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https://github.com/aslozada/kanon

Program to compute chirality indices and assess molecular symmetry
https://github.com/aslozada/kanon

chemistry chirality hausdorff molecule quaternions symmetry

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Program to compute chirality indices and assess molecular symmetry

Host: GitHub
URL: https://github.com/aslozada/kanon
Owner: aslozada
Created: 2020-12-22T14:24:36.000Z (about 4 years ago)
Default Branch: main
Last Pushed: 2024-07-12T14:44:32.000Z (6 months ago)
Last Synced: 2024-07-12T16:55:05.231Z (6 months ago)
Topics: chemistry, chirality, hausdorff, molecule, quaternions, symmetry
Language: Fortran
Homepage:
Size: 1.1 MB
Stars: 4
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md

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README

# Program to compute chirality indices and assess molecular symmetry

This is the official repository of the `kanon` program developed by Asdrubal Lozada-Blanco in the Laboratory of Theoretical Chemistry (Federal University of São Carlos - Brazil)

## Installation

### Building from source

To build kanon from source code you need to have:
- a Fortran compiler
- build systems: make or fpm
- [fpm](https://github.com/fortran-lang/fpm) version 0.2.0 or newer

#### Building with make

```
cp app/kanon.f90 src/
cp Makefile src/
cd src/
make clean
make
make clean
```

#### Building with fpm

```
fpm build
```

#### How to use kanon?

kanon uses a XYZFile as input

```
natom
comment
label1 xcoor1 ycoord1 zcoord1
label2 xcoor2 ycoord2 zcoord2
...
```

Examples
```
3
Water H2O.xyz
O 0.000000 0.000000 0.000000
H 0.000000 0.000000 0.947000
H 0.895670 0.000000 -0.316663

```

```
kanon --pattern H2O.xyz

---------------------------------------------------------------------------------
Cartesian coordinates input file: H2O.xyz
Number atoms: 3
O 0.00000 0.00000 0.00000
H 0.00000 0.00000 0.94700
H 0.89567 0.00000 -0.31666

```
```
kanon --single .xyz

-----------------------------------------------------------------------------
Diameter of molecule: 1.54889 ang.
-----------------------------------------------------------------------------
Center of masses: 0.05011 0.00000 0.03527
------------------------------------------------------------------------------
Moments of inertia: 1.74595 1.20907 0.53688
Eigenvectors
0.000 0.814 -0.580
1.000 0.000 0.000
0.000 0.580 0.814
---------------------------------------------------------------------------------
Symmetrical matrix in Diamond`s method to optimal rotation: B
---------------------------------------------------------------------------------
0.000 0.000 0.000 0.000
0.000 3.353 -0.000 -0.000
0.000 -0.000 2.399 -0.001
0.000 -0.000 -0.001 0.954
---------------------------------------------------------------------------------
Eigenvalues - Eigenvectors
---------------------------------------------------------------------------------
0.954 0.000 0.000 0.000 1.000
0.000 1.000 0.000 0.000 0.000
3.353 0.000 1.000 -0.000 -0.000
2.399 0.000 0.000 1.000 -0.000
--------------------------------------------------------------------------------
Check files: Pattern.xyz / Rotate_image.xyz
---------------------------------------------------------------------------------
Root-mean-square deviation
RMSD: 0.00000000
--------------------------------------------------------------------------------
Hausdorff-derived chirality Index
CHI: 0.00000000
--------------------------------------------------------------------------------
```

Comparing an object with any image

```
kanon --pattern .xyz --image .xyz

```

Delaunay triangulation of surfaces

```
kanon --pattern .xyz --delaunay .dat

```

```
output_grid.dat

GRID 1286
REF 6 2 1
6 2 1
6 3 2
4 70 3
4 69 70
70 69 74
71 70 74
...

```
With openmp
```
export OMP_NUM_THREADS=#
```

Example: Hausdorff Chirality Measure for biphenyl

Grid's effects

Electron density: Isovalue 0.05

Surface