From f38308c2d8b068724812d06a7b764a63469fa7fe Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 28 Jul 2023 10:13:17 +0200
Subject: [PATCH] Updated README.md
---
validation/README.md | 4 ++++
validation/test-suite.py | 4 +---
validation/test_files/working.cif | 2 --
validation/validate-mmcif-file.py | 5 +++++
4 files changed, 10 insertions(+), 5 deletions(-)
diff --git a/validation/README.md b/validation/README.md
index c5c1911..7072d9b 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 f038451..0e73fbe 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 6f39d88..046971f 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 f5aa7bf..ca0e97a 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
--
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