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''ucsfdock'' is a Python package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.
Deprecated. See [[pydock3]].
 
Programs:
* blastermaster: generate a specific docking configuration for a given receptor and ligand
* dockmaster: generate many different docking configurations and then evaluate & analyze them in parallel using a specified job scheduler (e.g. Slurm)
 
A '''docking configuration''' is a unique set of DOCK parameter files (e.g., ''matching_spheres.sph'') and INDOCK parameter values.
 
= Installation =
 
Coming soon.
 
= Instructions =
 
== Note for UCSF Shoichet Lab members ==
 
''ucsfdock'' is already installed on the following clusters. You can source the provided Python environment scripts to expose the relevant executables:
 
=== ''Wynton'' ===
 
source /wynton/home/irwin/isknight/envs/python3.8.5.sh
 
=== Gimel ===
 
Only nodes other than 'gimel' itself are supported, e.g., 'gimel5'.
 
source /nfs/soft/ian/python3.8.5.sh
 
== blastermaster ==
 
''blastermaster'' allows the generation of a specific docking configuration for a given receptor and ligand.
 
'''Note:''' Invoking ''blastermaster'' commands below will produce a log file called ''blastermaster.log'' in your current working directory.
 
=== blastermaster configure ===
 
First you need to create the directory for your blastermaster job. To do so, simply type
 
blastermaster configure
 
By default, the job directory is named ''blastermaster_job''. To specify a different name, type
 
blastermaster configure <JOB_DIR_NAME>
 
The job directory contains two sub-directories:
# ''working'': input files, intermediate blaster files, sub-directories for individual blastermaster subroutines
# ''dockfiles'': output files (DOCK parameter files & INDOCK)
 
If your current working directory contains any of the following files, then they will be automatically copied into the working directory within the created job directory. This feature is intended to simplify the process of configuring the blastermaster job.
 
* ''rec.pdb''
* ''xtal-lig.pdb''
* ''rec.crg.pdb''
* ''reduce_wwPDB_het_dict.txt''
* ''filt.params''
* ''radii''
* ''amb.crg.oxt''
* ''vdw.siz''
* ''delphi.def''
* ''vdw.parms.amb.mindock''
* ''prot.table.ambcrg.ambH''
 
Only the following are required. Default versions / generated versions will be used if the others are not provided.
* ''rec.pdb''
* ''xtal-lig.pdb''
 
If you would like to use files not present in your current working directory, copy them into your job's working directory, e.g.:
cp <FILE_PATH> <JOB_DIR_NAME>/working/
 
Finally, configure the ''blastermaster_config.yaml'' file in the job directory to your specifications. The parameters in this file govern the behavior of blastermaster.
 
=== blastermaster run ===
 
Once your job has been configured to your liking, navigate to the the job directory and run blastermaster:
cd <JOB_DIR_NAME>
blastermaster run
 
This will execute the many blastermaster subroutines in sequence. The state of the program will be printed to standard output as it runs.
 
== dockmaster ==
 
''dockmaster'' allows the evaluation of many different docking configurations in parallel using a specified job scheduler (e.g. Slurm).
 
The name "dockmaster", aside from being an uncreative rehash of the name "blastermaster", derives from the notion of a literal dockmaster, i.e., the person in charge of a dock who manages freight logistics and bosses around numerous dockworkers. In this analogy, a single dockworker corresponds to the processing of a single docking configuration.
 
'''Note:''' Invoking ''dockmaster'' commands will produce a log file called ''dockmaster.log'' in your current working directory.
 
=== dockmaster configure ===
First you need to create the directory for your blastermaster job. To do so, simply type
 
dockmaster configure
 
By default, the job directory is named ''dockmaster_job''. To specify a different name, type
 
dockmaster configure <JOB_DIR_NAME>
 
The job directory contains two sub-directories:
# ''working'': input files, intermediate blaster files, sub-directories for individual blastermaster subroutines
# ''retro_docking'': individual retro docking jobs for each docking configuration
 
The key difference between the working directories of ''blastermaster'' and ''dockmaster'' is that the working directory of ''dockmaster'' may contain multiple variants of the blaster files (prefixed by a number, e.g. "1_box"). These variant files are used to create the different docking configurations specified by the multi-valued entries of ''dockmaster_config.yaml''. They are created efficiently, such that the same variant used in multiple docking configurations is not created more than once.
 
If your current working directory contains any of the following files, then they will be automatically copied into the working directory within the created job directory. This feature is intended to simplify the process of configuring the dockmaster job.
 
* ''rec.pdb''
* ''xtal-lig.pdb''
* ''rec.crg.pdb''
* ''reduce_wwPDB_het_dict.txt''
* ''filt.params''
* ''radii''
* ''amb.crg.oxt''
* ''vdw.siz''
* ''delphi.def''
* ''vdw.parms.amb.mindock''
* ''prot.table.ambcrg.ambH''
 
Only the following are required. Default versions / generated versions will be used if the others are not provided.
* ''rec.pdb''
* ''xtal-lig.pdb''
 
If you would like to use files not present in your current working directory, copy them into your job's working directory, e.g.:
cp <FILE_PATH> <JOB_DIR_NAME>/working/
 
Finally, configure the ''dockmaster_config.yaml'' file in the job directory to your specifications. The parameters in this file govern the behavior of dockmaster.
 
'''Note:''' The ''dockmaster_config.yaml'' file differs from the ''blastermaster_config.yaml'' file in that every parameter of the former may accept either a single value or a ''list of comma-separated values'', which indicates a specific set of configuration parameter values to attempt. Multiple such multi-valued parameters may be provided, and all unique resultant docking configurations will be attempted.
 
Single-valued YAML line format:
 
distance_to_surface: 1.0
 
Multi-valued YAML line format:
 
distance_to_surface: [1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9]
 
=== environmental variables ===
 
Designate where the short cache and long cache should be located. E.g.:
 
export SHRTCACHE=/dev/shm  # temporary storage for job files
export LONGCACHE=/dev/shm  # long-term storage for files shared between jobs
 
In order for ''dockmaster'' to know which scheduler it should use, please configure the following environmental variables according to which one of the job schedulers you have.
 
==== Slurm ====
 
E.g., on the UCSF Shoichet Lab Gimel cluster (on any node other than 'gimel' itself, such as 'gimel5'):
 
export SBATCH_EXEC=/usr/bin/sbatch
export SQUEUE_EXEC=/usr/bin/squeue
 
==== SGE ====
 
E.g., on the UCSF Wynton cluster:
 
export QSTAT_EXEC=/opt/sge/bin/lx-amd64/qstat
export QSUB_EXEC=/opt/sge/bin/lx-amd64/qsub
 
The following is necessary on the UCSF Wynton cluster:
 
export SGE_SETTINGS=/opt/sge/wynton/common/settings.sh
 
On most clusters, this will probably be:
export SGE_SETTINGS=/opt/sge/default/common/settings.sh
 
=== dockmaster run ===
 
Once your job has been configured to your liking, navigate to the the job directory and run dockmaster:
cd <JOB_DIR_NAME>
dockmaster run <JOB_SCHEDULER_NAME>
 
where <JOB_SCHEDULER_NAME> is one of:
* ''sge''
* ''slurm''
 
This will execute the many dockmaster subroutines in sequence, except for the retro docking jobs run on each docking configuration, which are run in parallel via the scheduler. The state of the program will be printed to standard output as it runs.
 
You can also set the following flags to adjust retro docking job submission behavior. This example show the default values:
dockmaster run <JOB_SCHEDULER_NAME> --retro_docking_job_max_reattempts=0 --retro_docking_job_timeout_minutes=None
 
Once the dockmaster job is complete, the following files will be generated in the job directory:
* ''dockmaster_job_report.pdf'': contains (1) roc.png of best retro docking job, (2) box plots of enrichment for every multi-valued config parameter, and (3) heatmaps of enrichment for every pair of multi-valued config parameters
* ''dockmaster_job_results.csv'': enrichment metrics for each docking configuration
 
In addition, the best retro docking job will be copied to its own sub-directory ''best_retro_docking_job/''.
 
Within each retro docking job directory, there are the following files and sub-directories:
* ''working/'': intermediate files
* ''dockfiles/'': parameters files and INDOCK for given docking configuration
* ''output/'': contains:
** joblist
** sub-directories ''1/'' for actives and ''2/'' for decoys (each containing OUTDOCK and test.mol2 files)
** log files for the retro docking jobs
* ''retro_docking_job_results.csv'': data loaded from OUTDOCK files for both actives and decoys
* ''roc.png'': the ROC enrichment curve (log-scaled x-axis) for given docking configuration

Latest revision as of 06:40, 2 September 2022

Deprecated. See pydock3.

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