Atom positions are sometimes incorrect about alchex HOT 2 CLOSED

This appears to be due to an unknown error in the WAEditableResidue.scale_match_vector method.

from alchex.

This is probably caused by the scaling system currently used:

• Translate first pin to origin
• Scale so second pin matches
• Translate back

This will result in weird artefacts when scaling. What needs to be done instead is:

• Rotate about first pin so second pins are on the same vector
• Scale along this vector

This will require the following tools to be added:

• Tool to calculate rotation between two vectors
• Tool to calculate transformation matrix to align two vectors

This could be done using the existing SVD-based alignment tool

from alchex.