SDF (Structure Data File)
This chapter provides quick introductions about molecules, molecular formula, atomic bonds and molecule structures.
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
- SDF (Structure Data File)
is a file format to store multiple chemical structures records
and their associated data fields.
- Each molecule structure is separated from others by the "$$$$" line
in a SDF file.
- A single molecule structure in a SDF file has 6 blocks:
Header, Counts, Atoms, Bonds, Properties and Custom Fields.
- The key blocks in a SDF file are Counts, Atoms, Bonds, and Properties
which are called CTAB (Connection Table) blocks.
Table of Contents
About This Book
Introduction of Molecules
Molecule Names and Identifications
Molecule Mass and Weight
Protein and Amino Acid
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
Gene and Chromosome
Protein Kinase (PK)
►SDF (Structure Data File)
RDKit: Open-Source Cheminformatics Software
PyMol GUI and CLI
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)
HGNC (HUGO Gene Nomenclature Committee)
Resources and Tools
Molecule Related Terminologies
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