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run.009.descriptor_rescore.ranked.csh
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#!/bin/tcsh -fe
#
# Once the ligands have been minimized in Cartesian space, rescore each ligand with a footprint
# reference. The resulting output mol2 files will be transferred back to Cluster and fed into
# the MOE sorting / clustering protocol.
#
### Set some variables manually
set attractive = "6"
set repulsive = "12"
### Set some paths
set dockdir = "${DOCKHOMEWORK}/bin"
set amberdir = "${AMBERHOMEWORK}/bin"
set moedir = "${MOEHOMEWORK}/bin"
set rootdir = "${VS_ROOTDIR}"
set mpidir = "${VS_MPIDIR}/bin"
set masterdir = "${rootdir}/zzz.master"
set paramdir = "${rootdir}/zzz.parameters"
set scriptdir = "${rootdir}/zzz.scripts"
set descriptdir = "${rootdir}/zzz.descriptor"
set zincdir = "${rootdir}/zzz.zinclibs"
set system = "${VS_SYSTEM}"
set vendor = "${VS_VENDOR}"
### Compile with intel 2018.3 compiler in case this is not default for some system
### Choose parameters for cluster
### LIRED 24 ppn
### SeaWulf 28 ppn
### Rizzo 24 ppn
#-------!!!!!!!!!!! DO NOT SUBMIT THIS IN PARALLEL it will mess up the rank order mol2-----#
# This scripts ask for the entire node but ONLY USES one proc
# That is why we used dock6 and dock6.mpi
echo "\t ATTN: This script SHOULD not be run PARALLEL "
set wcl = 12:00:00
set nodes = 1
set ppn = 24
set queue = "long-24core"
@ numprocs = (${nodes} * ${ppn})
### Make the appropriate directory. If it already exists, remove previous dock results from only
### the same vendor.
if (! -e ${rootdir}/${system}/009.descriptor-rescore) then
mkdir -p ${rootdir}/${system}/009.descriptor-rescore/
endif
if (! -e ${rootdir}/${system}/009.descriptor-rescore/${vendor}) then
mkdir -p ${rootdir}/${system}/009.descriptor-rescore/${vendor}
endif
### Compute descriptor scores for the minimized crystal pose
echo "Computing Crystal pose descriptor scores..."
if (! -e ${rootdir}/${system}/009.descriptor-rescore/${vendor}/reference) then
mkdir -p ${rootdir}/${system}/009.descriptor-rescore/${vendor}/reference
endif
cd ${rootdir}/${system}/009.descriptor-rescore/${vendor}/reference
### Write the dock.in file
##################################################
cat <<EOF >${system}.${vendor}.reference.descriptor_rescore.in
conformer_search_type rigid
use_internal_energy yes
internal_energy_rep_exp 12
internal_energy_cutoff 100.0
ligand_atom_file ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd no
use_database_filter no
orient_ligand no
bump_filter no
score_molecules yes
contact_score_primary no
contact_score_secondary no
grid_score_primary no
grid_score_secondary no
multigrid_score_primary no
multigrid_score_secondary no
dock3.5_score_primary no
dock3.5_score_secondary no
continuous_score_primary no
continuous_score_secondary no
footprint_similarity_score_primary no
footprint_similarity_score_secondary no
pharmacophore_score_primary no
pharmacophore_score_secondary no
descriptor_score_primary yes
descriptor_score_secondary no
descriptor_use_grid_score no
descriptor_use_multigrid_score no
descriptor_use_continuous_score yes
descriptor_use_footprint_similarity yes
descriptor_use_pharmacophore_score yes
descriptor_use_tanimoto yes
descriptor_use_hungarian yes
descriptor_use_volume_overlap yes
descriptor_cont_score_rec_filename ${rootdir}/${system}/002.rec-prep/${system}.rec.clean.mol2
descriptor_cont_score_att_exp 6
descriptor_cont_score_rep_exp 12
descriptor_cont_score_rep_rad_scale 1
descriptor_cont_score_use_dist_dep_dielectric yes
descriptor_cont_score_dielectric 4.0
descriptor_cont_score_vdw_scale 1
descriptor_cont_score_es_scale 1
descriptor_fps_score_use_footprint_reference_mol2 yes
descriptor_fps_score_footprint_reference_mol2_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_fps_score_foot_compare_type Euclidean
descriptor_fps_score_normalize_foot no
descriptor_fps_score_foot_comp_all_residue yes
descriptor_fps_score_receptor_filename ${rootdir}/${system}/002.rec-prep/${system}.rec.clean.mol2
descriptor_fps_score_vdw_att_exp 6
descriptor_fps_score_vdw_rep_exp 12
descriptor_fps_score_vdw_rep_rad_scale 1
descriptor_fps_score_use_distance_dependent_dielectric yes
descriptor_fps_score_dielectric 4.0
descriptor_fps_score_vdw_fp_scale 1
descriptor_fps_score_es_fp_scale 1
descriptor_fps_score_hb_fp_scale 0
descriptor_fms_score_use_ref_mol2 yes
descriptor_fms_score_ref_mol2_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_fms_score_write_reference_pharmacophore_mol2 no
descriptor_fms_score_write_reference_pharmacophore_txt no
descriptor_fms_score_write_candidate_pharmacophore no
descriptor_fms_score_write_matched_pharmacophore no
descriptor_fms_score_compare_type overlap
descriptor_fms_score_full_match yes
descriptor_fms_score_match_rate_weight 5.0
descriptor_fms_score_match_dist_cutoff 1.0
descriptor_fms_score_match_proj_cutoff 0.7071
descriptor_fms_score_max_score 20
descriptor_fingerprint_ref_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_hms_score_ref_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_hms_score_matching_coeff -5
descriptor_hms_score_rmsd_coeff 1
descriptor_volume_score_reference_mol2_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_volume_score_overlap_compute_method analytical
descriptor_weight_cont_score 1
descriptor_weight_fps_score 1
descriptor_weight_pharmacophore_score 2
descriptor_weight_fingerprint_tanimoto -1
descriptor_weight_hms_score 10
descriptor_weight_volume_overlap_score -20
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
SASA_score_secondary no
amber_score_secondary no
minimize_ligand no
atom_model all
vdw_defn_file ${paramdir}/vdw_AMBER_parm99.defn
flex_defn_file ${paramdir}/flex.defn
flex_drive_file ${paramdir}/flex_drive.tbl
chem_defn_file ${paramdir}/chem.defn
pharmacophore_defn_file ${paramdir}/ph4.defn
ligand_outfile_prefix ${system}.reference.output
write_footprints yes
write_hbonds yes
write_orientations no
num_scored_conformers 1
rank_ligands no
EOF
##################################################
${dockdir}/dock6 -i ${system}.${vendor}.reference.descriptor_rescore.in -o ${system}.${vendor}.reference.descriptor_rescore.out
cd ../
foreach score (dce_sum fps_es fps_sum fps_vdw totalScore fms_score vo_score hms_score descriptor_score)
echo ${score}
rm -rf ${rootdir}/${system}/009.descriptor-rescore/${vendor}/${score}_rank
mkdir -p ${rootdir}/${system}/009.descriptor-rescore/${vendor}/${score}_rank
cd ${rootdir}/${system}/009.descriptor-rescore/${vendor}/${score}_rank
### Compute descriptor scores for the minimized poses
echo "Computing ${score} ranked descriptor scores..."
### Write the dock.in file
##################################################
cat <<EOF >${system}.${vendor}.${score}.descriptor_rescore.in
conformer_search_type rigid
use_internal_energy yes
internal_energy_rep_exp 12
internal_energy_cutoff 100.0
ligand_atom_file ${rootdir}/${system}/008.rank_mol/${vendor}/${score}_rank/${vendor}.${score}.output_ranked.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd no
use_database_filter no
orient_ligand no
bump_filter no
score_molecules yes
contact_score_primary no
contact_score_secondary no
grid_score_primary no
grid_score_secondary no
multigrid_score_primary no
multigrid_score_secondary no
dock3.5_score_primary no
dock3.5_score_secondary no
continuous_score_primary no
continuous_score_secondary no
footprint_similarity_score_primary no
footprint_similarity_score_secondary no
pharmacophore_score_primary no
pharmacophore_score_secondary no
descriptor_score_primary yes
descriptor_score_secondary no
descriptor_use_grid_score no
descriptor_use_multigrid_score no
descriptor_use_continuous_score yes
descriptor_use_footprint_similarity yes
descriptor_use_pharmacophore_score yes
descriptor_use_tanimoto yes
descriptor_use_hungarian yes
descriptor_use_volume_overlap yes
descriptor_cont_score_rec_filename ${rootdir}/${system}/002.rec-prep/${system}.rec.clean.mol2
descriptor_cont_score_att_exp 6
descriptor_cont_score_rep_exp 12
descriptor_cont_score_rep_rad_scale 1
descriptor_cont_score_use_dist_dep_dielectric yes
descriptor_cont_score_dielectric 4.0
descriptor_cont_score_vdw_scale 1
descriptor_cont_score_es_scale 1
descriptor_fps_score_use_footprint_reference_mol2 yes
descriptor_fps_score_footprint_reference_mol2_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_fps_score_foot_compare_type Euclidean
descriptor_fps_score_normalize_foot no
descriptor_fps_score_foot_comp_all_residue yes
descriptor_fps_score_receptor_filename ${rootdir}/${system}/002.rec-prep/${system}.rec.clean.mol2
descriptor_fps_score_vdw_att_exp 6
descriptor_fps_score_vdw_rep_exp 12
descriptor_fps_score_vdw_rep_rad_scale 1
descriptor_fps_score_use_distance_dependent_dielectric yes
descriptor_fps_score_dielectric 4.0
descriptor_fps_score_vdw_fp_scale 1
descriptor_fps_score_es_fp_scale 1
descriptor_fps_score_hb_fp_scale 0
descriptor_fms_score_use_ref_mol2 yes
descriptor_fms_score_ref_mol2_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_fms_score_write_reference_pharmacophore_mol2 no
descriptor_fms_score_write_reference_pharmacophore_txt no
descriptor_fms_score_write_candidate_pharmacophore no
descriptor_fms_score_write_matched_pharmacophore no
descriptor_fms_score_compare_type overlap
descriptor_fms_score_full_match yes
descriptor_fms_score_match_rate_weight 5.0
descriptor_fms_score_match_dist_cutoff 1.0
descriptor_fms_score_match_proj_cutoff 0.7071
descriptor_fms_score_max_score 20
descriptor_fingerprint_ref_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_hms_score_ref_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_hms_score_matching_coeff -5
descriptor_hms_score_rmsd_coeff 1
descriptor_volume_score_reference_mol2_filename ${rootdir}/${system}/007.cartesian-min/${vendor}/${system}.lig.python.min.mol2
descriptor_volume_score_overlap_compute_method analytical
descriptor_weight_cont_score 1
descriptor_weight_fps_score 1
descriptor_weight_pharmacophore_score 2
descriptor_weight_fingerprint_tanimoto -1
descriptor_weight_hms_score 10
descriptor_weight_volume_overlap_score -20
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
SASA_score_secondary no
amber_score_secondary no
minimize_ligand no
atom_model all
vdw_defn_file ${paramdir}/vdw_AMBER_parm99.defn
flex_defn_file ${paramdir}/flex.defn
flex_drive_file ${paramdir}/flex_drive.tbl
chem_defn_file ${paramdir}/chem.defn
pharmacophore_defn_file ${paramdir}/ph4.defn
ligand_outfile_prefix ${vendor}.${score}_rank.output
write_footprints yes
write_hbonds yes
write_orientations no
num_scored_conformers 1
rank_ligands no
EOF
##################################################
### Write the Cluster submit file to maui
##################################################
if (`hostname -f` == "login1.cm.cluster" || `hostname -f` == "login2.cm.cluster" ) then
cat <<EOF >${system}.${vendor}.${score}.descriptor_rescore.qsub.csh
#!/bin/tcsh
#PBS -l walltime=${wcl}
#PBS -l nodes=${nodes}:ppn=${ppn}
#PBS -N ${score}.${system}.${vendor}.descriptor
#PBS -q ${queue}
#PBS -V
#PBS -j oe
cd ${rootdir}/${system}/009.descriptor-rescore/${vendor}/${score}_rank
echo "Job Started"
date
${dockdir}/dock6 -v \
-i ${system}.${vendor}.${score}.descriptor_rescore.in \
-o ${system}.${vendor}.${score}.descriptor_rescore.out
echo "Job Finished"
date
EOF
##################################################
### Write the Cluster submit file to slurm
##################################################
###if (`hostname -f` == "login1.cm.cluster" || `hostname -f` == "login2.cm.cluster" ) then
else
cat <<EOF >${system}.${vendor}.${score}.descriptor_rescore.qsub.csh
#!/bin/tcsh
#SBATCH --time=${wcl}
#SBATCH --nodes=${nodes}
#SBATCH --ntasks=${ppn}
#SBATCH --job-name=${score}.${system}.${vendor}.descriptor
#SBATCH --output=${score}.${system}.${vendor}.descriptor
#SBATCH -p rn-long
cd ${rootdir}/${system}/009.descriptor-rescore/${vendor}/${score}_rank
echo "Job Started"
date
${dockdir}/dock6 -v \
-i ${system}.${vendor}.${score}.descriptor_rescore.in \
-o ${system}.${vendor}.${score}.descriptor_rescore.out
echo "Job Finished"
date
EOF
endif
##################################################
### Submit the job
echo "Submitting ${system}.${vendor}.${score}.descriptor_rescore"
qsub ${system}.${vendor}.${score}.descriptor_rescore.qsub.csh > & ${system}.${vendor}.${score}.descriptor_rescore.qsub.log
date
end
exit