Index

_

_bondfilename (moldesign.data attribute)

A

a1 (moldesign.Bond attribute), [1] (moldesign.molecules.Bond attribute) (moldesign.molecules.bonds.Bond attribute) a2 (moldesign.Bond attribute), [1] (moldesign.molecules.Bond attribute) (moldesign.molecules.bonds.Bond attribute) about() (in module moldesign.widgets), [1] (in module moldesign.widgets.computeconfig) AbstractFunction (class in moldesign.orbitals.gaussians) add() (moldesign.Chain method) (moldesign.Entity method), [1] (moldesign.Residue method), [1], [2] (moldesign.molecules.Chain method) (moldesign.molecules.Entity method) (moldesign.molecules.Residue method) (moldesign.molecules.biounits.Entity method) (moldesign.molecules.chain.Chain method) (moldesign.molecules.residue.Residue method) (moldesign.utils.classes.Categorizer method) add_click_callback() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) add_hydrogen() (in module moldesign), [1], [2] (in module moldesign.interfaces.openbabel) (in module moldesign.interfaces.pdbfixer_interface) (in module moldesign.tools) add_line() (moldesign.utils.utils.BaseTable method) add_missing_data() (in module moldesign), [1], [2] (in module moldesign.tools) (in module moldesign.tools.topology) add_orbitals() (in module moldesign.interfaces.nbo_interface) (moldesign.orbitals.wfn.ElectronicWfn method) add_water() (in module moldesign), [1], [2] (in module moldesign.interfaces.pdbfixer_interface) (in module moldesign.tools) addatom() (moldesign.Molecule method), [1], [2] (moldesign.molecules.Molecule method) (moldesign.molecules.molecule.Molecule method) addatoms() (moldesign.Molecule method), [1], [2] (moldesign.molecules.Molecule method) (moldesign.molecules.molecule.Molecule method) Alias (class in moldesign.utils.classes) align_orbital_phases() (moldesign.molecules.Trajectory method) (moldesign.Trajectory method), [1] (moldesign.molecules.trajectory.Trajectory method) (moldesign.orbitals.wfn.ElectronicWfn method), [1] align_phases() (moldesign.orbitals.orbitals.MolecularOrbitals method), [1] ALL_BASES (moldesign.data attribute) ALL_PROPERTIES (moldesign.models.base.EnergyModelBase attribute) (moldesign.models.PySCFPotential attribute) (moldesign.models.Spring attribute) (moldesign.models.base.QMBase attribute) (moldesign.models.base.QMMMBase attribute) (moldesign.models.pyscf.PySCFPotential attribute) (moldesign.models.sqm.SQMPotential attribute) (moldesign.models.toys.Spring attribute) amber_to_mol() (in module moldesign.interfaces.openmm) AmberParameters (class in moldesign.interfaces.ambertools) AMINO_NAMES (moldesign.data attribute) angle() (in module moldesign), [1], [2], [3] (in module moldesign.geom), [1] (in module moldesign.geom.coords) (moldesign.Trajectory method) (moldesign.molecules.Trajectory method) (moldesign.molecules.atomcollections.AtomContainer method) (moldesign.molecules.trajectory.Trajectory method) ANGLE_FORCE_CONSTANT (moldesign.geom attribute) angle_gradient() (in module moldesign), [1], [2], [3] (in module moldesign.geom), [1] (in module moldesign.geom.grads) ANGLE_TOLERANCE (moldesign.geom attribute) AngleConstraint (class in moldesign.geom), [1] (class in moldesign.geom.constraints) AngleMonitor (class in moldesign), [1], [2] (class in moldesign.geom) (class in moldesign.geom.monitor) angular (moldesign.orbitals.gaussians.CartesianGaussian attribute) animate() (moldesign.widgets.trajectory.TrajectoryViewer method) annotation (moldesign.molecules.trajectory.Frame attribute) aotype (moldesign.orbitals.gaussians.AtomicBasisFunction attribute) append() (moldesign.utils.classes.ExclusiveList method) append_frame() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) append_matrix() (in module moldesign.interfaces.nbo_interface) apply_4x4_transform() (in module moldesign.geom), [1] (in module moldesign.mathutils) apply_config() (moldesign.widgets.ComputeConfig method) (moldesign.widgets.RegistryConfig method) (moldesign.widgets.computeconfig.ComputeConfig method) (moldesign.widgets.computeconfig.RegistryConfig method)

apply_frame() (moldesign.molecules.Trajectory method) (moldesign.Trajectory method), [1] (moldesign.molecules.trajectory.Trajectory method) apply_selected_symmetry() (moldesign.widgets.Symmetrizer method) (moldesign.widgets.symmetry.Symmetrizer method) apply_values() (moldesign.widgets.configurator.Configurator method) args_from() (in module moldesign.utils.callsigs) Array (class in moldesign.units.quantity) array() (in module moldesign.units.tools) assert_atom() (moldesign.molecules.molecule.MolTopologyMixin method) assign_biopolymer_bonds() (in module moldesign.helpers.pdb) (moldesign.Chain method), [1], [2] (moldesign.molecules.Chain method) (moldesign.molecules.chain.Chain method) assign_forcefield() (in module moldesign), [1], [2] (in module moldesign.interfaces.ambertools) (in module moldesign.tools) assign_formal_charges() (in module moldesign), [1], [2] (in module moldesign.tools) (in module moldesign.tools.topology) assign_template_bonds() (moldesign.molecules.Residue method) (moldesign.Residue method), [1], [2] (moldesign.molecules.residue.Residue method) assign_unique_hydrogen_names() (in module moldesign.helpers.pdb) atnum (Atom attribute) (moldesign.Atom attribute), [1] (moldesign.data attribute) (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) ATNUM_VALENCE_CHARGE (moldesign.tools attribute) Atom (class in moldesign), [1], [2] (class in moldesign.molecules) (class in moldesign.molecules.atoms) atom_click() (moldesign.widgets.geombuilder.GeometryBuilder method) (moldesign.widgets.GeometryBuilder method) (moldesign.widgets.ResidueSelector method) (moldesign.widgets.selection.ResidueSelector method) AtomArray (class in moldesign.molecules.coord_arrays) AtomContainer (class in moldesign.molecules.atomcollections) AtomCoordinate (class in moldesign.molecules.coord_arrays) AtomDrawingMixin (class in moldesign.molecules.atoms) AtomGeometryMixin (class in moldesign.molecules.atoms) atomgrad() (moldesign.geom.AngleConstraint static method), [1] (moldesign.geom.DihedralConstraint static method), [1] (moldesign.geom.DistanceConstraint static method), [1] (moldesign.geom.FixedCoordinate method), [1] (moldesign.geom.FixedPosition method), [1] (moldesign.geom.constraints.AngleConstraint static method) (moldesign.geom.constraints.DihedralConstraint static method) (moldesign.geom.constraints.DistanceConstraint static method) (moldesign.geom.constraints.FixedCoordinate method) (moldesign.geom.constraints.FixedPosition method) ATOMIC_MASSES (moldesign.data attribute) ATOMIC_NUMBERS (moldesign.data attribute) AtomicBasisFunction (class in moldesign.orbitals.gaussians) AtomInspector (class in moldesign.uibase.components) atomkey() (moldesign.uibase.components.SelBase static method) (moldesign.widgets.ResidueSelector static method) (moldesign.widgets.selection.ResidueSelector static method) AtomList (class in moldesign), [1] (class in moldesign.molecules) (class in moldesign.molecules.atomcollections) atomnames (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) AtomPropertyMixin (class in moldesign.molecules.atoms) ATOMRADIUS (moldesign.viewer.bondclicker.BondClicker attribute) AtomReprMixin (class in moldesign.molecules.atoms) atoms (moldesign.AtomList attribute), [1] (Molecule attribute) (moldesign.Molecule attribute), [1] (moldesign.Residue attribute) (moldesign.molecules.AtomList attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.Residue attribute) (moldesign.molecules.atomcollections.AtomContainer attribute) (moldesign.molecules.atomcollections.AtomList attribute) (moldesign.molecules.biounits.ChildList attribute) (moldesign.molecules.molecule.Molecule attribute) (moldesign.molecules.residue.Residue attribute) atoms_within() (moldesign.molecules.atomcollections.AtomContainer method) (moldesign.molecules.atoms.AtomGeometryMixin method) Attribute (class in moldesign.utils.classes) autostyle() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method)

B

b (moldesign.data attribute) B3LYP (class in moldesign.models) (class in moldesign.models.models) backbone (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) BACKBONES (moldesign.data attribute) base (moldesign.data attribute) BASES (moldesign.data attribute) BaseTable (class in moldesign.utils.utils) basis_functions (moldesign.molecules.atoms.AtomPropertyMixin attribute) basis_values() (in module moldesign.interfaces.pyscf_interface) BasisSet (class in moldesign), [1] (class in moldesign.orbitals) (class in moldesign.orbitals.basis) BFGS (class in moldesign.min.scipy) bfgs() (in module moldesign) (in module moldesign.min) (in module moldesign.min.scipy) binomial_coefficient() (in module moldesign.utils.utils) BioAssembly (class in moldesign.helpers.pdb) biomol_summary_markdown() (moldesign.molecules.molecule.MolReprMixin method)

BIOPOLYMER_TYPES (moldesign.data attribute) biopy_to_mol() (in module moldesign.interfaces.biopython_interface) Bond (class in moldesign), [1] (class in moldesign.molecules) (class in moldesign.molecules.bonds) bond_click() (moldesign.widgets.geombuilder.GeometryBuilder method) (moldesign.widgets.GeometryBuilder method) bond_graph (moldesign.Atom attribute), [1], [2] (Molecule attribute) (moldesign.Molecule attribute), [1] (moldesign.molecules.Atom attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.atoms.Atom attribute) (moldesign.molecules.molecule.Molecule attribute) bond_to() (moldesign.Atom method), [1], [2] (moldesign.molecules.Atom method) (moldesign.molecules.atoms.Atom method) BondClicker (class in moldesign.viewer.bondclicker) BONDCOLOR (moldesign.viewer.bondclicker.BondClicker attribute) bondkey() (moldesign.widgets.BondSelector static method) (moldesign.widgets.selection.BondSelector static method) bonds (moldesign.Atom attribute), [1], [2] (moldesign.Molecule attribute), [1], [2] (moldesign.molecules.Atom attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.atoms.Atom attribute) (moldesign.molecules.molecule.Molecule attribute) BondSelector (class in moldesign.widgets) (class in moldesign.widgets.selection) broadcast_to() (in module moldesign.units.tools) build_assembly() (in module moldesign), [1], [2] (in module moldesign.tools) (in module moldesign.tools.build) build_bdna() (in module moldesign), [1], [2] (in module moldesign.interfaces.ambertools) (in module moldesign.tools) build_dna_helix() (in module moldesign), [1], [2] (in module moldesign.interfaces.ambertools) (in module moldesign.tools)

C

c_terminal (moldesign.Chain attribute), [1], [2] (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) calc_am1_bcc_charges() (in module moldesign), [1], [2] (in module moldesign.interfaces.ambertools) (in module moldesign.tools) calc_dipole() (moldesign.molecules.molecule.MolPropertyMixin method) calc_displacements() (moldesign.molecules.atomcollections.AtomContainer method) calc_distance_array() (moldesign.molecules.atomcollections.AtomContainer method) calc_distances() (moldesign.molecules.atoms.AtomGeometryMixin method) calc_forces() (moldesign.molecules.molecule.MolPropertyMixin method) calc_gasteiger_charges() (in module moldesign), [1], [2] (in module moldesign.interfaces.ambertools) (in module moldesign.tools) calc_orb_grid() (moldesign.GeometryViewer method), [1] (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) calc_potential_energy() (moldesign.molecules.molecule.MolPropertyMixin method) calc_property() (moldesign.molecules.molecule.MolPropertyMixin method) calc_wfn() (moldesign.molecules.molecule.MolPropertyMixin method) calculate() (moldesign.models.base.EnergyModelBase method) (moldesign.models.HarmonicOscillator method) (moldesign.models.OpenMMPotential method) (moldesign.models.PySCFPotential method) (moldesign.models.Spring method) (moldesign.models.openmm.OpenMMPotential method) (moldesign.models.pyscf.PySCFPotential method) (moldesign.models.sqm.SQMPotential method) (moldesign.models.toys.HarmonicOscillator method) (moldesign.models.toys.Spring method) (moldesign.molecules.molecule.MolSimulationMixin method) calculate_dipole() (moldesign.molecules.molecule.MolPropertyMixin method) calculate_forces() (moldesign.molecules.molecule.MolPropertyMixin method) calculate_potential_energy() (moldesign.molecules.molecule.MolPropertyMixin method) calculate_wfn() (moldesign.molecules.molecule.MolPropertyMixin method) callback() (moldesign.min.base.MinimizerBase method) cart_to_powers() (in module moldesign.orbitals.gaussians) CartesianGaussian (class in moldesign.orbitals.gaussians) CASSCF (class in moldesign.models) (class in moldesign.models.models) Categorizer (class in moldesign.utils.classes) center_of_mass (moldesign.molecules.atomcollections.AtomContainer attribute) chain (Atom attribute) (Chain attribute) Chain (class in moldesign), [1], [2] (class in moldesign.molecules) (class in moldesign.molecules.chain) chain (moldesign.Atom attribute), [1] (Residue attribute) (moldesign.Chain attribute), [1] (moldesign.Residue attribute), [1] (moldesign.molecules.Atom attribute) (moldesign.molecules.Chain attribute) (moldesign.molecules.Residue attribute) (moldesign.molecules.atoms.Atom attribute) (moldesign.molecules.chain.Chain attribute) (moldesign.molecules.residue.Residue attribute) CHAIN_MONOMER_NAMES (moldesign.data attribute) chains (moldesign.helpers.pdb.BioAssembly attribute) (Molecule attribute) (moldesign.Molecule attribute), [1] (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) change_resolution() (moldesign.widgets.orbitals.OrbitalUIPane method) ChangeLog (class in moldesign.widgets) (class in moldesign.widgets.computeconfig) charge (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) ChemicalGraphViewer (class in moldesign), [1] (class in moldesign.viewer) (class in moldesign.viewer.viewer2d) ChildList (class in moldesign.molecules.biounits) clear() (moldesign.utils.classes.ExclusiveList method) (moldesign.utils.classes.SortedCollection method) clear_constraints() (moldesign.molecules.molecule.MolConstraintMixin method)

clear_selection() (moldesign.widgets.geombuilder.GeometryBuilder method) (moldesign.widgets.GeometryBuilder method) clear_selections() (moldesign.uibase.components.SelBase method) (moldesign.widgets.BondSelector method) (moldesign.widgets.selection.BondSelector method) close() (moldesign.utils.databases.Hdf5Dbm method) code (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) color_by() (moldesign.uibase.selector.SelectionGroup method) (moldesign.viewer.common.ColorMixin method) COLOR_LIST (moldesign.data attribute) color_rotation (moldesign.data attribute) colormap() (in module moldesign.helpers.helpers) ColorMixin (class in moldesign.viewer.common) com (moldesign.molecules.atomcollections.AtomContainer attribute) compare() (moldesign.units.quantity.MdtQuantity method) CompressedJsonDbm (class in moldesign.utils.databases) ComputeConfig (class in moldesign.widgets) (class in moldesign.widgets.computeconfig) config (in module moldesign.compute.configuration) Configurator (class in moldesign.widgets.configurator) configure() (in module moldesign.widgets), [1] (in module moldesign.widgets.computeconfig) (moldesign.method.Method method) configure_methods() (moldesign.molecules.molecule.MolSimulationMixin method) ConstantTemperatureBase (class in moldesign.integrators.base) constrain() (moldesign.geom.Monitor method), [1] (moldesign.geom.monitor.Monitor method) constrain_angle() (moldesign.molecules.molecule.MolConstraintMixin method) constrain_atom() (moldesign.molecules.molecule.MolConstraintMixin method) constrain_dihedral() (moldesign.molecules.molecule.MolConstraintMixin method) constrain_distance() (moldesign.molecules.molecule.MolConstraintMixin method) CONSTRAINT (moldesign.AngleMonitor attribute), [1], [2] (moldesign.DihedralMonitor attribute), [1], [2] (moldesign.DistanceMonitor attribute), [1], [2] (moldesign.geom.AngleMonitor attribute) (moldesign.geom.DihedralMonitor attribute) (moldesign.geom.DistanceMonitor attribute) (moldesign.geom.monitor.AngleMonitor attribute) (moldesign.geom.monitor.DihedralMonitor attribute) (moldesign.geom.monitor.DistanceMonitor attribute) constraints (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) ConvergenceFailure convert() (moldesign.units.unitsystem.UnitSystem method) coord() (moldesign.forcefields.terms.HarmonicAngleTerm method) (moldesign.forcefields.terms.HarmonicBondTerm method) (moldesign.forcefields.terms.PeriodicTorsionTerm method) coords_changed() (moldesign.widgets.Symmetrizer method) (moldesign.widgets.symmetry.Symmetrizer method) copy() (moldesign.Atom method), [1], [2] (moldesign.Chain method), [1], [2] (moldesign.Residue method), [1], [2] (moldesign.molecules.Atom method) (moldesign.molecules.Chain method) (moldesign.molecules.Residue method) (moldesign.molecules.atomcollections.AtomContainer method) (moldesign.molecules.atoms.Atom method) (moldesign.molecules.chain.Chain method) (moldesign.molecules.molecule.MolTopologyMixin method) (moldesign.molecules.residue.Residue method) (moldesign.utils.classes.SortedCollection method) count() (moldesign.utils.classes.SortedCollection method) create_value_selector() (in module moldesign.uibase.selector) cross() (moldesign.units.quantity.MdtQuantity method) current() (moldesign.geom.AngleConstraint method), [1] (moldesign.geom.DihedralConstraint method), [1] (moldesign.geom.DistanceConstraint method), [1] (moldesign.geom.FixedCoordinate method), [1] (moldesign.geom.FixedPosition method), [1] (moldesign.geom.GeometryConstraint method), [1] (moldesign.geom.constraints.AngleConstraint method) (moldesign.geom.constraints.DihedralConstraint method) (moldesign.geom.constraints.DistanceConstraint method) (moldesign.geom.constraints.FixedCoordinate method) (moldesign.geom.constraints.FixedPosition method) (moldesign.geom.constraints.GeometryConstraint method) CyclicList (class in moldesign.data), [1]

D

DBASES (moldesign.data attribute) debug() (moldesign.uibase.logwidget.Logger method) DEF_CONFIG (in module moldesign.compute.configuration) DEF_PADDING (moldesign.GeometryViewer attribute) (moldesign.viewer.GeometryViewer attribute) (moldesign.viewer.viewer3d.GeometryViewer attribute) default() (moldesign.chemjson.JsonEncoder method) DEFAULT_COLOR_MAP() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) DEFAULT_CONFIG_PATH (in module moldesign.compute.configuration) DEFAULT_FORCE_TOLERANCE (moldesign.data attribute) DEFAULT_HEIGHT (moldesign.GeometryViewer attribute) (moldesign.viewer.GeometryViewer attribute) (moldesign.viewer.viewer3d.GeometryViewer attribute) DEFAULT_PROPERTIES (moldesign.models.base.EnergyModelBase attribute) (moldesign.models.OpenMMPotential attribute) (moldesign.models.PySCFPotential attribute) (moldesign.models.Spring attribute) (moldesign.models.base.QMBase attribute) (moldesign.models.base.QMMMBase attribute) (moldesign.models.openmm.OpenMMPotential attribute) (moldesign.models.pyscf.PySCFPotential attribute) (moldesign.models.sqm.SQMPotential attribute) (moldesign.models.toys.Spring attribute) DEFAULT_WIDTH (moldesign.GeometryViewer attribute) (moldesign.viewer.GeometryViewer attribute) (moldesign.viewer.viewer3d.GeometryViewer attribute) defunits() (moldesign.units.quantity.MdtQuantity method) defunits_inplace() (moldesign.units.quantity.MdtQuantity method) defunits_value() (moldesign.units.quantity.MdtQuantity method) DEGFMT (moldesign.widgets.geombuilder.GeometryBuilder attribute) (moldesign.widgets.GeometryBuilder attribute) deletebond() (moldesign.Molecule method), [1], [2] (moldesign.molecules.Molecule method) (moldesign.molecules.molecule.Molecule method) density_matrix (moldesign.BasisSet attribute) (moldesign.orbitals.BasisSet attribute) (moldesign.orbitals.basis.BasisSet attribute) desc (moldesign.geom.AngleConstraint attribute), [1] (moldesign.geom.DihedralConstraint attribute), [1] (moldesign.geom.DistanceConstraint attribute), [1] (moldesign.geom.FixedCoordinate attribute), [1] (moldesign.geom.FixedPosition attribute), [1] (moldesign.geom.GeometryConstraint attribute), [1] (moldesign.geom.constraints.AngleConstraint attribute) (moldesign.geom.constraints.DihedralConstraint attribute) (moldesign.geom.constraints.DistanceConstraint attribute) (moldesign.geom.constraints.FixedCoordinate attribute) (moldesign.geom.constraints.FixedPosition attribute) (moldesign.geom.constraints.GeometryConstraint attribute) (moldesign.helpers.pdb.BioAssembly attribute) description (moldesign.uibase.components.ReadoutFloatSlider attribute) DFT (class in moldesign.models) (class in moldesign.models.models) DictLike (class in moldesign.utils.classes) dihedral() (in module moldesign), [1], [2], [3] (in module moldesign.geom), [1] (in module moldesign.geom.coords) (moldesign.Trajectory method) (moldesign.molecules.Trajectory method) (moldesign.molecules.atomcollections.AtomContainer method) (moldesign.molecules.trajectory.Trajectory method) dihedral_gradient() (in module moldesign), [1], [2], [3] (in module moldesign.geom), [1] (in module moldesign.geom.grads) DihedralConstraint (class in moldesign.geom), [1] (class in moldesign.geom.constraints) DihedralMonitor (class in moldesign), [1], [2] (class in moldesign.geom) (class in moldesign.geom.monitor) dim_masses (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) dipole (moldesign.molecules.molecule.MolPropertyMixin attribute) display_log() (in module moldesign.uibase.logwidget) DIST_FORCE_CONSTANT (moldesign.geom attribute)

DIST_TOLERANCE (moldesign.geom attribute) distance() (in module moldesign), [1], [2], [3] (in module moldesign.geom), [1] (in module moldesign.geom.coords) (moldesign.Trajectory method) (moldesign.molecules.Trajectory method) (moldesign.molecules.atomcollections.AtomContainer method) (moldesign.molecules.atoms.AtomGeometryMixin method) (moldesign.molecules.trajectory.Trajectory method) distance_gradient() (in module moldesign), [1], [2], [3] (in module moldesign.geom), [1] (in module moldesign.geom.grads) DISTANCE_UNITS (moldesign.GeometryViewer attribute) (moldesign.viewer.GeometryViewer attribute) (moldesign.viewer.viewer3d.GeometryViewer attribute) DistanceConstraint (class in moldesign.geom), [1] (class in moldesign.geom.constraints) DistanceGraphViewer (class in moldesign), [1] (class in moldesign.viewer) (class in moldesign.viewer.viewer2d) DistanceMonitor (class in moldesign), [1], [2] (class in moldesign.geom) (class in moldesign.geom.monitor) doc_inherit (in module moldesign.utils.callsigs) DocInherit (class in moldesign.utils.callsigs) dof (moldesign.geom.AngleConstraint attribute), [1] (moldesign.geom.DihedralConstraint attribute), [1] (moldesign.geom.DistanceConstraint attribute), [1] (moldesign.geom.FixedCoordinate attribute), [1] (moldesign.geom.FixedPosition attribute), [1] (moldesign.geom.GeometryConstraint attribute), [1] (moldesign.geom.constraints.AngleConstraint attribute) (moldesign.geom.constraints.DihedralConstraint attribute) (moldesign.geom.constraints.DistanceConstraint attribute) (moldesign.geom.constraints.FixedCoordinate attribute) (moldesign.geom.constraints.FixedPosition attribute) (moldesign.geom.constraints.GeometryConstraint attribute) DONOTAPPLY (moldesign.molecules.Trajectory attribute) (moldesign.Trajectory attribute) (moldesign.molecules.trajectory.Trajectory attribute) dot() (moldesign.units.quantity.MdtQuantity method) DotDict (class in moldesign.utils.classes) DOUBLEOFFSET (moldesign.viewer.bondclicker.BondClicker attribute) DOUBLERADIUS (moldesign.viewer.bondclicker.BondClicker attribute) draw() (moldesign.molecules.atomcollections.AtomContainer method) (moldesign.Trajectory method), [1] (moldesign.molecules.Trajectory method) (moldesign.molecules.atoms.AtomDrawingMixin method) (moldesign.molecules.trajectory.Trajectory method) draw2d() (moldesign.molecules.atomcollections.AtomContainer method) (moldesign.molecules.atoms.AtomDrawingMixin method) draw3d() (moldesign.molecules.atomcollections.AtomContainer method) (moldesign.Trajectory method), [1] (moldesign.molecules.Trajectory method) (moldesign.molecules.atoms.AtomDrawingMixin method) (moldesign.molecules.trajectory.Trajectory method) draw_all_bonds() (moldesign.viewer.bondclicker.BondClicker method) draw_atom_vectors() (moldesign.GeometryViewer method), [1] (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) draw_axis() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) draw_bond() (moldesign.viewer.bondclicker.BondClicker method) draw_contacts() (moldesign.DistanceGraphViewer method) (moldesign.viewer.DistanceGraphViewer method) (moldesign.viewer.viewer2d.DistanceGraphViewer method) draw_forces() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) draw_momenta() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) draw_orbitals() (moldesign.molecules.molecule.MolDrawingMixin method) (moldesign.Trajectory method), [1] (moldesign.molecules.Trajectory method) (moldesign.molecules.trajectory.Trajectory method) DummyJob (class in moldesign.compute.compute) dynamic_dof (moldesign.molecules.molecule.MolPropertyMixin attribute)

E

ElectronicWfn (class in moldesign.orbitals.wfn), [1] elem (moldesign.Atom attribute), [1], [2] (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) element (Atom attribute) (moldesign.Atom attribute), [1], [2], [3], [4] (moldesign.molecules.Atom attribute), [1] (moldesign.molecules.atoms.Atom attribute), [1] ELEMENTS (moldesign.data attribute) emit() (moldesign.uibase.logwidget.WidgetValueHandler method) enable_logging_widgets() (in module moldesign.uibase.logwidget) energies (moldesign.orbitals.orbitals.MolecularOrbitals attribute), [1] energy (moldesign.orbitals.orbitals.Orbital attribute), [1] energy() (moldesign.forcefields.terms.HarmonicAngleTerm method) (moldesign.forcefields.terms.HarmonicBondTerm method) (moldesign.forcefields.terms.PeriodicTorsionTerm method) energy_model (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) EnergyModelBase (class in moldesign.models.base)

ENGINE_DISPLAY (moldesign.widgets attribute) ENGINES (moldesign.widgets attribute) Entity (class in moldesign), [1] (class in moldesign.molecules) (class in moldesign.molecules.biounits) ENVVAR (in module moldesign.compute.configuration) ERI4FoldTensor (class in moldesign.orbitals.gaussians) error() (moldesign.geom.AngleConstraint method), [1] (moldesign.geom.DihedralConstraint method), [1] (moldesign.geom.FixedPosition method), [1] (moldesign.geom.GeometryConstraint method), [1] (moldesign.geom.constraints.AngleConstraint method) (moldesign.geom.constraints.DihedralConstraint method) (moldesign.geom.constraints.FixedPosition method) (moldesign.geom.constraints.GeometryConstraint method) (moldesign.uibase.logwidget.Logger method) excited_state_properties (in module moldesign.parameters) ExclusiveList (class in moldesign.utils.classes) extend() (moldesign.utils.classes.ExclusiveList method) ExtraAmberParameters (in module moldesign.interfaces.ambertools)

F

ff (moldesign.Bond attribute), [1] (moldesign.molecules.Bond attribute) (moldesign.molecules.atoms.AtomPropertyMixin attribute) (moldesign.molecules.bonds.Bond attribute) FFParameters (class in moldesign.forcefields.forcefield) FFTerm (class in moldesign.forcefields.forcefield) find() (moldesign.utils.classes.SortedCollection method) find_ge() (moldesign.utils.classes.SortedCollection method) find_gt() (moldesign.utils.classes.SortedCollection method) find_le() (moldesign.utils.classes.SortedCollection method) find_lt() (moldesign.utils.classes.SortedCollection method) finite_difference_force() (moldesign.models.base.EnergyModelBase method) fire_selection_event() (moldesign.uibase.selector.Selector method) fiveprime_end (moldesign.Chain attribute), [1], [2] (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) FixedCoordinate (class in moldesign.geom), [1] (class in moldesign.geom.constraints) FixedPosition (class in moldesign.geom), [1] (class in moldesign.geom.constraints) fock (moldesign.BasisSet attribute) (moldesign.orbitals.BasisSet attribute) (moldesign.orbitals.basis.BasisSet attribute) (moldesign.orbitals.orbitals.MolecularOrbitals attribute), [1] fock_element() (moldesign.orbitals.orbitals.Orbital method), [1]

force (moldesign.Atom attribute), [1], [2] (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) (moldesign.units.unitsystem.UnitSystem attribute) FORCE_UNITS (moldesign.models.pyscf.PySCFPotential attribute) (moldesign.models.PySCFPotential attribute) (moldesign.models.sqm.SQMPotential attribute) ForceField (class in moldesign.models) (class in moldesign.models.models) ForceFieldMessage (class in moldesign.widgets.parameterization) forces (moldesign.molecules.molecule.MolPropertyMixin attribute) Frame (class in moldesign.molecules.trajectory) FrameInspector (class in moldesign.widgets.trajectory) frames (moldesign.molecules.Trajectory attribute) (moldesign.Trajectory attribute), [1] (moldesign.molecules.trajectory.Trajectory attribute) from_ao() (moldesign.orbitals.orbitals.MolecularOrbitals method), [1] from_filepath() (in module moldesign.utils.utils) from_name() (in module moldesign), [1] (in module moldesign.fileio) from_pdb() (in module moldesign), [1] (in module moldesign.fileio) from_smiles() (in module moldesign), [1] (in module moldesign.fileio) (in module moldesign.interfaces.openbabel) function_slice() (in module moldesign.uibase.plotting)

G

GAFF (class in moldesign.models) (class in moldesign.models.amber) Gaussian() (in module moldesign.orbitals.gaussians) geometry_matches() (moldesign.MolecularProperties method), [1] (moldesign.molecules.MolecularProperties method) (moldesign.molecules.molecule.MolecularProperties method) GeometryBuilder (class in moldesign.widgets) (class in moldesign.widgets.geombuilder) GeometryConstraint (class in moldesign.geom), [1] (class in moldesign.geom.constraints) GeometryViewer (class in moldesign), [1] (class in moldesign.viewer) (class in moldesign.viewer.viewer3d) get_aligned_coords() (in module moldesign.interfaces.symmol_interface) get_all_atoms() (in module moldesign.helpers.helpers) get_atom_index() (moldesign.ChemicalGraphViewer method), [1] (moldesign.viewer.ChemicalGraphViewer method) (moldesign.viewer.viewer2d.ChemicalGraphViewer method) get_atoms() (moldesign.molecules.atomcollections.AtomContainer method) get_axis() (moldesign.geom.symmetry.SymmetryElement method) (moldesign.geom.SymmetryElement method), [1] get_baseunit() (moldesign.units.unitsystem.UnitSystem method) get_child_listeners() (moldesign.uibase.selector.SelectionGroup method) get_conect_records() (in module moldesign.helpers.pdb) get_engine() (in module moldesign.compute.configuration) get_epsilon() (moldesign.forcefields.terms.LennardJonesSigmaEps method) get_eris_in_basis() (in module moldesign.interfaces.pyscf_interface) get_ffparams() (moldesign.forcefields.forcefield.ResidueTemplate method) get_forcefield() (moldesign.method.Method method) (moldesign.models.OpenMMPotential method) (moldesign.models.openmm.OpenMMPotential method) get_formal_charge() (moldesign.models.base.EnergyModelBase method) get_image_path() (in module moldesign.compute.compute) get_input_file() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) get_ligand() (moldesign.Chain method), [1], [2] (moldesign.molecules.Chain method) (moldesign.molecules.chain.Chain method) get_mmcif_assemblies() (in module moldesign.interfaces.biopython_interface) get_no_inst() (moldesign.utils.callsigs.DocInherit method) get_openmm_integrator() (moldesign.integrators.openmm.OpenMMLangevin method) (moldesign.integrators.OpenMMLangevin method) (moldesign.integrators.OpenMMVerlet method) (moldesign.integrators.openmm.OpenMMVerlet method) get_openmm_simulation() (moldesign.models.openmm.OpenMMPotential method) (moldesign.models.OpenMMPotential method) get_orbnames() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method)

get_output_files() (moldesign.compute.compute.DummyJob static method) get_parameters() (moldesign.method.Method class method) get_pdb_assemblies() (in module moldesign.helpers.pdb) get_positions() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) get_property() (moldesign.molecules.molecule.MolPropertyMixin method) get_qualified_name() (in module moldesign.utils.callsigs) get_residue_table() (moldesign.molecules.molecule.MolReprMixin method) get_sigma() (moldesign.forcefields.terms.LennardJonesSigmaEps method) get_stderr_stream() (moldesign.compute.compute.DummyJob method) get_stdout_stream() (moldesign.compute.compute.DummyJob method) get_stoichiometry() (moldesign.molecules.molecule.MolReprMixin method) get_symmetrized_coords() (moldesign.geom.MolecularSymmetry method), [1] (moldesign.geom.symmetry.MolecularSymmetry method) get_symmetry() (in module moldesign.geom), [1] get_units() (in module moldesign.units.tools) (moldesign.units.quantity.MdtQuantity method) get_with_inst() (moldesign.utils.callsigs.DocInherit method) getstring() (moldesign.utils.utils.BaseTable method) (moldesign.utils.utils.MarkdownTable method) (moldesign.utils.utils.PrintTable method) GETTER() (moldesign.AngleMonitor static method), [1], [2] (moldesign.DihedralMonitor static method), [1], [2] (moldesign.DistanceMonitor static method), [1], [2] (moldesign.geom.AngleMonitor static method) (moldesign.geom.DihedralMonitor static method) (moldesign.geom.DistanceMonitor static method) (moldesign.geom.monitor.AngleMonitor static method) (moldesign.geom.monitor.DihedralMonitor static method) (moldesign.geom.monitor.DistanceMonitor static method) GoogleDocArgumentInjector (class in moldesign.utils.docparsers.google) GRAD() (moldesign.AngleMonitor static method), [1], [2] (moldesign.DihedralMonitor static method), [1], [2] (moldesign.DistanceMonitor static method), [1], [2] (moldesign.geom.AngleMonitor static method) (moldesign.geom.DihedralMonitor static method) (moldesign.geom.DistanceMonitor static method) (moldesign.geom.monitor.AngleMonitor static method) (moldesign.geom.monitor.DihedralMonitor static method) (moldesign.geom.monitor.DistanceMonitor static method) grad() (moldesign.min.base.MinimizerBase method) gradient() (moldesign.geom.constraints.GeometryConstraint method) (moldesign.geom.GeometryConstraint method), [1] (moldesign.geom.Monitor method), [1] (moldesign.geom.monitor.Monitor method) gradient_descent() (in module moldesign), [1] (in module moldesign.min) (in module moldesign.min.descent) GradientDescent (class in moldesign.min.descent) grid_map() (in module moldesign.uibase.plotting) ground_state_properties (in module moldesign.parameters) guess_atnum_from_name() (in module moldesign.helpers.pdb) guess_bond_orders() (in module moldesign), [1], [2] (in module moldesign.interfaces.openbabel) (in module moldesign.tools) guess_histidine_states() (in module moldesign), [1], [2] (in module moldesign.tools) (in module moldesign.tools.topology)

H

h1e (moldesign.orbitals.orbitals.MolecularOrbitals attribute), [1] h2e (moldesign.orbitals.orbitals.MolecularOrbitals attribute), [1] handle_click() (moldesign.ChemicalGraphViewer method) (moldesign.GeometryViewer method) (moldesign.viewer.ChemicalGraphViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.bondclicker.BondClicker method) (moldesign.viewer.viewer2d.ChemicalGraphViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) handle_remove_button_click() (moldesign.uibase.components.SelBase method) (moldesign.widgets.BondSelector method) (moldesign.widgets.ResidueSelector method) (moldesign.widgets.selection.BondSelector method) (moldesign.widgets.selection.ResidueSelector method) handle_selection_event() (moldesign.ChemicalGraphViewer method), [1] (moldesign.GeometryViewer method), [1] (moldesign.uibase.components.AtomInspector method) (moldesign.uibase.selector.Selector method) (moldesign.uibase.selector.ValueSelector method) (moldesign.viewer.ChemicalGraphViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer2d.ChemicalGraphViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) (moldesign.widgets.orbitals.OrbitalUIPane method) (moldesign.widgets.trajectory.FrameInspector method) handled() (moldesign.uibase.logwidget.Logger method) HarmonicAngleTerm (class in moldesign.forcefields.terms) HarmonicBondTerm (class in moldesign.forcefields.terms) HarmonicOscillator (class in moldesign.models) (class in moldesign.models.toys)

has_next() (moldesign.utils.docparsers.google.peek_iter method) Hdf5Dbm (class in moldesign.utils.databases) heavy_atoms (moldesign.molecules.atomcollections.AtomContainer attribute) heavy_bonds (moldesign.Atom attribute), [1], [2] (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) highlight_atoms() (moldesign.GeometryViewer method), [1] (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) HIGHLIGHT_COLOR (moldesign.GeometryViewer attribute) (moldesign.viewer.GeometryViewer attribute) (moldesign.viewer.viewer3d.GeometryViewer attribute) HIGHLIGHTOPACITY (moldesign.widgets.geombuilder.GeometryBuilder attribute) (moldesign.widgets.GeometryBuilder attribute) homo (moldesign.molecules.molecule.MolPropertyMixin attribute)

I

if_not_none() (in module moldesign.utils.utils) improper_axis_from_matrix() (in module moldesign.geom), [1] (in module moldesign.geom.symmetry) index (Atom attribute), [1] (moldesign.Atom attribute), [1], [2], [3] (moldesign.molecules.Atom attribute), [1] (moldesign.molecules.atoms.Atom attribute), [1] index() (moldesign.utils.classes.SortedCollection method) info (moldesign.molecules.Trajectory attribute) (moldesign.Trajectory attribute), [1] (moldesign.molecules.trajectory.Trajectory attribute) info() (moldesign.uibase.logwidget.Logger method) init_config() (in module moldesign.compute.configuration) inpcrd (moldesign.interfaces.ambertools.AmberParameters attribute) insert() (moldesign.utils.classes.SortedCollection method) insert_right() (moldesign.utils.classes.SortedCollection method) insert_ter_records() (in module moldesign.helpers.pdb) Instance (class in moldesign), [1] (class in moldesign.molecules) (class in moldesign.molecules.biounits) integral (moldesign.orbitals.gaussians.CartesianGaussian attribute) integrator (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) IntegratorBase (class in moldesign.integrators.base)

INVALID (moldesign.uibase.components.UnitText attribute) ION_CHARGE (moldesign.tools attribute) IONS (moldesign.data attribute) is_3prime_end (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) is_5prime_end (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) is_biomolecule (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) is_c_terminal (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) is_color() (in module moldesign.utils.utils) is_monomer (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) is_n_terminal (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) is_printable() (in module moldesign.utils.utils) is_small_molecule (moldesign.Molecule attribute), [1], [2] (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) is_standard_residue (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) isin() (in module moldesign.parameters) iteratoms() (moldesign.molecules.biounits.ChildList method)

J

job (moldesign.interfaces.ambertools.AmberParameters attribute) JsonEncoder (class in moldesign.chemjson)

jsonify() (in module moldesign.chemjson)

K

key (moldesign.utils.classes.SortedCollection attribute) kill() (moldesign.compute.compute.DummyJob method) kinetic_energy (moldesign.molecules.molecule.MolPropertyMixin attribute) (moldesign.Trajectory attribute) (moldesign.molecules.Trajectory attribute) (moldesign.molecules.trajectory.Trajectory attribute) kinetic_energy() (in module moldesign.helpers.helpers)

kinetic_temperature (moldesign.molecules.molecule.MolPropertyMixin attribute) (moldesign.Trajectory attribute) (moldesign.molecules.Trajectory attribute) (moldesign.molecules.trajectory.Trajectory attribute) kinetic_temperature() (in module moldesign.helpers.helpers) kwargs_from() (in module moldesign.utils.callsigs)

L

label_atoms() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) (moldesign.widgets.GeometryBuilder method) (moldesign.widgets.geombuilder.GeometryBuilder method) LangevinBase (class in moldesign.integrators.base) ldot() (moldesign.units.quantity.MdtQuantity method) LEN (moldesign.interfaces.pyscf_interface.StatusLogger attribute)

LennardJonesSigmaEps (class in moldesign.forcefields.terms) lines() (moldesign.utils.docparsers.google.GoogleDocArgumentInjector method) Logger (class in moldesign.uibase.logwidget) lumo (moldesign.molecules.molecule.MolPropertyMixin attribute)

M

make_contact_view() (in module moldesign.viewer.viewer2d) make_controls() (moldesign.widgets.trajectory.TrajectoryViewer method) make_header() (moldesign.widgets.computeconfig.MDTConfig method) (moldesign.widgets.MDTConfig method) make_local_temp_dir() (in module moldesign.utils.utils) make_nbo_input_file() (in module moldesign.interfaces.nbo_interface) make_none() (in module moldesign.utils.utils) make_viewer() (moldesign.widgets.trajectory.TrajectoryOrbViewer method) (moldesign.widgets.trajectory.TrajectoryViewer method) markdown() (moldesign.utils.utils.MarkdownTable method) markdown_summary() (moldesign.molecules.atoms.AtomReprMixin method) (moldesign.Residue method), [1], [2] (moldesign.molecules.Residue method) (moldesign.molecules.molecule.MolReprMixin method) (moldesign.molecules.residue.Residue method) MarkdownTable (class in moldesign.utils.utils) mass (Atom attribute) (moldesign.Atom attribute), [1] (moldesign.data attribute) (moldesign.molecules.Atom attribute) (moldesign.molecules.atomcollections.AtomContainer attribute) (moldesign.molecules.atoms.Atom attribute) (moldesign.molecules.molecule.MolPropertyMixin attribute) masses (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) MAXATOMS (moldesign.ChemicalGraphViewer attribute) (moldesign.viewer.ChemicalGraphViewer attribute) (moldesign.viewer.viewer2d.ChemicalGraphViewer attribute) MAXDIST (moldesign.widgets.geombuilder.GeometryBuilder attribute) (moldesign.widgets.GeometryBuilder attribute) MDBase (class in moldesign.integrators.base) MDTConfig (class in moldesign.widgets) (class in moldesign.widgets.computeconfig) MdtQuantity (class in moldesign.units.quantity) MdtReporter() (in module moldesign.interfaces.openmm) MdtUnit (class in moldesign.units.quantity) Method (class in moldesign.method) methodcaller (class in moldesign.utils.utils) minimization_step (moldesign.molecules.trajectory.Frame attribute) minimize() (in module moldesign), [1] (in module moldesign.min) (in module moldesign.min.smart) (moldesign.models.OpenMMPotential method) (moldesign.models.base.EnergyModelBase method) (moldesign.models.openmm.OpenMMPotential method) (moldesign.molecules.molecule.MolSimulationMixin method) MinimizerBase (class in moldesign.min.base) MissingAtom (class in moldesign.widgets.parameterization) MMBase (class in moldesign.models.base) modifier (moldesign.utils.docparsers.google.modify_iter attribute) modify_iter (class in moldesign.utils.docparsers.google) mol (moldesign.method.Method attribute) (moldesign.Trajectory attribute), [1] (moldesign.molecules.Trajectory attribute) (moldesign.molecules.trajectory.Trajectory attribute) MOL_ATTRIBUTES (moldesign.molecules.Trajectory attribute) (moldesign.Trajectory attribute) (moldesign.molecules.trajectory.Trajectory attribute) mol_to_modeller() (in module moldesign.interfaces.openmm) mol_to_openmm_sim() (in module moldesign) (in module moldesign.fileio) mol_to_pybel() (in module moldesign.interfaces.openbabel) mol_to_pyscf() (in module moldesign.interfaces.pyscf_interface) mol_to_topology() (in module moldesign.interfaces.openmm) MolConstraintMixin (class in moldesign.molecules.molecule) moldesign (module), [1] moldesign.chemjson (module) moldesign.compute (module) moldesign.compute.compute (module) moldesign.compute.configuration (module) moldesign.compute.runsremotely (module) moldesign.data (module) moldesign.exceptions (module) moldesign.external (module) moldesign.external.transformations (module) moldesign.fileio (module) moldesign.forcefields (module) moldesign.forcefields.forcefield (module) moldesign.forcefields.terms (module) moldesign.geom (module), [1] moldesign.geom.constraints (module) moldesign.geom.coords (module) moldesign.geom.grads (module) moldesign.geom.monitor (module) moldesign.geom.setcoord (module) moldesign.geom.shake (module) moldesign.geom.symmetry (module) moldesign.helpers (module) moldesign.helpers.helpers (module) moldesign.helpers.pdb (module) moldesign.integrators (module) moldesign.integrators.base (module) moldesign.integrators.openmm (module) moldesign.integrators.verlet (module) moldesign.interfaces (module) moldesign.interfaces.ambertools (module) moldesign.interfaces.biopython_interface (module) moldesign.interfaces.nbo_interface (module) moldesign.interfaces.openbabel (module) moldesign.interfaces.openmm (module) moldesign.interfaces.opsin_interface (module) moldesign.interfaces.parmed_interface (module) moldesign.interfaces.pdbfixer_interface (module) moldesign.interfaces.pyscf_interface (module) moldesign.interfaces.qtrfit (module) moldesign.interfaces.symmol_interface (module) moldesign.mathutils (module) moldesign.method (module)

moldesign.min (module) moldesign.min.base (module) moldesign.min.descent (module) moldesign.min.scipy (module) moldesign.min.smart (module) moldesign.models (module) moldesign.models.amber (module) moldesign.models.base (module) moldesign.models.models (module) moldesign.models.openmm (module) moldesign.models.pyscf (module) moldesign.models.sqm (module) moldesign.models.toys (module) moldesign.molecules (module) moldesign.molecules.atomcollections (module) moldesign.molecules.atoms (module) moldesign.molecules.biounits (module) moldesign.molecules.bonds (module) moldesign.molecules.chain (module) moldesign.molecules.coord_arrays (module) moldesign.molecules.molecule (module) moldesign.molecules.residue (module) moldesign.molecules.trajectory (module) moldesign.orbitals (module) moldesign.orbitals.basis (module) moldesign.orbitals.gaussians (module) moldesign.orbitals.orbitals (module) moldesign.orbitals.wfn (module) moldesign.parameters (module) moldesign.tools (module) moldesign.tools.build (module) moldesign.tools.topology (module) moldesign.uibase (module) moldesign.uibase.components (module) moldesign.uibase.logwidget (module) moldesign.uibase.plotting (module) moldesign.uibase.selector (module) moldesign.units (module) moldesign.units.constants (module) moldesign.units.quantity (module) moldesign.units.tools (module) moldesign.units.unitsystem (module) moldesign.utils (module) moldesign.utils.callsigs (module) moldesign.utils.classes (module) moldesign.utils.databases (module) moldesign.utils.docparsers (module) moldesign.utils.docparsers.google (module) moldesign.utils.utils (module) moldesign.viewer (module) moldesign.viewer.bondclicker (module) moldesign.viewer.common (module) moldesign.viewer.viewer2d (module) moldesign.viewer.viewer3d (module) moldesign.widgets (module) moldesign.widgets.computeconfig (module) moldesign.widgets.configurator (module) moldesign.widgets.geombuilder (module) moldesign.widgets.orbitals (module) moldesign.widgets.parameterization (module) moldesign.widgets.selection (module) moldesign.widgets.symmetry (module) moldesign.widgets.trajectory (module) MolDrawingMixin (class in moldesign.molecules.molecule) molecular_orbitals (moldesign.orbitals.wfn.ElectronicWfn attribute), [1] MolecularOrbitals (class in moldesign.orbitals.orbitals), [1] MolecularProperties (class in moldesign), [1] (class in moldesign.molecules) (class in moldesign.molecules.molecule) MolecularSymmetry (class in moldesign.geom), [1] (class in moldesign.geom.symmetry) Molecule (class in moldesign), [1], [2] (class in moldesign.molecules) (class in moldesign.molecules.molecule) MolPropertyMixin (class in moldesign.molecules.molecule) MolReprMixin (class in moldesign.molecules.molecule) MolSimulationMixin (class in moldesign.molecules.molecule) MolTopologyMixin (class in moldesign.molecules.molecule) momenta (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) momentum (Atom attribute) (moldesign.Atom attribute), [1] (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) (moldesign.units.unitsystem.UnitSystem attribute) Monitor (class in moldesign.geom), [1] (class in moldesign.geom.monitor) MP2 (class in moldesign.models) (class in moldesign.models.models) multistate_properties (in module moldesign.parameters) mutate() (in module moldesign), [1], [2] (in module moldesign.interfaces.pdbfixer_interface) (in module moldesign.tools)

N

n_terminal (moldesign.Chain attribute), [1], [2] (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) name (Atom attribute) (Molecule attribute) (moldesign.Atom attribute), [1] (moldesign.Bond attribute), [1] (moldesign.Molecule attribute), [1] (moldesign.data attribute) (moldesign.molecules.Atom attribute) (moldesign.molecules.Bond attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.atoms.Atom attribute) (moldesign.molecules.bonds.Bond attribute) (moldesign.molecules.molecule.Molecule attribute) (moldesign.orbitals.gaussians.AtomicBasisFunction attribute) name_to_smiles() (in module moldesign.interfaces.opsin_interface) named_dict() (in module moldesign.parameters) namelist (moldesign.data attribute) natoms (moldesign.molecules.atomcollections.AtomContainer attribute) nbonds (moldesign.Atom attribute), [1], [2] (moldesign.Molecule attribute), [1], [2] (moldesign.molecules.Atom attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.atoms.Atom attribute) (moldesign.molecules.molecule.Molecule attribute) NBR1HIGHLIGHT (moldesign.widgets.geombuilder.GeometryBuilder attribute) (moldesign.widgets.GeometryBuilder attribute) NBR2HIGHLIGHT (moldesign.widgets.geombuilder.GeometryBuilder attribute) (moldesign.widgets.GeometryBuilder attribute) ndim (moldesign.orbitals.gaussians.CartesianGaussian attribute) ndims (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) (moldesign.orbitals.gaussians.CartesianGaussian attribute) new_docstring() (moldesign.utils.docparsers.google.GoogleDocArgumentInjector method) new_frame() (moldesign.molecules.Trajectory method) (moldesign.Trajectory method), [1] (moldesign.molecules.trajectory.Trajectory method) new_orb_type() (moldesign.widgets.orbitals.OrbitalUIPane method) new_orbital_selection() (moldesign.widgets.orbitals.OrbitalUIPane method) newbond() (moldesign.Molecule method), [1], [2] (moldesign.molecules.Molecule method) (moldesign.molecules.molecule.Molecule method) next() (moldesign.utils.docparsers.google.peek_iter method)

next_residue (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) norm (moldesign.orbitals.basis.PrimitiveBase attribute) (moldesign.orbitals.gaussians.AbstractFunction attribute) (moldesign.orbitals.gaussians.AtomicBasisFunction attribute) norm() (moldesign.units.quantity.MdtQuantity method) normalize() (moldesign.orbitals.gaussians.AbstractFunction method) (moldesign.orbitals.gaussians.AtomicBasisFunction method) normalized() (in module moldesign.geom), [1] (in module moldesign.mathutils) (moldesign.units.quantity.MdtQuantity method) NotCalculatedError nresidues (moldesign.Chain attribute) (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) NUCLEIC_NAMES (moldesign.data attribute) NUM_ATOMS (moldesign.AngleMonitor attribute), [1], [2] (moldesign.DihedralMonitor attribute), [1], [2] (moldesign.DistanceMonitor attribute), [1], [2] (moldesign.geom.AngleMonitor attribute) (moldesign.geom.DihedralMonitor attribute) (moldesign.geom.DistanceMonitor attribute) (moldesign.geom.monitor.AngleMonitor attribute) (moldesign.geom.monitor.DihedralMonitor attribute) (moldesign.geom.monitor.DistanceMonitor attribute) num_atoms (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.atomcollections.AtomContainer attribute) (moldesign.molecules.molecule.Molecule attribute) num_bonds (moldesign.Atom attribute), [1], [2] (Molecule attribute) (moldesign.Molecule attribute), [1], [2], [3], [4] (moldesign.molecules.Atom attribute) (moldesign.molecules.Molecule attribute), [1] (moldesign.molecules.atoms.Atom attribute) (moldesign.molecules.molecule.Molecule attribute), [1] num_dimensions (moldesign.orbitals.gaussians.CartesianGaussian attribute) num_electrons (moldesign.molecules.molecule.MolPropertyMixin attribute) num_frames (moldesign.molecules.Trajectory attribute) (moldesign.Trajectory attribute), [1] (moldesign.molecules.trajectory.Trajectory attribute) num_primitives (moldesign.orbitals.gaussians.AtomicBasisFunction attribute) num_residues (moldesign.Chain attribute) (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) numresidues (moldesign.Chain attribute) (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute)

O

objective() (moldesign.min.base.MinimizerBase method) occupations (moldesign.orbitals.orbitals.MolecularOrbitals attribute), [1] open() (moldesign.utils.databases.Hdf5Dbm class method) OpenMMLangevin (class in moldesign.integrators) (class in moldesign.integrators.openmm) OpenMMPickleMixin (class in moldesign.interfaces.openmm) OpenMMPotential (class in moldesign.models) (class in moldesign.models.openmm) OpenMMVerlet (class in moldesign.integrators) (class in moldesign.integrators.openmm) Orbital (class in moldesign.orbitals.orbitals), [1] orbital_is_selected (moldesign.GeometryViewer attribute) (moldesign.viewer.GeometryViewer attribute) (moldesign.viewer.viewer3d.GeometryViewer attribute)

OrbitalUIPane (class in moldesign.widgets.orbitals) OrbitalViewer (class in moldesign.widgets.orbitals) orbtype (moldesign.orbitals.gaussians.AtomicBasisFunction attribute) order (moldesign.Bond attribute), [1] (moldesign.molecules.Bond attribute) (moldesign.molecules.bonds.Bond attribute) OrderedDotDict (class in moldesign.utils.classes) origin() (moldesign.helpers.helpers.VolumetricGrid method) overlap() (moldesign.orbitals.basis.PrimitiveBase method) (moldesign.orbitals.gaussians.AbstractFunction method) (moldesign.orbitals.orbitals.MolecularOrbitals method), [1] (moldesign.orbitals.orbitals.Orbital method), [1] overlaps (moldesign.orbitals.orbitals.MolecularOrbitals attribute), [1]

P

PACKAGEPATH (moldesign.data attribute) pairwise_displacements() (in module moldesign.utils.utils) PARAM_SUPPORT (moldesign.method.Method attribute) (moldesign.models.PySCFPotential attribute) (moldesign.models.pyscf.PySCFPotential attribute) Parameter (class in moldesign.parameters) ParameterizationDisplay (class in moldesign.widgets.parameterization) ParameterizationError parameterize() (in module moldesign), [1], [2] (in module moldesign.interfaces.ambertools) (in module moldesign.tools) PARAMETERS (moldesign.integrators.base.ConstantTemperatureBase attribute) (moldesign.integrators.base.IntegratorBase attribute) (moldesign.integrators.base.LangevinBase attribute) (moldesign.integrators.base.MDBase attribute) (moldesign.method.Method attribute) (moldesign.models.GAFF attribute) (moldesign.models.HarmonicOscillator attribute) (moldesign.models.Spring attribute) (moldesign.models.amber.GAFF attribute) (moldesign.models.base.EnergyModelBase attribute) (moldesign.models.base.MMBase attribute) (moldesign.models.base.QMBase attribute) (moldesign.models.base.QMMMBase attribute) (moldesign.models.toys.HarmonicOscillator attribute) (moldesign.models.toys.Spring attribute) parent (Atom attribute) (Chain attribute) (Residue attribute) (moldesign.Atom attribute), [1] (moldesign.Chain attribute), [1] (moldesign.Residue attribute), [1] (moldesign.molecules.Atom attribute) (moldesign.molecules.Chain attribute) (moldesign.molecules.Residue attribute) (moldesign.molecules.atoms.Atom attribute) (moldesign.molecules.chain.Chain attribute) (moldesign.molecules.residue.Residue attribute) parmed_to_mdt() (in module moldesign.interfaces.parmed_interface) parse() (moldesign.utils.docparsers.google.GoogleDocArgumentInjector method) parse_mmcif() (in module moldesign.interfaces.biopython_interface) parse_nbo() (in module moldesign.interfaces.nbo_interface) parse_output() (in module moldesign.interfaces.symmol_interface) parse_pdb() (in module moldesign.interfaces.biopython_interface) parse_value() (moldesign.uibase.components.ReadoutFloatSlider method) partner() (moldesign.Bond method), [1] (moldesign.molecules.Bond method) (moldesign.molecules.bonds.Bond method) peek() (moldesign.utils.docparsers.google.peek_iter method) peek_iter (class in moldesign.utils.docparsers.google) PeriodicTorsionTerm (class in moldesign.forcefields.terms) perpendicular() (in module moldesign.geom), [1] (in module moldesign.mathutils) pint2simtk() (in module moldesign.interfaces.openmm)

PipedFile (class in moldesign.utils.utils) plot() (moldesign.molecules.Trajectory method) (moldesign.Trajectory method), [1] (moldesign.molecules.trajectory.Trajectory method) polymer_residues (moldesign.Chain attribute) (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) pop() (moldesign.utils.classes.ExclusiveList method) POSFMT (moldesign.widgets.geombuilder.GeometryBuilder attribute) (moldesign.widgets.GeometryBuilder attribute) position (Atom attribute) (moldesign.Atom attribute), [1] (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) positions (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.atomcollections.AtomContainer attribute) (moldesign.molecules.molecule.Molecule attribute) potential_energy (moldesign.molecules.molecule.MolPropertyMixin attribute) prep() (moldesign.integrators.base.IntegratorBase method) (moldesign.integrators.VelocityVerlet method) (moldesign.integrators.verlet.VelocityVerlet method) (moldesign.models.GAFF method) (moldesign.models.OpenMMPotential method) (moldesign.models.PySCFPotential method) (moldesign.models.Spring method) (moldesign.models.amber.GAFF method) (moldesign.models.base.EnergyModelBase method) (moldesign.models.openmm.OpenMMPotential method) (moldesign.models.pyscf.PySCFPotential method) (moldesign.models.toys.Spring method) prepare_docstring() (in module moldesign.utils.docparsers.google) prev_residue (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) PrimitiveBase (class in moldesign.orbitals.basis) print_environment() (in module moldesign.data), [1] print_parameters() (moldesign.method.Method class method) printflush() (in module moldesign.utils.utils) PrintTable (class in moldesign.utils.utils) prmtop (moldesign.interfaces.ambertools.AmberParameters attribute) progressbar (class in moldesign.utils.utils) properties (moldesign.molecules.atoms.AtomPropertyMixin attribute) (moldesign.molecules.molecule.MolPropertyMixin attribute) ProtectedArray (class in moldesign.molecules.coord_arrays) pybel_to_mol() (in module moldesign.interfaces.openbabel) PySCFPotential (class in moldesign.models) (class in moldesign.models.pyscf)

Q

QMBase (class in moldesign.models.base) QMConvergenceError

QMMMBase (class in moldesign.models.base) qtrfit() (in module moldesign.interfaces.qtrfit)

R

RBASES (moldesign.data attribute) read() (in module moldesign), [1] (in module moldesign.fileio) read_amber() (in module moldesign) (in module moldesign.fileio) read_file() (in module moldesign.interfaces.openbabel) read_orbital_set() (in module moldesign.interfaces.nbo_interface) read_stream() (in module moldesign.interfaces.openbabel) read_string() (in module moldesign.interfaces.openbabel) reader() (in module moldesign.chemjson) ReadOnlyDumb (class in moldesign.utils.databases) ReadOnlyRepr (class in moldesign.uibase.components) ReadoutFloatSlider (class in moldesign.uibase.components) rebuild() (moldesign.molecules.biounits.ChildList method) (moldesign.molecules.molecule.MolTopologyMixin method) recursionlimit_atleast() (in module moldesign.utils.utils) redirect_stderr (class in moldesign.utils.utils) redirect_stdout (class in moldesign.utils.utils) redraw_orbs() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) register_selection_listeners() (moldesign.uibase.selector.SelectionGroup method) registry_login() (in module moldesign.compute.configuration) RegistryConfig (class in moldesign.widgets) (class in moldesign.widgets.computeconfig) remove() (moldesign.utils.classes.ExclusiveList method) (moldesign.utils.classes.SortedCollection method) remove_atomlist_highlight() (moldesign.uibase.components.SelBase method) remove_bondlist_highlight() (moldesign.widgets.BondSelector method) (moldesign.widgets.selection.BondSelector method) remove_click_callback() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) remove_directories() (in module moldesign.utils.utils) remove_reslist_highlight() (moldesign.widgets.ResidueSelector method) (moldesign.widgets.selection.ResidueSelector method) reset_compute_engine() (in module moldesign.compute.configuration) reset_config() (moldesign.widgets.ComputeConfig method) (moldesign.widgets.RegistryConfig method) (moldesign.widgets.computeconfig.ComputeConfig method) (moldesign.widgets.computeconfig.RegistryConfig method) reset_constraints() (moldesign.models.openmm.OpenMMPotential method) (moldesign.models.OpenMMPotential method)

reset_coords() (moldesign.widgets.Symmetrizer method) (moldesign.widgets.symmetry.Symmetrizer method) reset_geometry() (moldesign.widgets.geombuilder.GeometryBuilder method) (moldesign.widgets.GeometryBuilder method) reset_values() (moldesign.widgets.configurator.Configurator method) residue (Atom attribute) Residue (class in moldesign), [1], [2] (class in moldesign.molecules) (class in moldesign.molecules.residue) residue (moldesign.Atom attribute), [1] (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) RESIDUE_BONDS (moldesign.data attribute) RESIDUE_DESCRIPTIONS (moldesign.data attribute) RESIDUE_ONE_LETTER (moldesign.data attribute) RESIDUE_TYPES (moldesign.data attribute) residues (moldesign.Chain attribute), [1], [2] (Molecule attribute) (moldesign.Molecule attribute), [1] (moldesign.molecules.Chain attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.chain.Chain attribute) (moldesign.molecules.molecule.Molecule attribute) ResidueSelector (class in moldesign.widgets) (class in moldesign.widgets.selection) ResidueTemplate (class in moldesign.forcefields.forcefield) reskey() (moldesign.widgets.ResidueSelector static method) (moldesign.widgets.selection.ResidueSelector static method) resname (moldesign.data attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.Residue attribute) (moldesign.molecules.residue.Residue attribute) restraint_penalty() (moldesign.geom.constraints.GeometryConstraint method) (moldesign.geom.GeometryConstraint method), [1] restraint_penalty_force() (moldesign.geom.constraints.GeometryConstraint method) (moldesign.geom.GeometryConstraint method), [1] RESTYPES (moldesign.data attribute) RHF (class in moldesign.models) (class in moldesign.models.models) rmsd() (moldesign.molecules.Trajectory method) (moldesign.Trajectory method), [1] (moldesign.molecules.trajectory.Trajectory method) rotate() (moldesign.molecules.atomcollections.AtomContainer method) run() (moldesign.integrators.base.IntegratorBase method) (moldesign.integrators.VelocityVerlet method) (moldesign.integrators.verlet.VelocityVerlet method) (moldesign.min.base.MinimizerBase method) (moldesign.min.descent.GradientDescent method) (moldesign.min.smart.SmartMin method) (moldesign.molecules.molecule.MolSimulationMixin method) run_job() (in module moldesign.compute.compute) run_nbo() (in module moldesign.interfaces.nbo_interface) (moldesign.orbitals.wfn.ElectronicWfn method) run_symmol() (in module moldesign.interfaces.symmol_interface) run_tleap() (in module moldesign.interfaces.ambertools) RunsRemotely (class in moldesign.compute.runsremotely) runsremotely (in module moldesign.compute.runsremotely)

S

safe_arccos() (in module moldesign.geom), [1] (in module moldesign.mathutils) satisfied() (moldesign.geom.constraints.GeometryConstraint method) (moldesign.geom.GeometryConstraint method), [1] save_config() (moldesign.widgets.ComputeConfig method) (moldesign.widgets.computeconfig.ComputeConfig method) Scalar (class in moldesign.units.quantity) scale_move() (moldesign.min.descent.GradientDescent method) SECTIONS (moldesign.utils.docparsers.google.GoogleDocArgumentInjector attribute) SelBase (class in moldesign.uibase.components) select_all_atoms() (moldesign.uibase.components.SelBase method) select_all_bonds() (moldesign.widgets.BondSelector method) (moldesign.widgets.selection.BondSelector method) selected_atoms (moldesign.uibase.components.SelBase attribute) selected_bonds (moldesign.widgets.BondSelector attribute) (moldesign.widgets.selection.BondSelector attribute) selected_residues (moldesign.widgets.ResidueSelector attribute) (moldesign.widgets.selection.ResidueSelector attribute) SelectionGroup (class in moldesign.uibase.selector) Selector (class in moldesign.uibase.selector) selectors (moldesign.widgets.configurator.Configurator attribute) sentinel (moldesign.utils.docparsers.google.peek_iter attribute) sequence (moldesign.Chain attribute), [1], [2] (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) sequential_least_squares() (in module moldesign) (in module moldesign.min) (in module moldesign.min.scipy) SequentialLeastSquares (class in moldesign.min.scipy) set_angle() (in module moldesign), [1], [2], [3] (in module moldesign.geom), [1] (in module moldesign.geom.setcoord) (moldesign.widgets.GeometryBuilder method) (moldesign.widgets.geombuilder.GeometryBuilder method) set_atom_x() (moldesign.widgets.geombuilder.GeometryBuilder method) (moldesign.widgets.GeometryBuilder method) set_atom_y() (moldesign.widgets.geombuilder.GeometryBuilder method) (moldesign.widgets.GeometryBuilder method) set_atom_z() (moldesign.widgets.geombuilder.GeometryBuilder method) (moldesign.widgets.GeometryBuilder method) set_bond_color() (moldesign.viewer.bondclicker.BondClicker method) set_canonical_mos() (moldesign.orbitals.wfn.ElectronicWfn method) set_color() (moldesign.GeometryViewer method) (moldesign.uibase.selector.SelectionGroup method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) set_colors() (moldesign.GeometryViewer method), [1] (moldesign.uibase.selector.SelectionGroup method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) set_dihedral() (in module moldesign), [1], [2], [3] (in module moldesign.geom), [1] (in module moldesign.geom.setcoord) (moldesign.widgets.GeometryBuilder method) (moldesign.widgets.geombuilder.GeometryBuilder method) set_distance() (in module moldesign), [1], [2], [3] (in module moldesign.geom), [1] (in module moldesign.geom.setcoord) (moldesign.widgets.GeometryBuilder method) (moldesign.widgets.geombuilder.GeometryBuilder method) set_energy_model() (moldesign.molecules.molecule.MolSimulationMixin method) set_highest_symmetry() (moldesign.widgets.Symmetrizer method) (moldesign.widgets.symmetry.Symmetrizer method) set_integrator() (moldesign.molecules.molecule.MolSimulationMixin method) set_positions() (moldesign.viewer.bondclicker.BondClicker method) set_progress() (moldesign.utils.utils.progressbar method)

set_wfn_guess() (moldesign.models.base.QMBase method) SETTER() (moldesign.AngleMonitor static method), [1], [2] (moldesign.DihedralMonitor static method), [1], [2] (moldesign.DistanceMonitor static method), [1], [2] (moldesign.geom.AngleMonitor static method) (moldesign.geom.DihedralMonitor static method) (moldesign.geom.DistanceMonitor static method) (moldesign.geom.monitor.AngleMonitor static method) (moldesign.geom.monitor.DihedralMonitor static method) (moldesign.geom.monitor.DistanceMonitor static method) shake_positions() (in module moldesign.geom), [1] (in module moldesign.geom.shake) shape (moldesign.units.quantity.MdtQuantity attribute) show() (moldesign.widgets.parameterization.MissingAtom method) (moldesign.widgets.parameterization.UnknownAtom method) (moldesign.widgets.parameterization.UnknownResidue method) (moldesign.widgets.parameterization.UnusualBond method) show_frame() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) show_relevant_fields() (moldesign.widgets.configurator.Configurator method) show_symmetry() (moldesign.widgets.Symmetrizer method) (moldesign.widgets.symmetry.Symmetrizer method) show_unbonded() (moldesign.GeometryViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) sidechain (moldesign.molecules.Residue attribute) (moldesign.Residue attribute), [1], [2] (moldesign.molecules.residue.Residue attribute) simtk2pint() (in module moldesign.interfaces.openmm) SINGLERADIUS (moldesign.viewer.bondclicker.BondClicker attribute) slice_frames() (moldesign.molecules.Trajectory method) (moldesign.Trajectory method), [1] (moldesign.molecules.trajectory.Trajectory method) SmartMin (class in moldesign.min.smart) solvent_residues (moldesign.Chain attribute) (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) SortedCollection (class in moldesign.utils.classes) SphericalGaussian (class in moldesign.orbitals.gaussians) Spring (class in moldesign.models) (class in moldesign.models.toys) SQMPotential (class in moldesign.models.sqm) status (moldesign.compute.compute.DummyJob attribute) status() (moldesign.uibase.logwidget.Logger method) StatusLogger (class in moldesign.interfaces.pyscf_interface) stderr (moldesign.compute.compute.DummyJob attribute) stdout (moldesign.compute.compute.DummyJob attribute) step() (moldesign.integrators.VelocityVerlet method) (moldesign.integrators.verlet.VelocityVerlet method) StyledTab (class in moldesign.uibase.components) sub_angles() (in module moldesign.geom), [1] (in module moldesign.mathutils) SubSelection (class in moldesign.molecules.trajectory) switch_display() (moldesign.widgets.parameterization.ParameterizationDisplay method) symbol (moldesign.Atom attribute), [1], [2] (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) SYMBOLS (moldesign.data attribute) Symmetrizer (class in moldesign.widgets) (class in moldesign.widgets.symmetry) SymmetryElement (class in moldesign.geom), [1] (class in moldesign.geom.symmetry) Synonym (class in moldesign.utils.classes)

T

Tensor (class in moldesign.units.quantity) test_connection() (moldesign.widgets.ComputeConfig method) (moldesign.widgets.computeconfig.ComputeConfig method) textnotify (class in moldesign.utils.utils) THEORIES (moldesign.models.sqm.SQMPotential attribute) theoryname (moldesign.models.pyscf.PySCFPotential attribute) (moldesign.models.PySCFPotential attribute) threeprime_end (moldesign.Chain attribute), [1], [2] (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) time (moldesign.Molecule attribute), [1] (Molecule attribute) (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute) (moldesign.molecules.trajectory.Frame attribute) time_to_steps() (moldesign.integrators.base.IntegratorBase static method) to_ao() (moldesign.orbitals.orbitals.MolecularOrbitals method), [1] to_graph() (moldesign.ChemicalGraphViewer method) (moldesign.DistanceGraphViewer method) (moldesign.viewer.ChemicalGraphViewer method) (moldesign.viewer.DistanceGraphViewer method) (moldesign.viewer.viewer2d.ChemicalGraphViewer method) (moldesign.viewer.viewer2d.DistanceGraphViewer method) to_json() (moldesign.Atom method), [1], [2] (moldesign.Bond method) (moldesign.Chain method) (moldesign.Residue method) (moldesign.method.Method method) (moldesign.molecules.Atom method) (moldesign.molecules.Bond method) (moldesign.molecules.Chain method) (moldesign.molecules.Residue method) (moldesign.molecules.atoms.Atom method) (moldesign.molecules.bonds.Bond method) (moldesign.molecules.chain.Chain method) (moldesign.molecules.molecule.MolTopologyMixin method) (moldesign.molecules.residue.Residue method) (moldesign.units.quantity.MdtQuantity method) to_simtk() (moldesign.units.quantity.MdtQuantity method) toggle_atom() (moldesign.uibase.components.SelBase method)

toggle_bond() (moldesign.widgets.BondSelector method) (moldesign.widgets.selection.BondSelector method) toggle_residue() (moldesign.widgets.ResidueSelector method) (moldesign.widgets.selection.ResidueSelector method) topology_to_mol() (in module moldesign.interfaces.openmm) Trajectory (class in moldesign), [1] (class in moldesign.molecules) (class in moldesign.molecules.trajectory) TrajectoryOrbViewer (class in moldesign.widgets.trajectory) TrajectoryViewer (class in moldesign.widgets.trajectory) transform() (moldesign.molecules.atomcollections.AtomContainer method) transforms (moldesign.helpers.pdb.BioAssembly attribute) translate() (moldesign.molecules.atomcollections.AtomContainer method) TRIPLEOFFSET (moldesign.viewer.bondclicker.BondClicker attribute) TRIPLERADIUS (moldesign.viewer.bondclicker.BondClicker attribute) type (moldesign.Chain attribute), [1], [2] (moldesign.Residue attribute), [1], [2] (moldesign.molecules.Chain attribute) (moldesign.molecules.Residue attribute) (moldesign.molecules.chain.Chain attribute) (moldesign.molecules.residue.Residue attribute) typename (moldesign.data attribute)

U

unclassified_residues (moldesign.Chain attribute) (moldesign.molecules.Chain attribute) (moldesign.molecules.chain.Chain attribute) UnhandledValenceError unit_system (moldesign.molecules.Trajectory attribute) (moldesign.Trajectory attribute), [1] (moldesign.molecules.trajectory.Trajectory attribute) UNITS (moldesign.helpers.helpers.VolumetricGrid attribute) units_transfer() (in module moldesign.units.tools) UnitSystem (class in moldesign.units.unitsystem) UnitText (class in moldesign.uibase.components) UnknownAtom (class in moldesign.widgets.parameterization) UnknownResidue (class in moldesign.widgets.parameterization)

unset_bond_color() (moldesign.viewer.bondclicker.BondClicker method) unset_color() (moldesign.ChemicalGraphViewer method) (moldesign.GeometryViewer method) (moldesign.uibase.selector.SelectionGroup method) (moldesign.viewer.ChemicalGraphViewer method) (moldesign.viewer.GeometryViewer method) (moldesign.viewer.viewer2d.ChemicalGraphViewer method) (moldesign.viewer.viewer3d.GeometryViewer method) unshow() (moldesign.widgets.parameterization.MissingAtom method) (moldesign.widgets.parameterization.UnknownAtom method) (moldesign.widgets.parameterization.UnknownResidue method) (moldesign.widgets.parameterization.UnusualBond method) UnusualBond (class in moldesign.widgets.parameterization) update_engine_display() (moldesign.widgets.ComputeConfig method) (moldesign.widgets.computeconfig.ComputeConfig method) update_properties() (moldesign.molecules.molecule.MolPropertyMixin method) update_readout (moldesign.uibase.components.ReadoutFloatSlider attribute) update_selections() (moldesign.uibase.selector.SelectionGroup method) use_parent_doc() (moldesign.utils.callsigs.DocInherit method)

V

valence (moldesign.Atom attribute), [1], [2] (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) VALID (moldesign.uibase.components.UnitText attribute) value (moldesign.geom.Monitor attribute), [1] (moldesign.geom.monitor.Monitor attribute) (moldesign.uibase.components.ReadOnlyRepr attribute) (moldesign.uibase.components.ReadoutFloatSlider attribute) (moldesign.uibase.components.UnitText attribute) value_in() (moldesign.units.quantity.MdtQuantity method) value_update() (moldesign.uibase.selector.ValueSelector method) ValueSelector (class in moldesign.uibase.selector) Vector (class in moldesign.units.quantity) velocities (moldesign.Molecule attribute), [1], [2] (moldesign.molecules.Molecule attribute) (moldesign.molecules.molecule.Molecule attribute)

velocity (moldesign.Atom attribute), [1], [2] (moldesign.molecules.Atom attribute) (moldesign.molecules.atoms.Atom attribute) VelocityVerlet (class in moldesign.integrators) (class in moldesign.integrators.verlet) version_check() (moldesign.widgets.ChangeLog static method) (moldesign.widgets.computeconfig.ChangeLog static method) viewer (moldesign.widgets.Symmetrizer attribute) (moldesign.widgets.symmetry.Symmetrizer attribute) ViewerToolBase (class in moldesign.uibase.components) VIEWERTYPE (moldesign.uibase.components.ViewerToolBase attribute) (moldesign.widgets.BondSelector attribute) (moldesign.widgets.GeometryBuilder attribute) (moldesign.widgets.geombuilder.GeometryBuilder attribute) (moldesign.widgets.selection.BondSelector attribute) VolumetricGrid (class in moldesign.helpers.helpers)

W

wait() (moldesign.compute.compute.DummyJob method) warn_assemblies() (in module moldesign.helpers.pdb) warning() (moldesign.uibase.logwidget.Logger method) wfn (moldesign.GeometryViewer attribute) (moldesign.molecules.molecule.MolPropertyMixin attribute) (moldesign.viewer.GeometryViewer attribute) (moldesign.viewer.viewer3d.GeometryViewer attribute) WhenParam (class in moldesign.parameters) WidgetValueHandler (class in moldesign.uibase.logwidget) write() (in module moldesign), [1] (in module moldesign.fileio) (moldesign.Molecule method), [1], [2] (moldesign.Trajectory method) (moldesign.molecules.Molecule method) (moldesign.molecules.Trajectory method) (moldesign.molecules.molecule.Molecule method) (moldesign.molecules.trajectory.Trajectory method)

write_config() (in module moldesign.compute.configuration) write_file() (in module moldesign.interfaces.openbabel) write_string() (in module moldesign.interfaces.openbabel) write_trajectory() (in module moldesign), [1] (in module moldesign.fileio) writeline() (moldesign.utils.utils.BaseTable method) (moldesign.utils.utils.MarkdownTable method) (moldesign.utils.utils.PrintTable method) writer() (in module moldesign.chemjson)

X

xyzlist() (moldesign.helpers.helpers.VolumetricGrid method)