What Are CTfile and CTAB
This section provides a quick introduction of the SDF (Structure Data File) format. An example of SDF file is also provided.
What CTfile (Chemical Table File)?
CTfile referes to six file formats that are used to
store chemical information in a table style.
All CTfile formats shares a common structure called CTAB (Connection Table),
which describes the structural relationships and
properties of a collection of atoms.
Below are short descriptions of CTfile formats:
- Molfile (Molecule File) - Describes a single molecular structure which can
contain disjoint fragments.
A Molfile is a 3-line header and CTAB structure.
- RGfile (Rgroup File) - Describes a single molecular query with Rgroups
(Relationship Groups). Each RGfile is a combination of CTABs defining the
root molecule and each
member of each Rgroup in the query.
- rxnfile (Reaction File) - Contains the structural information for
the reactants and products of a single reaction.
- SDfile (SDF - Structure Data File) - Contains structures and data for any
number of molecules.
A SDfile uses a Molfile and custom data to form a molecule structure.
And multiple molecule structures are concatenated to support multiple molecules.
- RDfile (RDF - Reaction Data File) - Contains reactions as well as molecules,
together with their associated data.
- XDfile (XML Data File) - XML-based data format for transferring recordsets
of structure or reaction information with associated data.
CTfile formats have 2 versions: V3000 and V2000.
For detailed specifications, see "CTfile Formats" at
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 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)
Resources and Tools
Molecule Related Terminologies
Full Version in PDF/EPUB