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Personal Chemistry Client (PCC)

FREE software for searching and integrating chemical structures and scientific data

A tool to view and search in (almost) any SDFile!

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PCC allows to search and view chemical structures and associated scientific data.
PCC supports structure based searches including exact match, substructure searches and similarity searches.
PCC allows to perform combined structure based searches and text or numerical searches.
PCC is a generic application that allows , without extensions, to access corporate data.

PCC is targeted for handling small to medium sized compound datasets (up to 5'000 compounds).
PCC is targeted to be used by either a personal scientist, a workgroup or a small company.

NEW: PCC v1.1 (released 22/03/2007)

Major new features:
  • Out of the box loading of MDL SDFiles
  • Validated query input
  • SMILES support for molstructure queries
  • Import/Export of PCC lists
  • enhanced help
Supported data sources
  • Delimited text file
  • Excel
  • Access
  •  MySQL
  • Oracle
  • SQL Server 
Chemical structures are stored in datasource using MDL molfile format.

PCC supports storage of chemical structures and scientific data in different data sources (e.g. molstructures stored in Excel and associated scientific data stored in Oracle or MySQL).

PCC supports access to both local and server (remote) RDBMS databases.

Contact Information

Dr. Alexander Kos

AKos Consulting & Solutions GmbH
Austr. 26
D-79585 Steinen
tel. +49 7627 970068
Fax +49 7627 970067
FaxToMail +49 1805 7447438318


Dr. Hans-Jürgen Himmler


Please use our PCC forum for Q&A

and visit www.openchemsoft.eu

Open Source Software for integrating chemical structures and scientific data.

PCC version 1.0 is FREE software that is licensed  according to the GPL license 2 or later. You can redistribute and/or modify PCC under the terms of the GNU General Public License as published by the Free Software Foundation either version 2 of this license, or any later version.

We are using the Chemistry Development Kit (CDK). This is a library for bio – and chemoinformatics and computational chemistry. The CDK project is hosted at SourceForge.net. The CDK originated in the lab of Christoph Steinbeck, see almost.cubic.uni-koeln.de/cdk/.


Services and Support

We provide services to configure PCC to access your corporate data and to customize PCC for your needs. These services are charged. Normally, we can do this remote with one day consulting costing 850 Euro.

We also offer support for PCC. Supported PCC users  get help and access to PCC bug fixes and enhancements. PCC support is charged.

We also offer maintenance and consulting services for your corporate chemoinformatic systems. Small pharma and biotech companies can use our services to save man power and to draw on our 20 year experience providing chemical information systems to the chemical and pharmaceutical industry.

Hardware and Software requirements

IBM PC or 100% IBM PC-compatible computer. We recommend 256MB RAM.

PCC is only tested on x86 computers.

Supported operating systems:
The Microsoft .NET Framework 2.0 supports the following operating systems: Windows 2000 SP3, Windows 98, Windows 98 2nd Edition, Windows ME, Windows Server 2003, Windows XP SP2.

PCC is tested under Windows XP SP2.  The PCC installation procedure requires 36 MB free hard disk space. Hard disk space required for the .NET 2.0 Framework: 280 MB (x86),
610 MB (x64).

Quick Start

After you have installed PCC, the Visualizer and if required the .Net 2.0 libraries, start PCC. Select first the data source, this is in Excel, click continue and open the demo Excel file.


We offer to use several schemes, in this case there is only one, select the NCI. We use a demo data set of the National Cancer Institute (NCI).


As next step you need to select the source for the structures. In our case the structures are in the same Excel sheet. Click continue, open the demo Excel file. Again, the structures could be in different sheets, we offer one, chose NCI.


Select a form, start with the nci_demo_mixed.frm:


For a substructure search you need to create an index:


If you are using ISIS/Draw make sure you have activated in the setting the options to write to the clipboard.

    select copy Mol/Rxnfile to clipboard

Copy a structure (i.e. benzene) (CTRL-C) and past it into the structure field (CTRL-V) or right click and start the search


Poster presentation

Free chemical structure search in MDL SDFiles using the open source Personal Chemistry Client (PCC)

Hans-Jürgen Himmler and Alexander Kos

AKos Consulting & Solutions Deutschland GmbH (AKos GmbH), Austr. 26, D-79585 Steinen, Germany

corresponding author email

from 3rd German Conference on Chemoinformatics
Goslar, Germany. 11-13 November 2007


Chemistry Central Journal 2008, 2(Suppl 1):P43doi:10.1186/1752-153X-2-S1-P43

The electronic version of this abstract is the complete one and can be found online at: http://www.journal.chemistrycentral.com/content/2/S1/P43

Published: 26 March 2008