SVG 2D depiction (svg)

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.

Multiple molecules are displayed in a grid of dimensions specified by the -xr and -xc options (number of rows and columns respectively and --rows, --cols with babel). When displayed in most modern browsers, like Firefox, there is javascript support for zooming (with the mouse wheel) and panning (by dragging with the left mouse button).

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.

Note

This is a write-only format.

Write Options

-u

no element-specific atom coloring

Use this option to produce a black and white diagram

-U

do not use internally-specified color

e.g. atom color read from cml or generated by internal code

-b <color>

background color, default white

e.g -xb yellow or -xb #88ff00 -xb none is transparent. Just -xb is black with white bonds. The atom symbol colors work with black and white backgrounds, but may not with other colors.

-B <color>

bond color, default black

e.g -xB yellow or -xB #88ff00

-C

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.

-a

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

-e

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)

-P <num>

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

-h <condition>

highlight mol if condition is met

The condition can use descriptors and properties, See documentation on --filter option for details. To highlight in a particular color, follow the condition by a color.

-i

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.

-j

do not embed javascript

Javascript is not usually embedded if there is only one molecule, but it is if the rows and columns have been specified as 1: -xr1 -xc1

-x

omit XML declaration (not displayed in GUI)

Useful if the output is to be embedded in another xml file.

-X

All atoms are explicitly declared

Useful if we don’t want any extra hydrogens drawn to fill the valence.

-A

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.

-S

Ball and stick depiction of molecules

Depicts the molecules as balls and sticks instead of the normal line style.

Comments

If the input molecule(s) contain explicit hydrogen, you could consider improving the appearance of the diagram by adding an option -d to make it implicit. Hydrogen on hetero atoms and on explicitly drawn C is always shown. For example, if input.smi had 10 molecules:

obabel input.smi -O out.svg -xb -xC -xe

would produce a svg file with a black background, with no explicit terminal carbon, and with an embedded cml representation of each molecule. The structures would be in two rows of four and one row of two.