Merge pull request #33 from xchem/xtalforms

Xtalforms

src/ligand_neighbourhood_alignment/cli.py

@@ -521,7 +521,16 @@ def _generate_assembly(
             #     op = gemmi.Op(generator.triplet)
             op = gemmi.Op(_transform)
             # chain_clone = structure[0][generator.chain].clone()
-            chain_clone = structure[0][_chain].clone()
+            try:
+                chain_clone = structure[0][_chain].clone()
+            except Exception as e:
+                raise Exception(
+                    'An Exception occurred in generating the biological assemblies\n'
+                    f'Based on the assembly, the expected chains were: {xtalform_assembly.chains}\n'
+                    f'However the chains in the structure were: {[_x.name for _x in structure[0]]}\n'
+                    'XCA does not currently handle datasets with a mis-match between the xtalform chains.\n'
+                    'You should ensure that the chain names are consistent with the reference dataset for the xtalforms.'
+                )
 
             for residue in chain_clone:
                 for atom in residue:
@@ -1283,6 +1292,7 @@ def _update(
                             _structure,
                             moving_ligand_id,
                             reference_ligand_id,
+                            ligand_neighbourhoods[moving_ligand_id],
                             alignability_graph,
                             ligand_neighbourhood_transforms,
                             conformer_site_transforms,

src/ligand_neighbourhood_alignment/generate_aligned_structures.py

@@ -267,6 +267,7 @@ def _align_structure(
         _structure,
         moving_ligand_id: tuple[str, str, str],
         reference_ligand_id: tuple[str, str, str],
+        neighbourhood: dt.Neighbourhood,
         g,
         neighbourhood_transforms: dict[tuple[tuple[str, str, str], tuple[str, str, str]], dt.Transform],
         conformer_site_transforms: dict[tuple[str, str], dt.Transform],
@@ -304,6 +305,13 @@ def _align_structure(
 
     _structure = superpose_structure(running_transform, _structure)
 
+    # Drop chains without atoms in neighbourhood
+    neighbourhood_chains = set([_atom_id[0] for _atom_id in neighbourhood.atoms])
+    for _model in _structure:
+        for _chain in _model:
+            if _chain.name not in neighbourhood_chains:
+                _model.remove_chain(_chain.name)
+
     # Write the fully aligned structure
     _structure.write_pdb(str(out_path))
 

src/ligand_neighbourhood_alignment/generate_sites_from_components.py

@@ -27,7 +27,8 @@
 )
 
 # from ligand_neighbourhood_alignment.save_sites import save_sites
-from ligand_neighbourhood_alignment.structures import get_structures, get_transform_from_residues, _get_transform_from_residues
+from ligand_neighbourhood_alignment.structures import get_structures, get_transform_from_residues, \
+    _get_transform_from_residues
 
 
 def get_components(g):
@@ -150,9 +151,9 @@ def get_sites_from_conformer_sites(conformer_sites: ConformerSites, neighbourhoo
 
 
 def get_xtalform_sites_from_canonical_sites(
-    canonical_sites: CanonicalSites,
-    assigned_xtalforms: AssignedXtalForms,
-    xtalforms: XtalForms,
+        canonical_sites: CanonicalSites,
+        assigned_xtalforms: AssignedXtalForms,
+        xtalforms: XtalForms,
 ):
     """
     Each canonical site may occur in several forms, depending on the
@@ -212,7 +213,6 @@ def get_xtalform_sites_from_canonical_sites(
 
 
 def get_subsite_transforms(sites: CanonicalSites, structures):
-
     transforms = {}
     for site_id, site in zip(sites.site_ids, sites.sites):
         rss = site.reference_ligand_id.dtag
@@ -227,21 +227,22 @@ def get_subsite_transforms(sites: CanonicalSites, structures):
 
     return transforms
 
+
 from ligand_neighbourhood_alignment import dt
+
+
 def _update_conformer_site_transforms(
-                conformer_site_transforms,
-                canonical_site: dt.CanonicalSite,
-                conformer_sites: dict[str, dt.ConformerSite],
+        conformer_site_transforms,
+        canonical_site: dt.CanonicalSite,
+        conformer_sites: dict[str, dt.ConformerSite],
         structures,
-            ):
-
+):
     ref_conformer_site = conformer_sites[canonical_site.reference_conformer_site_id]
     ref_conformer_site_residues = ref_conformer_site.residues
 
     for conformer_site_id in canonical_site.conformer_site_ids:
         key = (canonical_site.reference_conformer_site_id, conformer_site_id)
         if key not in conformer_site_transforms:
-
             conformer_site = conformer_sites[conformer_site_id]
             # conformer_site_residues = conformer_site.residues
 
@@ -253,8 +254,6 @@ def _update_conformer_site_transforms(
 
             conformer_site_transforms[key] = dt.Transform(transform.vec.tolist(), transform.mat.tolist())
 
-
-
     # transforms = {}
     # for site_id, site in zip(sites.site_ids, sites.sites):
     #     rss = site.reference_ligand_id.dtag
@@ -289,14 +288,15 @@ def get_site_transforms(sites: CanonicalSites, structures):
 
     return transforms
 
+
 def _update_canonical_site_transforms(
-            canonical_site_transforms: dict[str, dt.Transform],
+        canonical_site_transforms: dict[str, dt.Transform],
         canonical_site_id,
-            canonical_site: dt.CanonicalSite,
-            # canonical_sites: dict[str, dt.CanonicalSite],
+        canonical_site: dt.CanonicalSite,
+        # canonical_sites: dict[str, dt.CanonicalSite],
         conformer_sites: dict[str, dt.ConformerSite],
         structures,
-        ):
+):
     rss = structures[canonical_site.global_reference_dtag]
     ref_site_all_ress = [
         (chain.name, res.seqid.num) for model in rss for chain in model for res in chain
@@ -311,6 +311,7 @@ def _update_canonical_site_transforms(
         transform.mat.tolist(),
     )
 
+
 def _update_reference_structure_transforms(
         reference_structure_transforms,
         key,
@@ -327,8 +328,8 @@ def _update_reference_structure_transforms(
         transform.mat.tolist(),
     )
 
-def _generate_sites_from_components(_source_dir: Path):
 
+def _generate_sites_from_components(_source_dir: Path):
     logger.info(f"Source dir: {_source_dir}")
     g = read_graph(_source_dir)
     neighbourhoods: LigandNeighbourhoods = read_neighbourhoods(_source_dir)
@@ -395,4 +396,3 @@ def _generate_sites_from_components(_source_dir: Path):
     save_site_transforms(site_transforms, _source_dir)
 
     return canonical_sites
-