pidibble 1.5.2__tar.gz → 1.5.4__tar.gz

pidibble-1.5.4/.envrc

@@ -0,0 +1,4 @@
+# direnv: auto-activate this repo's uv-managed virtualenv on `cd` in.
+# Created with `uv venv .venv`. Run `direnv allow` once to trust this file.
+export VIRTUAL_ENV="$PWD/.venv"
+PATH_add "$VIRTUAL_ENV/bin"

pidibble-1.5.4/.github/workflows/release.yaml

@@ -0,0 +1,29 @@
+name: Release & Upload to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+jobs:
+  release:
+    uses: cameronabrams/workflows/.github/workflows/python-release.yml@main
+    with:
+      rtd_slug: pidibble
+      run_tests: true
+    secrets: inherit
+
+  publish:
+    needs: release
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - name: Download dist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

{pidibble-1.5.2 → pidibble-1.5.4}/.gitignore

@@ -136,3 +136,6 @@ dmypy.json
 .pyre/
 .vscode/settings.json
 
+
+# uv local lockfile (libraries: not committed)
+uv.lock

pidibble-1.5.4/CHANGELOG.md

@@ -0,0 +1,206 @@
+# Changelog
+
+All notable changes to this project are documented in this file.
+The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
+
+## [Unreleased]
+
+## [1.5.4] - 2026-07-14
+
+### Fixed
+- ATOM/HETATM/ANISOU `charge` field retyped from `Float` to `String`. The PDB charge column (79–80) is a formatted string (e.g. `1-`, `2+`), never a plain float, so every populated charge previously failed `float()` and emitted a spurious "Could not parse field charge" warning while discarding the value. Charges are now captured correctly (e.g. `1-`).
+- Off-by-one in `StringParser.report_record_error()` highlight: the error display dropped the character at the field's first column and coloured a window shifted one column to the right of the offending field. The highlight now wraps exactly the columns given by the field's byte range.
+
+## [1.5.3] - 2026-05-03
+
+### Fixed
+- `PDBParser(PDBcode=...)` legacy parameter silently swallowed by `**kwargs`; restored via explicit mapping to `source_id`/`source_db='rcsb'`
+- Eight bare `except:` clauses narrowed to specific exception types throughout
+- Bitwise `&=` used as logical AND in `BaseRecord.empty()` replaced with `all()`
+- `str2int_sig` raised `IndexError` on empty-string input; added guard before index access
+- `!= None` / `== None` comparisons replaced with `is not None` / `is None` throughout
+- `type(x) == T` identity comparisons replaced with `isinstance(x, T)` throughout
+- `elif type(p) == list:` in `parse_tokens()` was unreachable; corrected to `isinstance(p, PDBRecordList)`
+- Mutable default arguments `hold={}` and `hold=[]` in `gather_token` and `header_check` replaced with `None`
+
+### Changed
+- Global hex-tripped flag in `hex.py` replaced with `AtomSerialParser` callable class; each `PDBParser` instance owns its own state, eliminating thread-safety hazard and cross-parse contamination
+- `mappers` default argument changed from a mutable dict literal to `None`; default built inside `__init__`
+- Resource YAML files now loaded via `importlib.resources.files()` instead of `os.path.dirname(resources.__file__)`, ensuring correct behavior inside wheels and zip archives
+- `resources/__init__.py` removed; `resources/` is now a plain data directory, not a sub-package
+- `MANIFEST.in` removed; hatchling auto-discovers package data from git-tracked files
+- PEP 8 spacing applied throughout all source files
+- `parse_embedded()` refactored: `triggered`/`capturing` boolean pair replaced with explicit `_EmbedState` enum (`SEARCHING`, `PRE_CAPTURE`, `CAPTURING`); setup phase extracted into `_setup_embed_context()`
+
+### Added
+- `CHANGELOG.md` with full release history
+- `scripts/release.sh` for automated version rotation, tagging, and push
+- `[test]` optional dependency group in `pyproject.toml`
+
+---
+
+## [1.5.2] - 2025-09-16
+
+### Added
+- Capability to download structures from OPM and split DUM residues into a separate PDB file
+
+## [1.5.1] - 2025-09-15
+
+### Fixed
+- Minor fixes following 1.5.0
+
+## [1.5.0] - 2025-09-15
+
+### Added
+- Initial OPM support
+
+## [1.4.2] - 2025-08-11
+
+### Changed
+- Updated AlphaFold interface to current API
+
+## [1.4.1] - 2025-08-07
+
+### Fixed
+- Parsing bug in `PDBRecordList`
+
+## [1.4.0] - 2025-07-29
+
+### Added
+- `PDBRecordList` and `PDBRecordDict` classes
+
+## [1.3.3] - 2025-07-29
+
+### Fixed
+- Bugs where missing records were incorrectly assumed present during mmCIF parsing
+
+## [1.3.2] - 2025-07-25
+
+### Added
+- `filepath` parameter in `PDBParser()` for transparent reading of local files
+
+## [1.3.1] - 2025-07-25
+
+### Fixed
+- Minor fixes following 1.3.0
+
+## [1.3.0] - 2025-07-16
+
+### Changed
+- Streamlined class attribute usage throughout
+- Full API documentation published
+
+## [1.2.3] - 2025-03-06
+
+### Fixed
+- Negative residue sequence numbers now parsed correctly
+
+## [1.2.2] - 2025-03-04
+
+### Fixed
+- Minor fixes following 1.2.1
+
+## [1.2.1] - 2024-10-01
+
+### Fixed
+- Hexadecimal serial number parsing issues (again)
+
+## [1.2.0] - 2024-09-08
+
+### Fixed
+- Hexadecimal serial number parsing issues
+
+## [1.1.9] - 2024-08-08
+
+### Fixed
+- `nan` values and `*` filler characters in numeric fields now handled gracefully
+
+## [1.1.8] - 2024-07-15
+
+### Added
+- Unstructured REMARK records (e.g. from PACKMOL output) parsed as `REMARK.-1`
+
+## [1.1.6] - 2024-07-11
+
+### Fixed
+- Hexadecimal atom serial detection when no `a-f` characters are present, based on value exceeding 99999
+
+## [1.1.5] - 2024-07-11
+
+### Fixed
+- Hex-or-integer detection now restricted to atom serial number fields only
+
+## [1.1.4] - 2024-07-11
+
+### Added
+- Hexadecimal atom serial number support for files with more than 99999 atoms
+
+## [1.1.3] - 2024-03-21
+
+### Added
+- Ability to group records into models for multi-model PDB entries
+
+## [1.1.2] - 2024-02-28
+
+### Added
+- Ability to fetch structures from the AlphaFold database
+
+## [1.1.1] - 2023-09-19
+
+### Added
+- Version detection via `importlib.metadata`
+
+## [1.0.9.1] - 2023-08-28
+
+### Added
+- Limited mmCIF parsing: `ATOM`, `HETATM`, `SSBOND`, `LINK`, `SEQADV`, `REMARK 350`, and `REMARK 465` records
+
+## [1.0.8] - 2023-08-23
+
+### Fixed
+- Variations in how symmetry operation matrices are represented in PDB files
+
+## [1.0.7.7] - 2023-08-22
+
+### Changed
+- Cleaned up logging throughout
+
+## [1.0.7.6] - 2023-08-22
+
+### Fixed
+- Leading whitespace in `resName` field of `Residue10` record sometimes ignored
+
+## [1.0.7.5] - 2023-08-18
+
+### Added
+- Support for four-letter residue names
+
+## [1.0.7.4] - 2023-08-04
+
+### Added
+- Logging functionality
+
+## [1.0.7.3] - 2023-08-03
+
+### Changed
+- Improved parsing of BIOMT transforms
+
+## [1.0.7.2] - 2023-08-03
+
+### Added
+- Documentation stub on ReadTheDocs
+
+## [1.0.7.1] - 2023-08-03
+
+### Added
+- Support for split BIOMT tables and REMARK 280, 375, 650, and 700
+
+## [1.0.7] - 2023-08-01
+
+### Added
+- Pretty-print support for parsed records
+
+## [1.0] - 2023-07-01
+
+### Added
+- Initial release

{pidibble-1.5.2 → pidibble-1.5.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pidibble
-Version: 1.5.2
+Version: 1.5.4
 Summary: A complete Protein Data Bank (PDB) file parser
 Project-URL: Source, https://github.com/cameronabrams/pidibble
 Project-URL: Documentation, https://pidibble.readthedocs.io/en/latest/
@@ -14,6 +14,8 @@ Requires-Python: >=3.7
 Requires-Dist: mmcif
 Requires-Dist: numpy>=1.24
 Requires-Dist: pyyaml>=6
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
 Description-Content-Type: text/markdown
 
 # Pidibble 
@@ -90,66 +92,6 @@ ATOM
 
 ```
 
-## Release History
-* 1.5.2
-   * added capability to download from OPM and split out DUM resi's into a "dum" pdb
-* 1.4.2
-   * updated alphafold interface
-* 1.4.1
-   * Fixed parsing bug in `PDBRecordList`
-* 1.4.0
-   * Introduced `PDBRecordList` and `PDBRecordDict` classes
-* 1.3.3
-   * fixed bugs regarding assuming missing records actually present in mmcif parsing
-* 1.3.2
-   * implemented `filepath` parameter in `PDBParser()` to make
-     reading local files more transparent
-* 1.3.0
-   * streamline class attribute usage; full API documentation
-* 1.2.3:
-   * bugfix: negative resids allowed
-* 1.2.1:
-   * bugfix: hex issues AGAIN
-* 1.2.0
-   * bugfix: hex issues again
-* 1.1.9
-   * gently handles any nan values or '*' fillers
-* 1.1.8
-   * Allow unstructured REMARK records (thanks a lot, packmol) to be parsed as REMARK.-1
-* 1.1.6
-   * bugfix: detection of hex when no abcdef present based on a trip
-* 1.1.5
-   * bugfix: allow for ONLY atom serial numbers to be hex-or-int
-* 1.1.4
-   * Added ability to read hexadecimal atom indices for files with > 99999 atoms
-* 1.1.3
-   * Added ability to group into models for multiple-model entries
-* 1.1.2
-   * Added ability to retrieve pdbs from AlphaFold database
-* 1.1.1
-   * version detection
-* 1.0.9.1
-   * added limited functionality to parse mmCIF files, in particular to generate any
-     ATOM, HETATM, SSBOND, LINK, SEQADV, REMARK 350, and REMARK 465 records
-* 1.0.8
-    * bug fix: handle variations in how symmetry operation matrices are represented
-* 1.0.7.7
-    * cleaned up logging
-* 1.0.7.6
-    * bug fix: leading whitespace in resname field of Residue10 record sometimes ignored
-* 1.0.7.5
-    * support for four-letter residue names
-* 1.0.7.4
-    * added logging functionality
-* 1.0.7.3
-    * improved parsing of BIOMT transforms
-* 1.0.7.2
-    * added documentation stub at readthedocs
-* 1.0.7.1
-    * support for split BIOMT tables and REMARKS 280, 375, 650, and 700
-* 1.0.7
-    * pretty-print enabled
-* 1.0
-    * Initial version
-
+## Changelog
 
+See [CHANGELOG.md](CHANGELOG.md) for the full release history.

{pidibble-1.5.2 → pidibble-1.5.4}/README.md

@@ -72,66 +72,6 @@ ATOM
 
 ```
 
-## Release History
-* 1.5.2
-   * added capability to download from OPM and split out DUM resi's into a "dum" pdb
-* 1.4.2
-   * updated alphafold interface
-* 1.4.1
-   * Fixed parsing bug in `PDBRecordList`
-* 1.4.0
-   * Introduced `PDBRecordList` and `PDBRecordDict` classes
-* 1.3.3
-   * fixed bugs regarding assuming missing records actually present in mmcif parsing
-* 1.3.2
-   * implemented `filepath` parameter in `PDBParser()` to make
-     reading local files more transparent
-* 1.3.0
-   * streamline class attribute usage; full API documentation
-* 1.2.3:
-   * bugfix: negative resids allowed
-* 1.2.1:
-   * bugfix: hex issues AGAIN
-* 1.2.0
-   * bugfix: hex issues again
-* 1.1.9
-   * gently handles any nan values or '*' fillers
-* 1.1.8
-   * Allow unstructured REMARK records (thanks a lot, packmol) to be parsed as REMARK.-1
-* 1.1.6
-   * bugfix: detection of hex when no abcdef present based on a trip
-* 1.1.5
-   * bugfix: allow for ONLY atom serial numbers to be hex-or-int
-* 1.1.4
-   * Added ability to read hexadecimal atom indices for files with > 99999 atoms
-* 1.1.3
-   * Added ability to group into models for multiple-model entries
-* 1.1.2
-   * Added ability to retrieve pdbs from AlphaFold database
-* 1.1.1
-   * version detection
-* 1.0.9.1
-   * added limited functionality to parse mmCIF files, in particular to generate any
-     ATOM, HETATM, SSBOND, LINK, SEQADV, REMARK 350, and REMARK 465 records
-* 1.0.8
-    * bug fix: handle variations in how symmetry operation matrices are represented
-* 1.0.7.7
-    * cleaned up logging
-* 1.0.7.6
-    * bug fix: leading whitespace in resname field of Residue10 record sometimes ignored
-* 1.0.7.5
-    * support for four-letter residue names
-* 1.0.7.4
-    * added logging functionality
-* 1.0.7.3
-    * improved parsing of BIOMT transforms
-* 1.0.7.2
-    * added documentation stub at readthedocs
-* 1.0.7.1
-    * support for split BIOMT tables and REMARKS 280, 375, 650, and 700
-* 1.0.7
-    * pretty-print enabled
-* 1.0
-    * Initial version
-
+## Changelog
 
+See [CHANGELOG.md](CHANGELOG.md) for the full release history.

pidibble-1.5.4/docs/requirements.txt

@@ -0,0 +1,8 @@
+sphinx
+furo
+sphinx-copybutton
+sphinxcontrib-mermaid
+myst-parser
+readthedocs-sphinx-ext
+pyyaml
+pidibble

pidibble-1.5.4/docs/source/changelog.md

@@ -0,0 +1,5 @@
+# Changelog
+
+```{include} ../../CHANGELOG.md
+:heading-offset: 1
+```

pidibble-1.5.4/docs/source/changelog.rst

@@ -0,0 +1,7 @@
+.. _changelog:
+
+Changelog
+=========
+
+.. include:: ../../CHANGELOG.md
+   :parser: myst_parser.sphinx_

{pidibble-1.5.2 → pidibble-1.5.4}/docs/source/conf.py

@@ -22,6 +22,7 @@ extensions = [
     'sphinxcontrib.mermaid',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
+    'myst_parser',
 ]
 
 autosummary_generate = True  # Enable autosummary tables
@@ -49,7 +50,7 @@ html_theme_options = {
     "footer_icons": [
         {
             "name": "GitHub",
-            "url": "https://github.com/cameronabrams/ycleptic",
+            "url": "https://github.com/cameronabrams/pidibble",
             "html": """
     <svg role="img" width="24" height="24" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" fill="currentColor">
         <title>GitHub</title>

{pidibble-1.5.2 → pidibble-1.5.4}/docs/source/index.rst

@@ -30,3 +30,4 @@ Contents
    installation
    usage
    API <api/API>
+   changelog

{pidibble-1.5.2 → pidibble-1.5.4}/pidibble/baseparsers.py

@@ -7,21 +7,21 @@
 
 """
 import logging
-logger=logging.getLogger(__name__)
+logger = logging.getLogger(__name__)
 
 class ListParser:
     """
     A simple parser for lists of strings, with a customizable delimiter.
     """
 
-    def __init__(self,d=','):
-        self.d=d
-    
-    def parse(self,string):
+    def __init__(self, d=','):
+        self.d = d
+
+    def parse(self, string):
         """
         Parse a string into a list of strings, using the specified delimiter.
         If no delimiter is specified, it splits on whitespace.
-        
+
         Parameters
         ----------
         string : str
@@ -32,12 +32,12 @@ class ListParser:
         list
             A list of strings parsed from the input string.
         """
-        if self.d==None:
-            return [x for x in string.split() if x.strip()!='']
+        if self.d is None:
+            return [x for x in string.split() if x.strip() != '']
         else:
-            return [x.strip() for x in string.split(self.d) if x.strip()!='']
-    
-def list_parse(obj,d):
+            return [x.strip() for x in string.split(self.d) if x.strip() != '']
+
+def list_parse(obj, d):
     """
     A factory function to create a ListParser with a specific delimiter.
 
@@ -58,21 +58,21 @@ def list_parse(obj,d):
 """
 Define a dictionary of parsers for different list formats
 """
-ListParsers={
-    'CList':list_parse(ListParser,','),
-    'SList':list_parse(ListParser,';'),
-    'WList':list_parse(ListParser,None),
-    'DList':list_parse(ListParser,':'),
-    'LList':list_parse(ListParser,'\n')
+ListParsers = {
+    'CList': list_parse(ListParser, ','),
+    'SList': list_parse(ListParser, ';'),
+    'WList': list_parse(ListParser, None),
+    'DList': list_parse(ListParser, ':'),
+    'LList': list_parse(ListParser, '\n')
 }
 
-_cols="""
+_cols = """
          1         2         3         4         5         6         7         8
 12345678901234567890123456789012345678901234567890123456789012345678901234567890"""
 class StringParser:
     """
     A parser for fixed-width strings, with a customizable field map.
-    
+
     Parameters
     ----------
     fmtdict : dict
@@ -82,15 +82,15 @@ class StringParser:
     allowed : dict, optional
         A dictionary mapping field values to allowed values, for validation.
     """
-    def __init__(self,fmtdict,typemap,allowed={}):
-        self.typemap=typemap
-        self.fields={k:v for k,v in fmtdict.items()}
-        self.allowed=allowed
+    def __init__(self, fmtdict, typemap, allowed={}):
+        self.typemap = typemap
+        self.fields = {k: v for k, v in fmtdict.items()}
+        self.allowed = allowed
 
     def parse(self, record):
         """
         Parse a fixed-width string record into a dictionary of fields.
-        
+
         Parameters
         ----------
         record : str
@@ -101,39 +101,39 @@ class StringParser:
         dict
             A dictionary of fields parsed from the input record.
         """
-        if len(record)>80:
+        if len(record) > 80:
             logger.warning('The following record exceeds 80 bytes in length:')
             self.report_record_error(record)
             logger.warning('Stripping...')
             record = record.strip()
-            if len(record)>80:
-               raise ValueError(f'Record is too long; something wrong with your PDB file?')
-        input_dict={}
-        record+=' '*(80-len(record)) # pad
-        for k,v in self.fields.items():
-            typestring,byte_range=v
-            typ=self.typemap[typestring]
-            assert byte_range[1]<=len(record),f'{record} {byte_range}'
+            if len(record) > 80:
+                raise ValueError(f'Record is too long; something wrong with your PDB file?')
+        input_dict = {}
+        record += ' ' * (80 - len(record))  # pad
+        for k, v in self.fields.items():
+            typestring, byte_range = v
+            typ = self.typemap[typestring]
+            assert byte_range[1] <= len(record), f'{record} {byte_range}'
             # using columns beginning with "1" not "0"
-            fieldstring=record[byte_range[0]-1:byte_range[1]]
-            fieldstring=fieldstring.rstrip()
+            fieldstring = record[byte_range[0] - 1:byte_range[1]]
+            fieldstring = fieldstring.rstrip()
             try:
                 # if len(fieldstring)>0 and not typ==str:
                 #     fieldstring=''
-                input_dict[k]='' if fieldstring=='' else typ(fieldstring)
-            except:
-                self.report_field_error(record,k)
-                input_dict[k]=''
-            if typ==str:
-                input_dict[k]=input_dict[k].strip()
+                input_dict[k] = '' if fieldstring == '' else typ(fieldstring)
+            except (ValueError, TypeError):
+                self.report_field_error(record, k)
+                input_dict[k] = ''
+            if typ == str:
+                input_dict[k] = input_dict[k].strip()
             if fieldstring in self.allowed:
-                assert input_dict[k] in self.allowed[fieldstring],f'Value {input_dict[k]} is not allowed for field {k}; allowed values are {self.allowed[fieldstring]}'
+                assert input_dict[k] in self.allowed[fieldstring], f'Value {input_dict[k]} is not allowed for field {k}; allowed values are {self.allowed[fieldstring]}'
         return input_dict
-    
-    def report_record_error(self,record,byte_range=[]):
+
+    def report_record_error(self, record, byte_range=[]):
         """
         Report an error in parsing a fixed-width string record.
-        
+
         Parameters
         ----------
         record : str
@@ -143,14 +143,14 @@ class StringParser:
             If empty, the entire record is reported. 
         """
         if byte_range:
-            record=record[:byte_range[0]-1]+'\033[91m'+record[byte_range[0]:byte_range[1]+1]+'\033[0m'+record[byte_range[1]+1:]
-        repstr=_cols+'\n'+record+'|'
+            record = record[:byte_range[0] - 1] + '\033[91m' + record[byte_range[0] - 1:byte_range[1]] + '\033[0m' + record[byte_range[1]:]
+        repstr = _cols + '\n' + record + '|'
         logger.warning(repstr)
-        
-    def report_field_error(self,record,k):
+
+    def report_field_error(self, record, k):
         """
         Report an error in parsing a specific field from a fixed-width string record.
-        
+
         Parameters
         ----------
         record : str
@@ -158,26 +158,27 @@ class StringParser:
         k : str
             The field name that caused the error.
         """
-        byte_range=self.fields[k][1]
+        byte_range = self.fields[k][1]
         logger.warning(f'Could not parse field {k} from bytes {byte_range}:')
-        self.report_record_error(record,byte_range=byte_range)
+        self.report_record_error(record, byte_range=byte_range)
 
 def safe_float(x):
     """
     Convert a string to a float, returning 0.0 if the string is 'nan'.
     """
-    if x=='nan':
+    if x == 'nan':
         return 0.0
     return float(x)
 
-def str2int_sig(arg:str):
+def str2int_sig(arg: str):
     """
     Convert a string to an integer, returning -1 if the string is not numeric.
     If the string starts with a '-', it is returned as an integer.
     """
-    if not arg.strip().isnumeric():
-        if arg.strip()[0]=='-':
+    stripped = arg.strip()
+    if not stripped.isnumeric():
+        if stripped and stripped[0] == '-':
             return int(arg)
         else:
             return -1
-    return int(arg)
+    return int(arg)