How to obtain the full Kirchhoff matrix in GNM Prody - protein

[german12341212]

Hi users:

I want to display the full Kirchhoff matrix of a protein in GNM Prody

When using prody and asking for:

gnm.getKirchhoff()

I only obtain a summary like this:

array([[11., -1., -1., ..., 0., 0., 0.],
[-1., 15., -1., ..., 0., 0., 0.],
[-1., -1., 20., ..., 0., 0., 0.],
...,
[ 0., 0., 0., ..., 20., -1., -1.],
[ 0., 0., 0., ..., -1., 21., -1.],
[ 0., 0., 0., ..., -1., -1., 12.]])

Does anyone have a suggestion?

Thanks in advance
German

[jamesmkrieger]

We have a function under development to do this at #1085. You can try it by checking out my branch devel-9

If you have a development prody from github already then you can add my remote and fetch my branches and checkout this one as follows:

git remote add james https://github.com/jamesmkrieger/ProDy.git
git fetch james
git checkout devel-9

If you don't have any prody from github already then you can clone my remote and branch directly like this:
git clone -b devel-9 https://github.com/jamesmkrieger/ProDy.git
In this case, you would then need to install this prody in the development way:

python setup.py build_ext --inplace --force
pip install -Ue .

[AnthonyBogetti]

Hi @german12341212, did James' fix work for you? Please let me know. Thank you.