Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obabel -o svg" - Molecule Picture in SVG
This section provides a quick introduction on Open Babel 'obabel -o svg' command to generate molecule picture in SVG (Scalable Vector Graphics) format.
If you want to visualize a molecule structure as a 2-Dimensional picture, SVG (Scalable Vector Graphics) is a better format than any other formats like PNG (Portable Network Graphics). This is because SVG pictures are truly scalable. They can be enlarged at any size without losing any resolution.
To learn how to generate a good SVG picture from a molecule structure with the Open Babel "obabel" command, you should look at the SVG help text as shown below:
herong$ obabel -H svg svg SVG 2D depiction Scalable Vector Graphics 2D rendering of molecular structure. When called from command line 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. Write Options e.g. -xu 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 attached 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# px Scale to bond length(single mol only) P# px Single mol in defined size image The General option --px # is an alternative to the above. c# number of columns in table cols# number of columns in table(not displayed in GUI) r# number of rows in table rows# number of rows in table(not displayed in GUI) N# max number objects to be output l draw grid lines h <condition><color> highlight mol if condition is met The condition can use descriptors and properties, See documentation on ``--filter`` option for details. Specifying the highlight color is optional. 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. 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. This format is Write-only
Note that there are some nice features are supported for SVG format
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
►Generating SVG Pictures with Open Babel
►"obabel -o svg" - Molecule Picture in SVG
"obabel -:... -o svg" - Generate SVG from SMILES
"obabel ... -o svg -xi" - Show Atom Indices in SVG
"obabel ... -o svg -xS" - Ball/Stick Depiction in SVG
"obabel ... -o svg -xX" - Hide Implicit H in SVG
"obabel ... -o svg -xC" - Hide Terminal C in SVG
"obabel ... -o svg -xP300" - Control Image Size
"obabel ... -o svg" - Two "svg" XML Tag Levels
"obabel ... -o svg -xd" - Hide Molecule Name
"babel ... -o svg -xd -xP300" - Open Babel 2.4 Bug
Scale SVG Images using "viewBox" Attribute
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
RDKit: Open-Source Cheminformatics Software
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction