JW – Added AM1 rearrangement handlign to infrastructure roadmap - I know this is on CD’s backburner, I’ll probably get to it myself in a while.
CD – Any update on possible project handling post-translational modificaitons?
JW – We’re building out the infrastructure that will be required to start looking into that. I’ll know more in a few weeks.
JW – I can’t make this meeting time next week
CD – Let’s make this every-other-weekly
JW – Agree, I will have schedule conflicts every other week at this time.
JW updated the event to be every-other-weekly
Todos from last time
Connor will see if there’s a way to expand RDKit conformer generation energy window to allow better candidate ELF conformers to be generated.
CD – The only thing you have to do to get RDKit to generate way more conformers is to set the min RMSD to 0, and use max_conformers to control the number of outputs instead.
JW – Do we know whether these output conformers are substantially distinct?
CD – I suspect they are but haven’t verified. What you could do is generate more conformers than you want, and then prune them by diversity.
LW – I know that RDKit generates a alrge umber of conformers internally and then prunes them, possibly using the provided RMSD, util the desired number of conformers is achieved.
LW – Can we set an energy window in RDKit?
JW – I think we’d looked into this a little last time, and I don’t think we found a way to set this.
LW – I have some code that prunes conformers by an energy window that I specify (calculating energies using MMFF)
CD – Shows plot of ELF1 comparison now that RDKit is generating way more conformers
JW – I look at the bottom plot in terms of “should we throw out the current random conformer selection and implement ELF1 immediately?”, and the data is making me think “no”
Connor will evaluate whether OE vs. antechamber charge differences correlate with RMSD
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