mmtbx.ions.svm.utils module

Utility functions used within this module.

mmtbx.ions.svm.utils.filter_svm_outputs(chem_env, scatter_env, predictions)

Applies a simple set of filters to the accepted ions that might match a given chemical and scattering environment to help catch corner cases where the SVM might fail.

Parameters:
Return type:

list of str

mmtbx.ions.svm.utils.iterate_sites(pdb_hierarchy, split_sites=False, res_filter=None)

Returns a generator iterating over all atoms in pdb_hierarchy. Optionally skips sites with alternate conformations and can filter by residue name.

Parameters:

  • pdb_hierarchy (iotbx.pdb.hierarchy.root)

  • split_sites (bool, optional) – Indicates whether to iterate over sites with alternate conformations, by default they are not included.

  • res_filter (list of str, optional) – List of residue names to include, by default, all residues are examined.

Return type:

generator of iotbx.pdb.hierarchy.atom

mmtbx.ions.svm.utils.scale_to(matrix, source, target)

Given an upper and lower bound for each row of matrix, scales the values to be within the range specified by target.

Parameters:

  • matrix (numpy.array of float) – The matrix to be scaled.

  • source (tuple of numpy.array of float) – The upper and lower bound on the values of each row in the original matrix.

  • target (tuple of float) – The target range to scale to.

Returns:

matrix – The matrix with scaled values.

Return type:

numpy.array of float

Examples

>>> from mmtbx.ions.svm.utils import scale_to
>>> import numpy as np
>>> matrix = np.array([[0, 1, 2],
                       [2, 3, 4],
                       [1, 2, 3]])
>>> source = (np.array([2, 3, 4]),
              np.array([0, 1, 2]))
>>> target = (0, 1)
>>> scale_to(matrix, source, target)
array([[ 1. ,  1. ,  1. ],
       [ 0. ,  0. ,  0. ],
       [ 0.5,  0.5,  0.5]])