Auxiliary files¶
Auxiliary readers allow you to read in timeseries data accompanying a trajectory, that is not stored in the regular trajectory file.
Supported formats¶
Reader
Format
Extension (if file)
Remarks
XVGReader
XVG
xvg
(default)
Produced by Gromacs during simulation or analysis. Reads full file on initialisation.
XVGFileReader
XVG-F
xvg
Alternate xvg file reader, reading each step from the file in turn for a lower memory footprint.
XVGReader
is the default reader for .xvg files.
Reading data directly¶
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import XVG_BZ2 # cobrotoxin protein forces
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-2-1ab82d15e01a> in <module>
----> 1 from MDAnalysis.tests.datafiles import XVG_BZ2 # cobrotoxin protein forces
~/checkouts/readthedocs.org/user_builds/mdauserguide/conda/rms-1.0/lib/python3.8/site-packages/MDAnalysis/tests/datafiles.py in <module>
41
42 try:
---> 43 from MDAnalysisTests.datafiles import *
44 except ImportError:
45 print("*** ERROR ***")
~/checkouts/readthedocs.org/user_builds/mdauserguide/conda/rms-1.0/lib/python3.8/site-packages/MDAnalysisTests/__init__.py in <module>
124 try:
125 import matplotlib
--> 126 matplotlib.use('agg', warn=False)
127 except ImportError:
128 pass
TypeError: use() got an unexpected keyword argument 'warn'
In [3]: aux = mda.auxiliary.core.auxreader(XVG_BZ2)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-3-0c6e0f31d0f8> in <module>
----> 1 aux = mda.auxiliary.core.auxreader(XVG_BZ2)
NameError: name 'XVG_BZ2' is not defined
In [4]: aux
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-4-c1d93f0ef0f3> in <module>
----> 1 aux
NameError: name 'aux' is not defined
In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.
In [5]: for step in aux:
...: print(step.data)
...:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-5-2b2c8e575980> in <module>
----> 1 for step in aux:
2 print(step.data)
NameError: name 'aux' is not defined
Use slicing to skip steps.
In [6]: for step in aux[1:2]:
...: print(step.time)
...:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-6-4f8d5984773e> in <module>
----> 1 for step in aux[1:2]:
2 print(step.time)
NameError: name 'aux' is not defined
The auxreader()
function uses the get_auxreader_for()
to return an appropriate class. This can guess the format either from a filename, ‘
In [7]: mda.auxiliary.core.get_auxreader_for(XVG_BZ2)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-7-24dfee86a49a> in <module>
----> 1 mda.auxiliary.core.get_auxreader_for(XVG_BZ2)
NameError: name 'XVG_BZ2' is not defined
or return the reader for a specified format.
In [8]: mda.auxiliary.core.get_auxreader_for(format='XVG-F')
Out[8]: MDAnalysis.auxiliary.XVG.XVGFileReader
Loading data into a Universe¶
Auxiliary data may be added to a trajectory Reader through the
add_auxiliary()
method. Auxiliary data
may be passed in as a AuxReader instance, or directly as e.g. a filename, in
which case get_auxreader_for()
is used to
guess an appropriate reader.
In [9]: from MDAnalysis.tests.datafiles import PDB_xvf, TRR_xvf
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-9-6ccfd7da76ac> in <module>
----> 1 from MDAnalysis.tests.datafiles import PDB_xvf, TRR_xvf
~/checkouts/readthedocs.org/user_builds/mdauserguide/conda/rms-1.0/lib/python3.8/site-packages/MDAnalysis/tests/datafiles.py in <module>
41
42 try:
---> 43 from MDAnalysisTests.datafiles import *
44 except ImportError:
45 print("*** ERROR ***")
~/checkouts/readthedocs.org/user_builds/mdauserguide/conda/rms-1.0/lib/python3.8/site-packages/MDAnalysisTests/__init__.py in <module>
124 try:
125 import matplotlib
--> 126 matplotlib.use('agg', warn=False)
127 except ImportError:
128 pass
TypeError: use() got an unexpected keyword argument 'warn'
In [10]: u = mda.Universe(PDB_xvf, TRR_xvf)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-10-9948230bad34> in <module>
----> 1 u = mda.Universe(PDB_xvf, TRR_xvf)
NameError: name 'PDB_xvf' is not defined
In [11]: u.trajectory.add_auxiliary('protein_force', XVG_BZ2)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-11-34309ff5edd5> in <module>
----> 1 u.trajectory.add_auxiliary('protein_force', XVG_BZ2)
NameError: name 'u' is not defined
In [12]: for ts in u.trajectory:
....: print(ts.aux.protein_force)
....:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-12-3f68dbf72bd7> in <module>
----> 1 for ts in u.trajectory:
2 print(ts.aux.protein_force)
NameError: name 'u' is not defined
Passing arguments to auxiliary data¶
For alignment with trajectory data, auxiliary readers provide methods to assign each auxiliary step to the nearest trajectory timestep, read all steps assigned to a trajectory timestep and calculate ‘representative’ value(s) of the auxiliary data for that timestep.
To set a timestep or ??
‘Assignment’ of auxiliary steps to trajectory timesteps is determined from the time
of the auxiliary step, dt
of the trajectory and time at the first frame of the
trajectory. If there are no auxiliary steps assigned to a given timestep (or none within
cutoff
, if set), the representative value(s) are set to np.nan
.
Iterating over auxiliary data¶
Auxiliary data may not perfectly line up with the trajectory, or have missing data.
In [13]: from MDAnalysis.tests.datafiles import PDB, TRR
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-13-52c333738bd6> in <module>
----> 1 from MDAnalysis.tests.datafiles import PDB, TRR
~/checkouts/readthedocs.org/user_builds/mdauserguide/conda/rms-1.0/lib/python3.8/site-packages/MDAnalysis/tests/datafiles.py in <module>
41
42 try:
---> 43 from MDAnalysisTests.datafiles import *
44 except ImportError:
45 print("*** ERROR ***")
~/checkouts/readthedocs.org/user_builds/mdauserguide/conda/rms-1.0/lib/python3.8/site-packages/MDAnalysisTests/__init__.py in <module>
124 try:
125 import matplotlib
--> 126 matplotlib.use('agg', warn=False)
127 except ImportError:
128 pass
TypeError: use() got an unexpected keyword argument 'warn'
In [14]: u_long = mda.Universe(PDB, TRR)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-14-ca574921ef39> in <module>
----> 1 u_long = mda.Universe(PDB, TRR)
NameError: name 'PDB' is not defined
In [15]: u_long.trajectory.add_auxiliary('protein_force', XVG_BZ2, dt=200)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-15-53191d76ddcb> in <module>
----> 1 u_long.trajectory.add_auxiliary('protein_force', XVG_BZ2, dt=200)
NameError: name 'u_long' is not defined
In [16]: for ts in u_long.trajectory:
....: print(ts.time, ts.aux.protein_force[:4])
....:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-16-24060ca3ba09> in <module>
----> 1 for ts in u_long.trajectory:
2 print(ts.time, ts.aux.protein_force[:4])
NameError: name 'u_long' is not defined
The trajectory ProtoReader
methods
next_as_aux()
and
iter_as_aux()
allow for movement
through only trajectory timesteps for which auxiliary data is available.
In [17]: for ts in u_long.trajectory.iter_as_aux('protein_force'):
....: print(ts.time, ts.aux.protein_force[:4])
....:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-17-eb9c57d7b5fe> in <module>
----> 1 for ts in u_long.trajectory.iter_as_aux('protein_force'):
2 print(ts.time, ts.aux.protein_force[:4])
NameError: name 'u_long' is not defined
This may be used to
avoid representative values set to np.nan
, particularly when auxiliary data
is less frequent.
Sometimes the auxiliary data is longer than the trajectory.
In [18]: u_short = mda.Universe(PDB)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-18-aaa693c28066> in <module>
----> 1 u_short = mda.Universe(PDB)
NameError: name 'PDB' is not defined
In [19]: u_short.trajectory.add_auxiliary('protein_force', XVG_BZ2)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-19-9bf03c7a03c5> in <module>
----> 1 u_short.trajectory.add_auxiliary('protein_force', XVG_BZ2)
NameError: name 'u_short' is not defined
In [20]: for ts in u_short.trajectory:
....: print(ts.time, ts.aux.protein_force)
....:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-20-c24b04aeef54> in <module>
----> 1 for ts in u_short.trajectory:
2 print(ts.time, ts.aux.protein_force)
NameError: name 'u_short' is not defined
In order to acess auxiliary values at every individual step, including those
outside the time range of the trajectory,
iter_auxiliary()
allows iteration
over the auxiliary independent of the trajectory.
In [21]: for step in u_short.trajectory.iter_auxiliary('protein_force'):
....: print(step.data)
....:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-21-b3827dc427a3> in <module>
----> 1 for step in u_short.trajectory.iter_auxiliary('protein_force'):
2 print(step.data)
NameError: name 'u_short' is not defined
To iterate over only a certain section of the auxiliary:
In [22]: for step in u_short.trajectory.iter_auxiliary('protein_force', start=1, step=2):
....: print(step.time)
....:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-22-bf3fa2af3071> in <module>
----> 1 for step in u_short.trajectory.iter_auxiliary('protein_force', start=1, step=2):
2 print(step.time)
NameError: name 'u_short' is not defined
The trajectory remains unchanged, and the auxiliary will be returned to the current timestep after iteration is complete.
Accessing auxiliary attributes¶
To check the values of attributes of an added auxiliary, use
get_aux_attribute()
.
In [23]: u.trajectory.get_aux_attribute('protein_force', 'dt')
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-23-5b3164df381b> in <module>
----> 1 u.trajectory.get_aux_attribute('protein_force', 'dt')
NameError: name 'u' is not defined
If attributes are settable, they can be changed using
set_aux_attribute()
.
In [24]: u.trajectory.set_aux_attribute('protein_force', 'data_selector', [1])
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-24-de9e36c640bc> in <module>
----> 1 u.trajectory.set_aux_attribute('protein_force', 'data_selector', [1])
NameError: name 'u' is not defined
The auxiliary may be renamed using set_aux_attribute
with ‘auxname’, or more
directly by using rename_aux()
.
In [25]: u.trajectory.ts.aux.protein_force
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-25-eeb820e67c0b> in <module>
----> 1 u.trajectory.ts.aux.protein_force
NameError: name 'u' is not defined
In [26]: u.trajectory.rename_aux('protein_force', 'f')
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-26-2b6f1b68545f> in <module>
----> 1 u.trajectory.rename_aux('protein_force', 'f')
NameError: name 'u' is not defined
In [27]: u.trajectory.ts.aux.f
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-27-71c2bf052ebf> in <module>
----> 1 u.trajectory.ts.aux.f
NameError: name 'u' is not defined
Recreating auxiliaries¶
To recreate an auxiliary, the set of attributes necessary to replicate it can
first be obtained with get_description()
.
The returned dictionary can then be passed to
auxreader()
to load a new copy of the
original auxiliary reader.
In [28]: description = aux.get_description()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-28-1c956469c981> in <module>
----> 1 description = aux.get_description()
NameError: name 'aux' is not defined
In [29]: list(description.keys())
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-29-8acc739bb738> in <module>
----> 1 list(description.keys())
NameError: name 'description' is not defined
In [30]: del aux
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-30-501c038ea324> in <module>
----> 1 del aux
NameError: name 'aux' is not defined
In [31]: mda.auxiliary.core.auxreader(**description)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-31-46a012a8d339> in <module>
----> 1 mda.auxiliary.core.auxreader(**description)
NameError: name 'description' is not defined
The ‘description’ of any or all the auxiliaries added to a trajectory can be
obtained using get_aux_descriptions()
.
In [32]: descriptions = u.trajectory.get_aux_descriptions(['f'])
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-32-66db4ac34bff> in <module>
----> 1 descriptions = u.trajectory.get_aux_descriptions(['f'])
NameError: name 'u' is not defined
To reload, pass the dictionary into add_auxiliary()
.
In [1]: u2 = mda.Universe(PDB, TRR)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-1-80d0a701162a> in <module>
----> 1 u2 = mda.Universe(PDB, TRR)
NameError: name 'PDB' is not defined
In [2]: for desc in descriptions:
...: u2.trajectory.add_auxiliary(**desc)
...:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-2-73376cbc62d1> in <module>
----> 1 for desc in descriptions:
2 u2.trajectory.add_auxiliary(**desc)
NameError: name 'descriptions' is not defined