vvoelz / hpsandbox Goto Github PK

Just a couple minor suggestions:
1.
https://github.com/vvoelz/HPSandbox/blob/master/hpsandbox/__init__.py

• Unused variables:
  e.g., Is the variable __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

• paths are hard-coded: https://github.com/vvoelz/HPSandbox/blob/master/hpsandbox/Config.py#L55-L62
• use os.path.join for operating systems other than unix-like.
  e.g., line 56. self.SETUPDIR = self.EXPDIR + '/setup' should be self.SETUPDIR = os.path.join(self.EXPDIR, '/setup')
  ...this is also an issue here https://github.com/vvoelz/HPSandbox/blob/master/hpsandbox/Replica.py
  and
  https://github.com/vvoelz/HPSandbox/blob/master/hpsandbox/Trajectory.py#L106, as well as other instances.

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?
  Here's a possible change(?)

    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.