Saturday, July 20, 2019

molecular structure - Internal (Z-Matrix) to Cartesian coordinates conversion


Is there any way to convert from Internal to Cartesian coordinates using simple formulas?



I have studied and implemented: INTERNAL TO CARTESIAN by Jack D. Kunitz.


But somehow the x, y and z values are not correct. I am not implementing the transformation back to the initial frame as it says, because I do not understand that step. Is that the reason for not being able to get correct answers or is this not a good tutorial or solution to follow.



Answer



Sure, it's just trigonometry. There are a variety of open source implementations.


For example:



There are dozens in a search on GitHub if you don't like C++ or Python.


There's also a web app from Shodor for z-matrix conversion.


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