Comments (4)
Hi @xiki-tempula, I think the torsions are selected using a particular SMIRKS pattern. The idea is discussed in the docs here, and the SMIRKS itself is default value of the target_torsion_smirks
setting.
This is a particularly complicated SMIRKS - To read it you'll probably need to refer to the Daylight SMILES and SMARTS guides
from openff-bespokefit.
Like it wouldn't recognise the H-C-C-H dihedral in cyclopropane or dihedrals in cyclo molecules in general (as these won't go well with torsion scan).
The current value of the target torsion SMIRKS is '[!#1]~[!$(*#*)&!D1:1]-,=;!@[!$(*#*)&!D1:2]~[!#1]'
. The part that describes the central bond is -,=;!@
, which (I'm pretty sure) means "the central bond is single or double (-,=
), and must not be in a ring (;!@
)". So it should exclude all ring bonds.
And you don't do any downstream heuristics to do more filtering.
I don't think we do additional filtering, but I have low confidence in this answer, so I might escalate that question to @jthorton (who is out right now, so he may not get back to us on this for a few days).
from openff-bespokefit.
Hi @xiki-tempula, @j-wags is correct the SMIRKS pattern he shows is the only thing we use to identify torsions which should be targeted for optimisation and this is a fully customisable option in the workflow, we accept a list of patterns which can describe the target torsions so if you have a case in mind which is not hit by BespokeFit you can add a pattern for it to the list but this may uncover some issues when trying to scan in-ring torsions.
from openff-bespokefit.
@j-wags Thank you. Does this SMIRKS pattern captures everything? Like it wouldn't recognise the H-C-C-H dihedral in cyclopropane or dihedrals in cyclo molecules in general (as these won't go well with torsion scan).
And you don't do any downstream heuristics to do more filtering.
from openff-bespokefit.
Related Issues (20)
- About the way of adding more cpmds to an existing set
- Update installation docs HOT 2
- bespokefit gives the torsion a worse fit than the OpenFF HOT 19
- Automate running Psi4-based fits using default installation instructions HOT 5
- Use OpenFF 2.1.0 as default initial force field HOT 1
- Using psi4 HOT 11
- Test environments broken with OpenFF Toolkit 0.15.0 HOT 1
- SMILES shown in output is wrong HOT 11
- Provide a simple path to retrieving cached datasets, or package them with BespokeFit HOT 1
- BespokeFit appears to ignore `--qc-compute-n-cores` with XTB HOT 1
- Document environment variables HOT 4
- Python 3.12 support
- QCFractal 0.54 breaks tests HOT 1
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- Make docker container HOT 6
- Add API token support for HTTP endpoint? HOT 7
- LinearTorsionError for a nitrile group HOT 2
- Redis clash at localhost port, failed to run tutorial. HOT 5
- Optimization error encountered when following tutorial HOT 2
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from openff-bespokefit.