Module:CineMol/doc

This module is rated as beta. It is considered ready for widespread use, but as it is still relatively new, it should be applied with some caution to ensure results are as expected.

This module uses TemplateStyles:

Module:CineMol/styles.css^[e]

This module depends on the following other modules:

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
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

Module:CineMol/doc

Example

Usage

Template data

Content Disclaimer