Index

A

average_structure_file (model_workflow.mwf.MD property)

C

cg_residues (model_workflow.mwf.MD property) (model_workflow.mwf.Project property) cg_selection (model_workflow.mwf.MD property)

charges (model_workflow.mwf.Project property) check_is_time_dependent() (model_workflow.mwf.Project method) check_md_directories() (model_workflow.mwf.Project method)

D

dihedrals (model_workflow.mwf.Project property)

F

first_frame_file (model_workflow.mwf.MD property)

G

get_average_structure (model_workflow.mwf.MD attribute) get_average_structure_file() (model_workflow.mwf.MD method) get_cg_residues() (model_workflow.mwf.MD method) (model_workflow.mwf.Project method) get_cg_selection() (model_workflow.mwf.MD 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_dihedrals() (model_workflow.mwf.Project 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_input() (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_interaction_types (model_workflow.mwf.Project attribute) 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_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_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_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_map (model_workflow.mwf.Project attribute) get_screenshot_filename (model_workflow.mwf.Project attribute) 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) 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_input_topology_filepath() (model_workflow.mwf.Project method)

I

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_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) interaction_types (model_workflow.mwf.Project property) interactions (model_workflow.mwf.MD property) is_inputs_file_available() (model_workflow.mwf.Project method) is_time_dependent (model_workflow.mwf.Project property) is_trajectory_integral() (model_workflow.mwf.MD method)

L

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) must_check_stable_bonds (model_workflow.mwf.Project property)

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) process_input_files (model_workflow.mwf.MD 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)

R

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) residue_map (model_workflow.mwf.Project 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) snapshots (model_workflow.mwf.MD property) (model_workflow.mwf.Project property) standard_topology_file (model_workflow.mwf.Project property)

structure (model_workflow.mwf.MD property) (model_workflow.mwf.Project property) structure_file (model_workflow.mwf.MD property) (model_workflow.mwf.Project property)

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)