[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -11,20 +11,20 @@ repos:
     -   id: check-merge-conflict
     -   id: detect-private-key
 
--   repo: https://github.com/psf/black
-    rev: 24.1.1
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.1.0
     hooks:
     -   id: black
         language_version: python3
 
 -   repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 7.0.0
     hooks:
     -   id: isort
         args: ["--profile", "black"]
 
 -   repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.3.0
     hooks:
     -   id: flake8
         additional_dependencies: [flake8-docstrings]

README.md

@@ -1,6 +1,6 @@
 # Factory
 
-> **⚠️ This project is under active development.**  
+> **⚠️ This project is under active development.**
 
 A Python package for crystallographic data processing and analysis.
 

configs/config_example.yaml

@@ -22,7 +22,7 @@ model_settings:
   weight_decay: 0.000
   optimizer_eps: 1e-16
   weight_decouple: true
-  
+
   # Scheduler configuration
   # scheduler_step: 55
   scheduler_gamma: 0.1
@@ -41,18 +41,18 @@ model_settings:
   # scale_prior_variance: 6241.0
   # scale_distribution: FoldedNormalDistributionLayer
 
-  metadata_encoder: 
+  metadata_encoder:
     name: BaseMetadataEncoder
     params:
       depth: 10
 
-  # metadata_encoder: 
+  # metadata_encoder:
   #   name: SimpleMetadataEncoder
   #   params:
   #     hidden_dim: 256
   #     depth: 5
 
-  profile_encoder: 
+  profile_encoder:
     name: BaseShoeboxEncoder
     params:
       # in_channels: 1
@@ -91,7 +91,7 @@ model_settings:
     # params:
     #   concentration: 6.68
     #   rate: 0.001
-  
+
   background_prior_distribution:
     # name: TorchHalfNormal
     # params:
@@ -121,7 +121,3 @@ loss_settings:
 
 phenix_settings:
   r_values_reference_path: "/n/holylabs/LABS/hekstra_lab/Users/fgiehr/jobs/anomalous_peaks_files/pdb_model/refine_001.log"
-
-
-
-

docs/Makefile

@@ -20,4 +20,4 @@ help:
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 watch:
-	sphinx-autobuild . _build/html --open-browser --watch examples 
+	sphinx-autobuild . _build/html --open-browser --watch examples

docs/_templates/layout.html

@@ -7,4 +7,4 @@
         <li class="toctree-l1"><a class="reference internal" href="{{ pathto('index') }}">Home</a></li>
         <li class="toctree-l1"><a class="reference internal" href="{{ pathto('api/index') }}">API Reference</a></li>
     </ul>
-{% endblock %} 
+{% endblock %}

docs/api/index.rst

@@ -7,4 +7,4 @@ API Reference
    model
    distributions
 
-This section provides detailed API documentation for Factory's modules and functions. 
+This section provides detailed API documentation for Factory's modules and functions.

docs/conf.py

@@ -227,4 +227,4 @@ def linkcode_resolve(domain, info):
 
     fn = os.path.relpath(fn, start=os.path.dirname("../factory"))
 
-    return f"https://github.com/rs-station/factory/blob/main/factory/{fn}{linespec}"  # noqa 
+    return f"https://github.com/rs-station/factory/blob/main/factory/{fn}{linespec}"  # noqa

docs/convert_favicon.py

@@ -1,4 +1,9 @@
 import cairosvg
 
 # Convert SVG to PNG
-cairosvg.svg2png(url='images/favicon.svg', write_to='images/favicon_32x32.png', output_width=32, output_height=32) 
+cairosvg.svg2png(
+    url="images/favicon.svg",
+    write_to="images/favicon_32x32.png",
+    output_width=32,
+    output_height=32,
+)

docs/index.rst

@@ -16,4 +16,4 @@ Indices and tables
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search` 
+* :ref:`search`

docs/installation.rst

@@ -21,4 +21,4 @@ For development installation:
 
    git clone https://github.com/rs-station/factory.git
    cd factory
-   pip install -e ".[test,docs]" 
+   pip install -e ".[test,docs]"

docs/make.bat

@@ -32,4 +32,4 @@ goto end
 %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 
 :end
-popd 
+popd

docs/usage.rst

@@ -14,4 +14,4 @@ Here's a simple example of how to use Factory:
    # Create and use your model
    TODO
 
-For more detailed examples and API reference, see the :doc:`api/index` section. 
+For more detailed examples and API reference, see the :doc:`api/index` section.

pymol_figures/refine_001.pdb

@@ -8,24 +8,24 @@ REMARK   3               : Oeffner,Poon,Read,Richardson,Richardson,Sacchettini,
 REMARK   3               : Sauter,Sobolev,Storoni,Terwilliger,Williams,Zwart
 REMARK   3
 REMARK   3  X-RAY DATA.
-REMARK   3  
+REMARK   3
 REMARK   3  REFINEMENT TARGET : ML
-REMARK   3  
+REMARK   3
 REMARK   3  DATA USED IN REFINEMENT.
-REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10    
-REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 56.16   
-REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.33  
-REMARK   3   COMPLETENESS FOR RANGE        (%) : 90.85 
-REMARK   3   NUMBER OF REFLECTIONS             : 85983     
-REMARK   3   NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 45512     
-REMARK   3  
+REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10
+REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 56.16
+REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.33
+REMARK   3   COMPLETENESS FOR RANGE        (%) : 90.85
+REMARK   3   NUMBER OF REFLECTIONS             : 85983
+REMARK   3   NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 45512
+REMARK   3
 REMARK   3  FIT TO DATA USED IN REFINEMENT.
 REMARK   3   R VALUE     (WORKING + TEST SET) : 0.1221
 REMARK   3   R VALUE            (WORKING SET) : 0.1203
 REMARK   3   FREE R VALUE                     : 0.1386
-REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.24 
-REMARK   3   FREE R VALUE TEST SET COUNT      : 8804      
-REMARK   3  
+REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.24
+REMARK   3   FREE R VALUE TEST SET COUNT      : 8804
+REMARK   3
 REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
 REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE  CCWORK CCFREE
 REMARK   3     1   56.16 -    3.41    1.00     2849   309  0.1392 0.1691   0.948  0.914
@@ -58,21 +58,21 @@ REMARK   3    27    1.15 -    1.14    0.68     1903   241  0.3115 0.3307   0.747
 REMARK   3    28    1.14 -    1.12    0.54     1517   170  0.3396 0.3314   0.703  0.701
 REMARK   3    29    1.12 -    1.11    0.34      960    84  0.3824 0.4505   0.607  0.613
 REMARK   3    30    1.11 -    1.10    0.11      324    39  0.4270 0.4367   0.652  0.359
-REMARK   3  
+REMARK   3
 REMARK   3  BULK SOLVENT MODELLING.
 REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL
-REMARK   3   SOLVENT RADIUS     : 1.10    
-REMARK   3   SHRINKAGE RADIUS   : 0.90    
-REMARK   3   GRID STEP          : 0.60    
-REMARK   3  
+REMARK   3   SOLVENT RADIUS     : 1.10
+REMARK   3   SHRINKAGE RADIUS   : 0.90
+REMARK   3   GRID STEP          : 0.60
+REMARK   3
 REMARK   3  ERROR ESTIMATES.
-REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.10    
-REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.84   
-REMARK   3  
+REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.10
+REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.84
+REMARK   3
 REMARK   3  STRUCTURE FACTORS CALCULATION ALGORITHM : FFT
-REMARK   3  
+REMARK   3
 REMARK   3  B VALUES.
-REMARK   3   FROM WILSON PLOT           (A**2) : 15.22   
+REMARK   3   FROM WILSON PLOT           (A**2) : 15.22
 REMARK   3   Individual atomic B
 REMARK   3                  min    max   mean <Bi,j>   iso aniso
 REMARK   3     Overall:   11.38  62.75  20.78   1.59     0  1284
@@ -92,7 +92,7 @@ REMARK   3      42.20 - 47.34        24
 REMARK   3      47.34 - 52.48        11
 REMARK   3      52.48 - 57.61         2
 REMARK   3      57.61 - 62.75         3
-REMARK   3  
+REMARK   3
 REMARK   3  GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2
 REMARK   3  DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES.
 REMARK   3    BOND      :  0.008   0.066   1227  Z= 0.503
@@ -101,7 +101,7 @@ REMARK   3    CHIRALITY :  0.085   0.253    163
 REMARK   3    PLANARITY :  0.009   0.070    228
 REMARK   3    DIHEDRAL  : 12.968  82.313    464
 REMARK   3    MIN NONBONDED DISTANCE : 2.253
-REMARK   3  
+REMARK   3
 REMARK   3  MOLPROBITY STATISTICS.
 REMARK   3    ALL-ATOM CLASHSCORE : 0.00
 REMARK   3    RAMACHANDRAN PLOT:
@@ -118,7 +118,7 @@ REMARK   3      CIS-PROLINE     : 0.00 %
 REMARK   3      CIS-GENERAL     : 0.00 %
 REMARK   3      TWISTED PROLINE : 0.00 %
 REMARK   3      TWISTED GENERAL : 0.00 %
-REMARK   3  
+REMARK   3
 REMARK   3  RAMA-Z (RAMACHANDRAN PLOT Z-SCORE):
 REMARK   3  INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2.
 REMARK   3  SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY;
@@ -127,14 +127,14 @@ REMARK   3    WHOLE: -0.12 (0.63), RESIDUES: 173
 REMARK   3    HELIX: -1.09 (0.58), RESIDUES: 68
 REMARK   3    SHEET: -1.28 (0.81), RESIDUES: 14
 REMARK   3    LOOP :  1.25 (0.70), RESIDUES: 91
-REMARK   3  
+REMARK   3
 REMARK   3  MAX DEVIATION FROM PLANES:
 REMARK   3     TYPE  MAXDEV  MEANDEV LINEINFILE
-REMARK   3   TRP   0.041   0.009   TRP A 123 
-REMARK   3   HIS   0.005   0.003   HIS A  15 
-REMARK   3   PHE   0.037   0.008   PHE A  38 
-REMARK   3   TYR   0.017   0.006   TYR A  20 
-REMARK   3   ARG   0.009   0.002   ARG A 114 
+REMARK   3   TRP   0.041   0.009   TRP A 123
+REMARK   3   HIS   0.005   0.003   HIS A  15
+REMARK   3   PHE   0.037   0.008   PHE A  38
+REMARK   3   TYR   0.017   0.006   TYR A  20
+REMARK   3   ARG   0.009   0.002   ARG A 114
 REMARK   3
 HELIX    1 AA1 GLY A    4  HIS A   15  1                                  12
 HELIX    2 AA2 ASN A   19  TYR A   23  5                                   5
@@ -147,10 +147,10 @@ HELIX    8 AA8 ASP A  119  ARG A  125  5                                   7
 SHEET    1 AA1 3 THR A  43  ARG A  45  0
 SHEET    2 AA1 3 THR A  51  TYR A  53 -1  O  ASP A  52   N  ASN A  44
 SHEET    3 AA1 3 ILE A  58  ASN A  59 -1  O  ILE A  58   N  TYR A  53
-SSBOND   1 CYS A    6    CYS A  127 
-SSBOND   2 CYS A   30    CYS A  115 
-SSBOND   3 CYS A   64    CYS A   80 
-SSBOND   4 CYS A   76    CYS A   94 
+SSBOND   1 CYS A    6    CYS A  127
+SSBOND   2 CYS A   30    CYS A  115
+SSBOND   3 CYS A   64    CYS A   80
+SSBOND   4 CYS A   76    CYS A   94
 CRYST1   79.424   79.424   37.793  90.00  90.00  90.00 P 43 21 2
 SCALE1      0.012591  0.000000  0.000000        0.00000
 SCALE2      0.000000  0.012591  0.000000        0.00000