All modules for which code is available

• molsysmt.basic.add
• molsysmt.basic.append_structures
• molsysmt.basic.are_multiple_molecular_systems
• molsysmt.basic.compare
• molsysmt.basic.concatenate_structures
• molsysmt.basic.contains
• molsysmt.basic.conversion_report
• molsysmt.basic.convert
• molsysmt.basic.copy
• molsysmt.basic.extract
• molsysmt.basic.get
• molsysmt.basic.get_attributes
• molsysmt.basic.get_conversion_report
• molsysmt.basic.get_form
• molsysmt.basic.get_label
• molsysmt.basic.has_attribute
• molsysmt.basic.info
• molsysmt.basic.is_a_molecular_system
• molsysmt.basic.is_composed_of
• molsysmt.basic.iterator
• molsysmt.basic.merge
• molsysmt.basic.remove
• molsysmt.basic.select
• molsysmt.basic.set
• molsysmt.basic.view
• molsysmt.basic.where_is_attribute
• molsysmt.build.add_missing_bonds
• molsysmt.build.add_missing_heavy_atoms
• molsysmt.build.add_missing_hydrogens
• molsysmt.build.add_missing_terminal_cappings
• molsysmt.build.add_terminal_atoms
• molsysmt.build.assign_autodock_atom_types
• molsysmt.build.assign_partial_charges
• molsysmt.build.build_peptide
• molsysmt.build.editable
• molsysmt.build.get_covalent_bond_candidates
• molsysmt.build.get_disulfide_bonds
• molsysmt.build.get_missing_bonds
• molsysmt.build.get_missing_heavy_atoms
• molsysmt.build.get_missing_residues
• molsysmt.build.get_missing_terminal_cappings
• molsysmt.build.get_non_standard_residues
• molsysmt.build.get_peptide_bond_candidates
• molsysmt.build.get_residue_chemical_coverage
• molsysmt.build.has_hydrogens
• molsysmt.build.is_solvated
• molsysmt.build.make_bioassembly
• molsysmt.build.make_water_box
• molsysmt.build.mutate
• molsysmt.build.remove_overlapping_molecules
• molsysmt.build.solvate
• molsysmt.build.solve_atoms_with_alternate_location
• molsysmt.element.atom.get_atom_type_from_atom_name
• molsysmt.element.atom.is_atom_type
• molsysmt.element.atom.normalize_atom_types
• molsysmt.element.chain.get_chain_id
• molsysmt.element.chain.get_chain_index
• molsysmt.element.chain.get_chain_name
• molsysmt.element.chain.get_chain_type
• molsysmt.element.component.get_component_id
• molsysmt.element.component.get_component_index
• molsysmt.element.component.get_component_name
• molsysmt.element.component.get_component_type
• molsysmt.element.component.get_n_components
• molsysmt.element.component.is_component_type
• molsysmt.element.entity.get_entity_id
• molsysmt.element.entity.get_entity_index
• molsysmt.element.entity.get_entity_name
• molsysmt.element.entity.get_entity_type
• molsysmt.element.entity.get_n_entities
• molsysmt.element.group.amino_acid.get_1_letter_code_from_name
• molsysmt.element.group.amino_acid.get_bonded_atom_pairs
• molsysmt.element.group.amino_acid.get_expected_heavy_atoms
• molsysmt.element.group.amino_acid.get_expected_hydrogens
• molsysmt.element.group.amino_acid.get_group_db
• molsysmt.element.group.amino_acid.get_standard_name
• molsysmt.element.group.amino_acid.is_amino_acid
• molsysmt.element.group.get_bonded_atom_pairs
• molsysmt.element.group.get_group_type
• molsysmt.element.group.ion.get_bonded_atom_pairs
• molsysmt.element.group.ion.get_group_db
• molsysmt.element.group.ion.is_ion
• molsysmt.element.group.is_group_type
• molsysmt.element.group.lipid.is_lipid
• molsysmt.element.group.nucleotide.is_nucleotide
• molsysmt.element.group.saccharide.get_bonded_atom_pairs
• molsysmt.element.group.saccharide.get_group_db
• molsysmt.element.group.saccharide.is_saccharide
• molsysmt.element.group.small_molecule.get_bonded_atom_pairs
• molsysmt.element.group.small_molecule.get_group_db
• molsysmt.element.group.small_molecule.is_small_molecule
• molsysmt.element.group.small_molecule.small_molecule_is_amino_acid
• molsysmt.element.group.terminal_capping.get_bonded_atom_pairs
• molsysmt.element.group.terminal_capping.get_group_db
• molsysmt.element.group.terminal_capping.is_terminal_capping
• molsysmt.element.group.water.get_bonded_atom_pairs
• molsysmt.element.group.water.is_water
• molsysmt.element.is_composed_of
• molsysmt.element.is_element
• molsysmt.element.molecule.get_molecule_id
• molsysmt.element.molecule.get_molecule_index
• molsysmt.element.molecule.get_molecule_name
• molsysmt.element.molecule.get_molecule_type
• molsysmt.element.molecule.get_n_molecules
• molsysmt.element.molecule.is_molecule_type
• molsysmt.form
• molsysmt.form.get_attributes
• molsysmt.form.has_attribute
• molsysmt.form.is_file
• molsysmt.form.is_item
• molsysmt.form.is_string
• molsysmt.form.load_converter
• molsysmt.interactions.cation_pi.get_cation_pi_interactions
• molsysmt.interactions.disulfides.get_disulfide_candidates
• molsysmt.interactions.halogen_bonds.get_halogen_bonds
• molsysmt.interactions.hbonds.get_acceptor_atoms
• molsysmt.interactions.hbonds.get_buch_hbonds
• molsysmt.interactions.hbonds.get_donor_atoms
• molsysmt.interactions.hbonds.get_hbonds
• molsysmt.interactions.hbonds.get_luzard_chandler_hbonds
• molsysmt.interactions.hydrophobic.get_hydrophobic_interactions
• molsysmt.interactions.ionic.get_ionic_interactions
• molsysmt.interactions.metal_coordination.get_metal_coordination
• molsysmt.interactions.pi_pi.get_pi_pi_interactions
• molsysmt.interactions.water_bridges.get_water_bridges
• molsysmt.molecular_mechanics.get_degrees_of_freedom
• molsysmt.molecular_mechanics.get_engine_forcefield
• molsysmt.molecular_mechanics.get_forces
• molsysmt.molecular_mechanics.get_non_bonded_potential_energy
• molsysmt.molecular_mechanics.get_potential_energy
• molsysmt.molecular_mechanics.potential_energy_minimization
• molsysmt.pbc.get_angles_from_box
• molsysmt.pbc.get_box_from_lengths_and_angles
• molsysmt.pbc.get_box_with_shape
• molsysmt.pbc.get_lengths_and_angles_from_box
• molsysmt.pbc.get_lengths_from_box
• molsysmt.pbc.get_shape_from_angles
• molsysmt.pbc.get_shape_from_box
• molsysmt.pbc.get_volume_from_box
• molsysmt.pbc.get_volume_from_lengths_and_angles
• molsysmt.pbc.has_pbc
• molsysmt.pbc.unwrap
• molsysmt.pbc.wrap_to_mic
• molsysmt.pbc.wrap_to_pbc
• molsysmt.physchem.apply_chemical_template
• molsysmt.physchem.assess_chemical_template
• molsysmt.physchem.atoms.protor
• molsysmt.physchem.get_area_buried
• molsysmt.physchem.get_aromaticity
• molsysmt.physchem.get_atomic_radius
• molsysmt.physchem.get_autodock_atom_types
• molsysmt.physchem.get_buried_fraction
• molsysmt.physchem.get_charge
• molsysmt.physchem.get_charge_centers
• molsysmt.physchem.get_chemical_readiness
• molsysmt.physchem.get_cip_stereochemistry
• molsysmt.physchem.get_electronegativity
• molsysmt.physchem.get_halogen_bond_sites
• molsysmt.physchem.get_hbond_sites
• molsysmt.physchem.get_hydrogen_inventory
• molsysmt.physchem.get_hydrophobic_sites
• molsysmt.physchem.get_hydrophobicity
• molsysmt.physchem.get_mass
• molsysmt.physchem.get_metal_coordination_sites
• molsysmt.physchem.get_partial_charges
• molsysmt.physchem.get_peptide_chemical_template
• molsysmt.physchem.get_polarity
• molsysmt.physchem.get_sasa
• molsysmt.physchem.get_surface_area
• molsysmt.physchem.get_transmembrane_tendency
• molsysmt.physchem.get_volume
• molsysmt.physchem.get_water_sites
• molsysmt.physchem.normalize_aromatic_bond_orders
• molsysmt.structure.align_principal_axes
• molsysmt.structure.center
• molsysmt.structure.flip
• molsysmt.structure.get_angles
• molsysmt.structure.get_center
• molsysmt.structure.get_contacts
• molsysmt.structure.get_dihedral_angles
• molsysmt.structure.get_distances
• molsysmt.structure.get_least_rmsd
• molsysmt.structure.get_maximum_distances
• molsysmt.structure.get_minimum_distances
• molsysmt.structure.get_neighbors
• molsysmt.structure.get_principal_axes
• molsysmt.structure.get_radius_of_gyration
• molsysmt.structure.get_rmsd
• molsysmt.structure.get_rmsf
• molsysmt.structure.get_secondary_structure
• molsysmt.structure.least_rmsd_align
• molsysmt.structure.least_rmsd_fit
• molsysmt.structure.move_away
• molsysmt.structure.principal_component_analysis
• molsysmt.structure.rotate
• molsysmt.structure.set_dihedral_angles
• molsysmt.structure.shift_dihedral_angles
• molsysmt.structure.translate
• molsysmt.third_party.nglview.add_arrows
• molsysmt.third_party.nglview.add_contacts
• molsysmt.third_party.nglview.add_cylinders
• molsysmt.third_party.nglview.add_hbonds
• molsysmt.third_party.nglview.clear
• molsysmt.third_party.nglview.load_html_in_jupyter_notebook
• molsysmt.third_party.nglview.set_color
• molsysmt.third_party.nglview.set_color_by_value
• molsysmt.third_party.nglview.show_as_balls_and_sticks
• molsysmt.third_party.nglview.show_as_cartoon
• molsysmt.third_party.nglview.show_as_licorice
• molsysmt.third_party.nglview.show_as_surface
• molsysmt.third_party.nglview.show_gui
• molsysmt.third_party.nglview.standardize_view
• molsysmt.third_party.nglview.write_html
• molsysmt.third_party.openmm.forces.add_allowed_plane_region
• molsysmt.third_party.openmm.forces.add_allowed_z_region
• molsysmt.third_party.openmm.forces.add_constant_force
• molsysmt.third_party.openmm.forces.add_forbidden_plane_region
• molsysmt.third_party.openmm.forces.add_forbidden_z_region
• molsysmt.third_party.openmm.forces.add_harmonic_bond_force
• molsysmt.third_party.openmm.forces.add_plane_harmonic_restraint
• molsysmt.third_party.openmm.forces.add_point_harmonic_restraint
• molsysmt.third_party.openmm.forces.pin_atoms
• molsysmt.third_party.openmm.platforms.platforms
• molsysmt.third_party.openmm.reporters.StructuresDict
• molsysmt.third_party.openmm.reporters.h5msm
• molsysmt.third_party.openmm.reporters.tqdm
• molsysmt.topology.get_bondgraph
• molsysmt.topology.get_covalent_blocks
• molsysmt.topology.get_covalent_paths
• molsysmt.topology.get_dihedral_quartets
• molsysmt.topology.get_rigid_fragments
• molsysmt.topology.get_rotatable_bonds
• molsysmt.topology.get_sequence_alignment
• molsysmt.topology.get_sequence_identity
• molsysmt.topology.get_substructure_matches