diff --git a/validation/README.md b/validation/README.md index c5c191111e868aa09b8bd52550849df91d4ddd5f..7072d9b87e7f1c048b877ac047398da20ec2ef0d 100644 --- a/validation/README.md +++ b/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 diff --git a/validation/test-suite.py b/validation/test-suite.py index f03845142ffc628ae8345e727addbc4c138e04e5..0e73fbe3c83f9de9964685892027699a82b986e4 100644 --- a/validation/test-suite.py +++ b/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/. diff --git a/validation/test_files/working.cif b/validation/test_files/working.cif index 6f39d8881b1195bd606cc118e63e9ca572d5e868..046971f598dd54cbcc8fad5225f2e6aaed147d2f 100644 --- a/validation/test_files/working.cif +++ b/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 diff --git a/validation/validate-mmcif-file.py b/validation/validate-mmcif-file.py index f5aa7bfabe0d42b9a4b72d45233eea46fa35b1c4..ca0e97ae4fb84c124341138cdeba87ee30ba01f5 100755 --- a/validation/validate-mmcif-file.py +++ b/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