draw_sdf: draw_sdf

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

draw_sdf

Description

Draws an sdf object in the 2D plane using ggplot2 library. Permits customization of bond colors and atom colors.

Usage

	draw_sdf(sdf, filename = "test.jpg", alpha_edge = 0.5, alpha_node = 1, numbered = FALSE, font_size = 5, node_vertical_offset = 0, node_background_color = FALSE, bgcolor = rgb(1, 1, 1, 1), bgraster = NULL, node_policy = default_node_policy(), edge_policy = default_edge_policy(), bond_dist_offset = 0.05, fmcsR_sdf = NULL)

Arguments

sdf	An instance of a SDF or list of SDFs
filename	Filename to save image to. Defaults to 'test.jpg'. If set to NULL, does not save image.
alpha_edge	alpha of bonds in your image. Defaults to 0.5. 0 is fully transparent, 1 is fully opaque.
alpha_node	alpha of atoms in your image. Defaults to 1.0.
numbered	If 1 or TRUE, displays numbering of atoms at their location. If 2, displays a second numbering style.
font_size	Controls size of text to be displayed at atom locations. Beware when plotting multiple SDFs in one image. Ggplot will still scale fonts as if text is being plotted in one image.
node_vertical_offset	Upward shift of atom text. Upward shit is in SDF units, not ggplot units.
bgcolor	An rgb(r,g,b,alpha) or similar object. produces a background of the specified color.
node_background_color	A common color as a text string (e.g. 'white', 'pink') or an rgb(r,g,b,alpha). Draws a filled circle of the color specified before drawing text over each node.
bgraster	A readPNG object or a path to an object that can be understood using readPNG. Will be used as background.
node_policy	Mapping that defines how atom strings should be displayed. Simplest would be c('default'='black')
edge_policy	Mapping that defines how bonds should be displayed. Simplest is c('default'='black'), though this will display all Hydrogen bonds as well.
bond_dist_offset	Defines space between double or triple bonds, in SDF units.
fmcsR_sdf	A second SDF object to run fmcsR on.

Details

Requires ggplot2. Additional features require grid, gridExtra, fmcsR, or png. Most matrix operations vectorized.

Value

Returns a ggplot2 object. Calling draw_sdf(...) rather than assigning it will result in R trying to print a ggplot2 object.

Author(s)

John A. Sharifi

Examples

	library(ChemmineR) 		# if not already imported
	data(sdfsample)
	draw_sdf(sdfsample[[1]])

girke-lab/ChemmineR documentation built on July 28, 2023, 10:36 a.m.