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psfgen's Introduction

psfgen

Psfgen with a Python interface!

Read the Documentation!

Installation

To build and install, you'll need a C compiler:

python setup.py install

License

This software is classified as a "derivative work" of the original psfgen code. It uses the main psfgen code and a swig interface file that are the work of the original developers (Justin Gullingsrud and Jim Phillips). I have made it installable, and am fixing warnings in the C code. I will probably rewrite the Python interface at some point (this is early).

psfgen is licensed by the University of Illinois' Non-Exclusive, Non-Commercial use license.

"This software includes code developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."

psfgen's People

Contributors

eigenstate avatar al42and avatar penglian518 avatar

Stargazers

Miles avatar denis pan avatar Safaa Sader avatar avatar avatar Mingtian avatar avatar Markus Rauhalahti avatar Miquel Canyelles Niño avatar Francisco Adasme avatar Steven(Yuhang) Wang avatar avatar avatar

Watchers

James Cloos avatar avatar

Forkers

plin1112 al42and penglian518

psfgen's Issues

hydrogen mass repartition

Hi i'm version of PSFGen is very usefull,

I need know if are implementation use last psfgen 2 for enable hydrogen mass repartition

best

gen.alias_atom error

In python, I add this line.
gen.alias_atom(resname="ILE", top_atomname="CD", pdb_atomname="CD1")
When I run the script, the output for this alias.
"Aliasing residue CD1 atom CD1 to CD"
And it also print out the error message
"Warning: failed to set coordinate for atom CD1 ILE:14 B"

Cannot add_segment without pdbfile argument

Hi! Given the helpstring of add_segment:

        pdbfile (str): PDB file to read residue information from, or
            None to create an empty segment

My understanding is that I can create an empty segment with:
gen.add_segment('S')
but that fails with:
TypeError: add_segment() argument 3 must be str, not None
so it seems to demand a PDF filename. Is that intentional?

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