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Initial approach as suggested stakeholder consensus. |
👀 Overview
Summary | Create a QM dataset from an existing chemical structure databases running optimization, torsion-drive, and *new* electronic property calculation types. Datasets will be split into two sets, those with metal centers of primary interest (i.e., Pd, Fe, Zn, Mg, Cu, Li) and those of secondary interest Generate standard operating procedure for dataset continuity (DS-Continuity-SOP) to copy key OpenFF datasets into a secondary storage platform (i.e., Rh, Ir, Pt, Ni, Cr, Ag). Those of secondary interest will only be run with OPT calculation with GFN2-XTB. Those of primary interest will be run with a target level of theory, to be determined in this work, and have the target electronic properties evaluated. These dataset will be accompanied by organic compound elements: C, H, P, S, O, N, F, Cl, Br. To achieve this the standard OpenFF QCA dataset submission pipeline must be adapted in multiple ways. Address incompatibility with existing OpenFF infrastructure with Organometallic CMILES Add ability for conformers to be imported into qc-submit Zenodo) in a future-proof file format. | ||||||||||||||||||||||
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Status |
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\uD83D\uDEA9 Milestones and metrics
Datasets will be labeled as DS#-XXX-{1,2}, e.g. DS1-CCD-2, which denotes dataset 1, taken from the CCD database, with the metal centers of secondary interest. The first number and the middle three letter code are always paired to avoid confusion between similar database abbreviations, e.g. CCD vs COD vs CSD. The last number denotes inclusion of metal centers of primary and secondary interest:
1: primary interest: {Pd, Fe, Zn, Mg, Cu, Li}
2: secondary interest: {Rh, Ir, Pt, Ni, Cr, Ag}
Stage | Milestone/Benchmark | Contributors | Deadline | Status | ||||||||||||||||||||||||||||||||
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Add ability for conformers to be imported into qc-submit | Assess ability for conformers to be added into qc-submitGenerate Standard Operating Procedure | Determine qcportal capability to download datasets locally | Determine if RDKit functionality will perform adequately
| Resolve qc-submit CMILES incompatibility with organometallic complexes |
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Determine final future proof file format for datasets |
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Determine file conversion strategy from output of qcportal to future proof file format |
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If RDKit will handle CMILES, assess work around for OpenEye, or implement error handlingDetermine location to aggregate or reference Zenodo DOIs |
| Curate opt training dataset | Filter PDB Chemical Component Dictionary (CCD) and submit DS1-CCD-1 and DS1-CCD-2 at BP86 / def2-TZVP | Jennifer A Clark, Brent Westbrook | Jan. 15, 2025 |
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Submit DS1-CCD-1 and DS1-CCD-2 at alternative model chemistries for assessmentCombine pipeline elements into DS-continuity-SOP |
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Choose model chemistry based off of DS1-CCD-1 and DS1-CCD-2Create dataset collection on qcportal | Debug QCA-Dataset-Submission issues, or establish record keeping mechanism for direct QCPortal use. |
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Sage 2.0.0 |
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Sage 2.1.0 |
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Sage 2.2.0 |
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Submit DS2-COD-1 OPT at target model chemistryIndustry Benchmarking |
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Submit DS3-CSD-1 OPT at target model chemistryPublish OpenFF datasets | Apply DS-continuity-SOP to Sage 2.0.0 |
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Submit DS4Apply DS-MPTcontinuity-1 OPT at target model chemistrySOP to Sage 2.1.0 |
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Curate electronic properties training dataset | Define primary and secondary properties of interest | Jennifer A Clark , Chris Iacovella |
| Determine output protocol of primary properties of interest and implement |
| Determine output protocol of secondary properties of interest and implement |
| Submit DS1-CCD-1 Electronic Property calculation at target model chemistryApply DS-continuity-SOP to Sage 2.2.0 |
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Submit DS2Apply DS-COD-1 Electronic Property calculation at target model chemistrycontinuity-SOP to Industry Benchmarking dataset |
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Submit DS3-CSD-1 Electronic Property calculation at target model chemistryDetermine other benchmarking datasets of interest |
| Submit DS4-MPT-1 Electronic Property calculation at target model chemistry |
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📊 Progress and findings
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📊 Progress and findings
Generate Standard Operating Procedure
Although not supported now, within the timeframe of this project MolSSI is expected to have restored the qcportal capability of “dataset views” to allow downloading the files in some format. It should be trivial to export from there to qcschema molecules in hdf5 format. [QCA Users 2025-01-07]
Create Dataset Collection on QCPortal
This initiative was expected to be achieved by combining record lists from the published list from several datasets. However, after pushing to QCPortal additional specification keywords are added and new records are spawned. It is expected to have to do with the recent QCPortal upgrade? Strongly considering fallback to creating a collection directly with QCPortal, bypassing qc-submit… 2025-01-09 JCl/LW check-in