Index

Symbols

"rsfe"]) command line option "SGE"]) command line option

"switch"]) command line option

_

__eq__() (transformato.mutate.DummyRegion method) (transformato.mutate.MutationDefinition method) __hash__ (transformato.mutate.DummyRegion attribute) (transformato.mutate.MutationDefinition attribute) __init__() (transformato.mutate.CommonCoreTransformation method) (transformato.mutate.DummyRegion method) (transformato.mutate.Mutation method) (transformato.mutate.MutationDefinition method) (transformato.mutate.ProposeMutationRoute method) (transformato.restraints.Restraint method) (transformato.state.IntermediateStateFactory method) (transformato.system.SystemStructure method) __repr__() (transformato.mutate.DummyRegion method) (transformato.mutate.MutationDefinition method) __weakref__ (transformato.mutate.CommonCoreTransformation attribute) (transformato.mutate.DummyRegion attribute) (transformato.mutate.Mutation attribute) (transformato.mutate.MutationDefinition attribute) (transformato.mutate.ProposeMutationRoute attribute) (transformato.restraints.Restraint attribute) (transformato.state.IntermediateStateFactory attribute) (transformato.system.SystemStructure attribute) _add_flatbottom_parameters() (transformato.restraints.Restraint method) _calculate_order_of_LJ_mutations() (transformato.mutate.ProposeMutationRoute static method) _check_for_lp() (transformato.mutate.ProposeMutationRoute method) _check_hmr() (transformato.state.IntermediateStateFactory method) _compensate_charge() (transformato.mutate.Mutation method)

_copy_charmm_files() (transformato.state.IntermediateStateFactory method) _copy_files() (transformato.state.IntermediateStateFactory method) _copy_omm_files() (transformato.state.IntermediateStateFactory method) _create_sdf_from_pdb() (transformato.system.SystemStructure method) _determine_offset_and_set_possible_dummy_properties() (transformato.system.SystemStructure method) _find_mcs() (transformato.mutate.ProposeMutationRoute method) _find_terminal_atom() (transformato.mutate.ProposeMutationRoute static method) _generate_rdkit_mol() (transformato.system.SystemStructure method) _get_atom_mapping() (transformato.mutate.CommonCoreTransformation method) _get_common_core() (transformato.mutate.ProposeMutationRoute method) _init_base_dir() (transformato.state.IntermediateStateFactory method) _init_intermediate_state_dir() (transformato.state.IntermediateStateFactory method) _initialize_system() (transformato.system.SystemStructure method) _match_terminal_real_and_dummy_atoms() (transformato.mutate.ProposeMutationRoute static method) _match_terminal_real_and_dummy_atoms_for_mol1() (transformato.mutate.ProposeMutationRoute method) _match_terminal_real_and_dummy_atoms_for_mol2() (transformato.mutate.ProposeMutationRoute method) _mutate_atoms() (transformato.mutate.CommonCoreTransformation method) _mutate_to_common_core() (transformato.mutate.ProposeMutationRoute method) _mutate_vdw() (transformato.mutate.Mutation method) _overwrite_simulation_script_parameters() (transformato.state.IntermediateStateFactory method) _read_parameters() (transformato.system.SystemStructure method) _scale_epsilon_and_rmin() (transformato.mutate.Mutation static method) _show_common_core() (transformato.mutate.ProposeMutationRoute method) _transform_common_core() (transformato.mutate.ProposeMutationRoute method) _write_amber_files() (transformato.state.IntermediateStateFactory method) _write_psf() (transformato.state.IntermediateStateFactory static method) _write_rtf_file() (transformato.state.IntermediateStateFactory method) _write_workload_preamble() (transformato.state.IntermediateStateFactory method)

A

add_idx_to_common_core_of_mol1() (transformato.mutate.ProposeMutationRoute method) add_idx_to_common_core_of_mol2() (transformato.mutate.ProposeMutationRoute method)

analyze_traj_with command line option applyForce() (transformato.restraints.Restraint method)

C

check_switching_function() (transformato.utils method) command line option "rsfe"]) "SGE"]) "switch"]) analyze_traj_with config cons: default:, [1], [2] dt: engine extremities False]) free-energy-type: GPU: group1,group2 input_dir k, [1] max_snapshots mini_nstep: name, [1] None] nr_of_mutation_steps_cc nr_of_mutation_steps_charge nstdcd: nstep: nstout: other output_dir scaling shape, [1] switch: tlc wellsize, [1] workload-manager:

CommonCoreTransformation (class in transformato.mutate) config command line option cons: command line option create_restraints_from_config() (transformato.restraints method) createForce() (transformato.restraints.Restraint method)

D

default: command line option, [1], [2]

dt: command line option DummyRegion (class in transformato.mutate)

E

engine command line option

extremities command line option

F

False]) command line option

finish_common_core() (transformato.mutate.ProposeMutationRoute method) free-energy-type: command line option

G

generate_atom_tables_from_psf() (transformato.system.SystemStructure method) generate_extremities() (transformato.restraints method) generate_mutations_to_common_core_for_mol1() (transformato.mutate.ProposeMutationRoute method) generate_mutations_to_common_core_for_mol2() (transformato.mutate.ProposeMutationRoute method) generate_simple_selection() (transformato.restraints method) get3DDistance() (transformato.restraints method) get_bin_dir() (transformato.utils method) get_common_core_idx_mol1() (transformato.mutate.ProposeMutationRoute method)

get_common_core_idx_mol2() (transformato.mutate.ProposeMutationRoute method) get_idx_of_all_atoms() (transformato.mutate.ProposeMutationRoute method) get_structure_name() (transformato.utils method) get_test_output_dir() (transformato.utils method) get_toppar_dir() (transformato.utils method) GPU: command line option group1,group2 command line option

I

input_dir command line option

IntermediateStateFactory (class in transformato.state) isnotebook() (transformato.utils method)

K

k command line option, [1]

L

load_config_yaml() (transformato.utils method)

M

map_lj_mutations_to_atom_idx() (transformato.utils method) max_snapshots command line option mini_nstep: command line option module transformato.mutate, [1] transformato.restraints, [1] transformato.state, [1] transformato.system, [1] transformato.utils, [1]

mutate() (transformato.mutate.CommonCoreTransformation method) (transformato.mutate.Mutation method) Mutation (class in transformato.mutate) MutationDefinition (class in transformato.mutate)

N

name command line option, [1] None] command line option nr_of_mutation_steps_cc command line option nr_of_mutation_steps_charge command line option

nstdcd: command line option nstep: command line option nstout: command line option

O

other command line option

output_dir command line option

P

perform_mutations() (transformato.mutate method) postprocessing() (transformato.utils method)

propose_common_core() (transformato.mutate.ProposeMutationRoute method) ProposeMutationRoute (class in transformato.mutate) psf_correction() (transformato.utils method)

R

Restraint (class in transformato.restraints)

run_simulation() (transformato.utils method)

S

scaling command line option shape command line option, [1]

show_common_core_on_mol1() (transformato.mutate.ProposeMutationRoute method) show_common_core_on_mol2() (transformato.mutate.ProposeMutationRoute method) switch: command line option SystemStructure (class in transformato.system)

T

tlc command line option transformato.mutate module, [1] transformato.restraints module, [1]

transformato.state module, [1] transformato.system module, [1] transformato.utils module, [1]

W

wellsize command line option, [1] workload-manager: command line option

write_restraints_yaml() (transformato.restraints method) write_state() (transformato.state.IntermediateStateFactory method)