Index

_

__init__() (model_workflow.mwf.Project method)

A

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

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

B

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

C

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

check_is_time_dependent() (model_workflow.mwf.Project method) check_md_directories() (model_workflow.mwf.Project method) check_merged_residues() (model_workflow.utils.structures.Structure method) check_repeated_atoms() (model_workflow.utils.structures.Structure method) check_repeated_chains() (model_workflow.utils.structures.Structure method) check_repeated_residues() (model_workflow.utils.structures.Structure method) check_splitted_chains() (model_workflow.utils.structures.Structure method) classification (model_workflow.utils.structures.Chain property) (model_workflow.utils.structures.Residue property) copy() (model_workflow.utils.structures.Atom method) (model_workflow.utils.structures.Chain method) (model_workflow.utils.structures.Residue method) (model_workflow.utils.structures.Structure method) copy_bonds() (model_workflow.utils.structures.Structure method)

D

dihedrals (model_workflow.mwf.Project property)

display_summary() (model_workflow.utils.structures.Structure method) dummy_atom_indices (model_workflow.utils.structures.Structure property)

F

filter() (model_workflow.utils.structures.Structure method) find_fragments() (model_workflow.utils.structures.Structure method) find_ptms() (model_workflow.utils.structures.Structure method) find_residue() (model_workflow.utils.structures.Chain method) (model_workflow.utils.structures.Structure method) find_rings() (model_workflow.utils.structures.Residue method) (model_workflow.utils.structures.Structure method) find_whole_fragments() (model_workflow.utils.structures.Structure method) first_frame_file (model_workflow.mwf.MD property)

fix_atom_elements() (model_workflow.utils.structures.Structure method) fragments (model_workflow.utils.structures.Structure property) from_file() (model_workflow.utils.structures.Structure class method) from_mdanalysis() (model_workflow.utils.structures.Structure class method) from_mmcif() (model_workflow.utils.structures.Structure class method) from_mmcif_file() (model_workflow.utils.structures.Structure class method) from_pdb() (model_workflow.utils.structures.Structure class method) from_pdb_file() (model_workflow.utils.structures.Structure class method) from_prmtop_file() (model_workflow.utils.structures.Structure class method) from_tpr_file() (model_workflow.utils.structures.Structure class method)

G

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

get_ligand_map (model_workflow.mwf.Project attribute) get_ligand_references_file() (model_workflow.mwf.Project method) get_lipid_map (model_workflow.mwf.Project attribute) get_lipid_references_file() (model_workflow.mwf.Project method) get_md_directories() (model_workflow.mwf.Project method) get_md_inputs() (model_workflow.mwf.MD method) get_MDAnalysis_Universe (model_workflow.mwf.Project attribute) get_mds() (model_workflow.mwf.Project method) get_membrane_map (model_workflow.mwf.Project attribute) get_name_suggested_element() (model_workflow.utils.structures.Atom method) get_next_available_chain_name() (model_workflow.utils.structures.Structure method) get_pbc_residues() (model_workflow.mwf.MD method) (model_workflow.mwf.Project method) get_pbc_selection() (model_workflow.mwf.MD method) get_pdb_ids() (model_workflow.mwf.Project method) get_pdb_references (model_workflow.mwf.Project attribute) get_populations() (model_workflow.mwf.MD method) (model_workflow.mwf.Project method) get_populations_file() (model_workflow.mwf.Project method) get_processed_interactions (model_workflow.mwf.MD attribute) get_processed_interactions() (model_workflow.mwf.Project method) get_protein_map (model_workflow.mwf.Project attribute) get_protein_map() (model_workflow.mwf.MD method) get_protein_references_file() (model_workflow.mwf.Project method) get_pytraj_topology() (model_workflow.utils.structures.Structure method) get_reference_bonds (model_workflow.mwf.Project attribute) get_reference_bonds() (model_workflow.mwf.MD method) get_reference_frame (model_workflow.mwf.MD attribute) get_reference_md() (model_workflow.mwf.Project method) get_reference_md_index() (model_workflow.mwf.Project method) get_residue() (model_workflow.utils.structures.Atom method) get_residue_count() (model_workflow.utils.structures.Chain method) (model_workflow.utils.structures.Structure method) get_residue_index() (model_workflow.utils.structures.Atom method) get_residue_indices() (model_workflow.utils.structures.Chain method) get_residue_map (model_workflow.mwf.Project attribute) get_residues() (model_workflow.utils.structures.Chain method) get_screenshot_filename (model_workflow.mwf.Project attribute) get_selection() (model_workflow.utils.structures.Atom method) (model_workflow.utils.structures.Chain method) (model_workflow.utils.structures.Residue method) get_selection_chain_indices() (model_workflow.utils.structures.Structure method) get_selection_chains() (model_workflow.utils.structures.Structure method) get_selection_classification() (model_workflow.utils.structures.Structure method) get_selection_outer_bonds() (model_workflow.utils.structures.Structure method) get_selection_residue_indices() (model_workflow.utils.structures.Structure method) get_selection_residues() (model_workflow.utils.structures.Structure method) get_sequence() (model_workflow.utils.structures.Chain method) get_snaphsots() (model_workflow.mwf.Project method) get_snapshots (model_workflow.mwf.MD attribute) get_standard_topology_file() (model_workflow.mwf.Project method) get_structure() (model_workflow.mwf.MD method) (model_workflow.mwf.Project method) (model_workflow.utils.structures.Atom method) (model_workflow.utils.structures.Chain method) (model_workflow.utils.structures.Residue method) get_structure_file() (model_workflow.mwf.MD method) (model_workflow.mwf.Project method) get_topology_file() (model_workflow.mwf.MD method) (model_workflow.mwf.Project method) get_topology_filepath() (model_workflow.mwf.Project method) get_topology_reader() (model_workflow.mwf.Project method) get_trajectory_file() (model_workflow.mwf.MD method) (model_workflow.mwf.Project method) get_transitions() (model_workflow.mwf.MD method) (model_workflow.mwf.Project method) get_transitions_file() (model_workflow.mwf.Project method) guess_element() (model_workflow.utils.structures.Atom method)

H

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

I

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

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

L

label (model_workflow.utils.structures.Atom property) (model_workflow.utils.structures.Residue property) ligand_map (model_workflow.mwf.Project property)

ligand_references_file (model_workflow.mwf.Project property) lipid_map (model_workflow.mwf.Project property) lipid_references_file (model_workflow.mwf.Project property)

M

MD (class in model_workflow.mwf) md_directories (model_workflow.mwf.Project property) md_inputs (model_workflow.mwf.MD property)

mds (model_workflow.mwf.Project property) membrane_map (model_workflow.mwf.Project property) merge() (model_workflow.utils.structures.Structure method) must_check_stable_bonds (model_workflow.mwf.Project property)

N

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

P

pathify() (model_workflow.mwf.MD method) (model_workflow.mwf.Project method) pbc_residues (model_workflow.mwf.MD property) (model_workflow.mwf.Project property) pbc_selection (model_workflow.mwf.MD property) pdb_ids (model_workflow.mwf.Project property) pdb_references_file() (model_workflow.mwf.Project method) populations (model_workflow.mwf.MD property) (model_workflow.mwf.Project property) populations_file (model_workflow.mwf.Project property) prepare_metadata (model_workflow.mwf.MD attribute) (model_workflow.mwf.Project attribute)

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

R

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

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

S

screenshot_filename (model_workflow.mwf.Project property) select() (model_workflow.utils.structures.Structure method) select_all() (model_workflow.utils.structures.Structure method) select_atom_indices() (model_workflow.utils.structures.Structure method) select_by_classification() (model_workflow.utils.structures.Structure method) select_carbohydrates() (model_workflow.utils.structures.Structure method) select_cartoon() (model_workflow.utils.structures.Structure method) select_cg() (model_workflow.utils.structures.Structure method) select_counter_ions() (model_workflow.utils.structures.Structure method) select_heavy_atoms() (model_workflow.utils.structures.Structure method) select_ions() (model_workflow.utils.structures.Structure method) select_lipids() (model_workflow.utils.structures.Structure method) select_nucleic() (model_workflow.utils.structures.Structure method) select_pbc_guess() (model_workflow.utils.structures.Structure method) select_protein() (model_workflow.utils.structures.Structure method) select_residue_indices() (model_workflow.utils.structures.Structure method) select_water() (model_workflow.utils.structures.Structure method) select_water_and_counter_ions() (model_workflow.utils.structures.Structure method) set_atom_indices() (model_workflow.utils.structures.Residue method) set_atoms() (model_workflow.utils.structures.Residue method) set_bonds() (model_workflow.utils.structures.Structure method) set_chain() (model_workflow.utils.structures.Residue method) set_chain_index() (model_workflow.utils.structures.Residue method) set_classification() (model_workflow.utils.structures.Chain method) set_index() (model_workflow.utils.structures.Chain method) (model_workflow.utils.structures.Residue method)

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

T

topology_file (model_workflow.mwf.MD property) (model_workflow.mwf.Project property) topology_filepath (model_workflow.mwf.Project property) topology_reader (model_workflow.mwf.Project property)

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

U

universe (model_workflow.mwf.Project property)

update_inputs() (model_workflow.mwf.Project method)