schrodinger.comparison.neighbors module

methods for handling neighbors with ase

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

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

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.spherical_atomic_cluster(st, Rcut)

Construct a cluster of neighbors. This implementation includes any molecule that has any atom inside the cutoff radius with respect to the central molecule. The Nth value of the generator is centered about the Nth molecule.

params:

st (Structure): represents the conventional cell Rcut (float): cutoff for including molecules

returns:

Generator of clusters, if Z’=1 only the first cluster should be unique.

schrodinger.comparison.neighbors.search_cluster_radius(st, Ncluster_min=25, Ncluster_max=35, r=4.0, cluster_at_r=None, dRthresh=0.01) → 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.

Arguments:

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 (Structure or None): the cluster produced by spherical_atomic_cluster at radius r dRthresh (float): stop search if we can’t find Ncluster_min < N < Ncluster_max within precision dRthresh

Returns:

tuple of Structure, radius