pyemma.coordinates.data.MDFeaturizer

class pyemma.coordinates.data.MDFeaturizer(*args, **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

_Loggable__create_logger()
_MDFeaturizer__add_feature(f)
_SerializableMixIn__interpolate(state, klass)
__delattr__(name, /)	Implement delattr(self, name).
__dir__()	Default dir() implementation.
__eq__(value, /)	Return self==value.
__format__(format_spec, /)	Default object formatter.
__ge__(value, /)	Return self>=value.
__getattribute__(name, /)	Return getattr(self, name).
__getstate__()
__gt__(value, /)	Return self>value.
__hash__()	Return hash(self).
__init__(topfile, **kwargs)	extracts features from MD trajectories.
__init_subclass__(*args, **kwargs)	This method is called when a class is subclassed.
__le__(value, /)	Return self<=value.
__lt__(value, /)	Return self<value.
__ne__(value, /)	Return self!=value.
__new__(cls, *args, **kwargs)	Create and return a new object.
__reduce__()	Helper for pickle.
__reduce_ex__(protocol, /)	Helper for pickle.
__repr__()	Return repr(self).
__setattr__(name, value, /)	Implement setattr(self, name, value).
__setstate__(state)
__sizeof__()	Size of object in memory, in bytes.
__str__()	Return str(self).
__subclasshook__	Abstract classes can override this to customize issubclass().
_check_indices(pair_inds[, pair_n])	ensure pairs are valid (shapes, all atom indices available?, etc.)
_cleanup_logger(logger_id, logger_name)
_get_classes_to_inspect()	gets classes self derives from which 1.
_get_interpolation_map(cls)
_get_private_field(cls, name[, default])
_get_serialize_fields(cls)
_get_state_of_serializeable_fields(klass, state)	:return a dictionary {k:v} for k in self.serialize_fields and v=getattr(self, k)
_get_version(cls[, require])
_get_version_for_class_from_state(state, klass)	retrieves the version of the current klass from the state mapping from old locations to new ones.
_logger_is_active(level)	@param level: int log level (debug=10, info=20, warn=30, error=40, critical=50)
_set_state_from_serializeable_fields_and_state(…)	set only fields from state, which are present in klass.__serialize_fields
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

_Loggable__ids
_Loggable__refs
_MDFeaturizer__serialize_fields
_MDFeaturizer__serialize_version
_SerializableMixIn__serialize_fields
_SerializableMixIn__serialize_modifications_map
_SerializableMixIn__serialize_version
__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)
_loglevel_CRITICAL
_loglevel_DEBUG
_loglevel_ERROR
_loglevel_INFO
_loglevel_WARN
_save_data_producer
logger	The logger for this class instance
name	The name of this instance
topologyfile