schrodinger.geometry module¶

schrodinger::geometry C++ wrappers

class schrodinger.geometry.MomentsOfInertia¶

schrodinger::geometry::MomentsOfInertia

__init__(*args, **kwargs)¶

axes¶

moments¶

class schrodinger.geometry.PairPath¶

schrodinger::geometry::PairPath

__init__(*args, **kwargs)¶

a¶

b¶

schrodinger.geometry.cealign(arrayA, arrayB, windowSize, gapMax) → std::vector< schrodinger::geometry::PairPath,std::allocator< schrodinger::geometry::PairPath > >¶

schrodinger.geometry.center_of_mass(st) → Eigen::Vector3d¶

schrodinger.geometry.center_of_mass(st, atoms) → Eigen::Vector3d

Overload 1:

Calculates the center of mass of the given structure

Parameters:: st: – structure to consider
Return type:: Eigen::Vector3d
Returns:: : resulting center of mass coordinate

Overload 2:

Calculates the center of mass of the given structure

Parameters:

st: – structure to consider
atoms: – atoms for which calculation is desired

Return type:

Eigen::Vector3d

Returns:

: resulting center of mass coordinate

schrodinger.geometry.centroid(coordinates) → Eigen::Vector3d¶

schrodinger.geometry.centroid(st) → Eigen::Vector3d

schrodinger.geometry.centroid(st, atoms) → Eigen::Vector3d

Overload 1:

Calculates the centroid among a set of Cartesian coordinates

Parameters:: coordinates: – coordinates to consider
Return type:: Eigen::Vector3d
Returns:: : resulting centroid coordinate
Raises:: RuntimeError: if no coordinates are supplied

Overload 2:

Calculates the centroid of the given structure

Parameters:: st: – structure to consider
Return type:: Eigen::Vector3d
Returns:: : resulting centroid coordinate

Overload 3:

Calculates the centroid of the given structure

Parameters:

st: – structure to consider
atoms: – atoms for which calculation is desired

Return type:

Eigen::Vector3d

Returns:

: resulting centroid coordinate

schrodinger.geometry.principal_moments(coordinates, weights) → MomentsOfInertia¶

schrodinger.geometry.principal_moments(st) → MomentsOfInertia

schrodinger.geometry.principal_moments(st, atoms) → MomentsOfInertia

Overload 1:

Calculates the principal moments of inertia of a set of Cartesian coordinates and matching weights.

Notes: PBCs are not checked.

Parameters:

coordinates: – coordinates to consider
weights: – weights corresponding to each of the supplied coordinates

Return type:

MomentsOfInertia

Returns:

: principal axes and moments of inertia

Raises:

RuntimeError: if unable to find eigenvalues/eigenvectors

Overload 2:

Calculates the principal moments of inertia of the given structure. PBCs are checked for any crossing bonds.

Parameters:: st: – structure to consider
Return type:: MomentsOfInertia
Returns:: : principal axes and moments of inertia
Raises:: RuntimeError: on error checking if a bond crosses PBC
Raises:: InvalidArgument: if any PBC is crossed

Overload 3:

Calculates the principal moments of inertia of the requested atoms within the given structure.

Parameters:

st: – structure to consider
atoms: – atoms for which calculation is desired

Return type:

MomentsOfInertia

Returns:

: principal axes and moments of inertia

Raises:

RuntimeError: on error checking if a bond crosses PBC

Raises:

InvalidArgument: if any PBC is crossed

schrodinger.geometry.weighted_centroid(coordinates, weights) → Eigen::Vector3d¶

Calculates the weighted centroid among a set of Cartesian coordinates

Parameters:

coordinates: – coordinates to consider
weights: – weights corresponding to each of the supplied coordinates

Return type:

Eigen::Vector3d

Returns:

: resulting weighted centroid coordinate

Raises:

RuntimeError: if no coordinates are supplied

Raises:

RuntimeError: if coordinates and weights have different dimensions