Updated README.md

validation/README.md

@@ -154,9 +154,13 @@ The [`pyproject.toml`](pyproject.toml) we use can be found in the Git repository
 |Path       |Content                                                         |
 |-----------|----------------------------------------------------------------|
 |[Dockerfile](./Dockerfile)|Build instructions for the Docker image|
+|[NOTES](./NOTES)|A few notes to consider for further development|
 |[README.md](./README.md)|This README|
 |[entrypoint.sh](./entrypoint.sh)|Script executed on Docker container start|
 |[get-mmcif-dict-versions.py](./get-mmcif-dict-versions.py)|Extract versions of mmCIF dictionaries, used for building the Docker image. Copied into the image as `get-mmcif-dict-versions.py`.|
+|[requirements.txt](./requirements.txt)|List of Python packags needed for the validation tool.|
+|[test-suite.py](./test-suite.py)|Script to test the validation tool|
+|[test_files](./test_files)|Files used by the test suite|
 |[validate-mmcif-file.py](./validate-mmcif-file.py)|Validation tool, copied into the image as `validate-mmcif-file`.|
 
 <!--  LocalWords:  PDBx ModelCIF TOC JSON CifCheck RCSB mmcif cif pdbx dic dir

validation/test-suite.py

@@ -306,9 +306,7 @@ def _main():
             dic_version,
         )
     # Verify some version numbers inside the container
-    _do_step(
-        _verify_docker_image, "verifying Docker image", image, dic_version
-    )
+    _do_step(_verify_docker_image, "verifying Docker image", image, dic_version)
 
     # Run the actual tests of the validation script/ validate all files in
     # test_files/.

validation/test_files/working.cif

@@ -4,8 +4,6 @@ _struct.entry_id Q9Y5J9-Q9Y5L4_UNRELAXED_RANK_1_MODEL_5
 _struct.pdbx_model_details 'Dimer model generated for TIMM8B and TIMM13, produced using AlphaFold-Multimer (AlphaFold v2.2.0) as implemented by ColabFold (v1.2.0) which uses MMseqs2 for MSA generation (UniRef30 + Environmental).'
 _struct.pdbx_structure_determination_methodology computational
 _struct.title 'Predicted interaction between TIMM8B and TIMM13'
-_exptl.entry_id Q9Y5J9-Q9Y5L4_UNRELAXED_RANK_1_MODEL_5
-_exptl.method 'THEORETICAL MODEL'
 _audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/557bda7/base/mmcif_ma-core.dic
 _audit_conform.dict_name mmcif_ma.dic
 _audit_conform.dict_version 1.4.1

validation/validate-mmcif-file.py

@@ -10,6 +10,11 @@ and thus, won't be merged into the model mmCIF file and won't be checked.
 # pylint: disable=invalid-name
 # pylint: enable=invalid-name
 
+# ToDo: check that associated files (also non-cif) are actually in zip archive
+# ToDo: enable testing of gzipped files
+# ToDo: add "modelcif-pedantic" mode, fail on categories that are technically
+#       allowed but discouraged to be used, like _exptl
+
 from io import TextIOWrapper
 import argparse
 import atexit