gemmi-protools 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

gemmi_protools/peptide.py

@@ -0,0 +1,32 @@
+"""
+@Author: Luo Jiejian
+"""
+from copy import deepcopy
+
+from Bio.PDB.Polypeptide import nucleic_letters_3to1_extended, protein_letters_3to1_extended
+
+
+def strip_key_val(inputs):
+    outputs = dict()
+    for key, val in inputs.items():
+        outputs[key.strip()] = val.strip()
+    return outputs
+
+
+def __nucleic_3to1_mapper():
+    mapper = deepcopy(nucleic_letters_3to1_extended)
+    mapper["DN"] = "N"
+    mapper["N"] = "N"
+    new_mapper = strip_key_val(mapper)
+    return new_mapper
+
+
+def __protein_3to1_mapper():
+    mapper = deepcopy(protein_letters_3to1_extended)
+    mapper["UNK"] = "X"
+    new_mapper = strip_key_val(mapper)
+    return new_mapper
+
+
+nucleic_3to1_mapper = __nucleic_3to1_mapper()
+protein_3to1_mapper = __protein_3to1_mapper()

gemmi_protools/reader.py

@@ -9,7 +9,6 @@ from typing import Union, Optional, List
 
 import gemmi
 import numpy as np
-from Bio.PDB.Polypeptide import nucleic_letters_3to1_extended, protein_letters_3to1_extended
 from typeguard import typechecked
 
 from .cif_opts import _cif_block_for_output, _is_cif
@@ -17,12 +16,9 @@ from .parser import (_assign_digital_entity_names, _ent_from_structure,
                      pdb_parser, cif_parser, _chain_type, _chain_names2one_letter,
                      _assert_unique_chain_names_in_models, get_assembly)
 from .pdb_opts import _compound_source_string, _is_pdb
+from .peptide import nucleic_3to1_mapper, protein_3to1_mapper
 from .struct_info import Info
 
-nucleic_letters_3to1_extended["DN"] = "N"
-nucleic_letters_3to1_extended["N"] = "N"
-protein_letters_3to1_extended["UNK"] = "X"
-
 
 class StructureParser(object):
     """
@@ -417,9 +413,9 @@ class StructureParser(object):
         residues = self.chain_residues(polymer_only=True, with_water=False)[chain_id]
 
         if c_type == "protein":
-            one_letter_code = "".join([protein_letters_3to1_extended.get(r, "X") for r in residues])
+            one_letter_code = "".join([protein_3to1_mapper.get(r, "X") for r in residues])
         elif c_type in ["dna", "rna"]:
-            one_letter_code = "".join([nucleic_letters_3to1_extended.get(r, "N") for r in residues])
+            one_letter_code = "".join([nucleic_3to1_mapper.get(r, "N") for r in residues])
         else:
             one_letter_code = ""
         return one_letter_code

{gemmi_protools-0.1.3.dist-info → gemmi_protools-0.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmi_protools
-Version: 0.1.3
+Version: 0.1.4
 Summary: An Enhanced tool to process PDB structures based on Gemmi
 Author-email: Luo Jiejian <luojiejian12@mails.ucas.ac.cn>
 License-Expression: MIT

{gemmi_protools-0.1.3.dist-info → gemmi_protools-0.1.4.dist-info}/RECORD

@@ -6,11 +6,12 @@ gemmi_protools/dockq.py,sha256=JGPQ7Xs7gz9wubVVT9WSP5lZsLnfgcUH-_nLJ3c8I3U,4172
 gemmi_protools/parse_pdb_header.py,sha256=UOGMsE3-d3APhO7zaAEE0NT31n-iqt55VpDh_RPOicI,14223
 gemmi_protools/parser.py,sha256=QIJCOfK8FaFbLMvBG82zTOAjIvQJcf2WRwuFSxj4zvc,8982
 gemmi_protools/pdb_opts.py,sha256=NbXLDNNVF7tuG_bUM0Infylf5aYnOCP2Pd-ndqm5bK4,5652
+gemmi_protools/peptide.py,sha256=a2wiEutJmvhl6gDCIzzqRCbmyknk2mwgy2FZ53lXclU,750
 gemmi_protools/ppi.py,sha256=nRzRWv28SDjVt6hMShRL_QYKFsBO1xA5jSGIQrN0JBg,2313
-gemmi_protools/reader.py,sha256=4xuK7UmJVc6Nt9YhYS1FPsi5PL4QwZHilk8s3V-jf0Y,15499
+gemmi_protools/reader.py,sha256=u7872K-XeUW_sr0E1SaQWrPVWm88jPBUN8LLzf0flM0,15321
 gemmi_protools/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR58X8,2769
-gemmi_protools-0.1.3.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
-gemmi_protools-0.1.3.dist-info/METADATA,sha256=ymS32ZVWiYY7LDzrQkEqiatqY2qZBqenf3X0BvX5DT4,567
-gemmi_protools-0.1.3.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-gemmi_protools-0.1.3.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
-gemmi_protools-0.1.3.dist-info/RECORD,,
+gemmi_protools-0.1.4.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
+gemmi_protools-0.1.4.dist-info/METADATA,sha256=aKz2slj7fXafD3SnNaI0apr7PIxK87FFXnnwHcCVfvw,567
+gemmi_protools-0.1.4.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+gemmi_protools-0.1.4.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
+gemmi_protools-0.1.4.dist-info/RECORD,,