pytram

The pytram package is decprecated and no longer supported. We recommend to switch to PyEMMA.

This python package implements the transition-based reweighting analyis method (TRAM) estimators.

Installation

Using conda:

conda install -c https://conda.binstar.org/omnia pytram

Using pip from PyPI:

# you might have to install these dependencies manually
pip install cython
pip install numpy

# install pytram
pip install pytram

Using pip from github (this will install the latest development version):

# you might have to install these dependencies manually
pip install cython
pip install numpy

# install pytram - this might be slow
pip install git+https://github.com/markovmodel/pytram.git@devel

Authors

• Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
• Antonia Mey <antonia.mey@fu-berlin.de>
• Fabian Paul <fab@physik.tu-berlin.de>
• Hao Wu <hwu@zedat.fu-berlin.de>
• Frank Noé <frank.noe@fu-berlin.de>

References

• dTRAM: Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states, Hao Wu, Antonia S.J.S. Mey, Edina Rosta, and Frank Noé, J. Chem. Phys. 141, 214106 (2014).

  Download: <http://scitation.aip.org/content/aip/journal/jcp/141/21/10.1063/1.4902240>

• xTRAM: Estimating Equilibrium Expectations from Time-Correlated Simulation Data at Multiple Thermodynamic States, Antonia S.J.S. Mey, Hao Wu, and Frank Noé, Phys. Rev. X 4, 041018 (2014).

  Download: <http://journals.aps.org/prx/pdf/10.1103/PhysRevX.4.041018>

Copyright notice

Copyright (c) 2014, Computational Molecular Biology Group, FU Berlin, 14195 Berlin, Germany.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.