Merge pull request #725 from choderalab/fixing-tests

[WIP] writing tests for FAH suite

basesetup.py

@@ -3,7 +3,6 @@
 import sys
 import imp
 import json
-import string
 import shutil
 import subprocess
 import tempfile

perses/analysis/analyse_sams_convergence.py

@@ -1,5 +1,6 @@
 import matplotlib.pyplot as plt
-import os, sys
+import os
+import sys
 from glob import glob
 from perses.analysis import utils
 

perses/analysis/analysis.py

@@ -13,22 +13,15 @@
 # IMPORTS
 ################################################################################
 
-import os, os.path
-import sys, math
 import numpy as np
-import copy
-import time
-import netCDF4 as netcdf
 from openeye import oeiupac, oechem
-import pickle
-import json
 import itertools
 import pymbar
 from perses import storage
+import seaborn as sns
 
 import matplotlib as mpl
 mpl.use('Agg')
-import seaborn as sns
 
 from matplotlib.backends.backend_pdf import PdfPages
 import matplotlib.pyplot as plt

perses/analysis/fah_analysis.py

@@ -4,13 +4,10 @@
 from pymbar import BAR
 import matplotlib.pyplot as plt
 import seaborn
-import pickle
 from simtk.openmm import unit
-import bz2
 import json
 from tqdm.auto import tqdm
 from openmmtools.constants import kB
-import random
 import joblib
 import logging
 import os

perses/analysis/load_simulations.py

@@ -1,9 +1,3 @@
-import numpy as np
-import matplotlib.pyplot as plt
-import sys
-from openeye import oechem, oegraphsim
-from openmmtools.constants import kB
-
 import logging
 _logger = logging.getLogger()
 _logger.setLevel(logging.INFO)

perses/annihilation/lambda_protocol.py

@@ -2,12 +2,11 @@
 import numpy as np
 import logging
 import copy
-import traceback
 from openmmtools.alchemy import AlchemicalState
 
 logging.basicConfig(level=logging.NOTSET)
 _logger = logging.getLogger("lambda_protocol")
-_logger.setLevel(logging.DEBUG)
+_logger.setLevel(logging.INFO)
 
 
 class LambdaProtocol(object):
@@ -49,16 +48,16 @@ def __init__(self, functions='default'):
         default : ele and LJ terms of the old system are turned off between 0.0 -> 0.5
         ele and LJ terms of the new system are turned on between 0.5 -> 1.0
         core terms treated linearly
-        
+
         quarters : 0.25 of the protocol is used in turn to individually change the
         (a) off old ele, (b) off old sterics, (c) on new sterics (d) on new ele
         core terms treated linearly
-        
+
         namd : follows the protocol outlined here: https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00362#
-        Jiang, Wei, Christophe Chipot, and Benoît Roux. "Computing Relative Binding Affinity of Ligands 
-        to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD." 
+        Jiang, Wei, Christophe Chipot, and Benoît Roux. "Computing Relative Binding Affinity of Ligands
+        to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD."
         Journal of chemical information and modeling 59.9 (2019): 3794-3802.
-        
+
         ele-scaled : all terms are treated as in default, except for the old and new ele
         these are scaled with lambda^0.5, so as to be linear in energy, rather than lambda
 
@@ -120,17 +119,17 @@ def __init__(self, functions='default'):
                                   'lambda_torsions':
                                   lambda x: x}
             elif self.type == 'ele-scaled':
-                self.functions = {'lambda_electrostatics_insert': 
+                self.functions = {'lambda_electrostatics_insert':
                                    lambda x: 0.0 if x < 0.5 else ((2*(x-0.5))**0.5),
-                                  'lambda_electrostatics_delete': 
+                                  'lambda_electrostatics_delete':
                                    lambda x: (2*x)**2 if x < 0.5 else 1.0
                                  }
             elif self.type == 'user-defined':
                 self.functions = functions
             else:
                 _logger.warning(f"""LambdaProtocol type : {self.type} not
                                   recognised. Allowed values are 'default',
-                                  'namd' and 'quarters' and 'user-defined'. 
+                                  'namd' and 'quarters' and 'user-defined'.
                                   Setting LambdaProtocol functions to default. """)
                 self.functions = LambdaProtocol.default_functions
 

perses/annihilation/ncmc_switching.py

@@ -2,16 +2,14 @@
 import numpy as np
 import copy
 import logging
-import traceback
-from simtk import openmm, unit
-from perses.dispersed.feptasks import Particle, compute_reduced_potential
+from perses.dispersed.feptasks import compute_reduced_potential
 from perses.storage import NetCDFStorageView
 from perses.annihilation.relative import HybridTopologyFactory
-from perses.tests.utils import quantity_is_finite
 from openmmtools.constants import kB
 from openmmtools.cache import LRUCache, global_context_cache
 from openmmtools.states import ThermodynamicState, SamplerState, CompoundThermodynamicState
 from perses.annihilation.lambda_protocol import RelativeAlchemicalState, LambdaProtocol
+from simtk import unit
 
 default_temperature = 300.0*unit.kelvin
 default_nsteps = 1

perses/annihilation/relative.py

@@ -1,14 +1,9 @@
-import sys
 import simtk.openmm as openmm
-import simtk.openmm.app as app
 import simtk.unit as unit
 import mdtraj as md
 import numpy as np
 import copy
 import enum
-from io import StringIO
-import lxml.etree as etree
-from openmmtools.constants import ONE_4PI_EPS0
 
 InteractionGroup = enum.Enum("InteractionGroup", ['unique_old', 'unique_new', 'core', 'environment'])