Template:CineMol

Template documentation

This template is rated as alpha. It is ready for limited use and third-party feedback. It may be used on a small number of pages, but should be monitored closely. Suggestions for new features or adjustments to input and output are welcome.

This template uses TemplateStyles:

Module:CineMol/styles.css

This template uses Lua:

Attempt to make a template that can render molecule descriptions. Adapted from CineMol.

It can use Wikidata's P3636 or P683 to decide what to render.

Example

As an example, the following produces a picture of folic acid using its Wikidata number.

{{CineMol|wikidata=Q127060|style=tube|ry=1.3}}

In most cases you probably want to use {{Image frame}}

Penicillin-G (Style set to Spacefilling and look set to Glossy)

Penicillin-G (Tube style)

Vitamin B6 (style=ballandstick & look=cartoon)

{{Image frame|
|align=none
|style=width:250px
|caption=Caffine (wireframe mode)
|content=
  {{CineMol
  |style=wireframe
  |look=cartoon
  |pdb-ligand=CFF
  |rx=1.57
  |rz=1.9625
 }}
}}

Caffine (wireframe mode)

Usage

You can specify the molecule either by its pdb-ligand id, its wikidata Q number or the contents of a mol file. If unspecified will default to the Q number of the current page.

{{CineMol|wikidata=<Q id here>|...}}
{{CineMol|pdb-ligand=<ligand id here>|...}}
{{CineMol|mol=<SDF FILE HERE>|...}}

You can use the rx, ry, and rz parameters to adjust the viewpoint.

The style parameter determines the type of drawing. The choices are:

Space filling
Ball and stick
Tube
Wireframe

The look parameter determines the look of the drawing. There are two choices: Glossy and Cartoon.

By default hyrdogen atoms are not shown. To include them specify hydrogen=yes.

See template data for additional parameters.

Template data

Display diagrams of molecules based on a mol file or ligand id

Template parameters[Edit template data]
This template prefers block formatting of parameters.
Parameter		Description	Type	Status
style	`style`	Style of molecule drawing to do Suggested values `SpaceFilling` `BallAndStick` `Tube` `Wireframe` Default SpaceFilling	String	suggested
look	`look`	Look of rendering (Cartoon or glossy) Suggested values `Cartoon` `Glossy` Default Glossy	String	suggested
resolution	`resolution`	Resolution of drawing (Todo: Clarify this) Default 30	Number	optional
scale	`scale`	What scale to draw image at Default 5	Number	optional
focal_length	`focal_length`	focal length of camera (This might not work properly)	Number	optional
rotation over x axis	`rx`	How much to rotate the x axis Default 0	Number	optional
rotation over y axis	`ry`	How much to rotate the y axis Default 0	Number	optional
rotation over z axis	`rz`	How much to rotate over the z axis Default 0	Number	optional
hydrogen	`hydrogen`	Show hydrogen molecules Default no Example yes	Boolean	optional
lightbox	`lightbox`	Allow clicking to show a zoomed version of image. Default yes Example no	Boolean	optional
width	`width`	Width of images in pixels Default 250	Number	suggested
height	`height`	Height in pixels. (Note: supplying both height and width will adjust the aspect ratio)	Number	optional
mol	`mol`	Contents of mol/sdf file to render	String	optional
pdb-ligand	`pdb-ligand`	The id of a compound in PDB's chemical component dictionary	String	optional
ChEBI	`ChEBI`	ChEBI id of molecule to render	String	optional
wikidata	`wikidata`	A Wikidata Q-ID to use the value of P3636 to render a molecule. Will default to the current page	String	optional
css	`css`	Extra CSS to apply to the image	String	optional
alt	`alt`	Alternate text for screen readers that can't view images	String	optional
class	`class`	CSS class to apply to image	String	optional
title	`title`	Tooltip to display on hover	String	optional
link	`link`	Either url or pagename to link image to	String	optional
lightbox_caption	`lightbox_caption`	Caption for when user clicks to zoom. If unspecified and using a wikidata or pdb-ligend source, a caption will be automatically generated.	Content	optional

Editors can experiment in this template's sandbox and testcases pages.
Subpages of this template.