Merge pull request #53 from rs-station/phenix121

Add support for phenix 1.21

.gitignore

@@ -120,4 +120,5 @@ docs/images/logo.ai
 docs/images/logo2.ai
 
 # PyCharm files
-.idea/*
+.idea/*
+.idea/*

src/matchmaps/_compute_mr_diff.py

@@ -3,26 +3,21 @@
 import argparse
 import os
 import sys
-import subprocess
 import time
-from functools import partial
 from pathlib import Path
 
 import gemmi
-import numpy as np
 import reciprocalspaceship as rs
 
+from matchmaps._phenix_utils import rigid_body_refinement_wrapper, phaser_wrapper, _remove_waters
 from matchmaps._utils import (
     _handle_special_positions,
     make_floatgrid_from_mtz,
-    rigid_body_refinement_wrapper,
     _realspace_align_and_subtract,
     _rbr_selection_parser,
-    _remove_waters,
     _restore_ligand_occupancy,
     _validate_environment,
     _validate_inputs,
-    phaser_wrapper,
     _clean_up_files,
     _cif_or_pdb_to_pdb,
     _cif_or_mtz_to_mtz,
@@ -51,7 +46,8 @@ def compute_mr_difference_map(
     radius : float = 5,
     alpha : float = 0,
     no_bss = False,
-):
+    phenix_version: str = None,
+    ):
     """
     Compute a real-space difference map from mtzs in different spacegroups.
 
@@ -105,7 +101,12 @@ def compute_mr_difference_map(
         If True, skip bulk solvent scaling feature of phenix.refine
     """
 
-    _validate_environment(ccp4=False)
+    auto_phenix_version = _validate_environment(ccp4=False)
+
+    if phenix_version:
+        pass
+    else:
+        phenix_version = auto_phenix_version
 
     output_dir_contents = list(output_dir.glob("*"))
 
@@ -130,15 +131,8 @@ def compute_mr_difference_map(
         f"{time.strftime('%H:%M:%S')}: Running phenix.phaser to place 'off' model into 'on' data..."
     )
 
-    phaser_nickname = phaser_wrapper(
-        mtzfile=mtzon,
-        pdb=pdboff,
-        input_dir=input_dir,
-        output_dir=output_dir,
-        off_labels=f"{Fon},{SigFon}",
-        eff=None,
-        verbose=verbose,
-    )
+    phaser_nickname = phaser_wrapper(mtzfile=mtzon, pdb=pdboff, output_dir=output_dir, off_labels=f"{Fon},{SigFon}",
+                                     phenix_style=phenix_version, eff=None, verbose=verbose)
 
     # TO-DO: fix ligand occupancies in pdb_mr_to_on
     edited_mr_pdb = _restore_ligand_occupancy(
@@ -161,6 +155,7 @@ def compute_mr_difference_map(
         off_labels=f"{Fon},{SigFon}",  # workaround for compatibility
         mr_on=True,
         no_bss=no_bss,
+        phenix_style=phenix_version,
     )
 
     print(f"{time.strftime('%H:%M:%S')}: Running phenix.refine for the 'off' data...")
@@ -175,8 +170,8 @@ def compute_mr_difference_map(
         verbose=verbose,
         rbr_selections=rbr_phenix,
         off_labels=f"{Foff},{SigFoff}",
-        mr_off=True,
         no_bss=no_bss,
+        phenix_style=phenix_version,
     )
 
     # from here down I just copied over the stuff from the normal version
@@ -443,6 +438,16 @@ def parse_arguments():
         )
     )
 
+    parser.add_argument(
+        "--phenix-version",
+        required=False,
+        help=(
+            "Specify phenix version as a string, e.g. '1.20'. "
+            "If omitted, matchmaps will attempt to automatically detect the version in use "
+            "by analyzing the output of phenix.version"
+        )
+    )
+
     return parser
 
 
@@ -485,14 +490,16 @@ def main():
         alpha=args.alpha,
         on_as_stationary=args.on_as_stationary,
         keep_temp_files=args.keep_temp_files,
-        no_bss = args.no_bss
+        no_bss = args.no_bss,
+        phenix_version = args.phenix_version,
     )
 
     if args.script:
         _write_script(
             utility = 'matchmaps.mr', 
             arguments = sys.argv[1:],
             script_name = args.script,
+            phenix_version=args.phenix_version,
             )
 
     return

src/matchmaps/_compute_ncs_diff.py

@@ -3,23 +3,17 @@
 import argparse
 import os
 import sys
-import subprocess
 import time
-from functools import partial
 from pathlib import Path
 
 import gemmi
-import numpy as np
 import reciprocalspaceship as rs
 
-
+from matchmaps._phenix_utils import rigid_body_refinement_wrapper, _renumber_waters
 from matchmaps._utils import (
     _handle_special_positions,
     make_floatgrid_from_mtz,
-    rigid_body_refinement_wrapper,
-    _realspace_align_and_subtract,
     _rbr_selection_parser,
-    _renumber_waters,
     _ncs_align_and_subtract,
     _validate_environment,
     _validate_inputs,
@@ -48,6 +42,7 @@ def compute_ncs_difference_map(
     eff : str = None,
     keep_temp_files : str = None,
     no_bss = False,
+    phenix_version: str = None,
 ):
     """
     Compute an internal difference map across non-crystallographic symmetry
@@ -91,8 +86,13 @@ def compute_ncs_difference_map(
     no_bss : bool, optional
         If True, skip bulk solvent scaling feature of phenix.refine
     """
-    _validate_environment(ccp4=False)
-
+    auto_phenix_version = _validate_environment(ccp4=False)
+
+    if phenix_version:
+        pass
+    else:
+        phenix_version = auto_phenix_version
+
     output_dir_contents = list(output_dir.glob("*"))
 
     pdb = _cif_or_pdb_to_pdb(pdb, output_dir)
@@ -121,7 +121,8 @@ def compute_ncs_difference_map(
             verbose=verbose,
             rbr_selections=rbr_phenix,
             off_labels=f"{F},{SigF}",
-            no_bss=no_bss
+            no_bss=no_bss,
+            phenix_style=phenix_version,
         )
 
         # use phenix names for columns when computing FloatGrid
@@ -327,6 +328,16 @@ def parse_arguments():
             "Note that this file is written out in the current working directory, NOT the input or output directories"
         )
     )
+
+    parser.add_argument(
+        "--phenix-version",
+        required=False,
+        help=(
+            "Specify phenix version as a string, e.g. '1.20'. "
+            "If omitted, matchmaps will attempt to automatically detect the version in use "
+            "by analyzing the output of phenix.version"
+        )
+    )
 
     return parser
 
@@ -366,13 +377,15 @@ def main():
         spacing=args.spacing,
         keep_temp_files=args.keep_temp_files,
         no_bss=args.no_bss,
+        phenix_version=args.phenix_version,
     )
 
     if args.script:
         _write_script(
             utility = 'matchmaps.ncs', 
             arguments = sys.argv[1:],
             script_name = args.script,
+            phenix_version=args.phenix_version,
             )
 
     return

src/matchmaps/_compute_realspace_diff.py

@@ -1,27 +1,20 @@
 """Compute unbiased real space difference map."""
 
 import argparse
-import os
-import sys
-import glob
 import subprocess
+import sys
 import time
-from functools import partial
 from pathlib import Path
 
 import gemmi
-import numpy as np
 import reciprocalspaceship as rs
 
-from IPython import embed
-
+from matchmaps._phenix_utils import rigid_body_refinement_wrapper, _renumber_waters
 from matchmaps._utils import (
     _handle_special_positions,
     make_floatgrid_from_mtz,
-    rigid_body_refinement_wrapper,
     _realspace_align_and_subtract,
     _rbr_selection_parser,
-    _renumber_waters,
     _clean_up_files,
     _validate_environment,
     _validate_inputs,
@@ -51,7 +44,8 @@ def compute_realspace_difference_map(
     keep_temp_files : str = None,
     radius : float = 5,
     alpha : float = 0,
-    no_bss = False
+    no_bss = False,
+    phenix_version: str = None,
 ):
     """
     Compute a real-space difference map from mtzs.
@@ -103,9 +97,16 @@ def compute_realspace_difference_map(
         Alpha to use in error weighting of F-obs prior to Fourier Transform. Defaults to 0, e.g. no weighting.
     no_bss : bool, optional
         If True, skip bulk solvent scaling feature of phenix.refine
+    phenix_version: str, optional
+        Phenix version string to override the automatically detected version. I don't know why this would be necessary.
     """
 
-    _validate_environment(ccp4=True)
+    auto_phenix_version = _validate_environment(ccp4=True)
+
+    if phenix_version:
+        pass
+    else:
+        phenix_version = auto_phenix_version
 
     output_dir_contents = list(output_dir.glob("*"))
 
@@ -173,6 +174,7 @@ def compute_realspace_difference_map(
         verbose=verbose,
         rbr_selections=rbr_phenix,
         no_bss=no_bss,
+        phenix_style=phenix_version,
     )
 
     print(f"{time.strftime('%H:%M:%S')}: Running phenix.refine for the 'off' data...")
@@ -188,6 +190,7 @@ def compute_realspace_difference_map(
         rbr_selections=rbr_phenix,
         off_labels=f"{Foff},{SigFoff}",
         no_bss=no_bss,
+        phenix_style=phenix_version,
     )
 
     # read back in the files created by phenix
@@ -446,6 +449,16 @@ def parse_arguments():
             "Note that this file is written out in the current working directory, NOT the input or output directories"
         )
     )
+
+    parser.add_argument(
+        "--phenix-version",
+        required=False,
+        help=(
+            "Specify phenix version as a string, e.g. '1.20'. "
+            "If omitted, matchmaps will attempt to automatically detect the version in use "
+            "by analyzing the output of phenix.version"
+        )
+    )
 
     return parser
 
@@ -484,13 +497,15 @@ def main():
         on_as_stationary=args.on_as_stationary,
         keep_temp_files=args.keep_temp_files,
         no_bss = args.no_bss,
+        phenix_version = args.phenix_version,
     )
 
     if args.script:
         _write_script(
             utility = 'matchmaps', 
             arguments = sys.argv[1:],
             script_name = args.script,
+            phenix_version=args.phenix_version,
             )
 
     return