You are reading the documentation for version 3.1 of ProMod3. You may also want to read the documentation for: 3.0 1.3 2.0 3.2 2.1

Loading Precomputed Objects

Several data objects are used throughout the loop module. ProMod3 offers to load precomputed instances for direct usage.

promod3.loop.LoadTorsionSampler(seed=0)

Loads and returns a torsion sampler with an amino acid grouping as defined by [solis2006] that has been trained on non-redundant protein structures.

Parameters:seed (int) – Seed for internal random number generator
Returns:The torsion sampler
Return type:TorsionSampler
promod3.loop.LoadTorsionSamplerCoil(seed=0)

Loads and returns a torsion sampler with an amino acid grouping as defined by [solis2006] that has been trained on coil residues of non-redundant protein structures.

Parameters:seed (int) – Seed for internal random number generator
Returns:The torsion sampler
Return type:TorsionSampler
promod3.loop.LoadTorsionSamplerHelical(seed=0)

Loads and returns a torsion sampler with an amino acid grouping as defined by [solis2006] that has been trained on helical residues of non-redundant protein structures.

Parameters:seed (int) – Seed for internal random number generator
Returns:The torsion sampler
Return type:TorsionSampler
promod3.loop.LoadTorsionSamplerExtended(seed=0)

Loads and returns a torsion sampler with an amino acid grouping as defined by [solis2006] that has been trained on extended residues of non-redundant protein structures.

Parameters:seed (int) – Seed for internal random number generator
Returns:The torsion sampler
Return type:TorsionSampler
promod3.loop.LoadStructureDB()

Loads and returns a structure db containing roughly 21000 chains form the PDB with seqid redundancy cutoff of 60%

Returns:The structure db
Return type:StructureDB
promod3.loop.LoadFragDB()

Loads and returns a FragDB containing fragments up to the length of 14, therefore capable of bridging gaps up to the length of 12. The returned databases contains the location of fragments in the StructureDB returned by LoadStructureDB().

Returns:The Fragment database
Return type:FragDB

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