From 9bc58fb16cb3a5509ef29d9641d924ddce334d26 Mon Sep 17 00:00:00 2001
From: B13nch3n <b13nch3n_01@theb-si.de>
Date: Thu, 1 Feb 2024 10:38:22 +0100
Subject: [PATCH] Updated to latest ModelCIF dict verion
---
validation/Dockerfile | 10 +++++++---
validation/README.md | 2 +-
2 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/validation/Dockerfile b/validation/Dockerfile
index 34a884d..01d3c8d 100644
--- a/validation/Dockerfile
+++ b/validation/Dockerfile
@@ -80,7 +80,7 @@ COPY --chmod=755 validate-mmcif-file.py /usr/local/bin/validate-mmcif-file
## https://github.com/ihmwg/ModelCIF/blob/master/dist/mmcif_ma.dic.
## Dictionaries do not change that frequently therefore we skip the hassle of
## keeping them in an external volume.
-ARG USE_DICT_VERSION="1.4.5"
+ARG USE_DICT_VERSION="1.4.6"
ENV USE_DICT_VERSION=${USE_DICT_VERSION}
LABEL org.modelarchive.dict_release="${USE_DICT_VERSION}"
WORKDIR ${SRC_DIR}
@@ -91,7 +91,7 @@ RUN set -e pipefail; \
export _GIT_URL="https://raw.github.com/ihmwg/ModelCIF/master"; \
# Use the path of an actual commit to keep the dict immutable (RCSB refuses
# to use Git tags for versions).
- export _MA_DICT_URL="https://raw.githubusercontent.com/ihmwg/ModelCIF/ba728c4/archive/mmcif_ma-v${USE_DICT_VERSION}.dic"; \
+ export _MA_DICT_URL="https://raw.githubusercontent.com/ihmwg/ModelCIF/d18ba38/archive/mmcif_ma-v${USE_DICT_VERSION}.dic"; \
mkdir ${_DICT_DIR}; \
mkdir ${MMCIF_DICTS_DIR}; \
cd ${_DICT_DIR}; \
@@ -117,11 +117,15 @@ RUN set -e pipefail; \
## Build the PDBx/mmCIF SDB
DictToSdb -ddlFile mmcif_ddl.dic \
-dictFile mmcif_pdbx_v50.dic \
- -dictSdbFile ${MMCIF_DICTS_DIR}/mmcif_pdbx_v50.dic.sdb; \
+ -dictSdbFile ${MMCIF_DICTS_DIR}/mmcif_pdbx_v50.sdb; \
#
## Get versions of ModelCIF & PDBx/mmCIF dictionaries
get-mmcif-dict-versions --child-location ${_MA_DICT_URL} mmcif_ma.dic; \
mv mmcif_ma_version.json ${MMCIF_DICTS_DIR}/; \
+ get-mmcif-dict-versions --child-location ${_DICT_URL}/mmcif_pdbx_v50.dic \
+ --output mmcif_pdbx_v50_version.json \
+ mmcif_pdbx_v50.dic; \
+ mv mmcif_pdbx_v50_version.json ${MMCIF_DICTS_DIR}/; \
#
## Make SDBs readable and keep possible error logs from building them
mv *.log ${MMCIF_DICTS_DIR}/ 2>/dev/null || :; \
diff --git a/validation/README.md b/validation/README.md
index 7072d9b..24758bd 100644
--- a/validation/README.md
+++ b/validation/README.md
@@ -93,7 +93,7 @@ $
**`--help`** (**`-h`**) Print a help/ usage page for the validation tool.
-**`--dict-sdb <SDB FILE>`** (**`-d`**) Format dictionary in (binary) SDB format used for validating a ModelCIF file. The Docker container comes with a SDB for ModelCIF (`/usr/local/share/mmcif-dict-suite/mmcif_ma.sdb`) and one for the original PDBx/mmCIF (`/usr/local/share/mmcif-dict-suite/mmcif_pdbx_v50.dic.sdb`) format.
+**`--dict-sdb <SDB FILE>`** (**`-d`**) Format dictionary in (binary) SDB format used for validating a ModelCIF file. The Docker container comes with a SDB for ModelCIF (`/usr/local/share/mmcif-dict-suite/mmcif_ma.sdb`) and one for the original PDBx/mmCIF (`/usr/local/share/mmcif-dict-suite/mmcif_pdbx_v50.sdb`) format.
**`--out-file <JSON FILE>`** (**`-o`**) Instead of printing the output to `stdout`, store it in a JSON formatted file.
--
GitLab