Options

Indigo instance represents an environment for IndigoObjects. Many methods in Indigo has additional options that can be set via Indigo.setOption method:

indigo.setOption("render-comment", "text comment")
indigo.setOption("render-comment-color", "0, 0.4, 0.5")
indigo.setOption("ignore-stereochemistry-errors", True)

Contents

Options Table

Aromaticity options

Name

Type

Short description

Default

aromaticity-model

enum

Aromaticity model

basic

dearomatize-verification

boolean

Verify dearomatization method

true

unique-dearomatization

boolean

Find dearomatization if all possible configurations uniquely define hydrogens.

false

Deconvolution options

Name

Type

Short description

Default

deconvolution-aromatization

boolean

Aromatize input molecules

true

deco-save-ap-bond-orders

boolean

Save attachment points as separate atoms with explicit bond connected.

false

deco-ignore-errors

boolean

Ignore errors during decomposition

true

Fingerprints options

Name

Type

Short description

Default

fp-ord-qwords

integer

Size of "ordinary" part of a fingerprint, in 8-byte blocks.

25

fp-sim-qwords

integer

Size of "similarity" part of a fingerprint, in 8-byte blocks.

8

fp-any-qwords

integer

Size of "any" part of a fingerprint, in 8-byte blocks.

15

fp-tau-qwords

integer

Size of "tautomer" part of a fingerprint, in 8-byte blocks.

25

fp-ext-enabled

boolean

Sets whether to include or not 3-byte "EXT" part of the fingerprint.

true

Grid rendering options

Name

Type

Short description

Default

render-grid-margins

size

Horizontal and vertical margins around the grid cell, in pixels.

0, 0

render-grid-title-property

string

The name of the molecule's property that defines the title that is put under each molecule.

none

render-grid-title-alignment

enum

Cell title alignment

center

render-grid-title-font-size

int

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

20

render-grid-title-offset

int

Vertical space (in pixels) between the title and the rendered structure.

0

InChI options

Name

Type

Short description

Default

inchi-options

string

Options supported by the official InChI plugin.

none

Generic options

Name

Type

Short description

Default

ignore-noncritical-query-features

boolean

When true, the "bond topology", "stereo care", "ring bond count", and "unsaturation" specifications are ignored when a non-query molecule is being loaded.

false

treat-x-as-pseudoatom

boolean

Treat 'X' atoms in Molfiles/Rxnfiles as pseudoatoms, rather than "any halogen" query atoms.

false

skip-3d-chirality

boolean

Do not calculate chirality of 3D input structures.

false

molfile-saving-mode

enum (auto, 2000, 3000)

Molfile saving mode

auto

molfile-saving-no-chiral

boolean

Do no write the "Chiral" flag when saving Molfiles and Rxnfiles

false

molfile-saving-skip-date

boolean

Do no write the current date into Molfiles, Rxnfiles and RDFiles

false

smiles-saving-write-name

boolean

Write names when saving via generic saver interface in SMILES mode

false

filename-encoding

enum (ascii, utf-8)

File names encoding

ascii

serialize-preserve-ordering

boolean

Preserve atom and bond ordering in the serialization procedure

false

Layout options

Name

Type

Short description

Default

layout-max-iterations

int

The maximum number of iterations allowed for the layout procedure to run

0

smart-layout

boolean

whether to use "smart" layout or "simple"

false

pKa options

Name

Type

Short description

Default

pKa-model

string

pKa model type

simple

pKa-model-level

int

max level for advanced model

0

pKa-model-min-level

int

min level for advanced model

0

Reaction Products Enumeration and Transformation

Name

Type

Short description

Default

rpe-max-depth

int

Maximum level of representing product like a monomer (works only with ``rpe-multistep-reactions enabled``).

2

rpe-multistep-reactions

boolean

Enable multistep reactions (Products of the reaction can take part in further reactions)

false

rpe-mode

enum (grid, one-tube)

Monomers mixing mode

grid

rpe-self-reaction

boolean

Enable intramolecular reactions, where one molecule of monomers can play role of two (or more) reactants

false

rpe-max-products-count

int

Maximum amount of generated products.

1000

rpe-layout

boolean

Enable layout after product enumeration

true

transform-layout

boolean

Enable layout after transformation.

true

Rendering options

Name

Type

Short description

Default

render-output-format

string

Image file format.

automatic

render-image-size

size

Width and height of target image.

auto

render-bond-length

integer

Desired average bond length in pixels

100

render-relative-thickness

float

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

1.0

render-image-width

int

Image width

auto

render-image-height

int

Image height

auto

render-image-max-width

int

Maximum image width

auto

render-image-max-height

int

Maximum image height

auto

render-margins

size

Horizontal and vertical margins around the image, in pixels.

auto

render-coloring

boolean

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

false

render-base-color

coloring

The default color for atoms and bonds.

black (0, 0, 0)

render-background-color

color

Background color.

transparent

render-label-mode

enum

Atom label rendering mode

terminal-hetero

render-hdc-offset

offset

Offset for the rendering area

0, 0

render-comment

string

Put a comment at the top or bottom of the image

None

render-comment-font-size

integer

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

20

render-comment-alignment

enum

Comment alignment

center

render-comment-color

color

Color to use for the comment.

black

render-bond-line-width

float

Relative bond line width

1.0

render-comment-position

enum

top or bottom.

bottom

render-comment-offset

integer

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

0

render-implicit-hydrogens-visible

boolean

Show implicit hydrogens on visible atoms.

True

render-atom-ids-visible

boolean

Show atom numbers (for debugging purposes only).

False

render-bond-ids-visible

boolean

Show bond numbers (for debugging purposes only).

False

render-atom-bond-ids-from-one

boolean

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

False

render-aam-color

color

Atom-by-atom mapping indices color in reactions.

black

render-atom-color-property

string

S-group name for atom colors

none

render-bold-bond-detection

boolean

Detect and draw bold bond for Haworth projection

true

render-catalysts-placement

enum

Reaction catalysts place relative to the reaction arrow

above-and-below

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

boolean

Center double done if there is an attached stereobond

false

render-data-sgroup-color

color

Color for data-sgroups

black

render-stereo-style

enum (old, ext, none)

Stereocenters rendering mode

old

render-superatom-mode

enum (expand, collapse)

Superatoms rendering mode

expand

render-valences-visible

boolean

Render explicit valences

true

render-highlight-color

color

The color to be used for highlighting.

red

render-highlight-color-enabled

boolean

Enable highlighting with color.

true

render-highlight-thickness-enabled

boolean

Enable highlighting with thick bonds and bold atom labels.

false

render-highlighted-labels-visible

boolean

Always show labels of highlighted atoms.

False

Standardize options

Name

Type

Short description

Default

standardize-stereo

boolean

Sets or repairs the stereo on a molecule.

false

standardize-clear-stereo

boolean

Sets all atoms and bonds to NoStereo.

false

standardize-clear-enhanced-stereo

boolean

Removes all relative stereo groupings.

false

standardize-clear-unknown-stereo

boolean

Sets all atoms and bonds marked UnknownStereo to NoStereo.

false

standardize-clear-unknown-atom-stereo

boolean

Sets all atoms marked UnknownStereo to NoStereo.

false

standardize-clear-unknown-bond-stereo

boolean

Sets all bonds marked UnknownStereo to NoStereo.

false

standardize-clear-cis-trans

boolean

Sets all bonds marked CisStereo or TransStereo to UnknownStereo.

false

standardize-stereo-from-coordinates

boolean

Uses 2D coordinates and up/down bond markings (or 3D coordinates) to assign the stereochemistry of the atoms or bonds.

false

standardize-reposition-stereo-bonds

boolean

Repositions the stereo bond markings in an attempt to find the best bond to mark as a wedge bond for each stereo atom.

false

standardize-reposition-axial-stereo-bonds

boolean

Repositions the stereo bond markings for axial stereo centers (allenes and atropisomers) in an attempt to find the best bond to mark as a wedge bond for each center.

false

standardize-fix-direction-wedge-bonds

boolean

Checks the wedge bonds in the molecule to ensure that the wedge is drawn with the stereo atom at the narrow end of the wedge.

false

standardize-charges

boolean

Sets the charges on a molecule to a standard form.

false

standardize-clear-charges

boolean

Sets all formal charges to zero.

false

standardize-neutralize-zwitterions

boolean

Converts directly bonded zwitterions (positively charged atom bonded to negatively charged atom, A+B-) to the neutral representation (A=B).

false

standardize-center-molecule

boolean

Translates a molecule so its geometric center lies at the origin.

false

standardize-remove-single-atoms

boolean

Removes fragments that consist of only a single heavy atom.

false

standardize-keep-smallest

boolean

Keeps only the smallest fragment in the molecule.

false

standardize-keep-largest

boolean

Keeps only the largest fragment in the molecule.

false

standardize-remove-largest

boolean

Removes the largest fragment in the molecule.

false

standardize-clear-coordinates

boolean

Sets all x, y, z coordinates to zero.

false

standardize-straighten-triple-bonds

boolean

Finds atoms with triple bonds and non-linear geometry and fixes them so that the bond angles are 180 degrees.

false

standardize-straighten-allens

boolean

Finds atoms with two double-bonds and non-linear geometry and fixes them so that the bond angles are 180 degrees.

false

standardize-clear-molecule

boolean

Deletes all atoms and bonds in the molecule, keeping the molecule object in the data record.

false

standardize-make-non-h-to-c-atoms

boolean

Converts all non-Hydrogen atoms atoms in the molecule to carbon.

false

standardize-make-non-h-to-a-atoms

boolean

Converts all non-Hydrogen atoms in the molecule to the A query atom type.

false

standardize-make-non-h-c-to-q-atoms

boolean

Converts all non-Carbon, non-Hydrogen atoms in the molecule to the Q query atom type.

false

standardize-make-all-bonds-single

boolean

Converts all bonds in the molecule to single bonds.

false

standardize-highlight-colors

boolean

Clears any highlight colors from atoms and bonds.

false

standardize-clear-unusual-valences

boolean

Clears any atom valence query features and resets all implicit hydrogen counts to their standard values.

false

standardize-clear-isotopes

boolean

Clears all isotope markings from atoms.

false

standardize-clear-dative-bonds

boolean

Clears all explicit zero-order coordination bonds of dative type (V3000 type-9 bonds).

false

standardize-clear-hydrogen-bonds

boolean

Clears all explicit zero-order hydrogen bonds (V3000 type-10 bonds).

false

standardize-create-dative-bonds

boolean

Create coordination bond (zero-order bond) instead of wrong co-valent bond.

false

standardize-create-hydrogen-bonds

boolean

Create hydrogen bond (zero-order bond) instead of wrong co-valent bond.

false

Stereocenters options

Name

Type

Short description

Default

ignore-stereochemistry-errors

boolean

When reading a Molfile/Rxnfile with incorrectly marked stereobonds, ignore them rather than raise an error.

false

stereochemistry-bidirectional-mode

boolean

Treat stereobond direction bond not only for a pointed stereocenter, but for the neighbour as well.

false

stereochemistry-detect-haworth-projection

boolean

Detect Haworth projection

false

Substructure matching options

Name

Type

Short description

Default

embedding-uniqueness

enum

Defines how the uniqueness of a substructure match is determined when counting or iterating unique matches.

atoms

max-embeddings

int

The maximum number of embeddings allowed to enumerate when counting all embeddings.

0

Timeout options

Name

Type

Short description

Default

timeout

integer

Timeout (is ms) for Indigo operation. Zero means no timeout.

0

aam-timeout

integer

Timeout (is ms) for atom-to-atom mapping computation operation. Zero means no timeout.

0