DISI - User contributions [en]

How to do parameter scanning

2017-02-09T19:13:52Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep
|
|------ dockfiles
| |
| |----- working
| |
| ------ rec.pdb, xtal-lig.pdb, INDOCK and other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

mkdir ligands-decoys
cd ligands-decoys
mkdir ligands
mkdir decoys

now copy your decoys.db2.gz to decoys
now copy your ligands.db2.gz to ligands
now copy decoys.smi to the folder
now copy ligands.smi to the folder

7) Submit DOCK and enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh #1st change the path inside the script to your own dir
csh /path/to/script/AUCplot_of-lig-decoys.csh #1st change the path inside the script to your own dir

9) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

How to do parameter scanning

2017-02-09T19:09:30Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep
|
|------ dockfiles
| |
| |----- working
| |
| ------ rec.pdb, xtal-lig.pdb, INDOCK and other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

mkdir ligands-decoys
cd ligands-decoys
mkdir ligands
mkdir decoys

now copy your decoys.db2.gz to decoys
now copy your ligands.db2.gz to ligands

7) Submit DOCK and enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh #1st change the path inside the script to your own dir
csh /path/to/script/AUCplot_of-lig-decoys.csh #1st change the path inside the script to your own dir

9) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

How to do parameter scanning

2017-02-09T05:56:55Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep
|
|------ dockfiles
| |
| |----- working
| |
| ------ rec.pdb, xtal-lig.pdb, INDOCK and other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

mkdir ligands-decoys
cd ligands-decoys
mkdir ligands
mkdir decoys

now copy your decoys.db2.gz to decoys
now copy your ligands.db2.gz to ligands

7) Submit DOCK and enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh
csh /path/to/script/AUCplot_of-lig-decoys.csh

9) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

How to do parameter scanning

2017-02-09T05:56:29Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep
|
|------ dockfiles
| |
| |----- working
| |
| ------ rec.pdb, xtal-lig.pdb, INDOCK and other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

mkdir ligands-decoys
cd ligands-decoys
mkdir ligands
mkdir decoys

now copy your decoys.db2.gz to decoys
now copy your ligands.db2.gz to ligands

7) Submit DOCK and enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh
csh /path/to/script/AUCplot_of-lig-decoys.csh

9) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

How to do parameter scanning

2017-02-09T05:55:55Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep
|
|------ dockfiles
| |
| |----- working
| |
| ------ rec.pdb, xtal-lig.pdb, and other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

mkdir ligands-decoys
cd ligands-decoys
mkdir ligands
mkdir decoys

now copy your decoys.db2.gz to decoys
now copy your ligands.db2.gz to ligands

7) Submit DOCK and enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh
csh /path/to/script/AUCplot_of-lig-decoys.csh

9) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

How to do parameter scanning

2017-02-09T04:35:03Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles
| |
| |----- working
| |
| ------ other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

mkdir ligands-decoys
cd ligands-decoys
mkdir ligands
mkdir decoys

now copy your decoys.db2.gz to decoys
now copy your ligands.db2.gz to ligands

7) Submit DOCK and enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh
csh /path/to/script/AUCplot_of-lig-decoys.csh

9) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

How to do parameter scanning

2017-02-09T04:30:36Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles
| |
| |----- working
| |
| ------ other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

mkdir ligands-decoys
cd ligands-decoys
mkdir ligands
mkdir decoys

now copy your decoys.db2.gz to decoys
now copy your ligands.db2.gz to ligands

7) Submit enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh
csh /path/to/script/AUCplot_of-lig-decoys.csh

9) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

How to do parameter scanning

2017-02-09T04:29:58Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles
| |
| |----- working
| |
| ------ other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

mkdir decoys-ligands
cd decoys-ligands
mkdir ligands
mkdir decoys

now copy your decoys.db2.gz to decoys
now copy your ligands.db2.gz to ligands

7) Submit enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh
csh /path/to/script/AUCplot_of-lig-decoys.csh

9) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

How to do parameter scanning

2017-02-09T04:28:33Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles
| |
| |----- working
| |
| ------ other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) make the following subfolders

mkdir decoys-ligands
mkdir ligands inside decoys-ligands
mkdir decoys inside decoys-ligands

cp your decoys.db2.gz to decoys
cp your ligands.bd2.gz to ligands

7) Submit enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

8) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh
csh /path/to/script/AUCplot_of-lig-decoys.csh

9) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

How to do parameter scanning

2017-02-08T23:55:27Z

Mas:

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles
| |
| |----- working
| |
| ------ other files generated balstermaster.py
|
------- script ------ dockprep_thin_spheres_in_batches.csh
|
|------ submit_dockprep_thin_spheres.csh
|
|------ dockprep_thin_spheres.csh
|
|------ lig-decoy_enrichment.csh
|
|------ combineScoresAndPoses.csh
|
|------ AUCplot_of-lig-decoys.csh
|
|------ mk_matrix_logAUC.py
|
|------ sph_lib.py
|
|------ pdb_lib.py
|
------- close_sph.py

1) Make those directories above.
mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.
cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/lig-decoy_enrichment.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/combineScoresAndPoses.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/AUCplot_of-lig-decoys.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/mk_matrix_logAUC.py .

5) Run parameter scanning.
cd ../ # go back to thin_spheres_parameter_scanning folder
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

Note:- you can edit dockprep_thin_spheres_in_batches.csh to include more CPUs in Job Bound

6) Submit enrichment calculation.
csh /path/to/script/lig-decoy_enrichment.csh

7) Combine and analyze the docking results.
csh /path/to/script/combineScoresAndPoses.csh
csh /path/to/script/AUCplot_of-lig-decoys.csh

8) Visualize the logAUC by heatmap.
python /path/to/script/mk_matrix_logAUC.py

Using thin spheres in DOCK3.7

2016-11-10T00:31:18Z

Mas: /* Tutorial for using Thin Spheres in DOCK 3.7 */

==Tutorial for using Thin Spheres in DOCK 3.7==

Written by Trent E. Balius, 2016/11/03.

1) Run blastermaster.py. This will generate two directories: working and dockfiles

2) Make a new directory called mk_thin_spheres:
mkdir mk_thin_spheres
cd mk_thin_spheres

3) First lets make a molecular surface. We recommend that you make a less dense molecular surface by copying the rec.pdb and running the following command:
cp ../rec.pdb .
cp ../working/rec.site.dms .
$DOCKBASE/proteins/dms/bin/dms rec.pdb -a -d 0.2 -i rec.site.dms -g dms.log -p -n -o rec.ms

Here, the -d flag allows us to pass the program a scalar to modify the density of the surface points.
For example, with a -d set to 1.0 the density is will be 5.42 pts/sq.A, while with a -d 0.2, we will get a density of 1.18 pts/sq.A.

Instead, you could copy the molecular surface of the original surface (this is OK for small sites):
cp ../working/rec.ms .

4) Run the thin spheres code:
/mnt/nfs/home/tbalius/zzz.svn/dockenv/trunk/etc/thin_spheres.py -i rec.ms -o delphi.sph >& thin_spheres.log

Get the following python code:
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

python close_sph.py delphi.sph ../xtal-lig.pdb delphi_close.sph 2.0
head delphi_close.sph

if there are too many spheres (> 1,000), decrease the distance to, say, 1.2.

Note that this is available through the DOCK3.6 release.

cd ../
move back to the top directory.

5) Now lets setup a directory and files to run blastermaster with the Existing Low Dielectric Spheres
make a new directory call dockprep_w_thin_sph/
mkdir dockprep_w_thin_sph
cd dockprep_w_thin_sph
cp ../rec.pdb ../../xtal-lig.pdb .
mkdir working
cp ../../working/rec.crg.pdb working/.
cp ../mk_thin_spheres/delphi_close.sph working/lowdielectric.sph

Make sure the header of the sphere file is cluster 1.
head working/lowdielectric.sph
If it is not and says cluster 0 then run the following, because blaster master expects this to be cluster 1.
sed -i 's/cluster 0/cluster 1/g' working/lowdielectric.sph

6) Now lets run blastermaster with Existing Low Dielectric Spheres
$DOCKBASE/proteins/blastermaster/blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag

Using thin spheres in DOCK3.7

2016-11-10T00:27:59Z

Mas: /* Tutorial for using Thin Spheres in DOCK 3.7 */