Running ChemSTEP - Revision history

Kholland at 18:48, 22 June 2026

2026-06-22T18:48:26Z

← Older revision		Revision as of 18:48, 22 June 2026
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	<pre>		<pre>
	source /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/bin/activate		source /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/bin/activate
	</pre>		</pre>

Kholland at 18:44, 22 June 2026

2026-06-22T18:44:06Z

← Older revision		Revision as of 18:44, 22 June 2026
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	</pre>		</pre>

			TRIAZINES: 'n1cncnc1'

	=== Example: AmpC on 22B with minTD=0.50, No IFP ===		=== Example: AmpC on 22B with minTD=0.50, No IFP ===

Kholland at 18:43, 22 June 2026

2026-06-22T18:43:15Z

← Older revision		Revision as of 18:43, 22 June 2026
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	last update: ~~may 07~~ 2026 katie. current ver = 03 (integrated IFP).		last update: june 22 2026 katie. current ver = 04 (integrated IFP and smarts filtering).

	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 a subset of ZINC (22B or 72B) 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 a subset of ZINC (22B or 72B) 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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	! Library !! Path		! Library !! Path
	\|-		\|-
	\| 13B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/libraries/13B/13M_seeds.wynton.sdi</code>		\| 13B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/13B/13M_seeds.wynton.sdi</code>
	\|-		\|-
	\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/libraries/22B/22M_seeds.sdi</code>		\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/22B/22M_seeds.sdi</code>
	\|-		\|-
	\| 72B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/libraries/72B/72M_seeds.sdi</code>		\| 72B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/72B/72M_seeds.sdi</code>
	\|}		\|}

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	'''22B/72B library:'''		'''22B/72B library:'''
	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/get_scores.py 0		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/get_scores.py 0
	</pre>		</pre>

	'''13B library:'''		'''13B library:'''
	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/get_scores.py 0 MOL		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/get_scores.py 0 MOL
	</pre>		</pre>

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	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/convert_scores_to_npy.py 0 <mol_id_prefix>		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/convert_scores_to_npy.py 0 <mol_id_prefix>
	</pre>		</pre>

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	! Library !! Path		! Library !! Path
	\|-		\|-
	\| 13B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/libraries/13B/boltz_fplib.pickle</code>		\| 13B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/13B/boltz_fplib.pickle</code>
	\|-		\|-
	\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/libraries/22B/22B_fplib.pickle</code>		\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/22B/22B_fplib.pickle</code>
	\|-		\|-
	\| 72B \|\| <code>/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/libraries/72B/72B_fplib.pickle</code>		\| 72B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/libraries/72B/72B_fplib.pickle</code>
	\|}		\|}

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	Ionic/ASP-149 > 0		Ionic/ASP-149 > 0
	</pre>		</pre>


			=== Optional: SMARTS exclusion filter ===
			Integrated SMARTS filer can exclude problematic chemotypes from being built, docked, or selected as beacons. Multiple SMARTS patterns are tolerated. Comment in the following line in run_chemstep.py:

			<pre>
			filter_smarts=['n1cncnc1', 'c1cccnc1[SH]']
			</pre>


	=== Example: AmpC on 22B with minTD=0.50, No IFP ===		=== Example: AmpC on 22B with minTD=0.50, No IFP ===

	<pre>		<pre>
	lib_path = '/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/scripts/libraries/22B/22B_fplib.pickle'		lib_path = '/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/scripts/libraries/22B/22B_fplib.pickle'
	lib = load_library_from_pickle(lib_path)		lib = load_library_from_pickle(lib_path)
	algo = CSAlgo(lib, 'params.txt', 'output', 16, verbose=True,		algo = CSAlgo(lib, 'params.txt', 'output', 16, verbose=True,
	scheduler='sge', smi_id_prefix='CSLB',		scheduler='sge', smi_id_prefix='CSLB',
	python_exec="/wynton/group/bks/work/shared/kholland/~~chemstep_auto_v02~~/bin/python",		python_exec="/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/bin/python",
	dockfiles_path="/wynton/group/bks/work/kholland/chemstep_ampc_22B/seed_docking/dockfiles",		dockfiles_path="/wynton/group/bks/work/kholland/chemstep_ampc_22B/seed_docking/dockfiles",
	min_td_search=0.5,		min_td_search=0.5,
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	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/get_beacon_ids_smiles.py output/complete_info/beacons.df /path/to/fp/library output.txt		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/get_beacon_ids_smiles.py output/complete_info/beacons.df /path/to/fp/library output.txt
	</pre>		</pre>

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	In your ChemSTEP directory containing <code>chemstep_algo.log</code> and score files,		In your ChemSTEP directory containing <code>chemstep_algo.log</code> and score files,
	<pre>		<pre>
	bash /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/submit_hit_recovery.sh		bash /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/submit_hit_recovery.sh
	</pre>		</pre>

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	Get poses for Beacons:		Get poses for Beacons:
	<pre> python /wynton/group/bks/work/shared/kholland/~~chemstep_auto_v03_ifp~~/~~v03_ifp~~/scripts/get_beacon_poses.py output/complete_info/beacons.df /path/to/fp/library/ docked_poses.txt -o beacon_poses -j 8		<pre> python /wynton/group/bks/work/shared/kholland/chemstep_auto_v04/v04/scripts/get_beacon_poses.py output/complete_info/beacons.df /path/to/fp/library/ docked_poses.txt -o beacon_poses -j 8
	</pre>		</pre>

Kholland at 20:52, 12 June 2026

2026-06-12T20:52:17Z

← Older revision		Revision as of 20:52, 12 June 2026
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	<pre>		<pre>
	python /wynton/group/bks/work/bwhall61/for_beau/top_poses.py -t <pProp_energy_threshold> -s <num_poses_per_file> docked_poses.txt		python /wynton/group/bks/work/bwhall61/for_beau/top_poses.py -t <pProp_energy_threshold> -s <num_poses_per_file> docked_poses.txt
			</pre>

			Get poses for Beacons:
			<pre> python /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/get_beacon_poses.py output/complete_info/beacons.df /path/to/fp/library/ docked_poses.txt -o beacon_poses -j 8
	</pre>		</pre>

Kholland at 19:39, 12 June 2026

2026-06-12T19:39:07Z

← Older revision		Revision as of 19:39, 12 June 2026
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	<pre>		<pre>
	find /round_*_docking/bundle_paths -maxdepth 2 -name "test.mol2.gz.0" > docked_poses.txt		find round_*_docking/bundle_paths -maxdepth 2 -name "test.mol2.gz.0" > docked_poses.txt
	</pre>		</pre>

Kholland at 18:52, 12 June 2026

2026-06-12T18:52:42Z

← Older revision		Revision as of 18:52, 12 June 2026
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	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/get_beacon_ids_smiles.py /path/to/library~~/pickle chemstep_algo~~.~~log~~		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/get_beacon_ids_smiles.py output/complete_info/beacons.df /path/to/fp/library output.txt
	</pre>		</pre>

			{\| class="wikitable"
			! Library !! Path
			\|-
			\| 13B \|\| <code>/wynton/group/bks/work/omailhot/chunked_ampc_chemstep_lib</code>
			\|-
			\| 22B \|\| <code>/wynton/group/bks/work/kholland/22B_fp_library</code>
			\|-
			\| 72B \|\| <code>/wynton/group/bks/work/kholland/72B_fp_library</code>
			\|}

	Use the library pickle path from [[#7. Edit run_chemstep.py\|Step 7]].		Use the library pickle path from [[#7. Edit run_chemstep.py\|Step 7]].

Kholland at 18:47, 12 June 2026

2026-06-12T18:47:50Z

← Older revision		Revision as of 18:47, 12 June 2026
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	<pre>		<pre>
	python /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/~~get_beacon_smiles~~.py /path/to/library/pickle chemstep_algo.log		python /wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/get_beacon_ids_smiles.py /path/to/library/pickle chemstep_algo.log
	</pre>		</pre>

Kholland at 22:41, 10 June 2026

2026-06-10T22:41:42Z

← Older revision		Revision as of 22:41, 10 June 2026
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	<pre>		<pre>
	Hydrogen bond, ~~GLY19~~		Hydrogen bond, GLY-19
	Ionic, ~~ASP149~~		Ionic, ASP-149
	</pre>		</pre>

Kholland at 20:50, 26 May 2026

2026-05-26T20:50:53Z

← Older revision		Revision as of 20:50, 26 May 2026
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	<pre>		<pre>
	python /wynton/group/bks/work/bwhall61/for_beau/top_poses.py \		python /wynton/group/bks/work/bwhall61/for_beau/top_poses.py -t <pProp_energy_threshold> -s <num_poses_per_file> docked_poses.txt
	-t <~~pProp_threshold~~> \
	-s <num_poses_per_file> \
	~~-dock_results_path~~ docked_poses.txt
	</pre>		</pre>

Kholland at 22:54, 7 May 2026

2026-05-07T22:54:15Z

← Older revision		Revision as of 22:54, 7 May 2026
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	\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/22B/22M_seeds.sdi</code>		\| 22B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/22B/22M_seeds.sdi</code>
	\|-		\|-
	\| 72B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/72B/~~72B_seeds~~.sdi</code>		\| 72B \|\| <code>/wynton/group/bks/work/shared/kholland/chemstep_auto_v03_ifp/v03_ifp/scripts/libraries/72B/72M_seeds.sdi</code>
	\|}		\|}