Page Comparison

1. Generation of substituent list

• Removed phenyls with ortho-substituents

• Filter: cyclic substituents with (1) zero rotatable bond (2) # rings =1 or acyclic substituents with # rotatable bonds <2

• Combined Roche, Coverage, Pfizer, Bayer: 361 substituents (Acyclic aliphatic: 183, 2. aliphatic rings: 100, 3. 6-membered aromatic rings:50, 4. 5-membered aromatic rings:28)

  • Roche set

    • Acyclic aliphatic: 61, 2. aliphatic rings: 21, 3. 6-membered aromatic rings:5, 4. 5-membered aromatic rings:11

  • Coverage set

    • Acyclic aliphatic: 76, 2. aliphatic rings: 2, 3. 6-membered aromatic rings:6, 4. 5-membered aromatic rings:2

  • Pfizer set

    • Acyclic aliphatic: 24, 2. aliphatic rings: 9, 3. 6-membered aromatic rings:6, 4. 5-membered aromatic rings:7

  • eMolecules set

    • aliphatic chain: 148, 2. aliphatic rings: 75, 3. 6-membered aromatic rings:90, 4. 5-membered aromatic rings:51

  • Bayer set

    • Acyclic aliphatic: 116, 2. aliphatic rings: 86, 3. 6-membered aromatic rings:42, 4. 5-membered aromatic rings:16

...

• Using 361 substituents, generated 59086 molecules (align by mol weights )

3. Curation

3.1. Remove similar molecules using MACCS keys fingerprints and Check coverage of torsion parameters

(1) list molecules matching to each torsion parameter

...

(3) check coverage of torsion parameter (missing torsions)

→ now running*

• (1) Wnt to include all substituents in the final torsiondrive dataset (2) while choosing one from each cluster, currently choose center one(one with the largest sum of similarity indices) → constantly choose certain substituents?

  Image Added

3.2. Internal H bond forming mols : Better SMIRKS needed. How to consider spatial arrangement of 1-n chain

(1) Test filtering w/ oversimplified SMIRKS

...

• Filter  [n,N,o,O,F]([H])[!#1][!#1]~!@[!#1;r]([#7X2;r])

  • # molecules matched : 1430 (out of 59086)

  • Image RemovedImage Added

    Right hand side mols dont seem to form internal H bond

• Filter [n,N,o,O,F]([H])[!#1]~!@[!#1]~!@[!#1;r]([#7X2;r])

  • # molecules matched : 1060

    Image RemovedImage Added

  • How to exclude right mol?

...

TODO (2021-04-01)

•  1. Remove ortho substituents from substituent list, add ones with meta/para substituents
•  2. Remove similar molecules using MACCS keys fingerprints
•  3. Check coverage of torsion parameters → generate a draft of molecule set (~3000 entries)
•  4. Addition of intra H bond filter : by using SMIKRS pattern matching
•  5. Check the coverage of problematic substituents, which showed large discrepancies in Pavan’s 1.3.0 benchmarks
•  6. Range of WBOs of each training data subset, a list of scans training a certain torsion parameter
•  7. addition of double bond rotating torsion scans

...

damn installation

1. conda create --name constructure -c conda-forge -c openeye -c omnia pydantic openeye-toolkits cmiles ipykernel python=3.8

2. python setup.py develop (constructure)

3. python setup.py install (fragmenter)

4. conda install -c conda-forge pyyaml

* Additionally openforcefield has been installed