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MDTools

The MDTools suite is a collection of programs, scripts, and utilities we provide for researchers to make various modeling and simulation tasks easier, and to provide basic code and utilities which can be built up into larger toolsets. Each tool, script, or library is listed below and has its own separate distribution, documentation, etc. The programs in this collection are provided for the benefit of the research community, but are not officially supported unless otherwise stated. Each program may have a software license and/or citation suggestions which should be listed on its web page.

Simulation Tools

• CatDCD - Concatenates DCD multiple trajectory files, can select subset of atoms, think of Unix "cat".
• Chemical2vmd - Lets VMD act as a helper application for chemical/x-vmd MIME type in web browsers
• Conect2psf - Converts PDB "CONECT" records into a "PSF" file for proper bond display in VMD
• FlipDCD/FixDCD - DCD trajectory file endianism and header conversion
• Ionize - Parallelized ion placement tool
• JMV: Java Molecular Viewer - JMV is a molecular viewer written in Java and Java3D. JMV is designed to be an easy-to-use platform neutral molecular visualization tool, which can be used standalone or integrated into other programs.
• MDAPI - Application programming interface for molecular dynamics simulation engines
• MDEnergy - Calculate energies from DCD or PDB files
• MDTools for Python - Protein structure and dynamics analysis classes
• MDX - Collection of C libraries to enable development of methods for molecular dynamics of biomolecules
• MatDCD - A Matlab package for reading and writing DCD format trajectory files
• Mindy - A "minimal" molecular dynamics program based on the NAMD source code
• Mol_Volume - A program for calculating macromolecular volume
• PDBCat - A tool for PDB file text processing and conversion
• SODIUM - Arrange ions around biological macromolecules
• volutil - manipuate 3D volumetric data in VMD
• Wat2ions - Places ions in a water bath. A companion program to Delphi.

Web Database Application Framework

• DBIx::Frame - An extension of Perl DBI which a framework with better logging, and standardized interfaces to common operations. The basic framework for the below databases.
  • TCB::Publications - a publications database.
  • TCB::Seminar - a seminar database.
  • TCB::System - A sysadmin database, based on DBIx::Frame. Uses the following sub-packages:
    • TCB::Equipment - Equipment and Software
    • TCB::Loan - Equipment Loans
    • TCB::Help - Help Database
    • TCB::SysLoads - System Loads and Supercomputers
    • TCB::PortMap - Port Map
    • TCB::System::Obsolete - Obsolete Tables
  • TCB::Conference - a conference registration database.
  • TCB::Library - a library book database.
  • TCB::AddressBook - a basic address book.
  • TCB::mysql - interface to the mysql authorization database.

Web, Programming, and Administrative Tools

• TCB Script Library - small scripts that are too small to package separately, but may still be useful to many people.
• TapeChanger::MTX - Perl module to control tape changers, using the MTX package.
• TCB::Backup - perl scripts for performing our backups.
• TCB::RSS - code to manage RSS feeds and lists of updated web pages.
• Mail::SpamAssassin::UIUC - use the campus spam filtering service with SpamAssassin
• TCB::Internal - Perl module for performing TCB web page layouts
• TCB::AddUser - Perl module for adding and managing users
• CGI::SHTML - Perl module for parsing Server-Side Includes.
• TCB::Webdav - mount webdav partitions on Linux boxes, specifically BioCoRE and Netfiles.
• HTML::FormRemove - Perl module for removing form tags from HTML.
• make_tn - a script used to create thumbnail images and a web page to index them
• Projector - RS-232 control/automation software for Electrohome Marquee series CRT projectors
• SoftDB - A web-based, medium scale, field-specific software database
• Sysload - Machine load monitoring system for clusters, departments
• Usagemon - Software usage/event tracking system
• Swing Test - Java Swing Detection Applet for Web Browsers