GitLab

fixed bug in sideChainGen that caused a RuntimeWarning, when the sidechain direction was parallel to the z-axis

fixed a bug that produced an error, when no surface atoms were selected with a string in a boundary condition

changed implementation of the fps algorithm to calculate distances on-the-fly at each step in order to save memory usage

some rearranging and cleanup to make the new CodeRed the main one, old files are kept for the moment for easy code reuse if needed

red() includes keywords for SOAP now; own methods for structure assembly from combinations and vice versa

Handling of big combination arrays improved: boundary conditions are checked chunkwise, and the progress bar is updated more often.

structures are saved without the surface now, which makes some things easier; side chain generation is separated from the reduction part; first modifications of the reduction part to work with arbitrary representations and selection algorithms

side chain generation works properly now and is included as a red(...) method; error in angle boundary conditions fixed, and nearest neighbour selection included; codered specific exceptions added

added module with farthest point sampling methods; so far the approximate greedy method and the exact brute-force method are implemented.

added a min_dist check for the side chains, so they don't overlap with themselves or other atoms. the point in the code where this is done can be improved though...

codered object can find the positions associated with a boundary condition now and check the different boundary conditions