added source_file property to crystallographic_files entries

Author: tdudgeon

src/xchemalign/aligner.py

@@ -20,7 +20,6 @@
 import gemmi
 
 from rich.traceback import install
-install(show_locals=True)
 
 # Local alignment imports
 from ligand_neighbourhood_alignment import constants as lna_constants
@@ -66,6 +65,8 @@
 from xchemalign.utils import Constants
 from xchemalign.pdb_xtal import PDBXtal
 
+install(show_locals=True)
+
 
 def try_make(path):
     if not Path(path).exists():
@@ -461,10 +462,7 @@ def _perform_alignments(self, meta):
 
         # Get the assembly transforms
         if working_fs_model.assembly_transforms.exists():
-            assembly_transforms = ah.load_yaml(
-                working_fs_model.assembly_transforms,
-                lambda x: x
-            )
+            assembly_transforms = ah.load_yaml(working_fs_model.assembly_transforms, lambda x: x)
         else:
             assembly_transforms = {}
 
@@ -489,7 +487,6 @@ 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

src/xchemalign/collator.py

@@ -869,6 +869,7 @@ def _copy_files(self, meta):
                     data_to_add[Constants.META_XTAL_PDB] = {
                         Constants.META_FILE: str(fdata[1]),
                         Constants.META_SHA256: fdata[2],
+                        Constants.META_SOURCE_FILE: str(fdata[0]),
                     }
                     # copy MTZ file
                     fdata = files_to_copy.get(Constants.META_XTAL_MTZ)
@@ -882,6 +883,7 @@ def _copy_files(self, meta):
                             data_to_add[Constants.META_XTAL_MTZ] = {
                                 Constants.META_FILE: str(fdata[1]),
                                 Constants.META_SHA256: fdata[2],
+                                Constants.META_SOURCE_FILE: str(fdata[0]),
                             }
                     fdata = files_to_copy.get(Constants.META_XTAL_CIF)
 
@@ -896,6 +898,7 @@ def _copy_files(self, meta):
                             data_to_add[Constants.META_XTAL_CIF] = {
                                 Constants.META_FILE: str(fdata[1]),
                                 Constants.META_SHA256: fdata[2],
+                                Constants.META_SOURCE_FILE: str(fdata[0]),
                             }
                             try:
                                 mol = utils.gen_mol_from_cif(str(self.output_path / fdata[1]))
@@ -938,6 +941,7 @@ def _copy_files(self, meta):
                                 data = {
                                     Constants.META_FILE: str(attested_ligand_event_data[1]),
                                     Constants.META_SHA256: attested_ligand_event_data[2],
+                                    Constants.META_SOURCE_FILE: str(attested_ligand_event_data[0]),
                                     Constants.META_PROT_MODEL: ligand_key[0],
                                     Constants.META_PROT_CHAIN: ligand_key[1],
                                     Constants.META_PROT_RES: ligand_key[2],

src/xchemalign/utils.py

@@ -78,6 +78,7 @@ class Constants:
     META_REFERENCE = "reference"
     META_FILE = "file"
     META_SHA256 = "sha256"
+    META_SOURCE_FILE = "source_file"
     META_XTAL_FILES = "crystallographic_files"
     META_ALIGNED_FILES = "aligned_files"
     META_REFERENCE_ALIGNMENTS = "reference_aligned_files"