schrodinger.comparison.neighbors module

methods for handling neighbors with ase

class schrodinger.comparison.neighbors.MoleculeNeighbor(molecule_number, ix, iy, iz)

Bases: tuple

ix

Alias for field number 1

iy

Alias for field number 2

iz

Alias for field number 3

molecule_number

Alias for field number 0

schrodinger.comparison.neighbors.com_cell_atoms(st, unit_cell, symbol='C')

Construct an Atoms instance where each atom represents the COM of a molecule in st

params:

st (Structure): the input crystal unit_cell (3x3 np.array): lattice vectors are rows symbol (str): symbol for each atom in COM cell

returns:

An Atoms instance that gives the COM cell

schrodinger.comparison.neighbors.spherical_cluster(st, Rcut)

Construct a spherical cluster of radius Rcut about each molecules center of mass in st. The Nth value of the generator is centered about the Nth molecule.

params:

st (Structure): represents the conventional cell unit_cell (3x3 np.array): lattice vectors as rows Rcut (float): cutoff for including molecules

returns:

Generator of clusters

schrodinger.comparison.neighbors.spherical_atomic_cluster(st: schrodinger.structure._structure.Structure, Rcut: float, center_idx=1)

Construct a cluster of neighbors centered about the center_idx’th molecule. This implementation includes any molecule that has any atom inside the cutoff radius with respect to the central molecule.

Parameters

  • st – represents the conventional cell

  • Rcut – cutoff for including molecules

  • center_idx – molecule index for the spherical cluster center

schrodinger.comparison.neighbors.search_cluster_radius(st, Ncluster_min=25, Ncluster_max=35, r=4.0, cluster_at_r=None, dRthresh=0.01, center_idx=1) → Tuple[schrodinger.structure._structure.Structure, float]

Search for a cluster radius that gives a spherical cluster of a certain size. If a cluster that satisfies the limits is not found a RuntimeError.

Parameters

  • st (Structure) – the crystal

  • Ncluster_min (int) – minimum number of molecules in cluster

  • Ncluster_max (int) – maximum number of molecules in cluster

  • r (float) – radius to start search

  • cluster_at_r (Optional[Structure]) – the cluster produced by spherical_atomic_cluster at radius r

  • Rthresh (float) – stop search if we can’t find Ncluster_min < N < Ncluster_max within precision dRthresh

Returns

tuple of Structure, radius