Commit f18754b2 authored by Lukas Pravda's avatar Lukas Pravda
Browse files

Update README.md

Deleted pdbeccdutils/computations/__init__.py, pdbeccdutils/computations/parity_method.py, pdbeccdutils/core/__init__.py, pdbeccdutils/core/ccd_reader.py, pdbeccdutils/core/ccd_writer.py, pdbeccdutils/core/component.py, pdbeccdutils/core/depictions.py, pdbeccdutils/core/exceptions.py, pdbeccdutils/core/fragment_library.py, pdbeccdutils/core/models.py, pdbeccdutils/data/coordgen_templates/templates.mae, pdbeccdutils/data/general_templates/adamantane.sdf, pdbeccdutils/data/general_templates/cube.sdf, pdbeccdutils/data/general_templates/decahydrocorrin.sdf, pdbeccdutils/data/general_templates/hem.sdf, pdbeccdutils/data/general_templates/nonbornane.sdf, pdbeccdutils/data/general_templates/phorbine.sdf, pdbeccdutils/data/general_templates/porphin.sdf, pdbeccdutils/data/general_templates/porphycene.sdf, pdbeccdutils/data/general_templates/ru_complex.sdf, pdbeccdutils/data/general_templates/ru_complex2.sdf, pdbeccdutils/data/fragment_library.tsv, pdbeccdutils/helpers/__init__.py, pdbeccdutils/helpers/collection_ext.py, pdbeccdutils/helpers/conversions.py, pdbeccdutils/helpers/drawing.py, pdbeccdutils/helpers/logging.py, pdbeccdutils/helpers/mol_tools.py, pdbeccdutils/scripts/__init__.py, pdbeccdutils/scripts/process_components_cif_cli.py, pdbeccdutils/scripts/setup_pubchem_library_cli.py, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/0KA.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/11R.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/1CL.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/6KK.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/ADM.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/AXM.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/G2O.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/HDD.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/HEA.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/HEB.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/HEC.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/HEG.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/HEM.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/HME.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/HNN.cif, pdbeccdutils/tests/ccd_mmcif_test_files/depiction_test/SF4.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/000.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/007.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/00O.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/03R.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/08T.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/099.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/0OD.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/10R.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/3CD.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/7OM.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/880.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/ASX.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/ATP.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/BCD.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/CDL.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/CMO.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/D3O.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/DMS.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/EOH.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/FES.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/GLC.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/GLU.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/GOL.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/HEM.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/IBP.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/MAN.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/NA.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/NAD.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/NAG.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/SAC.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/SEH.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/SO4.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/SY9.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/V55.cif, pdbeccdutils/tests/ccd_mmcif_test_files/random_sample/VIA.cif, pdbeccdutils/tests/ccd_mmcif_test_files/UNL.cif, pdbeccdutils/tests/components_cif/cut_down_components.cif, pdbeccdutils/tests/conftest.py, pdbeccdutils/tests/test_file_writing.py, pdbeccdutils/tests/test_fragment_library.py, pdbeccdutils/tests/test_inchi_key_matches.py, pdbeccdutils/tests/test_load_eoh_cif.py, pdbeccdutils/tests/test_parity.py, pdbeccdutils/tests/test_process_components_cif_cli.py, pdbeccdutils/tests/test_property_generation.py, pdbeccdutils/tests/test_rdkit_fixtures.py, pdbeccdutils/tests/test_scaffold_generation.py, pdbeccdutils/tests/test_web_services.py, pdbeccdutils/tests/test_write_img.py, pdbeccdutils/tests/tst_utilities.py, pdbeccdutils/utils/__init__.py, pdbeccdutils/utils/config.py, pdbeccdutils/utils/pubchem_downloader.py, pdbeccdutils/utils/web_services.py, pdbeccdutils/__init__.py, doc/_static/HEM_300.svg, doc/_static/HEM_300_names.svg, doc/_static/pdbe_fragments.svg, doc/guide/depictions.md, doc/guide/fragments.md, doc/guide/intro.md, doc/guide/pipelines.md, doc/Makefile, doc/api.md, doc/conf.py, doc/index.md, doc/logo.png, doc/pdbeccdutils.computations.md, doc/pdbeccdutils.core.md, doc/pdbeccdutils.helpers.md, doc/pdbeccdutils.scripts.md, doc/pdbeccdutils.utils.md, .github/workflows/documentation.yml, .github/workflows/tests.yml, .gitignore, .gitlab-ci.yml, MANIFEST.in, CHANGELOG.md, LICENSE, Makefile, setup.py files
parent 9ee418d7
# This workflow will install Python dependencies, and generate documentation.
name: ccdutils documentation
on:
push:
branches:
- master
pull_request:
branches:
- master
jobs:
documentation:
name: Generate documentation
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
with:
persist-credentials: false
- name: Set up python
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: Set up environment and generate docs
uses: s-weigand/setup-conda@v1
with:
activate-conda: true
conda-channels: conda-forge
- run: |
conda install rdkit=2020.03.6
pip install -e ".[docs]"
- run: |
cd doc
make html
- name: Deploy pages
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./doc/_build/html
# This workflow will install Python dependencies, run pytests
name: ccdutils tests
on:
push:
branches:
- master
- dev
pull_request:
branches:
- master
- dev
jobs:
pytest:
name: Run unit tests
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
with:
persist-credentials: false
- name: Set up python
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: Set up environment and run pytest
uses: s-weigand/setup-conda@v1
with:
activate-conda: true
conda-channels: conda-forge
- run: |
conda install rdkit=2020.03.6
pip install -e ".[tests]"
- run: pytest --cov=pdbeccdutils
.idea
# Byte-compiled / optimized / DLL files
__pycache__/
.pytest_cache
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
*.egg-info/
.installed.cfg
*.egg
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*,cover
.hypothesis/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
# Flask stuff:
instance/
.webassets-cache
# Scrapy stuff:
.scrapy
# PyBuilder
target/
# IPython Notebook
.ipynb_checkpoints
# pyenv
.python-version
# celery beat schedule file
celerybeat-schedule
# dotenv
.env
# virtualenv
venv/
ENV/
# Spyder project settings
.spyderproject
# Rope project settings
.ropeproject
tests_out/
# vscode files
.vscode/*
# pytest files
pdbeccdutils/tests/out
# mypy cache
.mypy_cache
# Sphinx documentation
doc/_build/
.metrics
.DS_Store
\ No newline at end of file
image: continuumio/miniconda
before_script:
- apt-get update && apt-get install make
- conda create -c rdkit -n rdkit-doc rdkit python=3.7
- source activate rdkit-doc
- pip install -e .
- pip install pytest-cov sphinx sphinx_rtd_theme recommonmark sphinx-autodoc-typehints sphinx-markdown-tables
test:
script:
- pytest --cov=pdbeccdutils
only:
- master
pages:
script:
- cd doc
- make html
- mv _build/html/ ../public/
artifacts:
paths:
- public
only:
- master
# Changelog
## RELEASE 0.5 - May 15, 2019
### Features
* Add support for UniChem mapping.
* Add bond information to the SVG decomposition.
* Allow PARITY method to be atom/bond specific.
* Improve and extend physchem properties.
* Enhanced CIF export (physchem, scaffolds, fragments, 2D, mapping).
* Few improvements to match newest RDKit version (**breaking changes**).
## RELEASE 0.4 - January 12, 2019
### Features
* Add SVG decomposition in the SVG format.
* Protein-ligand interaction pipeline moved to separate [repository](https://gitlab.ebi.ac.uk/pdbe/release/interactions).
* Add basic properties calculation (Abhik).
* Extension and improvements of the Fragment library.
## RELEASE 0.3 - October 12, 2018
### Features
* Introduce CoordGen from RDKit.
* Refactored pdbeccdutils.core (**breaking changes**).
* Scaffolding (Abhik).
* Add protein-ligand interaction pipeline.
## RELEASE 0.2 - June 14, 2018
### Features
* PDBeChem pipeline.
* Support for PARITY method.
* Introduce EKTGv2() method for 3D conformer generation.
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include pdbeccdutils/data/general_templates/*
include pdbeccdutils/data/coordgen_templates/*
include pdbeccdutils/data/fragment_library.tsv
clean:
rm -rf build/* && rm -rf dist/* && rm -rf pdbeccdutils.egg-info && rm -rf htmlcov && rm .coverage
test-report:
pytest --cov=pdbeccdutils --cov-report=html
package:
pytest;\
python setup.py bdist_wheel;\
pip uninstall pdbeccdutils;\
pip install -e .;\
find dist -name "pdbeccdutils-*-py3*" -exec pip install {} \;
make upload:
twine upload dist/* --verbose
make pypi: package upload clean
[![CodeFactor](https://www.codefactor.io/repository/github/pdbeurope/ccdutils/badge/master)](https://www.codefactor.io/repository/github/pdbeurope/ccdutils/overview/master) ![PYPi](https://img.shields.io/pypi/v/pdbeccdutils?color=green&style=flat) ![GitHub](https://img.shields.io/github/license/pdbeurope/ccdutils) ![ccdutils documentation](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20documentation/badge.svg) ![ccdutils tests](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20tests/badge.svg)
# Repository was moved
# pdbeccdutils
* A set of python tools to deal with PDB chemical components definitions
for small molecules, taken from the [wwPDB Chemical Component Dictionary](https://www.wwpdb.org/data/ccd)
* The tools use:
* [RDKit](http://www.rdkit.org/) for chemistry
* [PDBeCIF](https://github.com/PDBeurope/pdbecif) cif parser.
* [scipy](https://www.scipy.org/) for depiction quality check.
* [numpy](https://www.numpy.org/) for molecular scaling.
* Please note that the project is under active development.
## Installation instructions
* `pdbeccdutils` requires RDKit to be installed.
The official RDKit documentation has [installation instructions for a variety of platforms](http://www.rdkit.org/docs/Install.html).
For linux/mac OS this is most easily done using the anaconda python with commands similar to:
```console
conda create -c conda-forge -n rdkit-env rdkit python=3.7
conda activate rdkit-env
```
* Once you have installed RDKit, as described above then install pdbeccdutils using pip:
```console
pip install pdbeccdutils
```
## Features
* mmCIF CCD read/write.
* Generation of 2D depictions (`No image available` generated if the flattening cannot be done) along with the quality check.
* Generation of 3D conformations.
* Fragment library search.
* Chemical scaffolds (Murcko scaffold, Murcko general, BRICS).
* Lightweight implementation of [parity method](https://doi.org/10.1016/j.str.2018.02.009) by Jon Tyczak.
* RDKit molecular properties per component.
* UniChem mapping.
## TODO list
* Add more unit/regression tests to get higher code coverage.
* Further improvements of the documentation.
## Notes
* Protein-ligand interaction has been extracted [here](https://gitlab.ebi.ac.uk/pdbe/release/interactions). This was because of the fact that at the end of the day it was not using any of the pdbeccdutils functionality and introduced additional dependencies on the package.
## Documentation
The documentation depends on the following packages:
* `sphinx`
* `sphinx_rtd_theme`
* `recommonmark`
* `sphinx-autodoc-typehints`
Note that `sphinx` needs to be a part of the virtual environment, if you want to generate documentation by yourself.
Otherwise it cannot pick `rdkit` module. `sphinx_rtd_theme` is a theme providing nice `ReadtheDocs` mobile friendly style.
* Generate *.rst* files to be included as a part of the documentation. Inside the directory `pdbeccdutils/doc` run the following commands to generate documentation.
* Alternatively, use the `recommonmark` package along with the proper configuration to get the Markdown working.
Use the following to generate initial markup files to be used by sphinx. This needs to be used when adding another sub-packages.
```console
sphinx-apidoc -f -o /path/to/output/dir ../pdbeccdutils/
```
Use this to re-generate the documentation from the doc/ directory:
```console
make html
```
Repository was moved to [GitHub](https://github.com/pdbeurope/ccdutils).
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = pdbeccdutils
SOURCEDIR = .
BUILDDIR = _build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
<?xml version='1.0' encoding='iso-8859-1'?>
<svg version='1.1' baseProfile='full'
xmlns='http://www.w3.org/2000/svg'
xmlns:rdkit='http://www.rdkit.org/xml'
xmlns:xlink='http://www.w3.org/1999/xlink'
xml:space='preserve'
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