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License: Other
a package of Python modules and example scripts for experimenting with the two-dimensional HP lattice model of Dill and Chan.
License: Other
Just a couple minor suggestions:
1.
https://github.com/vvoelz/HPSandbox/blob/master/hpsandbox/__init__.py
__all__
used for anything special? I don't see it in any other src code.https://github.com/vvoelz/HPSandbox/blob/master/hpsandbox/Config.py
os.path.join
for operating systems other than unix-like.self.SETUPDIR = self.EXPDIR + '/setup'
should be self.SETUPDIR = os.path.join(self.EXPDIR, '/setup')
Using more descriptive function names?
https://github.com/vvoelz/HPSandbox/blob/master/hpsandbox/Monty.py#L223-L246
D
might not be the best choice? maybe something more descriptive? def sum_squared_distances(self, chain):
"""Return the sum of squared-distances over the selected contacts."""
ssd = 0.0
for i in range(0,len(self.contacts)):
c = self.contacts[i][0]
d = self.contacts[i][1]
ssd += (chain.coords[c][0]-chain.coords[d][0])*(chain.coords[c][0]-chain.coords[d][0])
ssd += (chain.coords[c][1]-chain.coords[d][1])*(chain.coords[c][1]-chain.coords[d][1])
There are many standalone scripts from the 2014 work that need to have the print statements updated
Make HPSandbox a package that can be installed as
import hpsandbox as hp
or
from hpsandbox import *
All scripts in projects/build12merTmat require MSMBuilder. I have tried to install the latest version http://msmbuilder.org/3.8.0/ via conda in a separate environment but it is taking a long time....
This installation issue needs to be fixed before we can test the code.
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