Index _ | A | B | C | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W _ __init__() (molsysmt.basic.ConversionIssue method) (molsysmt.basic.ConversionReport method) (molsysmt.basic.Iterator method) (molsysmt.third_party.openmm.reporters.H5MSMReporter method) (molsysmt.third_party.openmm.reporters.StructuresDictReporter method) (molsysmt.third_party.openmm.reporters.TQDMReporter method) A add() (in module molsysmt.basic) add_allowed_plane_region() (in module molsysmt.third_party.openmm.forces) add_allowed_z_region() (in module molsysmt.third_party.openmm.forces) add_arrows() (in module molsysmt.third_party.nglview) add_constant_force() (in module molsysmt.third_party.openmm.forces) add_contacts() (in module molsysmt.third_party.nglview) add_cylinders() (in module molsysmt.third_party.nglview) add_forbidden_plane_region() (in module molsysmt.third_party.openmm.forces) add_forbidden_z_region() (in module molsysmt.third_party.openmm.forces) add_harmonic_bond_force() (in module molsysmt.third_party.openmm.forces) add_hbonds() (in module molsysmt.third_party.nglview) add_missing_bonds() (in module molsysmt.build) add_missing_heavy_atoms() (in module molsysmt.build) add_missing_hydrogens() (in module molsysmt.build) add_missing_terminal_cappings() (in module molsysmt.build) add_plane_harmonic_restraint() (in module molsysmt.third_party.openmm.forces) add_point_harmonic_restraint() (in module molsysmt.third_party.openmm.forces) add_terminal_atoms() (in module molsysmt.build) align_principal_axes() (in module molsysmt.structure) append_structures() (in module molsysmt.basic) apply_chemical_template() (in module molsysmt.physchem) are_multiple_molecular_systems() (in module molsysmt.basic) arguments (molsysmt.basic.Iterator attribute) assess_chemical_template() (in module molsysmt.physchem) assign_autodock_atom_types() (in module molsysmt.build) assign_partial_charges() (in module molsysmt.build) attribute (molsysmt.basic.ConversionIssue attribute) audited_scopes (molsysmt.basic.ConversionReport attribute) available_platforms() (in module molsysmt.third_party.openmm.platforms) B build_peptide() (in module molsysmt.build) C center() (in module molsysmt.structure) clear() (in module molsysmt.third_party.nglview) close() (in module molsysmt.form) compare() (in module molsysmt.basic) concatenate_structures() (in module molsysmt.basic) contains() (in module molsysmt.basic) ConversionIssue (class in molsysmt.basic) ConversionReport (class in molsysmt.basic) convert() (in module molsysmt.basic) copy() (in module molsysmt.basic) E editable() (in module molsysmt.build) element (molsysmt.basic.Iterator attribute) extract() (in module molsysmt.basic) F flip() (in module molsysmt.structure) from_form (molsysmt.basic.ConversionReport attribute) G get() (in module molsysmt.basic) get_1_letter_code_from_name() (in module molsysmt.element.group.amino_acid) get_acceptor_atoms() (in module molsysmt.hbonds) (in module molsysmt.interactions.hbonds) get_angles() (in module molsysmt.structure) get_angles_from_box() (in module molsysmt.pbc) get_area_buried() (in module molsysmt.physchem) get_aromaticity() (in module molsysmt.physchem) get_atom_type_from_atom_name() (in module molsysmt.element.atom) get_atomic_radius() (in module molsysmt.physchem) get_attributes() (in module molsysmt.basic) (in module molsysmt.form) get_autodock_atom_types() (in module molsysmt.physchem) get_bonded_atom_pairs() (in module molsysmt.element.group) (in module molsysmt.element.group.amino_acid) (in module molsysmt.element.group.ion) (in module molsysmt.element.group.saccharide) (in module molsysmt.element.group.small_molecule) (in module molsysmt.element.group.terminal_capping) (in module molsysmt.element.group.water) get_bondgraph() (in module molsysmt.topology) get_box_from_lengths_and_angles() (in module molsysmt.pbc) get_box_with_shape() (in module molsysmt.pbc) get_buch_hbonds() (in module molsysmt.hbonds) (in module molsysmt.interactions.hbonds) get_buried_fraction() (in module molsysmt.physchem) get_cation_pi_interactions() (in module molsysmt.interactions.cation_pi) get_center() (in module molsysmt.structure) get_chain_id() (in module molsysmt.element.chain) get_chain_index() (in module molsysmt.element.chain) get_chain_name() (in module molsysmt.element.chain) get_chain_type() (in module molsysmt.element.chain) get_charge() (in module molsysmt.physchem) get_charge_centers() (in module molsysmt.physchem) get_chemical_readiness() (in module molsysmt.physchem) get_cip_stereochemistry() (in module molsysmt.physchem) get_component_id() (in module molsysmt.element.component) get_component_index() (in module molsysmt.element.component) get_component_name() (in module molsysmt.element.component) get_component_type() (in module molsysmt.element.component) get_contacts() (in module molsysmt.structure) get_conversion_report() (in module molsysmt.basic) get_covalent_blocks() (in module molsysmt.topology) get_covalent_bond_candidates() (in module molsysmt.build) get_covalent_paths() (in module molsysmt.topology) get_degrees_of_freedom() (in module molsysmt.molecular_mechanics) get_dihedral_angles() (in module molsysmt.structure) get_dihedral_quartets() (in module molsysmt.topology) get_distances() (in module molsysmt.structure) get_disulfide_bonds() (in module molsysmt.build) get_disulfide_candidates() (in module molsysmt.interactions.disulfides) get_donor_atoms() (in module molsysmt.hbonds) (in module molsysmt.interactions.hbonds) get_electronegativity() (in module molsysmt.physchem) get_engine_forcefield() (in module molsysmt.molecular_mechanics) get_entity_id() (in module molsysmt.element.entity) get_entity_index() (in module molsysmt.element.entity) get_entity_name() (in module molsysmt.element.entity) get_entity_type() (in module molsysmt.element.entity) get_expected_heavy_atoms() (in module molsysmt.element.group.amino_acid) get_expected_hydrogens() (in module molsysmt.element.group.amino_acid) get_forces() (in module molsysmt.molecular_mechanics) get_form() (in module molsysmt.basic) get_group_db() (in module molsysmt.element.group.amino_acid) (in module molsysmt.element.group.ion) (in module molsysmt.element.group.saccharide) (in module molsysmt.element.group.small_molecule) (in module molsysmt.element.group.terminal_capping) get_group_type() (in module molsysmt.element.group) get_group_type_from_group_name() (in module molsysmt.element.group) get_halogen_bond_sites() (in module molsysmt.physchem) get_halogen_bonds() (in module molsysmt.interactions.halogen_bonds) get_hbond_sites() (in module molsysmt.physchem) get_hbonds() (in module molsysmt.interactions.hbonds) get_hydrogen_inventory() (in module molsysmt.physchem) get_hydrophobic_interactions() (in module molsysmt.interactions.hydrophobic) get_hydrophobic_sites() (in module molsysmt.physchem) get_hydrophobicity() (in module molsysmt.physchem) get_ionic_interactions() (in module molsysmt.interactions.ionic) get_label() (in module molsysmt.basic) get_least_rmsd() (in module molsysmt.structure) get_lengths_and_angles_from_box() (in module molsysmt.pbc) get_lengths_from_box() (in module molsysmt.pbc) get_luzard_chandler_hbonds() (in module molsysmt.hbonds) (in module molsysmt.interactions.hbonds) get_mass() (in module molsysmt.physchem) get_maximum_distances() (in module molsysmt.structure) get_metal_coordination() (in module molsysmt.interactions.metal_coordination) get_metal_coordination_sites() (in module molsysmt.physchem) get_minimum_distances() (in module molsysmt.structure) get_missing_bonds() (in module molsysmt.build) get_missing_heavy_atoms() (in module molsysmt.build) get_missing_residues() (in module molsysmt.build) get_missing_terminal_cappings() (in module molsysmt.build) get_molecule_id() (in module molsysmt.element.molecule) get_molecule_index() (in module molsysmt.element.molecule) get_molecule_name() (in module molsysmt.element.molecule) get_molecule_type() (in module molsysmt.element.molecule) get_n_components() (in module molsysmt.element.component) get_n_entities() (in module molsysmt.element.entity) get_n_molecules() (in module molsysmt.element.molecule) get_neighbors() (in module molsysmt.structure) get_non_bonded_potential_energy() (in module molsysmt.molecular_mechanics) get_non_standard_residues() (in module molsysmt.build) get_partial_charges() (in module molsysmt.physchem) get_peptide_bond_candidates() (in module molsysmt.build) get_peptide_chemical_template() (in module molsysmt.physchem) get_pi_pi_interactions() (in module molsysmt.interactions.pi_pi) get_polarity() (in module molsysmt.physchem) get_potential_energy() (in module molsysmt.molecular_mechanics) get_principal_axes() (in module molsysmt.structure) get_protor_atom_type() (in module molsysmt.physchem) get_protor_vdw_radius() (in module molsysmt.physchem) get_radius_of_gyration() (in module molsysmt.structure) get_residue_chemical_coverage() (in module molsysmt.build) get_rigid_fragments() (in module molsysmt.topology) get_rmsd() (in module molsysmt.structure) get_rmsf() (in module molsysmt.structure) get_rotatable_bonds() (in module molsysmt.topology) get_sasa() (in module molsysmt.physchem) get_secondary_structure() (in module molsysmt.structure) get_sequence_alignment() (in module molsysmt.topology) get_sequence_identity() (in module molsysmt.topology) get_shape_from_angles() (in module molsysmt.pbc) get_shape_from_box() (in module molsysmt.pbc) get_standard_name() (in module molsysmt.element.group.amino_acid) get_substructure_matches() (in module molsysmt.topology) get_surface_area() (in module molsysmt.physchem) get_transmembrane_tendency() (in module molsysmt.physchem) get_volume() (in module molsysmt.physchem) get_volume_from_box() (in module molsysmt.pbc) get_volume_from_lengths_and_angles() (in module molsysmt.pbc) get_water_bridges() (in module molsysmt.interactions.water_bridges) get_water_sites() (in module molsysmt.physchem) H H5MSMReporter (class in molsysmt.third_party.openmm.reporters) has_attribute() (in module molsysmt.basic) (in module molsysmt.form) has_hydrogens() (in module molsysmt.build) has_pbc() (in module molsysmt.pbc) I indices (molsysmt.basic.Iterator attribute) info() (in module molsysmt.basic) is_a_molecular_system() (in module molsysmt.basic) is_amino_acid() (in module molsysmt.element.group.amino_acid) is_atom_type() (in module molsysmt.element.atom) is_component_type() (in module molsysmt.element.component) is_composed_of() (in module molsysmt.basic) (in module molsysmt.element) is_element() (in module molsysmt.element) is_exhaustive (molsysmt.basic.ConversionReport attribute) is_file() (in module molsysmt.form) is_group_type() (in module molsysmt.element.group) is_ion() (in module molsysmt.element.group.ion) is_item() (in module molsysmt.form) is_lipid() (in module molsysmt.element.group.lipid) is_molecule_type() (in module molsysmt.element.molecule) is_nucleotide() (in module molsysmt.element.group.nucleotide) is_saccharide() (in module molsysmt.element.group.saccharide) is_small_molecule() (in module molsysmt.element.group.small_molecule) is_solvated() (in module molsysmt.build) is_string() (in module molsysmt.form) is_terminal_capping() (in module molsysmt.element.group.terminal_capping) is_water() (in module molsysmt.element.group.water) issues (molsysmt.basic.ConversionReport attribute) Iterator (class in molsysmt.basic) iterator_index (molsysmt.basic.Iterator attribute) K kind (molsysmt.basic.ConversionIssue attribute) L least_rmsd_align() (in module molsysmt.structure) least_rmsd_fit() (in module molsysmt.structure) load_converter() (in module molsysmt.form) load_html_in_jupyter_notebook() (in module molsysmt.third_party.nglview) loading_failures() (in module molsysmt.third_party.openmm.platforms) M make_bioassembly() (in module molsysmt.build) make_water_box() (in module molsysmt.build) merge() (in module molsysmt.basic) molecular_system (molsysmt.basic.Iterator attribute) move_away() (in module molsysmt.structure) mutate() (in module molsysmt.build) N normalize_aromatic_bond_orders() (in module molsysmt.physchem) normalize_atom_types() (in module molsysmt.element.atom) O outcome (molsysmt.basic.ConversionReport attribute) P pin_atoms() (in module molsysmt.third_party.openmm.forces) potential_energy_minimization() (in module molsysmt.molecular_mechanics) principal_component_analysis() (in module molsysmt.structure) R reason (molsysmt.basic.ConversionIssue attribute) remove() (in module molsysmt.basic) remove_overlapping_molecules() (in module molsysmt.build) rotate() (in module molsysmt.structure) S scope (molsysmt.basic.ConversionIssue attribute) select() (in module molsysmt.basic) set() (in module molsysmt.basic) set_color() (in module molsysmt.third_party.nglview) set_color_by_value() (in module molsysmt.third_party.nglview) set_dihedral_angles() (in module molsysmt.structure) shift_dihedral_angles() (in module molsysmt.structure) show_as_balls_and_sticks() (in module molsysmt.third_party.nglview) show_as_cartoon() (in module molsysmt.third_party.nglview) show_as_licorice() (in module molsysmt.third_party.nglview) show_as_surface() (in module molsysmt.third_party.nglview) show_gui() (in module molsysmt.third_party.nglview) small_molecule_is_amino_acid() (in module molsysmt.element.group.small_molecule) solvate() (in module molsysmt.build) solve_atoms_with_alternate_location() (in module molsysmt.build) standardize_view() (in module molsysmt.third_party.nglview) structure_indices (molsysmt.basic.Iterator attribute) StructuresDictReporter (class in molsysmt.third_party.openmm.reporters) T to_form (molsysmt.basic.ConversionReport attribute) TQDMReporter (class in molsysmt.third_party.openmm.reporters) translate() (in module molsysmt.structure) U unwrap() (in module molsysmt.pbc) V view() (in module molsysmt.basic) W where_is_attribute() (in module molsysmt.basic) wrap_to_mic() (in module molsysmt.pbc) wrap_to_pbc() (in module molsysmt.pbc) write_html() (in module molsysmt.third_party.nglview)
