Several approaches concerning atom type perception have been reported in the last 20 years ( Baber and Hodgkin, 1992 Froeyen and Herdewijn, 2005 Hendlich et al., 1997 Labute, 2005 Meng and Lewis, 1991 Sayle 2001 Zhao et al., 2007). Additional features and details are explained in the available tutorials. Rather we will give an overview with focus on the atom type perception and we provide the source code, not only to enable traceability of the applied methods but also to allow for user contributions and modifications. Thus, it is not possible to describe all features of this toolbox in detail.

The tasks performed by fconv cover a wide range in the field of handling molecular data. Therefore, we developed a new framework which grew rapidly and thus we implemented fconv as a command line front end, featuring easy access to most functions even for users without programming skills. Large-scale libraries like Open Babel ( ) did not fulfill our needs with respect to a flexible novel definition of own atom types and robustness. Ongoing development of several programs in our group demanded for a library that enables a robust handling of molecular data and consistent atom type perception. C++ sources and precompiled executables for LINUX/UNIX, Mac OS and Windows, as well as tutorials are available on. Apart from the predefined mapping of these types onto Sybyl types, the user is able to assign own mappings by providing modified template files, thus allowing for tailor-made atom type sets.Īvailability: fconv is free software available under GNU General Public License.

The atom type classification is based on a consistent assignment of internal atom types, which are by far more differentiated compared with e.g. Typical tasks are as follows: conversion and error correction of formats such as PDB(QT), MOL2, SDF, DLG and CIF extracting ligands from PDB as MOL2 automatic or ligand-based cavity detection rmsd calculation and clustering substructure searches alignment and structural superposition building of crystal packings adding hydrogens calculation of various properties like the number of rotatable bonds molecular weights or vdW volumes. It has become a very robust and comprehensive tool involved in a broad range of computational workflows that are currently applied in our drug design environment. Up to now, it has been developed and extensively tested for 3 years.

Summary: fconv is a program intended for parsing and manipulating multiple aspects and properties of molecular data.

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