Module:CineMol/doc

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}}

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Rendered based on the entry in the Chemical Component Dictionary for the molecule with id "FOL".

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

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

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Penicillin-G (Tube style)

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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
 }}
}}

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Rendered based on the entry in the Chemical Component Dictionary for the molecule with id "CFF".

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