Scalable Vector Graphics 2D rendering of molecular structure.
When called from commandline or GUI or otherwise via Convert(), single molecules are displayed at a fixed scale, as in normal diagrams, but multiple molecules are displayed in a table which expands to fill the containing element, such as a browser window. When WriteMolecule() is called directly, without going through WriteChemObject, e.g. via OBConversion::Write(), a fixed size image by default 200 x 200px containing a single molecule is written. The size can be specified by the P output option.
If both -xr and -xc are specified, they define the maximum number of molecules that are displayed. If only one of them is displayed, then the other is calculated so that ALL the molecules are displayed. If neither are specified, all the molecules are output in an approximately square table.
By default, 2D atom coordinates are generated (using gen2D) unless they are already present. This can be slow with a large number of molecules. (3D coordinates are ignored.) Include --gen2D explicitly if you wish any existing 2D coordinates to be recalculated.
This is a write-only format.
no element-specific atom coloring
Use this option to produce a black and white diagram
do not use internally-specified color
e.g. atom color read from cml or generated by internal code
The default is white. The atom colors work with both.
do not draw terminal C (and attached H) explicitly
The default is to draw all hetero atoms and terminal C explicitly, together with their attched hydrogens.
draw all carbon atoms
So propane would display as H3C-CH2-CH3
|d||do not display molecule name|
|s||use asymmetric double bonds|
|t||use thicker lines|
embed molecule as CML
OpenBabel can read the resulting svg file as a cml file.
|p <num>||px Scale to bond length(single mol only)|
px Single mol in defined size image
The General option –px # is an alternative to the above.
|c <num>||number of columns in table|
|c||ols<num> number of columns in table(not displayed in GUI)|
|r <num>||number of rows in table|
|r||ows<num> number of rows in table(not displayed in GUI)|
|N <num>||max number objects to be output|
|l||draw grid lines|
add index to each atom
These indices are those in sd or mol files and correspond to the order of atoms in a SMILES string.
omit XML declaration (not displayed in GUI)
Useful if the output is to be embedded in another xml file.
display aliases, if present
This applies to structures which have an alternative, usually shorter, representation already present. This might have been input from an A or S superatom entry in an sd or mol file, or can be generated using the –genalias option. For example:
obabel -:"c1cc(C=O)ccc1C(=O)O" -O out.svg --genalias -xA
would add a aliases COOH and CHO to represent the carboxyl and aldehyde groups and would display them as such in the svg diagram. The aliases which are recognized are in data/superatom.txt, which can be edited.