Index

_

__call__() (sknano.core.methodfunc method) (sknano.core.with_doc method) (sknano.testing.GeneratorTestFixtures method)

A

A (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) a (sknano.utils.geometric_shapes.Cube attribute) (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Ellipse attribute) (sknano.utils.geometric_shapes.Ellipsoid attribute) (sknano.utils.geometric_shapes.Rectangle attribute) (sknano.utils.geometric_shapes.Spheroid attribute) (sknano.utils.geometric_shapes.Square attribute) add_atom() (sknano.io.XYZ2DATAConverter method) add_atomtype() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) (sknano.io.XYZ2DATAConverter method) add_atomtypes() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) addCleanup() (sknano.testing.GeneratorTestFixtures method) addTypeEqualityFunc() (sknano.testing.GeneratorTestFixtures method) all() (sknano.core.math.Point method) (sknano.core.math.Vector method) analyze() (sknano.io.StructureData method) analyze_POAV() (sknano.utils.analysis.StructureAnalyzer method) angles (sknano.core.atoms.Bonds attribute) any() (sknano.core.math.Point method) (sknano.core.math.Vector method) append() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method) area (sknano.utils.geometric_shapes.Circle attribute) (sknano.utils.geometric_shapes.Ellipse attribute) (sknano.utils.geometric_shapes.Geometric2DRegion attribute) (sknano.utils.geometric_shapes.Parallelogram attribute) (sknano.utils.geometric_shapes.Rectangle attribute) (sknano.utils.geometric_shapes.Square attribute) argmax() (sknano.core.math.Point method) (sknano.core.math.Vector method) argmin() (sknano.core.math.Point method) (sknano.core.math.Vector method) argpartition() (sknano.core.math.Point method) (sknano.core.math.Vector method) argsort() (sknano.core.math.Point method) (sknano.core.math.Vector method) assert_() (sknano.testing.GeneratorTestFixtures method) assertAlmostEqual() (sknano.testing.GeneratorTestFixtures method) assertAlmostEquals() (sknano.testing.GeneratorTestFixtures method) assertDictContainsSubset() (sknano.testing.GeneratorTestFixtures method) assertDictEqual() (sknano.testing.GeneratorTestFixtures method) assertEqual() (sknano.testing.GeneratorTestFixtures method) assertEquals() (sknano.testing.GeneratorTestFixtures method) assertFalse() (sknano.testing.GeneratorTestFixtures method) assertGreater() (sknano.testing.GeneratorTestFixtures method) assertGreaterEqual() (sknano.testing.GeneratorTestFixtures method) assertIn() (sknano.testing.GeneratorTestFixtures method) assertIs() (sknano.testing.GeneratorTestFixtures method) assertIsInstance() (sknano.testing.GeneratorTestFixtures method) assertIsNone() (sknano.testing.GeneratorTestFixtures method) assertIsNot() (sknano.testing.GeneratorTestFixtures method) assertIsNotNone() (sknano.testing.GeneratorTestFixtures method) assertItemsEqual() (sknano.testing.GeneratorTestFixtures method)

assertLess() (sknano.testing.GeneratorTestFixtures method) assertLessEqual() (sknano.testing.GeneratorTestFixtures method) assertListEqual() (sknano.testing.GeneratorTestFixtures method) assertMultiLineEqual() (sknano.testing.GeneratorTestFixtures method) assertNotAlmostEqual() (sknano.testing.GeneratorTestFixtures method) assertNotAlmostEquals() (sknano.testing.GeneratorTestFixtures method) assertNotEqual() (sknano.testing.GeneratorTestFixtures method) assertNotEquals() (sknano.testing.GeneratorTestFixtures method) assertNotIn() (sknano.testing.GeneratorTestFixtures method) assertNotIsInstance() (sknano.testing.GeneratorTestFixtures method) assertNotRegexpMatches() (sknano.testing.GeneratorTestFixtures method) assertRaises() (sknano.testing.GeneratorTestFixtures method) assertRaisesRegexp() (sknano.testing.GeneratorTestFixtures method) assertRegexpMatches() (sknano.testing.GeneratorTestFixtures method) assertSequenceEqual() (sknano.testing.GeneratorTestFixtures method) assertSetEqual() (sknano.testing.GeneratorTestFixtures method) assertTrue() (sknano.testing.GeneratorTestFixtures method) assertTupleEqual() (sknano.testing.GeneratorTestFixtures method) assign_unique_ids() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) astype() (sknano.core.math.Point method) (sknano.core.math.Vector method) Atom (class in sknano.core.atoms) atom1 (sknano.core.atoms.Bond attribute) atom2 (sknano.core.atoms.Bond attribute) atom_ids (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) atom_style (sknano.io.DATAFormatSpec attribute) atom_tree (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) atomic_masses (in module sknano.core.refdata) atomic_numbers (in module sknano.core.refdata) atomID (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) Atoms (class in sknano.core.atoms) atoms (sknano.core.atoms.Bond attribute) (sknano.core.atoms.Bonds attribute) (sknano.core.atoms.Snapshot attribute) (sknano.generators.BilayerGrapheneGenerator attribute) (sknano.generators.FullereneGenerator attribute) (sknano.generators.GeneratorBase attribute) (sknano.generators.GrapheneGenerator attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.io.DATAData attribute) (sknano.io.DATAReader attribute) (sknano.io.StructureData attribute) (sknano.io.StructureIO attribute) (sknano.io.XYZData attribute) (sknano.io.XYZReader attribute) atomtype (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) atomtypes (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) axis_angle_from_rotation_matrix() (in module sknano.core.math)

B

b (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Ellipse attribute) (sknano.utils.geometric_shapes.Ellipsoid attribute) (sknano.utils.geometric_shapes.Rectangle attribute) base (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) BilayerGraphene (class in sknano.structures) BilayerGrapheneGenerator (class in sknano.generators) Bond (class in sknano.core.atoms) bond (sknano.generators.BilayerGrapheneGenerator attribute) (sknano.generators.GrapheneGenerator attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.BilayerGraphene attribute) (sknano.structures.Graphene attribute) (sknano.structures.GraphenePrimitiveCell attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) (sknano.structures.StructureBase attribute) bond_angle_pairs (sknano.core.atoms.Bonds attribute)

Bonds (class in sknano.core.atoms) bonds (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.io.StructureData attribute) bounds (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) bundle_density (sknano.generators.SWNTBundleGenerator attribute) (sknano.structures.SWNTBundle attribute) bundle_mass (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.NanotubeBundleBase attribute) (sknano.structures.NanotubeBundleMixin attribute) (sknano.structures.SWNTBundle attribute) bundle_packing (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.NanotubeBundleBase attribute) (sknano.structures.NanotubeBundleMixin attribute) (sknano.structures.SWNTBundle attribute) byteswap() (sknano.core.math.Point method) (sknano.core.math.Vector method)

C

c (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Ellipsoid attribute) (sknano.utils.geometric_shapes.Spheroid attribute) C_C (in module sknano.core.refdata) C_H (in module sknano.core.refdata) CCbond (in module sknano.core.refdata) center (sknano.utils.geometric_shapes.Circle attribute) (sknano.utils.geometric_shapes.Cube attribute) (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Ellipse attribute) (sknano.utils.geometric_shapes.Ellipsoid attribute) (sknano.utils.geometric_shapes.Parallelepiped attribute) (sknano.utils.geometric_shapes.Parallelogram attribute) (sknano.utils.geometric_shapes.Rectangle attribute) (sknano.utils.geometric_shapes.Sphere attribute) (sknano.utils.geometric_shapes.Spheroid attribute) (sknano.utils.geometric_shapes.Square attribute) center_CM() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) centroid (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) (sknano.utils.geometric_shapes.Circle attribute) (sknano.utils.geometric_shapes.Cube attribute) (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Ellipse attribute) (sknano.utils.geometric_shapes.Ellipsoid attribute) (sknano.utils.geometric_shapes.Geometric2DRegion attribute) (sknano.utils.geometric_shapes.Geometric3DRegion attribute) (sknano.utils.geometric_shapes.GeometricRegion attribute) (sknano.utils.geometric_shapes.Parallelepiped attribute) (sknano.utils.geometric_shapes.Parallelogram attribute) (sknano.utils.geometric_shapes.Rectangle attribute) (sknano.utils.geometric_shapes.Sphere attribute) (sknano.utils.geometric_shapes.Spheroid attribute) (sknano.utils.geometric_shapes.Square attribute) Ch (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) charges (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) CHbond (in module sknano.core.refdata) check_type() (in module sknano.core) chiral_angle (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) chiral_set (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) chiral_type (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) chiral_types (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) choose() (sknano.core.math.Point method) (sknano.core.math.Vector method) Circle (class in sknano.utils.geometric_shapes) clear() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method) (sknano.io.StructureData method) clip() (sknano.core.math.Point method) (sknano.core.math.Vector method) clip_bounds() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) CM (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) cmp_Ch() (in module sknano.structures) CN (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) comment_line (sknano.io.DATAData attribute) (sknano.io.DATAReader attribute) (sknano.io.StructureIO attribute) (sknano.io.XYZData attribute) (sknano.io.XYZReader attribute) compress() (sknano.core.math.Point method) (sknano.core.math.Vector method) compute_bundle_density() (in module sknano.structures) compute_bundle_params() (sknano.generators.MWNTBundleGenerator method) (sknano.generators.SWNTBundleGenerator method) (sknano.structures.MWNTBundle method) (sknano.structures.NanotubeBundleBase method) (sknano.structures.NanotubeBundleMixin method) (sknano.structures.SWNTBundle method) compute_centroid() (in module sknano.core.physics) compute_Ch() (in module sknano.structures) compute_chiral_angle() (in module sknano.structures) compute_d() (in module sknano.structures) compute_dR() (in module sknano.structures) compute_dt() (in module sknano.structures) compute_electronic_type() (in module sknano.structures) compute_inertia_tensor() (in module sknano.core.physics)

compute_linear_mass_density() (in module sknano.structures) compute_Lz() (in module sknano.structures) compute_M() (in module sknano.structures) compute_N() (in module sknano.structures) compute_Natoms() (in module sknano.structures) compute_Natoms_per_tube() (in module sknano.structures) compute_Natoms_per_unit_cell() (in module sknano.structures) compute_POAVs() (sknano.core.atoms.POAVAtoms method) compute_psi() (in module sknano.structures) compute_R() (in module sknano.structures) compute_R_chiral_angle() (in module sknano.structures) compute_rt() (in module sknano.structures) compute_symmetry_operation() (in module sknano.structures) compute_T() (in module sknano.structures) compute_t1() (in module sknano.structures) compute_t2() (in module sknano.structures) compute_tau() (in module sknano.structures) compute_tube_mass() (in module sknano.structures) compute_unit_cell_mass() (in module sknano.structures) conj() (sknano.core.math.Point method) (sknano.core.math.Vector method) conjugate() (sknano.core.math.Point method) (sknano.core.math.Vector method) contains_point() (sknano.utils.geometric_shapes.Circle method) (sknano.utils.geometric_shapes.Cube method) (sknano.utils.geometric_shapes.Cuboid method) (sknano.utils.geometric_shapes.Ellipse method) (sknano.utils.geometric_shapes.Ellipsoid method) (sknano.utils.geometric_shapes.Geometric2DRegion method) (sknano.utils.geometric_shapes.Geometric3DRegion method) (sknano.utils.geometric_shapes.GeometricRegion method) (sknano.utils.geometric_shapes.Parallelepiped method) (sknano.utils.geometric_shapes.Parallelogram method) (sknano.utils.geometric_shapes.Rectangle method) (sknano.utils.geometric_shapes.Sphere method) (sknano.utils.geometric_shapes.Spheroid method) (sknano.utils.geometric_shapes.Square method) convert() (sknano.io.DATA2XYZConverter method) (sknano.io.StructureConverter method) (sknano.io.XYZ2DATAConverter method) coordination_numbers (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) coords (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) copy() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Point method) (sknano.core.math.Points method) (sknano.core.math.Vector method) (sknano.core.math.Vectors method) count() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method) countTestCases() (sknano.testing.GeneratorTestFixtures method) ctypes (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) Cube (class in sknano.utils.geometric_shapes) Cuboid (class in sknano.utils.geometric_shapes) cull() (sknano.core.atoms.Trajectory method) cumprod() (sknano.core.math.Point method) (sknano.core.math.Vector method) cumsum() (sknano.core.math.Point method) (sknano.core.math.Vector method) cyclic_pairs() (in module sknano.core)

D

d (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) data (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) DATA2XYZConverter (class in sknano.io) DATAData (class in sknano.io) datafile (sknano.io.DATA2XYZConverter attribute) (sknano.io.XYZ2DATAConverter attribute) DATAFormatSpec (class in sknano.io) DATAIOError DATAReader (class in sknano.io) DATAWriter (class in sknano.io) debug() (sknano.testing.GeneratorTestFixtures method) defaultTestResult() (sknano.testing.GeneratorTestFixtures method)

delete() (sknano.io.DATAData method) deprecated() (in module sknano.core) diagonal() (sknano.core.math.Point method) (sknano.core.math.Vector method) doCleanups() (sknano.testing.GeneratorTestFixtures method) dot() (sknano.core.math.Point method) (sknano.core.math.Vector method) dr (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) dR (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) dt (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) dtype (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) dump() (sknano.core.math.Point method) (sknano.core.math.Vector method) dumps() (sknano.core.math.Point method) (sknano.core.math.Vector method)

E

electronic_type (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) element (sknano.core.atoms.Atom attribute) (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) element1 (sknano.generators.BilayerGrapheneGenerator attribute) (sknano.generators.GrapheneGenerator attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.BilayerGraphene attribute) (sknano.structures.Graphene attribute) (sknano.structures.GraphenePrimitiveCell attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) (sknano.structures.StructureBase attribute) element2 (sknano.generators.BilayerGrapheneGenerator attribute) (sknano.generators.GrapheneGenerator attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.BilayerGraphene attribute) (sknano.structures.Graphene attribute) (sknano.structures.GraphenePrimitiveCell attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) (sknano.structures.StructureBase attribute) element_names (in module sknano.core.refdata)

element_symbols (in module sknano.core.refdata) Ellipse (class in sknano.utils.geometric_shapes) Ellipsoid (class in sknano.utils.geometric_shapes) euclidean_distance() (sknano.core.math.Point method) extend() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method)

F

f (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) fail() (sknano.testing.GeneratorTestFixtures method) failIf() (sknano.testing.GeneratorTestFixtures method) failIfAlmostEqual() (sknano.testing.GeneratorTestFixtures method) failIfEqual() (sknano.testing.GeneratorTestFixtures method) failUnless() (sknano.testing.GeneratorTestFixtures method) failUnlessAlmostEqual() (sknano.testing.GeneratorTestFixtures method) failUnlessEqual() (sknano.testing.GeneratorTestFixtures method) failUnlessRaises() (sknano.testing.GeneratorTestFixtures method) fill() (sknano.core.math.Point method) (sknano.core.math.Vector method) filter() (sknano.core.atoms.Atoms method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method) filter_Ch() (in module sknano.structures) filter_Ch_list() (in module sknano.structures)

filter_ids() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) find_target_atom() (in module sknano.utils.analysis) fix_Lx (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.UnrolledSWNTMixin attribute) fix_Lz (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) flags (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) flat (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) flatten() (sknano.core.math.Point method) (sknano.core.math.Vector method) format_spec() (sknano.io.DATAData class method) Fullerene (class in sknano.structures) FullereneGenerator (class in sknano.generators) fx (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) fy (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) fz (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute)

G

generate_atoms() (in module sknano.testing) generate_bundle() (sknano.generators.MWNTBundleGenerator method) (sknano.generators.SWNTBundleGenerator method) generate_Ch_list() (in module sknano.structures) generate_Ch_property_grid() (in module sknano.structures) generate_structure_data() (sknano.generators.BilayerGrapheneGenerator method) (sknano.generators.FullereneGenerator method) (sknano.generators.GrapheneGenerator method) (sknano.generators.MWNTBundleGenerator method) (sknano.generators.MWNTGenerator method) (sknano.generators.SWNTBundleGenerator method) (sknano.generators.SWNTGenerator method) (sknano.generators.UnrolledSWNTGenerator method) generate_unit_cell() (sknano.generators.GrapheneGenerator method) (sknano.generators.MWNTBundleGenerator method) (sknano.generators.MWNTGenerator method) (sknano.generators.SWNTBundleGenerator method) (sknano.generators.SWNTGenerator method) (sknano.generators.UnrolledSWNTGenerator method) GeneratorBase (class in sknano.generators) GeneratorTestFixtures (class in sknano.testing) Geometric2DRegion (class in sknano.utils.geometric_shapes) Geometric3DRegion (class in sknano.utils.geometric_shapes) GeometricRegion (class in sknano.utils.geometric_shapes) get() (sknano.io.DATAData method) (sknano.io.DATAReader method) get_atom() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) get_atoms() (sknano.core.atoms.Atoms method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Snapshot method) (sknano.core.atoms.XAtoms method) get_Ch_indices() (in module sknano.structures)

get_Ch_type() (in module sknano.structures) get_coords() (sknano.core.atoms.KDTAtom method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtom method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtom method) (sknano.core.atoms.XAtoms method) get_fname() (in module sknano.core) get_fpath() (in module sknano.core) get_object_signature() (in module sknano.core) get_POAV_attr() (sknano.core.atoms.POAVAtoms method) getatomattr() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) getdoc() (sknano.core.methodfunc method) getfield() (sknano.core.math.Point method) (sknano.core.math.Vector method) grams_per_amu (in module sknano.core.refdata) grams_per_Da (in module sknano.core.refdata) Graphene (class in sknano.structures) GrapheneGenerator (class in sknano.generators) GraphenePrimitiveCell (class in sknano.structures)

H

H (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute)

headers (sknano.io.DATAData attribute) (sknano.io.DATAReader attribute)

I

id() (sknano.testing.GeneratorTestFixtures method) imag (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) index() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method) inertia_tensor (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute)

insert() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method) item() (sknano.core.math.Point method) (sknano.core.math.Vector method) itemset() (sknano.core.math.Point method) (sknano.core.math.Vector method) itemsize (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute)

K

KDTAtom (class in sknano.core.atoms) KDTAtoms (class in sknano.core.atoms)

kNN (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute)

L

length (sknano.core.atoms.Bond attribute) (sknano.core.math.Vector attribute) lengths (sknano.core.atoms.Bonds attribute) linear_mass_density (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) longMessage (sknano.testing.GeneratorTestFixtures attribute)

Lx (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.NanotubeBundleBase attribute) (sknano.structures.NanotubeBundleMixin attribute) (sknano.structures.SWNTBundle attribute) (sknano.structures.UnrolledSWNTMixin attribute) Ly (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.NanotubeBundleBase attribute) (sknano.structures.NanotubeBundleMixin attribute) (sknano.structures.SWNTBundle attribute) (sknano.structures.UnrolledSWNTMixin attribute) Lz (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute)

M

m (sknano.core.atoms.Atom attribute) M (sknano.core.atoms.Atoms attribute) m (sknano.core.atoms.KDTAtom attribute) M (sknano.core.atoms.KDTAtoms attribute) m (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVAtom attribute) M (sknano.core.atoms.POAVAtoms attribute) m (sknano.core.atoms.XAtom attribute) M (sknano.core.atoms.XAtoms attribute) (sknano.generators.SWNTBundleGenerator attribute) m (sknano.generators.SWNTBundleGenerator attribute) M (sknano.generators.SWNTGenerator attribute) m (sknano.generators.SWNTGenerator attribute) M (sknano.generators.UnrolledSWNTGenerator attribute) m (sknano.generators.UnrolledSWNTGenerator attribute) M (sknano.structures.SWNT attribute) m (sknano.structures.SWNT attribute) M (sknano.structures.SWNTBundle attribute) m (sknano.structures.SWNTBundle attribute) mag (sknano.core.math.Vector attribute) magnitude (sknano.core.math.Vector attribute) map() (sknano.io.DATAData method) map_Ch() (in module sknano.structures)

mapatomattr() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) mass (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) masses (sknano.core.atoms.Atoms attribute) (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) max() (sknano.core.math.Point method) (sknano.core.math.Vector method) maxbox() (sknano.io.DATAData method) maxDiff (sknano.testing.GeneratorTestFixtures attribute) maxtype() (sknano.io.DATAData method) mean() (sknano.core.math.Point method) (sknano.core.math.Vector method) mean_angle (sknano.core.atoms.Bonds attribute) mean_length (sknano.core.atoms.Bonds attribute) memoize() (in module sknano.core) method_function() (in module sknano.core) methodfunc (class in sknano.core) min() (sknano.core.math.Point method) (sknano.core.math.Vector method) misalignment_angles (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) moleculeID (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) MWNT (class in sknano.structures) MWNTBundle (class in sknano.structures) MWNTBundleGenerator (class in sknano.generators) MWNTGenerator (class in sknano.generators) MWNTMixin (class in sknano.structures)

N

n (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) N (sknano.generators.FullereneGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) n (sknano.generators.SWNTBundleGenerator attribute) N (sknano.generators.SWNTGenerator attribute) n (sknano.generators.SWNTGenerator attribute) N (sknano.generators.UnrolledSWNTGenerator attribute) n (sknano.generators.UnrolledSWNTGenerator attribute) N (sknano.structures.Fullerene attribute) (sknano.structures.SWNT attribute) n (sknano.structures.SWNT attribute) N (sknano.structures.SWNTBundle attribute) n (sknano.structures.SWNTBundle attribute) n1 (sknano.core.atoms.POAV2 attribute) n2 (sknano.core.atoms.POAV2 attribute) n3 (sknano.core.atoms.POAV2 attribute) NanoGen (class in sknano.scripts) nanogen() (in module sknano.scripts) (in module sknano.scripts.nanogen) NanotubeBundleBase (class in sknano.structures) NanotubeBundleMixin (class in sknano.structures) Natoms (sknano.core.atoms.Atoms attribute) (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) Natoms_per_bundle (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.NanotubeBundleBase attribute) (sknano.structures.NanotubeBundleMixin attribute) (sknano.structures.SWNTBundle attribute) Natoms_per_tube (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) Natoms_per_unit_cell (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute)

Nbonds (sknano.core.atoms.Bonds attribute) nbytes (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) ndim (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) nearest_neighbors (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) newbyteorder() (sknano.core.math.Point method) (sknano.core.math.Vector method) newxyz() (sknano.io.DATAData method) Nlayers (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.UnrolledSWNTMixin attribute) NN (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) NNrc (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) nonzero() (sknano.core.math.Point method) (sknano.core.math.Vector method) norm (sknano.core.math.Vector attribute) normalize() (sknano.core.math.Vector method) norms (sknano.core.math.Vectors attribute) Nshells (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) Nsnaps (sknano.core.atoms.Trajectory attribute) Ntubes (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.NanotubeBundleBase attribute) (sknano.structures.NanotubeBundleMixin attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) Ntypes (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) Nwalls (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) nx (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.NanotubeBundleBase attribute) (sknano.structures.NanotubeBundleMixin attribute) (sknano.structures.SWNTBundle attribute) (sknano.structures.UnrolledSWNTMixin attribute) ny (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.NanotubeBundleBase attribute) (sknano.structures.NanotubeBundleMixin attribute) (sknano.structures.SWNTBundle attribute) nz (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute)

O

o (sknano.utils.geometric_shapes.Parallelepiped attribute) (sknano.utils.geometric_shapes.Parallelogram attribute)

P

p (sknano.core.math.Vector attribute) p0 (sknano.core.math.Vector attribute) Parallelepiped (class in sknano.utils.geometric_shapes) Parallelogram (class in sknano.utils.geometric_shapes) partition() (sknano.core.math.Point method) (sknano.core.math.Vector method) pluralize() (in module sknano.core) pmax (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Rectangle attribute) pmin (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Rectangle attribute) POAV (class in sknano.core.atoms) POAV1 (class in sknano.core.atoms) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.POAVAtomMixin attribute) (sknano.core.atoms.POAVAtoms attribute) POAV2 (class in sknano.core.atoms) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.POAVAtomMixin attribute) (sknano.core.atoms.POAVAtoms attribute) POAVAtom (class in sknano.core.atoms)

POAVAtomMixin (class in sknano.core.atoms) POAVAtoms (class in sknano.core.atoms) POAVR (class in sknano.core.atoms) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.POAVAtomMixin attribute) (sknano.core.atoms.POAVAtoms attribute) Point (class in sknano.core.math) PointGroup (class in sknano.utils.symmetry_groups) Points (class in sknano.core.math) pop() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method) prod() (sknano.core.math.Point method) (sknano.core.math.Vector method) projection() (sknano.core.math.Vector method) ptp() (sknano.core.math.Point method) (sknano.core.math.Vector method) put() (sknano.core.math.Point method) (sknano.core.math.Vector method) pyramidalization_angles (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute)

Q

q (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtom attribute) (sknano.core.atoms.XAtoms attribute) query_atom_tree() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method)

query_ball_point() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method)

R

r (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) R (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) r (sknano.utils.geometric_shapes.Circle attribute) (sknano.utils.geometric_shapes.Sphere attribute) R1 (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) R2 (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) R3 (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) ravel() (sknano.core.math.Point method) (sknano.core.math.Vector method) read() (sknano.io.DATAData method) (sknano.io.DATAReader method) (sknano.io.StructureReader class method) (sknano.io.XYZData method) (sknano.io.XYZReader method) real (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) reciprocal_v1 (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) reciprocal_v2 (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) reciprocal_v3 (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) Rectangle (class in sknano.utils.geometric_shapes) reflection_matrix() (in module sknano.core.math) remove() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method) reorder() (sknano.io.DATAData method) repeat() (sknano.core.math.Point method) (sknano.core.math.Vector method) replace() (sknano.io.DATAData method)

reshape() (sknano.core.math.Point method) (sknano.core.math.Vector method) resize() (sknano.core.math.Point method) (sknano.core.math.Vector method) reverse() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Points method) (sknano.core.math.Vectors method) rezero() (sknano.core.atoms.KDTAtom method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtom method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtom method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Point method) (sknano.core.math.Points method) (sknano.core.math.Vector method) (sknano.core.math.Vectors method) rezero_array() (in module sknano.core) rezero_components() (sknano.core.math.Vector method) rezero_coords() (sknano.core.atoms.KDTAtom method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtom method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtom method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Point method) rezero_xyz() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) rotate() (in module sknano.core.math) (sknano.core.atoms.KDTAtom method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtom method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtom method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Point method) (sknano.core.math.Points method) (sknano.core.math.Vector method) (sknano.core.math.Vectors method) (sknano.utils.geometric_shapes.Circle method) (sknano.utils.geometric_shapes.Cube method) (sknano.utils.geometric_shapes.Cuboid method) (sknano.utils.geometric_shapes.Ellipse method) (sknano.utils.geometric_shapes.Ellipsoid method) (sknano.utils.geometric_shapes.Geometric2DRegion method) (sknano.utils.geometric_shapes.Geometric3DRegion method) (sknano.utils.geometric_shapes.Parallelepiped method) (sknano.utils.geometric_shapes.Parallelogram method) (sknano.utils.geometric_shapes.Rectangle method) (sknano.utils.geometric_shapes.Sphere method) (sknano.utils.geometric_shapes.Spheroid method) (sknano.utils.geometric_shapes.Square method) rotation_matrix() (in module sknano.core.math) round() (sknano.core.math.Point method) (sknano.core.math.Vector method) rt (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) run() (sknano.testing.GeneratorTestFixtures method) rx (sknano.utils.geometric_shapes.Ellipse attribute) Rx() (in module sknano.core.math) ry (sknano.utils.geometric_shapes.Ellipse attribute) Ry() (in module sknano.core.math) Rz() (in module sknano.core.math)

S

save_data() (sknano.generators.BilayerGrapheneGenerator method) (sknano.generators.FullereneGenerator method) (sknano.generators.GeneratorBase method) (sknano.generators.GrapheneGenerator method) (sknano.generators.MWNTBundleGenerator method) (sknano.generators.MWNTGenerator method) (sknano.generators.SWNTBundleGenerator method) (sknano.generators.SWNTGenerator method) (sknano.generators.UnrolledSWNTGenerator method) scale() (in module sknano.core.math) (sknano.core.math.Vector method) scaling_matrix() (in module sknano.core.math) searchsorted() (sknano.core.math.Point method) (sknano.core.math.Vector method) sections (sknano.io.DATAData attribute) (sknano.io.DATAReader attribute) select() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) select_within() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtoms method) setfield() (sknano.core.math.Point method) (sknano.core.math.Vector method) setflags() (sknano.core.math.Point method) (sknano.core.math.Vector method) setUp() (sknano.testing.GeneratorTestFixtures method) setUpClass() (sknano.testing.GeneratorTestFixtures method) shape (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) shortDescription() (sknano.testing.GeneratorTestFixtures method) sigma_pi_angles (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) size (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) skipTest() (sknano.testing.GeneratorTestFixtures method) sknano.apps (module) sknano.apps.nanogen_gui (module) sknano.core (module) sknano.core.atoms (module) sknano.core.math (module) sknano.core.physics (module) sknano.core.refdata (module) sknano.data (module) sknano.generators (module) sknano.io (module) sknano.scripts (module) sknano.scripts.nanogen (module) sknano.scripts.nanogenui (module) sknano.structures (module) sknano.testing (module) sknano.utils (module)

sknano.utils.analysis (module) sknano.utils.geometric_shapes (module) sknano.utils.symmetry_groups (module) Snapshot (class in sknano.core.atoms) sort() (sknano.core.atoms.Atoms method) (sknano.core.UserList method) (sknano.core.atoms.Bonds method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.Trajectory method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Point method) (sknano.core.math.Points method) (sknano.core.math.Vector method) (sknano.core.math.Vectors method) SpaceGroup (class in sknano.utils.symmetry_groups) Sphere (class in sknano.utils.geometric_shapes) Spheroid (class in sknano.utils.geometric_shapes) Square (class in sknano.utils.geometric_shapes) squeeze() (sknano.core.math.Point method) (sknano.core.math.Vector method) std() (sknano.core.math.Point method) (sknano.core.math.Vector method) strides (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) structure (sknano.generators.BilayerGrapheneGenerator attribute) (sknano.generators.FullereneGenerator attribute) (sknano.generators.GeneratorBase attribute) (sknano.generators.GrapheneGenerator attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) structure_data (sknano.generators.BilayerGrapheneGenerator attribute) (sknano.generators.FullereneGenerator attribute) (sknano.generators.GeneratorBase attribute) (sknano.generators.GrapheneGenerator attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) STRUCTURE_GENERATORS (in module sknano.generators) StructureAnalyzer (class in sknano.utils.analysis) StructureBase (class in sknano.structures) StructureConverter (class in sknano.io) StructureData (class in sknano.io) StructureFormatSpec (class in sknano.io) StructureIO (class in sknano.io) StructureIOError StructureReader (class in sknano.io) StructureWriter (class in sknano.io) sum() (sknano.core.math.Point method) (sknano.core.math.Vector method) swapaxes() (sknano.core.math.Point method) (sknano.core.math.Vector method) SWNT (class in sknano.structures) SWNTBundle (class in sknano.structures) SWNTBundleGenerator (class in sknano.generators) SWNTGenerator (class in sknano.generators) symbol (sknano.core.atoms.Atom attribute) (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) symbols (sknano.core.atoms.Atoms attribute) (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute)

T

T (sknano.core.atoms.POAV attribute) t (sknano.core.atoms.POAV attribute) T (sknano.core.atoms.POAV1 attribute) t (sknano.core.atoms.POAV1 attribute) T (sknano.core.atoms.POAV2 attribute) t (sknano.core.atoms.POAV2 attribute) T (sknano.core.atoms.POAVR attribute) t (sknano.core.atoms.POAVR attribute) T (sknano.core.math.Point attribute) (sknano.core.math.Vector attribute) (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) t1 (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) t2 (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) take() (sknano.core.math.Point method) (sknano.core.math.Vector method) tearDown() (sknano.testing.GeneratorTestFixtures method) tearDownClass() (sknano.testing.GeneratorTestFixtures method) timesteps() (sknano.core.atoms.Trajectory method)

timethis() (in module sknano.core) tobytes() (sknano.core.math.Point method) (sknano.core.math.Vector method) todict() (sknano.core.atoms.Atom method) (sknano.core.atoms.KDTAtom method) (sknano.core.atoms.POAV method) (sknano.core.atoms.POAV1 method) (sknano.core.atoms.POAV2 method) (sknano.core.atoms.POAVAtom method) (sknano.core.atoms.POAVR method) (sknano.core.atoms.XAtom method) (sknano.generators.MWNTBundleGenerator method) (sknano.generators.MWNTGenerator method) (sknano.generators.SWNTBundleGenerator method) (sknano.generators.SWNTGenerator method) (sknano.structures.MWNT method) (sknano.structures.MWNTBundle method) (sknano.structures.SWNT method) (sknano.structures.SWNTBundle method) tofile() (sknano.core.math.Point method) (sknano.core.math.Vector method) tolist() (sknano.core.math.Point method) (sknano.core.math.Vector method) tostring() (sknano.core.math.Point method) (sknano.core.math.Vector method) totient_func() (in module sknano.core.math) trace() (sknano.core.math.Point method) (sknano.core.math.Vector method) Trajectory (class in sknano.core.atoms) transformation_matrix() (in module sknano.core.math) translate() (in module sknano.core.math) (sknano.core.atoms.KDTAtom method) (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtom method) (sknano.core.atoms.POAVAtoms method) (sknano.core.atoms.XAtom method) (sknano.core.atoms.XAtoms method) (sknano.core.math.Point method) (sknano.core.math.Points method) (sknano.core.math.Vector method) (sknano.core.math.Vectors method) (sknano.utils.geometric_shapes.Circle method) (sknano.utils.geometric_shapes.Cube method) (sknano.utils.geometric_shapes.Cuboid method) (sknano.utils.geometric_shapes.Ellipse method) (sknano.utils.geometric_shapes.Ellipsoid method) (sknano.utils.geometric_shapes.Geometric2DRegion method) (sknano.utils.geometric_shapes.Geometric3DRegion method) (sknano.utils.geometric_shapes.Parallelepiped method) (sknano.utils.geometric_shapes.Parallelogram method) (sknano.utils.geometric_shapes.Rectangle method) (sknano.utils.geometric_shapes.Sphere method) (sknano.utils.geometric_shapes.Spheroid method) (sknano.utils.geometric_shapes.Square method) transpose() (sknano.core.math.Point method) (sknano.core.math.Vector method) tube_length (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) tube_mass (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute)

U

u (sknano.utils.geometric_shapes.Parallelepiped attribute) (sknano.utils.geometric_shapes.Parallelogram attribute) unit_cell_mass (sknano.generators.MWNTBundleGenerator attribute) (sknano.generators.MWNTGenerator attribute) (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.MWNT attribute) (sknano.structures.MWNTBundle attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) unit_cell_symmetry_params (sknano.generators.SWNTBundleGenerator attribute) (sknano.generators.SWNTGenerator attribute) (sknano.generators.UnrolledSWNTGenerator attribute) (sknano.structures.SWNT attribute) (sknano.structures.SWNTBundle attribute) unit_vector (sknano.core.atoms.Bond attribute) (sknano.core.math.Vector attribute) unit_vectors (sknano.core.atoms.Bonds attribute) UnrolledSWNTGenerator (class in sknano.generators) UnrolledSWNTMixin (class in sknano.structures)

update_attrs() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) update_bonds() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) update_coordination_numbers() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) update_nearest_neighbors() (sknano.core.atoms.KDTAtoms method) (sknano.core.atoms.POAVAtoms method) update_region_limits() (sknano.utils.geometric_shapes.Cube method) (sknano.utils.geometric_shapes.Cuboid method) (sknano.utils.geometric_shapes.Ellipsoid method) (sknano.utils.geometric_shapes.Parallelepiped method) (sknano.utils.geometric_shapes.Sphere method) (sknano.utils.geometric_shapes.Spheroid method) UserList (class in sknano.core)

V

v (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) (sknano.utils.geometric_shapes.Parallelepiped attribute) (sknano.utils.geometric_shapes.Parallelogram attribute) V1 (sknano.core.atoms.POAV attribute) v1 (sknano.core.atoms.POAV attribute) V1 (sknano.core.atoms.POAV1 attribute) v1 (sknano.core.atoms.POAV1 attribute) V1 (sknano.core.atoms.POAV2 attribute) v1 (sknano.core.atoms.POAV2 attribute) V1 (sknano.core.atoms.POAVR attribute) v1 (sknano.core.atoms.POAVR attribute) V2 (sknano.core.atoms.POAV attribute) v2 (sknano.core.atoms.POAV attribute) V2 (sknano.core.atoms.POAV1 attribute) v2 (sknano.core.atoms.POAV1 attribute) V2 (sknano.core.atoms.POAV2 attribute) v2 (sknano.core.atoms.POAV2 attribute) V2 (sknano.core.atoms.POAVR attribute) v2 (sknano.core.atoms.POAVR attribute) V3 (sknano.core.atoms.POAV attribute) v3 (sknano.core.atoms.POAV attribute) V3 (sknano.core.atoms.POAV1 attribute) v3 (sknano.core.atoms.POAV1 attribute) V3 (sknano.core.atoms.POAV2 attribute) v3 (sknano.core.atoms.POAV2 attribute)

V3 (sknano.core.atoms.POAVR attribute) v3 (sknano.core.atoms.POAVR attribute) var() (sknano.core.math.Point method) (sknano.core.math.Vector method) Vector (class in sknano.core.math) vector (sknano.core.atoms.Bond attribute) Vectors (class in sknano.core.math) vectors (sknano.core.atoms.Bonds attribute) velocities (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtoms attribute) view() (sknano.core.math.Point method) (sknano.core.math.Vector method) viz() (sknano.io.DATAData method) volume (sknano.utils.geometric_shapes.Cube attribute) (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Ellipsoid attribute) (sknano.utils.geometric_shapes.Geometric3DRegion attribute) (sknano.utils.geometric_shapes.Parallelepiped attribute) (sknano.utils.geometric_shapes.Sphere attribute) (sknano.utils.geometric_shapes.Spheroid attribute) Vpi (sknano.core.atoms.POAV attribute) vpi (sknano.core.atoms.POAV attribute) Vpi (sknano.core.atoms.POAV1 attribute) vpi (sknano.core.atoms.POAV1 attribute) Vpi (sknano.core.atoms.POAV2 attribute) vpi (sknano.core.atoms.POAV2 attribute) Vpi (sknano.core.atoms.POAVR attribute) vpi (sknano.core.atoms.POAVR attribute) Vv1v2v3 (sknano.core.atoms.POAV attribute) (sknano.core.atoms.POAV1 attribute) (sknano.core.atoms.POAV2 attribute) (sknano.core.atoms.POAVR attribute) vx (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) vy (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute) vz (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.XAtom attribute)

W

w (sknano.utils.geometric_shapes.Parallelepiped attribute) with_doc (class in sknano.core)

write() (sknano.io.DATAData method) (sknano.io.DATAWriter class method) (sknano.io.StructureWriter class method) (sknano.io.XYZData method) (sknano.io.XYZWriter class method)

X

x (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtom attribute) (sknano.core.atoms.XAtoms attribute) (sknano.core.math.Points attribute) XAtom (class in sknano.core.atoms) XAtoms (class in sknano.core.atoms) xmax (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Rectangle attribute) xmin (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Rectangle attribute) XYZ2DATAConverter (class in sknano.io)

XYZData (class in sknano.io) xyzfile (sknano.io.DATA2XYZConverter attribute) (sknano.io.XYZ2DATAConverter attribute) XYZFormatSpec (class in sknano.io) XYZIOError XYZReader (class in sknano.io) XYZWriter (class in sknano.io)

Y

y (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.KDTAtoms attribute) (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.POAVAtoms attribute) (sknano.core.atoms.XAtom attribute) (sknano.core.atoms.XAtoms attribute) (sknano.core.math.Points attribute) ymax (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Rectangle attribute)

ymin (sknano.utils.geometric_shapes.Cuboid attribute) (sknano.utils.geometric_shapes.Rectangle attribute)

Z

Z (sknano.core.atoms.Atom attribute) (sknano.core.atoms.KDTAtom attribute) z (sknano.core.atoms.KDTAtom attribute) (sknano.core.atoms.KDTAtoms attribute) Z (sknano.core.atoms.POAVAtom attribute) z (sknano.core.atoms.POAVAtom attribute) (sknano.core.atoms.POAVAtoms attribute)

Z (sknano.core.atoms.XAtom attribute) z (sknano.core.atoms.XAtom attribute) (sknano.core.atoms.XAtoms attribute) (sknano.core.math.Points attribute) zmax (sknano.utils.geometric_shapes.Cuboid attribute) zmin (sknano.utils.geometric_shapes.Cuboid attribute)