Department of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marburg, Germany.
Bioinformatics. 2011 Apr 1;27(7):1021-2. doi: 10.1093/bioinformatics/btr055. Epub 2011 Feb 18.
fconv is a program intended for parsing and manipulating multiple aspects and properties of molecular data. Up to now, it has been developed and extensively tested for 3 years. 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. 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. The atom type classification is based on a consistent assignment of internal atom types, which are by far more differentiated compared with e.g. Sybyl atom types. 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.
fconv is free software available under GNU General Public License. C++ sources and precompiled executables for LINUX/UNIX, Mac OS and Windows, as well as tutorials are available on http://www.agklebe.de.
fconv 是一个旨在解析和操作分子数据的多个方面和属性的程序。到目前为止，它已经开发和测试了 3 年。它已成为一个非常强大和全面的工具，涉及到广泛的计算工作流程，目前应用于我们的药物设计环境中。典型任务如下：转换和纠正 PDB(QT)、MOL2、SDF、DLG 和 CIF 等格式；从 PDB 中提取配体作为 MOL2；自动或基于配体的腔检测；均方根偏差计算和聚类；子结构搜索；对齐和结构叠加；晶体堆积；添加氢；计算各种性质，如可旋转键的数量；分子量或 vdW 体积。原子类型分类基于内部原子类型的一致赋值，与例如 Sybyl 原子类型相比，这些原子类型要精细得多。除了将这些类型预定义映射到 Sybyl 类型之外，用户还可以通过提供修改后的模板文件来分配自己的映射，从而允许定制原子类型集。
fconv 是根据 GNU 通用公共许可证提供的免费软件。C++源代码和适用于 LINUX/UNIX、Mac OS 和 Windows 的预编译可执行文件，以及教程都可以在 http://www.agklebe.de 上获得。
