Class representations of nature’s building blocks (sknano.core.atoms)¶
Getting Started¶
Of the classes implemented in atoms, there are two base
classes from which most classes in atoms inherit from:
Atom and Atoms.
The Atom class represents a single atom. The Atoms class is a container
class for Atom class instances. Sub-classes of Atom classes
add new atom attributes to the Atom class. Every Atom sub-class
has a corresponding container class that sub-classes the Atoms class.
Base Atom/Atoms classes¶
The Atom class represents a single atom. The Atoms class is a container
class for Atom class instances. Sub-classes of Atom classes
add new atom attributes to the Atom class. Every Atom sub-class
has a corresponding container class that sub-classes the Atoms class.
Mixins for extending functionality¶
The mixins sub-package provides mixin classes
which extend the existing Atom and/or Atoms sub-classes.
Classes for molecular dynamics simulations¶
There are two classes for molecular dynamics simulations Trajectory and
Snapshot.
Reference/API¶
sknano.core.atoms Package¶
Functions¶
check_operands(*atoms[, size]) |
Check atom operands. |
compute_angle(*atoms[, check_operands, degrees]) |
Compute bond angles. |
compute_bond(*atoms[, check_operands, degrees]) |
Compute bond angles. |
compute_dihedral(*atoms[, check_operands, ...]) |
Compute dihedral angle. |
compute_improper(*atoms[, check_operands, ...]) |
Compute improper angle. |
generate_vmd_selection_string(keyword, iterable) |
Generate a VMD keyword selection string from iterable. |
vdw_radius_from_basis(*args) |
Helper function to return the maximum van der Waals radius from a tuple of atoms. |
Classes¶
Angle(*args, **kwargs) |
Class representation of bond angle between 3 Atom objects. |
AngleStats(nobs, min, max, minmax, mean, ...) |
Attributes |
Angles(*args[, degrees]) |
TopologyCollection sub-class for collection of atom Angles. |
AngularTopology(*args[, degrees]) |
Topology sub-class for topology with angular measure. |
AngularTopologyCollection(*args[, degrees]) |
TopologyCollection sub-class for collection of angular topologies. |
Atom(*args[, element, mass, Z, parent]) |
Base class for abstract representation of structure atom. |
AtomAdapterMixin |
Mixin Atom class for 3rd party package compatibility. |
AtomTopologyMixin |
Mixin Atom topology class. |
AtomTransformationsMixin |
Mixin Atom class for performing affine transformations. |
Atoms([atoms, update_item_class]) |
Base class for collection of Atom objects. |
AtomsAdapterMixin |
Mixin Atoms class for 3rd party package compatibility. |
AtomsTopologyMixin |
Mixin Atoms topology class. |
AtomsTopologyStats(angles, bonds, dihedrals, ...) |
Attributes |
AtomsTransformationsMixin |
Mixin Atoms class for performing affine transformations. |
BasisAtom(*args[, lattice, xs, ys, zs]) |
An Atom sub-class for a crystal structure basis atom. |
BasisAtoms(*args[, xperiodic, yperiodic, ...]) |
An Atoms sub-class for crystal structure basis atoms. |
Bond(*args[, order]) |
Class representation of bond between 2 Atom objects. |
BondStats(nobs, min, max, minmax, mean, ...) |
Attributes |
Bonds([topolist, parent]) |
Base class for collection of atom Bonds. |
BoundingRegionsMixin |
Mixin Atoms class for computing bounding regions. |
CNAtom(*args[, CN]) |
An Atom class with a coordination number attribute. |
CNAtoms([atoms, update_item_class]) |
An Atoms sub-class for CNAtoms. |
ChargedAtom(*args[, q]) |
An Atom class with an electric charge attribute. |
ChargedAtoms([atoms, update_item_class]) |
An Atoms sub-class for ChargedAtoms. |
Dihedral(*args, **kwargs) |
Class representation of dihedral angle between 4 Atom objects. |
DihedralStats(nobs, min, max, minmax, mean, ...) |
Attributes |
Dihedrals(*args[, degrees]) |
Base class for collection of atom Dihedrals. |
DipoleAtom(*args[, px, py, pz]) |
An Atom sub-class with electric dipole moment attributes. |
DipoleAtoms([atoms, update_item_class]) |
An Atoms sub-class for DipoleAtoms. |
EnergyAtom(*args[, pe, ke, etotal]) |
An Atom class with energy attributes. |
EnergyAtoms([atoms, update_item_class]) |
An Atoms sub-class for EnergyAtoms. |
ForceAtom(*args[, fx, fy, fz]) |
An Atom sub-class with force attributes. |
ForceAtoms([atoms, update_item_class]) |
An Atoms sub-class for ForceAtoms. |
IDAtom(*args[, id, serial, mol]) |
An Atom sub-class with id attributes. |
IDAtoms([atoms, update_item_class]) |
An Atoms sub-class for IDAtoms. |
ImageAtom(*args[, ix, iy, iz]) |
An Atom sub-class with image count attributes. |
ImageAtoms([atoms, update_item_class]) |
An Atoms sub-class for ImageAtoms. |
Improper(*args, **kwargs) |
Class representation of improper angle between 4 Atom objects. |
ImproperStats(nobs, min, max, minmax, mean, ...) |
Attributes |
Impropers(*args[, degrees]) |
Base class for collection of atom Impropers. |
KDTreeAtomsMixin |
Mixin Atoms class for KDTree analysis. |
LatticeAtom(*args[, lattice, xs, ys, zs]) |
An Atom sub-class with crystal lattice attributes. |
LatticeAtoms(*args[, xperiodic, yperiodic, ...]) |
An Atoms sub-class for crystal structure lattice atoms. |
MDAtom(*args[, reference_atom]) |
An Atom sub-class for molecular dynamics trajectory analysis. |
MDAtoms(*args, **kwargs) |
An Atoms sub-class for molecular dynamics trajectory analysis. |
NeighborAtom(*args[, neighbors, neighbor_map]) |
An Atom sub-class for neighbor analysis. |
NeighborAtoms(*args[, kNN, NNrc, ...]) |
An Atoms sub-class for neighbor analysis. |
PBCAtomsMixin(*args[, xperiodic, yperiodic, ...]) |
Mixin Atoms class for PBC. |
POAV(atom) |
Base class for POAV analysis. |
POAV1(*args) |
POAV sub-class for POAV1 analysis. |
POAV2(*args) |
POAV sub-class for POAV2 analysis. |
POAVAtomMixin(*args, **kwargs) |
Mixin class for POAV analysis. |
POAVAtomsMixin(*args, **kwargs) |
Mixin class for POAV analysis. |
POAVR(*args) |
POAV sub-class for POAVR analysis. |
RingAtomMixin(*args, **kwargs) |
Mixin Atom class for ring statistics/network connectivity analysis. |
RingAtomsMixin(*args, **kwargs) |
Mixin Atoms class for ring statistics analysis. |
SelectionException(pstr[, loc, msg, elem]) |
Custom Exception class for Selections. |
SelectionParser([atoms, selstr]) |
Selection parser class. |
Snapshot([trajectory]) |
Container class for Trajectory data at single timestep |
StructureAtom(*args, **kwargs) |
An Atom class for structure analysis. |
StructureAtoms(*args, **kwargs) |
An Atoms sub-class for structure analysis. |
Topology(*atoms, size[, id, type, parent, ...]) |
Base Atom topology class. |
TopologyCollection([topolist, parent]) |
Base Atoms topology class. |
TopologyStats(nobs, min, max, minmax, mean, ...) |
Attributes |
Trajectory([snapshots]) |
Base class for trajectory analysis. |
TypeAtom(*args[, type]) |
An Atom class with an atom type attribute. |
TypeAtoms([atoms]) |
An Atoms sub-class for TypeAtoms. |
VMDAtomAdapterMixin |
An Atom mixin adapter class with atom attributes consistent with VMD atom attributes. |
VMDAtomsAdapterMixin |
An Atoms mixin adapter class with atom attributes consistent with VMD atom attributes. |
VanDerWaalsAtom(*args[, r_vdw]) |
An Atom class with a van der Waals radius attribute. |
VanDerWaalsAtoms([atoms, update_item_class]) |
An Atoms sub-class for VanDerWaalsAtoms. |
VelocityAtom(*args[, vx, vy, vz]) |
An Atom sub-class with velocity component attributes. |
VelocityAtoms([atoms, update_item_class]) |
An Atoms class for VelocityAtoms. |
XYZAtom(*args[, x, y, z]) |
An Atom sub-class with x, y, z attributes. |
XYZAtoms([atoms, update_item_class]) |
An Atoms sub-class for XYZAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.atoms Module¶
Base Atom classes (sknano.core.atoms.atoms)¶
Classes¶
Atom(*args[, element, mass, Z, parent]) |
Base class for abstract representation of structure atom. |
Atoms([atoms, update_item_class]) |
Base class for collection of Atom objects. |
Class Inheritance Diagram¶
sknano.core.atoms.basis_atoms Module¶
Atom classes for crystal structures (sknano.core.atoms.basis_atoms)¶
Classes¶
BasisAtom(*args[, lattice, xs, ys, zs]) |
An Atom sub-class for a crystal structure basis atom. |
BasisAtoms(*args[, xperiodic, yperiodic, ...]) |
An Atoms sub-class for crystal structure basis atoms. |
Class Inheritance Diagram¶
sknano.core.atoms.charged_atoms Module¶
Atom classes with a charge attribute (sknano.core.atoms.charged_atoms)¶
Classes¶
ChargedAtom(*args[, q]) |
An Atom class with an electric charge attribute. |
ChargedAtoms([atoms, update_item_class]) |
An Atoms sub-class for ChargedAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.cn_atoms Module¶
Atom classes with a coordination number (sknano.core.atoms.cn_atoms)¶
Classes¶
CNAtom(*args[, CN]) |
An Atom class with a coordination number attribute. |
CNAtoms([atoms, update_item_class]) |
An Atoms sub-class for CNAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.dipole_atoms Module¶
Atom classes with a dipole moment (sknano.core.atoms.dipole_atoms)¶
Classes¶
DipoleAtom(*args[, px, py, pz]) |
An Atom sub-class with electric dipole moment attributes. |
DipoleAtoms([atoms, update_item_class]) |
An Atoms sub-class for DipoleAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.energy_atoms Module¶
Atom classes with energy attributes (sknano.core.atoms.energy_atoms)¶
Classes¶
EnergyAtom(*args[, pe, ke, etotal]) |
An Atom class with energy attributes. |
EnergyAtoms([atoms, update_item_class]) |
An Atoms sub-class for EnergyAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.force_atoms Module¶
Atom classes with force attributes (sknano.core.atoms.force_atoms)¶
Classes¶
ForceAtom(*args[, fx, fy, fz]) |
An Atom sub-class with force attributes. |
ForceAtoms([atoms, update_item_class]) |
An Atoms sub-class for ForceAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.id_atoms Module¶
Atom classes with id attributes (sknano.core.atoms.id_atoms)¶
Classes¶
IDAtom(*args[, id, serial, mol]) |
An Atom sub-class with id attributes. |
IDAtoms([atoms, update_item_class]) |
An Atoms sub-class for IDAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.image_atoms Module¶
Atom classes with image id attributes (sknano.core.atoms.image_atoms)¶
Classes¶
ImageAtom(*args[, ix, iy, iz]) |
An Atom sub-class with image count attributes. |
ImageAtoms([atoms, update_item_class]) |
An Atoms sub-class for ImageAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.lattice_atoms Module¶
Atom classes for crystal lattices (sknano.core.atoms.lattice_atoms)¶
Classes¶
LatticeAtom(*args[, lattice, xs, ys, zs]) |
An Atom sub-class with crystal lattice attributes. |
LatticeAtoms(*args[, xperiodic, yperiodic, ...]) |
An Atoms sub-class for crystal structure lattice atoms. |
Class Inheritance Diagram¶
sknano.core.atoms.md_atoms Module¶
Atom classes for MD trajectory analysis (sknano.core.atoms.md_atoms)¶
An Atom class for molecular dynamics trajectory analysis.
Classes¶
MDAtom(*args[, reference_atom]) |
An Atom sub-class for molecular dynamics trajectory analysis. |
MDAtoms(*args, **kwargs) |
An Atoms sub-class for molecular dynamics trajectory analysis. |
Class Inheritance Diagram¶
sknano.core.atoms.molecules Module¶
Base molecule classes (sknano.core.atoms.molecules)¶
Classes¶
Molecule([atoms]) |
Base class for abstract representation of a molecule. |
Molecules([molecules, update_item_class]) |
Base class for collection of Molecule objects. |
Class Inheritance Diagram¶
sknano.core.atoms.neighbor_atoms Module¶
Atom classes for NN analysis (sknano.core.atoms.neighbor_atoms)¶
Classes¶
NeighborAtom(*args[, neighbors, neighbor_map]) |
An Atom sub-class for neighbor analysis. |
NeighborAtoms(*args[, kNN, NNrc, ...]) |
An Atoms sub-class for neighbor analysis. |
Class Inheritance Diagram¶
sknano.core.atoms.selections Module¶
Atom selection classes (sknano.core.atoms.selections)¶
Functions¶
generate_vmd_selection_string(keyword, iterable) |
Generate a VMD keyword selection string from iterable. |
Classes¶
SelectionException(pstr[, loc, msg, elem]) |
Custom Exception class for Selections. |
SelectionParser([atoms, selstr]) |
Selection parser class. |
Class Inheritance Diagram¶
sknano.core.atoms.structure_atoms Module¶
Atom classes for structure analysis (sknano.core.atoms.structure_atoms)¶
Classes¶
StructureAtom(*args, **kwargs) |
An Atom class for structure analysis. |
StructureAtoms(*args, **kwargs) |
An Atoms sub-class for structure analysis. |
Class Inheritance Diagram¶
sknano.core.atoms.trajectory Module¶
Trajectory class for MD simulations (sknano.core.atoms.trajectory)¶
Classes for analyzing the atom trajectories of molecular dynamics simulations.
Classes¶
Snapshot([trajectory]) |
Container class for Trajectory data at single timestep |
Trajectory([snapshots]) |
Base class for trajectory analysis. |
Class Inheritance Diagram¶
sknano.core.atoms.type_atoms Module¶
Atom classes with a ‘type’ attribute (sknano.core.atoms.type_atoms)¶
An Atom class with a type attribute.
Classes¶
TypeAtom(*args[, type]) |
An Atom class with an atom type attribute. |
TypeAtoms([atoms]) |
An Atoms sub-class for TypeAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.vdW_atoms Module¶
Atom classes with van der Waals radius (sknano.core.atoms.vdW_atoms)¶
Functions¶
vdw_radius_from_basis(*args) |
Helper function to return the maximum van der Waals radius from a tuple of atoms. |
Classes¶
VanDerWaalsAtom(*args[, r_vdw]) |
An Atom class with a van der Waals radius attribute. |
VanDerWaalsAtoms([atoms, update_item_class]) |
An Atoms sub-class for VanDerWaalsAtoms. |
Class Inheritance Diagram¶
sknano.core.atoms.velocity_atoms Module¶
Atom classes with velocity attributes (sknano.core.atoms.velocity_atoms)¶
Classes¶
VelocityAtom(*args[, vx, vy, vz]) |
An Atom sub-class with velocity component attributes. |
VelocityAtoms([atoms, update_item_class]) |
An Atoms class for VelocityAtoms. |
Class Inheritance Diagram¶
