Ptp generation finishing

[RiesBen]

No description provided.

[MTLehner]

Is this issue still valid?

As I see it the ptp files ar used. And @candidechamp is working on a solution to create the class in a non file based way

[candidechamp]

Just to clarify, what I did was to write functions to generate .ptp files for "hybrid" topologies, and I did it without using a Ptp() object (so not object oriented, because Ptp wasn't implemented yet) but my code could very easily be adapted.

Depending on what you've done @schroederb, I could adapt my code and have a createHybridTopo() class function, which would probably complement your createDualTopo() type function.

[RiesBen]

Hi,
my code is here:
https://github.com/rinikerlab/PyGromosTools/blob/release3/examples/dev/singleTop/example_ptp.ipynb

it builds up three functions for single, hybrid and dual topology with PyGromosTools. so its not done yet. The issue referred to the jnb that I wanted to integrate into PyGromosTools as functions for automatic build up. Following the definitions from the Restraintmaker manuscript.

Where is your Code @candidechamp?

[candidechamp]

@schroederb My code is just in a python file on my computer not linked to pyGromos whatsoever yet.

I somehow didn't see that the PERTATOMPARAM was already implemented so I didn't use that for my .ptp preparation, but could adapt it easily.

But other than that I was doing something very similar to you (i.e. building a normal topology by adding the proper bonds, angles, etc. and doing the perturbation topology at the very end which is a very simple step).

I can share my code with you if you want to look at it, but I would rather wait that we have one version on the pyGromos repo rather than 2 different ones which could be confusing for people.

[RiesBen]

hm so my jnb was planned to roll out to release3.
If you could share your code, I would check if there is a feature or cool addition, that I did not think of and add it. :)

[RiesBen]

This issue will be resolved with:
#220

I think we don't need this issue anymore.