Installation

git clone git@github.com:cbc-univie/mdy-newanalysis-package.git
cd mdy-newanalysis-package
pip install .

Info

If you want to install the package you have to connect an ssh key to your github account. Here are the instructions on how to generate ssh keys and link them to your github account:

https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent

https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account

The python package "newanalysis" contains all our homebrew functions for MDAnalysis, that formerly were embedded into the MDAnalysis package and are now available as a separate python module. Be aware that the API syntax of MDAnalysis has changed compared to the old version we have used for a long time.

CONTENTS OF THIS REPO (newanalysis_package)

• charmm_utilities: -- scripts for CHARMM

• newanalysis: -- the actual source for the newanalysis package

Test Cases are moved to new repo: mdy-newanalysis-package-testdata

• test_cases -- test cases, contain scripts for the new version (this package) in the new/ directories, as well as scripts for the old version of MDAnalysis (0.8.2dev, where newanalysis was embedded) -- please note that the trajectories were shortened considerably to reduce file size, so the results you will get for the test cases are obviously garbage

HOW TO INSTALL NEWANALYSIS

1. add new channel via conda config --add channels conda-forge

2. make a new conda environment that has MDAnalysis via conda create -n new_mdanalysis_environment python numpy scipy mdanalysis cython h5py ipython

3. activate that environment via conda activate new_mdanalysis_environment

4. go into the newanalysis_source folder

5. build and install the modules via python3 setup.py build python3 setup.py install

6. Esther says : In case of failure, look up the module where it failed, and delete the respective cpp file:

• src/helpers/correl.cpp
• src/helpers/diffusion.cpp
• src/helpers/helpers.cpp
• src/helpers/unfold.cpp
• src/voro/voro.cpp
• src/gfunction/gfunction.cpp Try to build again, if still not working, contact me.

HOW TO IMPORT INTO YOUR PYTHON SCRIPTS

• To be able to import these modules, change syntax in python script:

OLD: from MDAnalysis.newanalysis.helpers import calcEnergyAtomic from MDAnalysis.newanalysis.correl import correlate

NEW: from newanalysis.helpers import calcEnergyAtomic from newanalysis.correl import correlate

CHANGES COMPARED TO THE OLD MDANALYSIS VERSIONS

• use new CHARMM psf type (default in Versions >= 40, otherwise specify "psf xplor" instead of "psf" in the write statement)

• if you want to read CHARMM velocity files: reformat with the script charmm_utilities/transform_VELtoDCD.inp and make sure to convert the to the correct units!

• make sure to change syntax, e.g. OLD NEW u.trajectory.numframes u.trajectory.n_frames u.selectAtoms(...) u.select_atoms(...) sel.numberOfResidues() sel.n_residues sel.masses() sel.masses sel.charges() sel.charges sel.get_positions() sel.positions sel.centerOfMassByResidue(coor,masses) sel.center_of_mass(compound='residues')

• some previously available functions within an atom selection are now only accessible directly (and need to be imported from helpers), e.g. OLD NEW sel.dipoleMomentByResidue(coor,charges,masses) from newanalysis.functions import dipoleMomentByResidue dipoleMomentByResidue(sel,coor,charges,masses) sel.velcomByResidue(mass) from newanalysis.functions import velcomByResidue velcomByResidue(sel,vels,mass) same for atomsPerResidue(), residueFirstAtom(), centerOfMassByResidue(), dipoleMoment()