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UCL-CCS / TIES

Topology Superimposition based on joint graph traversal
MIT License
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Charges nullified #146

Closed bieniekmateusz closed 2 years ago

bieniekmateusz commented 4 years ago

Currently when the net charges are above 0.1, the largest mismatches are found across the molecules and removed first. One could consider checking another approach: remove the mismatches that are close to the removed sites. Ie remove mismatches in a way such that the molecule is not divided into sub-components.

The disadvantage of that would be that you want to largest mismatches to be removed so that their differences are accounted for.

bieniekmateusz commented 4 years ago

Investigate the case ~/code/BAC2020/resp_validation/cdk2/l20_l21/lig

Check if the problem is due to the cutting of of the entire molecule.

It might be more advisable to remove the net charges by first removing the atom pairs which are neighbouring the site(s) that is modified.