schrodinger.trajectory.BondRotator module

class schrodinger.trajectory.BondRotator.BondRotator(st, rb_atoms, angle_diff=10, ff=16, debug=False, canonicalize=True, prime_hmc=True, hmc_steps=20)

Bases: object

perform RB scan

getRotEnergy(offset=False)

potential(conf=None, degree=True)

get potential energy corresponding to ‘conf’ :param conf: conformation in degrees to get corresponding potential :type conf: float

:rtype float

prime_search_and_scan(nsteps=20)

Get best profile by using Prime HMC to generate multiple initial coordinates. Modify self.results to reflect the best profile.

run_hmc(nsteps=20, max_confs=10)

Run Prime’s Hybrid Monte Carlo (HMC), return top output cts that will be ‘deduplicated’ by energy and rmsd. :param nsteps: Number of MC steps :param max_confs: Number of maximum conformers to return :rtype: list(structure.Structure)