Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
W
_
__init__() (perses.analysis.Analysis method)
(perses.annihilation.HybridTopologyFactory method)
(perses.annihilation.ncmc_switching.NCMCEngine method)
(perses.bias.BiasEngine method)
(perses.bias.MinimizedPotentialBias method)
(perses.rjmc.geometry.BootstrapParticleFilter method)
(perses.rjmc.geometry.FFAllAngleGeometryEngine method)
(perses.rjmc.geometry.GeometryEngine method)
(perses.rjmc.geometry.GeometrySystemGenerator method)
(perses.rjmc.geometry.GeometrySystemGeneratorFast method)
(perses.rjmc.geometry.OmegaGeometryEngine method)
(perses.rjmc.geometry.PredAtomTopologyIndex method)
(perses.rjmc.geometry.PredHBond method)
(perses.rjmc.geometry.ProposalOrderTools method)
(perses.rjmc.topology_proposal.ButaneProposalEngine method)
(perses.rjmc.topology_proposal.NaphthaleneProposalEngine method)
(perses.rjmc.topology_proposal.NullProposalEngine method)
(perses.rjmc.topology_proposal.PeptideLibraryEngine method)
(perses.rjmc.topology_proposal.PointMutationEngine method)
(perses.rjmc.topology_proposal.PolymerProposalEngine method)
(perses.rjmc.topology_proposal.PremappedSmallMoleculeSetProposalEngine method)
(perses.rjmc.topology_proposal.PropaneProposalEngine method)
(perses.rjmc.topology_proposal.ProposalEngine method)
(perses.rjmc.topology_proposal.SmallMoleculeAtomMapper method)
(perses.rjmc.topology_proposal.SmallMoleculeSetProposalEngine method)
(perses.rjmc.topology_proposal.SystemGenerator method)
(perses.rjmc.topology_proposal.TopologyProposal method)
(perses.samplers.ExpandedEnsembleSampler method)
(perses.samplers.MultiTargetDesign method)
(perses.samplers.ProtonationStateSampler method)
(perses.samplers.SAMSSampler method)
(perses.storage.NetCDFStorage method)
A
Analysis (class in perses.analysis)
B
BiasEngine (class in perses.bias)
BootstrapParticleFilter (class in perses.rjmc.geometry)
build_system() (perses.rjmc.topology_proposal.SystemGenerator method)
ButaneProposalEngine (class in perses.rjmc.topology_proposal)
C
canonicalize_smiles() (perses.rjmc.topology_proposal.ButaneProposalEngine static method)
(perses.rjmc.topology_proposal.NaphthaleneProposalEngine static method)
(perses.rjmc.topology_proposal.NullProposalEngine static method)
(perses.rjmc.topology_proposal.PremappedSmallMoleculeSetProposalEngine static method)
(perses.rjmc.topology_proposal.PropaneProposalEngine static method)
(perses.rjmc.topology_proposal.SmallMoleculeSetProposalEngine static method)
clean_molecule_list() (perses.rjmc.topology_proposal.ButaneProposalEngine static method)
(perses.rjmc.topology_proposal.NaphthaleneProposalEngine static method)
(perses.rjmc.topology_proposal.NullProposalEngine static method)
(perses.rjmc.topology_proposal.PremappedSmallMoleculeSetProposalEngine static method)
(perses.rjmc.topology_proposal.PropaneProposalEngine static method)
(perses.rjmc.topology_proposal.SmallMoleculeSetProposalEngine static method)
close() (perses.storage.NetCDFStorage method)
compute_state_key() (perses.rjmc.topology_proposal.ButaneProposalEngine method)
(perses.rjmc.topology_proposal.NaphthaleneProposalEngine method)
(perses.rjmc.topology_proposal.NullProposalEngine method)
(perses.rjmc.topology_proposal.PeptideLibraryEngine method)
(perses.rjmc.topology_proposal.PointMutationEngine method)
(perses.rjmc.topology_proposal.PolymerProposalEngine method)
(perses.rjmc.topology_proposal.PremappedSmallMoleculeSetProposalEngine method)
(perses.rjmc.topology_proposal.PropaneProposalEngine method)
(perses.rjmc.topology_proposal.ProposalEngine method)
(perses.rjmc.topology_proposal.SmallMoleculeSetProposalEngine method)
CreatePredicateCopy() (perses.rjmc.geometry.PredAtomTopologyIndex method)
(perses.rjmc.geometry.PredHBond method)
D
determine_proposal_order() (perses.rjmc.geometry.ProposalOrderTools method)
E
ExpandedEnsembleSampler (class in perses.samplers)
extract_logP_values() (perses.analysis.Analysis method)
extract_state_trajectory() (perses.analysis.Analysis method)
F
FFAllAngleGeometryEngine (class in perses.rjmc.geometry)
from_json() (perses.rjmc.topology_proposal.SmallMoleculeAtomMapper class method)
G
g_k() (perses.bias.BiasEngine method)
(perses.bias.MinimizedPotentialBias method)
generate_and_check_proposal_matrix() (perses.rjmc.topology_proposal.SmallMoleculeAtomMapper method)
GeometryEngine (class in perses.rjmc.geometry)
GeometrySystemGenerator (class in perses.rjmc.geometry)
GeometrySystemGeneratorFast (class in perses.rjmc.geometry)
get_atom_maps() (perses.rjmc.topology_proposal.SmallMoleculeAtomMapper method)
get_environments() (perses.analysis.Analysis method)
get_free_energies() (perses.analysis.Analysis method)
get_log_weight() (perses.samplers.ExpandedEnsembleSampler method)
get_modified_system() (perses.rjmc.geometry.GeometrySystemGenerator method)
(perses.rjmc.geometry.GeometrySystemGeneratorFast method)
get_object() (perses.storage.NetCDFStorage method)
get_oemol_from_smiles() (perses.rjmc.topology_proposal.SmallMoleculeAtomMapper method)
get_smiles_index() (perses.rjmc.topology_proposal.SmallMoleculeAtomMapper method)
getForceField() (perses.rjmc.topology_proposal.SystemGenerator method)
H
handle_harmonic_angles() (perses.annihilation.HybridTopologyFactory method)
handle_harmonic_bonds() (perses.annihilation.HybridTopologyFactory method)
handle_nonbonded() (perses.annihilation.HybridTopologyFactory method)
handle_periodic_torsion_force() (perses.annihilation.HybridTopologyFactory method)
hybrid_positions (perses.annihilation.HybridTopologyFactory attribute)
hybrid_system (perses.annihilation.HybridTopologyFactory attribute)
hybrid_topology (perses.annihilation.HybridTopologyFactory attribute)
HybridTopologyFactory (class in perses.annihilation)
I
integrate() (perses.annihilation.ncmc_switching.NCMCEngine method)
L
logp_reverse() (perses.rjmc.geometry.FFAllAngleGeometryEngine method)
(perses.rjmc.geometry.GeometryEngine method)
(perses.rjmc.geometry.OmegaGeometryEngine method)
M
make_alchemical_system() (perses.annihilation.ncmc_switching.NCMCEngine method)
map_all_molecules() (perses.rjmc.topology_proposal.SmallMoleculeAtomMapper method)
MinimizedPotentialBias (class in perses.bias)
molecule_library_from_string() (perses.rjmc.topology_proposal.SmallMoleculeAtomMapper static method)
molecule_library_to_string() (perses.rjmc.topology_proposal.SmallMoleculeAtomMapper static method)
MultiTargetDesign (class in perses.samplers)
N
NaphthaleneProposalEngine (class in perses.rjmc.topology_proposal)
NCMCEngine (class in perses.annihilation.ncmc_switching)
NetCDFStorage (class in perses.storage)
new_positions() (perses.annihilation.HybridTopologyFactory method)
new_to_hybrid_atom_map (perses.annihilation.HybridTopologyFactory attribute)
NullProposalEngine (class in perses.rjmc.topology_proposal)
O
old_positions() (perses.annihilation.HybridTopologyFactory method)
old_to_hybrid_atom_map (perses.annihilation.HybridTopologyFactory attribute)
OmegaGeometryEngine (class in perses.rjmc.geometry)
omm_hybrid_topology (perses.annihilation.HybridTopologyFactory attribute)
P
PeptideLibraryEngine (class in perses.rjmc.topology_proposal)
plot_chemical_trajectory() (perses.analysis.Analysis method)
plot_exen_logp_components() (perses.analysis.Analysis method)
plot_ncmc_work_distributions() (perses.analysis.Analysis method)
plot_ncmc_work_old() (perses.analysis.Analysis method)
plot_sams_weights() (perses.analysis.Analysis method)
plot_work_trajectories() (perses.analysis.Analysis method)
PointMutationEngine (class in perses.rjmc.topology_proposal)
PolymerProposalEngine (class in perses.rjmc.topology_proposal)
precompute_gk() (perses.bias.MinimizedPotentialBias method)
PredAtomTopologyIndex (class in perses.rjmc.geometry)
PredHBond (class in perses.rjmc.geometry)
PremappedSmallMoleculeSetProposalEngine (class in perses.rjmc.topology_proposal)
PropaneProposalEngine (class in perses.rjmc.topology_proposal)
ProposalEngine (class in perses.rjmc.topology_proposal)
ProposalOrderTools (class in perses.rjmc.geometry)
propose() (perses.rjmc.geometry.FFAllAngleGeometryEngine method)
(perses.rjmc.geometry.GeometryEngine method)
(perses.rjmc.geometry.OmegaGeometryEngine method)
(perses.rjmc.topology_proposal.ButaneProposalEngine method)
(perses.rjmc.topology_proposal.NaphthaleneProposalEngine method)
(perses.rjmc.topology_proposal.NullProposalEngine method)
(perses.rjmc.topology_proposal.PeptideLibraryEngine method)
(perses.rjmc.topology_proposal.PointMutationEngine method)
(perses.rjmc.topology_proposal.PolymerProposalEngine method)
(perses.rjmc.topology_proposal.PremappedSmallMoleculeSetProposalEngine method)
(perses.rjmc.topology_proposal.PropaneProposalEngine method)
(perses.rjmc.topology_proposal.ProposalEngine method)
(perses.rjmc.topology_proposal.SmallMoleculeSetProposalEngine method)
ProtonationStateSampler (class in perses.samplers)
R
run() (perses.samplers.ExpandedEnsembleSampler method)
(perses.samplers.MultiTargetDesign method)
(perses.samplers.ProtonationStateSampler method)
(perses.samplers.SAMSSampler method)
S
SAMSSampler (class in perses.samplers)
set_growth_parameter_index() (perses.rjmc.geometry.GeometrySystemGenerator method)
(perses.rjmc.geometry.GeometrySystemGeneratorFast method)
SmallMoleculeAtomMapper (class in perses.rjmc.topology_proposal)
SmallMoleculeSetProposalEngine (class in perses.rjmc.topology_proposal)
sync() (perses.storage.NetCDFStorage method)
SystemGenerator (class in perses.rjmc.topology_proposal)
T
thisown (perses.rjmc.geometry.PredAtomTopologyIndex attribute)
(perses.rjmc.geometry.PredHBond attribute)
to_json() (perses.rjmc.topology_proposal.SmallMoleculeAtomMapper method)
TopologyProposal (class in perses.rjmc.topology_proposal)
U
update() (perses.samplers.ExpandedEnsembleSampler method)
(perses.samplers.MultiTargetDesign method)
(perses.samplers.ProtonationStateSampler method)
(perses.samplers.SAMSSampler method)
update_logZ_estimates() (perses.samplers.SAMSSampler method)
update_positions() (perses.samplers.ExpandedEnsembleSampler method)
update_sampler() (perses.samplers.SAMSSampler method)
update_samplers() (perses.samplers.MultiTargetDesign method)
(perses.samplers.ProtonationStateSampler method)
update_state() (perses.samplers.ExpandedEnsembleSampler method)
update_statistics() (perses.samplers.ExpandedEnsembleSampler method)
update_target_probabilities() (perses.samplers.MultiTargetDesign method)
(perses.samplers.ProtonationStateSampler method)
W
write_array() (perses.storage.NetCDFStorage method)
write_configuration() (perses.storage.NetCDFStorage method)
write_object() (perses.storage.NetCDFStorage method)
write_quantity() (perses.storage.NetCDFStorage method)
write_trajectory() (perses.analysis.Analysis method)
perses
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine
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Contents:
Installation
Changelog
Alchemical transformations
Bias engine
Molecular geometry generation via RJMC
Sampler stack
Storage handling
Analysis
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