| Option | Type | Description | Default |
|---|
ignore-stereochemistry-errors | boolean |
When reading a Molfile/Rxnfile with incorrectly marked stereobonds, ignore them rather than raise an error. |
false |
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. Otherwise, an error is raised. |
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 | string |
2000: force saving Molfiles and Rxnfiles to v2000 format, not regarding if there are features that can not be represented in v2000.3000: force saving Molfiles and Rxnfiles to v3000 format, not regarding if there are features that can not be represented in v2000.auto: detect if saving to v3000 is really needed, and then save to v3000. Otherwise, save to v2000.
|
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 |
| Option | Type | Description | Default |
|---|
render-output-format | string |
Obligatory. png, svg, pdf are allowed. On Windows, emf is also allowed. |
- |
render-bond-length | integer |
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. |
100 |
render-image-size | size |
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. |
- |
render-margins | size |
Horizontal and vertical margins around the image, in pixels. |
0x0 |
render-base-color | color |
The default color for atoms and bonds. |
black |
render-background-color | color |
Background color. |
transparent |
render-label-mode | string |
all: show all atomsterminal-hetero: show heteroatoms, terminal atoms, atoms with radical, charge, isotope, explicit valence, and atoms having two adjacent bonds in a linehetero: the same as terminal-hetero, but without terminal atomsnone: hide all labels, show only bonds
|
terminal-hetero |
render-highlighted-atoms-visible | boolean |
Always show labels of highlighted atoms. |
false |
render-implicit-hydrogens-visible | boolean |
Show implicit hydrogens on visible atoms. |
true |
render-superatom-mode | string |
expand: render expanded superatomscollapse: render just the superatoms' names
|
expand |
render-coloring | boolean |
Turn on atom coloring, e.g. nitrogen is blue, oxygen is red, etc. |
false |
render-highlight-thickness-enabled | boolean |
Enable highlighting with thick bonds and bold atom labels. |
false |
render-highlight-color-enabled | boolean |
Enable highlighting with color. |
true |
render-highlight-color | color |
The color to be used for highlighting. |
red |
render-data-sgroup-color | color |
Color of data SGroup labels. |
black |
render-aam-color | color |
Atom-by-atom mapping indices color in reactions. |
black |
render-stereo-style | string |
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.
|
old |
render-relative-thickness | float |
Set the thickness of a bond to X/30 of the average bond length. |
1.0 |
render-catalysts-placement | string |
above: place reaction catalysts above the reaction arrowabove-and-below: place reaction calalysts above and below the reaction arrow
|
above-and-below |
render-comment | string |
Put a single-line 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. |
- |
render-comment-position | string |
top or bottom. |
bottom |
render-comment-offset | integer |
Vertical space (in pixels) between the comment and the rendered structure or reaction. |
0 |
render-comment-alignment | float |
0 is for alignment to the left, 1 is for the alignment to the right, 0.5 is for centering the comment. Note that this setting has no effect if comment is larger than the molecule/reaction rendered. |
0.5 |
render-comment-font-size | integer |
Font size for the comment in absolute units, roughly equal to the height in pixels. |
20 |
render-comment-color | color |
Color to use for the comment. |
black |
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 |
| Option | Type | 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. If not defined, no titles are shown. The special value "^NAME" means to use the molecule's name as its title. |
- |
render-grid-title-alignment | float |
0 is for alignment to the left, 1 is for the alignment to the right, 0.5 is for centering the title. Note that this setting has no effect if the title is larger than the molecule rendered. |
0.5 |
render-grid-title-font-size | integer |
Font size for the title in absolute units, roughly equal to the height in pixels. |
20 |
render-grid-title-offset | integer |
Vertical space (in pixels) between the title and the rendered structure. |
0 |
