pna Namespace Reference

Functions
def	add_hbond_constraints (pose)

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

Function Documentation

add_hbond_constraints()

def pna.add_hbond_constraints

(

pose

)

References vancomycin.harm, pi, and numeric::constants::f.zero.

Variable Documentation

apc

float pna.apc = 0.1

Referenced by main().

best_score

int pna.best_score = 100000

big_pert_dock_rbpm

pna.big_pert_dock_rbpm = rigid.RigidBodyPerturbMover(1, 1.0, 1.5)

chm

pna.chm = rosetta.core.chemical.ChemicalManager.get_instance()

guaranteed_cart_scorefxn

pna.guaranteed_cart_scorefxn = ScoreFunctionFactory.create_score_function("talaris2013_cart")

min

pna.min = MinMover(min_mm, guaranteed_cart_scorefxn, "lbfgs_armijo_nonmonotone", 0.001, True)

min_mm

pna.min_mm = kinematics.MoveMap()

Referenced by HotspotPlacementMover.apply(), and zf_relax_test().

mm

pna.mm = kinematics.MoveMap()

pert_dock_rbpm

pna.pert_dock_rbpm = rigid.RigidBodyPerturbMover(1, 1.0, 0.5)

Referenced by DougsDockDesignMinimizeMagicMover.apply(), A3BHbsDockDesignMinimizeMover.apply(), TrizaolamerDockDesignMinimizeMover.apply(), HbsDesignMover.apply(), OopDesignMover.apply(), PeptoidDesignMover.apply(), and A3BHbsCreatorMover.do_mc().

pert_mc

pna.pert_mc = moves.MonteCarlo(pose, scorefxn, 3)

pna

pna.pna = residue_set_cap.name_map("APN")

pnc

pna.pnc = residue_set_cap.name_map("CPN")

png

pna.png = residue_set_cap.name_map("GPN")

Referenced by get_rotset().

pnt

pna.pnt = residue_set_cap.name_map("TPN")

Referenced by run().

pnu

pna.pnu = residue_set_cap.name_map("UPN")

pose

pna.pose = Pose()

res_pna

pna.res_pna = Residue(pna, True)

res_pna_cterm

pna.res_pna_cterm = Residue(residue_set_cap.name_map("APN:CtermProteinFull"), True)

res_pna_nterm

pna.res_pna_nterm = Residue(residue_set_cap.name_map("APN:NtermProteinFull"), True)

res_pnc

pna.res_pnc = Residue(pnc, True)

res_png

pna.res_png = Residue(png, True)

res_pnt

pna.res_pnt = Residue(pnt, True)

res_pnu

pna.res_pnu = Residue(pnu, True)

res_pnu_cterm

pna.res_pnu_cterm = Residue(residue_set_cap.name_map("UPN:CtermProteinFull"), True)

res_pnu_nterm

pna.res_pnu_nterm = Residue(residue_set_cap.name_map("UPN:NtermProteinFull"), True)

resi

int pna.resi = resim1 + 1

Referenced by add_constraints(), average_degree(), cal_distance(), calc_contacts(), ConstraintStatsMover.calc_native_stats(), ConstraintStatsMover.calc_stats(), calculate_burial(), create_starting_template(), get_aln_resi(), get_ca_distances(), get_linker_dihedrals(), main(), VallReader.make_fragment_lines(), VallReader.make_nmer_profile(), measure_sequence_recovery(), neighbor_count(), ConstraintStatsMover.print_stats(), read_distances(), read_in_cl_data(), removeConstraintsNearGap(), xtal_water_bunsat.report_sasa_if_contacting_water(), ConstraintConfig.resi_to_primary(), rotateUntilCys(), save_per_residue_scores(), DomainAssemblerNDocker.setup_cen_domains(), and verify_identical().

rts

pna.rts = chm.residue_type_set('fa_standard').get_self_ptr()

scorefxn

pna.scorefxn = get_score_function()

small_tor_mover

pna.small_tor_mover = RandomTorsionMover(mm, 1, 10)

test_score

pna.test_score = pose.energies().total_energies().dot(scorefxn.weights())

Referenced by gen_pep_bb_frag(), gen_pep_bb_frag_old(), gen_pep_bb_sequential(), main(), perturb_pep_bb(), and register_options().

trans_mover

pna.trans_mover = protocols.rigid.RigidBodyTransMover(pose, 1)

Referenced by fit_helix_in_map(), and main().