gemmi-protools 0.1.5__py3-none-any.whl → 0.1.6__py3-none-any.whl

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Files changed (7) hide show
  1. gemmi_protools/io/parser.py +7 -2
  2. gemmi_protools/io/pdb_opts.py +4 -2
  3. {gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.6.dist-info}/METADATA +1 -1
  4. {gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.6.dist-info}/RECORD +7 -7
  5. {gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.6.dist-info}/WHEEL +0 -0
  6. {gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.6.dist-info}/licenses/LICENSE +0 -0
  7. {gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.6.dist-info}/top_level.txt +0 -0
gemmi_protools/io/parser.py CHANGED
@@ -134,14 +134,19 @@ def pdb_parser(path: Union[str, pathlib.Path]):
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  block = struct.make_mmcif_block()
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  ent_t = _cif_entity_info(block)
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  rec = defaultdict(list)
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+
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  for cn, middle_eid in ent_t.polymer2eid.items():
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  rec[middle_eid].append(cn)
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  _mapper = _assign_digital_entity_names(struct)
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  _mapper_n = dict()
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+
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  for middle_eid, new_eid in _mapper.items():
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- old_eid = str(",".join(rec[middle_eid]))
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- _mapper_n[old_eid] = new_eid
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+ if middle_eid in rec:
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+ mid = rec[middle_eid]
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+ mid.sort()
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+ old_eid = str(",".join(mid))
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+ _mapper_n[old_eid] = new_eid
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  if _mapper_n:
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  _update_entity_names(ent_0, _mapper_n)
gemmi_protools/io/pdb_opts.py CHANGED
@@ -119,6 +119,8 @@ def _compound_source_string(entity: Entity) -> List[str]:
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  entity2polymer[v].append(k)
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  entity_labels = list(entity2polymer.keys())
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  entity_labels.sort()
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+ for v in entity2polymer.values():
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+ v.sort()
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  values = []
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  for i, el in enumerate(entity_labels):
@@ -136,9 +138,9 @@ def _compound_source_string(entity: Entity) -> List[str]:
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  compound_molecule = "COMPND {n_line:>3} MOLECULE: {molecule};"
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  compound_chain = "COMPND {n_line:>3} CHAIN: {chain};"
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- i = 0
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+ i = 1
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  for val in values:
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- if i == 0:
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+ if i == 1:
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  outputs.append(compound_mol0.format(**val))
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  i += 1
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  for c_str in [compound_molecule, compound_chain]:
{gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.6.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: gemmi_protools
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- Version: 0.1.5
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+ Version: 0.1.6
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  Summary: An Enhanced tool to process PDB structures based on Gemmi
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  Author-email: Luo Jiejian <luojiejian12@mails.ucas.ac.cn>
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  License-Expression: MIT
{gemmi_protools-0.1.5.dist-info → gemmi_protools-0.1.6.dist-info}/RECORD RENAMED
@@ -3,8 +3,8 @@ gemmi_protools/io/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E
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  gemmi_protools/io/cif_opts.py,sha256=TKND91aRGB5hYNdTFElCKMGabCg4klLk_c1evC3WZuA,6368
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  gemmi_protools/io/convert.py,sha256=780sQcwhslUD4Hj5UZMVlQdbicniJ6jNjncTl_7jaMk,3841
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  gemmi_protools/io/parse_pdb_header.py,sha256=UOGMsE3-d3APhO7zaAEE0NT31n-iqt55VpDh_RPOicI,14223
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- gemmi_protools/io/parser.py,sha256=lCeIzEnBhTl0AQPwa68PNrvj1d4vJdS99Mj-WypCvYo,9033
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- gemmi_protools/io/pdb_opts.py,sha256=VYIUsEGiFtbcK2eEUi4rsRKDCfMiV-WSXzz4zivxm7A,5686
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+ gemmi_protools/io/parser.py,sha256=NCLc9IHH-tb2hIm0jZeKu2nVw2Isr-n-pH4l7JbKA5w,9130
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+ gemmi_protools/io/pdb_opts.py,sha256=laUqxlecOe6goax12q8EJGZuZbHyIGsXVucMV3gVrgg,5741
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  gemmi_protools/io/peptide.py,sha256=a2wiEutJmvhl6gDCIzzqRCbmyknk2mwgy2FZ53lXclU,750
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  gemmi_protools/io/reader.py,sha256=oaJ5TTWLFCZ3tDq3R5dAyBqm4Q2sxmfl4D8cGvSOdl0,16060
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  gemmi_protools/io/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR58X8,2769
@@ -13,8 +13,8 @@ gemmi_protools/utils/align.py,sha256=CZcrvjy-ZbX2u7OAn-YGblbxaj9YFUDX4CFZcpbpnB8
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  gemmi_protools/utils/dockq.py,sha256=XmMwVEy-H4p6sH_HPcDWA3TP77OWdih0fE_BQJDr4pU,4189
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  gemmi_protools/utils/fixer.py,sha256=f1MAeYkFukijaBwTdINO0733Qbe5B9xSgRCE69nHkN4,8396
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  gemmi_protools/utils/ppi.py,sha256=VWYsdxWwQoS1xwEYj5KB96Zz3F8r5Eyuw6NT3ReD-wc,2330
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- gemmi_protools-0.1.5.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
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- gemmi_protools-0.1.5.dist-info/METADATA,sha256=0IypVyv4jYIvts3I3uoQC5R_6dG8dooo1B7XC9MgavQ,567
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- gemmi_protools-0.1.5.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
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- gemmi_protools-0.1.5.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
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- gemmi_protools-0.1.5.dist-info/RECORD,,
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+ gemmi_protools-0.1.6.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
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+ gemmi_protools-0.1.6.dist-info/METADATA,sha256=N8Os-XHbUKuRDyQw0Z3MjtYy5Z5fqLFpP1sxEZnoEbU,567
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+ gemmi_protools-0.1.6.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
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+ gemmi_protools-0.1.6.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
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+ gemmi_protools-0.1.6.dist-info/RECORD,,