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molovol / MoloVol

MoloVol is a free, cross-plattform, scientific software for volume and surface computations of single molecules and crystallographic unit cells.
https://molovol.com
MIT License
22 stars 4 forks source link

Cavities report #69

Closed rlavendomme closed 3 years ago

rlavendomme commented 3 years ago

Adapt unit cell code for the flood fill algorithm, Add cavity sorting by volume function. Add export list of cavities surface maps. Add list of cavity in report. Minor fixes.

rlavendomme commented 3 years ago

One thing I've noticed is that with my unit test for testing the two-probe mode, all volume values except probe 1 core volume have slightly changed. I couldn't find the reason for this. Do you have any idea what happened? I feel that at least the vdW volume should have stayed the same. Did you make changes to how the size of the space is determined in two probe mode? Now that I think of it I think I saw something along those lines.

The change you mentioned is probably due to the calibration of the voxel grid with the cartesian coordinate that was introduced in commit https://github.com/jmaglic/MoloVol/commit/03353efd9101e9538d058ef1a56c3b8a9774fd01 This is not directly related to this branch. At least for me, I have same volume values between the master branch and this development branch.

This calibration was done to simplify unit cell volume (and later surface) calculations. The values should have remained in a very small error range. Can you confirm that the difference is negligible or did you observe completely wrong values?

jmaglic commented 3 years ago

Just compiled the master branch and I can confirm that it's the same there, so I must have missed this change last time round. Seem to me quite minor deviations.