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These
pages discuss the development of new force field
assemblers.
The
Development link below will bring you to the pages
that discuss the development of new force field
assemblers. Force field assemblers are written in
Python (as objects and as procedures) and installed
as part of the Yup package. (This section is out of date.)
ENVIRONMENT
How to set up your environment for Yup development.
UTILITIES
There
are a number of modules that can be used as building blocks in the
construction of force field assemblers.
FFA provides the base class and the most basic of methods of a force field assembler. This module replaces Yup.Tools.FFA.
HookeFFA
provides an add-on to the FFA class. It will add the Hooke term to the
growing model and it provides for the addition of the individual
interactions of the term.
NonbondXFFA
provides an add-on to the FFA class. It will add one of two nonbond
terms that are based on the exclusion atom type. It can also generate an
exclusion list based on the close contacts in the initial conformation.
Chains ... This module replaces Yup.Tools.Chains and Yup.Tools.LinSeq.
PDBPartMap
is a module that provides a bridge between the Brookhaven PDB format
and YUP Models. The module provides several functions to convert
between PDB files and YUP Model objects.
Other modules that can be used to construct a force field assembler can be found in the Yup/Tools/ directory.
EXAMPLE
Worm is a force field assembler for a simple model type built on an older version of the Chains module. It is used here as an example.
MODEL TYPES
Model types that have found real-life use are documented in the User Manual.
rrDNAv1 is a reduced representation model of duplex DNA
rrRNAv1 is a reduced representation model of RNA and proteins
VirPack is a DNA virus packing model
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