pyemma.coordinates.data.MDFeaturizer¶

class pyemma.coordinates.data.MDFeaturizer(topfile, **kwargs)¶

Extracts features from MD trajectories.

__init__(topfile, **kwargs)¶

extracts features from MD trajectories.

Parameters

topfile (str or mdtraj.Topology) – a path to a topology file (pdb etc.) or an mdtraj Topology() object
use_cache (boolean, default=True) – Deprecated, topologies are always cached.

Methods

`__init__`(topfile, **kwargs)	extracts features from MD trajectories.
`add_all`([reference, atom_indices, …])	Adds all atom coordinates to the feature list.
`add_angles`(indexes[, deg, cossin, periodic])	Adds the list of angles to the feature list
`add_backbone_torsions`([selstr, deg, cossin, …])	Adds all backbone phi/psi angles or the ones specified in `selstr` to the feature list.
`add_chi1_torsions`([selstr, deg, cossin, …])	Adds all chi1 angles or the ones specified in `selstr` to the feature list.
`add_contacts`(indices[, indices2, threshold, …])	Adds the contacts to the feature list.
`add_custom_feature`(feature)	Adds a custom feature to the feature list.
`add_custom_func`(func, dim, args, *kwargs)	adds a user defined function to extract features
`add_dihedrals`(indexes[, deg, cossin, periodic])	Adds the list of dihedrals to the feature list
`add_distances`(indices[, periodic, indices2])	Adds the distances between atoms to the feature list.
`add_distances_ca`([periodic, excluded_neighbors])	Adds the distances between all Ca’s to the feature list.
`add_group_COM`(group_definitions[, ref_geom, …])	Adds the centers of mass (COM) in cartesian coordinates of a group or groups of atoms.
`add_group_mindist`(group_definitions[, …])	Adds the minimum distance between groups of atoms to the feature list.
`add_inverse_distances`(indices[, periodic, …])	Adds the inverse distances between atoms to the feature list.
`add_minrmsd_to_ref`(ref[, ref_frame, …])	Adds the minimum root-mean-square-deviation (minrmsd) with respect to a reference structure to the feature list.
`add_residue_COM`(residue_indices[, scheme, …])	Adds a per-residue center of mass (COM) in cartesian coordinates.
`add_residue_mindist`([residue_pairs, scheme, …])	Adds the minimum distance between residues to the feature list.
`add_selection`(indexes[, reference, …])	Adds the coordinates of the selected atom indexes to the feature list.
`add_sidechain_torsions`([selstr, deg, …])	Adds all side chain torsion angles or the ones specified in `selstr` to the feature list.
`describe`()	Returns a list of strings, one for each feature selected, with human-readable descriptions of the features.
`dimension`()	current dimension due to selected features
`load`(file_name[, model_name])	Loads a previously saved PyEMMA object from disk.
`pairs`(sel[, excluded_neighbors])	Creates all pairs between indexes.
`remove_all_custom_funcs`()	Remove all instances of CustomFeature from the active feature list.
`save`(file_name[, model_name, overwrite, …])	saves the current state of this object to given file and name.
`select`(selstring)	Returns the indexes of atoms matching the given selection
`select_Backbone`()	Returns the indexes of backbone C, CA and N atoms
`select_Ca`()	Returns the indexes of all Ca-atoms
`select_Heavy`([exclude_symmetry_related])	Returns the indexes of all heavy atoms (Mass >= 2), optionally excluding symmetry-related heavy atoms.
`transform`(traj)	Maps an mdtraj Trajectory object to the selected output features

Attributes

`logger`	The logger for this class instance
`name`	The name of this instance
`topologyfile`

add_all(reference=None, atom_indices=None, ref_atom_indices=None)¶

Adds all atom coordinates to the feature list. The coordinates are flattened as follows: [x1, y1, z1, x2, y2, z2, …]

Parameters

reference (mdtraj.Trajectory or None, default=None) – if given, all data is being aligned to the given reference with Trajectory.superpose
atom_indices (array_like, or None) – The indices of the atoms to superpose. If not supplied, all atoms will be used.
ref_atom_indices (array_like, or None) – Use these atoms on the reference structure. If not supplied, the same atom indices will be used for this trajectory and the reference one.

add_angles(indexes, deg=False, cossin=False, periodic=True)¶

Adds the list of angles to the feature list

Parameters

indexes (np.ndarray, shape=(num_pairs, 3), dtype=int) – an array with triplets of atom indices
deg (bool, optional, default = False) – If False (default), angles will be computed in radians. If True, angles will be computed in degrees.
cossin (bool, optional, default = False) – If True, each angle will be returned as a pair of (sin(x), cos(x)). This is useful, if you calculate the mean (e.g TICA/PCA, clustering) in that space.
periodic (bool, optional, default = True) – If periodic is True and the trajectory contains unitcell information, we will treat dihedrals that cross periodic images using the minimum image convention.

add_backbone_torsions(selstr=None, deg=False, cossin=False, periodic=True)¶

Adds all backbone phi/psi angles or the ones specified in selstr to the feature list.

Parameters

selstr (str, optional, default = "") – selection string specifying the atom selection used to specify a specific set of backbone angles If “” (default), all phi/psi angles found in the topology will be computed
deg (bool, optional, default = False) – If False (default), angles will be computed in radians. If True, angles will be computed in degrees.
cossin (bool, optional, default = False) – If True, each angle will be returned as a pair of (sin(x), cos(x)). This is useful, if you calculate the mean (e.g TICA/PCA, clustering) in that space.
periodic (bool, optional, default = True) – If periodic is True and the trajectory contains unitcell information, we will treat dihedrals that cross periodic images using the minimum image convention.

add_chi1_torsions(selstr='', deg=False, cossin=False, periodic=True)¶

Adds all chi1 angles or the ones specified in selstr to the feature list.

Parameters

selstr (str, optional, default = "") – selection string specifying the atom selection used to specify a specific set of backbone angles If “” (default), all chi1 angles found in the topology will be computed
deg (bool, optional, default = False) – If False (default), angles will be computed in radians. If True, angles will be computed in degrees.
cossin (bool, optional, default = False) – If True, each angle will be returned as a pair of (sin(x), cos(x)). This is useful, if you calculate the mean (e.g TICA/PCA, clustering) in that space.
periodic (bool, optional, default = True) – If periodic is True and the trajectory contains unitcell information, we will treat dihedrals that cross periodic images using the minimum image convention.

add_contacts(indices, indices2=None, threshold=0.3, periodic=True, count_contacts=False)¶

Adds the contacts to the feature list.

Parameters

indices (can be of two types:) –

ndarray((n, 2), dtype=int):
n x 2 array with the pairs of atoms between which the contacts shall be computed

iterable of integers (either list or ndarray(n, dtype=int)):
indices (not pairs of indices) of the atoms between which the contacts shall be computed.
indices2 (iterable of integers (either list or ndarray(n, dtype=int)), optional:) – Only has effect if indices is an iterable of integers. Instead of the above behaviour, only the contacts between the atoms in indices and indices2 will be computed.
threshold (float, optional, default = .3) – distances below this threshold (in nm) will result in a feature 1.0, distances above will result in 0.0. The default is set to .3 nm (3 Angstrom)
periodic (boolean, default True) – use the minimum image convention if unitcell information is available
count_contacts (boolean, default False) – If set to true, this feature will return the number of formed contacts (and not feature values with either 1.0 or 0) The ouput of this feature will be of shape (Nt,1), and not (Nt, nr_of_contacts)

Note

When using the iterable of integers input, indices and indices2 will be sorted numerically and made unique before converting them to a pairlist. Please look carefully at the output of describe() to see what features exactly have been added.

add_custom_feature(feature)¶

Adds a custom feature to the feature list.

Parameters: feature (object) – an object with interface like CustomFeature (map, describe methods)

add_custom_func(func, dim, *args, **kwargs)¶

adds a user defined function to extract features

Parameters

func (function) – a user-defined function, which accepts mdtraj.Trajectory object as first parameter and as many optional and named arguments as desired. Has to return a numpy.ndarray ndim=2.
dim (int) – output dimension of function
description (str or None) – a message for the describe feature list.
args (any number of positional arguments) – these have to be in the same order as func is expecting them
kwargs (dictionary) – named arguments passed to func

Notes

You can pass a description list to describe the output of your function by element, by passing a list of strings with the same lengths as dimensions. Alternatively a single element list or str will be expanded to match the output dimension.

add_dihedrals(indexes, deg=False, cossin=False, periodic=True)¶

Adds the list of dihedrals to the feature list

Parameters

indexes (np.ndarray, shape=(num_pairs, 4), dtype=int) – an array with quadruplets of atom indices
deg (bool, optional, default = False) – If False (default), angles will be computed in radians. If True, angles will be computed in degrees.
cossin (bool, optional, default = False) – If True, each angle will be returned as a pair of (sin(x), cos(x)). This is useful, if you calculate the mean (e.g TICA/PCA, clustering) in that space.
periodic (bool, optional, default = True) – If periodic is True and the trajectory contains unitcell information, we will treat dihedrals that cross periodic images using the minimum image convention.

add_distances(indices, periodic=True, indices2=None)¶

Adds the distances between atoms to the feature list.

Parameters

indices (can be of two types:) –

ndarray((n, 2), dtype=int):
n x 2 array with the pairs of atoms between which the distances shall be computed

iterable of integers (either list or ndarray(n, dtype=int)):
indices (not pairs of indices) of the atoms between which the distances shall be computed.
periodic (optional, boolean, default is True) – If periodic is True and the trajectory contains unitcell information, distances will be computed under the minimum image convention.
indices2 (iterable of integers (either list or ndarray(n, dtype=int)), optional:) – Only has effect if indices is an iterable of integers. Instead of the above behaviour, only the distances between the atoms in indices and indices2 will be computed.

Note

When using the iterable of integers input, indices and indices2 will be sorted numerically and made unique before converting them to a pairlist. Please look carefully at the output of describe() to see what features exactly have been added.

add_distances_ca(periodic=True, excluded_neighbors=2)¶

Adds the distances between all Ca’s to the feature list.

Parameters

periodic (boolean, default is True) – Use the minimum image convetion when computing distances
excluded_neighbors (int, default is 2) – Number of exclusions when compiling the list of pairs. Two CA-atoms are considered neighbors if they belong to adjacent residues.

add_group_COM(group_definitions, ref_geom=None, image_molecules=False, mass_weighted=True)¶

Adds the centers of mass (COM) in cartesian coordinates of a group or groups of atoms. If these group definitions coincide directly with residues, use add_residue_COM instead. No periodic boundaries are taken into account.

Parameters

group_definitions (iterable of integers) – List of the groups of atom indices for which the COM will be computed. The atoms are zero-indexed.
ref_geom (mdtraj.Trajectory, default is None) – The coordinates can be centered to a reference geometry before computing the COM.
image_molecules (boolean, default is False) – The method traj.image_molecules will be called before computing averages. The method tries to correct for molecules broken across periodic boundary conditions, but can be time consuming. See http://mdtraj.org/latest/api/generated/mdtraj.Trajectory.html#mdtraj.Trajectory.image_molecules for more details
mass_weighted (boolean, default is True) – Set to False if you want the geometric center and not the COM

Note

Centering (with ref_geom) and imaging (image_molecules=True) the trajectories can sometimes be time consuming. Consider doing that to your trajectory-files prior to the featurization.

add_group_mindist(group_definitions, group_pairs='all', threshold=None, periodic=True)¶

Adds the minimum distance between groups of atoms to the feature list. If the groups of atoms are identical to residues, use add_residue_mindist.

Parameters

group_definitions (list of 1D-arrays/iterables containing the group definitions via atom indices.) – If there is only one group_definition, it is assumed the minimum distance within this group (excluding the self-distance) is wanted. In this case, group_pairs is ignored.
group_pairs (Can be of two types:) –

‘all’
Computes minimum distances between all pairs of groups contained in the group definitions

ndarray((n, 2), dtype=int):
n x 2 array with the pairs of groups for which the minimum distances will be computed.
threshold (float, optional, default is None) – distances below this threshold (in nm) will result in a feature 1.0, distances above will result in 0.0. If left to None, the numerical value will be returned
periodic (bool, optional, default = True) – If periodic is True and the trajectory contains unitcell information, we will treat dihedrals that cross periodic images using the minimum image convention.

add_inverse_distances(indices, periodic=True, indices2=None)¶

Adds the inverse distances between atoms to the feature list.

Parameters

indices (can be of two types:) –

ndarray((n, 2), dtype=int):
n x 2 array with the pairs of atoms between which the inverse distances shall be computed

iterable of integers (either list or ndarray(n, dtype=int)):
indices (not pairs of indices) of the atoms between which the inverse distances shall be computed.
periodic (optional, boolean, default is True) – If periodic is True and the trajectory contains unitcell information, distances will be computed under the minimum image convention.
indices2 (iterable of integers (either list or ndarray(n, dtype=int)), optional:) – Only has effect if indices is an iterable of integers. Instead of the above behaviour, only the inverse distances between the atoms in indices and indices2 will be computed.

Note

When using the iterable of integers input, indices and indices2 will be sorted numerically and made unique before converting them to a pairlist. Please look carefully at the output of describe() to see what features exactly have been added.

add_minrmsd_to_ref(ref, ref_frame=0, atom_indices=None, precentered=False)¶

Adds the minimum root-mean-square-deviation (minrmsd) with respect to a reference structure to the feature list.

Parameters

ref –
Reference structure for computing the minrmsd. Can be of two types:
1. mdtraj.Trajectory object
2. filename for mdtraj to load. In this case, only the ref_frame of that file will be used.
ref_frame (integer, default=0) – Reference frame of the filename specified in ref. This parameter has no effect if ref is not a filename.
atom_indices (array_like, default=None) –
Atoms that will be used for:
1. aligning the target and reference geometries.
2. computing rmsd after the alignment.
If left to None, all atoms of ref will be used.
precentered (bool, default=False) – Use this boolean at your own risk to let mdtraj know that the target conformations are already centered at the origin, i.e., their (uniformly weighted) center of mass lies at the origin. This will speed up the computation of the rmsd.

add_residue_COM(residue_indices, scheme='all', ref_geom=None, image_molecules=False, mass_weighted=True)¶

Adds a per-residue center of mass (COM) in cartesian coordinates. No periodic boundaries are taken into account.

Parameters

residue_indices (iterable of integers) – The residue indices for which the COM will be computed. These are always zero-indexed that are not necessarily the residue sequence record of the topology (resSeq). resSeq indices start at least at 1 but can depend on the topology. See http://mdtraj.org/latest/atom_selection.html for more details.
scheme (str, default is 'all') – What atoms contribute to the COM computation. The supported keywords are: ‘all’, ‘backbone’, ‘sidechain’ . If the scheme yields no atoms for some residue, the selection falls back to ‘all’ for that residue.
ref_geom (obj:mdtraj.Trajectory, default is None) – The coordinates can be centered to a reference geometry before computing the COM.
image_molecules (boolean, default is False) – The method traj.image_molecules will be called before computing averages. The method tries to correct for molecules broken across periodic boundary conditions, but can be time consuming. See http://mdtraj.org/latest/api/generated/mdtraj.Trajectory.html#mdtraj.Trajectory.image_molecules for more details
mass_weighted (boolean, default is True) – Set to False if you want the geometric center and not the COM

Note

Centering (with ref_geom) and imaging (image_molecules=True) the trajectories can sometimes be time consuming. Consider doing that to your trajectory-files prior to the featurization.

add_residue_mindist(residue_pairs='all', scheme='closest-heavy', ignore_nonprotein=True, threshold=None, periodic=True)¶

Adds the minimum distance between residues to the feature list. See below how the minimum distance can be defined. If the topology generated out of topfile contains information on periodic boundary conditions, the minimum image convention will be used when computing distances.

Parameters

residue_pairs (can be of two types:) –

‘all’
Computes distances between all pairs of residues excluding first and second neighbors

ndarray((n, 2), dtype=int):
n x 2 array with the pairs residues for which distances will be computed
scheme ('ca', 'closest', 'closest-heavy', default is closest-heavy) – Within a residue, determines the sub-group atoms that will be considered when computing distances
ignore_nonprotein (boolean, default True) – Ignore residues that are not of protein type (e.g. water molecules, post-traslational modifications etc)
threshold (float, optional, default is None) – distances below this threshold (in nm) will result in a feature 1.0, distances above will result in 0.0. If left to None, the numerical value will be returned
periodic (bool, optional, default = True) – If periodic is True and the trajectory contains unitcell information, we will treat dihedrals that cross periodic images using the minimum image convention.

Note

Using scheme = ‘closest’ or ‘closest-heavy’ with residue pairs = ‘all’ will compute nearly all interatomic distances, for every frame, before extracting the closest pairs. This can be very time consuming. Those schemes are intended to be used with a subset of residues chosen via residue_pairs.

add_selection(indexes, reference=None, atom_indices=None, ref_atom_indices=None)¶

Adds the coordinates of the selected atom indexes to the feature list. The coordinates of the selection [1, 2, …] are flattened as follows: [x1, y1, z1, x2, y2, z2, …]

Parameters

indexes (ndarray((n), dtype=int)) – array with selected atom indexes
reference (mdtraj.Trajectory or None, default=None) – if given, all data is being aligned to the given reference with Trajectory.superpose
atom_indices (array_like, or None) – The indices of the atoms to superpose. If not supplied, all atoms will be used.
ref_atom_indices (array_like, or None) – Use these atoms on the reference structure. If not supplied, the same atom indices will be used for this trajectory and the reference one.

add_sidechain_torsions(selstr=None, deg=False, cossin=False, periodic=True, which='all')¶

Adds all side chain torsion angles or the ones specified in selstr to the feature list.

Parameters

selstr (str, optional, default=None) – selection string specifying the atom selection used to specify a specific set of backbone angles If “” (default), all chi1 angles found in the topology will be computed
deg (bool, optional, default=False) – If False (default), angles will be computed in radians. If True, angles will be computed in degrees.
cossin (bool, optional, default=False) – If True, each angle will be returned as a pair of (sin(x), cos(x)). This is useful, if you calculate the mean (e.g TICA/PCA, clustering) in that space.
periodic (bool, optional, default=True) – If periodic is True and the trajectory contains unitcell information, we will treat dihedrals that cross periodic images using the minimum image convention.
which (str or list of str, default='all') – one or combination of (‘all’, ‘chi1’, ‘chi2’, ‘chi3’, ‘chi4’, ‘chi5’)

describe()¶

Returns a list of strings, one for each feature selected, with human-readable descriptions of the features.

Returns: labels – An ordered list of strings, one for each feature selected, with human-readable descriptions of the features.
Return type: list of str

dimension()¶

current dimension due to selected features

Returns: dim – total dimension due to all selection features
Return type: int

classmethod load(file_name, model_name='default')¶

Loads a previously saved PyEMMA object from disk.

Parameters

file_name (str or file like object (has to provide read method)) – The file like object tried to be read for a serialized object.
model_name (str, default='default') – if multiple models are contained in the file, these can be accessed by their name. Use pyemma.list_models() to get a representation of all stored models.

Returns

obj

Return type

the de-serialized object

logger¶: The logger for this class instance

name¶: The name of this instance

static pairs(sel, excluded_neighbors=0)¶

Creates all pairs between indexes. Will exclude closest neighbors up to excluded_neighbors The self-pair (i,i) is always excluded

Parameters

sel (ndarray((n), dtype=int)) – array with selected atom indexes
excluded_neighbors (int, default = 0) – number of neighbors that will be excluded when creating the pairs

Returns

sel – m x 2 array with all pair indexes between different atoms that are at least excluded_neighbors indexes apart, i.e. if i is the index of an atom, the pairs [i,i-2], [i,i-1], [i,i], [i,i+1], [i,i+2], will not be in sel (n=excluded_neighbors) if excluded_neighbors = 2. Moreover, the list is non-redundant,i.e. if [i,j] is in sel, then [j,i] is not.

Return type

ndarray((m,2), dtype=int)

remove_all_custom_funcs()¶: Remove all instances of CustomFeature from the active feature list.

save(file_name, model_name='default', overwrite=False, save_streaming_chain=False)¶

saves the current state of this object to given file and name.

Parameters

file_name (str) – path to desired output file
model_name (str, default='default') – creates a group named ‘model_name’ in the given file, which will contain all of the data. If the name already exists, and overwrite is False (default) will raise a RuntimeError.
overwrite (bool, default=False) – Should overwrite existing model names?
save_streaming_chain (boolean, default=False) – if True, the data_producer(s) of this object will also be saved in the given file.

Examples

>>> import pyemma, numpy as np
>>> from pyemma.util.contexts import named_temporary_file
>>> m = pyemma.msm.MSM(P=np.array([[0.1, 0.9], [0.9, 0.1]]))

>>> with named_temporary_file() as file: # doctest: +SKIP
...    m.save(file, 'simple') # doctest: +SKIP
...    inst_restored = pyemma.load(file, 'simple') # doctest: +SKIP
>>> np.testing.assert_equal(m.P, inst_restored.P) # doctest: +SKIP

select(selstring)¶

Returns the indexes of atoms matching the given selection

Parameters: selstring (str) – Selection string. See mdtraj documentation for details: http://mdtraj.org/latest/atom_selection.html
Returns: indexes – array with selected atom indexes
Return type: ndarray((n), dtype=int)

select_Backbone()¶

Returns the indexes of backbone C, CA and N atoms

Returns: indexes – array with selected atom indexes
Return type: ndarray((n), dtype=int)

select_Ca()¶

Returns the indexes of all Ca-atoms

Returns: indexes – array with selected atom indexes
Return type: ndarray((n), dtype=int)

select_Heavy(exclude_symmetry_related=False)¶

Returns the indexes of all heavy atoms (Mass >= 2), optionally excluding symmetry-related heavy atoms.

Parameters: exclude_symmetry_related (boolean, default=False) – if True, exclude symmetry-related heavy atoms.
Returns: indexes – array with selected atom indexes
Return type: ndarray((n), dtype=int)

transform(traj)¶

Maps an mdtraj Trajectory object to the selected output features

Parameters: traj (mdtraj Trajectory) – Trajectory object used as an input
Returns: out – Output features: For each of T time steps in the given trajectory, a vector with all n output features selected.
Return type: ndarray((T, n), dtype=float32)