NAME¶

atomes - a toolbox to analyze, visualize and create/edit 3D atomic scale models

SYNOPSIS¶

atomes [OPTIONS] files...
atomes [IMAGES_OPTIONS] files...

DESCRIPTION¶

This manual page documents briefly the atomes command.

atomes is a toolbox to analyze, visualize and create/edit 3D atomic scale models.
It offers a workspace to open and manage project(s) that can exchange data: analysis results, atomic coordinates ...
atomes also provides an advanced input preparation system for calculations using well know molecular dynamics codes:

OPTIONS¶

This program uses a set of custom options to specify the file formats for atomic coordinates (ex: -xyz),
but otherwise follows the usual GNU command line syntax, with long options starting with two dashes (`-').
atomes will try to open a file based on its extension, however file type can be strictly enforced using the corresponding option.
A summary of options is presented below.

-h, --help

Show summary of options

-v, --version

Show version of program

-awf, -AWF

Open atomes workspace file

-apf, -APF

Open atomes project file(s)

-xyz, -XYZ

Import XYZ atomic coordinates(s)

-c3d, -C3D

Import Chem3D atomic coordinates(s)

-trj, -TRJ

Import CPMD atomic coordinates(s)

-xdatcar, -XDATCAR

Import VASP atomic coordinates(s)

-pdb, -PDB, -ent, -ENT

Import PDB atomic coordinates(s)

-cif, -CIF

Import CIF atomic coordinate(s)

-hist, -HIST

Import DL_POLY history file atomic coordinates(s)

-ipf, -IPF

Import I.S.A.A.C.S. project

EXEMPLES¶

atomes project.apf file.xyz -pdb other_file

atomes -awf workspace -apf project -xyz file -pdb other_file

IMAGE_OPTIONS¶

atomes can be used to generate image of atomic scale models directly from the command line.

-p, --png, --render-png

Render PNG image

-j, --jpg, --render-jpg

Render JPG image

-o, --output=[FILE]

Image name (default: image.png or image.jpg)

-W, --width=[X_SIZE]

Image width in pixels, X_SIZE must be > 0

-H, --height=[Y_SIZE]

Image height in pixels, Y_SIZE must be > 0

Depending on the file to be rendered, default parameters for the rendering are obtained:
- For an atomes project file (*.apf): from the project file itself.
- For any another type of atomic coordinates (ex: .xyz): from the user preferences in atomes.pml
In both cases some parameters can be momentarely overriden using command line options:

-s, --style=[STYLE]

Visual style, in:
- Balls and sticks: balls_and_sticks, ball_and_stick, b_and_s, bs, b
- Wireframes: wireframes, wireframe, wires, wire, wi, w
- Covalent radius: covalent_radius, covalent, cov_rad, cov, co, cr
- Ionic radius: ionic_radius, ionic_rad, ionic, ion, ir
- van der Waals radius: van_der_waals_radius, van_der_waals, vdw_radius, vdw_rad, vdw, vr
- In crystal radius: in_crystal_radius, crystal_radius, in_crystal, crystal, cryst, cr
- Spheres: spheres, sphere, sph, sp, s
- Cylinders: cylinders, cylinder, cyl, cy, c
- Dots: dots, dot, d

-r, --rep=[REP]

Representation style, in:
- Orthographic: orthograhpic, ortho, 0
- Perpsective (default): perspective, persp, 1

-b, --box=[STYLE]

Trigger box representation, if any, and set box style
Style, in:
- Wireframes: wireframes, wireframe, wires, wire, wi, w
- Cylinders: cylinders, cylinder, cyl, cy, c

-a, --axis=[STYLE]

Trigger axis representation and set axis style
Style, in:
- Wireframes: wireframes, wireframe, wires, wire, wi, w
- Cylinders: cylinders, cylinder, cyl, cy, c

-e, --acolor=[MAP]

Set color map for atoms and bonds
- Chemical specie(s): species, spec, sp, 0
- Total coordination(s): total_coordiantion, total_coord, tc, 1
- Partial coordination(s): partial_coordiantion, partial_coord, pc, 2
- Fragment(s)*: fragment, frag, fg, 3
- Molecule(s)*: molecule, mol, mo, 4
* if required trigger the corresponding analysis

-t, --pcolor=[MAP]

Trigger polyhedra representation, and set the corresponding color map

-C, --box_color=[COLOR]

Box color, COLOR in hexadecimal coding, 3 or 6 letters, with or without #

-G, --back_grad=[GRAD]

Background gradient type, in:
- No gradient: none, no, 0
- Linear: linear, lin, 1
- Circular: circular, circ, 2

-B, --back_color=[COLOR]

Background color, COLOR in hexadecimal coding, 3 or 6 letters, with or without #
Trigger single color mode (no gradient) for the background

-D, --back_dir=[DIR]

Background gradient direction, in:
- Linear gradient
- Right to left: 0
- Top to bottom: 1
- Bottom right to top left: 2
- Top right to bottom left: 3
- Circular gradient
- Right to left: 0
- Left to right: 1
- Top to bottom: 2
- Bottom to top: 3
- Bottom right to top left: 4
- Bottom left to top right: 5
- Top right to bottom left: 6
- Top left to bottom righ: 7
- From the center: 8

-P, --back_pos=[POS]

Gradient colors mixed position in [0.0 - 1.0]

-U, --grad_col_a=[COLOR]

Gradient initial color, COLOR in hexadecimal coding, 3 or 6 letters, with or without #

-V, --grad_col_b=[COLOR]

Gradient final color, COLOR in hexadecimal coding, 3 or 6 letters, with or without #

EXAMPLES¶

atomes --render-png --width=1920 --height=1024 -o project.png project.apf

atomes -j -W 1920 -H 1024 --output=my_file.jpg file.pdb -s cyl -e pc

SEE ALSO¶

https://atomes.ipcms.fr/

AUTHOR¶

This manual page was created by Dr. Sébastien Le Roux <sebastien.leroux@ipcms.unistra.fr>

BUGS¶

Report bugs at <https://github.com/Slookeur/atomes-GNU/issues>.