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20240801 complete fred docking#18

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apayne97 wants to merge 61 commits intomainchoderalab/asapdiscovery-sars-retrospective:mainfrom 20240801_complete_fred_dockingchoderalab/asapdiscovery-sars-retrospective:20240801_complete_fred_dockingCopy head branch name to clipboard

+223,604-9

Commits

Commits on Aug 12, 2024

• add fred docking scripts

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Commits on Aug 16, 2024

• update cluster script test

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Commits on Aug 21, 2024

• add test_import_speed test

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Commits on Sep 3, 2024

• add updated submission scripts

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• add scripts for calculting rmsd

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• add script for creating cached lig dir

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Commits on Sep 5, 2024

• add command for splitting up the 3d files

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• make executable

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• update file names

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• use correct input ligand files

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• fix typo

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Commits on Oct 11, 2024

• update cluster script

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• use any nodes in cpuqueue

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• add ben deduplication code

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• Merge remote-tracking branch 'origin/20240801_complete_fred_docking' into 20240801_complete_fred_docking

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• add updated molecule filtering code

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• add updated molecule filtering code

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• add updated molecule filtering code

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Commits on Oct 18, 2024

• add new fragalysis p series prep

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Commits on Oct 22, 2024

• add spruce reprepped fred script

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• update rmsd calculation and filtering script

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  495ff6d

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• examine missing structures

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• examine missing structures

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Commits on Nov 13, 2024

• update cluster submission script

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• update ligand rmsd array analysis

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• fix example submission

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• fix calculation script

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  e1b7d3b

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• fix calculation script

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Commits on Nov 15, 2024

• fix rmsd calculation output

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• update rmsd calculation script time

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Commits on Nov 21, 2024

• update rmsd calculation script time

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Commits on Dec 5, 2024

• update analysis processing

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• add chemical similarity csv to repo

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• remove call to 'bar' in mpi

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Commits on Dec 13, 2024

• add fred analysis

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Commits on Jan 7, 2025

• analyze results

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• test prepping and figure out the error

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Commits on Jan 10, 2025

• add slurm script for iris

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• use iris paths

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• change partition

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Commits on Jan 13, 2025

• update slurm prep script to correctly parallelize

  

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• add cross docking array script

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• add iris ligand cache splitting script

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• update lig directory creation

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• troubleshoot fixing P0097 automatically

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update prep cache for docking scripts

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• update slurm script

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• update slurm script

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• update slurm script

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Commits on Jan 16, 2025

• update slurm command with editable asapdiscovery repo and new cli

  

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