Rendering options

General

render-output-format

type

string

default

automatic

description

Image file format.

If this option is not set, then Indigo deduces image format from the file extension. Supported formats:

  • png

  • pdf

  • svg

  • emf (windows)

  • cdxml (not all options are supported)

render-image-size

type

size

default

auto

description

Width and height of target image.

If not set, is calculated automatically according to render-bond-length. To reset this setting, you can set the values of width and height to -1. This options defines both width and height that can be set independently via render-image-width and render-image-height options.

../../_images/indigorenderer_3c11ad279c390a28ce067ee73041a6b87ade9e3f0.svg ../../_images/indigorenderer_3c11ad279c390a28ce067ee73041a6b87ade9e3f1.svg

render-bond-length

type

integer

default

100

description

Desired average bond length in pixels

The actual average bond length may be less if the render-image-size option is set. To reset this setting, you can set its value to -1. This option scales label size as well.

../../_images/indigorenderer_f7be387e6db7f616aa9ba3ab3958a118e3313dea0.svg ../../_images/indigorenderer_f7be387e6db7f616aa9ba3ab3958a118e3313dea1.svg ../../_images/indigorenderer_f7be387e6db7f616aa9ba3ab3958a118e3313dea2.svg

render-relative-thickness

type

float

default

1.0

description

Set the thickness of bonds and atom labels to X/30 of the average bond length.

../../_images/indigorenderer_a07a656adc406186148b2958a3995aaeef6abc570.svg ../../_images/indigorenderer_a07a656adc406186148b2958a3995aaeef6abc571.svg ../../_images/indigorenderer_a07a656adc406186148b2958a3995aaeef6abc572.svg

render-image-width

type

int

default

auto

description

Image width

render-image-height

type

int

default

auto

description

Image height

render-image-max-width

type

int

default

auto

description

Maximum image width

render-image-max-height

type

int

default

auto

description

Maximum image height

render-margins

type

size

default

auto

description

Horizontal and vertical margins around the image, in pixels.

render-coloring

type

boolean

default

false

description

Turn on atom coloring, e.g. nitrogen is blue, oxygen is red, etc.

../../_images/indigorenderer_4c2f2f8b5b88aaa0cde640208fc5f2006c87a4c80.svg ../../_images/indigorenderer_4c2f2f8b5b88aaa0cde640208fc5f2006c87a4c81.svg

render-base-color

type

coloring

default

black (0, 0, 0)

description

The default color for atoms and bonds.

../../_images/indigorenderer_217893bd7c00aa95187cef8027eebbc6d77030ce0.svg ../../_images/indigorenderer_217893bd7c00aa95187cef8027eebbc6d77030ce1.svg

render-background-color

type

color

default

transparent

description

Background color.

../../_images/indigorenderer_dfbba4ab12e62b149d2d445a353832a6d4bd28d60.svg ../../_images/indigorenderer_dfbba4ab12e62b149d2d445a353832a6d4bd28d61.svg

Combination of both render-background-color and render-base-color can be used to get negative:

m = indigo.loadMoleculeFromFile('data/render_example1.mol')

indigo.setOption("render-background-color", "0, 0, 0")
indigo.setOption("render-base-color", "1, 1, 1")

indigoRenderer.renderToFile(m, "result.png")
../../_images/indigorenderer_5afc363772e39448d1cd4d5adbf562adbc786795.svg

render-label-mode

type

enum

default

terminal-hetero

description

Atom label rendering mode

all

show all atoms

terminal-hetero

show heteroatoms, terminal atoms, atoms with radical, charge, isotope, explicit valence, and atoms having two adjacent bonds in a line

hetero

the same as terminal-hetero, but without terminal atoms

none

hide all labels, show only bonds

../../_images/indigorenderer_56e221e816798873127eae5ff474f83b47516fb30.svg ../../_images/indigorenderer_56e221e816798873127eae5ff474f83b47516fb31.svg ../../_images/indigorenderer_56e221e816798873127eae5ff474f83b47516fb32.svg ../../_images/indigorenderer_56e221e816798873127eae5ff474f83b47516fb33.svg

render-hdc-offset

type

offset

default

0, 0

description

Offset for the rendering area

../../_images/indigorenderer_5f464c2e2487526b06b2a1470d133836ea5045a80.svg ../../_images/indigorenderer_5f464c2e2487526b06b2a1470d133836ea5045a81.svg

Comments

render-comment

type

string

default

None

description

Put a comment at the top or bottom of the image

If the image size is set explicitly, it must not be smaller than the size of the comment bounding box.

All the examples on this page contain comment with option value.

Comment can have multiple line:

../../_images/indigorenderer_bd0d6512e3230e62589572a289adf0ba004904ac0.svg

render-comment-font-size

type

integer

default

20

description

Font size for the comment in absolute units, roughly equal to the height in pixels.

../../_images/indigorenderer_466f5b8ed55a03de5496ec9ad39de337c9b72cbd0.svg ../../_images/indigorenderer_466f5b8ed55a03de5496ec9ad39de337c9b72cbd1.svg ../../_images/indigorenderer_466f5b8ed55a03de5496ec9ad39de337c9b72cbd2.svg

render-comment-alignment

type

enum

default

center

description

Comment alignment

Supported values: left, right, center, center-left

../../_images/indigorenderer_d85affdde4f867d5960bde527951095797c1d58d0.svg ../../_images/indigorenderer_d85affdde4f867d5960bde527951095797c1d58d1.svg ../../_images/indigorenderer_d85affdde4f867d5960bde527951095797c1d58d2.svg ../../_images/indigorenderer_d85affdde4f867d5960bde527951095797c1d58d3.svg

render-comment-color

type

color

default

black

description

Color to use for the comment.

../../_images/indigorenderer_fb119fbd66421752aca14a7c74518a6781b6133b0.svg ../../_images/indigorenderer_fb119fbd66421752aca14a7c74518a6781b6133b1.svg

render-bond-line-width

type

float

default

1.0

description

Relative bond line width

../../_images/indigorenderer_76584355aaca4915a4e67d873c0b81ab9ce6b5f00.svg ../../_images/indigorenderer_76584355aaca4915a4e67d873c0b81ab9ce6b5f01.svg ../../_images/indigorenderer_76584355aaca4915a4e67d873c0b81ab9ce6b5f02.svg

render-comment-position

type

enum

default

bottom

description

top or bottom.

../../_images/indigorenderer_720c541ef1469ab19d2838f359b7d5e75f9ef98e0.svg ../../_images/indigorenderer_720c541ef1469ab19d2838f359b7d5e75f9ef98e1.svg

render-comment-offset

type

integer

default

0

description

Vertical space (in pixels) between the comment and the rendered structure or reaction.

../../_images/indigorenderer_a29812dee01a7255f847acd27a8db84445731a580.svg ../../_images/indigorenderer_a29812dee01a7255f847acd27a8db84445731a581.svg ../../_images/indigorenderer_a29812dee01a7255f847acd27a8db84445731a582.svg

Chemistry

render-implicit-hydrogens-visible

type

boolean

default

True

description

Show implicit hydrogens on visible atoms.

../../_images/indigorenderer_bb170c86f5ee1dc585166e5390269a0d475c29bf0.svg ../../_images/indigorenderer_bb170c86f5ee1dc585166e5390269a0d475c29bf1.svg

render-atom-ids-visible

type

boolean

default

False

description

Show atom numbers (for debugging purposes only).

../../_images/indigorenderer_6f053b6acb6a81d303b625911c85a649227eac310.svg ../../_images/indigorenderer_6f053b6acb6a81d303b625911c85a649227eac311.svg

render-bond-ids-visible

type

boolean

default

False

description

Show bond numbers (for debugging purposes only).

../../_images/indigorenderer_a7b5ecc20c2aab239e409dc68c7c3ec162cd0b2e0.svg ../../_images/indigorenderer_a7b5ecc20c2aab239e409dc68c7c3ec162cd0b2e1.svg

render-atom-bond-ids-from-one

type

boolean

default

False

description

Show atom and bond numbers starting from one, not from zero.

render-aam-color

type

color

default

black

description

Atom-by-atom mapping indices color in reactions.

../../_images/indigorenderer_2d4b51b4095d744294e0a4b18dd40230c8e664f30.svg

render-atom-color-property

type

string

default

none

description

S-group name for atom colors

Indigo can use a specified color for each atom and interpolate these colors for bond rendering.

# Load structure
m = indigo.loadMolecule('CC(=C)C1=C(C)C(C)=CC(O)=C1NCCCCC=O')

# Add data sgroups with 'color' description
m.addDataSGroup([0, 1, 2, 3], [], "color", "0.155, 0.55, 0.955")
m.addDataSGroup([4, 5, 6, 16, 17, 18], [], "color", "0.955, 0.155, 0.155")

indigo.setOption("render-atom-color-property", "color")
indigo.setOption('render-coloring', False)
indigoRenderer.renderToFile(m, 'result.png')
../../_images/indigorenderer_bfb81f9acd9910b65776d216ac99637f46e02283.svg

See Atom Coloring for a larger example.

render-bold-bond-detection

type

boolean

default

true

description

Detect and draw bold bond for Haworth projection

Input: data/bold-bond.mol

../../_images/indigorenderer_1bc28b16c239ff2c4e4bd87858d8743f2b4a13cd0.svg ../../_images/indigorenderer_1bc28b16c239ff2c4e4bd87858d8743f2b4a13cd1.svg

render-catalysts-placement

type

enum

default

above-and-below

description

Reaction catalysts place relative to the reaction arrow

Input: data/catalysts3000.rxn

../../_images/indigorenderer_b6c60f30bd0cc1572a0865431b90994855115fa80.svg ../../_images/indigorenderer_b6c60f30bd0cc1572a0865431b90994855115fa81.svg

render-center-double-bond-when-stereo-adjacent

type

boolean

default

false

description

Center double done if there is an attached stereobond

../../_images/indigorenderer_e40818900fba8c7e8b4bf18e05a6552c536ce6a10.svg ../../_images/indigorenderer_e40818900fba8c7e8b4bf18e05a6552c536ce6a11.svg

render-data-sgroup-color

type

color

default

black

description

Color for data-sgroups

Input: data/render_example-sgroup.mol

../../_images/indigorenderer_e18eb2e98d5eea2b76442abaa014b5f81ef12eb80.svg ../../_images/indigorenderer_e18eb2e98d5eea2b76442abaa014b5f81ef12eb81.svg

render-stereo-style

type

enum (old, ext, none)

default

old

description

Stereocenters rendering mode

old:

Only display the “Chiral” sign when appropriate.

ext:

Display “abs”, “and”, “or” labels near each stereocenter.

none:

Hide all the information about the stereogroups.

Input: data/stereo-chiral.mol

../../_images/indigorenderer_45bbf8dc3fd3f1a657d113e5f8290004b699a5fe0.svg ../../_images/indigorenderer_45bbf8dc3fd3f1a657d113e5f8290004b699a5fe1.svg ../../_images/indigorenderer_45bbf8dc3fd3f1a657d113e5f8290004b699a5fe2.svg

Old style of rendering is used only with ordinary stereocenters, and enhanced stereocenters with and and or groups are rendered the same in the old and ext mode:

Input: data/stereo-chiral2.mol

../../_images/indigorenderer_2ffd17f6774edd33a8e5c7622aa0a8180955981a0.svg ../../_images/indigorenderer_2ffd17f6774edd33a8e5c7622aa0a8180955981a1.svg ../../_images/indigorenderer_2ffd17f6774edd33a8e5c7622aa0a8180955981a2.svg

render-superatom-mode

type

enum (expand, collapse)

default

expand

description

Superatoms rendering mode

Input: data/abbr.mol

../../_images/indigorenderer_47ecde5d4f564604570713bf01f4aa9513aee8a80.svg ../../_images/indigorenderer_47ecde5d4f564604570713bf01f4aa9513aee8a81.svg

render-valences-visible

type

boolean

default

true

description

Render explicit valences

../../_images/indigorenderer_0353c45c93208719837a25cd05e68583a4e2a73f0.svg ../../_images/indigorenderer_0353c45c93208719837a25cd05e68583a4e2a73f1.svg

Highlighting

render-highlight-color

type

color

default

red

description

The color to be used for highlighting.

Input: data/highlighting.mol

../../_images/indigorenderer_e905816881c8d623ce00c9e36c772bfd193700890.svg ../../_images/indigorenderer_e905816881c8d623ce00c9e36c772bfd193700891.svg

render-highlight-color-enabled

type

boolean

default

true

description

Enable highlighting with color.

Input: data/highlighting.mol

../../_images/indigorenderer_3d437ca521688ef7272f242d9f7139493fec3f110.svg ../../_images/indigorenderer_3d437ca521688ef7272f242d9f7139493fec3f111.svg

render-highlight-thickness-enabled

type

boolean

default

false

description

Enable highlighting with thick bonds and bold atom labels.

Input: data/highlighting.mol

../../_images/indigorenderer_c31cb16e30c5cc90f32e10593163cb2a0448691d0.svg ../../_images/indigorenderer_c31cb16e30c5cc90f32e10593163cb2a0448691d1.svg

render-highlighted-labels-visible

type

boolean

default

False

description

Always show labels of highlighted atoms.

Input: data/highlighting.mol

../../_images/indigorenderer_684946bb4d432e3399d9428862c423b9e7e9e1580.svg ../../_images/indigorenderer_684946bb4d432e3399d9428862c423b9e7e9e1581.svg