9.1.3. Compute observable timeseries from trajectories — MDAnalysis.core.Timeseries

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. To extract coordinates efficiently one can use MDAnalysis.analysis.base.AnalysisFromFunction as shown in Creating an in-memory trajectory with AnalysisFromFunction.

The collection of timeseries (such as Atom, Bond, Dihedral…) can be computed from a trajectory in one go, foregoing the need to iterate through the trajectory frame by frame in python. Inspired by CHARMM’s correl command.

The disadvantage is that the timeseries ‘plugins’ must be implemented in C-code. Hence not all trajectory readers (see MDAnalysis.coordinates) support them.

9.1.3.1. Basic classes

class MDAnalysis.core.Timeseries.Timeseries(*args, **kwds)[source]

Base timeseries class - define subclasses for specific timeseries computations.

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17

shape

shape tuple of the underlying numpy array

class MDAnalysis.core.Timeseries.TimeseriesCollection(*args, **kwds)[source]

A collection of timeseries objects.

The collection of timeseries (such as Atom, Bond, Dihedral…) can be computed from a trajectory in one go, foregoing the need to iterate through the trajectory frame by frame in python. Inspired by CHARMM’s correl command.

The disadvantage is that the timeseries ‘plugins’ must be implemented in C-code.

collection = TimeseriesCollection()
collection.addTimeseries(Timeseries.Atom(...)) - add a new Timeseries object
collection.compute(...)                        - compute the collection of timeseries from the trajectory
collection.clear()                             - clear the collection
collection[i]                                  - access the i'th timeseries
len(collection)                                - return the number of Timeseries added to the collection

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17

addTimeseries(ts)[source]

add a Timeseries object to the collection

clear()[source]

clear the timeseries collection

compute(trj, start=None, stop=None, skip=None, step=None)[source]

Iterate through the trajectory trj and compute the time series.

trj
dcd trajectory object (i.e. Universe.trajectory)
start
First frame of trajectory to analyse, Default: None becomes 0.
stop
Frame index to stop analysis. Default: None becomes n_frames. Iteration stops before this frame number, which means that the trajectory would be read until the end.
step
Step between frames to analyse, Default: None becomes 1.
Deprecated
Skip is deprecated in favor of step.

9.1.3.2. Timeseries of observables

class MDAnalysis.core.Timeseries.Atom(*args, **kwds)[source]

Create a timeseries that returns coordinate data for an atom or group of atoms

   t = Atom(code, atoms)

*code*
  is one of 'x', 'y', 'z', or 'v' ('vector', which returns all three
  dimensions)

*atoms*
  can be a single :class:`~MDAnalysis.core.groups.Atom` object,
  a list of :class:`~MDAnalysis.core.groups.Atom` objects, or an
  :class:`~MDAnalysis.core.groups.AtomGroup`

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17

class MDAnalysis.core.Timeseries.Bond(*args, **kwds)[source]

Create a timeseries that returns a timeseries for a bond

t = Bond(atoms)

atoms must contain 2 Atom instances, either as a list or an AtomGroup

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17

class MDAnalysis.core.Timeseries.Angle(*args, **kwds)[source]

Create a timeseries that returns a timeseries for an angle

t = Angle(atoms)

atoms must contain 3 Atom instances, either as a list or an AtomGroup

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17

class MDAnalysis.core.Timeseries.Dihedral(*args, **kwds)[source]

Create a timeseries that returns a timeseries for a dihedral angle

t = Dihedral(atoms)

atoms must contain 4 Atom objects, either as a list or an AtomGroup

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17

class MDAnalysis.core.Timeseries.Distance(*args, **kwds)[source]

Create a timeseries that returns distances between 2 atoms

t = Distance(code, atoms)

code is one of ‘d’ (distance vector), or ‘r’ (scalar distance) atoms must contain 2 Atom objects, either as a list or an AtomGroup

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17

class MDAnalysis.core.Timeseries.CenterOfGeometry(*args, **kwds)[source]

Create a timeseries that returns the center of geometry of a group of atoms

t = CenterOfGeometry(atoms)

atoms can be a list of Atom objects, or a AtomGroup

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17

class MDAnalysis.core.Timeseries.CenterOfMass(*args, **kwds)[source]

Create a timeseries that returns the center of mass of a group of atoms

t = CenterOfMass(atoms)

atoms can be a list of Atom objects or a AtomGroup

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17

class MDAnalysis.core.Timeseries.WaterDipole(*args, **kwds)[source]

Create a Timeseries that returns a timeseries for the bisector vector of a 3-site water

d = WaterDipole(atoms)

atoms must contain 3 Atom objects, either as a list or an AtomGroup; the first one must be the oxygen, the other two are the hydrogens.

The vector d, multiplied by the partial charge on the oxygen atom (e.g. q = -0.0.834 for TIP3P water), gives the actual dipole moment.

The vector is calculated from the positions of the oxygen atom (\(\mathbf{x}_{\text{O}}\)) and the two hydrogen atoms (\(\mathbf{x}_{\text{H}_1}\), \(\mathbf{x}_{\text{H}_2}\)) as

\[\mathbf{d} = \mathbf{x}_{\text{O}} - \frac{1}{2}(\mathbf{x}_{\text{H}_1} + \mathbf{x}_{\text{H}_2})\]

and the dipole moment vector is

\[\boldsymbol{\mu} = q_{\text{O}} \mathbf{d}\]

Note

This will only work for water models that have half of the oxygen charge on each hydrogen. The vector \(\mathbf{d}\) has the opposite direction of the dipole moment; multiplying with the oxygen charge (\(q_{\text{O}}<0\)) will flip the direction and produce the correct orientation.

There are no sanity checks; if the first atom in a water molecule is not oxygen then results will be wrong.

Deprecated since version 0.16.2: The Timeseries functionality (in particular correl) will be removed in the 0.17 release. See issue #1372 for more details. Use MDAnalysis.analysis.base.AnalysisFromFunction instead.

__init__ is deprecated! This class will be removed in 0.17