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Bugfix and typo corrections #7

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de55f37
Bugfixes
csecker May 8, 2023
21fa2f7
Merge branch 'VirtualFlow:vftools-1' into vftools-1
csecker Jan 15, 2024
0735ac0
Typo correction
csecker Jan 15, 2024
4d3909f
Merge remote-tracking branch 'origin/vftools-1' into vftools-1
csecker Jan 15, 2024
f505737
Typo correction, old_eollection_no -> old_collection_no
csecker Jan 15, 2024
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48 changes: 24 additions & 24 deletions bin/vfvs_pp_prepare_dockingposes.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ usage="vfvs_pp_prepare_docking_poses.sh <results folder> <folder_format> <rankin
Possible folder formats (for the results as well as pdbqt folders):
sub: for VFVS version < 8.0
tar: vfvs version >= 8.0
meta_tranch: Use this format if the output files are stored on the tranch level. This is the case when the setting 'outputfiles_level' was set to 'tranch' in the control file during the workflow.
meta_tranche: Use this format if the output files are stored on the tranche level. This is the case when the setting 'outputfiles_level' was set to 'tranche' in the control file during the workflow.
meta_collection: Use this format if the output files are stored on the collection level. This is the case when the setting 'outputfiles_level' was set to 'collection' in the control file during the workflow.

The <ranking file> needs to contain the collection in the first column and the compound name in the second column.
Expand Down Expand Up @@ -73,65 +73,65 @@ while read -r line; do
collection="${array[0]}"
#molecule=${array[1]/_*} # removing replicas
molecule=${array[1]}
tranch=${collection/_*}
tranche=${collection/_*}
collection_no=${collection/*_}
# name2_padded=$(printf "%05.f" ${collection:5})
echo -e "\n *** Preparing structure ${molecule} ***"
if [ -d ${output_folder}/${tranch}/${collection_no}/${molecule} ]; then
if [ -d ${output_folder}/${tranche}/${collection_no}/${molecule} ]; then
echo " * The directory for this ligand already exists. Skipping this ligand."
continue
fi
mkdir -p ${output_folder}/${tranch}/${collection_no}/${molecule}
cd ${output_folder}/${tranch}/${collection_no}/${molecule}
mkdir -p ${output_folder}/${tranche}/${collection_no}/${molecule}
cd ${output_folder}/${tranche}/${collection_no}/${molecule}

if [ "${format}" == "tar" ]; then
if ! tar -xvf ../../../../${results_folder}/${tranch}.tar --wildcards "${tranch}/${collection_no}*tar"; then
if ! tar -xvf ../../../../${results_folder/commplete/incomplete}/${tranch}.tar --wildcards "${tranch}/${collection_no}*tar"; then
if ! tar -xvf ../../../../${results_folder}/${tranche}.tar --wildcards "${tranche}/${collection_no}*tar"; then
if ! tar -xvf ../../../../${results_folder/complete/incomplete}/${tranche}.tar --wildcards "${tranche}/${collection_no}*tar"; then
echo " * Error, skipping this ligand"
cd ../../../../
continue
fi
fi
if ! tar -xvf ${tranch}/${collection_no}.gz.tar --wildcards "${molecule}*"; then
if ! tar -xvf ${tranche}/${collection_no}.gz.tar --wildcards "${molecule}*"; then
echo " * Error, skipping this ligand"
cd ../../../../
continue
fi
elif [ "${format}" == "sub" ]; then
if ! tar -xvf ../../../../${results_folder}/${tranch}/${collection_no}.gz.tar --wildcards "${molecule}_replica*"; then
if ! tar -xvf ../../../../${results_folder/commplete/incomplete}/${tranch}/${collection_no}.gz.tar --wildcards "${molecule}_replica*"; then
if ! tar -xvf ../../../../${results_folder}/${tranche}/${collection_no}.gz.tar --wildcards "${molecule}_replica*"; then
if ! tar -xvf ../../../../${results_folder/complete/incomplete}/${tranche}/${collection_no}.gz.tar --wildcards "${molecule}_replica*"; then
echo " * Error, skipping this ligand"
cd ../../../../
continue
fi
fi
elif [ "${format}" == "meta_tranch" ]; then
metatranch=${tranch:0:2}
if ! tar -xvf ../../../../${results_folder}/${metatranch}/${tranch}.tar --wildcards "${tranch}/${collection_no}.tar.gz"; then
if ! tar -xvf ../../../../${results_folder/commplete/incomplete}/${metatranch}/${tranch}.tar --wildcards "${tranch}/${collection_no}.tar.gz"; then
elif [ "${format}" == "meta_tranche" ]; then
metatranche=${tranche:0:2}
if ! tar -xvf ../../../../${results_folder}/${metatranche}/${tranche}.tar --wildcards "${tranche}/${collection_no}.tar.gz"; then
if ! tar -xvf ../../../../${results_folder/complete/incomplete}/${metatranche}/${tranche}.tar --wildcards "${tranche}/${collection_no}.tar.gz"; then
echo " * Error, skipping this ligand"
cd ../../../../
continue
fi
fi
if ! tar -xvf ${tranch}/${collection_no}.tar.gz --wildcards "${collection_no}/${molecule}_replica*"; then
if ! tar -xvf ${tranche}/${collection_no}.tar.gz --wildcards "${collection_no}/${molecule}_replica*"; then
echo " * Error, skipping this ligand"
cd ../../../../
continue
fi
mv ${collection_no}/*pdbqt ./
elif [ "${format}" == "meta_collection" ]; then
metatranch=${tranch:0:2}
if ! cp ../../../../${results_folder}/${metatranch}/${tranch}/${collection_no}.tar.gz ./; then
if ! cp ../../../..${results_folder/commplete/incomplete}/${metatranch}/${tranch}/${collection_no}.tar.gz ./; then
metatranche=${tranche:0:2}
if ! cp ../../../../${results_folder}/${metatranche}/${tranche}/${collection_no}.tar.gz ./; then
if ! cp ../../../..${results_folder/complete/incomplete}/${metatranche}/${tranche}/${collection_no}.tar.gz ./; then
echo " * Error, skipping this ligand"
cd ../../../../
continue
fi
fi
mkdir ${tranch}/
mv ${collection_no}.tar.gz ${tranch}/
if ! tar -xvf ${tranch}/${collection_no}.tar.gz --wildcards "${collection_no}/${molecule}_replica*"; then
mkdir ${tranche}/
mv ${collection_no}.tar.gz ${tranche}/
if ! tar -xvf ${tranche}/${collection_no}.tar.gz --wildcards "${collection_no}/${molecule}_replica*"; then
echo " * Error, skipping this ligand"
cd ../../../../
continue
Expand All @@ -150,21 +150,21 @@ while read -r line; do
replica=${file/*_}
replica=${replica/.*}
mkdir -p ${replica}
mv $file ${replica}/${tranch}_${collection_no}_${file}
mv $file ${replica}/${tranche}_${collection_no}_${file}
done
if [[ "${format}" == "tar" ]] || [[ "${format}" == "sub" ]]; then
rm *tar || true
fi

rm -r ${tranch}*
rm -r ${tranche}*
for replica_folder in $(ls -d replica*); do
cd ${replica_folder}
mv *pdbqt docking.out.pdbqt
obabel -m -ipdbqt docking.out.pdbqt -opdb -O "${molecule}.rank-.pdb"
energy=$(obenergy "${molecule}.rank-1.pdb" | tail -n 1 | awk '{print $4}')
obabel -m -ipdbqt docking.out.pdbqt -osdf -O "${molecule}.rank-.sdf"
obabel -ipdbqt docking.out.pdbqt -osdf -O "${molecule}.rank-all.sdf"
echo "${tranch}_${collection} ${molecule} ${replica_folder} ${energy}" >> "${molecule}.rank-1.energy"
echo "${tranche}_${collection} ${molecule} ${replica_folder} ${energy}" >> "${molecule}.rank-1.energy"
echo "${molecule} ${energy} ${replica_folder}" >> ../../../../../${ranking_file}.energies
cd ..
done
Expand Down
6 changes: 3 additions & 3 deletions bin/vfvs_prepare_newcollections.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ while read -r line; do
read -r -a array <<< "$line"
old_collection=${collection}
old_tranche=${tranche}
old_eollection_no=${collection_no}
old_collection_no=${collection_no}

collection_subno="1"
collection_subno_padded="0001"
Expand All @@ -83,8 +83,8 @@ while read -r line; do
else
collection="${array[0]}"
ligand="${array[1]}"
metatranche="${tranche:0:2}"
tranche="${collection/_*}"
metatranche="${tranche:0:2}"
collection_no=${collection/*_}
#collection_no="$(printf "%05.f" "${collection_no}")"
fi
Expand Down Expand Up @@ -146,7 +146,7 @@ while read -r line; do
elif [ "${pdbqt_folder_format}" == "hash_metatranche" ]; then
if [ "${new_collection}" == "true" ]; then
echo " * Extracting collection ${collection}"
rm -r ${old_eollection_no} &>/dev/null || true
rm -r ${old_collection_no} &>/dev/null || true
tar -xzf ../${pdbqt_input_folder}/${collection//smi/pdbqt}.tar.gz || true
fi
cp ${collection_no//smi/pdbqt}/${ligand}.pdbqt ../${output_folder}.tmp2/${collection_new}/${ligand}.pdbqt || true
Expand Down