Kholland at 21:34, 2 October 2026

2026-10-02T21:34:33Z

← Older revision		Revision as of 21:34, 2 October 2026
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	== 9. Monitor Job Status ==		== 9. Monitor Job Status ==

	Check job status with <code>squeue -u USER_ID</code>. The main job will run for up to '''6 days''' given no errors. ChemSTEP will launch search, building, and docking jobs in successive rounds.		Check job status with <code>squeue -u USER_ID</code>. The main job will run for up to '''14 days''' given no errors. ChemSTEP will launch search, building, and docking jobs in successive rounds.

	'''Note:''' If any building or docking subjobs hang, the main job will not proceed until those are canceled or finished. Monitor job statuses regularly and occasionally verify that docking output files (<code>scores_round_*.txt</code>) are being populated.		'''Note:''' If any building or docking subjobs hang, the main job will not proceed until those are canceled or finished. Monitor job statuses regularly and occasionally verify that docking output files (<code>scores_round_*.txt</code>) are being populated.

Frodo: /* 9. Monitor Job Status */ asdf

2026-10-02T20:24:38Z

9. Monitor Job Status: asdf

← Older revision		Revision as of 20:24, 2 October 2026
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	'''Note:''' If any building or docking subjobs hang, the main job will not proceed until those are canceled or finished. Monitor job statuses regularly and occasionally verify that docking output files (<code>scores_round_*.txt</code>) are being populated.		'''Note:''' If any building or docking subjobs hang, the main job will not proceed until those are canceled or finished. Monitor job statuses regularly and occasionally verify that docking output files (<code>scores_round_*.txt</code>) are being populated.


			[[Category:coreHPC]]

			[[Category:Transition 2027]]
			[[Category:Cluster]]

Kholland: Created page with "== 1. Source Environment ==

 source /mnt/fac/CX900007_DS1/soft/chemstep/env.sh

== 2. Dock the Seed Set == Copy the .sdi file for the library you want to use into a directory containing your dockfiles: {| class="wikitable" ! Library !! Path |- | 22B || cp -r /mnt/fac/CX900007_DS1/work/kholland/22B_seed_building/sdi ./sdi |} Then dock the seed set:

 bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh

== 3. Gather Scores f..."

2026-09-30T20:33:11Z

Created page with "== 1. Source Environment == <pre> source /mnt/fac/CX900007_DS1/soft/chemstep/env.sh </pre> == 2. Dock the Seed Set == Copy the <code>.sdi</code> file for the library you want to use into a directory containing your dockfiles: {| class="wikitable" ! Library !! Path |- | 22B || <code>cp -r /mnt/fac/CX900007_DS1/work/kholland/22B_seed_building/sdi ./sdi</code> |} Then dock the seed set: <pre> bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh </pre> == 3. Gather Scores f..."

New page

== 1. Source Environment ==

<pre>
source /mnt/fac/CX900007_DS1/soft/chemstep/env.sh
</pre>

== 2. Dock the Seed Set ==

Copy the <code>.sdi</code> file for the library you want to use into a directory containing your dockfiles:

{| class="wikitable"
! Library !! Path
|-
| 22B || <code>cp -r /mnt/fac/CX900007_DS1/work/kholland/22B_seed_building/sdi ./sdi</code>
|}

Then dock the seed set:
<pre>
bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh
</pre>

== 3. Gather Scores for the Seed Set ==

Once docking is complete, run the following from the directory '''one level above''' your docking output (<code>MOLECULES_DIR_TO_BIND</code>).

'''22B library:'''
<pre>
python python $CHEMSTEP_INSTALL_PATH/chemstep-development/accessory/get_scores.py 0
</pre>

Verify that <code>scores_round_0.txt</code> was correctly written:
<pre>
wc -l scores_round_0.txt
</pre>

== 4. Convert Scores to .npy Files ==

Convert scores to ChemSTEP-readable <code>.npy</code> files:

<pre>
python $CHEMSTEP_INSTALL_PATH/chemstep-development/accessory/convert_scores_to_npy.py 0 CSLB
</pre>

== 5. Set Up the ChemSTEP Run Directory ==

Create and enter a new run directory, then copy in the necessary files:

<pre>
mkdir chemstep_run
cd chemstep_run
chemstep-run-new
</pre>

This will populate the directory with <code>params.txt</code>, <code>run_chemstep.py</code>, and <code>launch_chemstep_as_job.sh</code>.

=== Optional: Integrated IFP ===

If running with integrated IFP for beacon selection, also run:

<pre>
chemstep-run-ifp
</pre>

This copies in the additional files <code>ifp_acceptance_criteria.txt</code> and <code>interactions.txt</code>.

== 6. Edit params.txt ==

Add the absolute paths to the ChemSTEP-readable score and indices <code>.npy</code> arrays generated in Step 4.

<pre>
seed_indices_file: /path/to/your/indices_round_0.npy
seed_scores_file: /path/to/your/scores_round_0.npy
hit_pprop: 5.5
n_docked_per_round: 2000000
bundle_size: 1000
max_beacons: 100
max_n_rounds: 250
</pre>

=== Parameter Reference ===

{| class="wikitable"
! Parameter !! Description
|-
| <code>hit_pprop</code> || Defines a "virtual hit." pProp = −log(rank%) within the total library score distribution. E.g., pProp 4 in 13B space ≈ top 0.01% (~1.3M molecules); pProp 5 ≈ 0.001% (~132K). The seed set should contain at least 10<sup>(pProp+2)</sup> molecules.
|-
| <code>n_docked_per_round</code> || Number of molecules prioritized per round. All must be built and docked between rounds. Too many slows throughput and may reduce diversity; too few slows virtual hit recovery. Recommended: 1-2 million
|-
| <code>max_beacons</code> || Diverse, well-scoring molecules used to guide prioritization. All molecules above the pProp threshold are candidates. Too many reduce inter-beacon diversity; too few hinder space exploration. Fewer beacons than specified may be assigned if an insufficient number of molecules clear the threshold. Recommended: 100
|-
| <code>bundle_size</code> || In auto docking mode, number of molecules submitted as a single build job.
|-
| <code>max_n_rounds</code> || No adjustment needed when running ChemSTEP prospectively as described here.
|}

== 7. Edit run_chemstep.py ==

'''Note:''' All paths must be '''absolute paths'''.

=== Required Settings ===

Set <code>lib_path</code> to the library pickle for your library:

{| class="wikitable"
! Library !! Path
|-
| 22B || <code>/mnt/fac/CX900007_DS1/work/kholland/22B_fp_lib/22B_fplib.pickle</code>
|}

<pre>
lib_path = '/full/path/to/library.pickle'
</pre>

Set <code>dockfiles_path</code>:

<pre>
dockfiles_path="/full/path/to/dockfiles"
</pre>

=== Optional: minTD Exclusion Zone ===

Molecules will not be prioritized from within a specified Tanimoto distance of beacons. Comment in the relevant lines and update the value. Consider also setting <code>enforce_n_docked_per_round = True</code> when using this option:

<pre>
min_td_search=0.5,
enforce_n_docked_per_round=True,
</pre>

=== Optional: Integrated IFP ===

Only selects beacons that satisfy user-defined interaction criteria. Comment in the following lines and update the paths to the necessary files (copied in Step 5 if you ran <code>chemstep-run-ifp</code>):

<pre>
use_IFP=True,
ifp_pdb_path='/full/path/to/rec.crg.pdb',
interactions_file='/full/path/to/interactions.txt',
ifp_acceptance_criteria_file='/full/path/to/ifp_acceptance_criteria.txt',
</pre>

'''<code>interactions.txt</code>''' — one interaction per line, comma-separated. Format: <code>interaction_type, residue_name_and_number</code>. Example:

<pre>
Hydrogen bond, GLY-19
Ionic, ASP-149
</pre>

Supported interaction types include: Proximal, Hydrogen bond, Ionic, Cation-pi, Hydrophobic, Halogen bond, and others. See LUNA and IFP documentation for the full list.

'''<code>ifp_acceptance_criteria.txt</code>''' — defines the number of unsatisfied donors/acceptors/specific interactions required for a molecule to pass IFP and be considered for beacon selection. Example:

<pre>
#_donors
#_acceptors
#_unstatisfied_donors == 0
#_unstatisfied_acceptors <= 4
Ionic/ASP-149 > 0
</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>

TRIAZINES: 'n1cncnc1'

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

<pre>
lib_path = '/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/scripts/libraries/22B/22B_fplib.pickle'
lib = load_library_from_pickle(lib_path)
algo = CSAlgo(lib, 'params.txt', 'output', 16, verbose=True,
scheduler='sge', smi_id_prefix='CSLB',
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",
min_td_search=0.5,
enforce_n_docked_per_round=True,
#use_IFP=True,
#ifp_pdb_path='/path/to/your/reference/rec.crg.pdb',
#interactions_file='/path/to/your/interactions.txt',
#ifp_acceptance_criteria_file='/path/to/your/ifp_acceptance_criteria.txt',
docking_method="auto", track_beacon_orig=True)
</pre>

== 8. Launch the Job ==

Submit the main ChemSTEP job:

<pre>
sbatch launch_chemstep_as_job.sh
</pre>

== 9. Monitor Job Status ==

Check job status with <code>squeue -u USER_ID</code>. The main job will run for up to '''6 days''' given no errors. ChemSTEP will launch search, building, and docking jobs in successive rounds.

'''Note:''' If any building or docking subjobs hang, the main job will not proceed until those are canceled or finished. Monitor job statuses regularly and occasionally verify that docking output files (<code>scores_round_*.txt</code>) are being populated.

Running ChemSTEP on CoreHPC - Revision history

Kholland at 21:34, 2 October 2026

Frodo: /* 9. Monitor Job Status */ asdf