Retropath2.0 Python wrapper

Implementation 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.

Prerequisites

• Python 3
• KNIME (code was tested on 4.6.4, 4.7.0 versions)

Install

Prerequisite

The conda package manager is required. Fresh instructions on how to install conda are available online.

The tool tries to install the KNIME Anlytical Platform as well as the RetroPath2.0 node dependancies.

conda package

Install in the <my_env> conda environment:

conda install -c conda-forge -n <my_env> retropath2_wrapper

Run

Disclaimer: we recommand to provide absolute path to files, problems can arise with relative paths.

From CLI (Linux, macOS)

python -m retropath2_wrapper <sink-file> <rules-file> <out-dir> --source_file <source-file>

From Python code

The minimal required arguments are sink_file, source_file, rules_file and outdir.

from retropath2_wrapper import retropath2

r_code = retropath2(
    sink_file='/path/to/sink/file',
    source_file='/path/to/source/file',
    rules_file='/path/to/rules/file',
    outdir='/path/to/outdir'
    )

Exploration settings have default values and can be tuned:

from retropath2_wrapper import retropath2

r_code = retropath2(
    sink_file='/path/to/sink/file',
    source_file='/path/to/source/file',
    rules_file='/path/to/rules/file',
    outdir='/path/to/outdir',
    max_steps=3,
    topx=100,
    dmin=0,
    dmax=100,
    mwmax_source=1000,
    )

Already installed KNIME app can hence be used that way, eg:

from retropath2_wrapper import retropath2
from retropath2_wrapper.knime import Knime

knime = Knime(
    kinstall="/path/to/knime/directory",
    workflow="/path/to/workflow",
)
r_code = retropath2(
    sink_file='/path/to/sink/file',
    source_file='/path/to/source/file',
    rules_file='/path/to/rules/file',
    outdir='/path/to/outdir'
    knime=knime,
    )

Executions can be timed out using the timeout arguments (in minutes).

Return codes

retropath2() function returns one of the following codes:

• 0: No error
• 1: File is not found
• 2: Running the RetroPath2.0 Knime program produced an OSError
• 3: InChI is malformated
• 4: Sink file is malformed
• 10: Source has been found in the sink (warning)
• 11: No solution is found (warning)

Tests

Test can be run with the following commands:

Natively

conda install -c conda-forge pytest
python -m pytest tests

To run functional tests, the environment variable RP2_FUNCTIONAL=TRUE is required.

Knime dependencies

Available options:

1. 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
2. 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.

python -m retropath2_wrapper.knime online \
    --kinstall "/path/to/knime/root/dir" \
    --kver {4.6.4,4.7.0}

Knime software and packages are available at:

• KNIME
• KNIME v4.6.4 - Zenodo
• KNIME v4.7.0 - Zenodo

All files from these repositories can be downloaded through the Download all button:

python -m retropath2_wrapper.knime local \
    --kinstall "/path/to/knime/root/dir" \
    --zenodo-zip "/path/to/7515771.zip"

Known issues

1. Could not load native RDKit library, libfreetype.so.6: cannot open shared object file Some Knime versions (like: 4.3.0) or environments can't load RDKit library. You need to append the $CONDA_PREFIX/lib path to the LD_LIBRARY_PATH variable where the libfreetype library is available:

conda activate <env_name>
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$CONDA_PREFIX/lib"

CI/CD

For further tests and development tools, a CI toolkit is provided in cicd-toolkit folder (see cicd-toolkit/README.md).

How to cite RetroPath2.0?

Please cite:

Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: https://doi.org/10.1016/j.ymben.2017.12.002