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

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

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

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

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

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

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

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

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