Added test for iteration 2

test-data/config_2.yaml

@@ -0,0 +1,11 @@
+target_name: Mpro
+base_dir: test-data/inputs_2
+output_dir: test-data/outputs
+ref_datasets:
+  - Mpro-IBM0045
+inputs:
+  - dir: dls/labxchem/data/2020/lb27995-1
+    type: model_building
+    soakdb: processing/database/soakDBDataFile.sqlite
+    panddas_event_files:
+    - processing/analysis/panddas/analyses/pandda_inspect_events.csv

xchemalign/aligner.py

@@ -570,6 +570,18 @@ def _perform_alignments(self, meta):
                             Constants.META_AIGNED_X_MAP: aligned_xmap_path,
                         }
 
+        ## Add the reference alignments
+        new_meta[Constants.META_REFERENCE_ALIGNMENTS] = {}
+        for dtag, crystal in crystals.items():
+            # Skip if no output for this dataset
+            if dtag not in fs_model.reference_alignments:
+                continue
+
+            crystal_output = new_meta[Constants.META_REFERENCE_ALIGNMENTS][dtag] = {}
+
+            for canonical_site_id, aligned_files in fs_model.reference_alignments.items():
+                crystal_output[canonical_site_id] = aligned_files
+
         new_meta[Constants.META_TRANSFORMS] = {}
 
         ## Get the observation to conformer site transforms

xchemalign/utils.py

@@ -73,6 +73,7 @@ class Constants:
     META_SHA256 = "sha256"
     META_XTAL_FILES = "crystallographic_files"
     META_ALIGNED_FILES = "aligned_files"
+    META_REFERENCE_ALIGNMENTS = "reference_aligned_files"
     META_XTAL_PDB = "xtal_pdb"
     META_XTAL_MTZ = "xtal_mtz"
     META_XTAL_CIF = "ligand_cif"