meld.system

Module for interacting with MELD systems.

The primary classes are:

• meld.system.meld_system.System is the main class that describes a MELD system. Systems are built using the builder objects described below. Once built, System objects may have a variety of restraints added.

• meld.system.options.RunOptions is a class that specifies options for a MELD run.

• meld.system.state.SystemState is a class that represents the current state of a MELD run.

The main classes to build a system are:

• meld.system.builders.amber.subsystem.AmberSubSystemFromSequence is used to build a sub-system starting from a sequence.

• meld.system.builders.amber.subsystem.AmberSubSystemFromPdbFile is used to build a sub-system from a PDB file.

• meld.system.builders.amber.builder.AmberSystemBuilder is used to combine SybSystems together into a system.

There are a few options for how to couple the temperature to the value of alpha:

• meld.system.temperature.ConstantTemperatureScaler

• meld.system.temperature.LinearTemperatureScaler

• meld.system.temperature.GeometricTemperatureScaler

• meld.system.temperature.REST2Scaler for explicit solvent

Modules

meld.system.amber	A module to read Amber parmtop and crd files
meld.system.builders
meld.system.density
meld.system.indexing	Look up atom and residue indices.
meld.system.mapping	Module to handle sampling the mappings of peaks to atom indices
meld.system.meld_system	A module to define MELD Systems
meld.system.montecarlo	A module to implement basic Monte Carlo moves.
meld.system.options	Module to handle options for a MELD run
meld.system.param_sampling
meld.system.patchers
meld.system.pdb_writer	Module for PDB output
meld.system.restraints	Implements all of the restraints available in MELD.
meld.system.scalers
meld.system.state	A module to define the SystemState
meld.system.temperature	Module to handle temperature scaling