MolecularProperties
An object whose sole purpose in life is to get molecular properties
A property should be implemented in two parts:
1) a classmethod called get_prop_
All properties should be appropriately vectorized to work on a single configuration or a set of configurations
@classmethod
mass_weighted_coords(cls, mol):
Computes the moments of inertia
mol:AbstractMolecule:returns:_
@classmethod
g_matrix(cls, mol):
mol:AbstractMolecule:returns:_
@classmethod
center_of_mass(cls, mol):
Computes the moments of inertia
mol:AbstractMolecule:returns:_
@classmethod
inertia_tensor(cls, mol):
Computes the inertia tensors for the stored geometries
mol:AbstractMolecule:returns:_
@classmethod
moments_of_inertia(cls, mol):
Computes the moments of inertia
mol:AbstractMolecule:returns:_
@classmethod
principle_axis_data(cls, mol, sel=None):
Generates the center of masses and inertial axes
mol:AbstractMolecule:returns:_
@classmethod
principle_axis_transformation(cls, mol, sel=None, inverse=False):
Generates the principle axis transformation for a Molecule
mol:AbstractMolecule:returns:_
@classmethod
eckart_embedding_data(cls, mol, coords, sel=None, in_paf=False, planar_ref_tolerance=None, proper_rotation=False):
mol:AbstractMoleculecoords:Anysel:Any:returns:_
@classmethod
eckart_transformation(cls, mol, ref_mol, sel=None, inverse=False, planar_ref_tolerance=None, proper_rotation=False):
ref_mol:AbstractMoleculereference geometry
mol:AbstractMoleculemolecules to get Eckart embeddings for
sel:Anycoordinate selection to use when doing the Eckart stuff
:returns:_
@classmethod
eckart_embedded_coords(cls, mol, coords, sel=None, in_paf=False, reset_com=True, planar_ref_tolerance=None, proper_rotation=False):
mol:AbstractMoleculecoords:Anysel:Any:returns:_
@classmethod
coriolis_constants(cls, mol):
@classmethod
translation_rotation_eigenvectors(cls, mol, sel=None):
mol:AbstractMoleculemolecules to get eigenvectors for
sel:Anycoordinate selection to use when doing the rotation/translation calculations
:returns:_
@classmethod
fragments(cls, mol):
mol:AbstractMolecule:returns:_
@classmethod
fragment_indices(cls, mol):
mol:AbstractMolecule:returns:_
@classmethod
edge_graph(cls, mol):
mol:AbstractMolecule:returns:_
@classmethod
guessed_bonds(cls, mol, tol=1.05, guess_type=True):
Guesses the bonds for the molecule by finding the ones that are less than some percentage of a single bond for that pair of elements
:returns:_
@classmethod
get_prop_chemical_formula(cls, atoms):
atoms:Tuple[str]:returns:_
@classmethod
chemical_formula(cls, mol):
mol:AbstractMolecule:returns:_