atomes - Man Page

atomes [Options] files...
atomes [IMAGES_OPTIONS] files...

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:

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

       atomes project.apf file.xyz -pdb other_file

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

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 #

       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

https://atomes.ipcms.fr/

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

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