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 |
---|---|---|---|
enum |
Aromaticity model |
basic |
|
boolean |
Verify dearomatization method |
true |
|
boolean |
Find dearomatization if all possible configurations uniquely define hydrogens. |
false |
Deconvolution options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
boolean |
Aromatize input molecules |
true |
|
boolean |
Save attachment points as separate atoms with explicit bond connected. |
false |
|
boolean |
Ignore errors during decomposition |
true |
Fingerprints options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
integer |
Size of "ordinary" part of a fingerprint, in 8-byte blocks. |
25 |
|
integer |
Size of "similarity" part of a fingerprint, in 8-byte blocks. |
8 |
|
integer |
Size of "any" part of a fingerprint, in 8-byte blocks. |
15 |
|
integer |
Size of "tautomer" part of a fingerprint, in 8-byte blocks. |
25 |
|
boolean |
Sets whether to include or not 3-byte "EXT" part of the fingerprint. |
true |
Grid rendering options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
size |
Horizontal and vertical margins around the grid cell, in pixels. |
0, 0 |
|
string |
The name of the molecule's property that defines the title that is put under each molecule. |
none |
|
enum |
Cell title alignment |
center |
|
int |
Font size for the title in absolute units, roughly equal to the height in pixels. |
20 |
|
int |
Vertical space (in pixels) between the title and the rendered structure. |
0 |
InChI options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
string |
Options supported by the official InChI plugin. |
none |
Generic options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
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 |
|
boolean |
Treat 'X' atoms in Molfiles/Rxnfiles as pseudoatoms, rather than "any halogen" query atoms. |
false |
|
boolean |
Do not calculate chirality of 3D input structures. |
false |
|
enum (auto, 2000, 3000) |
Molfile saving mode |
auto |
|
boolean |
Do no write the "Chiral" flag when saving Molfiles and Rxnfiles |
false |
|
boolean |
Do no write the current date into Molfiles, Rxnfiles and RDFiles |
false |
|
boolean |
Write names when saving via generic saver interface in SMILES mode |
false |
|
enum (ascii, utf-8) |
File names encoding |
ascii |
|
boolean |
Preserve atom and bond ordering in the serialization procedure |
false |
Layout options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
int |
The maximum number of iterations allowed for the layout procedure to run |
0 |
|
boolean |
whether to use "smart" layout or "simple" |
false |
pKa options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
string |
pKa model type |
simple |
|
int |
max level for advanced model |
0 |
|
int |
min level for advanced model |
0 |
Reaction Products Enumeration and Transformation¶
Name |
Type |
Short description |
Default |
---|---|---|---|
int |
Maximum level of representing product like a monomer (works only with ``rpe-multistep-reactions enabled``). |
2 |
|
boolean |
Enable multistep reactions (Products of the reaction can take part in further reactions) |
false |
|
enum (grid, one-tube) |
Monomers mixing mode |
grid |
|
boolean |
Enable intramolecular reactions, where one molecule of monomers can play role of two (or more) reactants |
false |
|
int |
Maximum amount of generated products. |
1000 |
|
boolean |
Enable layout after product enumeration |
true |
|
boolean |
Enable layout after transformation. |
true |
Rendering options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
string |
Image file format. |
automatic |
|
size |
Width and height of target image. |
auto |
|
integer |
Desired average bond length in pixels |
100 |
|
float |
Set the thickness of bonds and atom labels to X/30 of the average bond length. |
1.0 |
|
int |
Image width |
auto |
|
int |
Image height |
auto |
|
int |
Maximum image width |
auto |
|
int |
Maximum image height |
auto |
|
size |
Horizontal and vertical margins around the image, in pixels. |
auto |
|
boolean |
Turn on atom coloring, e.g. nitrogen is blue, oxygen is red, etc. |
false |
|
coloring |
The default color for atoms and bonds. |
black (0, 0, 0) |
|
color |
Background color. |
transparent |
|
enum |
Atom label rendering mode |
terminal-hetero |
|
offset |
Offset for the rendering area |
0, 0 |
|
string |
Put a comment at the top or bottom of the image |
None |
|
integer |
Font size for the comment in absolute units, roughly equal to the height in pixels. |
20 |
|
enum |
Comment alignment |
center |
|
color |
Color to use for the comment. |
black |
|
float |
Relative bond line width |
1.0 |
|
enum |
top or bottom. |
bottom |
|
integer |
Vertical space (in pixels) between the comment and the rendered structure or reaction. |
0 |
|
boolean |
Show implicit hydrogens on visible atoms. |
True |
|
boolean |
Show atom numbers (for debugging purposes only). |
False |
|
boolean |
Show bond numbers (for debugging purposes only). |
False |
|
boolean |
Show atom and bond numbers starting from one, not from zero. |
False |
|
color |
Atom-by-atom mapping indices color in reactions. |
black |
|
string |
S-group name for atom colors |
none |
|
boolean |
Detect and draw bold bond for Haworth projection |
true |
|
enum |
Reaction catalysts place relative to the reaction arrow |
above-and-below |
|
boolean |
Center double done if there is an attached stereobond |
false |
|
color |
Color for data-sgroups |
black |
|
enum (old, ext, none) |
Stereocenters rendering mode |
old |
|
enum (expand, collapse) |
Superatoms rendering mode |
expand |
|
boolean |
Render explicit valences |
true |
|
color |
The color to be used for highlighting. |
red |
|
boolean |
Enable highlighting with color. |
true |
|
boolean |
Enable highlighting with thick bonds and bold atom labels. |
false |
|
boolean |
Always show labels of highlighted atoms. |
False |
Standardize options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
boolean |
Sets or repairs the stereo on a molecule. |
false |
|
boolean |
Sets all atoms and bonds to NoStereo. |
false |
|
boolean |
Removes all relative stereo groupings. |
false |
|
boolean |
Sets all atoms and bonds marked UnknownStereo to NoStereo. |
false |
|
boolean |
Sets all atoms marked UnknownStereo to NoStereo. |
false |
|
boolean |
Sets all bonds marked UnknownStereo to NoStereo. |
false |
|
boolean |
Sets all bonds marked CisStereo or TransStereo to UnknownStereo. |
false |
|
boolean |
Uses 2D coordinates and up/down bond markings (or 3D coordinates) to assign the stereochemistry of the atoms or bonds. |
false |
|
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 |
|
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 |
|
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 |
|
boolean |
Sets the charges on a molecule to a standard form. |
false |
|
boolean |
Sets all formal charges to zero. |
false |
|
boolean |
Converts directly bonded zwitterions (positively charged atom bonded to negatively charged atom, A+B-) to the neutral representation (A=B). |
false |
|
boolean |
Translates a molecule so its geometric center lies at the origin. |
false |
|
boolean |
Removes fragments that consist of only a single heavy atom. |
false |
|
boolean |
Keeps only the smallest fragment in the molecule. |
false |
|
boolean |
Keeps only the largest fragment in the molecule. |
false |
|
boolean |
Removes the largest fragment in the molecule. |
false |
|
boolean |
Sets all x, y, z coordinates to zero. |
false |
|
boolean |
Finds atoms with triple bonds and non-linear geometry and fixes them so that the bond angles are 180 degrees. |
false |
|
boolean |
Finds atoms with two double-bonds and non-linear geometry and fixes them so that the bond angles are 180 degrees. |
false |
|
boolean |
Deletes all atoms and bonds in the molecule, keeping the molecule object in the data record. |
false |
|
boolean |
Converts all non-Hydrogen atoms atoms in the molecule to carbon. |
false |
|
boolean |
Converts all non-Hydrogen atoms in the molecule to the A query atom type. |
false |
|
boolean |
Converts all non-Carbon, non-Hydrogen atoms in the molecule to the Q query atom type. |
false |
|
boolean |
Converts all bonds in the molecule to single bonds. |
false |
|
boolean |
Clears any highlight colors from atoms and bonds. |
false |
|
boolean |
Clears any atom valence query features and resets all implicit hydrogen counts to their standard values. |
false |
|
boolean |
Clears all isotope markings from atoms. |
false |
|
boolean |
Clears all explicit zero-order coordination bonds of dative type (V3000 type-9 bonds). |
false |
|
boolean |
Clears all explicit zero-order hydrogen bonds (V3000 type-10 bonds). |
false |
|
boolean |
Create coordination bond (zero-order bond) instead of wrong co-valent bond. |
false |
|
boolean |
Create hydrogen bond (zero-order bond) instead of wrong co-valent bond. |
false |
Stereocenters options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
boolean |
When reading a Molfile/Rxnfile with incorrectly marked stereobonds, ignore them rather than raise an error. |
false |
|
boolean |
Treat stereobond direction bond not only for a pointed stereocenter, but for the neighbour as well. |
false |
|
boolean |
Detect Haworth projection |
false |
Substructure matching options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
enum |
Defines how the uniqueness of a substructure match is determined when counting or iterating unique matches. |
atoms |
|
int |
The maximum number of embeddings allowed to enumerate when counting all embeddings. |
0 |
Timeout options¶
Name |
Type |
Short description |
Default |
---|---|---|---|
integer |
Timeout (is ms) for Indigo operation. Zero means no timeout. |
0 |
|
integer |
Timeout (is ms) for atom-to-atom mapping computation operation. Zero means no timeout. |
0 |