Running ChemSTEP - Revision history

Kholland at 16:53, 16 March 2026

2026-03-16T16:53:01Z

Kholland at 20:29, 9 February 2026

2026-02-09T20:29:14Z

← Older revision		Revision as of 20:29, 9 February 2026
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	'''1. Source ChemSTEP virtual environment on Wynton'''		'''1. Source ChemSTEP virtual environment on Wynton'''
	source /wynton/group/bks/work/shared/kholland/~~chemstep_auto~~/bin/activate		source /wynton/group/bks/work/shared/kholland/chemstep_auto_v02/bin/activate

Kholland at 22:43, 12 January 2026

2026-01-12T22:43:34Z

← Older revision		Revision as of 22:43, 12 January 2026
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	'''5. Enter into or make a directory to run ChemSTEP in. Copy in necessary files for initiating ChemSTEP: params.txt, run_chemstep.py and launch_chemstep_as_job.sh. Copy in your score and indices numpy files as well, which should be in your docking directory.'''		'''5. Enter into or make a directory to run ChemSTEP in. Copy in necessary files for initiating ChemSTEP: params.txt, run_chemstep.py and launch_chemstep_as_job.sh. Copy in your score and indices numpy files as well, which should be in your docking directory.'''
	cp /wynton/group/bks/work/shared/kholland/chemstep_auto/params.txt .		cp /wynton/group/bks/work/shared/kholland/chemstep_auto/scripts/params.txt .
	cp /wynton/group/bks/work/shared/kholland/chemstep_auto/run_chemstep.py .		cp /wynton/group/bks/work/shared/kholland/chemstep_auto/scripts/run_chemstep.py .
	cp /wynton/group/bks/work/shared/kholland/chemstep_auto/launch_chemstep_as_job.sh .		cp /wynton/group/bks/work/shared/kholland/chemstep_auto/scripts/launch_chemstep_as_job.sh .

Kholland at 19:41, 16 December 2025

2025-12-16T19:41:19Z

← Older revision		Revision as of 19:41, 16 December 2025
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	cp /wynton/group/bks/work/shared/chemstep_13B_scripts_tutorial/launch_chemstep_iterative.sh .		cp /wynton/group/bks/work/shared/chemstep_13B_scripts_tutorial/launch_chemstep_iterative.sh .

	'''10. Run ChemSTEP'''		'''11. Run ChemSTEP'''
	qsub launch_chemstep_as_job.sh [round number]		qsub launch_chemstep_as_job.sh [round number]

Kholland at 19:30, 16 December 2025

2025-12-16T19:30:53Z

← Older revision		Revision as of 19:30, 16 December 2025
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	'''2. Copy seed-set SDI file into your docking directory'''		'''2. Copy seed-set SDI file into your docking directory'''
	This directory should already contain your dockfiles, with INDOCK parameters set to your liking. In this step, we are copying in a split database index file (SDI) containing paths to bundles of db2 files. This seed set contains ~~100~~ million molecules sampled randomly from the total virtual library, currently ~~1.1 trillion~~ molecules.		This directory should already contain your dockfiles, with INDOCK parameters set to your liking. In this step, we are copying in a split database index file (SDI) containing paths to bundles of db2 files. This seed set contains 92 million molecules sampled randomly from the total virtual library, currently 96 billion molecules (ZINC).
	cp /wynton/group/bks/work/shared/kholland/chemstep_auto/scripts/96M_seeds.wynton.sdi .		cp /wynton/group/bks/work/shared/kholland/chemstep_auto/scripts/96M_seeds.wynton.sdi .
	cp /wynton/group/bks/work/shared/kholland/chemstep_auto/scripts/rebuilt_seeds.wynton.sdi .		cp /wynton/group/bks/work/shared/kholland/chemstep_auto/scripts/rebuilt_seeds.wynton.sdi .

Kholland at 19:27, 16 December 2025

2025-12-16T19:27:09Z

← Older revision		Revision as of 19:27, 16 December 2025
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	'''7. Edit run_chemstep.py''' ~~note that the default parameters when copying over run_chemstep.py invoke the automatic building and docking pipeline.~~		'''7. Edit run_chemstep.py'''

	There are several configurable parameters that can be passed when first calling the CSAlgo object:		There are several configurable parameters that can be passed when first calling the CSAlgo object:
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	more optional parameters to come.		more optional parameters to come.

	At this time, we strongly suggest running ChemSTEP as a job array with 16 ~~or 32~~ CPU slots requested. The number of cores must be specified when calling CSAlgo (in run_chemstep.py) and the SGE wrapper(launch_chemstep_as_job.sh).		At this time, we strongly suggest running ChemSTEP as a job array with 8 or 16 CPU slots requested. The number of cores must be specified when calling CSAlgo (in run_chemstep.py) and the SGE wrapper(launch_chemstep_as_job.sh).

Kholland at 19:26, 16 December 2025

2025-12-16T19:26:00Z

← Older revision		Revision as of 19:26, 16 December 2025
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	last update: dec 15 2025 katie. current ver = 0.3.1.5 (automatic resubmission of failed SGE jobs).		last update: dec 16 2025 katie. current ver = 0.3.1.5 (automatic resubmission of failed SGE jobs).

	ChemSTEP (Chemical Space Traversal and Exploration Procedure) is an open-source, transparent acceleration algorithm for molecular docking capable of dealing with virtual libraries of several trillion compounds. This wiki page is a guide for BKS lab members to run ChemSTEP on Wynton HPC, using the current version of ZINC library (96B) or 13.3B library from Enamine REAL. '''for detailed instructions on the 13B space, see 'Running ChemSTEP on the 13B space' wiki page'''. For more general use directions, please refer to [ChemSTEP Read-the-Docs].		ChemSTEP (Chemical Space Traversal and Exploration Procedure) is an open-source, transparent acceleration algorithm for molecular docking capable of dealing with virtual libraries of several trillion compounds. This wiki page is a guide for BKS lab members to run ChemSTEP on Wynton HPC, using the current version of ZINC library (96B) or 13.3B library from Enamine REAL. '''for detailed instructions on the 13B space, see 'Running ChemSTEP on the 13B space' wiki page'''. For more general use directions, please refer to [ChemSTEP Read-the-Docs].
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	'''7. Edit run_chemstep.py'''		'''7. Edit run_chemstep.py''' note that the default parameters when copying over run_chemstep.py invoke the automatic building and docking pipeline.

	There are several configurable parameters that can be passed when first calling the CSAlgo object:		There are several configurable parameters that can be passed when first calling the CSAlgo object:

	'''docking_method=''' setting this to "auto" will set up and run iterative rounds of building, docking, and running ChemSTEP. If you choose the auto method, be sure to update the full path to your dockfiles in run_chemstep.py and check that all INDOCK parameters are set to your liking. NOTE: docking method is set to auto if you copy in the scripts as outlined above. Change if desired!!!!!		'''docking_method=''' setting this to "auto" will set up and run iterative rounds of building, docking, and running ChemSTEP. If you choose the auto method, be sure to update the full path to your dockfiles in run_chemstep.py and check that all INDOCK parameters are set to your liking. NOTE: docking method is set to auto if you copy in the scripts as outlined above. Change if desired!!!!!


	'''min_td_search=''' setting this parameter will ~~establich~~ a minimum-tanimoto distance "zone" around each beacon for prioritization. For example, setting a min_td_search=0.3 will require that each prioritized molecule be greater than 0.3 Td from each beacon.		'''min_td_search=''' setting this parameter will establish a minimum-tanimoto distance "zone" around each beacon for prioritization. For example, setting a min_td_search=0.3 will require that each prioritized molecule be greater than 0.3 Td from each beacon.

	more optional parameters to come.		more optional parameters to come.

Kholland at 22:06, 15 December 2025

2025-12-15T22:06:41Z

← Older revision		Revision as of 22:06, 15 December 2025
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	There are several configurable parameters that can be passed when first calling the CSAlgo object:		There are several configurable parameters that can be passed when first calling the CSAlgo object:

	'''docking_method=''' setting this to "auto" will set up and run iterative rounds of building, docking, and running ChemSTEP. If you choose the auto method, be sure to update the full path to your dockfiles in run_chemstep.py and check that all INDOCK parameters are set to your liking.		'''docking_method=''' setting this to "auto" will set up and run iterative rounds of building, docking, and running ChemSTEP. If you choose the auto method, be sure to update the full path to your dockfiles in run_chemstep.py and check that all INDOCK parameters are set to your liking. NOTE: docking method is set to auto if you copy in the scripts as outlined above. Change if desired!!!!!

Kholland at 22:04, 15 December 2025

2025-12-15T22:04:58Z

@@ Line 106: / Line 106: @@
 There are several configurable parameters that can be passed when first calling the CSAlgo object:
-'''docking_method='''
+'''docking_method=''' setting this to "auto" will set up and run iterative rounds of building, docking, and running ChemSTEP. If you choose the auto method, be sure to update the full path to your dockfiles in run_chemstep.py and check that all INDOCK parameters are set to your liking.
 At this time, we strongly suggest running ChemSTEP as a job array with 16 or 32 CPU slots requested. The number of cores must be specified when calling CSAlgo (in run_chemstep.py) and the SGE wrapper(launch_chemstep_as_job.sh).
-'''7. Run ChemSTEP''' with the following command:
+'''8. Run ChemSTEP''' with the following command:
      qsub launch_chemstep_as_job.sh
@@ Line 121: / Line 126: @@
 '''Troubleshooting:''' if no jobs are running and there is no SMI file, check the chemstep_submission.log first. Any traceback error or SGE error should give you some idea of why ChemSTEP failed. Some errors may be due to SGE or Wynton issues. If directed, look at a few .out files within /output/jobs/ . If a ChemSTEP run fails on your FIRST run, delete the output and log files, fix what needs to be fixed, and rerun. Errors in subsequent rounds during the chaining step can potentially corrupt chaining files within the /output directory that are needed for prioritization. At the very least, you will definitely have duplicates of beacons and information written to the log files. At this time, if your run fails during iterative rounds, it's best to start from the beginning.
-Prioritized molecules should be built, docked, and their scores fed back into ChemSTEP. More detailed instructions below:
+Prioritized molecules should be built, docked, and their scores fed back into ChemSTEP. More detailed instructions below for running in MANUAL mode:
-'''8. Build prioritized molecules (DOCK 3.8).''' /taken from docs.docking.org
+'''9. Build prioritized molecules (DOCK 3.8).''' /taken from docs.docking.org
        source /wynton/group/bks/soft/DOCK-3.8.5/env.sh
@@ Line 135: / Line 140: @@
-'''9. Set up for iterative rounds of ChemSTEP'''
+'''10. Set up for iterative rounds of ChemSTEP'''
        cp /wynton/group/bks/work/shared/kholland/chemstep_v0p0/run_chemstep_iterative.py .
@@ Line 149: / Line 154: @@
 For the first iterative round, the round number is [2], and should increase by one for every subsequent round of ChemSTEP. The output will be smi_round_****.smi file. Repeat steps 8-10 for as many rounds as needed. The performance is reported in outputy/complete_info/run_summary.df, which contains the number of beacons selected, the number of molecules docked, the number of hits found, the distance threshold for the selected molecules to dock, and the last added beacon's distance to all previous beacons.

Kholland at 21:59, 15 December 2025

2025-12-15T21:59:09Z

← Older revision		Revision as of 21:59, 15 December 2025
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	~~There should be no need to edit~~ run_chemstep.py or the ~~SGE wrapper script.~~ At this time, we strongly suggest running ChemSTEP as a job array with 16 or 32 CPU slots requested. The number of cores must be specified when calling CSAlgo (in run_chemstep.py) and the SGE wrapper(launch_chemstep_as_job.sh).
			'''7. Edit run_chemstep.py'''

			There are several configurable parameters that can be passed when first calling the CSAlgo object:

			'''docking_method='''

			At this time, we strongly suggest running ChemSTEP as a job array with 16 or 32 CPU slots requested. The number of cores must be specified when calling CSAlgo (in run_chemstep.py) and the SGE wrapper(launch_chemstep_as_job.sh).