@atomistics/xyz
An xyz chemical file format parser and tools for interacting with xyz files.
Install
For use in your scripts:
npm i --save @atomistics/xyz
To install it globally and use the provided cli scripts:
npm i -g @atomistics/xyz
Example
const xyz = require('@atomistics/xyz');
// xyz assumes we're going to get a trajectory, so it will return
// an array of images. Note that we grab the zeroth image.
const caffeine = xyz(`24
Caffeine
H -3.3804130 -1.1272367 0.5733036
N 0.9668296 -1.0737425 -0.8198227
C 0.0567293 0.8527195 0.3923156
N -1.3751742 -1.0212243 -0.0570552
C -1.2615018 0.2590713 0.5234135
C -0.3068337 -1.6836331 -0.7169344
C 1.1394235 0.1874122 -0.2700900
N 0.5602627 2.0839095 0.8251589
O -0.4926797 -2.8180554 -1.2094732
C -2.6328073 -1.7303959 -0.0060953
O -2.2301338 0.7988624 1.0899730
H 2.5496990 2.9734977 0.6229590
C 2.0527432 -1.7360887 -1.4931279
H -2.4807715 -2.7269528 0.4882631
H -3.0089039 -1.9025254 -1.0498023
H 2.9176101 -1.8481516 -0.7857866
H 2.3787863 -1.1211917 -2.3743655
H 1.7189877 -2.7489920 -1.8439205
C -0.1518450 3.0970046 1.5348347
C 1.8934096 2.1181245 0.4193193
N 2.2861252 0.9968439 -0.2440298
H -0.1687028 4.0436553 0.9301094
H 0.3535322 3.2979060 2.5177747
H -1.2074498 2.7537592 1.7203047
`)[0];
// The atomic numbers of each atom.
console.log(caffeine.numbers);
> [ 1, 7, 6, 7, 6, 6, 6, 7, 8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 6, 6, 7, 1, 1, 1 ]
// xyz will package the positions into an ndarray.
console.log(caffeine.positions.data);
> Float64Array [ -3.380413, -1.1272367, 0.5733036, ... 1.7203047 ]API
const xyz = require("@atomistics/xyz");
const trajectory = xyz(data);| Parameter | Type | Description |
|---|---|---|
| data | string | xyz file chemical format string |
Returns a list of images, where each image contains the atomic numbers and atom positions:
| Name | Type | Description |
|---|---|---|
| trajectory[N].numbers | int array | An array of atomic numbers. |
| trajectory[N].positions | ndarray | An ndarray of shape [atom count, 3] containing the position of each atom. |
CLI
xyz2json
xyz2json inputfile.xyz
Converts inputfile.xyz to json and prints the result to stdout.
Example:
$ xyz2json h2.xyz > h2.json
$ cat h2.json
[{"positions":[0,0,0,1,0,0],"numbers":[1,1]}]
xyz2js
xyz2js inputfile.xyz
Converts inputfile.xyz to a javascript module and prints the result to stdout.
Example:
$ xyz2js h2.xyz > h2.js
$ cat h2.js
const ndarray = require("ndarray");
const data = JSON.parse('[{"positions":[0,0,0,1,0,0],"numbers":[1,1]}]');
module.exports = data.map(d => {
return {
positions: ndarray(new Float64Array(d.positions), [d.positions.length/3, 3]),
numbers: d.numbers,
};
});