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.gameld	GaMELD Implementation Module.
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