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Badge](https://anaconda.org/conda-forge/retropath2_wrapper/badges/latest_release_date.svg)](https://anaconda.org/conda-forge/retropath2_wrapper)\n\nImplementation of the KNIME retropath2.0 workflow. Takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The tool expects the following files: `rules.csv`, `sink.csv` and `source.csv` and produces results in an output folder.\n\n## Prerequisites\n\n- Python 3\n- KNIME (code was tested on `4.6.4`, `4.7.0` versions)\n\n## Install\n\n### Prerequisite\n\nThe conda package manager is required. Fresh instructions on how to install conda are [available online](https://docs.conda.io/projects/conda/en/latest/user-guide/install/).\n\nThe tool tries to install the KNIME Anlytical Platform as well as the RetroPath2.0 node dependancies.\n\n### conda package\n\nInstall in the `\u003cmy_env\u003e` conda environment:\n\n```shell\nconda install -c conda-forge -n \u003cmy_env\u003e retropath2_wrapper\n```\n\n## Run\n\n**Disclaimer**: we recommand to provide absolute path to files, problems can arise with relative paths.\n\n### From CLI (Linux, macOS)\n\n```sh\npython -m retropath2_wrapper \u003csink-file\u003e \u003crules-file\u003e \u003cout-dir\u003e --source_file \u003csource-file\u003e\n```\n\n### From Python code\n\nThe minimal required arguments are `sink_file`, `source_file`, `rules_file` and `outdir`.\n\n```python\nfrom retropath2_wrapper import retropath2\n\nr_code = retropath2(\n    sink_file='/path/to/sink/file',\n    source_file='/path/to/source/file',\n    rules_file='/path/to/rules/file',\n    outdir='/path/to/outdir'\n    )\n```\n\nExploration settings have default values and can be tuned:\n\n```python\nfrom retropath2_wrapper import retropath2\n\nr_code = retropath2(\n    sink_file='/path/to/sink/file',\n    source_file='/path/to/source/file',\n    rules_file='/path/to/rules/file',\n    outdir='/path/to/outdir',\n    max_steps=3,\n    topx=100,\n    dmin=0,\n    dmax=100,\n    mwmax_source=1000,\n    )\n```\n\nAlready installed KNIME app can hence be used that way, eg:\n\n```python\nfrom retropath2_wrapper import retropath2\nfrom retropath2_wrapper.knime import Knime\n\nknime = Knime(\n    kinstall=\"/path/to/knime/directory\",\n    workflow=\"/path/to/workflow\",\n)\nr_code = retropath2(\n    sink_file='/path/to/sink/file',\n    source_file='/path/to/source/file',\n    rules_file='/path/to/rules/file',\n    outdir='/path/to/outdir'\n    knime=knime,\n    )\n```\n\nExecutions can be timed out using the `timeout` arguments (in minutes).\n\n### Return codes\n\n`retropath2()` function returns one of the following codes:\n\n- 0: No error\n- 1: File is not found\n- 2: Running the RetroPath2.0 Knime program produced an OSError\n- 3: InChI is malformated\n- 4: Sink file is malformed\n- 10: Source has been found in the sink (warning)\n- 11: No solution is found (warning)\n\n## Tests\n\nTest can be run with the following commands:\n\n### Natively\n\n```sh\nconda install -c conda-forge pytest\npython -m pytest tests\n```\n\nTo run functional tests, the environment variable `RP2_FUNCTIONAL=TRUE` is required.\n\n### Knime dependencies\n\nAvailable options:\n\n1. You provide a path of the Knime root directory through the argument `--kinstall`. You need to have the following libraries installed: `org.knime.features.chem.types.feature.group`, `org.knime.features.datageneration.feature.group`, `org.knime.features.python.feature.group`, `org.rdkit.knime.feature.feature.group`\n2. `retropath2_wrapper` will install Knime for you, at the root of the python package, by downloading the softwares available on Zenodo. You can choose a version among `4.6.4` or `4.7.0`. Optionally, you can locate a path for the installation. If an executable is found in the path, Knime will not be reinstalled.\n\n```bash\npython -m retropath2_wrapper.knime online \\\n    --kinstall \"/path/to/knime/root/dir\" \\\n    --kver {4.6.4,4.7.0}\n```\n\nKnime software and packages are available at:\n\n- [KNIME](https://www.knime.com/)\n- [KNIME v4.6.4 - Zenodo](https://zenodo.org/record/7515771)\n- [KNIME v4.7.0 - Zenodo](https://zenodo.org/record/7564938)\n\nAll files from these repositories can be downloaded through the `Download all` button:\n\n```bash\npython -m retropath2_wrapper.knime local \\\n    --kinstall \"/path/to/knime/root/dir\" \\\n    --zenodo-zip \"/path/to/7515771.zip\"\n```\n\n## Known issues\n\n1. Could not load native RDKit library, libfreetype.so.6: cannot open shared object file\n   Some Knime versions (like: 4.3.0) or environments can't load RDKit library.\n   You need to append the `$CONDA_PREFIX/lib` path to the `LD_LIBRARY_PATH` variable where the `libfreetype` library is available:\n\n```sh\nconda activate \u003cenv_name\u003e\nexport LD_LIBRARY_PATH=\"$LD_LIBRARY_PATH:$CONDA_PREFIX/lib\"\n```\n\n## CI/CD\n\nFor further tests and development tools, a CI toolkit is provided in `cicd-toolkit` folder (see [cicd-toolkit/README.md](cicd-toolit/README.md)).\n\n### How to cite RetroPath2.0?\n\nPlease cite:\n\nDelépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. 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