"sdf2svg" - PHP Script to Convert SDF to SVG

Provides a tutorial example on how to download and install sdf2svg, an open source PHP script developed by Ronnie Persson, to convert a molecule structure in a SDF file to a SVG (Scalable Vector Graphics) file.

If you want to convert molecule structures in SDF format to SVG (Scalable Vector Graphics) format to be viewed on Web pages directly, you can download and install the "sdf2svg" open source PHP script developed by Ronnie Persson.

1. Download "df2svg_beta_with_samples.zip" from sourceforge.net/projects/sdf2svg under the "beta_with_sample" folder.

2. Unzip all files from "df2svg_beta_with_samples.zip" into a folder called "sdf2svg". You should see the following contents:

herong$ ls -l sdf2svg
-rwxr-xr-x   1 herong  staff   1141 Apr  6 19:52 index.html
-rwxr-xr-x@  1 herong  staff   3416 Apr  6 19:46 outputsvg.php
-rwxr-xr-x@  1 herong  staff   2311 Apr  6 19:46 sample.php
-rwxr-xr-x@  1 herong  staff  14956 Apr  6 19:46 sample.sdf
-rwxr-xr-x@  1 herong  staff   3463 Apr  6 19:46 sample2.php
drwxr-xr-x@ 12 herong  staff    408 Apr  6 19:46 sdf2svg

3. Move this folder to the Apache Web server. And adjust owership and permission of this folder to be served as PHP scrits.

4. Run the first sample PHP page. You should see a picture of 4 molecules in SVG format converted from a SDF file.

sdf2svg - PHP Script to Convert SDF to SVG
sdf2svg - PHP Script to Convert SDF to SVG

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

SDF (Structure Data File)

 What Is SDF (Structure Data File)

 SDF Format Specification

 What Are CTfile and CTAB

 Convert SDF to SVG using Open Babel

"sdf2svg" - PHP Script to Convert SDF to SVG

 RDKit: Open-Source Cheminformatics Software

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB