Igor

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…

movers

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.