Program to compute chirality indices and assess molecular symmetry
July 12, 2024 · View on GitHub
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 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
-----------------------------------------------------------------------------
Diameter of molecule: 1.54889 ang.
--------------------------------------------------------------------------------
Center of masses
0.05011 0.00000 0.03527
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Principal moments of inertia
Ia Ib Ic
0.53688 1.20907 1.74595
--------------------------------------------------------------------------------
Inertia axis
0.00000 0.81430 -0.58045
1.00000 0.00000 0.00000
0.00000 0.58045 0.81430
--------------------------------------------------------------------------------
Symmetry elements. Tolerance: 0.05000
--------------------------------------------------------------------------------
kanon --single <H2O>.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 <object>.xyz --image <image>.xyz
Delaunay triangulation of surfaces
kanon --pattern <file>.xyz --delaunay <output_grid>.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