LigFlow/ScoreFlow search for ChemBase parametrized molecules

[diegoenry]

LigFlow/ScoreFlow should first search for a compound in ChemBase for parameters instead of recomputing all over again.

This is especially important for am1-bcc and even more for RESP which take a lot of time.

Another highlight here if to prevent recomputing the same parameters for the SAME molecule, in case a user wants to MMGBSA rescore multiple docking conformations.

[diegoenry]

Ideally, we must have a check at ChemFlow_functions to see if we have the pre-computed charges @ "$CHEMFLOW_HOME/ChemBase/${CHARGE}/"

If not, check it we have the pre-computed charges within "$PROJECT.chemflow/LigFlow/${CHARGE}/" (charge = bcc or resp )

If all fails, try to compute it, normally.

Quick update. I implemente the idea in a project folder.

PROJECT="hivpr"
PROTOCOL="bcc"
CHARGE="bcc"

WORKDIR=~/ChemFlow_paper/Benchmark_meso/
RUNDIR=~/ChemFlow_paper/Benchmark_meso/hivpr.chemflow/ScoreFlow/bcc/receptor/

LIGAND_LIST="CHEMBL158050"

for LIGAND in ${LIGAND_LIST} ; do

    FILENAME=${WORKDIR}/${PROJECT}.chemflow/LigFlow/${CHARGE}/${LIGAND}.mol2

    if [ -f ${FILENAME} ] ; then
        awk '/1 MOL/&&!/TEMP/ {print $9}'  ${FILENAME} > charges.dat
        antechamber -i ligand_gas.mol2 -o ligand_bcc.mol2 -fi mol2 -fo mol2 -cf charges.dat -c rc -pf yes &> /dev/null
    fi

done

[donadef]

What about when the charge option is rest ? what is the procedure ?

[donadef]

Done. @diegoenry you might want to test and then you can close this issue :)