Developer source API

Public library and developer interfaces are collected from source without importing optional backends. Private helpers and definitions nested inside functions are excluded.

• pele
• pele.accept_tests
• pele.accept_tests.dont_leave_basin
• pele.accept_tests.metropolis
• pele.accept_tests.spherical_container
• pele.amber
• pele.amber.amberSystem
• pele.amber.coords2pdb
• pele.amber.gmin_potential
• pele.amber.internal_coords
• pele.amber.measure
• pele.amber.obsolete.pdb2permlist
• pele.amber.openmm_potential
• pele.amber.read_amber
• pele.amber.sanity_checks
• pele.angleaxis
• pele.angleaxis._cpp_aa
• pele.angleaxis._otp_bulk
• pele.angleaxis._otp_cluster
• pele.angleaxis.aamindist
• pele.angleaxis.aaperiodicttransforms
• pele.angleaxis.aasystem
• pele.angleaxis.aatopology
• pele.angleaxis.bulk_rigid_mindist
• pele.angleaxis.rigidbody
• pele.basinhopping
• pele.concurrent
• pele.concurrent._connect_server
• pele.distance
• pele.distance._get_distance_cpp
• pele.distance._put_in_box_cpp
• pele.exceptions
• pele.gui
• pele.gui._list_views
• pele.gui.bhrunner
• pele.gui.connect_all
• pele.gui.connect_explorer_dlg
• pele.gui.connect_run_dlg
• pele.gui.double_ended_connect_runner
• pele.gui.graph_viewer
• pele.gui.neb_explorer
• pele.gui.normalmode_browser
• pele.gui.pymol_viewer
• pele.gui.run
• pele.gui.show3d
• pele.gui.show3d_with_slider
• pele.gui.takestep_explorer
• pele.gui.ui.dgraph_dlg
• pele.gui.ui.mplwidget
• pele.landscape
• pele.landscape._graph
• pele.landscape._smooth_path
• pele.landscape.connect_manager
• pele.landscape.connect_min
• pele.landscape.local_connect
• pele.landscape.singleended
• pele.mc
• pele.mindist
• pele.mindist._minpermdist_policies
• pele.mindist._pointgrouporder
• pele.mindist._wrapper_atomiccluster
• pele.mindist.backward_compatibility
• pele.mindist.exact_match
• pele.mindist.minpermdist_stochastic
• pele.mindist.periodic_exact_match
• pele.mindist.periodic_mindist
• pele.mindist.permutational_alignment
• pele.mindist.rmsfit
• pele.optimize
• pele.optimize._cosine_gradient_descent_cpp
• pele.optimize._fire
• pele.optimize._gradient_descent_cpp
• pele.optimize._lbfgs_cpp
• pele.optimize._lbfgs_py
• pele.optimize._modified_fire_cpp
• pele.optimize._mxd_end_only
• pele.optimize._mylbfgs
• pele.optimize._pele_opt
• pele.optimize._quench
• pele.optimize.cvode_opt
• pele.optimize.extended_mixed_descent
• pele.optimize.generic_mixed_descent
• pele.optimize.ode_linesearch
• pele.optimize.optimization_exceptions
• pele.optimize.result
• pele.potentials
• pele.potentials.ATLJ
• pele.potentials._fin_sin
• pele.potentials._frenkel
• pele.potentials._frozen_dof
• pele.potentials._gupta
• pele.potentials._harmonic_cpp
• pele.potentials._hs_wca_cpp
• pele.potentials._inversepower_cpp
• pele.potentials._inversepower_hs_cpp
• pele.potentials._inversepower_stillinger_cpp
• pele.potentials._inversepower_stillinger_cut_cpp
• pele.potentials._inversepower_stillinger_cut_quad
• pele.potentials._lj_cpp
• pele.potentials._morse_cpp
• pele.potentials._pele
• pele.potentials._pspin_spherical_cpp
• pele.potentials._pythonpotential
• pele.potentials._radial_gaussian_cpp
• pele.potentials._sumgaussianpot_cpp
• pele.potentials._sutton_chen
• pele.potentials._wca_cpp
• pele.potentials.atlj
• pele.potentials.combine_potentials
• pele.potentials.cpp_test_functions
• pele.potentials.gminpotential
• pele.potentials.heisenberg_spin
• pele.potentials.heisenberg_spin_RA
• pele.potentials.inverse_power_py
• pele.potentials.lammps_pele_cython
• pele.potentials.lammps_potential_python
• pele.potentials.lj
• pele.potentials.ljcut
• pele.potentials.ljpshiftfast
• pele.potentials.ml
• pele.potentials.morse
• pele.potentials.potential
• pele.potentials.xyspin
• pele.rates
• pele.rates._kmc
• pele.rates._ngt_cpp
• pele.rates._rate_calculations
• pele.rates._rates
• pele.rates._rates_linalg
• pele.storage
• pele.storage.database
• pele.storage.savenlowest
• pele.systems
• pele.systems._opengl_tools
• pele.systems.basesystem
• pele.systems.blj_bulk
• pele.systems.blj_bulk_frozen
• pele.systems.bljcluster
• pele.systems.cluster
• pele.systems.ljcluster
• pele.systems.ljcluster_frozen
• pele.systems.morse_bulk
• pele.systems.morse_cluster
• pele.systems.pspin_spherical_system
• pele.systems.spawn_OPTIM
• pele.takestep
• pele.takestep.adaptive
• pele.takestep.adaptive_step_temperature
• pele.takestep.buildingblocks
• pele.takestep.displace
• pele.takestep.generic
• pele.takestep.group
• pele.takestep.particle_exchange
• pele.thermodynamics
• pele.thermodynamics._normalmodes
• pele.thermodynamics._utils
• pele.thermodynamics.heat_capacity
• pele.transition_states
• pele.transition_states._NEB
• pele.transition_states._find_lowest_eig
• pele.transition_states._generalized_dimer
• pele.transition_states._interpolate
• pele.transition_states._nebdriver
• pele.transition_states._orthogopt
• pele.transition_states._transition_state_refinement
• pele.transition_states._tstools
• pele.transition_states._zeroev
• pele.transition_states.nebtesting.leps
• pele.utils
• pele.utils._cpp_utils
• pele.utils._pressure_tensor
• pele.utils.amber
• pele.utils.benchmark
• pele.utils.cell_scale
• pele.utils.disconnectivity_graph
• pele.utils.events
• pele.utils.frozen_atoms
• pele.utils.hessian
• pele.utils.histogram
• pele.utils.neighbor_list
• pele.utils.optim_compatibility
• pele.utils.pymolwrapper
• pele.utils.rbtools
• pele.utils.rotations
• pele.utils.vec3
• pele.utils.xyz