Tools and data formats for chemical data handling

From BlueObelisk

Enabling chemists to send experimental or theoretical data together with a publication requires software (commercial and open access) which can create, handle or transform chemistry related data. This includes chemical drawings, reactions, spectral data and chemical property data.

Data for publication supplements should be submitted in open data formats (XML, CML, ThermoML, JCAMP) or at least in data formats which are well defined (like SD format V3000).Chemical data supplements should not be submitted in PDF format, a format which destroys chemical information and hinders automated machine readability. The publishing of chemical molecule and reaction drawings as picture data (TIFF, BMP, PNG) is needed for the print process, but breaks any simple computer capturing process. Instead such chemical bitmap data needs to be run through an optical character recognition process (OCR) to capture the chemical formulas. This process is not error-free, has a poor accuracy and would not be needed if the chemical meta data is submitted as CML.

Every modern chemistry software can export CML for molecule and reaction drawings and every software which captures experimental thermodynamic or spectroscopic data must support open data exchange formats (JCAMP, netCDF, ThermoML and others).

Contents 1 Tools 1.1 Molecule drawings 1.2 Chemical reaction drawings 1.3 Building and visualising molecules 1.4 Chemical file format converters 1.5 Chemical property data handling and storage 1.6 Spectral data and hyphenated techniques data 2 Data Formats 2.1 Molecular data 2.2 Quantum Chemistry 2.3 Nuclear Magnetic Resonance (NMR) 2.4 Mass Spectrometry (IR) 2.5 Infrared Data (IR) 2.6 Optical Spectroscopy in general 2.7 Crystal Structures 2.8 GC-MS data 2.9 LC-MS data 2.10 Thermodynamic Property Data

Tools

Molecule drawings

This section includes tools and data formats for molecules (mol, sdf, cml, SMILES) and reaction data (rnx, rdx, cml, SMARTS, SMIRKS). Chemical drawings should be exported at CML (Chemical markup language) or mol format. No software or vendor specific format or even worse picture formats (BMP, JPEG, TIFF) should be used. If possible a list of InChI codes (InChIKey) should be created from all molecules. Examples see below.

Name	Vendor	Open/Closed Source	Operating System	Note
ISISDraw	MDL	Closed	Windows software	(deprecated no CML import/export; copy/paste into other programs is possible)
ChemDraw	CambridgeSoft	Closed	Windows software
ChemSketch	ACDLabs	Closed	Windows software
MarvinSketch	BioRad	Closed	Windows
KnowItAll	BioRad	Closed	Windows
XDrawChem	[1]	Open	Windows/LINUX/OSX
JChemPaint	[2]	Open	Platform Independent
Bioclipse	[3]	Open	Windows/Linux/OS-X

Chemical reaction drawings

Chemical drawings should be exported into CML or RNX format. Examples see below.

Name	Vendor	Open/Closed Source	Operating System	Note
ISISDraw	MDL	Closed	Windows software	(deprecated no CML import/export; copy/paste into other programs is possible)
ChemDraw	CambridgeSoft	Closed	Windows software
ChemSketch	ACDLabs	Closed	Windows software
MarvinSketch	BioRad	Closed	Windows
KnowItAll	BioRad	Closed	Windows
JChemPaint	[4]	Open	Platform Independent
Bioclipse	[5]	Open	Windows/Linux/OS-X

Building and visualising molecules

The below table provides is only intended to provide an overview of the functionality of a limited number of codes. The pages linked to in the "Special Features" section are places for users/developers to highlight particular strengths or unique features of a code.

For a more comprehensive list of the various builders and visualisers that are available, please see the Linux4Chemistry list or Mario Valle's list of Free Chemistry Visualisation Tools.

Program	Building				Visualising			Platforms			Open	Special Features
	Small Mol.	Large Struct.	Periodic Struct.	Internal Minimiser	Molecules	Isosurfaces	Vector Fields	Windows	Mac OSX	Linux
Aten	y	y	y	y	y	y	-	-	y	y	?	AtenFeatures
Avogadro	y	y	y	y	y	y	-	y	y	y	y	AvogadroFeatures
CCP1GUI	y	-	-	y	y	y	y	y	y	y	?	CCP1GUIFeatures
Jmol	y	y	y	y	y	y	-	y	y	y	y	JmolFeatures
Molden	y	-	-	y	y	y	-	y	y	y	?	MoldenFeatures
Molekel	-	-	-	-	y	y	-	y	y	y	?	MolekelFeatures
Zeobuilder	y	y	y	-	y	-	-	-	-	y	?	ZeobuilderFeatures
Jamberoo	y				y			y	y	y	y	ZeobuilderFeatures

Chemical file format converters

Such converter tools can be used to convert chemical data into accepted data formats (CML, MOL, SDF, PDB).

• OpenBabel an open source project - OpenBabel
• Molconvert a free converter - Molconvert

Chemical property data handling and storage

Pure experimental and calculated molecular property data (mp, bp, logP, pKa, solubility, toxicity, molecular descriptors, toxicity data) should be supplied in open data formats like XML, allowed but discouraged are also TXT (TAB separeated) or XLS (BIFF4 or later) format. If molecular data is available the files should can be exported in SDF format together with molecular information. Forbidden are supplements in PDF format. Large files should be compressed in .gz or .zip format.

Name	Vendor	Open/Closes Source	Note
Bioclipse	Bioclipse team	Open
EXCEL	Microsoft	Closed
Calc Spreadsheet	OpenOffice	Open
Instant-JChem	ChemAxon	Closed
ACDLabs		Closed	several spectral data packages
7ZIP		?	free compression and decompression tool for WIN/LINUX/OSX
TRC		?	tools for ThermoML conversion, capturing of experimental data and data format conversions

Spectral data and hyphenated techniques data

Here we are talking about NMR, MS, UV, IR, GC-MS, LC-MS, LC-UV.

• Vendor specfic software (hardware dependent)
• BioClipse - BioClipse team
• ACDLabs - several spectral data packages
• GRAMS - Thermo Grams/AI

Data Formats

Molecular data

Allowed but discouraged are vendor specific formats (like .skc in case of ISIS Draw or SMILES). Large files should be compressed in .gz format (GNU ZIP) or .zip format.

• CML (Chemical Markup Language)
• SD file format (V2000, V3000 form MDL)
• MOL format (MDL)
• PDB format
• SMARTS (Daylight)
• InChI (IUPAC and NIST)
• InChIKey (IUPAC and NIST) short InChI hash code - IUPAC

Quantum Chemistry

• Gaussian
  • Cubefile Format
    • Gaussian 03 Online Manual
    • http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube
    • http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
    • http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
    • gcube2plot source code

• GAMESS-UK
  • GukLogFile
  • GAMESS-UK Punchfile

• GAMESS - the US version GAMESS manual
  • log file
  • dat file
  • irc file

Nuclear Magnetic Resonance (NMR)

• JCAMP

Mass Spectrometry (IR)

• JCAMP

Infrared Data (IR)

• JCAMP

Optical Spectroscopy in general

• JCAMP

Crystal Structures

• CIF
• PDB

GC-MS data

• netCDF
• mzXML

LC-MS data

• netCDF
• mzXML

Thermodynamic Property Data

• ThermoML - IUPAC and NIST standard format for thermodynamic property data (bp, entropy, solubility and 120 other properties)

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