SYMBOL INDEX (1088 symbols across 80 files)

FILE: basesetup.py
  function find_packages (line 17) | def find_packages():
  function check_dependencies (line 32) | def check_dependencies(dependencies):
  class CompilerDetection (line 67) | class CompilerDetection(object):
    method __init__ (line 78) | def __init__(self, disable_openmp):
    method _print_compiler_version (line 120) | def _print_compiler_version(self, cc):
    method hasfunction (line 132) | def hasfunction(self, funcname, include=None, libraries=None, extra_po...
    method _print_support_start (line 190) | def _print_support_start(self, feature):
    method _print_support_end (line 193) | def _print_support_end(self, feature, status):
    method _detect_openmp (line 199) | def _detect_openmp(self):
    method _detect_sse3 (line 209) | def _detect_sse3(self):
    method _detect_sse41 (line 218) | def _detect_sse41(self):
  function git_version (line 231) | def git_version():
  function write_version_py (line 258) | def write_version_py(VERSION, ISRELEASED, filename='MDTraj/version.py'):
  class StaticLibrary (line 291) | class StaticLibrary(Extension):
    method __init__ (line 292) | def __init__(self, *args, **kwargs):
  class build_ext (line 297) | class build_ext(_build_ext):
    method build_extension (line 299) | def build_extension(self, ext):
    method build_static_extension (line 305) | def build_static_extension(self, ext):

FILE: benchmarks/benchmark_analysis.py
  function get_simdir_list (line 30) | def get_simdir_list(base_dir='.', is_reversed=False):
  function get_simulations_data (line 58) | def get_simulations_data(simulation_dirs):
  function to_arsenic_csv (line 72) | def to_arsenic_csv(experimental_data: dict, simulation_data: list, out_c...

FILE: benchmarks/run_benchmarks.py
  function concatenate_files (line 33) | def concatenate_files(input_files, output_file):
  function run_relative_perturbation (line 44) | def run_relative_perturbation(lig_a_idx, lig_b_idx, reverse=False, tidy=...

FILE: examples/moonshot-mainseries/00-prep-receptor.py
  function read_pdb_file (line 19) | def read_pdb_file(pdb_file):
  function prepare_receptor (line 37) | def prepare_receptor(complex_pdb_filename, output_basepath, assembly_sta...
  function prepare_receptor_wrapper (line 394) | def prepare_receptor_wrapper(complex_pdb_file):

FILE: examples/moonshot-mainseries/02-generate-poses-posit.py
  function GetFragments (line 12) | def GetFragments(mol, minbonds, maxbonds):
  function GetCommonFragments (line 30) | def GetCommonFragments(mollist, frags,
  function GetCoreFragment (line 57) | def GetCoreFragment(refmol, mols,
  function GetFragmentScore (line 81) | def GetFragmentScore(mol):
  function expand_stereochemistry_star (line 89) | def expand_stereochemistry_star(mol):
  function expand_stereochemistry (line 113) | def expand_stereochemistry(mols):
  function expand_stereochemistry_serial (line 143) | def expand_stereochemistry_serial(mols):
  function expand_protonation_states_oemols (line 167) | def expand_protonation_states_oemols(mols):
  class BumpCheck (line 215) | class BumpCheck:
    method __init__ (line 216) | def __init__(self, prot_mol, cutoff=2.0):
    method count (line 220) | def count(self, lig_mol):
  function mmff_energy (line 227) | def mmff_energy(mol):
  function generate_restricted_conformers (line 244) | def generate_restricted_conformers(receptor, refmol, mol, core_smarts=No...
  function has_ic50 (line 386) | def has_ic50(mol):
  function get_series (line 403) | def get_series(mol):
  function generate_restricted_conformers_star (line 477) | def generate_restricted_conformers_star(args):
  function generate_restricted_conformers_best (line 489) | def generate_restricted_conformers_best(args):
  function generate_poses (line 558) | def generate_poses(receptor, refmol, target_molecules, output_filename, ...
  function filter_by_series (line 622) | def filter_by_series(mols, filter_series='3-aminopyridine-like'):
  function filter_by_IC50s (line 640) | def filter_by_IC50s(mols):
  function load_molecules (line 648) | def load_molecules(filename, append_warts=False):
  function load_fragment (line 688) | def load_fragment(fragid, protonation_state, title=None):
  function prepend_fragment_molecules (line 725) | def prepend_fragment_molecules(mols, fragments):
  function write_molecules (line 747) | def write_molecules(mols, filename):
  function read_design_unit (line 762) | def read_design_unit(fragid, assembly_state, protonation_state):

FILE: examples/moonshot-mainseries/02-generate-poses.py
  function GetFragments (line 12) | def GetFragments(mol, minbonds, maxbonds):
  function GetCommonFragments (line 30) | def GetCommonFragments(mollist, frags,
  function GetCoreFragment (line 57) | def GetCoreFragment(refmol, mols,
  function GetFragmentScore (line 81) | def GetFragmentScore(mol):
  function expand_stereochemistry_star (line 89) | def expand_stereochemistry_star(mol):
  function expand_stereochemistry (line 113) | def expand_stereochemistry(mols):
  function expand_stereochemistry_serial (line 143) | def expand_stereochemistry_serial(mols):
  function expand_protonation_states_oemols (line 167) | def expand_protonation_states_oemols(mols):
  class BumpCheck (line 215) | class BumpCheck:
    method __init__ (line 216) | def __init__(self, prot_mol, cutoff=2.0):
    method count (line 220) | def count(self, lig_mol):
  function mmff_energy (line 227) | def mmff_energy(mol):
  function generate_restricted_conformers (line 244) | def generate_restricted_conformers(receptor, refmol, mol, core_smarts=No...
  function has_ic50 (line 460) | def has_ic50(mol):
  function get_series (line 477) | def get_series(mol):
  function generate_restricted_conformers_star (line 554) | def generate_restricted_conformers_star(args):
  function generate_restricted_conformers_best (line 597) | def generate_restricted_conformers_best(args):
  function generate_poses (line 672) | def generate_poses(receptor, refmol, target_molecules, output_filename, ...
  function filter_by_series (line 736) | def filter_by_series(mols, filter_series='3-aminopyridine-like'):
  function filter_by_IC50s (line 754) | def filter_by_IC50s(mols):
  function load_molecules (line 762) | def load_molecules(filename, append_warts=False):
  function load_fragment (line 802) | def load_fragment(fragid, protonation_state, title=None):
  function prepend_fragment_molecules (line 839) | def prepend_fragment_molecules(mols, fragments):
  function write_molecules (line 861) | def write_molecules(mols, filename):
  function read_receptor (line 876) | def read_receptor(fragid, assembly_state, protonation_state):

FILE: examples/moonshot-mainseries/03-list-absent-molecules.py
  function GetFragments (line 12) | def GetFragments(mol, minbonds, maxbonds):
  function GetCommonFragments (line 30) | def GetCommonFragments(mollist, frags,
  function GetCoreFragment (line 57) | def GetCoreFragment(refmol, mols,
  function GetFragmentScore (line 81) | def GetFragmentScore(mol):
  function expand_stereochemistry_star (line 89) | def expand_stereochemistry_star(mol):
  function expand_stereochemistry (line 113) | def expand_stereochemistry(mols):
  function expand_protonation_states (line 145) | def expand_protonation_states(mols):
  class BumpCheck (line 193) | class BumpCheck:
    method __init__ (line 194) | def __init__(self, prot_mol, cutoff=2.0):
    method count (line 198) | def count(self, lig_mol):
  function mmff_energy (line 205) | def mmff_energy(mol):
  function generate_restricted_conformers (line 222) | def generate_restricted_conformers(receptor, refmol, mol, core_smarts=No...
  function has_ic50 (line 424) | def has_ic50(mol):
  function get_series (line 441) | def get_series(mol):
  function generate_restricted_conformers_star (line 518) | def generate_restricted_conformers_star(args):
  function generate_poses (line 561) | def generate_poses(receptor, refmol, target_molecules, output_filename):
  function filter_by_series (line 620) | def filter_by_series(mols, filter_series='3-aminopyridine-like'):
  function filter_by_IC50s (line 638) | def filter_by_IC50s(mols):
  function load_molecules (line 646) | def load_molecules(filename, append_warts=False):
  function load_fragment (line 683) | def load_fragment(fragid, protonation_state, title=None):
  function prepend_fragment_molecules (line 720) | def prepend_fragment_molecules(mols, fragments):
  function write_molecules (line 742) | def write_molecules(mols, filename):
  function read_receptor (line 757) | def read_receptor(fragid, assembly_state, protonation_state):

FILE: examples/moonshot-mainseries/molecules/filter-cdd-export.py
  function pIC50 (line 34) | def pIC50(IC50_series):
  function DeltaG (line 37) | def DeltaG(pIC50):

FILE: examples/moonshot-mainseries/perses/analyze-benchmark-pKa.py
  function get_molecule_titles (line 14) | def get_molecule_titles(filename, add_warts=False):
  function get_experimental_data (line 64) | def get_experimental_data(filename):
  function get_microstate_info (line 91) | def get_microstate_info(filename):
  function get_experimental_data_network (line 133) | def get_experimental_data_network(filename):
  function collapse_states (line 186) | def collapse_states(perses_graph, microstates):
  function get_perses_realtime_statistics (line 273) | def get_perses_realtime_statistics(basepath, trajectory_prefix='out'):
  function get_perses_network_results (line 305) | def get_perses_network_results(basepath, trajectory_prefix='out'):
  function solve_mle (line 393) | def solve_mle(graph):
  function generate_arsenic_plots (line 410) | def generate_arsenic_plots(experimental_data_graph, perses_graph, arseni...
  function display_predictions (line 494) | def display_predictions(graph):
  function plot_sign_accuracy (line 540) | def plot_sign_accuracy(perses_graph, experimental_graph, filename):

FILE: examples/moonshot-mainseries/perses/extract-trajectories.py
  function new_positions (line 29) | def new_positions(htf, hybrid_positions):
  function old_positions (line 34) | def old_positions(htf, hybrid_positions):
  function extract_single_trajectory (line 39) | def extract_single_trajectory(phase, htf, state):
  function read_htfs (line 86) | def read_htfs(htf_filename):
  function extract_trajectories (line 110) | def extract_trajectories(path, prefix, extract, outpath, phase, index):

FILE: examples/moonshot-mainseries/perses/run-perses.py
  function load_molecules (line 6) | def load_molecules(filename, append_warts=False):
  function enumerate_transformations (line 47) | def enumerate_transformations():
  function cli (line 90) | def cli():
  function count (line 94) | def count():
  function run (line 106) | def run(index):

FILE: notebooks/plotting_tools.py
  class NonequilibriumSwitchingAnalysis (line 6) | class NonequilibriumSwitchingAnalysis(object):
    method __init__ (line 11) | def __init__(self, trajectory_directory, trajectory_prefix):
    method get_nonequilibrium_trajectory (line 65) | def get_nonequilibrium_trajectory(self, direction, trajectory_index):
    method lambda_zero_traj (line 94) | def lambda_zero_traj(self):
    method lambda_one_traj (line 107) | def lambda_one_traj(self):
    method cumulative_work (line 120) | def cumulative_work(self):

FILE: perses/__init__.py
  function get_datadir (line 3) | def get_datadir():

FILE: perses/_version.py
  function get_keywords (line 20) | def get_keywords():
  class VersioneerConfig (line 33) | class VersioneerConfig:
  function get_config (line 37) | def get_config():
  class NotThisMethod (line 51) | class NotThisMethod(Exception):
  function register_vcs_handler (line 59) | def register_vcs_handler(vcs, method):  # decorator
  function run_command (line 70) | def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
  function versions_from_parentdir (line 105) | def versions_from_parentdir(parentdir_prefix, root, verbose):
  function git_get_keywords (line 131) | def git_get_keywords(versionfile_abs):
  function git_versions_from_keywords (line 160) | def git_versions_from_keywords(keywords, tag_prefix, verbose):
  function git_pieces_from_vcs (line 219) | def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_comma...
  function plus_or_dot (line 313) | def plus_or_dot(pieces):
  function render_pep440 (line 320) | def render_pep440(pieces):
  function render_pep440_pre (line 345) | def render_pep440_pre(pieces):
  function render_pep440_post (line 361) | def render_pep440_post(pieces):
  function render_pep440_old (line 388) | def render_pep440_old(pieces):
  function render_git_describe (line 410) | def render_git_describe(pieces):
  function render_git_describe_long (line 430) | def render_git_describe_long(pieces):
  function render (line 450) | def render(pieces, style):
  function get_versions (line 482) | def get_versions():

FILE: perses/analysis/analysis.py
  class Analysis (line 39) | class Analysis(object):
    method __init__ (line 43) | def __init__(self, storage_filename):
    method get_environments (line 59) | def get_environments(self):
    method _state_transition_to_iupac (line 73) | def _state_transition_to_iupac(self, state_transition):
    method plot_work_trajectories (line 98) | def plot_work_trajectories(self, environment, filename):
    method plot_sams_weights (line 137) | def plot_sams_weights(self, environment):
    method plot_chemical_trajectory (line 144) | def plot_chemical_trajectory(self, environment, filename):
    method get_free_energies (line 179) | def get_free_energies(self, environment):
    method _get_state_transitions (line 214) | def _get_state_transitions(self):
    method write_trajectory (line 252) | def write_trajectory(self, environmnent, pdb_filename):
    method extract_logP_values (line 265) | def extract_logP_values(self, environment, logP_accept_component, subt...
    method _prepare_logP_accept (line 307) | def _prepare_logP_accept(self, environment):
    method extract_state_trajectory (line 337) | def extract_state_trajectory(self, environment):
    method plot_ncmc_work_distributions (line 362) | def plot_ncmc_work_distributions(self, environment, output_filename):
    method plot_exen_logp_components (line 404) | def plot_exen_logp_components(self, environment, filename_prefix=None,...
    method plot_ncmc_work_old (line 478) | def plot_ncmc_work_old(self, filename):

FILE: perses/analysis/cycles.py
  function pathway (line 18) | def pathway(nodes):
  function get_attr (line 39) | def get_attr(G, nodeA, nodeB, attr='dg'):
  function combine_errors (line 60) | def combine_errors(errors):
  function cycle_closure (line 63) | def cycle_closure(G, steps, verbose=False):
  function plot_comparison (line 107) | def plot_comparison(x,y,X,Y, title='',shaded=True,color='blue'):

FILE: perses/analysis/extract_trajectory.py
  function get_hybrid_topology (line 12) | def get_hybrid_topology(file):
  function get_positions (line 38) | def get_positions(file):
  function write_trajectory (line 50) | def write_trajectory(positions, topology, outputfile='trajectory.pdb',ce...

FILE: perses/analysis/fah_analysis.py
  function _strip_outliers (line 19) | def _strip_outliers(w, max_value=1e4, n_devs=5):
  function _get_works (line 41) | def _get_works(df, run, project, GEN=None):
  function free_energies (line 71) | def free_energies(

FILE: perses/analysis/load_simulations.py
  class Simulation (line 7) | class Simulation(object):
    method __init__ (line 68) | def __init__(self, directory):
    method _load_data (line 104) | def _load_data(self):
    method report (line 156) | def report(self):
    method historic_fes (line 163) | def historic_fes(self, stepsize=100):
    method sample_history (line 221) | def sample_history(self, method='binding'):
    method reset_history (line 251) | def reset_history(self):

FILE: perses/analysis/resample.py
  function samples_correlated (line 6) | def samples_correlated(arrays, seed=None):
  function samples_uncorrelated (line 53) | def samples_uncorrelated(arrays, seed=None):
  function _bootstrap (line 94) | def _bootstrap(get_samples, f, n_iters, seed):
  function bootstrap_correlated (line 117) | def bootstrap_correlated(f, n_iters=100, seed=None):
  function bootstrap_uncorrelated (line 154) | def bootstrap_uncorrelated(f, n_iters=100, seed=None):

FILE: perses/analysis/utils.py
  function open_netcdf (line 6) | def open_netcdf(filename):
  function get_offline_free_energies (line 18) | def get_offline_free_energies(filename,offline_frequency=10):
  function get_t0 (line 34) | def get_t0(filename):
  function plot_replica_mixing (line 44) | def plot_replica_mixing(ncfile_name, title='',filename='replicas.png'):

FILE: perses/analysis/visualization.py
  function _check_pymol (line 32) | def _check_pymol():
  function _check_mpy (line 39) | def _check_mpy():
  class Visualization (line 61) | class Visualization(object):
    method __init__ (line 85) | def __init__(self, old_pdb,
    method load (line 167) | def load(self):
    method format (line 214) | def format(self,
    method _set_transparency (line 332) | def _set_transparency(self, old_transparency, new_transparency, old_se...
    method save_frames (line 353) | def save_frames(self,
    method save_mp4 (line 398) | def save_mp4(frames, outfile="movie.mp4", fps=25):

FILE: perses/annihilation/lambda_protocol.py
  class LambdaProtocol (line 11) | class LambdaProtocol(object):
    method __init__ (line 38) | def __init__(self, functions='default'):
    method _validate_functions (line 138) | def _validate_functions(self,n=10):
    method _check_for_naked_charges (line 175) | def _check_for_naked_charges(self,n=10):
    method get_functions (line 196) | def get_functions(self):
    method plot_functions (line 199) | def plot_functions(self,n=50):
  class RESTProtocol (line 212) | class RESTProtocol(object):
    method __init__ (line 221) | def __init__(self):
  class RESTCapableLambdaProtocol (line 224) | class RESTCapableLambdaProtocol(object):
    method __init__ (line 281) | def __init__(self, functions='default'):
  class RelativeAlchemicalState (line 293) | class RelativeAlchemicalState(AlchemicalState):
    class _LambdaParameter (line 312) | class _LambdaParameter(AlchemicalState._LambdaParameter):
    method set_alchemical_parameters (line 322) | def set_alchemical_parameters(self, global_lambda,
  class RESTState (line 337) | class RESTState(AlchemicalState):
    class _LambdaParameter (line 350) | class _LambdaParameter(AlchemicalState._LambdaParameter):
      method lambda_validator (line 352) | def lambda_validator(self, instance, parameter_value):
    method set_alchemical_parameters (line 362) | def set_alchemical_parameters(self,
  class RESTCapableRelativeAlchemicalState (line 379) | class RESTCapableRelativeAlchemicalState(AlchemicalState):
    class _LambdaParameter (line 432) | class _LambdaParameter(AlchemicalState._LambdaParameter):
      method lambda_validator (line 434) | def lambda_validator(self, instance, parameter_value):
    method set_alchemical_parameters (line 462) | def set_alchemical_parameters(self, global_lambda, beta0, beta, lambda...

FILE: perses/annihilation/ncmc_switching.py
  class NaNException (line 20) | class NaNException(Exception):
    method __init__ (line 21) | def __init__(self, *args, **kwargs):
  class NCMCEngine (line 24) | class NCMCEngine(object):
    method __init__ (line 45) | def __init__(self, temperature=default_temperature, functions=None, ns...
    method beta (line 126) | def beta(self):
    method _compute_energy_contribution (line 131) | def _compute_energy_contribution(self, hybrid_thermodynamic_state, ini...
    method _topology_proposal_to_thermodynamic_states (line 160) | def _topology_proposal_to_thermodynamic_states(self, topology_proposal):
    method make_alchemical_system (line 185) | def make_alchemical_system(self, topology_proposal, current_positions,...
    method integrate (line 223) | def integrate(self, topology_proposal, initial_sampler_state, proposed...

FILE: perses/annihilation/relative.py
  class HybridTopologyFactory (line 16) | class HybridTopologyFactory(object):
    method __init__ (line 65) | def __init__(self,
    method _validate_disjoint_sets (line 371) | def _validate_disjoint_sets(self):
    method _handle_virtual_sites (line 386) | def _handle_virtual_sites(self):
    method _determine_core_atoms_in_topology (line 411) | def _determine_core_atoms_in_topology(self, topology, unique_atoms, ma...
    method _determine_atom_classes (line 453) | def _determine_atom_classes(self):
    method _translate_nonbonded_method_to_custom (line 494) | def _translate_nonbonded_method_to_custom(self, standard_nonbonded_met...
    method _handle_constraints (line 518) | def _handle_constraints(self):
    method _determine_interaction_group (line 542) | def _determine_interaction_group(self, atoms_in_interaction):
    method _add_bond_force_terms (line 588) | def _add_bond_force_terms(self):
    method _add_angle_force_terms (line 626) | def _add_angle_force_terms(self):
    method _add_torsion_force_terms (line 698) | def _add_torsion_force_terms(self, add_custom_core_force=True, add_uni...
    method _add_nonbonded_force_terms (line 741) | def _add_nonbonded_force_terms(self, add_custom_sterics_force=True):
    method _nonbonded_custom_sterics_common (line 852) | def _nonbonded_custom_sterics_common(self):
    method _nonbonded_custom (line 872) | def _nonbonded_custom(self, v2):
    method _nonbonded_custom_mixing_rules (line 897) | def _nonbonded_custom_mixing_rules(self):
    method _find_bond_parameters (line 915) | def _find_bond_parameters(self, bond_force, index1, index2):
    method handle_harmonic_bonds (line 942) | def handle_harmonic_bonds(self):
    method _find_angle_parameters (line 1069) | def _find_angle_parameters(self, angle_force, indices):
    method _find_torsion_parameters (line 1098) | def _find_torsion_parameters(self, torsion_force, indices):
    method handle_harmonic_angles (line 1131) | def handle_harmonic_angles(self):
    method handle_periodic_torsion_force (line 1292) | def handle_periodic_torsion_force(self):
    method handle_nonbonded (line 1386) | def handle_nonbonded(self):
    method _generate_dict_from_exceptions (line 1493) | def _generate_dict_from_exceptions(self, force):
    method _handle_interaction_groups (line 1517) | def _handle_interaction_groups(self):
    method _handle_hybrid_exceptions (line 1562) | def _handle_hybrid_exceptions(self):
    method _handle_original_exceptions (line 1660) | def _handle_original_exceptions(self):
    method handle_old_new_exceptions (line 1803) | def handle_old_new_exceptions(self):
    method _find_exception (line 1903) | def _find_exception(self, force, index1, index2):
    method _compute_hybrid_positions (line 1930) | def _compute_hybrid_positions(self):
    method _create_topology (line 1963) | def _create_topology(self):
    method _impose_virtual_bonds (line 2038) | def _impose_virtual_bonds(self):
    method _impose_rmsd_restraint (line 2099) | def _impose_rmsd_restraint(self):
    method old_positions (line 2153) | def old_positions(self, hybrid_positions):
    method new_positions (line 2175) | def new_positions(self, hybrid_positions):
    method hybrid_system (line 2198) | def hybrid_system(self):
    method new_to_hybrid_atom_map (line 2210) | def new_to_hybrid_atom_map(self):
    method old_to_hybrid_atom_map (line 2222) | def old_to_hybrid_atom_map(self):
    method hybrid_positions (line 2234) | def hybrid_positions(self):
    method hybrid_topology (line 2247) | def hybrid_topology(self):
    method omm_hybrid_topology (line 2259) | def omm_hybrid_topology(self):
  class RepartitionedHybridTopologyFactory (line 2269) | class RepartitionedHybridTopologyFactory(HybridTopologyFactory):
    method __init__ (line 2276) | def __init__(self,
    method _handle_bonds (line 2447) | def _handle_bonds(self):
    method _handle_angles (line 2492) | def _handle_angles(self):
    method _handle_torsions (line 2538) | def _handle_torsions(self):
    method _handle_nonbonded (line 2587) | def _handle_nonbonded(self):
    method _handle_exceptions (line 2658) | def _handle_exceptions(self):
  class RESTCapableHybridTopologyFactory (line 2701) | class RESTCapableHybridTopologyFactory(HybridTopologyFactory):
    method __init__ (line 3027) | def __init__(self,
    method _generate_rest_region (line 3200) | def _generate_rest_region(self):
    method _build_hybrid_particles (line 3234) | def _build_hybrid_particles(self):
    method _validate_disjoint_sets (line 3267) | def _validate_disjoint_sets(self):
    method get_rest_identifier (line 3281) | def get_rest_identifier(self, particles):
    method get_alch_identifier (line 3338) | def get_alch_identifier(self, particles):
    method _create_bond_force (line 3380) | def _create_bond_force(self):
    method _copy_bonds (line 3447) | def _copy_bonds(self):
    method _create_angle_force (line 3542) | def _create_angle_force(self):
    method _copy_angles (line 3592) | def _copy_angles(self):
    method _create_torsion_force (line 3693) | def _create_torsion_force(self):
    method _copy_torsions (line 3749) | def _copy_torsions(self):
    method _create_electrostatics_force (line 3879) | def _create_electrostatics_force(self):
    method _create_scaled_sterics_force (line 3945) | def _create_scaled_sterics_force(self):
    method _create_reciprocal_space_force (line 4037) | def _create_reciprocal_space_force(self):
    method _create_nonscaled_sterics_force (line 4085) | def _create_nonscaled_sterics_force(self):
    method _copy_nonbondeds (line 4127) | def _copy_nonbondeds(self):
    method _create_exceptions_force (line 4236) | def _create_exceptions_force(self):
    method _copy_exceptions (line 4296) | def _copy_exceptions(self):

FILE: perses/annihilation/rest.py
  class RESTTopologyFactory (line 18) | class RESTTopologyFactory(HybridTopologyFactory):
    method __init__ (line 33) | def __init__(self, system, solute_region, use_dispersion_correction=Fa...
    method _handle_constraints (line 106) | def _handle_constraints(self):
    method _add_bond_force_terms (line 111) | def _add_bond_force_terms(self):
    method scaling_expression (line 128) | def scaling_expression(self, nb=False):
    method _add_angle_force_terms (line 140) | def _add_angle_force_terms(self):
    method _add_torsion_force_terms (line 157) | def _add_torsion_force_terms(self):
    method _add_nonbonded_force_terms (line 175) | def _add_nonbonded_force_terms(self):
    method get_identifier (line 208) | def get_identifier(self, particles):
    method _add_bonds (line 222) | def _add_bonds(self):
    method _add_angles (line 232) | def _add_angles(self):
    method _add_torsions (line 239) | def _add_torsions(self):
    method _add_nonbondeds (line 246) | def _add_nonbondeds(self):
    method REST_system (line 276) | def REST_system(self):

FILE: perses/app/cli.py
  function _check_openeye_license (line 69) | def _check_openeye_license():
  function _test_platform (line 75) | def _test_platform(platform_name):
  function cli (line 88) | def cli(yaml, platform_name, override):

FILE: perses/app/fah_generator.py
  class TimeFilter (line 18) | class TimeFilter(logging.Filter):
    method filter (line 22) | def filter(self, record):
  function make_neq_integrator (line 68) | def make_neq_integrator(nsteps_eq=250000, nsteps_neq=250000, neq_splitti...
  function make_core_file (line 99) | def make_core_file(numSteps,
  function relax_structure (line 160) | def relax_structure(temperature,
  function run_neq_fah_setup (line 235) | def run_neq_fah_setup(ligand_file,
  function run (line 620) | def run(yaml_filename=None):

FILE: perses/app/relative_hydration.py
  function simulate_hybrid (line 12) | def simulate_hybrid(hybrid_system,functions, lambda_value, positions, ns...
  function check_alchemical_hybrid_elimination_bar (line 23) | def check_alchemical_hybrid_elimination_bar(topology_proposal, old_posit...

FILE: perses/app/relative_point_mutation_setup.py
  class PointMutationExecutor (line 34) | class PointMutationExecutor(object):
    method __init__ (line 107) | def __init__(self,
    method generate_htf (line 475) | def generate_htf(self, factory, topology_proposal, old_positions, new_...
    method get_complex_htf (line 549) | def get_complex_htf(self):
    method get_apo_htf (line 558) | def get_apo_htf(self):
    method get_complex_rhtf_0 (line 567) | def get_complex_rhtf_0(self):
    method get_apo_rhtf_0 (line 576) | def get_apo_rhtf_0(self):
    method get_complex_rhtf_1 (line 585) | def get_complex_rhtf_1(self):
    method get_apo_rhtf_1 (line 594) | def get_apo_rhtf_1(self):
    method get_apo_rest_htf (line 603) | def get_apo_rest_htf(self):
    method get_complex_rest_htf (line 612) | def get_complex_rest_htf(self):
    method _solvate (line 621) | def _solvate(self,
    method _handle_charge_changes (line 688) | def _handle_charge_changes(self, topology_proposal, new_positions):

FILE: perses/app/relative_setup.py
  class RelativeFEPSetup (line 37) | class RelativeFEPSetup(object):
    method __init__ (line 43) | def __init__(self,
    method _setup_complex_phase (line 592) | def _setup_complex_phase(self):
    method _generate_solvent_topologies (line 641) | def _generate_solvent_topologies(self, topology_proposal, old_positions):
    method _generate_vacuum_topologies (line 730) | def _generate_vacuum_topologies(self, topology_proposal, old_positions):
    method _make_new_deterministic_positions (line 799) | def _make_new_deterministic_positions(self, phase):
    method _solvate_system (line 824) | def _solvate_system(self, topology, positions, model='tip3p',phase='co...
    method _handle_charge_changes (line 887) | def _handle_charge_changes(self, topology_proposal, new_positions):
    method _store_phase_topologies (line 919) | def _store_phase_topologies(self, phase: str):
    method complex_topology_proposal (line 976) | def complex_topology_proposal(self):
    method complex_old_positions (line 980) | def complex_old_positions(self):
    method complex_new_positions (line 984) | def complex_new_positions(self):
    method solvent_topology_proposal (line 988) | def solvent_topology_proposal(self):
    method solvent_old_positions (line 992) | def solvent_old_positions(self):
    method solvent_new_positions (line 996) | def solvent_new_positions(self):
    method vacuum_topology_proposal (line 1000) | def vacuum_topology_proposal(self):
    method vacuum_old_positions (line 1004) | def vacuum_old_positions(self):
    method vacuum_new_positions (line 1008) | def vacuum_new_positions(self):
  class DaskClient (line 1011) | class DaskClient(object):
    method __init__ (line 1024) | def __init__(self):
    method activate_client (line 1027) | def activate_client(self,
    method deactivate_client (line 1053) | def deactivate_client(self):
    method scatter (line 1062) | def scatter(self, df):
    method deploy (line 1072) | def deploy(self, func, arguments):
    method gather_results (line 1095) | def gather_results(self, futures):
    method wait (line 1113) | def wait(self, futures):
  class NonequilibriumSwitchingFEP (line 1123) | class NonequilibriumSwitchingFEP(DaskClient):
    method __init__ (line 1128) | def __init__(self,
    method compute_nonalchemical_perturbations (line 1305) | def compute_nonalchemical_perturbations(self, start, end, sampler_stat...
    method instantiate_particles (line 1381) | def instantiate_particles(self,
    method algorithm_4 (line 1504) | def algorithm_4(self,
    method gather_neq_results (line 1668) | def gather_neq_results(self):
    method compute_sMC_free_energy (line 1708) | def compute_sMC_free_energy(self):
    method attempt_resample (line 1721) | def attempt_resample(self, observable = 'ESS', resampling_method = 'mu...
    method ESS (line 1793) | def ESS(works_prev, works_incremental):
    method CESS (line 1818) | def CESS(works_prev, works_incremental):
    method multinomial_resample (line 1845) | def multinomial_resample(cumulative_works, sampler_states, num_resampl...
    method binary_search (line 1878) | def binary_search(self,
    method equilibrate (line 1966) | def equilibrate(self,
    method modify_thermodynamic_state (line 2092) | def modify_thermodynamic_state(self, thermodynamic_state, current_lamb...
    method pull_trajectory_snapshot (line 2101) | def pull_trajectory_snapshot(self, endstate):
    method _adjust_for_correlation (line 2132) | def _adjust_for_correlation(self, timeseries_array: np.array):
    method _endpoint_perturbations (line 2153) | def _endpoint_perturbations(self, direction = None, num_subsamples = 1...
    method _alchemical_free_energy (line 2208) | def _alchemical_free_energy(self, num_subsamples = 100):
    method current_free_energy_estimate (line 2230) | def current_free_energy_estimate(self):

FILE: perses/app/setup_relative_calculation.py
  class TimeFilter (line 23) | class TimeFilter(logging.Filter):
    method filter (line 24) | def filter(self, record):
  function getSetupOptions (line 47) | def getSetupOptions(filename, override_string=None):
  function get_openmm_platform (line 341) | def get_openmm_platform(platform_name=None):
  function run_setup (line 372) | def run_setup(setup_options, serialize_systems=True, build_samplers=True):
  function run (line 753) | def run(yaml_filename=None, override_string=None):
  function _resume_run (line 991) | def _resume_run(setup_options):
  function _process_overrides (line 1051) | def _process_overrides(overrides, yaml_options):
  function _generate_htf (line 1093) | def _generate_htf(phase: str, topology_proposal_dictionary: dict, setup_...
  function _validate_endstate_energies_for_htf (line 1134) | def _validate_endstate_energies_for_htf(hybrid_topology_factory_dict: di...
  function _generate_parsed_yaml (line 1165) | def _generate_parsed_yaml(setup_options, input_yaml_file_path):

FILE: perses/bias/bias_engine.py
  class BiasEngine (line 14) | class BiasEngine(object):
    method __init__ (line 24) | def __init__(self, metadata):
    method g_k (line 27) | def g_k(self, molecule_smiles):
  class MinimizedPotentialBias (line 43) | class MinimizedPotentialBias(BiasEngine):
    method __init__ (line 58) | def __init__(self, smiles_list, implicit_solvent=None, constraints=app...
    method _create_molecule_list (line 69) | def _create_molecule_list(self, smiles_list):
    method _create_implicit_solvent_openmm (line 92) | def _create_implicit_solvent_openmm(self, mol):
    method g_k (line 122) | def g_k(self, molecule_smiles):
    method precompute_gk (line 151) | def precompute_gk(self):

FILE: perses/data/constant-pH/imidazole/generate-protomers-from-smiles.py
  function read_molecules (line 18) | def read_molecules(filename):
  function DumpSDData (line 49) | def DumpSDData(mol):
  function retrieve_url (line 58) | def retrieve_url(url, filename):
  function read_molecule (line 67) | def read_molecule(filename):
  function fix_mol2_resname (line 77) | def fix_mol2_resname(filename, residue_name):
  function write_mol2_preserving_atomnames (line 87) | def write_mol2_preserving_atomnames(filename, molecules, residue_name):
  function enumerate_conformations (line 101) | def enumerate_conformations(name, smiles=None, pdbname=None):

FILE: perses/dispersed/feptasks.py
  class Particle (line 29) | class Particle():
    method __init__ (line 116) | def __init__(self,
    method anneal (line 244) | def anneal(self, new, num_integration_steps = 1):
    method attempt_termination (line 310) | def attempt_termination(self):
    method compute_incremental_work (line 333) | def compute_incremental_work(self, _lambda):
    method save_configuration (line 345) | def save_configuration(self, iteration):
    method launch_particle (line 378) | def launch_particle(task):
    method distribute_anneal (line 444) | def distribute_anneal(task, new, num_integration_steps = 1):
    method update_incremental_work (line 468) | def update_incremental_work(task, index):
    method pull_sampler_state (line 480) | def pull_sampler_state(task):
    method pull_cumulative_work (line 488) | def pull_cumulative_work(task):
    method pull_cumulative_work_profile (line 495) | def pull_cumulative_work_profile(task):
    method pull_work_increments (line 503) | def pull_work_increments(task):
    method pull_current_lambda (line 516) | def pull_current_lambda(task):
    method pull_shadow_work (line 528) | def pull_shadow_work(task):
    method pull_timers (line 535) | def pull_timers(task):
    method pull_success (line 542) | def pull_success(task):
    method pull_labels (line 549) | def pull_labels(task):
    method pull_last_label (line 556) | def pull_last_label(task):
    method push_resamples (line 564) | def push_resamples(task, sampler_state, label, work):
    method push_cumulative_work (line 577) | def push_cumulative_work(task, work):
    method check_NonequilibriumFEPTask (line 585) | def check_NonequilibriumFEPTask(task):
    method write_nonequilibrium_trajectory (line 618) | def write_nonequilibrium_trajectory(nonequilibrium_trajectory, traject...
  function check_EquilibriumFEPTask (line 639) | def check_EquilibriumFEPTask(task):
  function minimize (line 659) | def minimize(thermodynamic_state: states.ThermodynamicState, sampler_sta...
  function compute_reduced_potential (line 692) | def compute_reduced_potential(thermodynamic_state: states.ThermodynamicS...
  function write_nonequilibrium_trajectory (line 714) | def write_nonequilibrium_trajectory(nonequilibrium_trajectory, trajector...
  function write_equilibrium_trajectory (line 735) | def write_equilibrium_trajectory(trajectory: md.Trajectory, trajectory_f...
  function compute_nonalchemical_perturbation (line 759) | def compute_nonalchemical_perturbation(alchemical_thermodynamic_state: s...
  function compute_timeseries (line 814) | def compute_timeseries(reduced_potentials: np.array) -> list:
  function run_equilibrium (line 827) | def run_equilibrium(task):

FILE: perses/dispersed/parallel.py
  class Parallelism (line 9) | class Parallelism(object):
    method activate_client (line 23) | def activate_client(self,
    method deactivate_client (line 81) | def deactivate_client(self):
    method scatter (line 107) | def scatter(self, df, workers = None):
    method deploy (line 137) | def deploy(self, func, arguments, workers = None):
    method run_all (line 170) | def run_all(self, func, arguments, workers):
    method gather_results (line 198) | def gather_results(self, futures, omit_errors = False):
    method gather_actor_result (line 226) | def gather_actor_result(self, future):
    method launch_actor (line 246) | def launch_actor(self, _class):
    method progress (line 272) | def progress(self, futures):
    method wait (line 291) | def wait(self, futures):

FILE: perses/dispersed/smc.py
  class SequentialMonteCarlo (line 22) | class SequentialMonteCarlo():
    method __init__ (line 33) | def __init__(self,
    method implement_parallelism (line 187) | def implement_parallelism(self, external_parallelism, internal_paralle...
    method _activate_annealing_workers (line 223) | def _activate_annealing_workers(self):
    method _deactivate_annealing_workers (line 260) | def _deactivate_annealing_workers(self):
    method AIS (line 281) | def AIS(self,
    method sMC (line 403) | def sMC(self,
    method compute_sMC_free_energy (line 712) | def compute_sMC_free_energy(self, cumulative_work_dict):
    method minimize_sampler_states (line 734) | def minimize_sampler_states(self):
    method pull_trajectory_snapshot (line 743) | def pull_trajectory_snapshot(self, endstate):
    method equilibrate (line 772) | def equilibrate(self,
    method _resample (line 916) | def _resample(self,
    method compute_lambda_increment (line 978) | def compute_lambda_increment(self, new_val, sampler_states, observable...
    method binary_search (line 989) | def binary_search(self,

FILE: perses/dispersed/utils.py
  function check_platform (line 37) | def check_platform(platform):
  function check_system (line 53) | def check_system(system):
  function configure_platform (line 77) | def configure_platform(platform_name='Reference', fallback_platform_name...
  function compute_survival_rate (line 120) | def compute_survival_rate(sMC_particle_ancestries):
  function compute_potential_components (line 145) | def compute_potential_components(context, beta=beta, platform=DEFAULT_PL...
  function minimize (line 188) | def minimize(thermodynamic_state,
  function multinomial_resample (line 220) | def multinomial_resample(total_works, num_resamples):
  function ESS (line 244) | def ESS(works_prev, works_incremental):
  function CESS (line 266) | def CESS(works_prev, works_incremental):
  function compute_timeseries (line 288) | def compute_timeseries(reduced_potentials):
  function run_equilibrium (line 318) | def run_equilibrium(task):
  function write_equilibrium_trajectory (line 451) | def write_equilibrium_trajectory(trajectory: md.Trajectory, trajectory_f...
  function write_nonequilibrium_trajectory (line 477) | def write_nonequilibrium_trajectory(nonequilibrium_trajectory, trajector...
  function compute_reduced_potential (line 498) | def compute_reduced_potential(thermodynamic_state: states.ThermodynamicS...
  function create_endstates (line 522) | def create_endstates(first_thermostate, last_thermostate):
  function generate_endpoint_thermodynamic_states (line 584) | def generate_endpoint_thermodynamic_states(system, topology_proposal, re...
  function create_endstates_from_real_systems (line 643) | def create_endstates_from_real_systems(htf, for_testing=False):
  function validate_endstate_energies (line 830) | def validate_endstate_energies(topology_proposal,
  function validate_endstate_energies_point (line 951) | def validate_endstate_energies_point(input_htf, endstate=0, minimize=Fal...
  function activate_LocallyOptimalAnnealing (line 1103) | def activate_LocallyOptimalAnnealing(thermodynamic_state,
  function deactivate_worker_attributes (line 1141) | def deactivate_worker_attributes(remote_worker):
  function call_anneal_method (line 1158) | def call_anneal_method(remote_worker,
  class LocallyOptimalAnnealing (line 1190) | class LocallyOptimalAnnealing():
    method initialize (line 1198) | def initialize(self,
    method anneal (line 1273) | def anneal(self,
    method attempt_termination (line 1419) | def attempt_termination(self, noneq_trajectory_filename):
    method reset_dimensions (line 1435) | def reset_dimensions(self):
    method compute_incremental_work (line 1443) | def compute_incremental_work(self, _lambda):
    method update_context (line 1474) | def update_context(self, _lambda):
    method save_configuration (line 1487) | def save_configuration(self, iteration, sampler_state):

FILE: perses/rjmc/atom_mapping.py
  class InvalidMappingException (line 28) | class InvalidMappingException(Exception):
    method __init__ (line 33) | def __init__(self, message):
  class AtomMapping (line 50) | class AtomMapping(object):
    method __init__ (line 89) | def __init__(self, old_mol, new_mol, new_to_old_atom_map=None, old_to_...
    method __repr__ (line 133) | def __repr__(self):
    method __str__ (line 136) | def __str__(self):
    method __hash__ (line 139) | def __hash__(self):
    method _validate (line 143) | def _validate(self):
    method new_to_old_atom_map (line 168) | def new_to_old_atom_map(self):
    method new_to_old_atom_map (line 173) | def new_to_old_atom_map(self, value):
    method old_to_new_atom_map (line 178) | def old_to_new_atom_map(self):
    method old_to_new_atom_map (line 183) | def old_to_new_atom_map(self, value):
    method n_mapped_atoms (line 188) | def n_mapped_atoms(self):
    method render_image (line 192) | def render_image(self, filename, format=None, width=1200, height=600):
    method _ipython_display_ (line 322) | def _ipython_display_(self):
    method creates_or_breaks_rings (line 327) | def creates_or_breaks_rings(self):
    method unmap_partially_mapped_cycles (line 366) | def unmap_partially_mapped_cycles(self):
    method preserve_chirality (line 470) | def preserve_chirality(self):
  class AtomMapper (line 560) | class AtomMapper(object):
    method __init__ (line 653) | def __init__(self,
    method get_all_mappings (line 751) | def get_all_mappings(self, old_mol, new_mol):
    method get_best_mapping (line 957) | def get_best_mapping(self, old_mol, new_mol):
    method get_sampled_mapping (line 1008) | def get_sampled_mapping(self, old_mol, new_mol):
    method propose_mapping (line 1043) | def propose_mapping(old_mol, new_mol):
    method score_mapping (line 1079) | def score_mapping(self, atom_mapping):
    method generate_atom_mapping_from_positions (line 1186) | def generate_atom_mapping_from_positions(self, old_mol, new_mol):
    method _get_all_maps (line 1262) | def _get_all_maps(old_oemol, new_oemol,
    method _create_pattern_to_target_map (line 1343) | def _create_pattern_to_target_map(old_oemol, new_oemol, match, matchin...
    method _create_atom_mapping (line 1379) | def _create_atom_mapping(old_oemol, new_oemol, match, matching_criteri...
    method _assign_ring_ids (line 1433) | def _assign_ring_ids(oemol, max_ring_size=10, assign_atoms=True, assig...
    method _get_scaffold (line 1493) | def _get_scaffold(oemol, adjustHcount=False):
  function _convert_opemol_to_offmol (line 1559) | def _convert_opemol_to_offmol(oemol, allow_undefined_stereo: bool=False,...
  function _convert_positions_to_angstroms (line 1835) | def _convert_positions_to_angstroms(positions):

FILE: perses/rjmc/coordinate_numba.py
  function _cross_vec3 (line 5) | def _cross_vec3(a, b):
  function _norm (line 13) | def _norm(a):
  function _rotation_matrix (line 18) | def _rotation_matrix(axis, angle):
  function internal_to_cartesian (line 46) | def internal_to_cartesian(bond_position, angle_position, torsion_positio...
  function torsion_scan (line 79) | def torsion_scan(bond_position, angle_position, torsion_position, intern...
  function calculate_angle (line 88) | def calculate_angle(atom_position, bond_position, angle_position):
  function cartesian_to_internal (line 104) | def cartesian_to_internal(atom_position, bond_position, angle_position, ...

FILE: perses/rjmc/coordinate_tools.py
  function _rotation_matrix (line 3) | def _rotation_matrix(axis, angle):
  function _cartesian_to_internal (line 26) | def _cartesian_to_internal(atom_position, bond_position, angle_position,...
  function _internal_to_cartesian (line 69) | def _internal_to_cartesian(bond_position, angle_position, torsion_positi...

FILE: perses/rjmc/geometry.py
  function check_dimensionality (line 34) | def check_dimensionality(quantity, compatible_units):
  class GeometryEngine (line 71) | class GeometryEngine(object):
    method __init__ (line 81) | def __init__(self, metadata=None, storage=None):
    method propose (line 85) | def propose(self, top_proposal, current_positions, beta):
    method logp_reverse (line 103) | def logp_reverse(self, top_proposal, new_coordinates, old_coordinates,...
  class FFAllAngleGeometryEngine (line 128) | class FFAllAngleGeometryEngine(GeometryEngine):
    method __init__ (line 160) | def __init__(self,
    method propose (line 195) | def propose(self, top_proposal, current_positions, beta, validate_ener...
    method logp_reverse (line 250) | def logp_reverse(self, top_proposal, new_coordinates, old_coordinates,...
    method _write_partial_pdb (line 295) | def _write_partial_pdb(self, pdbfile, topology, positions, atoms_with_...
    method _logp_propose (line 327) | def _logp_propose(self, top_proposal, old_positions, beta, new_positio...
    method _corrected_reduced_potential (line 707) | def _corrected_reduced_potential(self, growth_system_generator, positi...
    method _define_no_nb_system (line 746) | def _define_no_nb_system(self,
    method _copy_positions (line 822) | def _copy_positions(self, atoms_with_positions, top_proposal, current_...
    method _get_relevant_bond (line 854) | def _get_relevant_bond(self, atom1, atom2):
    method _get_bond_constraint (line 883) | def _get_bond_constraint(self, atom1, atom2, system):
    method _get_relevant_angle (line 917) | def _get_relevant_angle(self, atom1, atom2, atom3):
    method _add_bond_units (line 961) | def _add_bond_units(self, bond):
    method _add_angle_units (line 988) | def _add_angle_units(self, angle):
    method _add_torsion_units (line 1015) | def _add_torsion_units(self, torsion):
    method _rotation_matrix (line 1042) | def _rotation_matrix(self, axis, angle):
    method _cartesian_to_internal (line 1077) | def _cartesian_to_internal(self, atom_position, bond_position, angle_p...
    method _internal_to_cartesian (line 1135) | def _internal_to_cartesian(self, bond_position, angle_position, torsio...
    method _bond_log_pmf (line 1191) | def _bond_log_pmf(self, bond, beta, n_divisions):
    method _bond_logp (line 1257) | def _bond_logp(self, r, bond, beta, n_divisions):
    method _propose_bond (line 1301) | def _propose_bond(self, bond, beta, n_divisions):
    method _angle_log_pmf (line 1345) | def _angle_log_pmf(self, angle, beta, n_divisions):
    method _angle_logp (line 1413) | def _angle_logp(self, theta, angle, beta, n_divisions):
    method _propose_angle (line 1457) | def _propose_angle(self, angle, beta, n_divisions):
    method _torsion_scan (line 1500) | def _torsion_scan(self, torsion_atom_indices, positions, r, theta, n_d...
    method _torsion_log_pmf (line 1557) | def _torsion_log_pmf(self, growth_context, torsion_atom_indices, posit...
    method _propose_torsion (line 1655) | def _propose_torsion(self, growth_context, torsion_atom_indices, posit...
    method _torsion_logp (line 1710) | def _torsion_logp(self, growth_context, torsion_atom_indices, position...
  class GeometrySystemGenerator (line 1759) | class GeometrySystemGenerator(object):
    method __init__ (line 1769) | def __init__(self,
    method set_growth_parameter_index (line 2136) | def set_growth_parameter_index(self, growth_parameter_index, context=N...
    method get_modified_system (line 2145) | def get_modified_system(self):
    method _determine_extra_torsions (line 2157) | def _determine_extra_torsions(self,
    method adjust_phase (line 2354) | def adjust_phase(self, phase):
    method _select_torsions_without_h (line 2380) | def _select_torsions_without_h(self, torsion_list):
    method _determine_extra_angles (line 2403) | def _determine_extra_angles(self, angle_force, reference_topology, gro...
    method _calculate_growth_idx (line 2475) | def _calculate_growth_idx(self, particle_indices, growth_indices):
  class NetworkXProposalOrder (line 2500) | class NetworkXProposalOrder(object):
    method __init__ (line 2505) | def __init__(self, topology_proposal, direction="forward"):
    method _create_reference_connectivity_graph (line 2566) | def _create_reference_connectivity_graph(self):
    method determine_proposal_order (line 2583) | def determine_proposal_order(self):
    method _propose_atoms_in_order (line 2637) | def _propose_atoms_in_order(self, atom_group):
  class NoTorsionError (line 2705) | class NoTorsionError(Exception):
    method __init__ (line 2706) | def __init__(self, message):

FILE: perses/rjmc/topology_proposal.py
  function add_method (line 35) | def add_method(object, function):
  function set_residue_oemol_and_openmm_topology_attributes (line 48) | def set_residue_oemol_and_openmm_topology_attributes(object, residue_oem...
  function _get_networkx_molecule (line 75) | def _get_networkx_molecule(self):
  function augment_openmm_topology (line 140) | def augment_openmm_topology(topology, residue_oemol, residue_topology, r...
  function append_topology (line 158) | def append_topology(destination_topology, source_topology, exclude_resid...
  function deepcopy_topology (line 192) | def deepcopy_topology(source_topology):
  class TopologyProposal (line 206) | class TopologyProposal(object):
    method __init__ (line 279) | def __init__(self,
    method new_topology (line 311) | def new_topology(self):
    method new_system (line 314) | def new_system(self):
    method old_topology (line 317) | def old_topology(self):
    method old_system (line 320) | def old_system(self):
    method logp_proposal (line 323) | def logp_proposal(self):
    method new_to_old_atom_map (line 326) | def new_to_old_atom_map(self):
    method old_to_new_atom_map (line 329) | def old_to_new_atom_map(self):
    method unique_new_atoms (line 332) | def unique_new_atoms(self):
    method unique_old_atoms (line 335) | def unique_old_atoms(self):
    method new_alchemical_atoms (line 338) | def new_alchemical_atoms(self):
    method old_alchemical_atoms (line 341) | def old_alchemical_atoms(self):
    method new_environment_atoms (line 344) | def new_environment_atoms(self):
    method old_environment_atoms (line 347) | def old_environment_atoms(self):
    method n_atoms_new (line 350) | def n_atoms_new(self):
    method n_atoms_old (line 353) | def n_atoms_old(self):
    method new_chemical_state_key (line 356) | def new_chemical_state_key(self):
    method old_chemical_state_key (line 359) | def old_chemical_state_key(self):
    method old_residue_name (line 362) | def old_residue_name(self):
    method new_residue_name (line 365) | def new_residue_name(self):
    method metadata (line 368) | def metadata(self):
    method core_new_to_old_atom_map (line 371) | def core_new_to_old_atom_map(self):
  class ProposalEngine (line 374) | class ProposalEngine(object):
    method __init__ (line 392) | def __init__(self, system_generator, proposal_metadata=None, always_ch...
    method propose (line 397) | def propose(self, current_system, current_topology, current_metadata=N...
    method compute_state_key (line 418) | def compute_state_key(self, topology):
    method chemical_state_list (line 435) | def chemical_state_list(self):
  class PolymerProposalEngine (line 438) | class PolymerProposalEngine(ProposalEngine):
    method _get_neutrals (line 451) | def _get_neutrals(aminos, positive, negative):
    method __init__ (line 458) | def __init__(self, system_generator, chain_id, proposal_metadata=None,...
    method generate_oemol_from_pdb_template (line 485) | def generate_oemol_from_pdb_template(pdbfile):
    method _get_charge_difference (line 501) | def _get_charge_difference(current_resname, new_resname):
    method propose (line 531) | def propose(self,
    method _find_adjacent_residue_atoms (line 725) | def _find_adjacent_residue_atoms(self, old_topology, new_topology, mut...
    method _choose_mutant (line 783) | def _choose_mutant(self, topology, metadata):
    method _generate_residue_map (line 804) | def _generate_residue_map(self, topology, index_to_new_residues):
    method _identify_differences (line 824) | def _identify_differences(self, topology, residue_map):
    method _delete_atoms (line 939) | def _delete_atoms(self, topology, to_delete):
    method _add_new_atoms (line 982) | def _add_new_atoms(self, topology, missing_atoms, missing_bonds, resid...
    method _is_residue_equal (line 1046) | def _is_residue_equal(self, residue, other_residue):
    method _construct_atom_map (line 1059) | def _construct_atom_map(self,
    method _get_mol_atom_matches (line 1191) | def _get_mol_atom_matches(self, current_molecule, proposed_molecule, f...
    method compute_state_key (line 1275) | def compute_state_key(self, topology):
    method validate_core_atoms_with_system (line 1292) | def validate_core_atoms_with_system(topology_proposal):
  class PointMutationEngine (line 1389) | class PointMutationEngine(PolymerProposalEngine):
    method __init__ (line 1406) | def __init__(self,
    method _choose_mutant (line 1478) | def _choose_mutant(self, topology, metadata):
    method _undo_old_mutants (line 1525) | def _undo_old_mutants(self, topology, chain_id, old_key):
    method _choose_mutation_from_allowed (line 1565) | def _choose_mutation_from_allowed(self, topology, chain_id, allowed_mu...
    method _propose_mutation (line 1673) | def _propose_mutation(self, topology, chain_id, index_to_new_residues):
    method _mutable_residues (line 1749) | def _mutable_residues(self, chain):
    method _save_mutations (line 1753) | def _save_mutations(self, topology, index_to_new_residues):
    method _compute_mutant_key (line 1770) | def _compute_mutant_key(self,
  class PeptideLibraryEngine (line 1821) | class PeptideLibraryEngine(PolymerProposalEngine):
    method __init__ (line 1838) | def __init__(self, system_generator, library, chain_id, proposal_metad...
    method _choose_mutant (line 1844) | def _choose_mutant(self, topology, metadata):
    method _one_to_three_letter_code (line 1892) | def _one_to_three_letter_code(self, residue_one_letter):
  class SmallMoleculeSetProposalEngine (line 1918) | class SmallMoleculeSetProposalEngine(ProposalEngine):
    method __init__ (line 1960) | def __init__(self, list_of_oemols, system_generator, residue_name='MOL...
    method propose (line 2014) | def propose(self,
    method canonicalize_smiles (line 2186) | def canonicalize_smiles(smiles):
    method _topology_to_smiles (line 2210) | def _topology_to_smiles(self, topology):
    method compute_state_key (line 2247) | def compute_state_key(self, topology):
    method _find_mol_start_index (line 2266) | def _find_mol_start_index(self, topology):
    method _build_new_topology (line 2292) | def _build_new_topology(self, current_receptor_topology, oemol_proposed):
    method _remove_small_molecule (line 2324) | def _remove_small_molecule(self, topology):
    method _constraint_repairs (line 2349) | def _constraint_repairs(atom_map, old_system, new_system, old_topology...
    method _propose_molecule (line 2414) | def _propose_molecule(self, system, topology, current_mol_id, exclude_...
    method _calculate_probability_matrix (line 2462) | def _calculate_probability_matrix(self):
    method chemical_state_list (line 2512) | def chemical_state_list(self):
    method clean_molecule_list (line 2517) | def clean_molecule_list(smiles_list, atom_opts, bond_opts):

FILE: perses/samplers/multistate.py
  class HybridCompatibilityMixin (line 22) | class HybridCompatibilityMixin(object):
    method __init__ (line 28) | def __init__(self, *args, hybrid_factory=None, **kwargs):
    method setup (line 33) | def setup(self, n_states, temperature, storage_file, minimisation_step...
  class HybridSAMSSampler (line 120) | class HybridSAMSSampler(HybridCompatibilityMixin, sams.SAMSSampler):
    method __init__ (line 125) | def __init__(self, *args, hybrid_factory=None, **kwargs):
  class HybridRepexSampler (line 130) | class HybridRepexSampler(HybridCompatibilityMixin, replicaexchange.Repli...
    method __init__ (line 135) | def __init__(self, *args, hybrid_factory=None, **kwargs):

FILE: perses/samplers/samplers.py
  function log_sum_exp (line 43) | def log_sum_exp(a_n):
  class ExpandedEnsembleSampler (line 60) | class ExpandedEnsembleSampler(object):
    method __init__ (line 129) | def __init__(self, sampler, topology, state_key, proposal_engine, geom...
    method state_keys (line 218) | def state_keys(self):
    method get_log_weight (line 221) | def get_log_weight(self, state_key):
    method _system_to_thermodynamic_state (line 244) | def _system_to_thermodynamic_state(self, system):
    method _geometry_forward (line 261) | def _geometry_forward(self, topology_proposal, old_sampler_state):
    method _geometry_reverse (line 295) | def _geometry_reverse(self, topology_proposal, new_sampler_state, old_...
    method _ncmc_hybrid (line 320) | def _ncmc_hybrid(self, topology_proposal, old_sampler_state, new_sampl...
    method _geometry_ncmc_geometry (line 353) | def _geometry_ncmc_geometry(self, topology_proposal, sampler_state, ol...
    method update_positions (line 442) | def update_positions(self, n_iterations=1):
    method update_state (line 448) | def update_state(self):
    method update (line 510) | def update(self):
    method run (line 532) | def run(self, niterations=1):
    method update_statistics (line 544) | def update_statistics(self):
  class SAMSSampler (line 556) | class SAMSSampler(object):
    method __init__ (line 607) | def __init__(self, sampler, logZ=None, log_target_probabilities=None, ...
    method state_keys (line 687) | def state_keys(self):
    method _num_dof_compensation (line 690) | def _num_dof_compensation(self, smiles):
    method update_sampler (line 725) | def update_sampler(self):
    method update_logZ_estimates (line 731) | def update_logZ_estimates(self):
    method update (line 776) | def update(self):
    method run (line 790) | def run(self, niterations=1):
  class MultiTargetDesign (line 806) | class MultiTargetDesign(object):
    method __init__ (line 823) | def __init__(self, target_samplers, storage=None, verbose=False):
    method state_keys (line 868) | def state_keys(self):
    method update_samplers (line 871) | def update_samplers(self):
    method update_target_probabilities (line 878) | def update_target_probabilities(self):
    method update (line 908) | def update(self):
    method run (line 922) | def run(self, niterations=1):
  class ProtonationStateSampler (line 940) | class ProtonationStateSampler(object):
    method __init__ (line 956) | def __init__(self, complex_sampler, solvent_sampler, log_state_penalti...
    method state_keys (line 990) | def state_keys(self):
    method update_samplers (line 993) | def update_samplers(self):
    method update_target_probabilities (line 1000) | def update_target_probabilities(self):
    method update (line 1011) | def update(self):
    method run (line 1025) | def run(self, niterations=1):

FILE: perses/samplers/thermodynamics.py
  class ThermodynamicState (line 51) | class ThermodynamicState(object):
    method __init__ (line 87) | def __init__(self, system, temperature, pressure=None):
    method _create_context (line 151) | def _create_context(self, platform=None):
    method _cleanup_context (line 180) | def _cleanup_context(self):
    method _compute_potential (line 185) | def _compute_potential(self, coordinates, box_vectors):
    method reduced_potential (line 198) | def reduced_potential(self, coordinates, box_vectors=None, platform=No...
    method beta (line 307) | def beta(self):
    method reduced_potential_multiple (line 310) | def reduced_potential_multiple(self, coordinates_list, box_vectors_lis...
    method is_compatible_with (line 409) | def is_compatible_with(self, state):
    method __repr__ (line 458) | def __repr__(self):
    method __str__ (line 485) | def __str__(self):
  function volume (line 490) | def volume(box_vectors):

FILE: perses/storage/storage.py
  class NetCDFStorage (line 35) | class NetCDFStorage(object):
    method __init__ (line 39) | def __init__(self, filename, mode='w'):
    method _find_group (line 61) | def _find_group(self):
    method _encode_string (line 73) | def _encode_string(string, encoding='ascii'):
    method sync (line 81) | def sync(self):
    method close (line 86) | def close(self):
    method write_configuration (line 91) | def write_configuration(self, varname, positions, topology, iteration=...
    method write_object (line 159) | def write_object(self, varname, obj, iteration=None):
    method get_object (line 186) | def get_object(self, envname, modname, varname, iteration=None):
    method write_quantity (line 217) | def write_quantity(self, varname, value, iteration=None):
    method write_array (line 242) | def write_array(self, varname, array, iteration=None):
  class NetCDFStorageView (line 296) | class NetCDFStorageView(NetCDFStorage):
    method __init__ (line 299) | def __init__(self, storage, envname=None, modname=None):

FILE: perses/tests/benchmark.py
  function plot_logPs (line 39) | def plot_logPs(logps, molecule_name, scheme, component):
  function benchmark_exen_ncmc_protocol (line 74) | def benchmark_exen_ncmc_protocol(analyses, molecule_name, scheme):
  function benchmark_ncmc_work_during_protocol (line 121) | def benchmark_ncmc_work_during_protocol():

FILE: perses/tests/conftest.py
  function pytest_addoption (line 5) | def pytest_addoption(parser):
  function pytest_configure (line 11) | def pytest_configure(config):
  function pytest_collection_modifyitems (line 17) | def pytest_collection_modifyitems(config, items):
  function in_tmpdir (line 26) | def in_tmpdir(tmpdir):
  function input_yaml_template (line 31) | def input_yaml_template():
  function input_template_obj_default_selection (line 61) | def input_template_obj_default_selection(input_yaml_template):
  function input_template_not_water_selection (line 67) | def input_template_not_water_selection(input_template_obj_default_select...

FILE: perses/tests/test_GPU.py
  function test_gpu_platforms (line 6) | def test_gpu_platforms(platform_type):

FILE: perses/tests/test_analysis.py
  function test_analysis (line 29) | def test_analysis():

FILE: perses/tests/test_atom_mapping.py
  class TestAtomMapping (line 20) | class TestAtomMapping(unittest.TestCase):
    method setUp (line 22) | def setUp(self):
    method test_create (line 29) | def test_create(self):
    method test_validation_fail (line 39) | def test_validation_fail(self):
    method test_set_and_get_mapping (line 53) | def test_set_and_get_mapping(self):
    method test_repr (line 64) | def test_repr(self):
    method test_str (line 68) | def test_str(self):
    method test_render_image (line 72) | def test_render_image(self):
    method test_ring_breaking_detection (line 79) | def test_ring_breaking_detection(self):
    method test_unmap_partially_mapped_cycles (line 92) | def test_unmap_partially_mapped_cycles(self):
    method test_preserve_chirality (line 109) | def test_preserve_chirality(self):
  class TestAtomMapper (line 127) | class TestAtomMapper(unittest.TestCase):
    method setUp (line 128) | def setUp(self):
    method test_molecular_atom_mapping (line 137) | def test_molecular_atom_mapping(self):
    method test_map_strategy (line 166) | def test_map_strategy(self):
    method test_sampled_mappings (line 196) | def test_sampled_mappings(self):
    method test_generate_atom_mapping_from_positions (line 225) | def test_generate_atom_mapping_from_positions(self):
    method test_atom_mappings_moonshot (line 245) | def test_atom_mappings_moonshot(self):
    method test_simple_heterocycle_mapping (line 279) | def test_simple_heterocycle_mapping(self):
    method test_mapping_strength_levels (line 300) | def test_mapping_strength_levels(self):

FILE: perses/tests/test_cli.py
  function default_input_yaml_template_cli (line 12) | def default_input_yaml_template_cli():
  function input_template_obj_cli (line 49) | def input_template_obj_cli(default_input_yaml_template_cli):
  function input_template_obj_tip5p_cli (line 54) | def input_template_obj_tip5p_cli(input_template_obj_cli):
  function test_dummy_cli_with_override (line 62) | def test_dummy_cli_with_override(input_params, in_tmpdir, request):
  function test_s3_yaml_read (line 94) | def test_s3_yaml_read(in_tmpdir):

FILE: perses/tests/test_coordinate_numba.py
  function test_coordinate_conversion (line 21) | def test_coordinate_conversion():
  function test_openmm_dihedral (line 46) | def test_openmm_dihedral():
  function test_try_random_itoc (line 117) | def test_try_random_itoc():

FILE: perses/tests/test_fah.py
  function test_pipeline_small_molecule (line 32) | def test_pipeline_small_molecule():
  function test_pipeline_small_molecule_solvent (line 60) | def test_pipeline_small_molecule_solvent():
  function test_pipeline_protein (line 83) | def test_pipeline_protein():
  function test_core_file (line 107) | def test_core_file():
  function test_neq_integrator (line 119) | def test_neq_integrator():

FILE: perses/tests/test_geometry_engine.py
  class GeometryTestSystem (line 81) | class GeometryTestSystem(object):
    method topology (line 103) | def topology(self):
    method system (line 107) | def system(self):
    method structure (line 111) | def structure(self):
    method growth_order (line 115) | def growth_order(self):
    method positions (line 119) | def positions(self):
    method energy (line 123) | def energy(self):
  class FourAtomValenceTestSystem (line 127) | class FourAtomValenceTestSystem(GeometryTestSystem):
    method __init__ (line 147) | def __init__(self, bond=True, angle=True, torsion=True):
    method internal_coordinates (line 231) | def internal_coordinates(self):
    method internal_coordinates (line 239) | def internal_coordinates(self, internal_coordinates):
    method bond_parameters (line 248) | def bond_parameters(self):
    method angle_parameters (line 253) | def angle_parameters(self):
    method torsion_parameters (line 258) | def torsion_parameters(self):
  function test_propose_bond (line 262) | def test_propose_bond():
  function test_propose_angle (line 311) | def test_propose_angle():
  function test_bond_logp (line 361) | def test_bond_logp():
  function test_angle_logp (line 420) | def test_angle_logp():
  function test_add_bond_units (line 486) | def test_add_bond_units():
  function test_add_angle_units (line 514) | def test_add_angle_units():
  function test_add_torsion_units (line 545) | def test_add_torsion_units():
  function test_torsion_scan (line 575) | def test_torsion_scan():
  function test_torsion_log_discrete_pdf (line 622) | def test_torsion_log_discrete_pdf():
  function calculate_torsion_discrete_log_pdf_manually (line 659) | def calculate_torsion_discrete_log_pdf_manually(beta, torsion, phis):
  function test_torsion_logp (line 695) | def test_torsion_logp():
  function test_propose_torsion (line 741) | def test_propose_torsion():
  function _get_internal_from_omm (line 794) | def _get_internal_from_omm(atom_coords, bond_coords, angle_coords, torsi...
  function oemol_to_openmm_system (line 864) | def oemol_to_openmm_system(oemol):
  function oemol_to_openmm_system_amber (line 869) | def oemol_to_openmm_system_amber(oemol, molecule_name):
  function align_molecules (line 890) | def align_molecules(mol1, mol2):
  function test_mutate_from_all_to_all (line 917) | def test_mutate_from_all_to_all(): # TODO: fix protein mutations
  function test_propose_lysozyme_ligands (line 979) | def test_propose_lysozyme_ligands(): # TODO: fix protein mutations
  function test_propose_kinase_inhibitors (line 994) | def test_propose_kinase_inhibitors(): # TODO: fix protein mutations
  function run_proposals (line 1001) | def run_proposals(proposal_list):
  function make_geometry_proposal_array (line 1042) | def make_geometry_proposal_array(smiles_list, forcefield=['data/gaff.xml...
  function load_pdbid_to_openmm (line 1090) | def load_pdbid_to_openmm(pdbid):
  function _guessFileFormat (line 1112) | def _guessFileFormat(file, filename):
  function test_existing_coordinates (line 1132) | def test_existing_coordinates():
  function run_logp_reverse (line 1155) | def run_logp_reverse():
  function _get_capped_amino_acid (line 1186) | def _get_capped_amino_acid(amino_acid='ALA'):
  function _tleap_all (line 1221) | def _tleap_all():
  function _oemol_from_residue (line 1226) | def _oemol_from_residue(res):
  function _print_failed_SMILES (line 1252) | def _print_failed_SMILES(failed_mol_list):
  function _generate_ffxmls (line 1258) | def _generate_ffxmls():
  class LinearValenceTestSystem (line 1286) | class LinearValenceTestSystem(GeometryTestSystem):
    method __init__ (line 1293) | def __init__(self, bond=True, angle=True, torsion=True, n_atoms=4, add...
    method internal_coordinates (line 1418) | def internal_coordinates(self):
    method internal_coordinates (line 1425) | def internal_coordinates(self, internal_coordinates):
    method bond_parameters (line 1436) | def bond_parameters(self):
    method angle_parameters (line 1440) | def angle_parameters(self):
    method torsion_parameters (line 1444) | def torsion_parameters(self):
  class AnalyticalBeadSystems (line 1450) | class AnalyticalBeadSystems(object):
    method __init__ (line 1456) | def __init__(self, transformation, num_iterations):
    method convert_to_md (line 1482) | def convert_to_md(self, openmm_positions):
    method minimize (line 1501) | def minimize(self, system, positions):
    method compute_rp (line 1525) | def compute_rp(self, system, positions):
    method create_simple_topology_proposal (line 1552) | def create_simple_topology_proposal(self, sys_pos_top, n_atoms_initial...
    method run_rj_simple_system (line 1602) | def run_rj_simple_system(self, configurations_initial, topology_propos...
    method create_iid_bead_systems (line 1647) | def create_iid_bead_systems(self, printer=False):
    method forward_transformation (line 1687) | def forward_transformation(self, iid_positions_A, printer=False):
    method backward_transformation (line 1719) | def backward_transformation(self, proposed_positions, printer=False):
    method work_comparison (line 1754) | def work_comparison(self, printer=False):
  function test_AnalyticalBeadSystems (line 1789) | def test_AnalyticalBeadSystems(transformation=[[3,4], [4,5], [3,5]], num...
  function test_logp_forward_check_for_vacuum_topology_proposal (line 1826) | def test_logp_forward_check_for_vacuum_topology_proposal(current_mol_nam...

FILE: perses/tests/test_lambda_protocol.py
  function test_lambda_protocol (line 14) | def test_lambda_protocol():
  function test_lambda_protocol_failure_ends (line 32) | def test_lambda_protocol_failure_ends():
  function test_lambda_protocol_naked_charges (line 37) | def test_lambda_protocol_naked_charges():

FILE: perses/tests/test_ncmc_integrator.py
  function collect_switching_data (line 22) | def collect_switching_data(system, positions, functions, temperature, co...

FILE: perses/tests/test_parallel.py
  function test_Parallelism_local (line 18) | def test_Parallelism_local():
  function test_Parallelism_distributed (line 40) | def test_Parallelism_distributed():
  function run_parallelism (line 57) | def run_parallelism(_parallel, data):
  function dummy_function (line 122) | def dummy_function(_arg):

FILE: perses/tests/test_relative.py
  function run_hybrid_endpoint_overlap (line 39) | def run_hybrid_endpoint_overlap(topology_proposal, current_positions, ne...
  function calculate_cross_variance (line 89) | def calculate_cross_variance(all_results):
  function check_result (line 108) | def check_result(results, threshold=3.0, neffmin=10):
  function test_networkx_proposal_order (line 129) | def test_networkx_proposal_order():
  function test_explosion (line 140) | def test_explosion():
  function test_vacuum_overlap_with_constraints (line 151) | def test_vacuum_overlap_with_constraints():
  function test_valence_overlap (line 157) | def test_valence_overlap():
  function test_bonds_angles_overlap (line 166) | def test_bonds_angles_overlap():
  function test_sterics_overlap (line 175) | def test_sterics_overlap():
  function test_simple_overlap_pairs (line 184) | def test_simple_overlap_pairs(pairs=None):
  function test_simple_overlap (line 214) | def test_simple_overlap(name1='pentane', name2='butane', forcefield_kwar...
  function test_hostguest_overlap (line 244) | def test_hostguest_overlap():
  function test_difficult_overlap (line 260) | def test_difficult_overlap():
  function run_endpoint_perturbation (line 289) | def run_endpoint_perturbation(lambda_thermodynamic_state, nonalchemical_...
  function compare_energies (line 405) | def compare_energies(mol_name="naphthalene", ref_mol_name="benzene",atom...
  function test_compare_energies (line 473) | def test_compare_energies():
  function test_position_output (line 479) | def test_position_output():
  function test_generate_endpoint_thermodynamic_states (line 497) | def test_generate_endpoint_thermodynamic_states():
  function HybridTopologyFactory_energies (line 515) | def HybridTopologyFactory_energies(current_mol = 'toluene', proposed_mol...
  function test_HybridTopologyFactory_energies (line 571) | def test_HybridTopologyFactory_energies(molecule_perturbation_list = [['...
  function test_RMSD_restraint (line 579) | def test_RMSD_restraint():
  function RepartitionedHybridTopologyFactory_energies (line 656) | def RepartitionedHybridTopologyFactory_energies(topology, chain, system,...
  function test_RepartitionedHybridTopologyFactory_energies (line 758) | def test_RepartitionedHybridTopologyFactory_energies():
  function flattenedHybridTopologyFactory_energies (line 796) | def flattenedHybridTopologyFactory_energies(topology, chain, system, pos...
  function test_flattenedHybridTopologyFactory_energies (line 932) | def test_flattenedHybridTopologyFactory_energies():
  function run_RESTCapableHybridTopologyFactory_energies (line 948) | def run_RESTCapableHybridTopologyFactory_energies(test_name, phase, use_...
  function test_RESTCapableHybridTopologyFactory_energies (line 1021) | def test_RESTCapableHybridTopologyFactory_energies():
  function test_RESTCapableHybridTopologyFactory_energies_GPU (line 1038) | def test_RESTCapableHybridTopologyFactory_energies_GPU():
  function run_unsampled_endstate_energies (line 1055) | def run_unsampled_endstate_energies(test_name, use_point_energies=True, ...
  function test_unsampled_endstate_energies (line 1192) | def test_unsampled_endstate_energies():
  function test_unsampled_endstate_energies_GPU (line 1204) | def test_unsampled_endstate_energies_GPU():
  class TestHybridTopologyFactory (line 1223) | class TestHybridTopologyFactory:
    method test_custom_nonbonded_cutoff (line 1225) | def test_custom_nonbonded_cutoff(self):

FILE: perses/tests/test_relative_point_mutation_setup.py
  function test_PointMutationExecutor (line 4) | def test_PointMutationExecutor():
  function test_PointMutationExecutor_endstate_validation (line 35) | def test_PointMutationExecutor_endstate_validation():
  function test_PointMutationExecutor_solvated (line 63) | def test_PointMutationExecutor_solvated():
  function test_PointMutationExecutor_without_counterion (line 92) | def test_PointMutationExecutor_without_counterion():

FILE: perses/tests/test_relative_setup.py
  function generate_example_waterbox_states (line 21) | def generate_example_waterbox_states(temperature=300.0*unit.kelvin, pres...
  function test_parsed_yaml_generation (line 45) | def test_parsed_yaml_generation():
  function test_run_nonequilibrium_switching_move (line 84) | def test_run_nonequilibrium_switching_move():
  function test_run_cdk2_iterations_repex (line 158) | def test_run_cdk2_iterations_repex():
  function test_run_bace_spectator (line 209) | def test_run_bace_spectator():
  function test_relative_setup_charge_change (line 259) | def test_relative_setup_charge_change():
  function test_relative_setup_solvent_padding (line 310) | def test_relative_setup_solvent_padding():
  function test_relative_setup_list_ligand_input (line 329) | def test_relative_setup_list_ligand_input():
  function test_relative_setup_topologies_storage (line 366) | def test_relative_setup_topologies_storage(tmp_path):

FILE: perses/tests/test_repex.py
  function test_RESTCapableHybridTopologyFactory_repex_neutral_mutation (line 8) | def test_RESTCapableHybridTopologyFactory_repex_neutral_mutation():
  function test_RESTCapableHybridTopologyFactory_repex_charge_mutation (line 95) | def test_RESTCapableHybridTopologyFactory_repex_charge_mutation():
  function test_RESTCapableHybridTopologyFactory_repex_neutral_transformation (line 203) | def test_RESTCapableHybridTopologyFactory_repex_neutral_transformation():
  function test_RESTCapableHybridTopologyFactory_repex_charge_transformation (line 315) | def test_RESTCapableHybridTopologyFactory_repex_charge_transformation():

FILE: perses/tests/test_rest.py
  function compare_energy_components (line 25) | def compare_energy_components(rest_system, other_system, positions, plat...
  function test_bookkeeping (line 75) | def test_bookkeeping():
  function compare_energies (line 139) | def compare_energies(REST_system, other_system, positions, rest_atoms, T...
  function test_energy_scaling (line 240) | def test_energy_scaling():

FILE: perses/tests/test_resume.py
  function test_cli_resume_repex (line 24) | def test_cli_resume_repex(input_params, request):
  function test_resume_small_molecule (line 63) | def test_resume_small_molecule():
  function test_resume_protein_mutation_with_checkpoint (line 137) | def test_resume_protein_mutation_with_checkpoint(tmp_path):
  function test_resume_protein_mutation_no_checkpoint (line 206) | def test_resume_protein_mutation_no_checkpoint(tmp_path):

FILE: perses/tests/test_samplers.py
  function test_valence (line 32) | def test_valence():
  function test_testsystems_gh_actions (line 68) | def test_testsystems_gh_actions():
  function test_testsystems_advanced (line 82) | def test_testsystems_advanced():
  function run_samplers (line 89) | def run_samplers(testsystem_names, niterations=5):

FILE: perses/tests/test_smc.py
  function sMC_setup (line 43) | def sMC_setup():
  function test_local_AIS (line 112) | def test_local_AIS():
  function test_configure_platform (line 166) | def test_configure_platform():
  function test_compute_survival_rate (line 173) | def test_compute_survival_rate():
  function test_multinomial_resample (line 194) | def test_multinomial_resample():
  function test_ESS (line 205) | def test_ESS():
  function test_CESS (line 213) | def test_CESS():
  function test_compute_timeseries (line 221) | def test_compute_timeseries():
  function test_create_endstates (line 229) | def test_create_endstates():

FILE: perses/tests/test_storage.py
  function test_storage_create (line 27) | def test_storage_create():
  function test_storage_append (line 34) | def test_storage_append():
  function test_sync (line 43) | def test_sync():
  function test_storage_view (line 50) | def test_storage_view():
  function test_write_quantity (line 61) | def test_write_quantity():
  function test_write_array (line 76) | def test_write_array():
  function test_write_object (line 100) | def test_write_object():
  function run_sampler (line 126) | def run_sampler(sampler, niterations):
  function test_storage_with_samplers (line 131) | def test_storage_with_samplers():

FILE: perses/tests/test_topology_proposal.py
  function test_small_molecule_proposals (line 43) | def test_small_molecule_proposals():
  function test_small_molecule_constraint_repair_mapping (line 78) | def test_small_molecule_constraint_repair_mapping():
  function load_pdbid_to_openmm (line 128) | def load_pdbid_to_openmm(pdbid):
  function _guessFileFormat (line 150) | def _guessFileFormat(file, filename):
  function create_simple_protein_system_generator (line 170) | def create_simple_protein_system_generator():
  function create_insulin_topology_engine (line 181) | def create_insulin_topology_engine(chain_id = 'A', allowed_mutations = N...
  function generate_atp (line 197) | def generate_atp(phase = 'vacuum'):
  function generate_dipeptide_top_pos_sys (line 252) | def generate_dipeptide_top_pos_sys(topology,
  function test_mutate_from_alanine (line 409) | def test_mutate_from_alanine():
  function test_protein_atom_maps (line 428) | def test_protein_atom_maps():
  function test_specify_allowed_mutants (line 492) | def test_specify_allowed_mutants():
  function test_propose_self (line 539) | def test_propose_self():
  function test_run_point_mutation_propose (line 571) | def test_run_point_mutation_propose():
  function test_alanine_dipeptide_map (line 599) | def test_alanine_dipeptide_map():
  function test_mutate_from_every_amino_to_every_other (line 643) | def test_mutate_from_every_amino_to_every_other():
  function test_limiting_allowed_residues (line 777) | def test_limiting_allowed_residues():
  function test_always_change (line 815) | def test_always_change():
  function test_run_peptide_library_engine (line 868) | def test_run_peptide_library_engine():
  function test_protein_counterion_topology_fix_positive (line 902) | def test_protein_counterion_topology_fix_positive():
  function test_protein_counterion_topology_fix_negitive (line 949) | def test_protein_counterion_topology_fix_negitive():
  function test_protein_counterion_topology_fix_zero (line 997) | def test_protein_counterion_topology_fix_zero():

FILE: perses/tests/test_utils.py
  function test_get_data_filename (line 19) | def test_get_data_filename(datafile='data/gaff2.xml'):
  function test_extractPositionsFromOEMol (line 40) | def test_extractPositionsFromOEMol(molecule=smiles_to_oemol('CC')):
  function test_giveOpenmmPositionsToOEMol (line 66) | def test_giveOpenmmPositionsToOEMol(positions=None, molecule=smiles_to_o...
  function test_OEMol_to_omm_ff (line 105) | def test_OEMol_to_omm_ff(molecule=smiles_to_oemol('CC')):
  function run_oemol_test_suite (line 147) | def run_oemol_test_suite(iupac='ethane'):
  function test_generate_expression (line 181) | def test_generate_expression():

FILE: perses/tests/test_visualization.py
  function test_protein_mutation (line 11) | def test_protein_mutation():
  function test_small_molecule (line 31) | def test_small_molecule():

FILE: perses/tests/testsystems.py
  class PersesTestSystem (line 63) | class PersesTestSystem(object):
    method __init__ (line 91) | def __init__(self, storage_filename=None, mode='w', ncmc_nsteps=5, mcm...
  class AlanineDipeptideTestSystem (line 124) | class AlanineDipeptideTestSystem(PersesTestSystem):
    method __init__ (line 163) | def __init__(self, constraints=app.HBonds, **kwargs):
  class AlanineDipeptideValenceTestSystem (line 280) | class AlanineDipeptideValenceTestSystem(PersesTestSystem):
    method __init__ (line 319) | def __init__(self, **kwargs):
  function load_via_pdbfixer (line 408) | def load_via_pdbfixer(filename=None, pdbid=None):
  class T4LysozymeMutationTestSystem (line 422) | class T4LysozymeMutationTestSystem(PersesTestSystem):
    method __init__ (line 461) | def __init__(self, **kwargs):
  class MybTestSystem (line 629) | class MybTestSystem(PersesTestSystem):
    method __init__ (line 667) | def __init__(self, **kwargs):
  class AblImatinibResistanceTestSystem (line 800) | class AblImatinibResistanceTestSystem(PersesTestSystem):
    method __init__ (line 838) | def __init__(self, **kwargs):
  class AblAffinityTestSystem (line 979) | class AblAffinityTestSystem(PersesTestSystem):
    method __init__ (line 1019) | def __init__(self, **kwargs):
  class AblImatinibProtonationStateTestSystem (line 1193) | class AblImatinibProtonationStateTestSystem(PersesTestSystem):
    method __init__ (line 1231) | def __init__(self, **kwargs):
  class ImidazoleProtonationStateTestSystem (line 1418) | class ImidazoleProtonationStateTestSystem(PersesTestSystem):
    method __init__ (line 1456) | def __init__(self, **kwargs):
  function minimize_wrapper (line 1641) | def minimize_wrapper(testsystem):
  class SmallMoleculeLibraryTestSystem (line 1664) | class SmallMoleculeLibraryTestSystem(PersesTestSystem):
    method __init__ (line 1705) | def __init__(self, constraints=app.HBonds, premapped_json_dict=None, *...
  class AlkanesTestSystem (line 1829) | class AlkanesTestSystem(SmallMoleculeLibraryTestSystem):
    method __init__ (line 1833) | def __init__(self, **kwargs):
  class KinaseInhibitorsTestSystem (line 1837) | class KinaseInhibitorsTestSystem(SmallMoleculeLibraryTestSystem):
    method __init__ (line 1841) | def __init__(self, **kwargs):
  class T4LysozymeInhibitorsTestSystem (line 1858) | class T4LysozymeInhibitorsTestSystem(SmallMoleculeLibraryTestSystem):
    method read_smiles (line 1862) | def read_smiles(self, filename):
    method __init__ (line 1874) | def __init__(self, **kwargs):
  class FusedRingsTestSystem (line 1903) | class FusedRingsTestSystem(SmallMoleculeLibraryTestSystem):
    method __init__ (line 1907) | def __init__(self, **kwargs):
  class ValenceSmallMoleculeLibraryTestSystem (line 1911) | class ValenceSmallMoleculeLibraryTestSystem(PersesTestSystem):
    method __init__ (line 1951) | def __init__(self, **kwargs):
    method _canonicalize_smiles (line 2044) | def _canonicalize_smiles(self, list_of_smiles):
  function check_topologies (line 2075) | def check_topologies(testsystem):
  function checktestsystem (line 2091) | def checktestsystem(testsystem_class):
  function test_testsystems (line 2099) | def test_testsystems():
  function run_t4_inhibitors (line 2112) | def run_t4_inhibitors():
  function run_alkanes (line 2131) | def run_alkanes():
  function run_t4 (line 2145) | def run_t4():
  function run_myb (line 2163) | def run_myb():
  function run_abl_imatinib_resistance (line 2178) | def run_abl_imatinib_resistance():
  function run_kinase_inhibitors (line 2196) | def run_kinase_inhibitors():
  function run_valence_system (line 2210) | def run_valence_system():
  function run_alanine_system (line 2222) | def run_alanine_system(sterics=False):
  function test_valence_write_pdb_ncmc_switching (line 2241) | def test_valence_write_pdb_ncmc_switching():
  function run_abl_affinity_write_pdb_ncmc_switching (line 2249) | def run_abl_affinity_write_pdb_ncmc_switching():
  function run_constph_abl (line 2271) | def run_constph_abl():
  function run_imidazole (line 2307) | def run_imidazole():
  function run_fused_rings (line 2328) | def run_fused_rings():

FILE: perses/tests/utils.py
  function enter_temp_directory (line 44) | def enter_temp_directory():
  class NaNException (line 58) | class NaNException(Exception):
  function quantity_is_finite (line 62) | def quantity_is_finite(quantity):
  function compare_at_lambdas (line 82) | def compare_at_lambdas(context, functions):
  function get_atoms_with_undefined_stereocenters (line 115) | def get_atoms_with_undefined_stereocenters(molecule, verbose=False):
  function has_undefined_stereocenters (line 154) | def has_undefined_stereocenters(molecule, verbose=False):
  function enumerate_undefined_stereocenters (line 193) | def enumerate_undefined_stereocenters(molecule, verbose=False):
  function test_sanitizeSMILES (line 242) | def test_sanitizeSMILES():
  function compute_potential (line 266) | def compute_potential(system, positions, platform=None):
  function generate_solvated_hybrid_test_topology (line 294) | def generate_solvated_hybrid_test_topology(current_mol_name="naphthalene...
  function generate_vacuum_hostguest_proposal (line 429) | def generate_vacuum_hostguest_proposal(current_mol_name="B2", proposed_m...
  function validate_rjmc_work_variance (line 489) | def validate_rjmc_work_variance(top_prop, positions, geometry_method = 0...
  function validate_endstate_energies_md (line 607) | def validate_endstate_energies_md(input_htf, T_max=300 * unit.kelvin, en...
  function validate_unsampled_endstates_point (line 749) | def validate_unsampled_endstates_point(htf, hybrid_system, endstate=0, m...
  function validate_unsampled_endstates_md (line 831) | def validate_unsampled_endstates_md(htf, hybrid_system, endstate=0, n_st...
  function track_torsions (line 937) | def track_torsions(hybrid_factory):

FILE: perses/utils/charge_changing.py
  function modify_atom_classes (line 9) | def modify_atom_classes(water_atoms, topology_proposal):
  function get_charge_difference (line 30) | def get_charge_difference(current_oemol, new_oemol):
  function get_water_indices (line 53) | def get_water_indices(charge_diff,
  function get_ion_and_water_parameters (line 105) | def get_ion_and_water_parameters(system, topology, positive_ion_name="NA...
  function transform_waters_into_ions (line 169) | def transform_waters_into_ions(water_atoms, system, charge_diff, particl...

FILE: perses/utils/data.py
  function get_data_filename (line 12) | def get_data_filename(relative_path):
  function generate_gaff_xml (line 39) | def generate_gaff_xml():
  function forcefield_directory (line 63) | def forcefield_directory():
  function load_smi (line 77) | def load_smi(smi_file,index=None):
  function serialize (line 103) | def serialize(item, filename):

FILE: perses/utils/openeye.py
  function system_generator_wrapper (line 19) | def system_generator_wrapper(oemols,
  function smiles_to_oemol (line 57) | def smiles_to_oemol(smiles, title='MOL', max_confs=1):
  function iupac_to_oemol (line 113) | def iupac_to_oemol(iupac, title='MOL', max_confs=1):
  function extractPositionsFromOEMol (line 157) | def extractPositionsFromOEMol(molecule,units=unit.angstrom):
  function giveOpenmmPositionsToOEMol (line 177) | def giveOpenmmPositionsToOEMol(positions, molecule):
  function OEMol_to_omm_ff (line 201) | def OEMol_to_omm_ff(molecule, system_generator):
  function createSystemFromIUPAC (line 225) | def createSystemFromIUPAC(iupac_name, title="MOL", **system_generator_kw...
  function createSystemFromSMILES (line 263) | def createSystemFromSMILES(smiles,title='MOL', **system_generator_kwargs):
  function describe_oemol (line 298) | def describe_oemol(mol):
  function createOEMolFromSDF (line 323) | def createOEMolFromSDF(sdf_filename, index=0, add_hydrogens=True, allow_...
  function calculate_mol_similarity (line 374) | def calculate_mol_similarity(molA, molB):
  function createSMILESfromOEMol (line 392) | def createSMILESfromOEMol(molecule):
  function generate_unique_atom_names (line 401) | def generate_unique_atom_names(molecule):
  function has_undefined_stereocenters (line 447) | def has_undefined_stereocenters(mol):
  function generate_expression (line 478) | def generate_expression(list):

FILE: perses/utils/smallmolecules.py
  function sanitizeSMILES (line 11) | def sanitizeSMILES(smiles_list, mode='drop', verbose=False):
  function canonicalize_SMILES (line 91) | def canonicalize_SMILES(smiles_list):
  function show_topology (line 119) | def show_topology(topology):
  function render_single_molecule (line 138) | def render_single_molecule(filename, molecule, width=1200, height=600):
  function render_atom_mapping (line 157) | def render_atom_mapping(filename, molecule1, molecule2, new_to_old_atom_...
  function render_protein_residue_atom_mapping (line 275) | def render_protein_residue_atom_mapping(topology_proposal, filename, wid...
  function generate_ligands_figure (line 302) | def generate_ligands_figure(molecules,figsize=None,filename='ligands.png'):

FILE: perses/utils/url_utils.py
  function retrieve_file_url (line 22) | def retrieve_file_url(url, retries=5):
  function fetch_url_contents (line 44) | def fetch_url_contents(url, retries=5):

FILE: setup.py
  function find_package_data (line 32) | def find_package_data(data_root, package_root):

FILE: versioneer.py
  class VersioneerConfig (line 285) | class VersioneerConfig:
  function get_root (line 289) | def get_root():
  function get_config_from_root (line 328) | def get_config_from_root(root):
  class NotThisMethod (line 357) | class NotThisMethod(Exception):
  function register_vcs_handler (line 366) | def register_vcs_handler(vcs, method):  # decorator
  function run_command (line 377) | def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
  function git_get_keywords (line 941) | def git_get_keywords(versionfile_abs):
  function git_versions_from_keywords (line 970) | def git_versions_from_keywords(keywords, tag_prefix, verbose):
  function git_pieces_from_vcs (line 1029) | def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_comma...
  function do_vcs_install (line 1123) | def do_vcs_install(manifest_in, versionfile_source, ipy):
  function versions_from_parentdir (line 1161) | def versions_from_parentdir(parentdir_prefix, root, verbose):
  function versions_from_file (line 1204) | def versions_from_file(filename):
  function write_to_version_file (line 1221) | def write_to_version_file(filename, versions):
  function plus_or_dot (line 1232) | def plus_or_dot(pieces):
  function render_pep440 (line 1239) | def render_pep440(pieces):
  function render_pep440_pre (line 1264) | def render_pep440_pre(pieces):
  function render_pep440_post (line 1280) | def render_pep440_post(pieces):
  function render_pep440_old (line 1307) | def render_pep440_old(pieces):
  function render_git_describe (line 1329) | def render_git_describe(pieces):
  function render_git_describe_long (line 1349) | def render_git_describe_long(pieces):
  function render (line 1369) | def render(pieces, style):
  class VersioneerBadRootError (line 1401) | class VersioneerBadRootError(Exception):
  function get_versions (line 1405) | def get_versions(verbose=False):
  function get_version (line 1481) | def get_version():
  function get_cmdclass (line 1486) | def get_cmdclass(cmdclass=None):
  function do_setup (line 1730) | def do_setup():
  function scan_setup_py (line 1812) | def scan_setup_py():