gemmi-protools 0.1.9__py3-none-any.whl → 0.1.11__py3-none-any.whl

gemmi_protools/io/cif_opts.py

@@ -135,6 +135,12 @@ def _cif_entity_info(block: gemmi.cif.Block) -> Entity:
 def _cif_block_for_output(structure: gemmi.Structure, entity: Entity) -> gemmi.cif.Block:
     block = structure.make_mmcif_block()
 
+    reflns = block.find_mmcif_category(category="_reflns.")
+    resolution = "%.2f" % structure.resolution
+    reflns.erase()
+    reflns_loop = block.init_loop(prefix="_reflns.", tags=["d_resolution_high", "d_resolution_low"])
+    reflns_loop.add_row([resolution, resolution])
+
     ta = block.find_mmcif_category(category="_entity.")
     da = pd.DataFrame(list(ta), columns=list(ta.tags))
     if "_entity.id" in da.columns:

gemmi_protools/io/parser.py

@@ -2,7 +2,7 @@
 @Author: Luo Jiejian
 """
 import pathlib
-from collections import defaultdict, Counter
+from collections import Counter
 from typing import Union, Optional, Dict, List
 
 import gemmi
@@ -114,6 +114,19 @@ def _update_entity_names(entity: Entity, mapper: Dict[str, str]):
             tmp[mapper[key]] = entity[super_key][key]
         entity.__setattr__(super_key, tmp)
 
+    new_polymer2eid = dict()
+    for c, old_eid in entity.polymer2eid.items():
+        new_polymer2eid[c] = mapper[old_eid]
+    entity.__setattr__(name="polymer2eid", value=new_polymer2eid)
+
+
+def _melt_dict(inputs: dict):
+    outputs = dict()
+    for keys, val in inputs.items():
+        for k in keys.split(","):
+            outputs[k] = val
+    return outputs
+
 
 @typechecked
 def pdb_parser(path: Union[str, pathlib.Path]):
@@ -126,39 +139,34 @@ def pdb_parser(path: Union[str, pathlib.Path]):
         struct = gemmi.read_structure(str(path))
         struct.resolution = _get_pdb_resolution(struct.raw_remarks)
         ent_0 = _pdb_entity_info(path)
+        ch2desc = _melt_dict(ent_0.eid2desc)
+        ch2specie = _melt_dict(ent_0.eid2specie)
+        ch2taxid = _melt_dict(ent_0.eid2taxid)
 
         struct.setup_entities()
-
-        # pdb have "A,B,C" chains
-        # after setup, entities will merge
         block = struct.make_mmcif_block()
         ent_t = _cif_entity_info(block)
-        rec = defaultdict(list)
-
-        for cn, middle_eid in ent_t.polymer2eid.items():
-            rec[middle_eid].append(cn)
 
-        _mapper = _assign_digital_entity_names(struct)
-        _mapper_n = dict()
+        # set non-polymer entity names
+        non_polymer_entities = [e.name for e in struct.entities if e.polymer_type.name == "Unknown"]
+        for k in non_polymer_entities:
+            assert k in ent_t.eid2desc
+            if ent_t.eid2desc[k] == "?":
+                ent_t.eid2desc[k] = k
 
-        for middle_eid, new_eid in _mapper.items():
-            if middle_eid in rec:
-                mid = rec[middle_eid]
-                mid.sort()
-                old_eid = str(",".join(mid))
-                _mapper_n[old_eid] = new_eid
+        for k in ent_t.eid2desc.keys():
+            if k not in non_polymer_entities:
+                ent_t.eid2desc[k] = ch2desc.get(k, "?")
 
-        if _mapper_n:
-            _update_entity_names(ent_0, _mapper_n)
+        polymer_chs_used_as_eid = set(ch2specie.keys()).intersection(ent_t.eid2desc.keys())
+        for k in polymer_chs_used_as_eid:
+            ent_t.eid2specie[k] = ch2specie.get(k, "?")
+            ent_t.eid2taxid[k] = ch2taxid.get(k, "?")
 
-        ent_1 = _ent_from_structure(struct)
+        m = _assign_digital_entity_names(struct)
+        _update_entity_names(ent_t, m)
 
-        # update ent_0 with ent_1
-        for super_key in ["eid2desc", "polymer2eid"]:
-            for key, val in ent_1[super_key].items():
-                if key not in ent_0[super_key]:
-                    ent_0[super_key][key] = val
-        return struct, ent_0
+        return struct, ent_t
     else:
         raise ValueError("Only support .pdb or .pdb.gz file, but got %s" % path)
 

gemmi_protools/io/reader.py

@@ -83,6 +83,19 @@ class StructureParser(object):
     def to_pdb(self, outfile: str, write_minimal_pdb=False):
         compound_source = _compound_source_string(self.ENTITY)
         struct = self.STRUCT.clone()
+
+        rs = "REMARK   2 RESOLUTION.    %.2f ANGSTROMS." % struct.resolution
+        resolution_remarks = ["%-80s" % "REMARK   2",
+                              "%-80s" % rs]
+
+        resolution_remark_exist = False
+        for line in struct.raw_remarks:
+            if "REMARK   2 RESOLUTION" in line:
+                resolution_remark_exist = True
+
+        if not resolution_remark_exist:
+            struct.raw_remarks = resolution_remarks + struct.raw_remarks
+
         struct.raw_remarks = compound_source + struct.raw_remarks
         if write_minimal_pdb:
             struct.write_minimal_pdb(outfile)

{gemmi_protools-0.1.9.dist-info → gemmi_protools-0.1.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmi_protools
-Version: 0.1.9
+Version: 0.1.11
 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-0.1.9.dist-info → gemmi_protools-0.1.11.dist-info}/RECORD

@@ -1,20 +1,20 @@
 gemmi_protools/__init__.py,sha256=hwUw-EieCG0kwzHjTjzHF9Bc3D-J5R_l6G8PCcFegkw,331
 gemmi_protools/io/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E,29
-gemmi_protools/io/cif_opts.py,sha256=TKND91aRGB5hYNdTFElCKMGabCg4klLk_c1evC3WZuA,6368
+gemmi_protools/io/cif_opts.py,sha256=cYEhubRP2rymbwSlB3ZQPGUFQiXGb2UQ0gdXdTd3c-I,6646
 gemmi_protools/io/convert.py,sha256=780sQcwhslUD4Hj5UZMVlQdbicniJ6jNjncTl_7jaMk,3841
 gemmi_protools/io/parse_pdb_header.py,sha256=UOGMsE3-d3APhO7zaAEE0NT31n-iqt55VpDh_RPOicI,14223
-gemmi_protools/io/parser.py,sha256=NCLc9IHH-tb2hIm0jZeKu2nVw2Isr-n-pH4l7JbKA5w,9130
+gemmi_protools/io/parser.py,sha256=HFc4Kovr6rxEpLAEDUtF_e-RnA5OsWMeMFjuVNm7UYY,9507
 gemmi_protools/io/pdb_opts.py,sha256=laUqxlecOe6goax12q8EJGZuZbHyIGsXVucMV3gVrgg,5741
 gemmi_protools/io/peptide.py,sha256=a2wiEutJmvhl6gDCIzzqRCbmyknk2mwgy2FZ53lXclU,750
-gemmi_protools/io/reader.py,sha256=oaJ5TTWLFCZ3tDq3R5dAyBqm4Q2sxmfl4D8cGvSOdl0,16060
+gemmi_protools/io/reader.py,sha256=lI9JTXqsct3D719qVN7Dsvg-zHudElojpW5-odtXa8A,16527
 gemmi_protools/io/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR58X8,2769
 gemmi_protools/utils/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E,29
 gemmi_protools/utils/align.py,sha256=CZcrvjy-ZbX2u7OAn-YGblbxaj9YFUDX4CFZcpbpnB8,6959
 gemmi_protools/utils/dockq.py,sha256=XmMwVEy-H4p6sH_HPcDWA3TP77OWdih0fE_BQJDr4pU,4189
 gemmi_protools/utils/fixer.py,sha256=RDmpoZpTrGdwuJQTTK1eif132MHV1I-T6Nt47ezgxTM,10236
 gemmi_protools/utils/ppi.py,sha256=VWYsdxWwQoS1xwEYj5KB96Zz3F8r5Eyuw6NT3ReD-wc,2330
-gemmi_protools-0.1.9.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
-gemmi_protools-0.1.9.dist-info/METADATA,sha256=OFqx1MONnQTZ7b65AspnNX0FIvtrE2gQVWT7yCTGhqE,567
-gemmi_protools-0.1.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-gemmi_protools-0.1.9.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
-gemmi_protools-0.1.9.dist-info/RECORD,,
+gemmi_protools-0.1.11.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
+gemmi_protools-0.1.11.dist-info/METADATA,sha256=liLlq__4RA0P1MW4gE_HmpyGfqDPQPMF8n0E3sGpKN4,568
+gemmi_protools-0.1.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+gemmi_protools-0.1.11.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
+gemmi_protools-0.1.11.dist-info/RECORD,,