rmsd
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charnley
Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
This issue report evolves from an earlier discussion [here](https://github.com/charnley/rmsd/discussions/85). With the test data provided in the .zip attached below, the RMSD of an alignment works fine e.g., ```bash $ calculate_rmsd...
I'm looking for a method that lets me specify a list of distances to minimize the RMSD against. i.e. Given two point clouds each with size N, and a 1-1...
Mostly white space updates, Parameters/Returns updates, changed makeQ and makeW to have quaternion_ in front
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,...
The get_coordinates_pdb function in calculate_rmsd.py would benefit from the inclusion of 'HETATM' when reading in coordinates and atoms. https://github.com/charnley/rmsd/blob/cd8af499fb63529a1b5b1f880fdb2dab2731544a/rmsd/calculate_rmsd.py#L688 I was able to change line 688 to: `if line.startswith("ATOM") or...
` if x_column == None: try: # look for x column for i, x in enumerate(tokens): if "." in x and "." in tokens[i + 1] and "." in tokens[i...
I calculate the RMSD value for two xyz files (opt.xyz and sp.xyz) with all possible methods, and the smallest value I take for a specific example is 2.1. Then I...
pdb: 8xgo 8xgn [CsFAOMT.zip](https://github.com/charnley/rmsd/files/13936962/CsFAOMT.zip)
The first file contain hydrogen but when i use --no-hydrogen and --reorder ,it's still reported that structure not same size .They are both 169 residues.
Sometimes I am interested in knowing the rmsd value for the modified structure. Now I need to run calculate_rmsd.py twice (with and without -p). With this simple change the rmsd...
