vermouth.processors.water_bias module¶
- class vermouth.processors.water_bias.ComputeWaterBias(auto_bias, water_bias, idr_regions)[source]¶
Bases:
Processor
Processor which computes the water bias for the Martini Go and Martini IDP model.
The water bias strength is defined per secondary structure element in water_bias and assigned if auto_bias is set to True. Using the idr_regions argument the water_bias can be changed for intrinsically disordered regions (IDRs). The IDR bias superseeds the auto bias.
This Processor updates the system.gmx_topology_params attribute.
Subclassing¶
If the procedure by which to assign the water bias is to be changed this processor is best subclassed and the assign_residue_water_bias method overwritten.
- param auto_bias:
apply the automatic secondary structure dependent water biasing
- type auto_bias:
bool
- param water_bias:
a dict of secondary structure codes and epsilon value for the water bias in kJ/mol
- type water_bias:
dict[str, float]
- param idr_regions:
list of tuples of residue regions defining the IDRs
- type idr_regions:
list
- param prefix:
prefix of the Go virtual-site atomtypes
- type prefix:
str
- param system:
the system of the molecules is used for storing the nonbonded parameters
- type system:
vermouth.system.System
- assign_residue_water_bias(molecule, res_graph)[source]¶
Assign the residue water bias for all residues with a secondary structure element or that are defined by the region selector. Region selectors supercede the auto assignment.
- Parameters:
molecule (
vermouth.molecule.Molecule
) – the moleculeres_graph (
vermouth.molecule.Molecule
) – the residue graph of the molecule
- remove_cross_nb_interactions(molecule, res_graph)[source]¶
Remove Go bonds between folded and disordered regions of a molecule
- Parameters:
molecule (
vermouth.molecule.Molecule
) – the moleculeres_graph (
vermouth.molecule.Molecule
) – the residue graph of the molecule
- run_system(system)[source]¶
Assign the water bias of the Go model to file. Biasing is always molecule specific i.e. no two different vermouth molecules can have the same bias.
- Parameters:
system (
vermouth.system.System
)