add mass-weight to RMSD calculations

[rsysadmin-com]

Hi all!

I trust you guys are all safe and healthy during this COVID-19 pandemic.

Quick question: is there any way to calculate the RMSD contemplating the mass-weighting? If not, would someone be willing to add it? :-)

Please see http://archive.ambermd.org/200805/0482.html for further info.

Compared to, for example, QMol, it seems like enabling/disabling such an option yields different results.

For example:
Results from calculate_rmsd.py and QMol with "mass weighting" disabled:
01 vs v2 10.902
v1 vs v3 0.179
v1 vs v4 5.950
v1 vs v5 10.929

They are identical.

Now with QMol and "mass weighting" enabled:
01 vs v2 10.874
v1 vs v3 0.179
v1 vs v4 5.933
v1 vs v5 10.902

As you can appreciate, there is a slight difference but it makes a rather huge change...

QMol's source-code can be downloaded here:
http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml

I only found references to "mass weight" in QMol's kabsch.cpp and kabsch.h

I know that there is a weighted Kabsch algorithm (thanks Jimmy for the info)
https://github.com/charnley/rmsd/blob/master/rmsd/calculate_rmsd.py#L229

but, from what I see in the calculate_rmsd.py options, there are no ways to call that function.

Volunteers? :-)

Thanks a lot in advance for your time and consideration!

I look forward to hearing from you soon!

Please stay safe!

Best,
Martin