Index

_

__call__() (sknano.core.Cached method) (sknano.core.NoInstances method) (sknano.core.Singleton method) (sknano.core.meta.Cached method) (sknano.core.meta.NoInstances method) (sknano.core.meta.Singleton method) (sknano.core.meta.method_func method) (sknano.core.meta.with_doc method) (sknano.core.method_func method) (sknano.core.with_doc method)

A

A (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) a (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.geometric_regions.Cube attribute) (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Parallelepiped attribute) (sknano.core.geometric_regions.Rectangle attribute) (sknano.core.geometric_regions.Square attribute) a1 (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Direct2DLatticeMixin attribute) (sknano.core.crystallography.Direct3DLatticeMixin attribute) a2 (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Direct2DLatticeMixin attribute) (sknano.core.crystallography.Direct3DLatticeMixin attribute) a3 (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Direct3DLatticeMixin attribute) a_star (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) abc (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Parallelepiped attribute) abs_cap() (in module sknano.core.math) add_atom() (sknano.io.xyz.XYZConverter method) (sknano.io.XYZConverter method) add_default_arguments() (in module sknano.scripts) add_ring() (sknano.core.atoms.mixins.RingAtomsMixin method) (sknano.core.atoms.RingAtomsMixin method) add_type() (sknano.io.xyz.XYZConverter method) (sknano.io.XYZConverter method) ALL (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) all_angles (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) all_bonds (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) all_dihedrals (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) all_equal() (in module sknano.core) (in module sknano.core.itertools) all_impropers (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) all_selection_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) alpha (sknano.core.crystallography.Crystal3DLattice attribute) alpha_star (sknano.core.crystallography.Reciprocal3DLattice attribute) AlphaQuartz (class in sknano.core.structures) AlphaQuartzGenerator (class in sknano.generators) analyze_network() (sknano.core.atoms.mixins.RingAtomsMixin method) (sknano.core.atoms.RingAtomsMixin method) analyze_POAV() (sknano.utils.analysis.StructureAnalyzer method) analyze_POAVs() (sknano.core.atoms.mixins.POAVAtomsMixin method) (sknano.core.atoms.POAVAtomsMixin method) analyze_structure() (in module sknano.scripts) AND (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) Angle (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) angle (sknano.core.atoms.AngularTopology attribute) (sknano.core.atoms.mixins.AngularTopology attribute) (sknano.core.math.Quaternion attribute) angle() (in module sknano.core.math) (in module sknano.core.math.vector) (sknano.core.math.Vector method) (sknano.core.math.vector.Vector method) angle_style (sknano.io.DATAFormatter attribute) (sknano.io.lammps_data.DATAFormatter attribute) Angles (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) angles (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.AtomTopologyMixin attribute) (sknano.core.atoms.mixins.AtomTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) angles_in_degrees (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) AngleStats (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) AngularTopology (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) AngularTopologyCollection (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) area (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.geometric_regions.Circle attribute) (sknano.core.geometric_regions.Ellipse attribute) (sknano.core.geometric_regions.Geometric2DRegion attribute) (sknano.core.geometric_regions.Parallelogram attribute) (sknano.core.geometric_regions.Rectangle attribute) (sknano.core.geometric_regions.Square attribute) (sknano.core.geometric_regions.Triangle attribute) (sknano.core.structures.GrapheneMixin attribute)

armchair_edge_length (sknano.apps.nanogen_gui.GrapheneModel attribute) asbool() (in module sknano.core) (in module sknano.core.strings) asdict() (in module sknano.core) (in module sknano.core.strings) aselect (sknano.core.atoms.Snapshot attribute) (sknano.core.atoms.trajectory.Snapshot attribute) asfloat() (in module sknano.core) (in module sknano.core.strings) asint() (in module sknano.core) (in module sknano.core.strings) aslist() (in module sknano.core) (in module sknano.core.strings) asset() (in module sknano.core) (in module sknano.core.strings) astuple() (in module sknano.core) (in module sknano.core.strings) Atom (class in sknano.core.atoms) (class in sknano.core.atoms.atoms) atom1 (sknano.core.atoms.Angle attribute) (sknano.core.atoms.Bond attribute) (sknano.core.atoms.Dihedral attribute) (sknano.core.atoms.Improper attribute) (sknano.core.atoms.mixins.Angle attribute) (sknano.core.atoms.mixins.Bond attribute) (sknano.core.atoms.mixins.Dihedral attribute) (sknano.core.atoms.mixins.Improper attribute) atom2 (sknano.core.atoms.Angle attribute) (sknano.core.atoms.Bond attribute) (sknano.core.atoms.Dihedral attribute) (sknano.core.atoms.Improper attribute) (sknano.core.atoms.mixins.Angle attribute) (sknano.core.atoms.mixins.Bond attribute) (sknano.core.atoms.mixins.Dihedral attribute) (sknano.core.atoms.mixins.Improper attribute) atom3 (sknano.core.atoms.Angle attribute) (sknano.core.atoms.Dihedral attribute) (sknano.core.atoms.Improper attribute) (sknano.core.atoms.mixins.Angle attribute) (sknano.core.atoms.mixins.Dihedral attribute) (sknano.core.atoms.mixins.Improper attribute) atom4 (sknano.core.atoms.Dihedral attribute) (sknano.core.atoms.Improper attribute) (sknano.core.atoms.mixins.Dihedral attribute) (sknano.core.atoms.mixins.Improper attribute) ATOM_ATTRIBUTE (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) atom_ids (sknano.core.atoms.mixins.Topology attribute) (sknano.core.atoms.Topology attribute) atom_selection (sknano.core.atoms.Snapshot attribute) (sknano.core.atoms.trajectory.Snapshot attribute) atom_style (sknano.io.DATAFormatter attribute) (sknano.io.lammps_data.DATAFormatter attribute) atom_tree (sknano.core.atoms.KDTreeAtomsMixin attribute) (sknano.core.atoms.mixins.KDTreeAtomsMixin attribute) AtomAdapterMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) atomattrs (sknano.io.DUMPFormatter attribute) (sknano.io.lammps_dump.DUMPFormatter attribute) atomattrs2str() (sknano.io.DUMPFormatter method) (sknano.io.lammps_dump.DUMPFormatter method) ATOMICNUMBER (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) atomID (sknano.core.atoms.id_atoms.IDAtom attribute) (sknano.core.atoms.IDAtom attribute) Atoms (class in sknano.core.atoms) (class in sknano.core.atoms.atoms) atoms (sknano.core.atoms.mixins.Topology attribute) (sknano.core.atoms.Snapshot attribute) (sknano.core.atoms.Topology attribute) (sknano.core.atoms.trajectory.Snapshot attribute) (sknano.core.structures.StructureMixin attribute) (sknano.testing.AtomsTestFixture attribute) AtomsAdapterMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) AtomsTestFixture (class in sknano.testing) AtomsTopologyMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) AtomsTopologyStats (class in sknano.core.atoms) AtomsTransformationsMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) AtomTopologyMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) AtomTransformationsMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) atomtype (sknano.core.atoms.type_atoms.TypeAtom attribute) (sknano.core.atoms.TypeAtom attribute) attach_wrapper() (in module sknano.core) (in module sknano.core.meta) attr_dtypes (sknano.io.DUMPFormatter attribute) (sknano.io.lammps_dump.DUMPFormatter attribute) attr_selection_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) axis (sknano.core.geometric_regions.Cone attribute) (sknano.core.geometric_regions.Cylinder attribute) (sknano.core.math.Quaternion attribute) axis_angle_from_rotation_matrix() (in module sknano.core.math) (in module sknano.core.math.transforms)

B

b (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Parallelepiped attribute) (sknano.core.geometric_regions.Rectangle attribute) b1 (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal2DLatticeMixin attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.crystallography.Reciprocal3DLatticeMixin attribute) b2 (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal2DLatticeMixin attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.crystallography.Reciprocal3DLatticeMixin attribute) b3 (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.crystallography.Reciprocal3DLatticeMixin attribute) b_star (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) BaseClass (class in sknano.core) (class in sknano.core.meta) basis (sknano.core.crystallography.CrystalCell attribute) (sknano.core.structures.NanoStructureBase attribute) (sknano.core.structures.StructureMixin attribute) BasisAtom (class in sknano.core.atoms) (class in sknano.core.atoms.basis_atoms) BasisAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.basis_atoms) BCCGenerator (class in sknano.generators) BCCStructure (class in sknano.core.structures) BCCStructureGenerator (in module sknano.generators) beta (sknano.core.crystallography.Crystal3DLattice attribute) beta_star (sknano.core.crystallography.Reciprocal3DLattice attribute) BetaQuartz (class in sknano.core.structures) bilayer_graphene (sknano.testing.AtomsTestFixture attribute) BilayerGraphene (class in sknano.core.structures) BilayerGrapheneGenerator (class in sknano.generators)

Bond (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) bond (sknano.core.atoms.Bond attribute) (sknano.core.atoms.mixins.Bond attribute) bond_pairs (sknano.core.atoms.Angle attribute) (sknano.core.atoms.mixins.Angle attribute) bond_style (sknano.io.DATAFormatter attribute) (sknano.io.lammps_data.DATAFormatter attribute) Bonds (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) bonds (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.AtomTopologyMixin attribute) (sknano.core.atoms.mixins.AtomTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) BondStats (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) bounding_box (sknano.core.atoms.BoundingRegionsMixin attribute) (sknano.core.atoms.mixins.BoundingRegionsMixin attribute) (sknano.core.crystallography.LatticeBase attribute) (sknano.core.geometric_regions.Geometric2DRegion attribute) (sknano.core.geometric_regions.Geometric3DRegion attribute) bounding_region (sknano.core.atoms.BoundingRegionsMixin attribute) (sknano.core.atoms.mixins.BoundingRegionsMixin attribute) bounding_sphere (sknano.core.atoms.BoundingRegionsMixin attribute) (sknano.core.atoms.mixins.BoundingRegionsMixin attribute) BoundingRegionsMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) bounds (sknano.core.atoms.BoundingRegionsMixin attribute) (sknano.core.atoms.mixins.BoundingRegionsMixin attribute) buckyball (sknano.testing.AtomsTestFixture attribute) BulkStructureModel (class in sknano.apps.nanogen_gui) bundle_density (sknano.core.structures.NanotubeBundleMixin attribute) bundle_geometry (sknano.core.structures.NanotubeBundleMixin attribute) bundle_mass (sknano.core.structures.NanotubeBundleMixin attribute) bundle_packing (sknano.core.structures.NanotubeBundleMixin attribute)

C

c (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Parallelepiped attribute) c_star (sknano.core.crystallography.Reciprocal3DLattice attribute) Cached (class in sknano.core) (class in sknano.core.meta) CaesiumChlorideGenerator (class in sknano.generators) CaesiumChlorideStructure (class in sknano.core.structures) CaesiumChlorideStructureGenerator (in module sknano.generators) call_signature (sknano.generators.GeneratorConfigParser attribute) (sknano.generators.LayeredStructureGenerator attribute) CappedNanotubeGeneratorMixin (class in sknano.generators) cartesian_to_fractional() (sknano.core.crystallography.LatticeBase method) CCPStructure (in module sknano.core.structures) cell (sknano.core.crystallography.LatticeBase attribute) cell_area (sknano.core.crystallography.Crystal2DLattice attribute) cell_matrix (sknano.core.crystallography.LatticeBase attribute) cell_volume (sknano.core.crystallography.Crystal3DLattice attribute) center (sknano.core.atoms.Angle attribute) (sknano.core.atoms.mixins.Angle attribute) (sknano.core.geometric_regions.Circle attribute) (sknano.core.geometric_regions.Cube attribute) (sknano.core.geometric_regions.Ellipse attribute) (sknano.core.geometric_regions.Ellipsoid attribute) (sknano.core.geometric_regions.GeometricRegion attribute) (sknano.core.geometric_regions.Sphere attribute) (sknano.core.geometric_regions.Square attribute) center_centroid() (sknano.core.geometric_regions.GeometricRegion method) centroid (sknano.core.atoms.mixins.Topology attribute) (sknano.core.atoms.Topology attribute) (sknano.core.crystallography.LatticeBase attribute) (sknano.core.geometric_regions.Circle attribute) (sknano.core.geometric_regions.Cone attribute) (sknano.core.geometric_regions.Cube attribute) (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Cylinder attribute) (sknano.core.geometric_regions.Ellipse attribute) (sknano.core.geometric_regions.Ellipsoid attribute) (sknano.core.geometric_regions.GeometricRegion attribute) (sknano.core.geometric_regions.Parallelepiped attribute) (sknano.core.geometric_regions.Parallelogram attribute) (sknano.core.geometric_regions.Rectangle attribute) (sknano.core.geometric_regions.Sphere attribute) (sknano.core.geometric_regions.Square attribute) (sknano.core.geometric_regions.Triangle attribute) Ch (sknano.apps.nanogen_gui.MWNTModel attribute) (sknano.core.structures.SWNTMixin attribute) Ch_list (sknano.apps.nanogen_gui.MWNTModel attribute) (sknano.core.structures.MWNTMixin attribute) Ch_vec (sknano.core.structures.SWNTMixin attribute) ChargedAtom (class in sknano.core.atoms) (class in sknano.core.atoms.charged_atoms) ChargedAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.charged_atoms) check_operands() (in module sknano.core.atoms) (in module sknano.core.atoms.mixins) check_type() (in module sknano.core) (in module sknano.core.meta) chiral_angle (sknano.core.structures.SWNTMixin attribute) chiral_set (sknano.core.structures.MWNTMixin attribute) chiral_type (sknano.core.structures.SWNTMixin attribute) chiral_types (sknano.apps.nanogen_gui.MWNTModel attribute) (sknano.core.structures.MWNTMixin attribute) Circle (class in sknano.core.geometric_regions) circle (sknano.testing.Geometric2DRegionsTestFixture attribute) ClassSignature (class in sknano.core) (class in sknano.core.meta) clear() (sknano.core.structures.StructureMixin method) cmp_Ch() (in module sknano.core.structures) CN (sknano.core.atoms.cn_atoms.CNAtom attribute) (sknano.core.atoms.CNAtom attribute) (sknano.core.atoms.NeighborAtom attribute) (sknano.core.atoms.neighbor_atoms.NeighborAtom attribute) CNAtom (class in sknano.core.atoms) (class in sknano.core.atoms.cn_atoms) CNAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.cn_atoms) column_matrix (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) (sknano.core.math.point.Point attribute) (sknano.core.math.vector.Vector attribute) comment_line (sknano.io.StructureData attribute) Composition (class in sknano.core.structures) Compositions (class in sknano.core.structures) compute_angle() (in module sknano.core.atoms) (in module sknano.core.atoms.mixins) compute_bond() (in module sknano.core.atoms) (in module sknano.core.atoms.mixins) compute_bundle_density() (in module sknano.core.structures) compute_centroid() (in module sknano.core.physics) compute_Ch() (in module sknano.core.structures) compute_chiral_angle() (in module sknano.core.structures) compute_d() (in module sknano.core.structures) compute_dihedral() (in module sknano.core.atoms) (in module sknano.core.atoms.mixins) compute_dR() (in module sknano.core.structures) compute_dt() (in module sknano.core.structures) compute_electronic_type() (in module sknano.core.structures) compute_improper() (in module sknano.core.atoms) (in module sknano.core.atoms.mixins) compute_inertia_tensor() (in module sknano.core.physics) compute_linear_mass_density() (in module sknano.core.structures) compute_Lx() (in module sknano.core.structures) compute_Ly() (in module sknano.core.structures) compute_Lz() (in module sknano.core.structures) compute_M() (in module sknano.core.structures) compute_measure() (sknano.core.atoms.Angle method) (sknano.core.atoms.Bond method) (sknano.core.atoms.Dihedral method) (sknano.core.atoms.Improper method) (sknano.core.atoms.Topology method) (sknano.core.atoms.mixins.Angle method) (sknano.core.atoms.mixins.Bond method) (sknano.core.atoms.mixins.Dihedral method) (sknano.core.atoms.mixins.Improper method) (sknano.core.atoms.mixins.Topology method) compute_N() (in module sknano.core.structures) compute_Natoms() (in module sknano.core.structures) compute_Natoms_per_tube() (in module sknano.core.structures) compute_Natoms_per_unit_cell() (in module sknano.core.structures)

compute_POAVs() (sknano.core.atoms.mixins.POAVAtomsMixin method) (sknano.core.atoms.POAVAtomsMixin method) compute_psi() (in module sknano.core.structures) compute_R() (in module sknano.core.structures) compute_R_chiral_angle() (in module sknano.core.structures) compute_rt() (in module sknano.core.structures) compute_strain() (sknano.core.atoms.mixins.Topology method) (sknano.core.atoms.Topology method) compute_symmetry_chiral_angle() (in module sknano.core.structures) compute_symmetry_operation() (in module sknano.core.structures) compute_T() (in module sknano.core.structures) compute_t1() (in module sknano.core.structures) compute_t2() (in module sknano.core.structures) compute_tau() (in module sknano.core.structures) compute_tube_diameter() (in module sknano.core.structures) compute_tube_length() (in module sknano.core.structures) compute_tube_mass() (in module sknano.core.structures) compute_tube_radius() (in module sknano.core.structures) compute_unit_cell_mass() (in module sknano.core.structures) compute_unit_cell_symmetry_params() (in module sknano.core.structures) Cone (class in sknano.core.geometric_regions) CONE (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) cone (sknano.testing.Geometric3DRegionsTestFixture attribute) conjugate (sknano.core.math.Quaternion attribute) consume() (in module sknano.core) (in module sknano.core.itertools) contains() (sknano.core.geometric_regions.Circle method) (sknano.core.geometric_regions.Cone method) (sknano.core.geometric_regions.Cube method) (sknano.core.geometric_regions.Cuboid method) (sknano.core.geometric_regions.Cylinder method) (sknano.core.geometric_regions.Ellipse method) (sknano.core.geometric_regions.Ellipsoid method) (sknano.core.geometric_regions.GeometricRegion method) (sknano.core.geometric_regions.Parallelepiped method) (sknano.core.geometric_regions.Parallelogram method) (sknano.core.geometric_regions.Rectangle method) (sknano.core.geometric_regions.Sphere method) (sknano.core.geometric_regions.Square method) (sknano.core.geometric_regions.Triangle method) ConventionalCellGraphene (class in sknano.core.structures) ConventionalCellGrapheneGenerator (class in sknano.generators) convert() (sknano.io.DATA2XYZConverter method) (sknano.io.StructureDataConverter method) (sknano.io.XYZ2DATAConverter method) (sknano.io.lammps_data.DATA2XYZConverter method) (sknano.io.xyz.XYZ2DATAConverter method) convert_condition_str() (in module sknano.core.math) coordinates_bounding_box (sknano.core.atoms.BoundingRegionsMixin attribute) (sknano.core.atoms.mixins.BoundingRegionsMixin attribute) Copper (class in sknano.core.structures) CopperGenerator (class in sknano.generators) copy() (sknano.core.math.Vector method) (sknano.core.math.vector.Vector method) cos_alpha (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Direct3DLatticeMixin attribute) cos_alpha_star (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.crystallography.Reciprocal3DLatticeMixin attribute) cos_beta (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Direct3DLatticeMixin attribute) cos_beta_star (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.crystallography.Reciprocal3DLatticeMixin attribute) cos_gamma (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Direct2DLatticeMixin attribute) (sknano.core.crystallography.Direct3DLatticeMixin attribute) cos_gamma_star (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal2DLatticeMixin attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.crystallography.Reciprocal3DLatticeMixin attribute) count_neighbors() (sknano.core.atoms.KDTreeAtomsMixin method) (sknano.core.atoms.mixins.KDTreeAtomsMixin method) cross() (in module sknano.core.math) (in module sknano.core.math.vector) (sknano.core.math.Vector method) (sknano.core.math.vector.Vector method) Crystal2DLattice (class in sknano.core.crystallography) Crystal2DStructure (class in sknano.core.structures) Crystal3DLattice (class in sknano.core.crystallography) Crystal3DStructure (class in sknano.core.structures) crystal_cell (sknano.core.structures.StructureMixin attribute) CrystalCell (class in sknano.core.crystallography) CrystalStructureBase (class in sknano.core.structures) CrystalStructureGenerator (class in sknano.generators) CsClGenerator (in module sknano.generators) CsClStructure (in module sknano.core.structures) Cube (class in sknano.core.geometric_regions) CUBE (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) cube (sknano.testing.Geometric3DRegionsTestFixture attribute) cubic() (sknano.core.crystallography.Crystal3DLattice class method) (sknano.core.crystallography.Reciprocal3DLattice class method) CubicClosePackedStructure (class in sknano.core.structures) CubicStructure (class in sknano.core.structures) Cuboid (class in sknano.core.geometric_regions) CUBOID (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) cuboid (sknano.testing.Geometric3DRegionsTestFixture attribute) cyclic_pairs() (in module sknano.core) (in module sknano.core.itertools) Cylinder (class in sknano.core.geometric_regions) CYLINDER (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) cylinder (sknano.testing.Geometric3DRegionsTestFixture attribute)

D

d (sknano.core.structures.SWNTMixin attribute) DATA (in module sknano.io) (in module sknano.io.lammps_data) data (sknano.core.structures.Fullerene attribute) (sknano.core.structures.Fullerenes attribute) DATA2XYZConverter (class in sknano.io) (class in sknano.io.lammps_data) data_reader (sknano.testing.IOTestFixture attribute) DATAConverter (class in sknano.io) (class in sknano.io.lammps_data) DATAData (class in sknano.io) (class in sknano.io.lammps_data) datadata (sknano.testing.IOTestFixture attribute) DATAError, [1] datafile (sknano.core.structures.Fullerene attribute) (sknano.io.DATAConverter attribute) (sknano.io.XYZ2DATAConverter attribute) (sknano.io.lammps_data.DATAConverter attribute) (sknano.io.xyz.XYZ2DATAConverter attribute) DATAFormatSpec (in module sknano.io) (in module sknano.io.lammps_data) DATAFormatter (class in sknano.io) (class in sknano.io.lammps_data) DATAIO (in module sknano.io) (in module sknano.io.lammps_data) DATAIOError (in module sknano.io) (in module sknano.io.lammps_data) DATAIOFormatter (in module sknano.io) (in module sknano.io.lammps_data) DATAIOReader (in module sknano.io) (in module sknano.io.lammps_data) DATAIOWriter (in module sknano.io) (in module sknano.io.lammps_data) DATAReader (class in sknano.io) (class in sknano.io.lammps_data) DATAWriter (class in sknano.io) (class in sknano.io.lammps_data) dedupe() (in module sknano.core) (in module sknano.core.itertools) delete() (sknano.io.DATAData method) (sknano.io.lammps_data.DATAData method) deprecate_kwarg() (in module sknano.core) (in module sknano.core.meta) deprecated() (in module sknano.core) (in module sknano.core.meta) DiamondGenerator (class in sknano.generators) DiamondStructure (class in sknano.core.structures) DiamondStructureGenerator (in module sknano.generators) Dihedral (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) dihedral (sknano.core.atoms.Dihedral attribute) (sknano.core.atoms.mixins.Dihedral attribute) dihedral_style (sknano.io.DATAFormatter attribute) (sknano.io.lammps_data.DATAFormatter attribute) Dihedrals (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) dihedrals (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.AtomTopologyMixin attribute) (sknano.core.atoms.mixins.AtomTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) DihedralStats (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) DipoleAtom (class in sknano.core.atoms) (class in sknano.core.atoms.dipole_atoms)

DipoleAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.dipole_atoms) Direct2DLatticeMixin (class in sknano.core.crystallography) Direct3DLatticeMixin (class in sknano.core.crystallography) DirectLatticeMixin (in module sknano.core.crystallography) Domain (class in sknano.core.crystallography) domain (sknano.io.DATAReader attribute) (sknano.io.lammps_data.DATAReader attribute) dot() (in module sknano.core.math) (in module sknano.core.math.vector) (sknano.core.math.Vector method) (sknano.core.math.vector.Vector method) dotproduct() (in module sknano.core) (in module sknano.core.itertools) dr (sknano.core.atoms.xyz_atoms.XYZAtom attribute) (sknano.core.atoms.XYZAtom attribute) dR (sknano.core.structures.SWNTMixin attribute) dt (sknano.core.structures.MWNTMixin attribute) (sknano.core.structures.SWNTMixin attribute) dt_list (sknano.core.structures.MWNTMixin attribute) DUMP (in module sknano.io) (in module sknano.io.lammps_dump) dump_bond_data() (in module sknano.core.refdata) dump_reader (sknano.testing.IOTestFixture attribute) dumpattrs (sknano.io.DUMPFormatter attribute) (sknano.io.lammps_dump.DUMPFormatter attribute) dumpattrs2index (sknano.io.DUMPFormatter attribute) (sknano.io.lammps_dump.DUMPFormatter attribute) dumpattrs2str() (sknano.io.DUMPFormatter method) (sknano.io.lammps_dump.DUMPFormatter method) DUMPData (class in sknano.io) (class in sknano.io.lammps_dump) dumpdata (sknano.testing.IOTestFixture attribute) dumpdata1 (sknano.testing.AtomsTestFixture attribute) DUMPError, [1] DUMPFormatter (class in sknano.io) (class in sknano.io.lammps_dump) DUMPIO (in module sknano.io) (in module sknano.io.lammps_dump) DUMPIOError (in module sknano.io) (in module sknano.io.lammps_dump) DUMPIOFormatter (in module sknano.io) (in module sknano.io.lammps_dump) DUMPIOReader (in module sknano.io) (in module sknano.io.lammps_dump) DUMPIOWriter (in module sknano.io) (in module sknano.io.lammps_dump) dumpobj() (in module sknano.core) (in module sknano.core.io) DUMPReader (class in sknano.io) (class in sknano.io.lammps_dump) DUMPTestFixture (class in sknano.testing) DUMPWriter (class in sknano.io) (class in sknano.io.lammps_dump)

E

edge_length (sknano.apps.nanogen_gui.GrapheneModel attribute) electronic_type (sknano.core.structures.SWNTMixin attribute) element (sknano.core.atoms.Atom attribute) (sknano.core.atoms.atoms.Atom attribute) ELEMENT (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) element1 (sknano.core.structures.NanoStructureBase attribute) element2 (sknano.core.structures.NanoStructureBase attribute) Ellipse (class in sknano.core.geometric_regions) ellipse (sknano.testing.Geometric2DRegionsTestFixture attribute) Ellipsoid (class in sknano.core.geometric_regions) ELLIPSOID (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute)

ellipsoid (sknano.testing.Geometric3DRegionsTestFixture attribute) end (sknano.core.atoms.Bond attribute) (sknano.core.atoms.mixins.Bond attribute) EnergyAtom (class in sknano.core.atoms) (class in sknano.core.atoms.energy_atoms) EnergyAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.energy_atoms) etotal (sknano.core.atoms.energy_atoms.EnergyAtom attribute) (sknano.core.atoms.EnergyAtom attribute) euclidean_distance() (sknano.core.math.Point method) (sknano.core.math.point.Point method) expr (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) expr_term (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) EXWITHIN (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) exwithin_selection_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute)

F

f (sknano.core.atoms.force_atoms.ForceAtom attribute) (sknano.core.atoms.ForceAtom attribute) FCCGenerator (class in sknano.generators) FCCStructure (class in sknano.core.structures) FCCStructureGenerator (in module sknano.generators) filter_Ch() (in module sknano.core.structures) filter_Ch_list() (in module sknano.core.structures) filter_vmd_indices() (sknano.core.atoms.mixins.VMDAtomsAdapterMixin method) (sknano.core.atoms.VMDAtomsAdapterMixin method) filtered_vmd_indices() (sknano.core.atoms.mixins.VMDAtomsAdapterMixin method) (sknano.core.atoms.VMDAtomsAdapterMixin method) finalize() (sknano.generators.GeneratorBase method) (sknano.generators.MWNTGenerator method) (sknano.generators.SWNTGenerator method) find_defect_chains() (in module sknano.utils.analysis) find_mod_objs() (in module sknano.core) (in module sknano.core.meta) find_rings() (in module sknano.core.analysis) find_target_atom() (in module sknano.utils.analysis) first_neighbors (sknano.core.atoms.neighbor_atoms.NeighborAtom attribute) (sknano.core.atoms.NeighborAtom attribute) first_true() (in module sknano.core) (in module sknano.core.itertools) fix_Lx (sknano.core.structures.UnrolledSWNTMixin attribute) fix_Lz (sknano.core.structures.SWNTMixin attribute) flatten() (in module sknano.core) (in module sknano.core.itertools) fmtstr (sknano.core.BaseClass attribute) (sknano.core.meta.BaseClass attribute) ForceAtom (class in sknano.core.atoms) (class in sknano.core.atoms.force_atoms) ForceAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.force_atoms)

format() (sknano.io.DATAFormatter method) (sknano.io.DUMPFormatter method) (sknano.io.PDBFormatter method) (sknano.io.XYZFormatter method) (sknano.io.lammps_data.DATAFormatter method) (sknano.io.lammps_dump.DUMPFormatter method) (sknano.io.pdb.PDBFormatter method) (sknano.io.xyz.XYZFormatter method) formatter (sknano.core.atoms.Snapshot attribute) (sknano.core.atoms.trajectory.Snapshot attribute) formatter() (sknano.io.DATAData class method) (sknano.io.lammps_data.DATAData class method) fractional_diff() (sknano.core.crystallography.LatticeBase method) fractional_matrix (sknano.core.crystallography.LatticeBase attribute) fractional_to_cartesian() (sknano.core.crystallography.LatticeBase method) from_components() (sknano.core.math.Quaternion class method) from_conventional_cell() (sknano.core.structures.Graphene class method) (sknano.generators.GrapheneGenerator class method) from_primitive_cell() (sknano.core.structures.Graphene class method) (sknano.generators.GrapheneGenerator class method) from_pymatgen_structure() (sknano.core.structures.Crystal2DStructure class method) (sknano.core.structures.Crystal3DStructure class method) from_spacegroup() (sknano.core.structures.Crystal2DStructure class method) (sknano.core.structures.Crystal3DStructure class method) (sknano.core.structures.CubicStructure class method) (sknano.core.structures.HexagonalStructure class method) frozendict (class in sknano.core) (class in sknano.core.collections) Fullerene (class in sknano.core.structures) FullereneGenerator (class in sknano.generators) FullereneModel (class in sknano.apps.nanogen_gui) Fullerenes (class in sknano.core.structures) fullerenes (sknano.apps.nanogen_gui.FullereneModel attribute) (sknano.core.structures.Fullerenes attribute) fx (sknano.core.atoms.force_atoms.ForceAtom attribute) (sknano.core.atoms.ForceAtom attribute) fy (sknano.core.atoms.force_atoms.ForceAtom attribute) (sknano.core.atoms.ForceAtom attribute) fz (sknano.core.atoms.force_atoms.ForceAtom attribute) (sknano.core.atoms.ForceAtom attribute)

G

gamma (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) gamma_star (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) generate() (sknano.generators.GeneratorBase method) (sknano.generators.GeneratorMixin method) (sknano.generators.GrapheneGeneratorBase method) (sknano.generators.LayeredStructureGenerator method) (sknano.generators.MWNTGeneratorBase method) (sknano.generators.NanotubeBundleGeneratorBase method) (sknano.generators.UnrolledSWNTGenerator method) generate_atoms() (in module sknano.testing) generate_bounding_box() (in module sknano.core.geometric_regions) generate_bundle_coords() (sknano.core.structures.NanotubeBundleMixin method) generate_Ch_list() (in module sknano.core.structures) (sknano.core.structures.MWNTMixin method) generate_Ch_property_grid() (in module sknano.core.structures) generate_dt_mask() (sknano.core.structures.MWNTMixin method) generate_endcaps() (sknano.generators.CappedNanotubeGeneratorMixin method) generate_fname() (sknano.generators.ConventionalCellGrapheneGenerator class method) (sknano.generators.FullereneGenerator class method) (sknano.generators.GrapheneGeneratorBase class method) (sknano.generators.LayeredStructureGenerator method) (sknano.generators.MWNTGenerator class method) (sknano.generators.PrimitiveCellGrapheneGenerator class method) (sknano.generators.SWNTGenerator class method) (sknano.generators.UnrolledSWNTGenerator class method) generate_lattice() (in module sknano.core.crystallography) generate_structure() (in module sknano.testing) generate_unit_cell() (sknano.core.structures.Fullerene method) (sknano.core.structures.MWNTBase method) (sknano.core.structures.UnrolledSWNT method) generate_vmd_selection_string() (in module sknano.core.atoms) (in module sknano.core.atoms.selections) GeneratorBase (class in sknano.generators) GeneratorConfigParser (class in sknano.generators) GeneratorMixin (class in sknano.generators) GeneratorTestFixture (class in sknano.testing) Geometric2DRegion (class in sknano.core.geometric_regions) Geometric2DRegionsTestFixture (class in sknano.testing) Geometric3DRegion (class in sknano.core.geometric_regions) Geometric3DRegionsTestFixture (class in sknano.testing) GeometricRegion (class in sknano.core.geometric_regions) GeometricRegionsTestFixture (class in sknano.testing) GeometricTransformsMixin (class in sknano.core.geometric_regions) get() (sknano.io.DATAReader method) (sknano.io.lammps_data.DATAReader method) get_angle() (sknano.core.atoms.AtomsTopologyMixin method) (sknano.core.atoms.mixins.AtomsTopologyMixin method) get_angles() (sknano.core.atoms.AtomsTopologyMixin method) (sknano.core.atoms.mixins.AtomsTopologyMixin method) get_atom_from_vmd_index() (sknano.core.atoms.mixins.VMDAtomsAdapterMixin method) (sknano.core.atoms.VMDAtomsAdapterMixin method) get_atoms() (sknano.core.atoms.Snapshot method) (sknano.core.atoms.trajectory.Snapshot method) get_bond() (sknano.core.atoms.AtomsTopologyMixin method) (sknano.core.atoms.mixins.AtomsTopologyMixin method) get_bonds() (sknano.core.atoms.AtomsTopologyMixin method) (sknano.core.atoms.mixins.AtomsTopologyMixin method) get_Ch_indices() (in module sknano.core.structures)

get_Ch_type() (in module sknano.core.structures) get_chiral_indices() (in module sknano.core.structures) get_chiral_indices_from_str() (in module sknano.core.structures) get_chiral_type() (in module sknano.core.structures) get_coords() (sknano.core.atoms.xyz_atoms.XYZAtom method) (sknano.core.atoms.XYZAtom method) get_dihedral() (sknano.core.atoms.AtomsTopologyMixin method) (sknano.core.atoms.mixins.AtomsTopologyMixin method) get_dihedrals() (sknano.core.atoms.AtomsTopologyMixin method) (sknano.core.atoms.mixins.AtomsTopologyMixin method) get_fname() (in module sknano.core) (in module sknano.core.io) get_fpath() (in module sknano.core) (in module sknano.core.io) get_improper() (sknano.core.atoms.AtomsTopologyMixin method) (sknano.core.atoms.mixins.AtomsTopologyMixin method) get_impropers() (sknano.core.atoms.AtomsTopologyMixin method) (sknano.core.atoms.mixins.AtomsTopologyMixin method) get_lattice() (sknano.core.structures.CubicStructure class method) (sknano.core.structures.HexagonalStructure class method) get_nth_nearest_neighbors() (sknano.core.atoms.neighbor_atoms.NeighborAtom method) (sknano.core.atoms.NeighborAtom method) get_object_signature() (in module sknano.core) (in module sknano.core.meta) get_POAV_attr() (sknano.core.atoms.mixins.POAVAtomsMixin method) (sknano.core.atoms.POAVAtomsMixin method) get_points() (sknano.core.geometric_regions.GeometricRegion method) get_vmd_selection_string() (sknano.core.atoms.mixins.VMDAtomsAdapterMixin method) (sknano.core.atoms.VMDAtomsAdapterMixin method) get_wall() (sknano.core.structures.MWNTMixin method) getattr() (sknano.core.atoms.Atom method) (sknano.core.atoms.atoms.Atom method) getdoc() (sknano.core.meta.method_func method) (sknano.core.method_func method) Gold (class in sknano.core.structures) GoldGenerator (class in sknano.generators) Graphene (class in sknano.core.structures) graphene (sknano.testing.AtomsTestFixture attribute) GrapheneBase (class in sknano.core.structures) GrapheneConventionalCell (class in sknano.core.structures) GrapheneGenerator (class in sknano.generators) GrapheneGeneratorBase (class in sknano.generators) GrapheneMixin (class in sknano.core.structures) GrapheneModel (class in sknano.apps.nanogen_gui) GrapheneNanoribbon (class in sknano.core.structures) GraphenePrimitiveCell (class in sknano.core.structures) grouped_expr (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) grouper() (in module sknano.core) (in module sknano.core.itertools)

H

H (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) HCPStructure (in module sknano.core.structures) headers (sknano.io.DATAReader attribute) (sknano.io.lammps_data.DATAReader attribute) hexagonal() (sknano.core.crystallography.Crystal2DLattice class method) (sknano.core.crystallography.Crystal3DLattice class method) (sknano.core.crystallography.Reciprocal2DLattice class method) (sknano.core.crystallography.Reciprocal3DLattice class method) HexagonalCellGraphene (in module sknano.core.structures)

HexagonalCellGrapheneGenerator (in module sknano.generators) HexagonalClosePackedStructure (class in sknano.core.structures) HexagonalGraphene (in module sknano.core.structures) HexagonalGrapheneGenerator (in module sknano.generators) HexagonalStructure (class in sknano.core.structures)

I

i (sknano.core.atoms.image_atoms.ImageAtom attribute) (sknano.core.atoms.ImageAtom attribute) id (sknano.core.atoms.id_atoms.IDAtom attribute) (sknano.core.atoms.IDAtom attribute) ID (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) id_selection_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) IDAtom (class in sknano.core.atoms) (class in sknano.core.atoms.id_atoms) IDAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.id_atoms) imag (sknano.core.math.Quaternion attribute) ImageAtom (class in sknano.core.atoms) (class in sknano.core.atoms.image_atoms) ImageAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.image_atoms) Improper (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) improper (sknano.core.atoms.Improper attribute) (sknano.core.atoms.mixins.Improper attribute) improper_style (sknano.io.DATAFormatter attribute) (sknano.io.lammps_data.DATAFormatter attribute) Impropers (class in sknano.core.atoms) (class in sknano.core.atoms.mixins)

impropers (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.AtomTopologyMixin attribute) (sknano.core.atoms.mixins.AtomTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) ImproperStats (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) INDEX (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) init_bundle_parameters() (sknano.core.structures.NanotubeBundleMixin method) invalidate() (sknano.core.lazy_property class method) (sknano.core.meta.lazy_property class method) inverse (sknano.core.math.Quaternion attribute) IOTestFixture (class in sknano.testing) Iron (class in sknano.core.structures) IronGenerator (class in sknano.generators) iter_except() (in module sknano.core) (in module sknano.core.itertools) ix (sknano.core.atoms.image_atoms.ImageAtom attribute) (sknano.core.atoms.ImageAtom attribute) iy (sknano.core.atoms.image_atoms.ImageAtom attribute) (sknano.core.atoms.ImageAtom attribute) iz (sknano.core.atoms.image_atoms.ImageAtom attribute) (sknano.core.atoms.ImageAtom attribute)

K

KDTreeAtomsMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins)

ke (sknano.core.atoms.energy_atoms.EnergyAtom attribute) (sknano.core.atoms.EnergyAtom attribute)

L

LAMMPSDATA (in module sknano.io) (in module sknano.io.lammps_data) LAMMPSDATA2XYZConverter (in module sknano.io) (in module sknano.io.lammps_data) LAMMPSDATAFormatSpec (in module sknano.io) (in module sknano.io.lammps_data) LAMMPSDATAFormatter (in module sknano.io) (in module sknano.io.lammps_data) LAMMPSDATAIOError (in module sknano.io) (in module sknano.io.lammps_data) LAMMPSDATAReader (in module sknano.io) (in module sknano.io.lammps_data) LAMMPSDATAWriter (in module sknano.io) (in module sknano.io.lammps_data) lattice (sknano.core.atoms.lattice_atoms.LatticeAtom attribute) (sknano.core.atoms.LatticeAtom attribute) (sknano.core.crystallography.CrystalCell attribute) (sknano.core.structures.StructureMixin attribute) lattice_parameters (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) lattice_region (sknano.core.atoms.BoundingRegionsMixin attribute) (sknano.core.atoms.mixins.BoundingRegionsMixin attribute) lattice_shift (sknano.core.structures.StructureMixin attribute) lattice_vectors (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) LatticeAtom (class in sknano.core.atoms) (class in sknano.core.atoms.lattice_atoms) LatticeAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.lattice_atoms) LatticeBase (class in sknano.core.crystallography) layer_rotation_increment (sknano.apps.nanogen_gui.GrapheneModel attribute) LayeredStructureGenerator (class in sknano.generators) lazy_property (class in sknano.core) (class in sknano.core.meta) lbond (sknano.core.atoms.Angle attribute) (sknano.core.atoms.mixins.Angle attribute) length (sknano.core.atoms.Bond attribute) (sknano.core.atoms.mixins.Bond attribute) (sknano.core.math.Vector attribute) (sknano.core.math.vector.Vector attribute)

lengths (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Domain attribute) (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Parallelepiped attribute) (sknano.core.geometric_regions.Rectangle attribute) lengths_and_angles (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) linear_mass_density (sknano.core.structures.SWNTMixin attribute) ListBasedSet (class in sknano.core) (class in sknano.core.collections) listdir() (in module sknano.core) (in module sknano.core.io) listdir_dirnames() (in module sknano.core) (in module sknano.core.io) listdir_fnames() (in module sknano.core) (in module sknano.core.io) lneighbor (sknano.core.atoms.Angle attribute) (sknano.core.atoms.mixins.Angle attribute) load_bond_data() (in module sknano.core.refdata) load_fullerene_data() (in module sknano.core.structures) loadobj() (in module sknano.core) (in module sknano.core.io) logged() (in module sknano.core) (in module sknano.core.meta) LPAR (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) lx (sknano.core.crystallography.Domain attribute) (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Rectangle attribute) Lx (sknano.core.structures.NanotubeBundleMixin attribute) (sknano.core.structures.UnrolledSWNTMixin attribute) ly (sknano.core.crystallography.Domain attribute) (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Rectangle attribute) Ly (sknano.core.structures.NanotubeBundleMixin attribute) (sknano.core.structures.UnrolledSWNTMixin attribute) lz (sknano.core.crystallography.Domain attribute) (sknano.core.geometric_regions.Cuboid attribute) Lz (sknano.core.structures.MWNTMixin attribute) (sknano.core.structures.SWNTMixin attribute) Lz_list (sknano.core.structures.MWNTMixin attribute)

M

m (sknano.core.atoms.Atom attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.atoms.Atom attribute) (sknano.core.atoms.mixins.POAV1 attribute) (sknano.core.atoms.mixins.POAV2 attribute) M (sknano.core.structures.SWNTMixin attribute) m (sknano.core.structures.SWNTMixin attribute) mag (sknano.core.math.Vector attribute) (sknano.core.math.vector.Vector attribute) magnitude (sknano.core.math.Vector attribute) (sknano.core.math.vector.Vector attribute) make_sig() (in module sknano.core) (in module sknano.core.meta) make_supercell() (sknano.core.structures.StructureMixin method) map() (sknano.io.DATAData method) (sknano.io.DUMPReader method) (sknano.io.lammps_data.DATAData method) (sknano.io.lammps_dump.DUMPReader method) map_Ch() (in module sknano.core.structures) map_function() (in module sknano.core) (in module sknano.core.strings) map_operator() (in module sknano.core) (in module sknano.core.strings) mass (sknano.core.atoms.Atom attribute) (sknano.core.atoms.atoms.Atom attribute) (sknano.core.structures.MWNTMixin attribute) (sknano.core.structures.NanotubeBundleMixin attribute) (sknano.core.structures.SWNTMixin attribute) (sknano.generators.GeneratorBase attribute) matrix (sknano.core.crystallography.LatticeBase attribute) max_wall_diameter (sknano.apps.nanogen_gui.MWNTModel attribute) (sknano.core.structures.MWNTMixin attribute) max_walls (sknano.core.structures.MWNTMixin attribute) maxbox() (sknano.io.DATAData method) (sknano.io.lammps_data.DATAData method) maxtype() (sknano.io.DATAData method) (sknano.io.lammps_data.DATAData method) MDAtom (class in sknano.core.atoms) (class in sknano.core.atoms.md_atoms) MDAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.md_atoms) measure (sknano.core.atoms.mixins.Topology attribute) (sknano.core.atoms.Topology attribute) (sknano.core.geometric_regions.Geometric2DRegion attribute) (sknano.core.geometric_regions.Geometric3DRegion attribute) (sknano.core.geometric_regions.GeometricRegion attribute) memoize() (in module sknano.core) (in module sknano.core.meta)

method_func (class in sknano.core) (class in sknano.core.meta) metric_tensor (sknano.core.crystallography.LatticeBase attribute) min_wall_diameter (sknano.apps.nanogen_gui.MWNTModel attribute) (sknano.core.structures.MWNTMixin attribute) minmax() (in module sknano.core) (in module sknano.core.array) misalignment_angles (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) mol (sknano.core.atoms.id_atoms.IDAtom attribute) (sknano.core.atoms.IDAtom attribute) Molecule (class in sknano.core.atoms.molecules) moleculeID (sknano.core.atoms.id_atoms.IDAtom attribute) (sknano.core.atoms.IDAtom attribute) Molecules (class in sknano.core.atoms.molecules) molid (sknano.core.atoms.id_atoms.IDAtom attribute) (sknano.core.atoms.IDAtom attribute) MOLID (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) molid_selection_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) monoclinic() (sknano.core.crystallography.Crystal3DLattice class method) (sknano.core.crystallography.Reciprocal3DLattice class method) MoS2 (class in sknano.core.structures) MoS2Generator (class in sknano.generators) MWNT (class in sknano.core.structures) MWNTBase (class in sknano.core.structures) MWNTGenerator (class in sknano.generators) MWNTGeneratorBase (class in sknano.generators) MWNTMixin (class in sknano.core.structures) MWNTModel (class in sknano.apps.nanogen_gui)

N

n (sknano.core.atoms.mixins.POAV1 attribute) (sknano.core.atoms.POAV1 attribute) N (sknano.core.structures.Fullerene attribute) (sknano.core.structures.Fullerenes attribute) (sknano.core.structures.GrapheneMixin attribute) (sknano.core.structures.SWNTMixin attribute) n (sknano.core.structures.SWNTMixin attribute) n1 (sknano.core.atoms.mixins.POAV2 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.structures.GrapheneMixin attribute) n2 (sknano.core.atoms.mixins.POAV2 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.structures.GrapheneMixin attribute) n3 (sknano.core.atoms.mixins.POAV2 attribute) (sknano.core.atoms.POAV2 attribute) NaClGenerator (in module sknano.generators) NaClStructure (in module sknano.core.structures) NAME (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) name (sknano.core.structures.Fullerene attribute) nanogen() (in module sknano.scripts) (in module sknano.scripts.nanogen) nanogen_parser() (in module sknano.scripts) NanoGenModel (class in sknano.apps.nanogen_gui) NanoStructureBase (class in sknano.core.structures) NanoStructureGenerator (class in sknano.generators) Nanotube (in module sknano.core.structures) NanotubeBundleBase (class in sknano.core.structures) NanotubeBundleGeneratorBase (class in sknano.generators) NanotubeBundleMixin (class in sknano.core.structures) NanotubeMixin (in module sknano.core.structures) NanotubeUnitCell (class in sknano.core.structures) Natoms (sknano.core.structures.Fullerene attribute) (sknano.core.structures.GrapheneMixin attribute) (sknano.core.structures.MWNTMixin attribute) (sknano.core.structures.NanotubeBundleMixin attribute) (sknano.core.structures.SWNTMixin attribute) (sknano.generators.GeneratorBase attribute) Natoms_list (sknano.core.structures.MWNTMixin attribute) (sknano.core.structures.NanotubeBundleMixin attribute) Natoms_per_bundle (sknano.core.structures.NanotubeBundleMixin attribute) Natoms_per_layer (sknano.core.structures.GrapheneMixin attribute) Natoms_per_tube (sknano.core.structures.MWNTMixin attribute) (sknano.core.structures.NanotubeBundleMixin attribute) (sknano.core.structures.SWNTMixin attribute) Natoms_per_unit_cell (sknano.core.structures.GrapheneMixin attribute) (sknano.core.structures.SWNTMixin attribute) Natoms_per_wall (sknano.core.structures.MWNTMixin attribute) ncycles() (in module sknano.core) (in module sknano.core.itertools) ndim (sknano.core.geometric_regions.Geometric2DRegion attribute) (sknano.core.geometric_regions.Geometric3DRegion attribute) (sknano.core.geometric_regions.GeometricRegion attribute) neighbor_distances (sknano.core.atoms.neighbor_atoms.NeighborAtom attribute) (sknano.core.atoms.NeighborAtom attribute)

neighbor_map (sknano.core.atoms.neighbor_atoms.NeighborAtom attribute) (sknano.core.atoms.NeighborAtom attribute) NeighborAtom (class in sknano.core.atoms) (class in sknano.core.atoms.neighbor_atoms) NeighborAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.neighbor_atoms) neighbors (sknano.core.atoms.neighbor_atoms.NeighborAtom attribute) (sknano.core.atoms.NeighborAtom attribute) new_dumpattr() (sknano.io.DUMPReader method) (sknano.io.lammps_dump.DUMPReader method) newcolumn() (sknano.io.DUMPReader method) (sknano.io.lammps_dump.DUMPReader method) newxyz() (sknano.io.DATAData method) (sknano.io.lammps_data.DATAData method) Niso (sknano.core.structures.Fullerene attribute) Nisomers (sknano.core.structures.Fullerene attribute) nlayers (sknano.apps.nanogen_gui.GrapheneModel attribute) (sknano.core.structures.UnrolledSWNTMixin attribute) NN (sknano.core.atoms.neighbor_atoms.NeighborAtom attribute) (sknano.core.atoms.NeighborAtom attribute) Nneighbors (sknano.core.atoms.neighbor_atoms.NeighborAtom attribute) (sknano.core.atoms.NeighborAtom attribute) NoInstances (class in sknano.core) (class in sknano.core.meta) NONE (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) none_selection_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) norm (sknano.core.math.Quaternion attribute) (sknano.core.math.Vector attribute) (sknano.core.math.vector.Vector attribute) normalize() (sknano.core.math.Vector method) (sknano.core.math.vector.Vector method) NOT (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) notify_observers() (sknano.apps.nanogen_gui.ObserverModelMixin method) nselect (sknano.core.atoms.Snapshot attribute) (sknano.core.atoms.trajectory.Snapshot attribute) nselected (sknano.core.atoms.Snapshot attribute) (sknano.core.atoms.trajectory.Snapshot attribute) nth() (in module sknano.core) (in module sknano.core.itertools) Ntubes (sknano.core.structures.NanotubeBundleMixin attribute) NullVector (class in sknano.core.math) (class in sknano.core.math.vector) NUMBONDS (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) Nwalls (sknano.apps.nanogen_gui.MWNTModel attribute) (sknano.core.structures.MWNTMixin attribute) nx (sknano.core.structures.NanotubeBundleMixin attribute) (sknano.core.structures.UnrolledSWNTMixin attribute) ny (sknano.core.structures.NanotubeBundleMixin attribute) (sknano.core.structures.UnrolledSWNTMixin attribute) nz (sknano.core.structures.MWNTMixin attribute) (sknano.core.structures.SWNTMixin attribute) nz_list (sknano.core.structures.MWNTMixin attribute)

O

o (sknano.core.geometric_regions.Parallelepiped attribute) (sknano.core.geometric_regions.Parallelogram attribute) obj_mro_str() (in module sknano.core) (in module sknano.core.strings) oblique() (sknano.core.crystallography.Crystal2DLattice class method) (sknano.core.crystallography.Reciprocal2DLattice class method) ObserverModelMixin (class in sknano.apps.nanogen_gui) OF (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) offset (sknano.core.crystallography.LatticeBase attribute) optional_debug() (in module sknano.core) (in module sknano.core.meta)

OR (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) order (sknano.core.atoms.Bond attribute) (sknano.core.atoms.mixins.Bond attribute) ordinal_form() (in module sknano.core) (in module sknano.core.strings) origin (sknano.core.atoms.Bond attribute) (sknano.core.atoms.mixins.Bond attribute) ortho_matrix (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.LatticeBase attribute) orthorhombic() (sknano.core.crystallography.Crystal3DLattice class method) (sknano.core.crystallography.Reciprocal3DLattice class method) otherattrs (sknano.io.DUMPFormatter attribute) (sknano.io.lammps_dump.DUMPFormatter attribute)

P

p (sknano.core.atoms.dipole_atoms.DipoleAtom attribute) (sknano.core.atoms.DipoleAtom attribute) (sknano.core.math.Vector attribute) (sknano.core.math.vector.Vector attribute) p0 (sknano.core.math.Vector attribute) (sknano.core.math.vector.Vector attribute) p1 (sknano.core.geometric_regions.Cone attribute) (sknano.core.geometric_regions.Cylinder attribute) (sknano.core.geometric_regions.Triangle attribute) p2 (sknano.core.geometric_regions.Cone attribute) (sknano.core.geometric_regions.Cylinder attribute) (sknano.core.geometric_regions.Triangle attribute) p3 (sknano.core.geometric_regions.Triangle attribute) padnone() (in module sknano.core) (in module sknano.core.itertools) pair_style (sknano.io.DATAFormatter attribute) (sknano.io.lammps_data.DATAFormatter attribute) pairwise() (in module sknano.core) (in module sknano.core.itertools) Parallelepiped (class in sknano.core.geometric_regions) PARALLELEPIPED (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) parallelepiped (sknano.testing.Geometric3DRegionsTestFixture attribute) Parallelogram (class in sknano.core.geometric_regions) parallelogram (sknano.testing.Geometric2DRegionsTestFixture attribute) parse() (sknano.core.atoms.SelectionParser method) (sknano.core.atoms.selections.SelectionParser method) partition() (in module sknano.core) (in module sknano.core.itertools) partner() (sknano.core.atoms.Bond method) (sknano.core.atoms.mixins.Bond method) pbc (sknano.core.atoms.mixins.PBCAtomsMixin attribute) (sknano.core.atoms.PBCAtomsMixin attribute) pbc_diff() (in module sknano.core.crystallography) PBCAtomsMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) PDB (in module sknano.io) (in module sknano.io.pdb) pdb_reader (sknano.testing.IOTestFixture attribute) PDBData (class in sknano.io) (class in sknano.io.pdb) pdbdata (sknano.testing.IOTestFixture attribute) PDBError, [1] PDBFormatSpec (in module sknano.io) (in module sknano.io.pdb) PDBFormatter (class in sknano.io) (class in sknano.io.pdb) PDBIO (in module sknano.io) (in module sknano.io.pdb) PDBIOError (in module sknano.io) (in module sknano.io.pdb) PDBIOFormatter (in module sknano.io) (in module sknano.io.pdb) PDBIOReader (in module sknano.io) (in module sknano.io.pdb) PDBIOWriter (in module sknano.io) (in module sknano.io.pdb) PDBReader (class in sknano.io) (class in sknano.io.pdb) PDBTokenizer (class in sknano.io.tokenizers) PDBWriter (class in sknano.io) (class in sknano.io.pdb)

pe (sknano.core.atoms.energy_atoms.EnergyAtom attribute) (sknano.core.atoms.EnergyAtom attribute) periodic_table (sknano.testing.AtomsTestFixture attribute) PeriodicCKDTree (class in sknano.core.analysis) PeriodicKDTree (class in sknano.core.analysis) PG (sknano.core.structures.Fullerene attribute) plural_word_check() (in module sknano.core) (in module sknano.core.strings) pluralize() (in module sknano.core) (in module sknano.core.strings) pmax (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.GeometricRegion attribute) (sknano.core.geometric_regions.Rectangle attribute) pmin (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.GeometricRegion attribute) (sknano.core.geometric_regions.Rectangle attribute) POAV (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) POAV1 (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) (sknano.core.atoms.POAVAtomMixin attribute) (sknano.core.atoms.POAVAtomsMixin attribute) (sknano.core.atoms.mixins.POAVAtomMixin attribute) (sknano.core.atoms.mixins.POAVAtomsMixin attribute) POAV2 (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) (sknano.core.atoms.POAVAtomMixin attribute) (sknano.core.atoms.POAVAtomsMixin attribute) (sknano.core.atoms.mixins.POAVAtomMixin attribute) (sknano.core.atoms.mixins.POAVAtomsMixin attribute) POAVAtomMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) POAVAtomsMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) POAVdict() (sknano.core.atoms.mixins.POAV method) (sknano.core.atoms.POAV method) (sknano.core.atoms.POAV1 method) (sknano.core.atoms.POAV2 method) (sknano.core.atoms.mixins.POAV1 method) (sknano.core.atoms.mixins.POAV2 method) POAVR (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) (sknano.core.atoms.POAVAtomMixin attribute) (sknano.core.atoms.POAVAtomsMixin attribute) (sknano.core.atoms.mixins.POAVAtomMixin attribute) (sknano.core.atoms.mixins.POAVAtomsMixin attribute) Point (class in sknano.core.math) (class in sknano.core.math.point) point_groups (sknano.core.structures.Fullerene attribute) PointDefect (class in sknano.core.structures) PointGroup (class in sknano.utils.symmetry) Points (class in sknano.core.math) (class in sknano.core.math.points) points (sknano.core.geometric_regions.GeometricRegion attribute) powerset() (in module sknano.core) (in module sknano.core.itertools) PrimitiveCellGraphene (class in sknano.core.structures) PrimitiveCellGrapheneGenerator (class in sknano.generators) print_dumpattrs() (sknano.testing.DUMPTestFixture method) print_regions() (sknano.testing.GeometricRegionsTestFixture method) projection() (in module sknano.core.math) (in module sknano.core.math.vector) (sknano.core.math.Vector method) (sknano.core.math.vector.Vector method) px (sknano.core.atoms.dipole_atoms.DipoleAtom attribute) (sknano.core.atoms.DipoleAtom attribute) py (sknano.core.atoms.dipole_atoms.DipoleAtom attribute) (sknano.core.atoms.DipoleAtom attribute) py_find_rings() (in module sknano.core.analysis) pymatgen_structure() (in module sknano.core.structures) pyramidalization_angles (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) pz (sknano.core.atoms.dipole_atoms.DipoleAtom attribute) (sknano.core.atoms.DipoleAtom attribute)

Q

q (sknano.core.atoms.charged_atoms.ChargedAtom attribute) (sknano.core.atoms.ChargedAtom attribute) quantify() (in module sknano.core) (in module sknano.core.itertools) Quaternion (class in sknano.core.math) query() (sknano.core.analysis.PeriodicCKDTree method)

query_atom_tree() (sknano.core.atoms.KDTreeAtomsMixin method) (sknano.core.atoms.mixins.KDTreeAtomsMixin method) query_ball_point() (sknano.core.analysis.PeriodicCKDTree method) (sknano.core.atoms.KDTreeAtomsMixin method) (sknano.core.atoms.mixins.KDTreeAtomsMixin method) query_ball_tree() (sknano.core.atoms.KDTreeAtomsMixin method) (sknano.core.atoms.mixins.KDTreeAtomsMixin method) query_pairs() (sknano.core.atoms.KDTreeAtomsMixin method) (sknano.core.atoms.mixins.KDTreeAtomsMixin method)

R

r (sknano.core.atoms.xyz_atoms.XYZAtom attribute) (sknano.core.atoms.XYZAtom attribute) (sknano.core.geometric_regions.Circle attribute) (sknano.core.geometric_regions.Cone attribute) (sknano.core.geometric_regions.Cylinder attribute) (sknano.core.geometric_regions.Sphere attribute) R (sknano.core.structures.SWNTMixin attribute) r0 (sknano.core.atoms.xyz_atoms.XYZAtom attribute) (sknano.core.atoms.XYZAtom attribute) R1 (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) r1 (sknano.core.structures.GrapheneMixin attribute) R2 (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) r2 (sknano.core.structures.GrapheneMixin attribute) R3 (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) r_vdw (sknano.core.atoms.VanDerWaalsAtom attribute) (sknano.core.atoms.vdW_atoms.VanDerWaalsAtom attribute) random_combination() (in module sknano.core) (in module sknano.core.itertools) random_combination_with_replacement() (in module sknano.core) (in module sknano.core.itertools) random_permutation() (in module sknano.core) (in module sknano.core.itertools) random_product() (in module sknano.core) (in module sknano.core.itertools) rbond (sknano.core.atoms.Angle attribute) (sknano.core.atoms.mixins.Angle attribute) read() (sknano.io.DATAReader method) (sknano.io.DUMPReader method) (sknano.io.PDBReader method) (sknano.io.StructureDataReader class method) (sknano.io.StructureDataReaderMixin method) (sknano.io.XYZReader method) (sknano.io.lammps_data.DATAReader method) (sknano.io.lammps_dump.DUMPReader method) (sknano.io.pdb.PDBReader method) (sknano.io.xyz.XYZReader method) read_data() (sknano.io.StructureDataReaderMixin method) read_dump() (sknano.io.StructureDataReaderMixin method) read_pdb() (sknano.io.StructureDataReaderMixin method) read_snapshot() (sknano.io.DUMPReader method) (sknano.io.lammps_dump.DUMPReader method) read_xyz() (sknano.io.StructureDataReaderMixin method) real (sknano.core.math.Quaternion attribute) Reciprocal2DLattice (class in sknano.core.crystallography) Reciprocal2DLatticeMixin (class in sknano.core.crystallography) Reciprocal3DLattice (class in sknano.core.crystallography) Reciprocal3DLatticeMixin (class in sknano.core.crystallography) reciprocal_lattice (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) reciprocal_v1 (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) reciprocal_v2 (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) reciprocal_v3 (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) ReciprocalLatticeBase (class in sknano.core.crystallography) ReciprocalLatticeMixin (in module sknano.core.crystallography) record_dict() (sknano.io.pdb.PDBFormatter method) (sknano.io.PDBFormatter method) Rectangle (class in sknano.core.geometric_regions) rectangle (sknano.testing.Geometric2DRegionsTestFixture attribute) rectangular() (sknano.core.crystallography.Crystal2DLattice class method) (sknano.core.crystallography.Reciprocal2DLattice class method) RectangularCellGraphene (in module sknano.core.structures) RectangularCellGrapheneGenerator (in module sknano.generators) RectangularGraphene (in module sknano.core.structures) RectangularGrapheneGenerator (in module sknano.generators) reference_atom (sknano.core.atoms.md_atoms.MDAtom attribute) (sknano.core.atoms.MDAtom attribute) reference_atom_bonds (sknano.core.atoms.md_atoms.MDAtom attribute) (sknano.core.atoms.MDAtom attribute) reference_atom_neighbors (sknano.core.atoms.md_atoms.MDAtom attribute) (sknano.core.atoms.MDAtom attribute) reference_index (sknano.io.DUMPReader attribute) (sknano.io.lammps_dump.DUMPReader attribute) reference_timestep (sknano.io.DUMPReader attribute) (sknano.io.lammps_dump.DUMPReader attribute) reflection_matrix() (in module sknano.core.math) (in module sknano.core.math.transforms) region (sknano.core.crystallography.LatticeBase attribute)

region_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) REGIONS (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) register_observer() (sknano.apps.nanogen_gui.ObserverModelMixin method) rejection() (in module sknano.core.math) (in module sknano.core.math.vector) (sknano.core.math.Vector method) (sknano.core.math.vector.Vector method) remapdumpattrs() (sknano.io.DUMPFormatter method) (sknano.io.lammps_dump.DUMPFormatter method) remove_observer() (sknano.apps.nanogen_gui.ObserverModelMixin method) removed_package_warning() (in module sknano.core) (in module sknano.core.meta) reorder() (sknano.io.DATAData method) (sknano.io.lammps_data.DATAData method) repeatfunc() (in module sknano.core) (in module sknano.core.itertools) replace() (sknano.io.DATAData method) (sknano.io.lammps_data.DATAData method) reset() (sknano.testing.Timer method) reset_attrs() (sknano.core.atoms.Atom method) (sknano.core.atoms.POAVAtomsMixin method) (sknano.core.atoms.RingAtomsMixin method) (sknano.core.atoms.atoms.Atom method) (sknano.core.atoms.mixins.POAVAtomsMixin method) (sknano.core.atoms.mixins.RingAtomsMixin method) reset_poav_atoms_attrs() (sknano.core.atoms.mixins.POAVAtomsMixin method) (sknano.core.atoms.POAVAtomsMixin method) reset_ring_atoms_attrs() (sknano.core.atoms.mixins.RingAtomsMixin method) (sknano.core.atoms.RingAtomsMixin method) RESIDUE (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) rezero() (in module sknano.core) (in module sknano.core.array) (sknano.core.atoms.Atom method) (sknano.core.atoms.DipoleAtom method) (sknano.core.atoms.ForceAtom method) (sknano.core.atoms.VelocityAtom method) (sknano.core.atoms.XYZAtom method) (sknano.core.atoms.atoms.Atom method) (sknano.core.atoms.dipole_atoms.DipoleAtom method) (sknano.core.atoms.force_atoms.ForceAtom method) (sknano.core.atoms.molecules.Molecule method) (sknano.core.atoms.velocity_atoms.VelocityAtom method) (sknano.core.atoms.xyz_atoms.XYZAtom method) (sknano.core.math.Point method) (sknano.core.math.Vector method) (sknano.core.math.point.Point method) (sknano.core.math.vector.Vector method) (sknano.core.structures.Composition method) rezero_array() (in module sknano.core) (in module sknano.core.array) rezero_components() (sknano.core.math.Vector method) (sknano.core.math.vector.Vector method) rezero_coords() (sknano.core.atoms.xyz_atoms.XYZAtom method) (sknano.core.atoms.XYZAtom method) (sknano.core.math.Point method) (sknano.core.math.point.Point method) rezero_xyz() (sknano.core.atoms.xyz_atoms.XYZAtom method) (sknano.core.atoms.XYZAtom method) ring_stats (sknano.core.atoms.mixins.RingAtomsMixin attribute) (sknano.core.atoms.RingAtomsMixin attribute) RingAtomMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) RingAtomsMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) rings_per_atom (sknano.core.atoms.mixins.RingAtomsMixin attribute) (sknano.core.atoms.RingAtomsMixin attribute) Rn_counter (sknano.core.atoms.mixins.RingAtomsMixin attribute) (sknano.core.atoms.RingAtomsMixin attribute) rneighbor (sknano.core.atoms.Angle attribute) (sknano.core.atoms.mixins.Angle attribute) RocksaltGenerator (class in sknano.generators) RocksaltStructure (class in sknano.core.structures) RockSaltStructure (in module sknano.core.structures) RocksaltStructureGenerator (in module sknano.generators) rotate() (in module sknano.core.math) (in module sknano.core.math.transforms) (sknano.core.atoms.AtomTransformationsMixin method) (sknano.core.atoms.AtomsTransformationsMixin method) (sknano.core.atoms.DipoleAtom method) (sknano.core.atoms.ForceAtom method) (sknano.core.atoms.Topology method) (sknano.core.atoms.VelocityAtom method) (sknano.core.atoms.dipole_atoms.DipoleAtom method) (sknano.core.atoms.force_atoms.ForceAtom method) (sknano.core.atoms.mixins.AtomTransformationsMixin method) (sknano.core.atoms.mixins.AtomsTransformationsMixin method) (sknano.core.atoms.mixins.Topology method) (sknano.core.atoms.molecules.Molecule method) (sknano.core.atoms.velocity_atoms.VelocityAtom method) (sknano.core.crystallography.CrystalCell method) (sknano.core.crystallography.LatticeBase method) (sknano.core.crystallography.UnitCell method) (sknano.core.geometric_regions.GeometricTransformsMixin method) (sknano.core.math.Point method) (sknano.core.math.Vector method) (sknano.core.math.point.Point method) (sknano.core.math.vector.Vector method) (sknano.core.structures.Composition method) (sknano.core.structures.StructureMixin method) rotation_matrix() (in module sknano.core.math) (in module sknano.core.math.transforms) rotation_matrix_from_augmented_matrix() (in module sknano.core.math) (in module sknano.core.math.transforms) roundrobin() (in module sknano.core) (in module sknano.core.itertools) row_matrix (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) (sknano.core.math.point.Point attribute) (sknano.core.math.vector.Vector attribute) RPAR (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) rs (sknano.core.atoms.lattice_atoms.LatticeAtom attribute) (sknano.core.atoms.LatticeAtom attribute) rt (sknano.core.structures.MWNTMixin attribute) (sknano.core.structures.SWNTMixin attribute) rt_list (sknano.core.structures.MWNTMixin attribute) running (sknano.testing.Timer attribute) rx (sknano.core.geometric_regions.Ellipse attribute) (sknano.core.geometric_regions.Ellipsoid attribute) Rx() (in module sknano.core.math) (in module sknano.core.math.transforms) ry (sknano.core.geometric_regions.Ellipse attribute) (sknano.core.geometric_regions.Ellipsoid attribute) Ry() (in module sknano.core.math) (in module sknano.core.math.transforms) rz (sknano.core.geometric_regions.Ellipsoid attribute) Rz() (in module sknano.core.math) (in module sknano.core.math.transforms)

S

save() (sknano.generators.ConventionalCellGrapheneGenerator method) (sknano.generators.CrystalStructureGenerator method) (sknano.generators.FullereneGenerator method) (sknano.generators.GeneratorBase method) (sknano.generators.GrapheneGeneratorBase method) (sknano.generators.LayeredStructureGenerator method) (sknano.generators.MWNTGenerator method) (sknano.generators.PrimitiveCellGrapheneGenerator method) (sknano.generators.SWNTGenerator method) (sknano.generators.UnrolledSWNTGenerator method) scalar_projection() (in module sknano.core.math) (in module sknano.core.math.vector) scalar_triple_product() (in module sknano.core.math) (in module sknano.core.math.vector) scale() (sknano.core.math.Vector method) (sknano.core.math.vector.Vector method) (sknano.io.DUMPReader method) (sknano.io.lammps_dump.DUMPReader method) scaling_matrix (sknano.core.crystallography.CrystalCell attribute) (sknano.core.structures.StructureMixin attribute) scaling_matrix() (in module sknano.core.math) (in module sknano.core.math.transforms) second_neighbors (sknano.core.atoms.neighbor_atoms.NeighborAtom attribute) (sknano.core.atoms.NeighborAtom attribute) sections (sknano.io.DATAReader attribute) (sknano.io.lammps_data.DATAReader attribute) selected (sknano.core.atoms.Snapshot attribute) (sknano.core.atoms.trajectory.Snapshot attribute) selection_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) SelectionException, [1] SelectionParser (class in sknano.core.atoms) (class in sknano.core.atoms.selections) serial (sknano.core.atoms.id_atoms.IDAtom attribute) (sknano.core.atoms.IDAtom attribute) SERIAL (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) set_nth_nearest_neighbors() (sknano.core.atoms.neighbor_atoms.NeighborAtom method) (sknano.core.atoms.NeighborAtom method) set_pbc() (sknano.core.atoms.mixins.PBCAtomsMixin method) (sknano.core.atoms.PBCAtomsMixin method) setUp() (sknano.testing.GeometricRegionsTestFixture method) (sknano.testing.TempfileTestFixture method) sigma_pi_angles (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) sin_alpha (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Direct3DLatticeMixin attribute) sin_alpha_star (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.crystallography.Reciprocal3DLatticeMixin attribute) sin_beta (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Direct3DLatticeMixin attribute) sin_beta_star (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.crystallography.Reciprocal3DLatticeMixin attribute) sin_gamma (sknano.core.crystallography.Crystal2DLattice attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.crystallography.Direct2DLatticeMixin attribute) (sknano.core.crystallography.Direct3DLatticeMixin attribute) sin_gamma_star (sknano.core.crystallography.Reciprocal2DLattice attribute) (sknano.core.crystallography.Reciprocal2DLatticeMixin attribute) (sknano.core.crystallography.Reciprocal3DLattice attribute) (sknano.core.crystallography.Reciprocal3DLatticeMixin attribute) Singleton (class in sknano.core) (class in sknano.core.meta) sknano() (in module sknano.scripts) sknano.apps.nanogen_gui (module) sknano.core (module) sknano.core.analysis (module) sknano.core.array (module) sknano.core.atoms (module) sknano.core.atoms.atoms (module) sknano.core.atoms.basis_atoms (module) sknano.core.atoms.charged_atoms (module) sknano.core.atoms.cn_atoms (module) sknano.core.atoms.dipole_atoms (module) sknano.core.atoms.energy_atoms (module) sknano.core.atoms.force_atoms (module) sknano.core.atoms.id_atoms (module) sknano.core.atoms.image_atoms (module) sknano.core.atoms.lattice_atoms (module) sknano.core.atoms.md_atoms (module) sknano.core.atoms.mixins (module) sknano.core.atoms.molecules (module) sknano.core.atoms.neighbor_atoms (module) sknano.core.atoms.selections (module) sknano.core.atoms.structure_atoms (module) sknano.core.atoms.trajectory (module) sknano.core.atoms.type_atoms (module) sknano.core.atoms.vdW_atoms (module) sknano.core.atoms.velocity_atoms (module) sknano.core.atoms.xyz_atoms (module) sknano.core.collections (module) sknano.core.crystallography (module) sknano.core.geometric_regions (module) sknano.core.io (module) sknano.core.itertools (module) sknano.core.math (module) sknano.core.math.point (module) sknano.core.math.points (module) sknano.core.math.transforms (module) sknano.core.math.vector (module) sknano.core.math.vectors (module) sknano.core.meta (module) sknano.core.physics (module) sknano.core.refdata (module) sknano.core.strings (module) sknano.core.structures (module)

sknano.data (module) sknano.generators (module) sknano.io (module) sknano.io.lammps_data (module) sknano.io.lammps_dump (module) sknano.io.pdb (module) sknano.io.tokenizers (module), [1] sknano.io.xyz (module) sknano.scripts (module) sknano.scripts.nanogen (module) sknano.scripts.nanogenui (module) sknano.testing (module) sknano.utils (module) sknano.utils.analysis (module) sknano.utils.symmetry (module) sknano_parser() (in module sknano.scripts) Snapshot (class in sknano.core.atoms) (class in sknano.core.atoms.trajectory) SpaceGroup (class in sknano.utils.symmetry) SphaleriteStructure (in module sknano.core.structures) Sphere (class in sknano.core.geometric_regions) SPHERE (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) sphere (sknano.testing.Geometric3DRegionsTestFixture attribute) Square (class in sknano.core.geometric_regions) square (sknano.testing.Geometric2DRegionsTestFixture attribute) square() (sknano.core.crystallography.Crystal2DLattice class method) (sknano.core.crystallography.Reciprocal2DLattice class method) start() (sknano.testing.Timer method) stop() (sknano.testing.Timer method) strain (sknano.core.atoms.mixins.Topology attribute) (sknano.core.atoms.Topology attribute) structure (sknano.core.structures.StructureMixin attribute) (sknano.testing.AtomsTestFixture attribute) StructureAnalyzer (class in sknano.utils.analysis) StructureAtom (class in sknano.core.atoms) (class in sknano.core.atoms.structure_atoms) StructureAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.structure_atoms) StructureBase (class in sknano.core.structures) StructureData (class in sknano.io) StructureDataConverter (class in sknano.io) StructureDataError StructureDataFormatter (class in sknano.io) StructureDataMixin (class in sknano.io) StructureDataReader (class in sknano.io) StructureDataReaderMixin (class in sknano.io) StructureDataWriter (class in sknano.io) StructureDataWriterMixin (class in sknano.io) StructureFormatSpec (in module sknano.io) StructureIO (in module sknano.io) StructureIOConverter (in module sknano.io) StructureIOError (in module sknano.io) StructureIOFormatter (in module sknano.io) StructureIOMixin (in module sknano.io) StructureIOReader (in module sknano.io) StructureIOReaderMixin (in module sknano.io) StructureIOWriter (in module sknano.io) StructureIOWriterMixin (in module sknano.io) StructureMixin (class in sknano.core.structures) StructureReader (in module sknano.io) StructureReaderMixin (in module sknano.io) StructureWriter (in module sknano.io) StructureWriterMixin (in module sknano.io) style (sknano.io.DUMPFormatter attribute) (sknano.io.lammps_dump.DUMPFormatter attribute) SuperCell (class in sknano.core.crystallography) supercell_lattice_points() (in module sknano.core.crystallography) SWNT (class in sknano.core.structures) swnt (sknano.testing.AtomsTestFixture attribute) SWNTBase (class in sknano.core.structures) SWNTGenerator (class in sknano.generators) SWNTGeneratorBase (class in sknano.generators) SWNTMixin (class in sknano.core.structures) SWNTModel (class in sknano.apps.nanogen_gui) symbol (sknano.core.atoms.Atom attribute) (sknano.core.atoms.atoms.Atom attribute)

T

T (sknano.core.atoms.mixins.POAV attribute) t (sknano.core.atoms.mixins.POAV attribute) T (sknano.core.atoms.mixins.POAV2 attribute) (sknano.core.atoms.POAV attribute) (sknano.core.atoms.mixins.POAVR attribute) t (sknano.core.atoms.POAV attribute) T (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) (sknano.core.structures.SWNTMixin attribute) t1 (sknano.core.structures.SWNTMixin attribute) t2 (sknano.core.structures.SWNTMixin attribute) T_list (sknano.core.structures.MWNTMixin attribute) tabulate() (in module sknano.core) (in module sknano.core.itertools) TabulateMixin (class in sknano.core) (class in sknano.core.strings) tail() (in module sknano.core) (in module sknano.core.itertools) take() (in module sknano.core) (in module sknano.core.itertools) tearDown() (sknano.testing.GeometricRegionsTestFixture method) (sknano.testing.TempfileTestFixture method) TempfileTestFixture (class in sknano.testing) tetragonal() (sknano.core.crystallography.Crystal3DLattice class method) (sknano.core.crystallography.Reciprocal3DLattice class method) third_neighbors (sknano.core.atoms.neighbor_atoms.NeighborAtom attribute) (sknano.core.atoms.NeighborAtom attribute) tilt_factors (sknano.core.crystallography.Domain attribute) Timer (class in sknano.testing) timethis() (in module sknano.core) (in module sknano.core.meta) todict() (sknano.core.atoms.Angle method) (sknano.core.BaseClass method) (sknano.core.atoms.AngularTopology method) (sknano.core.atoms.Atom method) (sknano.core.atoms.Bond method) (sknano.core.atoms.CNAtom method) (sknano.core.atoms.ChargedAtom method) (sknano.core.atoms.Dihedral method) (sknano.core.atoms.DipoleAtom method) (sknano.core.atoms.EnergyAtom method) (sknano.core.atoms.ForceAtom method) (sknano.core.atoms.IDAtom method) (sknano.core.atoms.ImageAtom method) (sknano.core.atoms.Improper method) (sknano.core.atoms.LatticeAtom method) (sknano.core.atoms.MDAtom method) (sknano.core.atoms.NeighborAtom method) (sknano.core.atoms.POAV method) (sknano.core.atoms.SelectionParser method) (sknano.core.atoms.Snapshot method) (sknano.core.atoms.Topology method) (sknano.core.atoms.TypeAtom method) (sknano.core.atoms.VanDerWaalsAtom method) (sknano.core.atoms.VelocityAtom method) (sknano.core.atoms.XYZAtom method) (sknano.core.atoms.atoms.Atom method) (sknano.core.atoms.charged_atoms.ChargedAtom method) (sknano.core.atoms.cn_atoms.CNAtom method) (sknano.core.atoms.dipole_atoms.DipoleAtom method) (sknano.core.atoms.energy_atoms.EnergyAtom method) (sknano.core.atoms.force_atoms.ForceAtom method) (sknano.core.atoms.id_atoms.IDAtom method) (sknano.core.atoms.image_atoms.ImageAtom method) (sknano.core.atoms.lattice_atoms.LatticeAtom method) (sknano.core.atoms.md_atoms.MDAtom method) (sknano.core.atoms.mixins.Angle method) (sknano.core.atoms.mixins.AngularTopology method) (sknano.core.atoms.mixins.Bond method) (sknano.core.atoms.mixins.Dihedral method) (sknano.core.atoms.mixins.Improper method) (sknano.core.atoms.mixins.POAV method) (sknano.core.atoms.mixins.Topology method) (sknano.core.atoms.molecules.Molecule method) (sknano.core.atoms.neighbor_atoms.NeighborAtom method) (sknano.core.atoms.selections.SelectionParser method) (sknano.core.atoms.trajectory.Snapshot method) (sknano.core.atoms.type_atoms.TypeAtom method) (sknano.core.atoms.vdW_atoms.VanDerWaalsAtom method) (sknano.core.atoms.velocity_atoms.VelocityAtom method) (sknano.core.atoms.xyz_atoms.XYZAtom method) (sknano.core.crystallography.Crystal2DLattice method) (sknano.core.crystallography.Crystal3DLattice method) (sknano.core.crystallography.CrystalCell method) (sknano.core.crystallography.Domain method) (sknano.core.crystallography.Reciprocal2DLattice method) (sknano.core.crystallography.Reciprocal3DLattice method) (sknano.core.crystallography.UnitCell method) (sknano.core.geometric_regions.Circle method) (sknano.core.geometric_regions.Cone method) (sknano.core.geometric_regions.Cube method) (sknano.core.geometric_regions.Cuboid method) (sknano.core.geometric_regions.Cylinder method) (sknano.core.geometric_regions.Ellipse method) (sknano.core.geometric_regions.Ellipsoid method) (sknano.core.geometric_regions.Parallelepiped method) (sknano.core.geometric_regions.Parallelogram method) (sknano.core.geometric_regions.Rectangle method) (sknano.core.geometric_regions.Sphere method) (sknano.core.geometric_regions.Square method) (sknano.core.geometric_regions.Triangle method) (sknano.core.meta.BaseClass method) (sknano.core.structures.Composition method) (sknano.core.structures.ConventionalCellGraphene method) (sknano.core.structures.CrystalStructureBase method) (sknano.core.structures.Fullerene method) (sknano.core.structures.GrapheneBase method) (sknano.core.structures.MWNTBase method) (sknano.core.structures.NanoStructureBase method) (sknano.core.structures.NanotubeBundleBase method) (sknano.core.structures.PointDefect method) (sknano.core.structures.PrimitiveCellGraphene method) (sknano.core.structures.SWNTBase method) (sknano.core.structures.UnrolledSWNTBase method) (sknano.generators.GeneratorConfigParser method) (sknano.generators.LayeredStructureGenerator method) (sknano.io.DATAFormatter method) (sknano.io.DATAReader method) (sknano.io.DUMPFormatter method) (sknano.io.DUMPReader method) (sknano.io.PDBFormatter method) (sknano.io.StructureData method) (sknano.io.StructureDataConverter method) (sknano.io.StructureDataFormatter method) (sknano.io.XYZFormatter method) (sknano.io.lammps_data.DATAFormatter method) (sknano.io.lammps_data.DATAReader method) (sknano.io.lammps_dump.DUMPFormatter method) (sknano.io.lammps_dump.DUMPReader method) (sknano.io.pdb.PDBFormatter method) (sknano.io.xyz.XYZFormatter method) tolist() (sknano.core.math.Point method) (sknano.core.math.Quaternion method) (sknano.core.math.Vector method) (sknano.core.math.point.Point method) (sknano.core.math.vector.Vector method) Topology (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) topology_stats (sknano.core.atoms.AtomsTopologyMixin attribute) (sknano.core.atoms.mixins.AtomsTopologyMixin attribute) TopologyCollection (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) TopologyStats (class in sknano.core.atoms) (class in sknano.core.atoms.mixins)

totient_func() (in module sknano.core.math) Trajectory (class in sknano.core.atoms) (class in sknano.core.atoms.trajectory) trajectory (sknano.io.DUMPReader attribute) (sknano.io.lammps_dump.DUMPReader attribute) transform_lattice() (sknano.core.structures.StructureMixin method) transformation_matrix() (in module sknano.core.math) (in module sknano.core.math.transforms) translate() (sknano.core.atoms.AtomsTransformationsMixin method) (sknano.core.atoms.AtomTransformationsMixin method) (sknano.core.atoms.mixins.AtomTransformationsMixin method) (sknano.core.atoms.mixins.AtomsTransformationsMixin method) (sknano.core.atoms.molecules.Molecule method) (sknano.core.crystallography.CrystalCell method) (sknano.core.crystallography.LatticeBase method) (sknano.core.crystallography.UnitCell method) (sknano.core.geometric_regions.GeometricTransformsMixin method) (sknano.core.math.Point method) (sknano.core.math.Vector method) (sknano.core.math.point.Point method) (sknano.core.math.vector.Vector method) (sknano.core.structures.Composition method) (sknano.core.structures.StructureMixin method) translation_from_augmented_matrix() (in module sknano.core.math) (in module sknano.core.math.transforms) translation_from_matrix() (in module sknano.core.math) (in module sknano.core.math.transforms) translation_matrix() (in module sknano.core.math) (in module sknano.core.math.transforms) Triangle (class in sknano.core.geometric_regions) triangle (sknano.testing.Geometric2DRegionsTestFixture attribute) triclinic() (sknano.core.crystallography.Crystal3DLattice class method) (sknano.core.crystallography.Reciprocal3DLattice class method) tselect (sknano.core.atoms.Snapshot attribute) (sknano.core.atoms.trajectory.Snapshot attribute) tube_length (sknano.core.structures.SWNTMixin attribute) tube_mass (sknano.core.structures.MWNTMixin attribute) (sknano.core.structures.SWNTMixin attribute) Tvec (sknano.core.structures.SWNTMixin attribute) TYPE (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) type (sknano.core.atoms.type_atoms.TypeAtom attribute) (sknano.core.atoms.TypeAtom attribute) type_check_chiral_indices() (in module sknano.core.structures) type_selection_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) typeassert() (in module sknano.core) (in module sknano.core.meta) TypeAtom (class in sknano.core.atoms) (class in sknano.core.atoms.type_atoms) TypeAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.type_atoms) typed_property() (in module sknano.core) (in module sknano.core.meta)

U

u (sknano.core.geometric_regions.Parallelepiped attribute) (sknano.core.geometric_regions.Parallelogram attribute) unique_elements() (in module sknano.core) (in module sknano.core.itertools) unique_everseen() (in module sknano.core) (in module sknano.core.itertools) unique_justseen() (in module sknano.core) (in module sknano.core.itertools) unit_cell (sknano.core.crystallography.CrystalCell attribute) (sknano.core.structures.StructureMixin attribute) unit_cell_mass (sknano.core.structures.SWNTMixin attribute) unit_cell_symmetry_params (sknano.core.structures.SWNTMixin attribute) unit_quaternion (sknano.core.math.Quaternion attribute) unit_vector (sknano.core.atoms.Bond attribute) (sknano.core.atoms.mixins.Bond attribute) (sknano.core.math.Vector attribute) (sknano.core.math.vector.Vector attribute) UnitCell (class in sknano.core.crystallography) UnrolledSWNT (class in sknano.core.structures) UnrolledSWNTBase (class in sknano.core.structures)

UnrolledSWNTGenerator (class in sknano.generators) UnrolledSWNTMixin (class in sknano.core.structures) unscale() (sknano.io.DUMPReader method) (sknano.io.lammps_dump.DUMPReader method) unset_pbc() (sknano.core.atoms.mixins.PBCAtomsMixin method) (sknano.core.atoms.PBCAtomsMixin method) unwrap() (sknano.io.DUMPReader method) (sknano.io.lammps_dump.DUMPReader method) update() (sknano.core.crystallography.Domain method) update_attrs() (sknano.core.atoms.Atom method) (sknano.core.atoms.AtomsTopologyMixin method) (sknano.core.atoms.POAVAtomsMixin method) (sknano.core.atoms.RingAtomsMixin method) (sknano.core.atoms.atoms.Atom method) (sknano.core.atoms.mixins.AtomsTopologyMixin method) (sknano.core.atoms.mixins.POAVAtomsMixin method) (sknano.core.atoms.mixins.RingAtomsMixin method) update_basis() (sknano.core.crystallography.CrystalCell method) update_Ch_list() (sknano.core.structures.MWNTMixin method) update_dumpattr() (sknano.io.DUMPReader method) (sknano.io.lammps_dump.DUMPReader method) update_ring_stats() (sknano.core.atoms.mixins.RingAtomsMixin method) (sknano.core.atoms.RingAtomsMixin method) UserList (class in sknano.core) (class in sknano.core.collections)

V

v (sknano.core.atoms.velocity_atoms.VelocityAtom attribute) (sknano.core.atoms.VelocityAtom attribute) (sknano.core.geometric_regions.Parallelepiped attribute) (sknano.core.geometric_regions.Parallelogram attribute) (sknano.core.math.Quaternion attribute) V1 (sknano.core.atoms.mixins.POAV attribute) v1 (sknano.core.atoms.mixins.POAV attribute) V1 (sknano.core.atoms.POAV attribute) v1 (sknano.core.atoms.POAV attribute) V2 (sknano.core.atoms.mixins.POAV attribute) v2 (sknano.core.atoms.mixins.POAV attribute) V2 (sknano.core.atoms.POAV attribute) v2 (sknano.core.atoms.POAV attribute) V3 (sknano.core.atoms.mixins.POAV attribute) v3 (sknano.core.atoms.mixins.POAV attribute) V3 (sknano.core.atoms.POAV attribute) v3 (sknano.core.atoms.POAV attribute) Vacancy (class in sknano.core.structures) VanDerWaalsAtom (class in sknano.core.atoms) (class in sknano.core.atoms.vdW_atoms) VanDerWaalsAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.vdW_atoms) vdw_distance (sknano.core.structures.NanoStructureBase attribute) vdw_radius (sknano.core.structures.NanoStructureBase attribute) vdw_radius_from_basis() (in module sknano.core.atoms) (in module sknano.core.atoms.vdW_atoms) Vector (class in sknano.core.math) (class in sknano.core.math.vector) vector (sknano.core.atoms.Bond attribute) (sknano.core.atoms.mixins.Bond attribute)

vector_projection() (in module sknano.core.math) (in module sknano.core.math.vector) vector_rejection() (in module sknano.core.math) (in module sknano.core.math.vector) vector_triple_product() (in module sknano.core.math) (in module sknano.core.math.vector) Vectors (class in sknano.core.math) (class in sknano.core.math.vectors) vectors (sknano.core.geometric_regions.GeometricRegion attribute) VelocityAtom (class in sknano.core.atoms) (class in sknano.core.atoms.velocity_atoms) VelocityAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.velocity_atoms) viz() (sknano.io.DATAData method) (sknano.io.lammps_data.DATAData method) vmd_index (sknano.core.atoms.mixins.VMDAtomAdapterMixin attribute) (sknano.core.atoms.VMDAtomAdapterMixin attribute) vmd_indices (sknano.core.atoms.mixins.VMDAtomsAdapterMixin attribute) (sknano.core.atoms.VMDAtomsAdapterMixin attribute) VMDAtomAdapterMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) VMDAtomsAdapterMixin (class in sknano.core.atoms) (class in sknano.core.atoms.mixins) volume (sknano.core.atoms.BoundingRegionsMixin attribute) (sknano.core.atoms.mixins.BoundingRegionsMixin attribute) (sknano.core.crystallography.Crystal3DLattice attribute) (sknano.core.geometric_regions.Cone attribute) (sknano.core.geometric_regions.Cube attribute) (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Cylinder attribute) (sknano.core.geometric_regions.Ellipsoid attribute) (sknano.core.geometric_regions.Geometric3DRegion attribute) (sknano.core.geometric_regions.Parallelepiped attribute) (sknano.core.geometric_regions.Sphere attribute) Vpi (sknano.core.atoms.mixins.POAV attribute) vpi (sknano.core.atoms.mixins.POAV attribute) Vpi (sknano.core.atoms.POAV attribute) vpi (sknano.core.atoms.POAV attribute) Vv1v2v3 (sknano.core.atoms.mixins.POAV attribute) (sknano.core.atoms.POAV attribute) vx (sknano.core.atoms.velocity_atoms.VelocityAtom attribute) (sknano.core.atoms.VelocityAtom attribute) vy (sknano.core.atoms.velocity_atoms.VelocityAtom attribute) (sknano.core.atoms.VelocityAtom attribute) vz (sknano.core.atoms.velocity_atoms.VelocityAtom attribute) (sknano.core.atoms.VelocityAtom attribute)

W

w (sknano.core.geometric_regions.Parallelepiped attribute) (sknano.core.math.Quaternion attribute) wall_diameters (sknano.core.structures.MWNTMixin attribute) wall_masses (sknano.core.structures.MWNTMixin attribute) wall_radii (sknano.core.structures.MWNTMixin attribute) wall_spacing (sknano.apps.nanogen_gui.MWNTModel attribute) (sknano.core.structures.MWNTMixin attribute) walls (sknano.core.structures.MWNTMixin attribute) with_doc (class in sknano.core) (class in sknano.core.meta) WITHIN (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute) within_region() (sknano.core.atoms.BoundingRegionsMixin method) (sknano.core.atoms.mixins.BoundingRegionsMixin method) within_selection_expression (sknano.core.atoms.SelectionParser attribute) (sknano.core.atoms.selections.SelectionParser attribute)

wrap() (sknano.io.DUMPReader method) (sknano.io.lammps_dump.DUMPReader method) wrap_cartesian_coordinate() (sknano.core.crystallography.LatticeBase method) wrap_cartesian_coordinates() (sknano.core.crystallography.LatticeBase method) wrap_fractional_coordinate() (sknano.core.crystallography.LatticeBase method) wrap_fractional_coordinates() (sknano.core.crystallography.LatticeBase method) write() (sknano.io.DATAData method) (sknano.io.DATAWriter class method) (sknano.io.DUMPData method) (sknano.io.DUMPWriter class method) (sknano.io.PDBData method) (sknano.io.PDBWriter class method) (sknano.io.StructureDataWriter class method) (sknano.io.StructureDataWriterMixin method) (sknano.io.XYZData method) (sknano.io.XYZWriter class method) (sknano.io.lammps_data.DATAData method) (sknano.io.lammps_data.DATAWriter class method) (sknano.io.lammps_dump.DUMPData method) (sknano.io.lammps_dump.DUMPWriter class method) (sknano.io.pdb.PDBData method) (sknano.io.pdb.PDBWriter class method) (sknano.io.xyz.XYZData method) (sknano.io.xyz.XYZWriter class method) write_data() (sknano.io.StructureDataWriterMixin method) write_dump() (sknano.io.StructureDataWriterMixin method) write_pdb() (sknano.io.StructureDataWriterMixin method) write_xyz() (sknano.io.StructureDataWriterMixin method)

X

x (sknano.core.atoms.xyz_atoms.XYZAtom attribute) (sknano.core.atoms.XYZAtom attribute) (sknano.core.math.Quaternion attribute) xhi (sknano.core.crystallography.Domain attribute) xhi_bound (sknano.core.crystallography.Domain attribute) xlo (sknano.core.crystallography.Domain attribute) xlo_bound (sknano.core.crystallography.Domain attribute) xmax (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Rectangle attribute) xmin (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Rectangle attribute) xperiodic (sknano.core.atoms.mixins.PBCAtomsMixin attribute) (sknano.core.atoms.PBCAtomsMixin attribute) xs (sknano.core.atoms.lattice_atoms.LatticeAtom attribute) (sknano.core.atoms.LatticeAtom attribute) XYZ (in module sknano.io) (in module sknano.io.xyz) XYZ2DATAConverter (class in sknano.io) (class in sknano.io.xyz) xyz_reader (sknano.testing.IOTestFixture attribute) XYZAtom (class in sknano.core.atoms) (class in sknano.core.atoms.xyz_atoms) XYZAtoms (class in sknano.core.atoms) (class in sknano.core.atoms.xyz_atoms) XYZConverter (class in sknano.io) (class in sknano.io.xyz)

XYZData (class in sknano.io) (class in sknano.io.xyz) xyzdata (sknano.testing.IOTestFixture attribute) XYZError, [1] xyzfile (sknano.io.DATA2XYZConverter attribute) (sknano.io.XYZConverter attribute) (sknano.io.lammps_data.DATA2XYZConverter attribute) (sknano.io.xyz.XYZConverter attribute) XYZFormatSpec (in module sknano.io) (in module sknano.io.xyz) XYZFormatter (class in sknano.io) (class in sknano.io.xyz) XYZIO (in module sknano.io) (in module sknano.io.xyz) XYZIOConverter (in module sknano.io) (in module sknano.io.xyz) XYZIOError (in module sknano.io) (in module sknano.io.xyz) XYZIOFormatter (in module sknano.io) (in module sknano.io.xyz) XYZIOReader (in module sknano.io) (in module sknano.io.xyz) XYZIOWriter (in module sknano.io) (in module sknano.io.xyz) XYZReader (class in sknano.io) (class in sknano.io.xyz) XYZWriter (class in sknano.io) (class in sknano.io.xyz)

Y

y (sknano.core.atoms.xyz_atoms.XYZAtom attribute) (sknano.core.atoms.XYZAtom attribute) (sknano.core.math.Quaternion attribute) yhi (sknano.core.crystallography.Domain attribute) yhi_bound (sknano.core.crystallography.Domain attribute) ylo (sknano.core.crystallography.Domain attribute) ylo_bound (sknano.core.crystallography.Domain attribute)

ymax (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Rectangle attribute) ymin (sknano.core.geometric_regions.Cuboid attribute) (sknano.core.geometric_regions.Rectangle attribute) yperiodic (sknano.core.atoms.mixins.PBCAtomsMixin attribute) (sknano.core.atoms.PBCAtomsMixin attribute) ys (sknano.core.atoms.lattice_atoms.LatticeAtom attribute) (sknano.core.atoms.LatticeAtom attribute)

Z

Z (sknano.core.atoms.Atom attribute) (sknano.core.atoms.atoms.Atom attribute) z (sknano.core.atoms.xyz_atoms.XYZAtom attribute) (sknano.core.atoms.XYZAtom attribute) (sknano.core.math.Quaternion attribute) zhi (sknano.core.crystallography.Domain attribute) zhi_bound (sknano.core.crystallography.Domain attribute) zigzag_edge_length (sknano.apps.nanogen_gui.GrapheneModel attribute) ZincblendeGenerator (class in sknano.generators) ZincblendeStructure (class in sknano.core.structures) ZincBlendeStructure (in module sknano.core.structures)

ZincblendeStructureGenerator (in module sknano.generators) zlo (sknano.core.crystallography.Domain attribute) zlo_bound (sknano.core.crystallography.Domain attribute) zmax (sknano.core.geometric_regions.Cuboid attribute) zmin (sknano.core.geometric_regions.Cuboid attribute) zperiodic (sknano.core.atoms.mixins.PBCAtomsMixin attribute) (sknano.core.atoms.PBCAtomsMixin attribute) zs (sknano.core.atoms.lattice_atoms.LatticeAtom attribute) (sknano.core.atoms.LatticeAtom attribute)