Benchmark for MDA 2.4.3 (#5)

* switch to chembl33 and update env * formatting with black * standardization code modifies mol inplace * benchmark results * simplify conda env * add scaffold analysis * use rdkit.js to generate images on hover * add link to scaffold network viz in readme * cleanup
MDAnalysis · Aug 7, 2024 · 8b6e4f5 · 8b6e4f5
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diff --git a/Makefile b/Makefile
@@ -1,7 +1,5 @@
 # MDAnalysis fork to use
-GITHUB_USER ?= cbouy
-# Branch of MDAnalysis to install
-BRANCH ?= fix-converter
+MDA_VERSION ?= 2.4.3
 # Use conda or mamba
 CONDA ?= conda
 # Number of threads to use in parallel
@@ -15,9 +13,9 @@ MAX_ATOMS ?= 50
 
 SHELL := /bin/bash
 SET_CONDA_ENV := source $$(conda info --base)/etc/profile.d/conda.sh && conda activate && conda activate rdkitconverter
-CHEMBL_SDF := ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_30/chembl_30.sdf.gz
+CHEMBL_SDF := ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_33/chembl_33.sdf.gz
 
-fetch := data/chembl_30.sdf.gz
+fetch := data/chembl_33.sdf.gz
 process := data/chembl_processed_unique.smi.gz
 benchmark := data/chembl_failed.smi
 report := results/failed_molecules.html
@@ -30,7 +28,7 @@ help:
 	@echo 'targets:'
 	@echo '  help                      Show this help'
 	@echo '  install                   Install dependencies'
-	@echo '  fetch                     Fetch ChEMBL 30'
+	@echo '  fetch                     Fetch ChEMBL 33'
 	@echo '  process                   Filter, standardize and remove duplicate molecules'
 	@echo '  benchmark                 Run the benchmark'
 	@echo '  report                    Generate the report'
@@ -42,7 +40,7 @@ help:
 install:
 	$(CONDA) env create -f environment.yaml
 	@$(SET_CONDA_ENV)
-	@pip install git+https://github.com/$(GITHUB_USER)/mdanalysis.git@$(BRANCH)#subdirectory=package
+	@$(CONDA) install 'mdanalysis==$(MDA_VERSION)'
 
 $(fetch):
 	@export CHEMBL_SDF=$(CHEMBL_SDF)

diff --git a/README.md b/README.md
@@ -12,16 +12,19 @@ To cite this repository, please use the following DOI:
 
 | Description | Value |
 | --- | --- |
-| **MDAnalysis version** | 2.2.0-dev0 |
-| **Accuracy** | 99.14% |
-| **Number of molecules fetched** | 2,136,187 |
-| **Number of molecules processed** | 1,942,004 |
-| **Number of molecules failed** | 16,615 |
+| **MDAnalysis version** | 2.4.3 |
+| **Accuracy** | 99.19% |
+| **Number of molecules fetched** | 2,372,174 |
+| **Number of molecules processed** | 2,166,327 |
+| **Number of molecules failed** | 17,577 |
 
 Details on the benchmark can also be found [here](results/results.json).
 
 The **interactive list of molecules** currently failing can be accessed [here](https://raw.githack.com/MDAnalysis/RDKitConverter-benchmark/main/results/failed_molecules.html) (click on a molecule's image to zoom in).
 
+Failing **scaffolds** can be accessed [here](https://raw.githack.com/MDAnalysis/RDKitConverter-benchmark/main/results/failed_scaffolds.html). The scaffold network used to
+create this file can be viewed [here](https://raw.githack.com/MDAnalysis/RDKitConverter-benchmark/main/results/scaffold_network.html).
+
 ## Instructions
 
 Running the benchmark requires conda (or mamba) on a Linux machine.
@@ -53,7 +56,7 @@ The results are available in the `results/` directory:
 
 ## Methods
 
-The benchmark will fetch ChEMBL 30 as an SDF file and process the molecules the following way:
+The benchmark will fetch ChEMBL 33 as an SDF file and process the molecules the following way:
 - Discard molecules that could not be read or sanitized by RDKit
 - Keep only the largest fragment
 - Keep only molecules with 2 to 50 heavy atoms

diff --git a/environment.yaml b/environment.yaml
@@ -1,165 +1,18 @@
 name: rdkitconverter
 channels:
+  - uclcheminformatics 
   - conda-forge
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1=conda_forge
-  - _openmp_mutex=4.5=1_gnu
-  - alsa-lib=1.2.3=h516909a_0
-  - biopython=1.79=py39h3811e60_1
-  - boost=1.74.0=py39h5472131_5
-  - boost-cpp=1.74.0=h6cacc03_7
-  - brotli=1.0.9=h7f98852_6
-  - brotli-bin=1.0.9=h7f98852_6
-  - brotlipy=0.7.0=py39h3811e60_1003
-  - bzip2=1.0.8=h7f98852_4
-  - c-ares=1.18.1=h7f98852_0
-  - ca-certificates=2022.2.1=h06a4308_0
-  - cairo=1.16.0=ha12eb4b_1010
-  - certifi=2021.10.8=py39hf3d152e_1
-  - cffi=1.15.0=py39h4bc2ebd_0
-  - charset-normalizer=2.0.12=pyhd8ed1ab_0
-  - colorama=0.4.4=pyh9f0ad1d_0
-  - cryptography=36.0.0=py39h9ce1e76_0
-  - cycler=0.11.0=pyhd8ed1ab_0
-  - cython=0.29.28=py39he80948d_0
-  - dbus=1.13.18=hb2f20db_0
-  - easydict=1.9=py_0
-  - expat=2.4.7=h27087fc_0
-  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
-  - font-ttf-inconsolata=3.000=h77eed37_0
-  - font-ttf-source-code-pro=2.038=h77eed37_0
-  - font-ttf-ubuntu=0.83=hab24e00_0
-  - fontconfig=2.13.96=h8e229c2_2
-  - fonts-conda-ecosystem=1=0
-  - fonts-conda-forge=1=0
-  - fonttools=4.30.0=py39hb9d737c_0
-  - freetype=2.11.0=h70c0345_0
-  - gettext=0.21.0=hf68c758_0
-  - gevent=21.12.0=py39h3811e60_0
-  - giflib=5.2.1=h36c2ea0_2
-  - glib=2.70.2=h780b84a_4
-  - glib-tools=2.70.2=h780b84a_4
-  - greenlet=1.1.2=py39he80948d_1
-  - grequests=0.6.0=pyh9f0ad1d_0
-  - griddataformats=0.7.0=pyhd8ed1ab_0
-  - gst-plugins-base=1.18.5=hf529b03_3
-  - gstreamer=1.18.5=h9f60fe5_3
-  - icu=69.1=h9c3ff4c_0
-  - idna=3.3=pyhd8ed1ab_0
-  - jbig=2.1=h7f98852_2003
-  - jinja2=3.0.3=pyhd8ed1ab_0
-  - jpeg=9e=h7f98852_0
-  - keyutils=1.6.1=h166bdaf_0
-  - kiwisolver=1.4.0=py39hf939315_0
-  - krb5=1.19.3=h3790be6_0
-  - lcms2=2.12=hddcbb42_0
-  - ld_impl_linux-64=2.36.1=hea4e1c9_2
-  - lerc=3.0=h9c3ff4c_0
-  - libblas=3.9.0=13_linux64_openblas
-  - libbrotlicommon=1.0.9=h7f98852_6
-  - libbrotlidec=1.0.9=h7f98852_6
-  - libbrotlienc=1.0.9=h7f98852_6
-  - libcblas=3.9.0=13_linux64_openblas
-  - libclang=13.0.1=default_hc23dcda_0
-  - libdeflate=1.10=h7f98852_0
-  - libedit=3.1.20210910=h7f8727e_0
-  - libev=4.33=h516909a_1
-  - libevent=2.1.10=h9b69904_4
-  - libffi=3.4.2=h7f98852_5
-  - libgcc-ng=11.2.0=h1d223b6_14
-  - libgfortran-ng=11.2.0=h69a702a_14
-  - libgfortran5=11.2.0=h5c6108e_14
-  - libglib=2.70.2=h174f98d_4
-  - libgomp=11.2.0=h1d223b6_14
-  - libiconv=1.16=h516909a_0
-  - liblapack=3.9.0=13_linux64_openblas
-  - libllvm13=13.0.1=hf817b99_2
-  - libnsl=2.0.0=h7f98852_0
-  - libogg=1.3.5=h27cfd23_1
-  - libopenblas=0.3.18=pthreads_h8fe5266_0
-  - libopus=1.3.1=h7f98852_1
-  - libpng=1.6.37=h21135ba_2
-  - libpq=14.2=hd57d9b9_0
-  - libstdcxx-ng=11.2.0=he4da1e4_14
-  - libtiff=4.3.0=h542a066_3
-  - libuuid=2.32.1=h7f98852_1000
-  - libuv=1.43.0=h7f98852_0
-  - libvorbis=1.3.7=h9c3ff4c_0
-  - libwebp=1.2.2=h3452ae3_0
-  - libwebp-base=1.2.2=h7f98852_1
-  - libxcb=1.13=h7f98852_1004
-  - libxkbcommon=1.0.3=he3ba5ed_0
-  - libxml2=2.9.12=h885dcf4_1
-  - libzlib=1.2.11=h36c2ea0_1013
-  - lz4-c=1.9.3=h9c3ff4c_1
-  - markupsafe=2.1.1=py39hb9d737c_0
-  - matplotlib=3.5.1=py39hf3d152e_0
-  - matplotlib-base=3.5.1=py39h2fa2bec_0
-  - mmtf-python=1.1.2=py_0
-  - mols2grid=0.2.1=pyhd8ed1ab_0
-  - mrcfile=1.3.0=pyh44b312d_0
-  - msgpack-python=1.0.3=py39h1a9c180_0
-  - munkres=1.1.4=pyh9f0ad1d_0
-  - mysql-common=8.0.28=ha770c72_0
-  - mysql-libs=8.0.28=hfa10184_0
-  - ncurses=6.3=h9c3ff4c_0
-  - networkx=2.7.1=pyhd8ed1ab_0
-  - nspr=4.33=h295c915_0
-  - nss=3.74=hb5efdd6_0
-  - numpy=1.22.3=py39h18676bf_0
-  - openjpeg=2.4.0=hb52868f_1
-  - openssl=1.1.1m=h7f8727e_0
-  - packaging=21.3=pyhd8ed1ab_0
-  - pandas=1.4.1=py39hde0f152_0
-  - pcre=8.45=h9c3ff4c_0
-  - pillow=9.0.1=py39hae2aec6_2
-  - pip=22.0.4=pyhd8ed1ab_0
-  - pixman=0.40.0=h36c2ea0_0
-  - pthread-stubs=0.4=h36c2ea0_1001
-  - pycairo=1.21.0=py39h0934665_0
-  - pycparser=2.21=pyhd8ed1ab_0
-  - pyopenssl=22.0.0=pyhd8ed1ab_0
-  - pyparsing=3.0.7=pyhd8ed1ab_0
-  - pyqt=5.12.3=py39hf3d152e_8
-  - pyqt-impl=5.12.3=py39hde8b62d_8
-  - pyqt5-sip=4.19.18=py39he80948d_8
-  - pyqtchart=5.12=py39h0fcd23e_8
-  - pyqtwebengine=5.12.1=py39h0fcd23e_8
-  - pysocks=1.7.1=py39hf3d152e_4
-  - python=3.9.10=h85951f9_2_cpython
-  - python-dateutil=2.8.2=pyhd8ed1ab_0
-  - python_abi=3.9=2_cp39
-  - pytz=2021.3=pyhd8ed1ab_0
-  - qt=5.12.9=ha98a1a1_5
-  - rdkit=2020.03.6=py39h54e287e_1
-  - readline=8.1.2=h7f8727e_1
-  - requests=2.27.1=pyhd8ed1ab_0
-  - requests_cache=0.4.13=py_0
-  - scipy=1.8.0=py39hee8e79c_1
-  - setuptools=60.10.0=py39hf3d152e_0
-  - six=1.16.0=pyh6c4a22f_0
-  - sqlite=3.38.0=hc218d9a_0
-  - tk=8.6.12=h27826a3_0
-  - tornado=6.1=py39h3811e60_2
-  - tqdm=4.63.0=pyhd8ed1ab_0
-  - tzdata=2022a=h191b570_0
-  - unicodedata2=14.0.0=py39h3811e60_0
-  - urllib3=1.26.9=pyhd8ed1ab_0
-  - wheel=0.37.1=pyhd8ed1ab_0
-  - xorg-kbproto=1.0.7=h7f98852_1002
-  - xorg-libice=1.0.10=h7f98852_0
-  - xorg-libsm=1.2.3=hd9c2040_1000
-  - xorg-libx11=1.7.2=h7f98852_0
-  - xorg-libxau=1.0.9=h7f98852_0
-  - xorg-libxdmcp=1.1.3=h7f98852_0
-  - xorg-libxext=1.3.4=h7f98852_1
-  - xorg-libxrender=0.9.10=h7f98852_1003
-  - xorg-renderproto=0.11.1=h7f98852_1002
-  - xorg-xextproto=7.3.0=h7f98852_1002
-  - xorg-xproto=7.0.31=h7f98852_1007
-  - xz=5.2.5=h516909a_1
-  - zlib=1.2.11=h36c2ea0_1013
-  - zope.event=4.5.0=pyh9f0ad1d_0
-  - zope.interface=5.4.0=py39h3811e60_1
-  - zstd=1.5.2=ha95c52a_0
+  - bokeh=3.2.0
+  - mols2grid=1.1.1
+  - networkx=3.1
+  - pandas=2.0.2
+  - python=3.10.11
+  - rdkit=2022.09.1
+  - scaffoldgraph=1.1.2
+  - tqdm=4.65.0
+  - numpy=1.25.0
+  - pydot=1.4.2
+  - pygraphviz=1.11
+  - scipy=1.9.3
diff --git a/results/badge.json b/results/badge.json
@@ -1 +1 @@
-{"schemaVersion": 1, "label": "accuracy", "message": "99.14%", "color": "success"}
+{"schemaVersion": 1, "label": "accuracy", "message": "99.19%", "color": "success"}
diff --git a/results/failed_molecules.html b/results/failed_molecules.html