I want to add hydrogens to some linear polymer molecules (polyethylenes).I know some working methods like using PyMOL internal function h_add. This method works, but hydrogens are added at distances from the backbone carbon atoms that vary from 1.07 to 1.1 ngstroms. I need to control the hydrogen distances from the backbone atoms and also the HCH and CCH angles to constant values that I choose every time (for example, HC = 1.5 , HCH = 108.5, CCH = 109.5).Is there a geometry algorithm which I can use to understand the process of hydrogen adding? I know that it can be implemented nicely to a Fortran code but is there an easier way to do this, e.g. a script in Python, or better yet, a bash script?The molecule coordinate files I am using are in the PDB format.
Algorithms for adding hydrogens on a molecule
algorithms;simulation;molecular dynamics