pidibble 1.2.0__tar.gz → 1.3.1__tar.gz

pidibble-1.3.1/.github/workflows/release.yaml

@@ -0,0 +1,41 @@
+name: Release & Upload to PyPI (Hatch)
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+
+      - name: Install Hatch
+        run: python -m pip install --upgrade pip hatch
+
+      - name: Clean previous builds
+        run: rm -rf dist/
+        
+      - name: Build the package with Hatch
+        run: hatch build
+
+      - name: Upload to GitHub Release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: |
+            dist/*.tar.gz
+            dist/*.whl
+
+      - name: Publish to PyPI using Hatch
+        env:
+          HATCH_INDEX_USER: __token__
+          HATCH_INDEX_AUTH: ${{ secrets.PYPI_API_TOKEN }}
+        run: hatch publish

{pidibble-1.2.0 → pidibble-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pidibble
-Version: 1.2.0
+Version: 1.3.1
 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/
@@ -88,6 +88,8 @@ ATOM
 ```
 
 ## Release History
+* 1.2.1:
+   * bugfix: hex issues AGAIN
 * 1.2.0
    * bugfix: hex issues again
 * 1.1.9

{pidibble-1.2.0 → pidibble-1.3.1}/README.md

@@ -70,6 +70,8 @@ ATOM
 ```
 
 ## Release History
+* 1.2.1:
+   * bugfix: hex issues AGAIN
 * 1.2.0
    * bugfix: hex issues again
 * 1.1.9

{pidibble-1.2.0 → pidibble-1.3.1}/docs/source/conf.py

@@ -6,8 +6,8 @@ project = 'Pidibble'
 copyright = '2023-2024, Cameron F. Abrams'
 author = 'cfa22@drexel.edu'
 
-release = '1.1'
-version = '1.1.4'
+release = '1.3'
+version = '1.3.0'
 
 # -- General configuration
 

pidibble-1.3.1/docs/source/generated/pidibble.rst

@@ -0,0 +1,6 @@
+pidibble
+========
+
+.. automodule:: pidibble
+
+   

{pidibble-1.2.0 → pidibble-1.3.1}/docs/source/usage.rst

@@ -175,4 +175,6 @@ Currently, only ``ATOM``, ``HETATM``, ``SEQADV``, ``REMARK 350``, and ``REMARK 4
 >>> ', '.join(list(p.parsed.keys()))
 'ATOM, HETATM, LINK, SSBOND, SEQADV, REMARK.350.BIOMOLECULE1.TRANSFORM1, REMARK.350.BIOMOLECULE1.TRANSFORM2, REMARK.350.BIOMOLECULE1.TRANSFORM3, REMARK.465'
 
-These records are the bare minimum needed to generate (say) input coordinate and topology files for an MD simulation.  Future versions of ``pidibble`` will provide complete PDB-like parsings of ``mmCIF`` files.  This is probably not useful.
+These records are the bare minimum needed to generate (say) input coordinate and topology files for an MD simulation.  Future versions of ``pidibble`` will provide complete PDB-like parsings of ``mmCIF`` files.  This is probably not useful.
+
+Importantly:  ``pidibble`` parses mmCIF input to generate a structure that is the equivalent of the PDB format; that is, it uses ``auth`` fields instead of ``label`` fields.  

{pidibble-1.2.0 → pidibble-1.3.1}/pidibble/hex.py

@@ -4,7 +4,7 @@ def str2atomSerial(arg):
     assert type(arg)==str
     if arg=='nan':
         return_object=0
-    elif __hex_tripped__ or any([(x in arg) for x in 'abcdef']):
+    elif __hex_tripped__ or any([(x in arg) for x in 'abcdefABCDEF']):
         return_object=int(arg,16)
     elif '*' in arg:
         return_object=0

{pidibble-1.2.0 → pidibble-1.3.1}/pidibble/mmcif_parse.py

@@ -101,8 +101,15 @@ class MMCIF_Parser:
                                 if k in map_values:
                                     mapper=self.global_maps[map_values[k]]
                                     if type(val)==list:
-                                        val=list(set([mapper[x] for x in val]))
-                                        val.sort()
+                                        logger.debug(f'mapper {mapper}')
+                                        logger.debug(f'list before mapping {val}')
+                                        mapped_val=list(set([str(mapper[x]) for x in val]))
+                                        logger.debug(f'list after mapping {mapped_val}')
+                                        try:
+                                            mapped_val.sort()
+                                            val=mapped_val
+                                        except:
+                                            raise TypeError(f'could not sort list {mapped_val} at key {k}')
                                     else:
                                         val=mapper[val]
                         idict[k]=val

{pidibble-1.2.0 → pidibble-1.3.1}/pidibble/resources/mmcif_format.yaml

@@ -74,6 +74,10 @@ LINK:
       resName: ptnr1_auth_comp_id
       seqNum: ptnr1_auth_seq_id
       iCode: pdbx_ptnr1_PDB_ins_code
+    residue1_label:
+      chainID: ptnr1_label_asym_id 
+      resName: ptnr1_label_comp_id
+      seqNum: ptnr1_label_seq_id
     ptnr1_label_atom_id: ptnr1_label_atom_id
     ptnr1_label_comp_id: ptnr1_label_comp_id
     ptnr1_label_asym_id: ptnr1_label_asym_id
@@ -85,6 +89,10 @@ LINK:
       resName: ptnr2_auth_comp_id
       seqNum: ptnr2_auth_seq_id
       iCode: pdbx_ptnr2_PDB_ins_code
+    residue2_label:
+      chainID: ptnr2_label_asym_id 
+      resName: ptnr2_label_comp_id
+      seqNum: ptnr2_label_seq_id
     ptnr2_label_atom_id: ptnr2_label_atom_id
     ptnr2_label_comp_id: ptnr2_label_comp_id
     ptnr2_label_asym_id: ptnr2_label_asym_id
@@ -103,6 +111,10 @@ SSBOND:
       resName: ptnr1_auth_comp_id
       seqNum: ptnr1_auth_seq_id
       iCode: pdbx_ptnr1_PDB_ins_code
+    residue1_label:
+      chainID: ptnr1_label_asym_id
+      resName: ptnr1_label_comp_id
+      seqNum: ptnr1_label_seq_id
     ptnr1_label_atom_id: ptnr1_label_atom_id
     ptnr1_label_comp_id: ptnr1_label_comp_id
     ptnr1_label_asym_id: ptnr1_label_asym_id
@@ -112,6 +124,10 @@ SSBOND:
       resName: ptnr2_auth_comp_id
       seqNum: ptnr2_auth_seq_id
       iCode: pdbx_ptnr2_PDB_ins_code
+    residue2_label:
+      chainID: ptnr2_label_asym_id
+      resName: ptnr2_label_comp_id
+      seqNum: ptnr2_label_seq_id
     ptnr2_label_atom_id: ptnr2_label_atom_id
     ptnr2_label_comp_id: ptnr2_label_comp_id
     ptnr2_label_asym_id: ptnr2_label_asym_id

{pidibble-1.2.0 → pidibble-1.3.1}/pidibble/resources/pdb_format.yaml

@@ -405,7 +405,7 @@ record_formats:
   HELIX:
     type: 3
     fields:
-      serNum: [nteger,[8,10]]
+      serNum: [Integer,[8,10]]
       helixID: [String,[12,14]]
       initRes: [Residue11,[16,26]]
       endRes: [Residue11,[28,38]]

{pidibble-1.2.0 → pidibble-1.3.1}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 [project]
 name = "pidibble"
-version = "1.2.0"
+version = "1.3.1"
 authors = [
   { name="Cameron F Abrams", email="cfa22@drexel.edu" },
 ]