pna.py File Reference

Look for structure in peptide nucleic acids. More...

Namespaces
	pna

Functions
def	pna.add_hbond_constraints (pose)

Variables
	pna.pose = Pose()
	pna.scorefxn = get_score_function()
	pna.guaranteed_cart_scorefxn = ScoreFunctionFactory.create_score_function("talaris2013_cart")
	pna.chm = rosetta.core.chemical.ChemicalManager.get_instance()
	pna.rts = chm.residue_type_set('fa_standard').get_self_ptr()
	pna.pna = residue_set_cap.name_map("APN")
	pna.pnc = residue_set_cap.name_map("CPN")
	pna.png = residue_set_cap.name_map("GPN")
	pna.pnt = residue_set_cap.name_map("TPN")
	pna.pnu = residue_set_cap.name_map("UPN")
	pna.res_pna_nterm = Residue(residue_set_cap.name_map("APN:NtermProteinFull"), True)
	pna.res_pna_cterm = Residue(residue_set_cap.name_map("APN:CtermProteinFull"), True)
	pna.res_pna = Residue(pna, True)
	pna.res_pnc = Residue(pnc, True)
	pna.res_png = Residue(png, True)
	pna.res_pnt = Residue(pnt, True)
	pna.res_pnu = Residue(pnu, True)
	pna.res_pnu_nterm = Residue(residue_set_cap.name_map("UPN:NtermProteinFull"), True)
	pna.res_pnu_cterm = Residue(residue_set_cap.name_map("UPN:CtermProteinFull"), True)
	pna.trans_mover = protocols.rigid.RigidBodyTransMover(pose, 1)
	pna.big_pert_dock_rbpm = rigid.RigidBodyPerturbMover(1, 1.0, 1.5)
	pna.pert_dock_rbpm = rigid.RigidBodyPerturbMover(1, 1.0, 0.5)
	pna.mm = kinematics.MoveMap()
	pna.min_mm = kinematics.MoveMap()
int	pna.resi = resim1 + 1
	pna.small_tor_mover = RandomTorsionMover(mm, 1, 10)
	pna.min = MinMover(min_mm, guaranteed_cart_scorefxn, "lbfgs_armijo_nonmonotone", 0.001, True)
	pna.pert_mc = moves.MonteCarlo(pose, scorefxn, 3)
float	pna.apc = 0.1
int	pna.best_score = 100000
	pna.test_score = pose.energies().total_energies().dot(scorefxn.weights())

Detailed Description

Look for structure in peptide nucleic acids.

Author

Andrew Watkins