msmbuilder.metrics.ContinuousContact.__init__

ContinuousContact.__init__(metric='euclidean', p=2, contacts='all', scheme='closest-heavy', V=None, VI=None)

Create a distance calculator based on the distances between pairs of atoms in a sturcture – like the contact map except without casting to boolean.

Parameters:

metric : {‘braycurtis’, ‘canberra’, ‘chebyshev’, ‘cityblock’,

‘correlation’, ‘cosine’, ‘euclidean’, ‘minkowski’, ‘sqeuclidean’}

distance metric to equip the space with

p : int

exponent for p-norm, used only for metric=’minkowski’

contacts : {ndarray, ‘all’}

contacts can be an n by 2 array, where each row is a pair of integers giving the indices of 2 residues whose distance you care about. Alternatively, contacts can be the string ‘all’. This is a shortcut for supplying a contacts list that includes all (N-2 * N-3) / 2 pairs of residues which are more than 2 residues apart.

scheme: {‘CA’, ‘closest’, ‘closest-heavy’} :

scheme can be ‘CA’, ‘closest’, or ‘closest-heavy’ and gives the sense in which the ‘distance between two residues’ is computed. If scheme is ‘CA’, then we’ll use the cartesian distance between the residues’ C-alpha atoms as their distance for the purpose of calculating whether or not they have exceeded the cutoff. If scheme is ‘closest’, we’ll use the distance between the closest pair of atoms where one belongs to residue i and to residue j. If scheme is ‘closest-heavy’, we’ll use the distance between the closest pair of non-hydrogen atoms where one belongs to reside i and one to residue j.