Merge pull request #33 from xchem/issue_1480

Issue 1480

DEV-GUIDE.md

@@ -12,19 +12,16 @@ This supersedes [Fragalysis-API](https://github.com/xchem/fragalysis-api).
 
 Project dependencies are defined in the `pyproject.toml` file.
 
-You will need to use Python 3.10 or 3.11 (a requirement of the `pyproject.toml` file).
-Python 3.12 cannot currently be used.
-
+You will need to use Python 3.10 or later (a requirement of the `pyproject.toml` file).
 If you prefer to use [conda] you can create a Python 3.10 environment using the
-`environment.yaml` in this project, otherwise, if you have Python 3.10 or 3.11,
+`environment.yaml` in this project, otherwise, if you have Python 3.10 or later,
 you can create an environment using the built-in `venv` module: -
 
     python -m venv venv
     source venv/bin/activate
     pip install --upgrade pip
 
-Make sure you create the venv using Python 3.10 or 3.11 (e.g. change the first command to `python3.11 -m venv venv`
-if needed).
+Make sure you create the venv using Python 3.10 (or later).
 
 From your clean virtual environment you can now install the run-time and development
 dependencies like this: -

src/xchemalign/aligner.py

@@ -20,6 +20,7 @@
 import gemmi
 
 from rich.traceback import install
+install(show_locals=True)
 
 # Local alignment imports
 from ligand_neighbourhood_alignment import constants as lna_constants
@@ -65,8 +66,6 @@
 from xchemalign.utils import Constants
 from xchemalign.pdb_xtal import PDBXtal
 
-install(show_locals=True)
-
 
 def try_make(path):
     if not Path(path).exists():
@@ -461,8 +460,11 @@ def _perform_alignments(self, meta):
             assembly_landmarks = {}
 
         # Get the assembly transforms
-        if working_fs_model.assembly_landmarks.exists():
-            assembly_transforms = ah.load_yaml(working_fs_model.assembly_landmarks, lambda x: x)
+        if working_fs_model.assembly_transforms.exists():
+            assembly_transforms = ah.load_yaml(
+                working_fs_model.assembly_transforms,
+                lambda x: x
+            )
         else:
             assembly_transforms = {}
 
@@ -487,14 +489,15 @@ def _perform_alignments(self, meta):
             assembly_landmarks,
             assembly_transforms,
             self.version_dir.name[7:],
+
         )
 
         # Update the metadata_file with aligned file locations and site information
         new_meta = {}
 
         # Add the xtalform information
         meta_xtalforms = {}
-        xtalforms = read_yaml(updated_fs_model.xtalforms)
+        xtalforms = readπ_yaml(updated_fs_model.xtalforms)
         for xtalform_id, xtalform in xtalforms[Constants.META_XTALFORMS].items():
             xtalform_reference = xtalform[Constants.META_REFERENCE]
             reference_structure = gemmi.read_structure(datasets[xtalform_reference].pdb)  # (xtalform_reference).pdb)