class sknano.core.atoms.MDAtoms(atoms=None, kNN=16, NNrc=2.0, **kwargs)[source][source]

An Atoms sub-class for molecular dynamics trajectory analysis.

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


atoms : {None, sequence, MDAtoms}, optional

if not None, then a list of MDAtom instance objects or an existing MDAtoms instance object.


CM Alias for center_of_mass.
CN_counts Alias for coordination_number_counts.
M Total mass of Atoms.
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.
atom_ids Alias for IDAtoms.ids.
atom_tree KDTree of
atomtypes Alias for types.
bounds Bounds of Atoms.
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.
coordination_counts Alias for coordination_number_counts.
coordination_number_counts Coordination number counts.
coordination_numbers ndarray of CNAtom.CNs.
coords Alias for Atoms.r.
distances Neighbor atoms distances.
dr ndarray of Atom.dr displacement Vectors
elements ndarray of Atom.elements in Atoms.
f Alias for forces.
forces ndarray of ForceAtom forces.
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.
inertia_tensor Inertia tensor.
ix ndarray of Atoms \(i_x\) values.
iy ndarray of Atoms \(i_y\) values.
iz ndarray of Atoms \(i_z\) values.
kNN Number of nearest neighbors to return when querying the kd-tree.
kinetic_energies ndarray of
masses ndarray of Atom.masss in Atoms.
mol_ids Alias for IDAtoms.mols.
molecule_ids Alias for IDAtoms.mols.
mols Return array of IDAtom.mols.
nearest_neighbors Return array of nearest-neighbor atoms for each KDTAtom.
neighbors Return array of neighbor atoms.
potential_energies ndarray of
q Return the total net charge of ChargedAtoms.
r ndarray of Atom.r position Vectors
rs ndarray of Atom.r position Vectors
symbols ndarray of Atom.symbols in Atoms.
total_energies ndarray of EnergyAtom.etotal.
typemap dict of TypeAtom.types.
types ndarray of TypeAtom.types.
v Alias for velocities.
velocities ndarray of VelocityAtom velocities.
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 Atoms \(x\) coordinates.
xs ndarray of Atoms \(x\) coordinates.
y ndarray of Atoms \(y\) coordinates.
ys ndarray of Atoms \(y\) coordinates.
z ndarray of Atoms \(z\) coordinates.
zs ndarray of Atoms \(z\) coordinates.


add_atomtype(atom) Alias for add_type.
add_atomtypes([atoms]) Alias for add_types.
add_type(atom) Add atom type to typemap.
add_types([atoms]) Add atom type for each atom in atoms to TypeAtom.typemap dictionary.
assign_unique_ids([starting_id]) Assign unique 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.
clip_bounds(region[, center_before_clipping]) Remove atoms outside the given region.
compute_POAVs() Compute POAV1, POAV2, POAVR.
filter(condition[, invert]) Filter Atoms by condition.
filter_ids(atom_ids[, invert]) Filter Atoms by IDAtoms.ids in atom_ids.
filtered(condition[, invert]) Return new list of Atoms filtered by condition.
filtered_ids(atom_ids[, invert]) Return new Atoms filtered by IDAtoms.ids in atom_ids.
get_POAV_attr(POAV_class, attr) Return list of POAVAtom POAV1 POAV2 or POAVR attribute.
get_atom(id) Get IDAtom with == id.
get_atoms([asarray]) Return list of Atoms.
get_atomtypes([asdict]) Alias for get_types.
get_coords([asdict]) Return atom coords.
get_types([asdict]) Return list of TypeAtom TypeAtom.types.
getatomattr(attr) Get ndarray of atom attributes attr.
index(item, *args)
insert(i, item)
mapatomattr([from_attr, to_attr, attrmap]) Set/update atom attribute from another atom attribute with dict.
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.
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.
set_pbc([xperiodic, yperiodic, zperiodic])
sort([key, reverse])
translate(t[, fix_anchor_points]) Translate Atom vectors by Vector t.
update_attrs() Update KDTAtoms attributes.
update_bonds() Update KDTAtom.bonds.