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