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集成/传统嵌合体扩展:分子集成数据和传统建模程序的标准化用户与程序员界面。

The Ensemble/Legacy Chimera extension: standardized user and programmer interface to molecular Ensemble data and Legacy modeling programs.

作者信息

Konerding D E

机构信息

Graduate Group in Biophysics, UCSF 94143-0446, USA.

出版信息

Pac Symp Biocomput. 2000:254-65. doi: 10.1142/9789814447331_0024.

Abstract

Ensemble/Legacy is a toolkit extension of the Object Technology Framework (OTF) that exposes an object oriented interface for accessing and manipulating ensembles (collections of molecular conformations that share a common chemical topology) and driving Legacy programs (such as MSMS, AMBER, X-PLOR, CORMA/MARDIGRAS, Dials and Windows, and CURVES). Ensemble/Legacy provides a natural programming interface for running Legacy programs on ensembles of molecules and accessing the resulting data. Using the OTF reduces the time cost of developing a new library to store and manipulate molecular data and also allows Ensemble/Legacy to integrate into the Chimera visualization program. The extension to Chimera exposes the Legacy functionality using a graphical user interface that greatly simplifies the process of modeling and analyzing conformational ensembles. Furthermore, all the C++ functionality of the Ensemble/Legacy toolkit is "wrapped" for use in the Python programming language. More detailed documentation on using Ensemble/Legacy is available online (http:¿picasso.nmr.ucsf.edu/dek/ensemble. html).

摘要

Ensemble/Legacy是对象技术框架(OTF)的一个工具包扩展,它提供了一个面向对象的接口,用于访问和操作集合(共享共同化学拓扑结构的分子构象集合)以及驱动传统程序(如MSMS、AMBER、X-PLOR、CORMA/MARDIGRAS、Dials和Windows以及CURVES)。Ensemble/Legacy为在分子集合上运行传统程序并访问结果数据提供了一个自然的编程接口。使用OTF减少了开发用于存储和操作分子数据的新库的时间成本,并且还允许Ensemble/Legacy集成到Chimera可视化程序中。对Chimera的扩展通过图形用户界面展示了传统功能,这极大地简化了构象集合的建模和分析过程。此外,Ensemble/Legacy工具包的所有C++功能都被“包装”起来以便在Python编程语言中使用。有关使用Ensemble/Legacy的更详细文档可在线获取(http:¿picasso.nmr.ucsf.edu/dek/ensemble. html)。

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