MDAtoms

class sknano.core.atoms.MDAtoms(*args, **kwargs)

Bases: sknano.core.atoms.energy_atoms.EnergyAtoms, sknano.core.atoms.force_atoms.ForceAtoms, sknano.core.atoms.velocity_atoms.VelocityAtoms, sknano.core.atoms.structure_atoms.StructureAtoms

An Atoms sub-class for molecular dynamics trajectory analysis.

Sub-class of StructureAtoms class, and a container class for lists of MDAtom instances.

Parameters:atoms ({None, sequence, MDAtoms}, optional) – if not None, then a list of MDAtom instance objects or an existing MDAtoms instance object.

Attributes

CM	Alias for center_of_mass.
CN_counts	Alias for coordination_number_counts.
M	Total mass of Atoms.
NNN	Number of first nearest-neighbors.
NNrc	Nearest neighbor radius cutoff.
Natoms	Number of atoms in Atoms.
Ntypes	Number of unique types.
POAV1	List of POAVAtom POAV1 POAV1 attribute.
POAV2	List of POAVAtom POAV2 POAV2 attribute.
POAVR	List of POAVAtom POAVR POAVR attribute.
Rn_counter	Return rings per atom counter.
all_angles	Angles.
all_bonds	Bonds.
all_dihedrals	Dihedrals.
all_impropers	Impropers.
angles	Angles.
angles_in_degrees	bool setting for returning angles in degrees.
atom_ids	Alias for ids.
atom_tree	Concrete implementation of atom_tree.
atomtypes	Alias for types.
bonds	Bonds.
bounding_box	Axis-aligned bounding box of Atoms.
bounding_region	Bounding Geometric3DRegion.
bounding_sphere	Bounding Sphere of Atoms.
bounds	Alias for bounding_region.
cell	Alias for LatticeAtoms.cell_matrix.
cell_matrix	Return the Crystal3DLattice.cell_matrix.
center_of_mass	Center-of-Mass coordinates of Atoms.
centroid	Centroid of Atoms.
charges	Return array of ChargedAtom charges.
com	Alias for center_of_mass.
coordinates_bounding_box	Bounding box of atom coordinates.
coordination_counts	Alias for coordination_number_counts.
coordination_number_counts	Coordination number counts.
coordination_numbers	ndarray of NeighborAtom.CNs.
coords	Alias for Atoms.r.
dihedrals	Dihedrals.
distances	Neighbor atoms distances.
dr	Vectors of Atom.dr displacement Vectors
elements	ndarray of Atom.elements.
etotal	ndarray of EnergyAtom.etotal.
f	Vectors of ForceAtom forces.
first_neighbors	First neighbors.
fmtstr	Format string.
forces	Alias for f.
fx	ndarray of Atoms \(f_x\) components.
fy	ndarray of Atoms \(f_y\) components.
fz	ndarray of Atoms \(f_z\) components.
i	Alias for images.
ids	Return array of IDAtom.ids.
images	ndarray of ImageAtom images.
impropers	Impropers.
indices	Return array of IDAtom.indexs.
inertia_tensor	Return inertia tensor about the origin.
ix	ndarray of Atoms \(i_x\) values.
iy	ndarray of Atoms \(i_y\) values.
iz	ndarray of Atoms \(i_z\) values.
kNN	Max number of nearest-neighbors to return from kd-tree search.
ke	ndarray of EnergyAtom.ke.
kinetic_energies	An alias for EnergyAtoms.ke.
lattice	Return the LatticeAtom.lattice of the first atom in self.
lattice_region	lattice region.
masses	ndarray of Atom.masss.
mol_ids	Alias for mols.
molecule_ids	Alias for mols.
mols	Return array of IDAtom.mols.
moment_of_inertia	Alias for inertia_tensor.
nearest_neighbors	Return array of nearest-neighbor atoms for each KDTAtom.
neighbor_cutoffs	Nearest neighbor radius cutoff.
neighbor_distances	Neighbor distances
neighbors	Return array of neighbor atoms.
neighbors_analyzed	Return True if neighbors have been analyzed.
nn_adjacency_list	Return nearest-neighbor adjacency list
nn_adjacency_map	Return nearest-neighbor adjacency map
nn_adjacency_matrix	Return nearest-neighbor adjacency matrix.
nn_seed	Return nearest-neighbor seed list
nn_vectors	Return nearest-neighbor vectors.
pbc	Return boolean array of periodic boundaries set along x,y,z axes.
pe	ndarray of EnergyAtom.pe.
positions	Alias for Atoms.r.
potential_energies	An alias for EnergyAtoms.pe.
principal_axes	Return principal axes of rotation computed from the inertia tensor.
principal_moments_of_inertia	Return principal moments of inertia.
q	Return the total net charge of ChargedAtoms.
r	Vectors of Atom.r position Vectors
radius_of_gyration	Return radius of gyration.
ring_stats	dict of ring statistics.
rings_per_atom	Rings per atom list.
rs	Vectors of LatticeAtom.rs Vectors
second_neighbors	Second neighbors.
serials	Alias for ids.
symbols	ndarray of Atom.symbols.
third_neighbors	Third neighbors.
topology_stats	dict of topology statistics.
total_energies	An alias for EnergyAtoms.etotal.
typemap	dict of TypeAtom.types.
types	ndarray of TypeAtom.types.
v	Returns a Vectors object of VelocityAtom.v Vectors
velocities	Alias for v.
vmd_indices	Array of VMD atom index attribute.
volume	Volume of region containing atoms.
vx	ndarray of Atoms \(v_x\) components.
vy	ndarray of Atoms \(v_y\) components.
vz	ndarray of Atoms \(v_z\) components.
x	ndarray of XYZAtom.x coordinates.
xperiodic	Return True if periodic along the x axis.
xs	ndarray of LatticeAtom.xs values
y	ndarray of XYZAtom.y coordinates.
yperiodic	Return True if periodic along the y axis.
ys	ndarray of LatticeAtom.ys values
z	ndarray of XYZAtom.z coordinates.
zperiodic	Return True if periodic along the z axis.
zs	ndarray of LatticeAtom.zs values

Methods

add_atomtype(atom)	Alias for add_type.
add_atomtypes([atoms])	Alias for add_types.
add_ring(nodes)	Append ring atoms to rings.
add_type(atom)	Add atom type to typemap.
add_types([atoms])	Add atom type for each atom in atoms to TypeAtom.typemap dictionary.
align_principal_axis(index, vector)	Align principal_axes`[`index] along vector.
analyze_POAVs(**kwargs)	Compute POAV1, POAV2, POAVR.
analyze_network([cutoff, max_ring_size, ...])	Analyze the network connectivity.
append(atom)
assign_unique_ids([starting_id])	Assign unique IDAtom.id to each IDAtom in IDAtoms.
assign_unique_types([from_attr])	Assign unique TypeAtom.types to each TypeAtom in TypeAtoms from an existing unique atom attribute.
center_CM([axis])	Alias for center_center_of_mass.
center_center_of_mass([axis])	Center atoms on center-of-mass coordinates.
center_centroid()	Center centroid on origin.
center_com([axis])	Alias for center_center_of_mass.
clear()
clip_bounds(region[, center_before_clipping])	Remove atoms outside the given region.
compute_POAVs(**kwargs)	Alias for analyze_POAVs.
copy()
count(item)
count_neighbors(other, r[, p])	Count how many nearby neighbor pairs can be formed.
count_neighbors_in_self(r[, p])	Count number of neighbor pairs for each atom in self.
extend(other)
filter(condition[, invert])	Filter Atoms by condition.
filter_ids(atom_ids[, invert])	Filter Atoms by IDAtoms.ids in atom_ids.
filter_vmd_indices(vmd_indices[, invert])	Filter Atoms by VMDAtomsAdapterMixin.vmd_indices.
filtered(condition[, invert])	Return new list of Atoms filtered by condition.
filtered_ids(atom_ids[, invert])	Return new Atoms object filtered by atom_ids.
filtered_vmd_indices(vmd_indices[, invert])	Return new Atoms filtered by vmd_indices.
get_POAV_attr(POAV_class, attr)	Return list of POAVAtom POAV1 POAV2 or POAVR attribute.
get_angle(*triplet[, check_operands, degrees])	Compute bond angles.
get_angles([neighbors_only, unique, ids_only])	Return list of bond angles.
get_atom(id)	Get IDAtom with Xatom.id == id.
get_atom_from_vmd_index(vmd_index)	Get Atom by VMD atom index.
get_atoms([ids])	Overrides parent class Atoms.get_atoms.
get_atomtypes([asdict])	Alias for get_types.
get_bond(*pair[, check_operands, degrees])	Compute bond lengths.
get_bonds([neighbors_only, unique, ids_only])	Return list of bonds.
get_coords([asdict])	Return atom coords.
get_dihedral(*ids[, check_operands, degrees])	Compute dihedral angles.
get_dihedrals([neighbors_only, unique, ids_only])	Return list of Dihedrals
get_improper(*ids[, check_operands, degrees])	Compute improper angles.
get_impropers([neighbors_only, unique, ids_only])	Return list of Improperss
get_nth_nearest_neighbors(n[, exclusive])	Return `n`th nearest neighbors.
get_types([asdict])	Return list of TypeAtom TypeAtom.types.
get_vmd_selection_string(keyword)	Get a VMD selection string for the VMD keyword.
getattr(attr[, default, recursive])	Get ndarray of atom attributes attr.
index(item, *args)
insert(i, atom)
mapatomattr([from_attr, to_attr, attrmap])	Set/update atom attribute from another atom attribute with dict.
pop([i])
query_atom_tree([k, eps, p, rc])	Query atom tree for nearest neighbors distances and indices.
query_ball_point(pts, r[, p, eps])	Find all Atoms within distance r of point(s) pts.
query_ball_tree(other, r[, p, eps])	Find all pairs of Atoms whose distance is at more r.
query_pairs(r[, p, eps])	Find all pairs of points within a distance r.
remove(item)
reset_attrs([poavs])	Reset the POAVAtomsMixin class attributes, then call parent class reset_attrs method.
reset_poav_atoms_attrs()	Reset the POAVAtomsMixin class attributes.
reset_ring_atoms_attrs()	Reset the RingAtomsMixin class attributes.
reverse()
rezero([epsilon])	Set values with absolute value less than epsilon to zero.
rezero_coords([epsilon])	Alias for Atoms.rezero_xyz.
rezero_xyz([epsilon])	Rezero position vector components with absolute value less than epsilon.
rotate(**kwargs)	Rotate Atom vectors.
select([selstr, selstrlist, verbose])	Return Atom or Atoms from selection command.
set_pbc(dims)	Set periodic boundaries along dims.
sort([key, reverse])
todict()	Return dict of constructor parameters.
translate(t[, fix_anchor_points, cartesian])	Translate Atom vectors by Vector t.
unset_pbc()	Turn of PBCs along all dimensions.
update_attrs([topology])	Update AtomsTopologyMixin class attributes.
update_neighbor_lists()	Update neighbor lists
update_neighbors(**kwargs)	Update NeighborAtom.neighbors.
update_ring_stats([angle_reference, ...])
within_region(region)	Returns new Atoms object containing atoms within region.
wrap_coords([pbc])	Wrap coordinates into lattice.