Application to antagonists of the adenosine receptor

Follow these instructions to reproduce the results of the "Application to antagonists of the adenosine receptor" study.

1. Install the latest versions of eMolFrag and eSynth.

2. Extract donor molecules from input.tar.gz and fragment them with eMolFrag into sets of bricks and linkers:

[example]$ tar xzf input.tar.gz

[example]$ python eMolFrag_2017_01_18_01/eMolFrag.py -i input/ -o output-emolfrag/ -p 1 -m 0 -c 1

This command will create a directory output-emolfrag containing output files from eMolFrag. You can check files you generated against our output files.

3. Now you can generate a series of new molecules with eSynth. First, you may need to set the environment, e.g.:

[example]$ export LD_LIBRARY_PATH=/home/tliu7/apps/openbabel-2.3.2/lib/:/home/tliu7/apps/gsl-1.16/lib/

and then run eSynth:

[example]$ esynth-1.1/esynth output-emolfrag/BrickUnique.sdf output-emolfrag/LinkerUnique.sdf -nopen -serial -smi-only -prob-level 4 2>err

This command will create a directory synth_output_dir containing output files from eSynth. You can check files you generated against our output files.

4. If eSynth completes within a given time limit, all output files will be saved as *.zlib files, otherwise some files will be saved as *.smi. You can use the command below to combine all output files into a single text file, output-esynth.smi:

[example]$ for i in `ls synth_output_dir` ; do if [[ $i == *zlib ]] ; then cat synth_output_dir/$i | /usr/bin/openssl zlib -d >> output-esynth.smi ; else cat synth_output_dir/$i >> output-esynth.smi ; fi ; done

You can check the file you generated against our file output-esynth.smi.gz.

 

© Michal Brylinski
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