self.chain_label+".cif"
self.file = path_to_3D_data+"rna_only/"+self.chain_label+".cif"
# Check if file exists, if yes, abort (do not recompute)
if os.path.exists(self.file):
......@@ -1517,9 +1516,9 @@ class Pipeline:
# extract chains of pure RNA
os.makedirs(path_to_3D_data + "rna_only")
'''
if (not self.HOMOLOGY) and not os.path.isdir(path_to_3D_data + "renumbered_rna_only"):
if (not self.HOMOLOGY) and not os.path.isdir(path_to_3D_data + "rna_only"):
# extract chains of pure RNA
os.makedirs(path_to_3D_data + "renumbered_rna_only")
os.makedirs(path_to_3D_data + "rna_only")
# define and run jobs
joblist = []
......
......@@ -1503,7 +1503,7 @@ def measure_from_structure(f):
warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.PDBConstructionWarning)
warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.BiopythonWarning)
parser=MMCIFParser()
s = parser.get_structure(f, os.path.abspath(path_to_3D_data+ "renumbered_rna_only/" + f))
s = parser.get_structure(f, os.path.abspath(path_to_3D_data+ "rna_only/" + f))
measures_aa(name, s, thr_idx)
if DO_HIRE_RNA_MEASURES:
......@@ -1837,7 +1837,7 @@ def measures_hrna(name, s, thr_idx):
@trace_unhandled_exceptions
def measures_hrna_basepairs(name, s, thr_idx):
"""
Open a renumbered_rna_only/ file, and run measures_hrna_basepairs_chain() on every chain
Open a rna_only/ file, and run measures_hrna_basepairs_chain() on every chain
"""
setproctitle(f"RNANet statistics.py Worker {thr_idx+1} measures_hrna_basepairs({name})")
......@@ -2884,7 +2884,7 @@ if __name__ == "__main__":
# if n_unmapped_chains:
# os.makedirs(runDir+"/results/geometry/all-atoms/distances/", exist_ok=True)
# liste_struct = os.listdir(path_to_3D_data + "renumbered_rna_only")
# liste_struct = os.listdir(path_to_3D_data + "rna_only")
# if '4zdo_1_E.cif' in liste_struct:
# liste_struct.remove('4zdo_1_E.cif') # weird cases to remove for now
# if '4zdp_1_E.cif' in liste_struct:
......