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.