contact_map

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Regenerate webhook for read the docs

2

@dwhswenson I assume you got the same emails as me, but I don't have the permissions to fix it. (don't have admin rights on this repo or on RtD) Our...

sroet

The calculated results are inconsistent with those calculated by amber cpptraj

1

Dear Developers, I'm counting multiple different peptides binding to a receptor and analyzing the differences in the contacts they make. Firstly, I used cpptraj to calculate a nativecontacts as a...

astomer2

I'm a bit confused why I am getting this behavior, I am using chain A of PDBs 1mmi and 1jql Looking at the contact map difference ``` import mdtraj as...

sam-mahdi

[WIP]: cythonisation

1

Here I am trying to see if we can get a speedup with cythonization of the `contactobject` via type hinting (as is done in for the scheduler in `dask/distributed`). To...

sroet

Renaming `master` branch to `main`

2

I'm planning to rename the `master` branch here to `main`. My thoughts on this are fully discussed in https://github.com/openpathsampling/openpathsampling/issues/956, so I won't repeat them here. With the exceptions of Contact...

dwhswenson

As mentioned in #101 , there are some limitations on the DaskContactFrequency, mainly: - The whole trajectory has to fit into memory as it is loaded once to figure out...

sroet

Enhancement: ContactTrajectory class (with movies!)

6

It might be nice to add a `ContactTrajectory` class. This would store a separate (single frame) contact map for each time slice. Then you could do interesting things like create...

dwhswenson

Renaming `ContactFrequency` to `ContactMap`; removing old `ContactMap`

2

***Current status (tl;dr for users):*** For a single-frame contact map, you should use `ContactFrequency` with a single-frame trajectory. ```python #cmap = ContactMap(traj, frame=0) # old cmap = ContactFrequency(traj[0]) # new...

dwhswenson

ContactFrequency to pandas dataframe

7

Dear all, I really like using ContactMap Explorer! I was wandering if there is a way to create a pandas dataframe out of a ContactFrequency calculation. Like: ``` traj=mdt.load('trajectory.h5') peptide...

PeptideSimulator01

To handle contact pairs, we frequently use dictionaries/counters where the keys are a `frozenset` of the indices. This gets very annoying to deal with, especially when writing unit tests (so...

dwhswenson