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choderalab / yank

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
http://getyank.org
MIT License
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Bond Order Preservation #801

Open Lnaden opened 6 years ago

Lnaden commented 6 years ago

We need to trap bond order information for small molecules.

We can do this either through extending the MDTraj Topology object in Topography, or by switching to the OpenMM Topology in Topography.

YANK will still need to capture this information from small molecules when available, even after the molecule is piped through Antechamber. Alternately, this information needs to be accepted if not stored at times when it is needed (e.g. SMARTS selection at Topography.select, maybe a .select(..., **kwargs) which get passed down to selector)?

If we need to switch to OpenEye Molecules from OpenMM Topology, use the oess/oemmtools repo code for openmmTop_to_oemol which should be permissively copiable.

davidlmobley commented 6 years ago

👍 for this issue. :)

Lnaden commented 6 years ago

The plan right now is to extend MDTraj to support bond orders where applicable by effectively porting the OpenMM implementation of it to support both Type and Order keywords

jchodera commented 6 years ago

Maybe open an issue there before we begin implementing it? https://github.com/mdtraj/mdtraj/issues

Lnaden commented 6 years ago

Probably a good idea