Chemical file format
Encyclopedia
This article discusses some common molecular file formats, including usage and converting between them.
or streams and many formats have been created, with varying degrees of documentation. The format can be found by three means (see chemical MIME section)
(CML) is an open standard for representing molecular and other chemical data. The open source project includes XML Schema, source code for parsing and working with CML data, and an active community. The articles Tools for Working with Chemical Markup Language and XML for Chemistry and Biosciences discusses CML in more detail. CML data files are accepted by many tools, including JChemPaint
, Jmol
, XDrawChem
and MarvinView.
is commonly used for proteins but it can be used for other types of molecules as well. It was originally designed as, and continues to be, a fixed-column-width format and thus officially has a built-in maximum number of atoms, of residues, and of chains; this currently results in splitting very large structures such as ribosomes into multiple files (e.g., 3I1M, 3I1N, 3I1O, 3I1P). However, many tools can read files that exceed those limits. Some PDB files contain an optional section describing atom connectivity as well as position. Because these files are sometimes used to describe macromolecular assemblies or molecules represented in explicit solvent, they can grow very large and are often compressed. Some tools, such as Jmol and KiNG, can read PDB files in gzipped format. The PDB maintains the specifications of the PDB file format and its XML alternative, PDBML. There was a fairly major change in PDB format specification (to version 3.0) in August 2007, and a remediation of many file problems in the existing database. The typical file extension for a PDB file is .pdb, although some older files use .ent or .brk. Some molecular modeling tools write nonstandard PDB-style files that adapt the basic format to their own needs.
simulations, so it allows for additional numerical precision and optionally retains information about particle velocity
as well as position at a given point in the simulation trajectory. It does not allow for the storage of connectivity information, which in GROMACS is obtained from separate molecule and system topology files. The typical file extension for a GROMACS file is .gro.
molecular dynamics package can read and write a number of standard chemical and biochemical file formats; however, the CARD (coordinate) and PSF (protein structure
file) are largely unique to CHARMM. The CARD format is fixed-column-width, resembles the PDB format, and is used exclusively for storing atomic coordinates. The PSF file contains atomic connectivity information (which describes atomic bonds) and is required before beginning a simulation. The typical file extensions used are .crd and .psf respectively.
software can use OpenBabel to import and export a number of file formats. However, by default, it uses the GPR format. This file is composed of several parts, separated by a tag (!Header, !Info, !Atoms, !Bonds, !Coord, !PartialCharges and !End).
The proposed MIME type for this format is application/x-ghemical.
(SLN) is a chemical line notation
. Based on SMILES, it incorporates a complete syntax for specifying relative stereochemistry. SLN has a rich query syntax that allows for the specification of Markush queries. The syntax also supports the specification of combinatorial libraries of CD.
Example SLNs
(SMILES) is a line notation
for molecules. SMILES strings include connectivity but do not include 2D or 3D coordinates.
Hydrogen atoms are not represented. Other atoms are represented by their element symbols B, C, N, O, F, P, S, Cl, Br, and I. The symbol "=" represents double bonds and "#" represents triple bonds. Branching is indicated by . Rings are indicated by pairs of digits.
Some examples are
is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates.
formats, like the Structure Data Format (SDF) files. They are text files that adhere to a strict format for representing multiple chemical structure records and associated data fields. The format was originally developed and published by Molecular Design Limited (MDL).
MOL is another file format from MDL. It is documented in Chapter 4 of the white paper Media:MDL CTfile Formats.
PubChem also has XML and ASN1 file formats, which are export options from the PubChem online database. They are both text based (ASN1 is most often a binary format).
There are a large number of other formats listed in the table below
and JOELib
are freely available open source tools specifically designed for converting between file formats. Their chemical expert systems support a large atom type conversion tables.
babel -i input_format input_file -o output_format output_file
For example, to convert the file epinephrine.sdf in SDF to CML use the command
babel -i sdf epinephrine.sdf -o cml epinephrine.cml
The resulting file is epinephrine.cml.
A number of tools intended for viewing and editing molecular structures are able to read in files in a number of formats and write them out in other formats. The tools JChemPaint
(based on the Chemistry Development Kit
), XDrawChem
(based on OpenBabel
), Chime
, Jmol
and Mol2mol fit into this category.
MDL MOL file can be converted to wikipedia
recommended SVG graphics format by Mol2Svg converter freeware.
types to chemical streams.
The definitive specification is at http://www.ch.ic.ac.uk/chemime/ which is updated when major new types appear.
on your system. Programs can then register as viewer, editor or processor for these formats so that full support for
chemical MIME types is available.
chemical-mime-data: http://downloads.sourceforge.net/chemical-mime/
Distinguishing formats
Chemical information is usually provided as filesComputer file
A computer file is a block of arbitrary information, or resource for storing information, which is available to a computer program and is usually based on some kind of durable storage. A file is durable in the sense that it remains available for programs to use after the current program has finished...
or streams and many formats have been created, with varying degrees of documentation. The format can be found by three means (see chemical MIME section)
- file extension (usually 3 letters). This is widely used, but fragile as common suffixes such as ".mol" and ".dat" are used by many systems, including non-chemical ones.
- self-describing files where the format information is included in the file. Examples are CIF and CML.
- chemical/MIME type added by a chemically-aware server.
Chemical Markup Language
Chemical Markup LanguageChemical Markup Language
CML is an approach to managing molecular information using tools such as XML and Java. It was the first domain specific implementation based strictly on XML, first based on a DTD and later on XML Schema, the most robust and widely used system for precise information management in many areas...
(CML) is an open standard for representing molecular and other chemical data. The open source project includes XML Schema, source code for parsing and working with CML data, and an active community. The articles Tools for Working with Chemical Markup Language and XML for Chemistry and Biosciences discusses CML in more detail. CML data files are accepted by many tools, including JChemPaint
JChemPaint
JChemPaint is an editor and viewer for chemical structures in 2D.It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems...
, Jmol
Jmol
Jmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...
, XDrawChem
XDrawChem
XDrawChem is a free software program for drawing chemical structural formulas, available for Windows, Unix, and Mac OS. It is distributed under the GNU GPL.- Major features :* Fixed length and fixed angle drawing* Automatic alignment of figures...
and MarvinView.
Protein Data Bank Format
The Protein Data Bank FormatProtein Data Bank (file format)
The Protein Data Bank file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed...
is commonly used for proteins but it can be used for other types of molecules as well. It was originally designed as, and continues to be, a fixed-column-width format and thus officially has a built-in maximum number of atoms, of residues, and of chains; this currently results in splitting very large structures such as ribosomes into multiple files (e.g., 3I1M, 3I1N, 3I1O, 3I1P). However, many tools can read files that exceed those limits. Some PDB files contain an optional section describing atom connectivity as well as position. Because these files are sometimes used to describe macromolecular assemblies or molecules represented in explicit solvent, they can grow very large and are often compressed. Some tools, such as Jmol and KiNG, can read PDB files in gzipped format. The PDB maintains the specifications of the PDB file format and its XML alternative, PDBML. There was a fairly major change in PDB format specification (to version 3.0) in August 2007, and a remediation of many file problems in the existing database. The typical file extension for a PDB file is .pdb, although some older files use .ent or .brk. Some molecular modeling tools write nonstandard PDB-style files that adapt the basic format to their own needs.
GROMACS format
The GROMACS file format family was created for use with the molecular simulation software package GROMACS. It closely resembles the PDB format but was designed for storing output from molecular dynamicsMolecular dynamics
Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
simulations, so it allows for additional numerical precision and optionally retains information about particle velocity
Velocity
In physics, velocity is speed in a given direction. Speed describes only how fast an object is moving, whereas velocity gives both the speed and direction of the object's motion. To have a constant velocity, an object must have a constant speed and motion in a constant direction. Constant ...
as well as position at a given point in the simulation trajectory. It does not allow for the storage of connectivity information, which in GROMACS is obtained from separate molecule and system topology files. The typical file extension for a GROMACS file is .gro.
CHARMM format
The CHARMMCHARMM
CHARMM is the name of a widely used set of force fields for molecular dynamics as well as the name for the molecular dynamics simulation and analysis package associated with them...
molecular dynamics package can read and write a number of standard chemical and biochemical file formats; however, the CARD (coordinate) and PSF (protein structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
file) are largely unique to CHARMM. The CARD format is fixed-column-width, resembles the PDB format, and is used exclusively for storing atomic coordinates. The PSF file contains atomic connectivity information (which describes atomic bonds) and is required before beginning a simulation. The typical file extensions used are .crd and .psf respectively.
Ghemical file format
The GhemicalGhemical
Ghemical is a computational chemistry software package written in C++ and released under the GNU GPL. The program has GUI based on GTK+2 and supports quantum mechanical and molecular mechanic models, with geometry optimization, molecular dynamics, and a large set of visualization tools...
software can use OpenBabel to import and export a number of file formats. However, by default, it uses the GPR format. This file is composed of several parts, separated by a tag (!Header, !Info, !Atoms, !Bonds, !Coord, !PartialCharges and !End).
The proposed MIME type for this format is application/x-ghemical.
SYBYL Line Notation
SYBYL Line NotationSYBYL Line Notation
The SYBYL line notation or SLN is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings....
(SLN) is a chemical line notation
Line notation
Line notation is a typographical notation system using ASCII characters, most often used for chemical nomenclature.Line notation is a word and symbol description of an electrochemical cell widely used in chemistry.-Chemistry:...
. Based on SMILES, it incorporates a complete syntax for specifying relative stereochemistry. SLN has a rich query syntax that allows for the specification of Markush queries. The syntax also supports the specification of combinatorial libraries of CD.
Example SLNs
| Description | SLN String |
|---|---|
| Benzene Benzene Benzene is an organic chemical compound. It is composed of 6 carbon atoms in a ring, with 1 hydrogen atom attached to each carbon atom, with the molecular formula C6H6.... |
C[1]H:CH:CH:CH:CH:CH:@1 |
| Alanine Alanine Alanine is an α-amino acid with the chemical formula CH3CHCOOH. The L-isomer is one of the 20 amino acids encoded by the genetic code. Its codons are GCU, GCC, GCA, and GCG. It is classified as a nonpolar amino acid... |
NH2C[s=n]H(CH3)C(=O)OH |
| Query showing R sidechain | R1[hac>1]C[1]:C:C:C:C:C:@1 |
| Query for amide/sulfamide | NHC=M1{M1:O,S} |
SMILES
The Simplified Molecular Input Line Entry SpecificationSimplified molecular input line entry specification
The simplified molecular-input line-entry specification or SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings...
(SMILES) is a line notation
Line notation
Line notation is a typographical notation system using ASCII characters, most often used for chemical nomenclature.Line notation is a word and symbol description of an electrochemical cell widely used in chemistry.-Chemistry:...
for molecules. SMILES strings include connectivity but do not include 2D or 3D coordinates.
Hydrogen atoms are not represented. Other atoms are represented by their element symbols B, C, N, O, F, P, S, Cl, Br, and I. The symbol "=" represents double bonds and "#" represents triple bonds. Branching is indicated by . Rings are indicated by pairs of digits.
Some examples are
| Name | Formula | SMILES String |
|---|---|---|
| Methane Methane Methane is a chemical compound with the chemical formula . It is the simplest alkane, the principal component of natural gas, and probably the most abundant organic compound on earth. The relative abundance of methane makes it an attractive fuel... |
CH4 | C |
| Ethanol Ethanol Ethanol, also called ethyl alcohol, pure alcohol, grain alcohol, or drinking alcohol, is a volatile, flammable, colorless liquid. It is a psychoactive drug and one of the oldest recreational drugs. Best known as the type of alcohol found in alcoholic beverages, it is also used in thermometers, as a... |
C2H6O | CCO |
| Benzene Benzene Benzene is an organic chemical compound. It is composed of 6 carbon atoms in a ring, with 1 hydrogen atom attached to each carbon atom, with the molecular formula C6H6.... |
C6H6 | C1=CC=CC=C1 or c1ccccc1 |
| Ethylene Ethylene Ethylene is a gaseous organic compound with the formula . It is the simplest alkene . Because it contains a carbon-carbon double bond, ethylene is classified as an unsaturated hydrocarbon. Ethylene is widely used in industry and is also a plant hormone... |
C2H4 | C=C |
XYZ
The XYZ file formatXYZ file format
The XYZ file format is a chemical file format. There is no formal standard and several variations exist, but a typical XYZ format specifies the molecule geometry by giving the number of atoms with Cartesian coordinates that will be read on the first line, a comment on the second, and the lines of...
is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates.
MDL number
The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number.Other Common Formats
One of the widest used industry standards are chemical table fileChemical table file
- File formats :Chemical table files come in various formats. In addition to the formats discussed below, other formats include RGfiles, Rxnfiles, RDfiles, XDfiles and Clipboard.- Molfile :...
formats, like the Structure Data Format (SDF) files. They are text files that adhere to a strict format for representing multiple chemical structure records and associated data fields. The format was originally developed and published by Molecular Design Limited (MDL).
MOL is another file format from MDL. It is documented in Chapter 4 of the white paper Media:MDL CTfile Formats.
PubChem also has XML and ASN1 file formats, which are export options from the PubChem online database. They are both text based (ASN1 is most often a binary format).
There are a large number of other formats listed in the table below
Converting Between Formats
OpenBabelOpenBabel
OpenBabel is free software, a chemical expert system mainly used for converting chemical file formats. Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, and Mac OS...
and JOELib
JOELib
JOELib is a free software chemical expert system mainly used for converting chemical file formats. Because of its strong relationship to informatics, this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix and other systems supporting...
are freely available open source tools specifically designed for converting between file formats. Their chemical expert systems support a large atom type conversion tables.
babel -i input_format input_file -o output_format output_file
For example, to convert the file epinephrine.sdf in SDF to CML use the command
babel -i sdf epinephrine.sdf -o cml epinephrine.cml
The resulting file is epinephrine.cml.
A number of tools intended for viewing and editing molecular structures are able to read in files in a number of formats and write them out in other formats. The tools JChemPaint
JChemPaint
JChemPaint is an editor and viewer for chemical structures in 2D.It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems...
(based on the Chemistry Development Kit
Chemistry Development Kit
The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics. It is available for Windows, Unix, and Mac OS...
), XDrawChem
XDrawChem
XDrawChem is a free software program for drawing chemical structural formulas, available for Windows, Unix, and Mac OS. It is distributed under the GNU GPL.- Major features :* Fixed length and fixed angle drawing* Automatic alignment of figures...
(based on OpenBabel
OpenBabel
OpenBabel is free software, a chemical expert system mainly used for converting chemical file formats. Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, and Mac OS...
), Chime
Chime
-Musical instrument or tone:* Chime , an array of large bells, typically housed in a tower and played from a keyboard.** An instrument of this kind with 23 bells or more is known as a carillon...
, Jmol
Jmol
Jmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...
and Mol2mol fit into this category.
MDL MOL file can be converted to wikipedia
Wikipedia
Wikipedia is a free, web-based, collaborative, multilingual encyclopedia project supported by the non-profit Wikimedia Foundation. Its 20 million articles have been written collaboratively by volunteers around the world. Almost all of its articles can be edited by anyone with access to the site,...
recommended SVG graphics format by Mol2Svg converter freeware.
The Chemical MIME Project
"Chemical MIME" is a de facto approach for adding MIMEMIME
Multipurpose Internet Mail Extensions is an Internet standard that extends the format of email to support:* Text in character sets other than ASCII* Non-text attachments* Message bodies with multiple parts...
types to chemical streams.
This project started in January 1994, and was first announced during the Chemistry workshop at the First WWW International Conference, held at CERN in May 1994. The first version of an Internet draft was published during May–October 1994, and the second revised version during April–September 1995. A paper presented to the CPEP (Committee on Printed and Electronic Publications) at the IUPAC meeting in August 1996 is available for discussion.
| file extension | MIME MIME Multipurpose Internet Mail Extensions is an Internet standard that extends the format of email to support:* Text in character sets other than ASCII* Non-text attachments* Message bodies with multiple parts... type |
proper name | description |
|---|---|---|---|
| alc | chemical/x-alchemy | Alchemy Format | |
| csf | chemical/x-cache-csf | CAChe MolStruct CSF | |
| cbin, cascii, ctab | chemical/x-cactvs-binary | CACTVS format | |
| cdx | chemical/x-cdx | ChemDraw eXchange file | |
| cer | chemical/x-cerius | MSI Cerius II format | |
| c3d | chemical/x-chem3d | Chem3D Format | |
| chm | chemical/x-chemdraw | ChemDraw file | |
| cif | chemical/x-cif | Crystallographic Information File Crystallographic Information File Crystallographic Information File is a standard text file format for representing crystallographic information, promulgated by the International Union of Crystallography . CIF was developed by the IUCr Working Party on Crystallographic Information in an effort sponsored by the IUCr Commission on... , Crystallographic Information Framework |
Promulgated by the International Union of Crystallography |
| cmdf | chemical/x-cmdf | CrystalMaker Data format | |
| cml | chemical/x-cml | Chemical Markup Language Chemical Markup Language CML is an approach to managing molecular information using tools such as XML and Java. It was the first domain specific implementation based strictly on XML, first based on a DTD and later on XML Schema, the most robust and widely used system for precise information management in many areas... |
XML XML Extensible Markup Language is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards.... based Chemical Markup Language Chemical Markup Language CML is an approach to managing molecular information using tools such as XML and Java. It was the first domain specific implementation based strictly on XML, first based on a DTD and later on XML Schema, the most robust and widely used system for precise information management in many areas... . |
| cpa | chemical/x-compass | Compass program of the Takahashi | |
| bsd | chemical/x-crossfire | Crossfire file | |
| csm, csml | chemical/x-csml | Chemical Style Markup Language | |
| ctx | chemical/x-ctx | Gasteiger group CTX file format | |
| cxf, cef | chemical/x-cxf | Chemical eXchange Format | |
| emb, embl | chemical/x-embl-dl-nucleotide | EMBL Nucleotide Format | |
| spc | chemical/x-galactic-spc | SPC format for spectral and chromatographic data | |
| inp, gam, gamin | chemical/x-gamess-input | GAMESS Input format | |
| fch, fchk | chemical/x-gaussian-checkpoint | Gaussian Checkpoint Format | |
| cub | chemical/x-gaussian-cube | Gaussian Cube (Wavefunction) Forma | |
| gau, gjc, gjf | chemical/x-gaussian-input | Gaussian Input Format | |
| gcg | chemical/x-gcg8-sequence | Protein Sequence Format | |
| gen | chemical/x-genbank | ToGenBank Format | |
| istr,ist | chemical/x-isostar | IsoStar Library of Intermolecular Interactions | |
| jdx, dx | chemical/x-jcamp-dx | JCAMP Spectroscopic Data Exchange Format | |
| kin | chemical/x-kinemage | Kinetic (Protein Structure) Images; Kinemage Kinemage A kinemage is an interactive graphic scientific illustration. It often is used to visualize molecules, especially proteins and nucleic acids, although it can also represent other types of 3-dimensional data... |
|
| mcm | chemical/x-macmolecule | MacMolecule File Format | |
| mmd, mmod | chemical/x-macromodel-input | MacroModel MacroModel MacroModel is a computer program for molecular modelling of organic compounds and biopolymers. It features various force fields coupled with energy minimization algorithms for the prediction of geometry and relative conformational energies of molecules... Molecular Mechanics |
|
| mol | chemical/x-mdl-molfile | MDL Molfile | |
| smiles, smi | chemical/x-daylight-smiles | Simplified molecular input line entry specification Simplified molecular input line entry specification The simplified molecular-input line-entry specification or SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings... |
A line notation for molecules. |
| sdf | chemical/x-mdl-sdfile | Structure-Data File | |
| el | chemical/x-sketchel | SketchEl Molecule | |
| ds | chemical/x-datasheet | SketchEl XML DataSheet | |
| inchi | chemical/x-inchi | The IUPAC International Chemical Identifier | |
| jsd, jsdraw | chemical/x-jsdraw | JSDraw native file format |
The definitive specification is at http://www.ch.ic.ac.uk/chemime/ which is updated when major new types appear.
Chemical MIME Support
For Unix/Linux there is a tar.gz available which registers chemical MIME typeson your system. Programs can then register as viewer, editor or processor for these formats so that full support for
chemical MIME types is available.
chemical-mime-data: http://downloads.sourceforge.net/chemical-mime/
Sources of Chemical Data
Here is a short list of sources of freely available molecular data. There are many more resources than listed here out there on the Internet. Links to these sources are given in the references below.- The US National Institute of Health PubChemPubChemPubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information , a component of the National Library of Medicine, which is part of the United States National Institutes of Health . PubChem can...
database is a huge source of chemical data. All of the data is in two-dimensions. Data includes SDF, SMILES, PubChem XML, and PubChem ASN1 formats. - The worldwide Protein Data Bank (wwPDB) is an excellent source of protein and nucleic acid molecular coordinate data. The data is three-dimensional and provided in Protein Data Bank (PDB) format.
- eMoleculesEMoleculeseMolecules is a search engine for chemical molecules. The system was first launched in November 2005.-Database:* The database contains more than 7.0M unique molecules from commercial suppliers, like Acros, ASINEX, ChemBridge, ChemDiv, Comgenex, Enamine Ltd, Fluka, InterBioScreen, Key Organics, Life...
is a commercial database for molecular data. The data includes a two-dimensional structure diagram and a smiles string for each compound. eMolecules supports fast substructure searching based on parts of the molecular structure. - ChemExper is a commercial data base for molecular data. The search results include a two-dimensional structure diagram and a mole file for many compounds.
- New York UniversityNew York UniversityNew York University is a private, nonsectarian research university based in New York City. NYU's main campus is situated in the Greenwich Village section of Manhattan...
Library of 3-D Molecular Structures. - The US Environmental Protection Agency's The Distributed Structure-Searchable Toxicity (DSSTox) Database Network is a project of EPA's Computational Toxicology Program. The database provides SDF molecular files with a focus on carcinogenic and otherwise toxic substances.
See also
- File formatFile formatA file format is a particular way that information is encoded for storage in a computer file.Since a disk drive, or indeed any computer storage, can store only bits, the computer must have some way of converting information to 0s and 1s and vice-versa. There are different kinds of formats for...
- OpenBabelOpenBabelOpenBabel is free software, a chemical expert system mainly used for converting chemical file formats. Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, and Mac OS...
, JOELibJOELibJOELib is a free software chemical expert system mainly used for converting chemical file formats. Because of its strong relationship to informatics, this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix and other systems supporting...
, OELibOELibOELib was an Open Source Cheminformatics library. Its actual GPLed C++ and Java successors are OpenBabel and JOELib. Its commercial successor is called OEChem.- External links :* *... - Chemistry Development KitChemistry Development KitThe Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics. It is available for Windows, Unix, and Mac OS...
- Chemical Markup LanguageChemical Markup LanguageCML is an approach to managing molecular information using tools such as XML and Java. It was the first domain specific implementation based strictly on XML, first based on a DTD and later on XML Schema, the most robust and widely used system for precise information management in many areas...
- Software for molecular modeling
- NCI/CADD Chemical Identifier Resolver
External links
- /chemical/structure Blog at cactus.nci.nih.gov description of a REST-like chemical structure format converter
- Online Molecule Format Converter based on Open Babel
- E-Babel Applet for Online Molecule Format Converter based on Open Babel