Calculate root-mean-square deviation (RMSD) between two sets of cartesian coordinates (XYZ or PDB format), using rotation (fx. Kabsch algorithm), atom reordering (fx. Hungarian algorithm), and axis reflections, resulting in the minimal RMSD.

## Project description

## Calculate Root-mean-square deviation (RMSD) of Two Molecules Using Rotation

The root-mean-square deviation (RMSD) is calculated, using Kabsch algorithm
(1976) or Quaternion algorithm (1991) for rotation, between two Cartesian
coordinates in either `.xyz` or `.pdb` format, resulting in the minimal
RMSD.

For more information please read RMSD and Kabsch algorithm.

### Motivation

You have molecule A and B and want to calculate the structural difference between those two. If you just calculate the RMSD straight-forward you might get a too big of a value as seen below. You would need to first recenter the two molecules and then rotate them unto each other to get the true minimal RMSD. This is what this script does.

No Changes | Re-centered | Rotated |
---|---|---|

RMSD 2.50 | RMSD 1.07 | RMSD 0.25 |

### Citation

**Implementation**:- Calculate Root-mean-square deviation (RMSD) of Two Molecules Using Rotation, GitHub, http://github.com/charnley/rmsd, <git commit hash or version number>

**Kabsch algorithm**:- Kabsch W., 1976, A solution for the best rotation to relate two sets of vectors, Acta Crystallographica, A32:922-923, doi: http://dx.doi.org/10.1107/S0567739476001873

**Quaternion algorithm**:- Michael W. Walker and Lejun Shao and Richard A. Volz, 1991, Estimating 3-D location parameters using dual number quaternions, CVGIP: Image Understanding, 54:358-367, doi: http://dx.doi.org/10.1016/1049-9660(91)90036-o

Please cite this project when using it for scientific publications.

### Installation

Easiest is to get the program vis PyPi under the package name `rmsd`,

pip install rmsd

or download the project from GitHub via

git clone https://github.com/charnley/rmsd

There is only one Python file, so you can also download calculate_rmsd.py and put it in your bin folder.

wget -O calculate_rmsd https://raw.githubusercontent.com/charnley/rmsd/master/rmsd/calculate_rmsd.py chmod +x calculate_rmsd

### Usage examples

Use `calculate_rmsd --help` to see all the features. Usage is pretty straight
forward, call `calculate_rmsd` with two structures in either `.xyz` or
`.pdb`. In this example Ethane has the exact same structure, but is
translated in space, so the RMSD should be zero.

calculate_rmsd tests/ethane.xyz tests/ethane_translate.xyz

It is also possible to ignore all hydrogens (useful for larger molecules where hydrogens move around indistinguishable) and print the rotated structure for visual comparison. The output will be in XYZ format.

calculate_rmsd --no-hydrogen --print tests/ethane.xyz tests/ethane_mini.xyz

If the atoms are scrambled and not aligned you can use the `--reorder`
argument which will align the atoms from structure B unto A. Use
`--reorder-method` to select what method for reordering. Choose between
Hungarian (default), distance (very approximate) and brute force (slow).

calculate_rmsd --reorder tests/water_16.xyz tests/water_16_idx.xyz

It is also possible to use RMSD as a library in other scripts, see example.py for example usage.

### Problems?

Submit issues or pull requests on GitHub.

## Project details

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Filename, size | File type | Python version | Upload date | Hashes |
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Filename, size rmsd-1.3.2.tar.gz (11.8 kB) | File type Source | Python version None | Upload date | Hashes View |