Igor minimises the Fragmenstein monster in the protein using PyRosetta.
Igor uses the package rdkit_to_params to parameterise the compounds.
Igor has three minimisers that I tried:
- a modified cartesian FastRelax which works effectively.
- cartesian MinMover which gets stuck in local minimum in hard cases.
- PertMinMover which behaves weirdly...
Igor gets run as follows:
e = Igor(pose, constraint_filename)
e.minimize(10)
Where pose is a pyrosetta.Pose instance.
But Igor can be initialised with Igor.from_pdbfile(..) or Igor.from_pdbblock(..).
Do note that when Victor calls Igor the constraint file used will have the atoms that should be constrained by position.
The Igor.coordinate_constraint (default = 1) controls the stringency.
Victor will make Igor repeat the minimisation with increasingly lower stringency until the ∆∆G is negative
or when the weight is near zero.
In the absence of coordinate constraints in the constraint file (Victor generates it from the constraints),
the argument default_coord_constraint=True passed to .minimise will set relax.constrain_relax_to_start_coords(True).
Note that the get_mod_FastRelax has a weight in case it runs of constrain to position alone.
As Victor sets the constraints, the class attribute of Victor constraint_function_type can be HARMONIC, FLAT_HARMONIC (default) or FADE.