Index

_

__call__() (pele.accept_tests.Metropolis method) (pele.accept_tests.SphericalContainer method) (pele.angleaxis.ExactMatchAACluster method) (pele.angleaxis.MinPermDistAACluster method) (pele.mindist.ExactMatchAtomicCluster method) (pele.mindist.ExactMatchCluster method) (pele.mindist.ExactMatchPeriodic method) (pele.mindist.MinPermDistAtomicCluster method) (pele.mindist.MinPermDistCluster method) (pele.mindist.PointGroupOrderCluster method) (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) (pele.takestep.AdaptiveStepsize method) (pele.takestep.AdaptiveStepsizeTemperature method) (pele.takestep.BlockMoves method) (pele.takestep.GroupSteps method) (pele.takestep.ParticleExchange method) (pele.takestep.RandomDisplacement method) (pele.takestep.Reseeding method) (pele.takestep.RotationalDisplacement method) (pele.takestep.Takestep method) (pele.takestep.TakestepInterface method) (pele.takestep.TakestepSlice method) (pele.takestep.UniformDisplacement method) (pele.utils.histogram.EnergyHistogram method) (pele.utils.histogram.PrintHistogram method)

A

aa2mx() (in module pele.utils.rotations) aa2q() (in module pele.utils.rotations) accept() (pele.accept_tests.SphericalContainer method) accept_fortran() (pele.accept_tests.SphericalContainer method) acceptRejectE() (pele.accept_tests.Metropolis method) acceptWrapper() (pele.accept_tests.SphericalContainer method) accuracy (pele.storage.Database attribute) AdaptiveStepsize (class in pele.takestep) AdaptiveStepsizeTemperature (class in pele.takestep) add_atom() (pele.angleaxis.RigidFragment method) add_minimum() (pele.concurrent.ConnectServer method) add_properties() (pele.storage.Database method) add_property() (pele.storage.Database method) add_sites() (pele.angleaxis.RBTopology method) add_ts() (pele.concurrent.ConnectServer method)

addBlock() (pele.takestep.BlockMoves method) addEventAfterStep() (pele.basinhopping.BasinHopping method) (pele.mc.MonteCarlo method) addMinimum() (pele.landscape.TSGraph method) (pele.storage.Database method) addTransitionState() (pele.landscape.TSGraph method) (pele.storage.Database method) adjustStep() (pele.takestep.AdaptiveStepsize method) (pele.takestep.AdaptiveStepsizeTemperature method) adjustStepSize() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) adjustTemp() (pele.takestep.AdaptiveStepsizeTemperature method) align() (pele.angleaxis.MeasureRigidBodyCluster method) align_path() (pele.angleaxis.RBTopology method) align_structures() (pele.angleaxis.MinPermDistAACluster method) (pele.mindist.MinPermDistAtomicCluster method) (pele.mindist.MinPermDistCluster method) apply_transformation() (pele.angleaxis.ExactMatchAACluster method) (pele.mindist.ExactMatchAtomicCluster method) (pele.mindist.ExactMatchCluster method) areConnected() (pele.landscape.TSGraph method) ATLJ (class in pele.potentials) AtomicCluster (class in pele.systems) attachEvent() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method)

B

BaseParameters (class in pele.systems) BasePotential (class in pele.potentials) BaseSystem (class in pele.systems) BasinHopping (class in pele.basinhopping)

BLJCluster (class in pele.systems) BlockMoves (class in pele.takestep) buildList() (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListSubsetBuild method)

C

calculate() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) can_invert() (pele.angleaxis.TransformAngleAxisCluster method) (pele.mindist.TransformPolicy method) cg() (in module pele.optimize) check_match() (pele.angleaxis.ExactMatchAACluster method) (pele.angleaxis.MinPermDistAACluster method) (pele.mindist.ExactMatchAtomicCluster method) (pele.mindist.ExactMatchCluster method) (pele.mindist.ExactMatchPeriodic method) (pele.mindist.MinPermDistAtomicCluster method) (pele.mindist.MinPermDistCluster method) clear() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) color_by_group() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) color_by_value() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) compareMinima (pele.storage.Database attribute) connect() (pele.landscape.DoubleEndedConnect method) (pele.landscape.LocalConnect method) connection (pele.storage.Database attribute) ConnectManager (class in pele.landscape)

ConnectServer (class in pele.concurrent) ConnectWorker (class in pele.concurrent) converged() (pele.optimize.Fire method) coords (pele.storage.Minimum attribute) (pele.storage.TransitionState attribute) (pele.utils.rbtools.CoordsAdapter attribute) coords_adapter() (pele.angleaxis.RBTopology method) CoordsAdapter (class in pele.utils.rbtools) copy() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) (pele.transition_states.NEB method) (pele.utils.rbtools.CoordsAdapter method) cpp_topology (pele.angleaxis.RBTopology attribute) create_database() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) createNEB() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) current (pele.transition_states.InterpolatedPath attribute)

D

Database (class in pele.storage) database2graph() (in module pele.landscape) DisconnectivityGraph (class in pele.utils.disconnectivity_graph) distance_squared() (pele.angleaxis.RBTopology method) (pele.angleaxis.RigidFragment method) distance_squared_grad() (pele.angleaxis.RBTopology method) (pele.angleaxis.RigidFragment method) dos_to_cv() (in module pele.thermodynamics)

DoubleEndedConnect (class in pele.landscape) draw() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) draw_box() (in module pele.utils.pymolwrapper) draw_minima() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) draw_rigid() (in module pele.utils.pymolwrapper) draw_spheres() (in module pele.utils.pymolwrapper)

E

eigenval (pele.storage.TransitionState attribute) eigenvec (pele.storage.TransitionState attribute) energy (pele.storage.Minimum attribute) (pele.storage.TransitionState attribute) EnergyHistogram (class in pele.utils.histogram) engine (pele.storage.Database attribute) ExactMatchAACluster (class in pele.angleaxis)

ExactMatchAtomicCluster (class in pele.mindist) ExactMatchCluster (class in pele.mindist) ExactMatchPeriodic (class in pele.mindist) examples.getting_started.example1_minimization (module) examples.getting_started.example2_global_optimization (module)

F

final (pele.transition_states.InterpolatedPath attribute) finalize_best_match() (pele.angleaxis.MinPermDistAACluster method) (pele.mindist.MinPermDistAtomicCluster method) (pele.mindist.MinPermDistCluster method) finalize_setup() (pele.angleaxis.RBTopology method) (pele.angleaxis.RigidFragment method) find_best_permutation() (in module pele.mindist) find_permutation() (pele.angleaxis.MeasureRigidBodyCluster method) (pele.mindist.MeasurePolicy method) find_rotation() (pele.angleaxis.MeasureRigidBodyCluster method) (pele.mindist.MeasurePolicy method) find_transformation() (pele.angleaxis.ExactMatchAACluster method) (pele.mindist.ExactMatchAtomicCluster method) (pele.mindist.ExactMatchCluster method) findLowestEigenVector() (in module pele.transition_states) findMinimum() (pele.storage.Database method) findrotation() (in module pele.mindist)

findrotation_kabsch() (in module pele.mindist) findrotation_kearsley() (in module pele.mindist) FindTransitionState (class in pele.transition_states) findTransitionState() (in module pele.transition_states) Fire (class in pele.optimize) fire() (in module pele.optimize) forceAccept() (pele.accept_tests.Metropolis method) FreezePot (class in pele.utils.frozen_atoms) fromkeys() (pele.optimize.Result static method) (pele.systems.BaseParameters static method) (pele.systems.Parameters static method) fvib (pele.storage.Minimum attribute) (pele.storage.TransitionState attribute)

G

generate_path() (pele.transition_states.NEBDriver method) get() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) get_1d_indices() (pele.utils.frozen_atoms.FreezePot method) get_atom_labels() (pele.angleaxis.RBTopology method) get_atommasses() (pele.angleaxis.RBTopology method) get_atomtypes() (pele.angleaxis.RBTopology method) get_basinhopping() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_com() (pele.angleaxis.MeasureRigidBodyCluster method) (pele.mindist.MeasurePolicy method) get_compare_exact() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_compare_minima() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_connect_job() (pele.concurrent.ConnectServer method) (pele.landscape.ConnectManager method) get_dist() (pele.angleaxis.MeasureRigidBodyCluster method) (pele.mindist.MeasurePolicy method) get_double_ended_connect() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_eig() (in module pele.utils.hessian) get_eigvals() (in module pele.utils.hessian) get_energy() (pele.transition_states.FindTransitionState method) get_gradient() (pele.transition_states.FindTransitionState method) get_log_product_normalmode_freq() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_lowest_energy_minimum() (pele.storage.Database method) get_metric_tensor() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_mindist() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_minima_layout() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) get_minimizer() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_ndof() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_normalmodes() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_nrigid() (pele.angleaxis.RBTopology method) get_nzero_modes() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_orthogonalize_to_zero_eigenvectors() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_permlist() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.LJCluster method) get_pgorder() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_phases() (pele.potentials.XYModel method) get_potential() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_property() (pele.storage.Database method)

get_random_configuration() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_random_minimized_configuration() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_result() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) get_smallest_eig() (in module pele.utils.hessian) get_smallest_rij() (pele.angleaxis.RigidFragment method) get_sorted_eig() (in module pele.utils.hessian) get_spin_energies() (pele.potentials.XYModel method) get_state() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) get_system() (pele.concurrent.ConnectServer method) get_system_properties() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_takestep() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) get_thermodynamic_information() (in module pele.thermodynamics) get_tree_layout() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) getCoords() (pele.potentials.GMINPotential method) getDist() (pele.landscape.DoubleEndedConnect method) getEnergy() (pele.potentials.BasePotential method) (pele.potentials.GMINPotential method) (pele.potentials.HeisenbergModel method) (pele.potentials.HeisenbergModelRA method) (pele.potentials.LJ method) (pele.potentials.LJCut method) (pele.potentials.LJpshift method) (pele.potentials.XYModel method) (pele.transition_states.NEB method) (pele.utils.frozen_atoms.FreezePot method) (pele.utils.neighbor_list.MultiComponentSystem method) (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListPotentialMulti method) (pele.utils.neighbor_list.NeighborListSubsetBuild method) getEnergyGradient() (pele.potentials.BasePotential method) (pele.potentials.GMINPotential method) (pele.potentials.HeisenbergModel method) (pele.potentials.HeisenbergModelRA method) (pele.potentials.LJ method) (pele.potentials.LJCut method) (pele.potentials.LJpshift method) (pele.potentials.XYModel method) (pele.transition_states.NEB method) (pele.utils.frozen_atoms.FreezePot method) (pele.utils.neighbor_list.MultiComponentSystem method) (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListPotentialMulti method) (pele.utils.neighbor_list.NeighborListSubsetBuild method) getEnergyGradientHessian() (pele.potentials.BasePotential method) (pele.potentials.GMINPotential method) (pele.potentials.HeisenbergModel method) (pele.potentials.HeisenbergModelRA method) (pele.potentials.LJ method) (pele.potentials.LJpshift method) (pele.potentials.XYModel method) (pele.utils.frozen_atoms.FreezePot method) (pele.utils.neighbor_list.MultiComponentSystem method) (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListPotentialMulti method) (pele.utils.neighbor_list.NeighborListSubsetBuild method) getEnergyGradientList() (pele.potentials.LJCut method) (pele.utils.frozen_atoms.FreezePot method) getEnergyGradientNumerical() (pele.potentials.BasePotential method) (pele.potentials.GMINPotential method) (pele.potentials.HeisenbergModel method) (pele.potentials.HeisenbergModelRA method) (pele.potentials.LJpshift method) (pele.potentials.XYModel method) (pele.utils.frozen_atoms.FreezePot method) (pele.utils.neighbor_list.MultiComponentSystem method) (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListPotentialMulti method) (pele.utils.neighbor_list.NeighborListSubsetBuild method) getEnergyList() (pele.potentials.LJCut method) (pele.utils.frozen_atoms.FreezePot method) getGradient() (pele.potentials.BasePotential method) (pele.potentials.GMINPotential method) (pele.potentials.HeisenbergModel method) (pele.potentials.HeisenbergModelRA method) (pele.potentials.LJ method) (pele.potentials.LJpshift method) (pele.potentials.XYModel method) (pele.utils.frozen_atoms.FreezePot method) (pele.utils.neighbor_list.MultiComponentSystem method) (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListPotentialMulti method) (pele.utils.neighbor_list.NeighborListSubsetBuild method) getHessian() (pele.potentials.BasePotential method) (pele.potentials.GMINPotential method) (pele.potentials.HeisenbergModel method) (pele.potentials.HeisenbergModelRA method) (pele.potentials.LJ method) (pele.potentials.LJpshift method) (pele.potentials.XYModel method) (pele.utils.frozen_atoms.FreezePot method) (pele.utils.neighbor_list.MultiComponentSystem method) (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListPotentialMulti method) (pele.utils.neighbor_list.NeighborListSubsetBuild method) getMinimum() (pele.storage.Database method) getPath() (pele.landscape.TSGraph method) getStep() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) getTransitionState() (pele.storage.Database method) getTransitionStateFromID() (pele.storage.Database method) getTransitionStatesMinimum() (pele.storage.Database method) GMINPotential (class in pele.potentials) gramm_schmidt() (in module pele.transition_states) GroupSteps (class in pele.takestep)

H

has_key() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) HeisenbergModel (class in pele.potentials)

HeisenbergModelRA (class in pele.potentials)

I

id() (pele.storage.Minimum method) (pele.storage.TransitionState method) initial (pele.transition_states.InterpolatedPath attribute) initialize() (pele.optimize.Fire method) insert() (pele.utils.histogram.EnergyHistogram method) insert_rejected (pele.basinhopping.BasinHopping attribute) (pele.mc.MonteCarlo attribute) insertWrapper() (pele.utils.histogram.EnergyHistogram method) interpolate() (pele.angleaxis.RBTopology method) InterpolatedPath (class in pele.transition_states)

InterpolatedPathDensity() (in module pele.transition_states) interpolator (pele.transition_states.InterpolatedPath attribute) invalid (pele.storage.Minimum attribute) (pele.storage.TransitionState attribute) invert() (pele.angleaxis.TransformAngleAxisCluster method) (pele.mindist.TransformPolicy method) items() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) iteritems() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) iterkeys() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) itervalues() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method)

K

keys() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method)

L

label_minima() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) lattice (pele.utils.rbtools.CoordsAdapter attribute) LBFGS (class in pele.optimize) lbfgs_py() (in module pele.optimize) lbfgs_scipy() (in module pele.optimize) LJ (class in pele.potentials)

LJCluster (class in pele.systems) LJCut (class in pele.potentials) LJpshift (class in pele.potentials) load_coords_pymol() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) LocalConnect (class in pele.landscape) logproduct_freq2() (in module pele.thermodynamics)

M

make_sparse() (in module pele.utils.hessian) MakeAllMaximaClimbing() (pele.transition_states.NEB method) makeBLJNeighborListPotFreeze() (in module pele.utils.frozen_atoms) MakeHighestImageClimbing() (pele.transition_states.NEB method) MeasurePolicy (class in pele.mindist) MeasureRigidBodyCluster (class in pele.angleaxis) mergeMinima() (pele.landscape.DoubleEndedConnect method) (pele.landscape.TSGraph method) (pele.storage.Database method) metadata (pele.storage.Minimum attribute) (pele.storage.TransitionState attribute) metric_tensor() (pele.angleaxis.RBTopology method) (pele.angleaxis.RigidFragment method) metric_tensor_cog() (pele.angleaxis.RigidFragment method) Metropolis (class in pele.accept_tests) minima() (pele.storage.Database method) minima_from_ts() (in module pele.transition_states) minima_to_cv() (in module pele.thermodynamics)

Minimum (class in pele.storage) minimum1 (pele.storage.TransitionState attribute) minimum2 (pele.storage.TransitionState attribute) minimum_adder() (pele.storage.Database method) MinPermDistAACluster (class in pele.angleaxis) MinPermDistAtomicCluster (class in pele.mindist) MinPermDistCluster (class in pele.mindist) MonteCarlo (class in pele.mc) MultiComponentSystem (class in pele.utils.neighbor_list) mx2aa() (in module pele.utils.rotations) mx2q() (in module pele.utils.rotations) MYLBFGS (class in pele.optimize) mylbfgs() (in module pele.optimize)

N

natoms (pele.utils.rbtools.CoordsAdapter attribute) NEB (class in pele.transition_states) neb_distance() (pele.angleaxis.RBTopology method) NEBDriver (class in pele.transition_states) NEBForce() (pele.transition_states.NEB method) needNewList() (pele.utils.neighbor_list.NeighborListPotentialMulti method) NeighborListPotentialBuild (class in pele.utils.neighbor_list) NeighborListPotentialMulti (class in pele.utils.neighbor_list) NeighborListSubsetBuild (class in pele.utils.neighbor_list)

next() (pele.mindist.StandardClusterAlignment method) nimages (pele.transition_states.InterpolatedPath attribute) nlattice (pele.utils.rbtools.CoordsAdapter attribute) normalmode_frequencies() (in module pele.thermodynamics) nrigid (pele.utils.rbtools.CoordsAdapter attribute) number_of_minima() (pele.storage.Database method) number_of_transition_states() (pele.storage.Database method) NumericalDerivative() (pele.potentials.BasePotential method) (pele.potentials.GMINPotential method) (pele.potentials.HeisenbergModel method) (pele.potentials.HeisenbergModelRA method) (pele.potentials.LJ method) (pele.potentials.LJpshift method) (pele.potentials.XYModel method) (pele.utils.frozen_atoms.FreezePot method) (pele.utils.neighbor_list.MultiComponentSystem method) (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListPotentialMulti method) (pele.utils.neighbor_list.NeighborListSubsetBuild method) NumericalHessian() (pele.potentials.BasePotential method) (pele.potentials.GMINPotential method) (pele.potentials.HeisenbergModel method) (pele.potentials.HeisenbergModelRA method) (pele.potentials.LJ method) (pele.potentials.LJpshift method) (pele.potentials.XYModel method) (pele.utils.frozen_atoms.FreezePot method) (pele.utils.neighbor_list.MultiComponentSystem method) (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListPotentialMulti method) (pele.utils.neighbor_list.NeighborListSubsetBuild method)

O

one_iteration() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) optimize() (pele.transition_states.NEB method) optimize_permutations() (in module pele.mindist)

orthogopt() (in module pele.transition_states) (pele.angleaxis.RBTopology method) orthogopt_translation_only() (in module pele.transition_states)

P

Parameters (class in pele.systems) params() (pele.transition_states.FindTransitionState class method) (pele.transition_states.NEBDriver class method) ParticleExchange (class in pele.takestep) pele.accept_tests (module) pele.angleaxis (module) pele.concurrent (module) pele.gui (module) pele.landscape (module) pele.mindist (module) pele.optimize (module) pele.potentials (module) pele.rates (module) pele.storage (module) pele.systems (module) pele.takestep (module), [1] pele.thermodynamics (module) pele.transition_states (module) pele.utils (module) pele.utils.amber (module) pele.utils.frozen_atoms (module) pele.utils.hessian (module) pele.utils.histogram (module)

pele.utils.neighbor_list (module) pele.utils.pymolwrapper (module) pele.utils.rbtools (module) pele.utils.rotations (module) pele.utils.xyz (module) permute() (pele.angleaxis.TransformAngleAxisCluster method) (pele.mindist.TransformPolicy method) pgorder (pele.storage.Minimum attribute) (pele.storage.TransitionState attribute) plot() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) PointGroupOrderCluster (class in pele.mindist) pop() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) popitem() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) populateBondConn() (pele.utils.amber.readAmberParam method) posAtoms (pele.utils.rbtools.CoordsAdapter attribute) posRigid (pele.utils.rbtools.CoordsAdapter attribute) prepare() (pele.transition_states.NEBDriver method) printBondConn() (pele.utils.amber.readAmberParam method) printEvent() (pele.utils.histogram.PrintHistogram method) printHis() (pele.utils.histogram.PrintHistogram method) PrintHistogram (class in pele.utils.histogram) printState() (pele.transition_states.NEB method) printStep() (pele.basinhopping.BasinHopping method) (pele.mc.MonteCarlo method) properties() (pele.storage.Database method)

Q

q2aa() (in module pele.utils.rotations) q2mx() (in module pele.utils.rotations)

q_multiply() (in module pele.utils.rotations) q_slerp() (in module pele.utils.rotations)

R

random_aa() (in module pele.utils.rotations) random_q() (in module pele.utils.rotations) RandomDisplacement (class in pele.takestep) RBTopology (class in pele.angleaxis) read_xyz() (in module pele.utils.xyz) readAmberParam (class in pele.utils.amber) redistribute_forces() (pele.angleaxis.RigidFragment method) redistribute_gradient() (pele.angleaxis.RBTopology method) reduced_coordinates_displace() (in module pele.takestep) refresh() (pele.landscape.TSGraph method) remove_transition_state() (pele.storage.Database method) removeMinimum() (pele.storage.Database method)

Reseeding (class in pele.takestep) reset() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) (pele.takestep.AdaptiveStepsizeTemperature method) Result (class in pele.optimize) returnPath() (pele.landscape.DoubleEndedConnect method) RigidFragment (class in pele.angleaxis) rotate() (in module pele.takestep) (pele.angleaxis.TransformAngleAxisCluster method) (pele.mindist.TransformPolicy method) rotate_aa() (in module pele.utils.rotations) RotationalDisplacement (class in pele.takestep) rotRigid (pele.utils.rbtools.CoordsAdapter attribute) run() (pele.basinhopping.BasinHopping method) (pele.concurrent.ConnectServer method) (pele.concurrent.ConnectWorker method) (pele.mc.MonteCarlo method) (pele.optimize.Fire method) (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) (pele.transition_states.FindTransitionState method) (pele.transition_states.NEBDriver method) run_gui() (in module pele.gui)

S

savefig() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) scale() (pele.takestep.AdaptiveStepsize method) (pele.takestep.AdaptiveStepsizeTemperature method) (pele.takestep.BlockMoves method) (pele.takestep.GroupSteps method) (pele.takestep.ParticleExchange method) (pele.takestep.RandomDisplacement method) (pele.takestep.Reseeding method) (pele.takestep.RotationalDisplacement method) (pele.takestep.Takestep method) (pele.takestep.TakestepInterface method) (pele.takestep.TakestepSlice method) (pele.takestep.UniformDisplacement method) session (pele.storage.Database attribute) set_connect_manager() (pele.concurrent.ConnectServer method) set_cpp_topology() (pele.angleaxis.RBTopology method) set_energy_levels() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) set_state() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) set_up_neighborlists() (pele.potentials.XYModel method) setdefault() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) setPrinting() (pele.basinhopping.BasinHopping method) (pele.mc.MonteCarlo method) show() (pele.utils.disconnectivity_graph.DisconnectivityGraph method) Sm (pele.angleaxis.RigidFragment attribute)

small_random_aa() (in module pele.utils.rotations) smooth_path() (pele.systems.AtomicCluster method) (pele.systems.BLJCluster method) (pele.systems.BaseSystem method) (pele.systems.LJCluster method) smoothPath() (in module pele.landscape) SphericalContainer (class in pele.accept_tests) standard_alignments() (pele.angleaxis.ExactMatchAACluster method) (pele.mindist.ExactMatchAtomicCluster method) (pele.mindist.ExactMatchCluster method) StandardClusterAlignment (class in pele.mindist) start() (in module pele.utils.pymolwrapper) steepest_descent() (in module pele.optimize) step() (pele.optimize.Fire method) stop_criterion_satisfied() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) success() (pele.landscape.DoubleEndedConnect method) symmetriesaa (pele.angleaxis.RigidFragment attribute)

T

takeOneStep() (pele.basinhopping.BasinHopping method) (pele.mc.MonteCarlo method) Takestep (class in pele.takestep) takeStep() (pele.takestep.AdaptiveStepsize method) (pele.takestep.AdaptiveStepsizeTemperature method) (pele.takestep.BlockMoves method) (pele.takestep.GroupSteps method) (pele.takestep.ParticleExchange method) (pele.takestep.RandomDisplacement method) (pele.takestep.Reseeding method) (pele.takestep.RotationalDisplacement method) (pele.takestep.Takestep method) (pele.takestep.TakestepInterface method) (pele.takestep.TakestepSlice method) (pele.takestep.UniformDisplacement method) takestep_aa() (in module pele.utils.rotations) TakestepInterface (class in pele.takestep) TakestepSlice (class in pele.takestep) tangent() (pele.transition_states.NEB method) tangent_old() (pele.transition_states.NEB method) test_potential() (pele.potentials.BasePotential method) (pele.potentials.GMINPotential method) (pele.potentials.HeisenbergModel method) (pele.potentials.HeisenbergModelRA method) (pele.potentials.LJpshift method) (pele.potentials.XYModel method) (pele.utils.frozen_atoms.FreezePot method) (pele.utils.neighbor_list.MultiComponentSystem method) (pele.utils.neighbor_list.NeighborListPotentialBuild method) (pele.utils.neighbor_list.NeighborListPotentialMulti method) (pele.utils.neighbor_list.NeighborListSubsetBuild method)

to_atomistic() (pele.angleaxis.RBTopology method) (pele.angleaxis.RigidFragment method) transform_grad() (pele.angleaxis.RigidFragment method) transform_gradient() (pele.angleaxis.RBTopology method) TransformAngleAxisCluster (class in pele.angleaxis) TransformPolicy (class in pele.mindist) transition_states() (pele.storage.Database method) TransitionState (class in pele.storage) translate() (pele.angleaxis.TransformAngleAxisCluster method) (pele.mindist.TransformPolicy method) TSGraph (class in pele.landscape)

U

uniform_displace() (in module pele.takestep) UniformDisplacement (class in pele.takestep) untried() (pele.landscape.ConnectManager method) update() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) (pele.utils.neighbor_list.NeighborListPotentialMulti method)

update_coords() (pele.optimize.LBFGS method) (pele.optimize.MYLBFGS method) updateCoords() (pele.utils.rbtools.CoordsAdapter method) updateStep() (pele.takestep.AdaptiveStepsize method) (pele.takestep.AdaptiveStepsizeTemperature method) (pele.takestep.BlockMoves method) (pele.takestep.GroupSteps method) (pele.takestep.ParticleExchange method) (pele.takestep.RandomDisplacement method) (pele.takestep.Reseeding method) (pele.takestep.RotationalDisplacement method) (pele.takestep.Takestep method) (pele.takestep.TakestepInterface method) (pele.takestep.TakestepSlice method) (pele.takestep.UniformDisplacement method) user_data (pele.storage.Minimum attribute) (pele.storage.TransitionState attribute)

V

values() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) vec_random() (in module pele.utils.rotations) vec_random_ndim() (in module pele.utils.rotations) vector_random_uniform_hypersphere() (in module pele.utils.rotations)

viewitems() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) viewkeys() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method) viewvalues() (pele.optimize.Result method) (pele.systems.BaseParameters method) (pele.systems.Parameters method)

W

write_xyz() (in module pele.utils.xyz)

X

XYModel (class in pele.potentials)

Z

zeroEV() (pele.angleaxis.RBTopology method) zeroEV_cluster() (in module pele.transition_states)

zeroEV_rotation() (in module pele.transition_states) zeroEV_translation() (in module pele.transition_states)