Index

_

__init__() (mddb_workflow.mwf.Project method)

A

add_atom() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) add_residue() (mddb_workflow.utils.structures.Chain method) aiida_data_file (mddb_workflow.mwf.Project property) Atom (class in mddb_workflow.utils.structures) atom_count (mddb_workflow.utils.structures.Chain property) (mddb_workflow.utils.structures.Residue property) (mddb_workflow.utils.structures.Structure property)

atom_indices (mddb_workflow.utils.structures.Chain property) (mddb_workflow.utils.structures.Residue property) atoms (mddb_workflow.utils.structures.Chain property) (mddb_workflow.utils.structures.Residue property) auto_chainer() (mddb_workflow.utils.structures.Structure method) average_structure_file (mddb_workflow.mwf.MD property)

B

bonds (mddb_workflow.utils.structures.Atom property) (mddb_workflow.utils.structures.Structure property)

C

cg_residues (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) cg_selection (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) Chain (class in mddb_workflow.utils.structures) chain (mddb_workflow.utils.structures.Atom property) (mddb_workflow.utils.structures.Residue property) chain_count (mddb_workflow.utils.structures.Structure property) chain_index (mddb_workflow.utils.structures.Atom property) (mddb_workflow.utils.structures.Residue property) chainer() (mddb_workflow.utils.structures.Structure method) charges (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) check_available_chains() (mddb_workflow.utils.structures.Structure method) check_incoherent_bonds() (mddb_workflow.utils.structures.Structure method) check_is_time_dependent() (mddb_workflow.mwf.Project method)

check_merged_residues() (mddb_workflow.utils.structures.Structure method) check_repeated_atoms() (mddb_workflow.utils.structures.Structure method) check_repeated_chains() (mddb_workflow.utils.structures.Structure method) check_repeated_residues() (mddb_workflow.utils.structures.Structure method) check_splitted_chains() (mddb_workflow.utils.structures.Structure method) classification (mddb_workflow.utils.structures.Chain property) (mddb_workflow.utils.structures.Residue property) clone() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) copy() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) (mddb_workflow.utils.structures.Structure method) copy_bonds() (mddb_workflow.utils.structures.Structure method) create_cache() (mddb_workflow.mwf.Project static method)

D

del_bonds() (mddb_workflow.utils.structures.Structure method) dihedrals (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property)

display_summary() (mddb_workflow.utils.structures.Structure method) dummy_atom_indices (mddb_workflow.utils.structures.Structure property) dummy_selection (mddb_workflow.mwf.MD property)

F

filter() (mddb_workflow.utils.structures.Structure method) filter_away() (mddb_workflow.utils.structures.Structure method) find_chain() (mddb_workflow.utils.structures.Structure method) find_covalent_bonds() (mddb_workflow.utils.structures.Structure method) find_fragments() (mddb_workflow.utils.structures.Structure method) find_or_create_chain() (mddb_workflow.utils.structures.Structure method) find_or_create_residue() (mddb_workflow.utils.structures.Chain method) find_ptms() (mddb_workflow.utils.structures.Structure method) find_residue() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Structure method) find_rings() (mddb_workflow.utils.structures.Residue method) (mddb_workflow.utils.structures.Structure method) find_whole_fragments() (mddb_workflow.utils.structures.Structure method)

first_frame_file (mddb_workflow.mwf.MD property) fix_atom_elements() (mddb_workflow.utils.structures.Structure method) force_classifications() (mddb_workflow.utils.structures.Structure method) forced_class_selections (mddb_workflow.mwf.MD property) fragments (mddb_workflow.utils.structures.Structure property) from_file() (mddb_workflow.utils.structures.Structure class method) from_mdanalysis() (mddb_workflow.utils.structures.Structure class method) from_mmcif() (mddb_workflow.utils.structures.Structure class method) from_mmcif_file() (mddb_workflow.utils.structures.Structure class method) from_pdb() (mddb_workflow.utils.structures.Structure class method) from_pdb_file() (mddb_workflow.utils.structures.Structure class method) from_pdb_id() (mddb_workflow.utils.structures.Structure class method) from_prmtop_file() (mddb_workflow.utils.structures.Structure class method) from_tpr_file() (mddb_workflow.utils.structures.Structure class method)

G

generate_pdb() (mddb_workflow.utils.structures.Structure method) generate_pdb_file() (mddb_workflow.utils.structures.Structure method) get_aiida_data_file() (mddb_workflow.mwf.Project method) get_atom_by_name() (mddb_workflow.utils.structures.Residue method) get_atom_count() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) (mddb_workflow.utils.structures.Structure method) get_atom_indices() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) get_atoms() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) get_available_chain_name() (mddb_workflow.utils.structures.Structure method) get_average_structure (mddb_workflow.mwf.MD attribute) get_average_structure_file() (mddb_workflow.mwf.MD method) get_bonded_atom_indices() (mddb_workflow.utils.structures.Residue method) get_bonded_atoms() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Residue method) get_bonded_residue_indices() (mddb_workflow.utils.structures.Residue method) get_bonded_residues() (mddb_workflow.utils.structures.Residue method) get_bonds() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Structure method) get_cg_residues() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_cg_selection() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_chain() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Residue method) get_chain_count() (mddb_workflow.utils.structures.Structure method) get_chain_index() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Residue method) get_chain_references (mddb_workflow.mwf.Project attribute) get_charges (mddb_workflow.mwf.MD attribute) get_charges() (mddb_workflow.mwf.Project method) get_check_stable_bonds() (mddb_workflow.mwf.MD method) get_classification() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) get_classification_by_name() (mddb_workflow.utils.structures.Residue method) get_dihedrals() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_dummy_atom_indices() (mddb_workflow.utils.structures.Structure method) get_dummy_selection() (mddb_workflow.mwf.MD method) get_file() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_first_frame (mddb_workflow.mwf.MD attribute) get_first_frame_file() (mddb_workflow.mwf.MD method) get_forced_class_selections() (mddb_workflow.mwf.MD method) get_formula() (mddb_workflow.utils.structures.Residue method) get_fragments() (mddb_workflow.utils.structures.Structure method) get_inchi_references (mddb_workflow.mwf.Project attribute) get_inchikeys (mddb_workflow.mwf.Project attribute) get_index() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) get_input() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_input_structure_file() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_input_structure_filepath() (mddb_workflow.mwf.MD method) get_input_topology_file() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_input_topology_filepath() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_input_trajectory_filepaths() (mddb_workflow.mwf.MD method) get_input_trajectory_files() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_inputs() (mddb_workflow.mwf.Project method) get_inputs_file() (mddb_workflow.mwf.Project method) get_ion_atom_indices() (mddb_workflow.utils.structures.Structure method) get_label() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Residue method) get_letter() (mddb_workflow.utils.structures.Residue method) get_ligand_references (mddb_workflow.mwf.Project attribute)

get_lipid_references (mddb_workflow.mwf.Project attribute) get_md_charges() (mddb_workflow.mwf.Project method) get_MDAnalysis_Universe (mddb_workflow.mwf.MD attribute) get_mds() (mddb_workflow.mwf.Project method) get_membrane_map (mddb_workflow.mwf.Project attribute) get_name_suggested_element() (mddb_workflow.utils.structures.Atom method) get_next_available_chain_name() (mddb_workflow.utils.structures.Structure method) get_parsed_chains() (mddb_workflow.utils.structures.Structure method) get_pbc_residues() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_pbc_selection() (mddb_workflow.mwf.MD method) get_pdb_ids() (mddb_workflow.mwf.Project method) get_pdb_references (mddb_workflow.mwf.Project attribute) get_populations() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_populations_file() (mddb_workflow.mwf.Project method) get_processed_interactions (mddb_workflow.mwf.MD attribute) get_processed_interactions() (mddb_workflow.mwf.Project method) get_project_directory() (mddb_workflow.mwf.Project static method) get_protein_map (mddb_workflow.mwf.Project attribute) get_protein_map() (mddb_workflow.mwf.MD method) get_protein_references_file() (mddb_workflow.mwf.Project method) get_pytraj_topology() (mddb_workflow.utils.structures.Structure method) get_rechained_structure() (mddb_workflow.utils.structures.Structure method) get_reference_bonds (mddb_workflow.mwf.MD attribute) get_reference_frame (mddb_workflow.mwf.MD attribute) get_reference_md() (mddb_workflow.mwf.Project method) get_reference_md_index() (mddb_workflow.mwf.Project method) get_residue() (mddb_workflow.utils.structures.Atom method) get_residue_count() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Structure method) get_residue_index() (mddb_workflow.utils.structures.Atom method) get_residue_indices() (mddb_workflow.utils.structures.Chain method) get_residue_map (mddb_workflow.mwf.Project attribute) get_residues() (mddb_workflow.utils.structures.Chain method) get_screenshot_filename (mddb_workflow.mwf.Project attribute) get_selection() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) get_selection_chain_indices() (mddb_workflow.utils.structures.Structure method) get_selection_chains() (mddb_workflow.utils.structures.Structure method) get_selection_classification() (mddb_workflow.utils.structures.Structure method) get_selection_outer_bonds() (mddb_workflow.utils.structures.Structure method) get_selection_residue_indices() (mddb_workflow.utils.structures.Structure method) get_selection_residues() (mddb_workflow.utils.structures.Structure method) get_sequence() (mddb_workflow.utils.structures.Chain method) get_sequences() (mddb_workflow.utils.structures.Structure method) get_snapshots (mddb_workflow.mwf.MD attribute) get_snapshots() (mddb_workflow.mwf.Project method) get_standard_topology_file() (mddb_workflow.mwf.Project method) get_structure() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) get_structure_file() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_thickness_analysis (mddb_workflow.mwf.MD attribute) get_topology_file() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_topology_filepath() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_topology_reader() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_trajectory_file() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_transitions() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) get_transitions_file() (mddb_workflow.mwf.Project method) get_universe() (mddb_workflow.mwf.Project method) get_warnings() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) guess_element() (mddb_workflow.utils.structures.Atom method)

H

has_cg() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Structure method)

I

inchikey_map (mddb_workflow.mwf.Project property) inchikeys (mddb_workflow.mwf.Project property) index (mddb_workflow.utils.structures.Atom property) (mddb_workflow.utils.structures.Chain property) (mddb_workflow.utils.structures.Residue property) inherit_topology_filename() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) input_authors (mddb_workflow.mwf.Project property) input_boxtype (mddb_workflow.mwf.Project property) input_cg_selection (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) input_chain_names (mddb_workflow.mwf.Project property) input_citation (mddb_workflow.mwf.Project property) input_collections (mddb_workflow.mwf.Project property) input_contact (mddb_workflow.mwf.Project property) input_customs (mddb_workflow.mwf.Project property) input_cv19_abs (mddb_workflow.mwf.Project property) input_cv19_nanobs (mddb_workflow.mwf.Project property) input_cv19_startconf (mddb_workflow.mwf.Project property) input_cv19_unit (mddb_workflow.mwf.Project property) input_dataset (mddb_workflow.mwf.Project property) input_description (mddb_workflow.mwf.Project property) input_dummy_selection (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) input_ensemble (mddb_workflow.mwf.Project property) input_files_processing (mddb_workflow.mwf.MD attribute) input_force_fields (mddb_workflow.mwf.Project property) input_forced_class_selections (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) input_framestep (mddb_workflow.mwf.Project property) input_getter() (mddb_workflow.mwf.MD method) input_groups (mddb_workflow.mwf.Project property) input_interactions (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) input_license (mddb_workflow.mwf.Project property) input_ligands (mddb_workflow.mwf.Project property) input_linkcense (mddb_workflow.mwf.Project property) input_links (mddb_workflow.mwf.Project property) input_metadditions (mddb_workflow.mwf.Project property) input_method (mddb_workflow.mwf.Project property) input_multimeric (mddb_workflow.mwf.Project property)

input_name (mddb_workflow.mwf.Project property) input_orientation (mddb_workflow.mwf.Project property) input_pbc_selection (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) input_pdb_ids (mddb_workflow.mwf.Project property) input_program (mddb_workflow.mwf.Project property) input_protein_references (mddb_workflow.mwf.Project property) input_structure_file (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) input_temperature (mddb_workflow.mwf.Project property) input_thanks (mddb_workflow.mwf.Project property) input_timestep (mddb_workflow.mwf.Project property) input_topology_file (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) input_trajectory_files (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) input_type (mddb_workflow.mwf.Project property) input_version (mddb_workflow.mwf.Project property) input_water (mddb_workflow.mwf.Project property) inputs (mddb_workflow.mwf.Project property) inputs_file (mddb_workflow.mwf.Project property) inputs_property() (mddb_workflow.mwf.Project method) interactions (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) invert_selection() (mddb_workflow.utils.structures.Structure method) ion_atom_indices (mddb_workflow.utils.structures.Structure property) is_bonded_with_residue() (mddb_workflow.utils.structures.Residue method) is_carbohydrate_candidate() (mddb_workflow.utils.structures.Atom method) is_cg() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Residue method) is_coherent() (mddb_workflow.utils.structures.Residue method) is_fatty_candidate() (mddb_workflow.utils.structures.Atom method) is_inputs_file_available() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) is_ion() (mddb_workflow.utils.structures.Atom method) is_large_aa() (mddb_workflow.utils.structures.Residue method) is_missing_any_bonds() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) (mddb_workflow.utils.structures.Structure method) is_time_dependent (mddb_workflow.mwf.Project property) is_trajectory_integral() (mddb_workflow.mwf.MD method)

L

label (mddb_workflow.utils.structures.Atom property) (mddb_workflow.utils.structures.Residue property)

ligand_references (mddb_workflow.mwf.Project property) lipid_references (mddb_workflow.mwf.Project property)

M

MD (class in mddb_workflow.mwf) md_charges (mddb_workflow.mwf.Project property) mds (mddb_workflow.mwf.Project property)

membrane_map (mddb_workflow.mwf.Project property) merge() (mddb_workflow.utils.structures.Structure method) must_check_stable_bonds (mddb_workflow.mwf.MD property)

N

name_selection() (mddb_workflow.utils.structures.Structure method)

P

pathify() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method) pbc_residues (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) pbc_selection (mddb_workflow.mwf.MD property) pdb_ids (mddb_workflow.mwf.Project property) pdb_references (mddb_workflow.mwf.Project property) pdb_references_file() (mddb_workflow.mwf.Project method) populations (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) populations_file (mddb_workflow.mwf.Project property)

prepare_metadata (mddb_workflow.mwf.MD attribute) (mddb_workflow.mwf.Project attribute) prepare_standard_topology (mddb_workflow.mwf.Project attribute) print_tests_summary() (mddb_workflow.mwf.MD method) produce_provenance (mddb_workflow.mwf.Project attribute) Project (class in mddb_workflow.mwf) protein_map (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) protein_references_file (mddb_workflow.mwf.Project property) ptm_options (mddb_workflow.utils.structures.Structure attribute) purge_chain() (mddb_workflow.utils.structures.Structure method) purge_residue() (mddb_workflow.utils.structures.Structure method)

R

raw_protein_chainer() (mddb_workflow.utils.structures.Structure method) reference_bonds (mddb_workflow.mwf.MD property) reference_frame (mddb_workflow.mwf.MD property) reference_md (mddb_workflow.mwf.Project property) reference_md_index (mddb_workflow.mwf.Project property) remove_atom() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) remove_residue() (mddb_workflow.utils.structures.Chain method) Residue (class in mddb_workflow.utils.structures) residue (mddb_workflow.utils.structures.Atom property) residue_count (mddb_workflow.utils.structures.Chain property) (mddb_workflow.utils.structures.Structure property) residue_index (mddb_workflow.utils.structures.Atom property) residue_indices (mddb_workflow.utils.structures.Chain property) residue_map (mddb_workflow.mwf.Project property) residues (mddb_workflow.utils.structures.Chain property) run_apl_analysis (mddb_workflow.mwf.MD attribute) run_channels_analysis (mddb_workflow.mwf.MD attribute)

run_clusters_analysis (mddb_workflow.mwf.MD attribute) run_density_analysis (mddb_workflow.mwf.MD attribute) run_dihedral_energies (mddb_workflow.mwf.MD attribute) run_dist_perres_analysis (mddb_workflow.mwf.MD attribute) run_energies_analysis (mddb_workflow.mwf.MD attribute) run_hbonds_analysis (mddb_workflow.mwf.MD attribute) run_helical_analysis (mddb_workflow.mwf.MD attribute) run_lipid_interactions_analysis (mddb_workflow.mwf.MD attribute) run_lipid_order_analysis (mddb_workflow.mwf.MD attribute) run_markov_analysis (mddb_workflow.mwf.MD attribute) run_pca_analysis (mddb_workflow.mwf.MD attribute) run_pockets_analysis (mddb_workflow.mwf.MD attribute) run_rgyr_analysis (mddb_workflow.mwf.MD attribute) run_rmsd_pairwise_analysis (mddb_workflow.mwf.MD attribute) run_rmsd_perres_analysis (mddb_workflow.mwf.MD attribute) run_rmsds_analysis (mddb_workflow.mwf.MD attribute) run_rmsf_analysis (mddb_workflow.mwf.MD attribute) run_sas_analysis (mddb_workflow.mwf.MD attribute) run_tmscores_analysis (mddb_workflow.mwf.MD attribute)

S

screenshot_filename (mddb_workflow.mwf.Project property) select() (mddb_workflow.utils.structures.Structure method) select_all() (mddb_workflow.utils.structures.Structure method) select_atom_indices() (mddb_workflow.utils.structures.Structure method) select_by_classification() (mddb_workflow.utils.structures.Structure method) select_carbohydrates() (mddb_workflow.utils.structures.Structure method) select_cartoon() (mddb_workflow.utils.structures.Structure method) select_cg() (mddb_workflow.utils.structures.Structure method) select_counter_ions() (mddb_workflow.utils.structures.Structure method) select_dummy() (mddb_workflow.utils.structures.Structure method) select_heavy_atoms() (mddb_workflow.utils.structures.Structure method) select_ions() (mddb_workflow.utils.structures.Structure method) select_ligands() (mddb_workflow.utils.structures.Structure method) select_lipids() (mddb_workflow.utils.structures.Structure method) select_missing_bonds() (mddb_workflow.utils.structures.Structure method) select_nucleic() (mddb_workflow.utils.structures.Structure method) select_pbc_guess() (mddb_workflow.utils.structures.Structure method) select_protein() (mddb_workflow.utils.structures.Structure method) select_residue_indices() (mddb_workflow.utils.structures.Structure method) select_water() (mddb_workflow.utils.structures.Structure method) select_water_and_counter_ions() (mddb_workflow.utils.structures.Structure method) set_atom_indices() (mddb_workflow.utils.structures.Residue method) set_atoms() (mddb_workflow.utils.structures.Residue method) set_bonds() (mddb_workflow.utils.structures.Structure method) set_chain() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Residue method) set_chain_index() (mddb_workflow.utils.structures.Atom method) (mddb_workflow.utils.structures.Residue method)

set_classification() (mddb_workflow.utils.structures.Chain method) set_index() (mddb_workflow.utils.structures.Chain method) (mddb_workflow.utils.structures.Residue method) set_new_atom() (mddb_workflow.utils.structures.Structure method) set_new_chain() (mddb_workflow.utils.structures.Structure method) set_new_coordinates() (mddb_workflow.utils.structures.Structure method) set_new_residue() (mddb_workflow.utils.structures.Structure method) set_residue() (mddb_workflow.utils.structures.Atom method) set_residue_index() (mddb_workflow.utils.structures.Atom method) set_residue_indices() (mddb_workflow.utils.structures.Chain method) set_residues() (mddb_workflow.utils.structures.Chain method) set_selection_chain_name() (mddb_workflow.utils.structures.Structure method) snapshots (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) sort_residues() (mddb_workflow.utils.structures.Structure method) split() (mddb_workflow.utils.structures.Residue method) split_by_atom_names() (mddb_workflow.utils.structures.Residue method) standard_topology_file (mddb_workflow.mwf.Project property) Structure (class in mddb_workflow.utils.structures) structure (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) (mddb_workflow.utils.structures.Atom property) (mddb_workflow.utils.structures.Chain property) (mddb_workflow.utils.structures.Residue property) structure_file (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) SUPPORTED_SELECTION_SYNTAXES (mddb_workflow.utils.structures.Structure attribute)

T

thickness_analysis (mddb_workflow.mwf.MD property) topology_file (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) topology_filepath (mddb_workflow.mwf.MD property) topology_reader (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property)

trajectory_file (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) transitions (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property) transitions_file (mddb_workflow.mwf.Project property)

U

universe (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property)

update_inputs() (mddb_workflow.mwf.MD method) (mddb_workflow.mwf.Project method)

W

warnings (mddb_workflow.mwf.MD property) (mddb_workflow.mwf.Project property)