Biotite Bump to >=1 (#737)

* update for biotite 1.1 * additional CIF fixes * completely remove oldcif * update readme with some examples (#738) --------- Co-authored-by: Brady Johnston <[email protected]> Co-authored-by: Brady Johnston <[email protected]>
BradyAJohnston · Feb 13, 2025 · ca52651 · ca52651
1 parent ecd852d
commit ca52651
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Showing 5 changed files with 42 additions and 350 deletions.
diff --git a/molecularnodes/entities/molecule/oldcif.py b/molecularnodes/entities/molecule/oldcif.py
diff --git a/molecularnodes/entities/molecule/pdbx.py b/molecularnodes/entities/molecule/pdbx.py
@@ -3,6 +3,7 @@
 import biotite.structure as struc
 import biotite.structure.io.pdbx as pdbx
 import numpy as np
+from biotite import InvalidFileError
 
 from .molecule import Molecule
 
@@ -67,13 +68,21 @@ def get_structure(
         bonds=True,
         model: int | None = None,
     ):
-        array = pdbx.get_structure(self.file, model=model, extra_fields=extra_fields)
-        array = self.set_extra_annotations(array, self.file)
-
-        if not array.bonds and bonds:
-            array.bonds = struc.bonds.connect_via_residue_names(
-                array, inter_residue=True
+        try:
+            array = pdbx.get_structure(
+                self.file, model=model, extra_fields=extra_fields
             )
+            array = self.set_extra_annotations(array, self.file)
+            if not array.bonds and bonds:
+                array.bonds = struc.bonds.connect_via_residue_names(
+                    array, inter_residue=True
+                )
+        except InvalidFileError:
+            array = pdbx.get_component(self.file)
+            if not array.bonds and bonds:
+                array.bonds = struc.bonds.connect_via_residue_names(
+                    array, inter_residue=True
+                )
 
         return array
 

diff --git a/molecularnodes/entities/molecule/ui.py b/molecularnodes/entities/molecule/ui.py
@@ -9,7 +9,6 @@
 
 from ...download import FileDownloadPDBError, download, CACHE_DIR
 from ...blender import path_resolve
-from .oldcif import OldCIF
 from .molecule import Molecule
 from .pdb import PDB
 from .pdbx import BCIF, CIF
@@ -38,12 +37,8 @@ def parse(filepath) -> Molecule:
 
     if suffix not in parser:
         raise ValueError(f"Unable to open local file. Format '{suffix}' not supported.")
-    try:
-        molecule = parser[suffix](filepath)
-    except InvalidFileError:
-        molecule = OldCIF(filepath)
 
-    return molecule
+    return parser[suffix](filepath)
 
 
 def fetch(