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6 additions
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7 deletions
... | @@ -321,8 +321,7 @@ class Chain: | ... | @@ -321,8 +321,7 @@ class Chain: |
321 | self.file = path_to_3D_data+"rna_mapped_to_Rfam/"+self.chain_label+".cif" | 321 | self.file = path_to_3D_data+"rna_mapped_to_Rfam/"+self.chain_label+".cif" |
322 | else: | 322 | else: |
323 | status = f"Extract {self.pdb_id}-{self.pdb_chain_id}" | 323 | status = f"Extract {self.pdb_id}-{self.pdb_chain_id}" |
324 | - self.file = path_to_3D_data+"renumbered_rna_only/"+self.chain_label+".cif" | 324 | + self.file = path_to_3D_data+"rna_only/"+self.chain_label+".cif" |
325 | - #self.file = path_to_3D_data+"rna_only/"+self.chain_label+".cif" | ||
326 | 325 | ||
327 | # Check if file exists, if yes, abort (do not recompute) | 326 | # Check if file exists, if yes, abort (do not recompute) |
328 | if os.path.exists(self.file): | 327 | if os.path.exists(self.file): |
... | @@ -1517,9 +1516,9 @@ class Pipeline: | ... | @@ -1517,9 +1516,9 @@ class Pipeline: |
1517 | # extract chains of pure RNA | 1516 | # extract chains of pure RNA |
1518 | os.makedirs(path_to_3D_data + "rna_only") | 1517 | os.makedirs(path_to_3D_data + "rna_only") |
1519 | ''' | 1518 | ''' |
1520 | - if (not self.HOMOLOGY) and not os.path.isdir(path_to_3D_data + "renumbered_rna_only"): | 1519 | + if (not self.HOMOLOGY) and not os.path.isdir(path_to_3D_data + "rna_only"): |
1521 | # extract chains of pure RNA | 1520 | # extract chains of pure RNA |
1522 | - os.makedirs(path_to_3D_data + "renumbered_rna_only") | 1521 | + os.makedirs(path_to_3D_data + "rna_only") |
1523 | 1522 | ||
1524 | # define and run jobs | 1523 | # define and run jobs |
1525 | joblist = [] | 1524 | joblist = [] | ... | ... |
... | @@ -1503,7 +1503,7 @@ def measure_from_structure(f): | ... | @@ -1503,7 +1503,7 @@ def measure_from_structure(f): |
1503 | warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.PDBConstructionWarning) | 1503 | warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.PDBConstructionWarning) |
1504 | warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.BiopythonWarning) | 1504 | warnings.simplefilter('ignore', Bio.PDB.PDBExceptions.BiopythonWarning) |
1505 | parser=MMCIFParser() | 1505 | parser=MMCIFParser() |
1506 | - s = parser.get_structure(f, os.path.abspath(path_to_3D_data+ "renumbered_rna_only/" + f)) | 1506 | + s = parser.get_structure(f, os.path.abspath(path_to_3D_data+ "rna_only/" + f)) |
1507 | 1507 | ||
1508 | measures_aa(name, s, thr_idx) | 1508 | measures_aa(name, s, thr_idx) |
1509 | if DO_HIRE_RNA_MEASURES: | 1509 | if DO_HIRE_RNA_MEASURES: |
... | @@ -1837,7 +1837,7 @@ def measures_hrna(name, s, thr_idx): | ... | @@ -1837,7 +1837,7 @@ def measures_hrna(name, s, thr_idx): |
1837 | @trace_unhandled_exceptions | 1837 | @trace_unhandled_exceptions |
1838 | def measures_hrna_basepairs(name, s, thr_idx): | 1838 | def measures_hrna_basepairs(name, s, thr_idx): |
1839 | """ | 1839 | """ |
1840 | - Open a renumbered_rna_only/ file, and run measures_hrna_basepairs_chain() on every chain | 1840 | + Open a rna_only/ file, and run measures_hrna_basepairs_chain() on every chain |
1841 | """ | 1841 | """ |
1842 | 1842 | ||
1843 | setproctitle(f"RNANet statistics.py Worker {thr_idx+1} measures_hrna_basepairs({name})") | 1843 | setproctitle(f"RNANet statistics.py Worker {thr_idx+1} measures_hrna_basepairs({name})") |
... | @@ -2884,7 +2884,7 @@ if __name__ == "__main__": | ... | @@ -2884,7 +2884,7 @@ if __name__ == "__main__": |
2884 | 2884 | ||
2885 | # if n_unmapped_chains: | 2885 | # if n_unmapped_chains: |
2886 | # os.makedirs(runDir+"/results/geometry/all-atoms/distances/", exist_ok=True) | 2886 | # os.makedirs(runDir+"/results/geometry/all-atoms/distances/", exist_ok=True) |
2887 | - # liste_struct = os.listdir(path_to_3D_data + "renumbered_rna_only") | 2887 | + # liste_struct = os.listdir(path_to_3D_data + "rna_only") |
2888 | # if '4zdo_1_E.cif' in liste_struct: | 2888 | # if '4zdo_1_E.cif' in liste_struct: |
2889 | # liste_struct.remove('4zdo_1_E.cif') # weird cases to remove for now | 2889 | # liste_struct.remove('4zdo_1_E.cif') # weird cases to remove for now |
2890 | # if '4zdp_1_E.cif' in liste_struct: | 2890 | # if '4zdp_1_E.cif' in liste_struct: | ... | ... |
-
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