MR and NCS functions accept sfCIFs

src/matchmaps/_compute_mr_diff.py

@@ -23,6 +23,7 @@
     phaser_wrapper,
     _clean_up_files,
     _cif_or_pdb_to_pdb,
+    _cif_or_mtz_to_mtz,
 )
 
 
@@ -94,17 +95,16 @@ def compute_mr_difference_map(
 
     output_dir_contents = list(output_dir.glob("*"))
 
-    off_name = mtzoff.name.removesuffix(".mtz")
-    on_name = mtzon.name.removesuffix(".mtz")
-
     pdboff = _cif_or_pdb_to_pdb(pdboff, output_dir)
 
+    mtzoff, off_name = _cif_or_mtz_to_mtz(mtzoff, output_dir)
+    mtzon, on_name = _cif_or_mtz_to_mtz(mtzon, output_dir)
+
     # take in the list of rbr selections and parse them into phenix and gemmi selection formats
     # if rbr_groups = None, just returns (None, None)
     rbr_phenix, rbr_gemmi = _rbr_selection_parser(rbr_selections)
 
     # this is where scaling takes place in the usual pipeline, but that doesn't make sense with different-spacegroup inputs
-    # side note: I need to test the importance of scaling even in the normal case!! Might be more artifact than good, who knows
 
     pdboff = _handle_special_positions(pdboff, output_dir)
 
@@ -133,8 +133,6 @@ def compute_mr_difference_map(
         output_dir=output_dir,
     )
 
-    # the refinement process *should* be identical. Waters are gone already
-    # I just need to make sure that the phaser outputs go together
     print(f"{time.strftime('%H:%M:%S')}: Running phenix.refine for the 'on' data...")
 
     nickname_on = rigid_body_refinement_wrapper(
@@ -166,7 +164,6 @@ def compute_mr_difference_map(
     )
 
     # from here down I just copied over the stuff from the normal version
-    # this should be proofread for compatibility but should all work
 
     # read back in the files created by phenix
     # these have knowable names

src/matchmaps/_compute_ncs_diff.py

@@ -24,6 +24,7 @@
     _validate_inputs,
     _clean_up_files,
     _cif_or_pdb_to_pdb,
+    _cif_or_mtz_to_mtz,
 )
 
 
@@ -51,6 +52,8 @@ def compute_ncs_difference_map(
 
     pdb = _cif_or_pdb_to_pdb(pdb, output_dir)
 
+    mtz, _ = _cif_or_mtz_to_mtz(mtz, output_dir)
+
     rbr_phenix, rbr_gemmi = _rbr_selection_parser(ncs_chains)
 
     if Phi is None:  # do rigid-body refinement to get phases
@@ -109,7 +112,7 @@ def compute_ncs_difference_map(
     )
 
     print(f"{time.strftime('%H:%M:%S')}: Cleaning up files...")
-    print(keep_temp_files)
+
     _clean_up_files(output_dir, output_dir_contents, keep_temp_files)
 
     print(f"{time.strftime('%H:%M:%S')}: Done!")

src/matchmaps/_compute_realspace_diff.py

@@ -94,9 +94,6 @@ def compute_realspace_difference_map(
 
     output_dir_contents = list(output_dir.glob("*"))
 
-    # off_name = mtzoff.name.removesuffix(".mtz")
-    # on_name = mtzon.name.removesuffix(".mtz")
-
     pdboff = _cif_or_pdb_to_pdb(pdboff, output_dir)
 
     mtzoff, off_name = _cif_or_mtz_to_mtz(mtzoff, output_dir)

src/matchmaps/_utils.py

@@ -891,9 +891,9 @@ def _cif_or_mtz_to_mtz(input_file, output_dir):
 
     Parameters
     ----------
-    input_file : _type_
+    input_file : pathlib.Path
         _description_
-    output_dir : _type_
+    output_dir : pathlib.Path
         _description_
 
     Returns
@@ -923,6 +923,24 @@ def _cif_or_mtz_to_mtz(input_file, output_dir):
             input_file.name.removesuffix(input_file.suffix))
 
 def _cif_or_pdb_to_pdb(input_file, output_dir):
+    """
+    _summary_
+
+    Parameters
+    ----------
+    input_file : pathlib.Path
+    output_dir : pathlib.Path
+
+    Returns
+    -------
+    pathlib.Path
+        path to output file
+
+    Raises
+    ------
+    ValueError
+        _description_
+    """
 
     if input_file.suffix.lower() == '.pdb':