Molecular Modelling Toolkit
Encyclopedia
The Molecular Modelling Toolkit (MMTK) is an open source
software package written in Python
, which performs common tasks in molecular modelling
.
, MMTK consists of about 18,000 lines of Python code, 12,000 lines of hand-written C code, and some machine-generated C code.
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
software package written in Python
Python (programming language)
Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...
, which performs common tasks in molecular modelling
Molecular modelling
Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...
.
, MMTK consists of about 18,000 lines of Python code, 12,000 lines of hand-written C code, and some machine-generated C code.
Features
- construction of molecular systems, with special support for proteins and nucleic acids
- infinite systems or periodic boundary conditions (orthorhombic elementary cells)
- common geometrical operations on coordinates
- rigid-body fits
- visualization using external PDB and VRML viewers; animation of dynamics trajectories and normal modes
- the AMBER 94 force field, with several options for handling electrostatic interactions
- a deformation force field for fast normal mode calculations on proteins
- energy minimization (steepest descent and conjugate gradient)
- molecular dynamics (with optional thermostat, barostat, and distance constraints)
- normal mode analysis
- trajectory operations
- point charge fits
- molecular surface calculations
- interfaces to other programs
See also
- Software for molecular mechanics modelling