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:
- 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:
- 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:
- 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:
- 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:
- 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
StructureDBreturned byLoadStructureDB().- Returns:
The Fragment database
- Return type: