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simonbraysimonbray
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remove ignite completely! use rocksdb instead
1 parent e4f7793 commit 0587daf

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‎chemicaltoolbox/lirasearch/lirasearch.xml‎

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@@ -8,20 +8,19 @@
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</requirements>
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<command detect_errors="exit_code">
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<![CDATA[
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ln -sf ${database_select.fields.path}/* /opt/ignite/storage &&
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nohup /opt/ignite/bin/ignite.sh config/lira_ignite.xml &
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ln -sf ${database_select.fields.path}/* /opt/storage/ &&
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export HOME=`pwd` &&
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#if $ligand.ext == 'pdb':
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ln -s $ligand ligand.pdb &&
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#else
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python /opt/ignite/scripts/convert_sdf_to_pdb.py $ligand ligand.pdb &&
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python /opt/scripts/convert_sdf_to_pdb.py $ligand ligand.pdb &&
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#end if
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python -m esp_dnn.predict -m ligand -i . -o . &&
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esp-surface-generator ligand.pdb.pqr ligand.pdb.tmesh &&
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sh-coeff-calculator . &&
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echo 'y' | /opt/ignite/bin/control.sh --set-state ACTIVE_READ_ONLY &&
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micromamba run -n lirasearch python /opt/ignite/scripts/lira_search_sdf.py --in_file rid_coeffs.csv --out_file output --database /opt/ignite/storage/rid_coeffs.csv --ignite_address 127.0.0.1:10800 --num_results $num_results --out_folder search_results &&
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micromamba run -n lirasearch python /opt/ignite/scripts/lira_super.py --target ligand.pdb --folder search_results &&
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micromamba run -n lirasearch python /opt/scripts/lira_search_sdf.py --in_file rid_coeffs.csv --out_file output --out_keys keys.txt --database /opt/storage/rid_coeffs.csv --num_results $num_results &&
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mkdir search_results && rocksdb_to_sdf /opt/storage keys.txt search_results &&
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micromamba run -n lirasearch python /opt/scripts/lira_super.py --target ligand.pdb --folder search_results &&
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cat search_results/*rotated.sdf >> '$output_sdf'
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]]>
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</command>

‎chemicaltoolbox/lirasearch/test-data/lirasearch_output.sdf‎

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M END
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$$$$
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ZINCae0000002oHX.0
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RDKit 3D
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M END
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$$$$
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ZINCae0000002oRr.0
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RDKit 3D
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M END
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$$$$

‎chemicaltoolbox/lirasearch/test-data/storage/000004.log‎

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‎chemicaltoolbox/lirasearch/test-data/storage/CURRENT‎

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MANIFEST-000005

‎chemicaltoolbox/lirasearch/test-data/storage/IDENTITY‎

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a04d2a72-b1ab-4ef4-8bd4-bab49ae2ee58

chemicaltoolbox/lirasearch/test-data/storage/node00-bfcdcb74-02d8-4121-b8f8-af2d7efdb83e/maintenance_tasks.mntc renamed to chemicaltoolbox/lirasearch/test-data/storage/LOCK

File renamed without changes.

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