gemmi-protools 0.1.0__py3-none-any.whl

gemmi_protools/struct_info.py

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+"""
+@Author: Luo Jiejian
+"""
+from dataclasses import dataclass, field
+from datetime import datetime
+from typing import Dict, Optional
+
+import gemmi
+from typeguard import typechecked
+
+
+@typechecked
+@dataclass
+class Entity:
+    eid2desc: Dict[str, str] = field(default_factory=dict)
+    eid2specie: Dict[str, str] = field(default_factory=dict)
+    eid2taxid: Dict[str, str] = field(default_factory=dict)
+    polymer2eid: Dict[str, str] = field(default_factory=dict)
+
+    @typechecked
+    def __setattr__(self, name: str, value: Dict[str, str]):
+        super().__setattr__(name, value)
+
+    @typechecked
+    def update(self, inputs: Dict[str, Dict[str, str]]):
+        for key, value in inputs.items():
+            if hasattr(self, key):
+                self.__setattr__(key, value)
+
+    def get(self, name: str, default: Optional[str] = None):
+        if hasattr(self, name):
+            return self.__getitem__(name)
+        else:
+            return default
+
+    def __getitem__(self, name: str):
+        return getattr(self, name)
+
+    def keys(self):
+        return list(self.__dict__.keys())
+
+
+@typechecked
+@dataclass
+class Info:
+    cell_Z: str = ""
+    pdb_id: str = ""
+    exp_method: str = ""
+    deposition_date: str = "1909-01-08"
+    title: str = ""
+    keywords: str = ""
+    keywords_text: str = ""
+
+    @property
+    def __attributes_mapper(self):
+        return {'cell_Z': '_cell.Z_PDB',
+                'pdb_id': '_entry.id',
+                'exp_method': '_exptl.method',
+                'deposition_date': '_pdbx_database_status.recvd_initial_deposition_date',
+                'title': '_struct.title',
+                'keywords': '_struct_keywords.pdbx_keywords',
+                'keywords_text': '_struct_keywords.text'}
+
+    def to_gemmi_structure_infomap(self) -> gemmi.InfoMap:
+        outputs = dict()
+        for name, target_name in self.__attributes_mapper.items():
+            value = self.__getattribute__(name)
+            if isinstance(value, str):
+                v = str(value)
+                if len(v) > 1:
+                    outputs[target_name] = v
+        return gemmi.InfoMap(outputs)
+
+    @typechecked
+    def from_gemmi_structure_infomap(self, infomap: gemmi.InfoMap):
+        mapper_iv = {v: k for k, v in self.__attributes_mapper.items()}
+        for key, val in infomap.items():
+            if key in mapper_iv:
+                name = mapper_iv[key]
+                self.__setattr__(name, val)
+
+    @typechecked
+    def __setattr__(self, name: str, value: str):
+        if name == "deposition_date":
+            try:
+                datetime.strptime(value, "%Y-%m-%d")
+            except ValueError as e:
+                raise ValueError(f"{e}")
+
+        if hasattr(self, name):
+            super().__setattr__(name, value)

gemmi_protools-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: gemmi_protools
+Version: 0.1.0
+Summary: An Enhanced tool to process PDB structures based on Gemmi
+Author-email: Luo Jiejian <luojiejian12@mails.ucas.ac.cn>
+License-Expression: MIT
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: gemmi>=0.7.0
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: typeguard>=4.1.2
+Requires-Dist: numpy
+Requires-Dist: biopython>=1.84
+Requires-Dist: scipy>=1.14.1
+Requires-Dist: dockq
+Dynamic: license-file
+
+# An Enhanced tool to process PDB structures based on Gemmi

gemmi_protools-0.1.0.dist-info/RECORD

@@ -0,0 +1,16 @@
+gemmi_protools/__init__.py,sha256=SvBS-OBVhYsoHCWw4Rwp-6p8vaFhJC9FQMlx0vYpITQ,237
+gemmi_protools/align.py,sha256=LoN2xlZbvEwceQiz6F_VQBxlsNTKfGnJQ1LM937t1qw,6925
+gemmi_protools/cif_opts.py,sha256=bfJuUQSYzz_703cIgxgvEVxXalfVYEZwpVjuYEB9O2U,6351
+gemmi_protools/convert.py,sha256=780sQcwhslUD4Hj5UZMVlQdbicniJ6jNjncTl_7jaMk,3841
+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/ppi.py,sha256=nRzRWv28SDjVt6hMShRL_QYKFsBO1xA5jSGIQrN0JBg,2313
+gemmi_protools/reader.py,sha256=0VjMxOogqB1dccucQU2I703W5Ro4JYBakE2eXftUTPU,13194
+gemmi_protools/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR58X8,2769
+gemmi_protools-0.1.0.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
+gemmi_protools-0.1.0.dist-info/METADATA,sha256=XFZBAmfQXoij0iJFUkox30Y-acNtssncQsbR9tX6lOs,567
+gemmi_protools-0.1.0.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
+gemmi_protools-0.1.0.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
+gemmi_protools-0.1.0.dist-info/RECORD,,

gemmi_protools-0.1.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (77.0.3)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

gemmi_protools-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Roger
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

gemmi_protools-0.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+gemmi_protools