delete junk files

docs/conf.py

@@ -17,14 +17,15 @@
 import os
 import sys
 import sphinx
+import sphinx_rtd_theme
 sys.path.insert(0, os.path.abspath('..'))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'HPS-Urry'
-copyright = '2021, Quyen Vu'
-author = 'Quyen Vu'
+project = u'HPS-Urry'
+copyright = u'2021, Quyen Vu'
+author = u'Quyen Vu'
 
 # The short X.Y version
 version = '2021.0'
@@ -46,18 +47,25 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
-    'numpydoc'
+    'numpydoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.doctest',
+    'sphinx.ext.coverage'
 ]
 
+autosummary_generate = True
+#numpydoc_show_class_members = False
+autodoc_default_flags = ['members', 'inherited-members']
+
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 # If true, the current module name will be prepended to all description unit titles.
 add_module_names = False
 
-# html_sidebars = {
-#    '**': ['localtoc.html', 'searchbox.html'],
-# }
-
+html_sidebars = {
+        '**': ['localtoc.html', 'sourcelink.html', 'searchbox.html'],
+}
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

hps/core/system.py

@@ -53,7 +53,7 @@ class system:
     yukawaForce : :code:`openmm.CustomNonbondedForce`
         Stores the OpenMM :code:`CustomNonbondedForce` initialized-class.
         Implements the Debye-Huckle potential.
-    pairWiseForce : :code:`openmm.CustomNonbondedForce`
+    ashbaughHatchForces : :code:`openmm.CustomNonbondedForce`
         Stores the OpenMM :code:`CustomNonbondedForce` initialized-class. Implements the pairwise short-range
         potential.
     forceGroups : :code:`collections.OrderedDict`
@@ -92,7 +92,7 @@ class system:
         class using their defined forcefield parameters.
     addYukawaForces()
         Creates a nonbonded force term for electrostatic interaction DH potential.
-    addPairWiseForces()
+    addAshbaughHatchForces()
         Creates a nonbonded force term for pairwise interaction (customize LJ 12-6 potential).
     createSystemObject()
         Creates OpenMM system object adding particles, masses and forces.
@@ -171,7 +171,7 @@ def __init__(self, structure_path, particles_mass=1.0):
 
         # self.exclusions = []
         # PairWise potential
-        self.pairWiseForce = None
+        self.ashbaugh_HatchForce = None
         # self.muy = 1
         # self.delta = 0.08
         self.epsilon = 0.8368
@@ -552,7 +552,7 @@ def addAshbaughHatchForces(self):
         \\epsilon = 0.8368 kj/mol`
 
         The
-        The force object is stored at the :code:`pairWiseForce` attribute.
+        The force object is stored at the :code:`ashbaugh_HatchForce` attribute.
 
         Parameters
         ----------
@@ -573,26 +573,26 @@ def addAshbaughHatchForces(self):
         energy_function += '+(1-step(2^(1/6)*sigma-r)) * (hps*4*epsilon*((sigma/r)^12-(sigma/r)^6));'
         energy_function += 'sigma=0.5*(sigma1+sigma2);'
         energy_function += 'hps=0.5*(hps1+hps2)'
-        self.pairWiseForce = CustomNonbondedForce(energy_function)
-        self.pairWiseForce.addGlobalParameter('epsilon', self.epsilon)
-        self.pairWiseForce.addPerParticleParameter('sigma')
-        self.pairWiseForce.addPerParticleParameter('hps')
-        self.pairWiseForce.setNonbondedMethod(NonbondedForce.CutoffNonPeriodic)
-        self.pairWiseForce.setCutoffDistance(self.cutoff_Ashbaugh_Hatch)
+        self.ashbaugh_HatchForce = CustomNonbondedForce(energy_function)
+        self.ashbaugh_HatchForce.addGlobalParameter('epsilon', self.epsilon)
+        self.ashbaugh_HatchForce.addPerParticleParameter('sigma')
+        self.ashbaugh_HatchForce.addPerParticleParameter('hps')
+        self.ashbaugh_HatchForce.setNonbondedMethod(NonbondedForce.CutoffNonPeriodic)
+        self.ashbaugh_HatchForce.setCutoffDistance(self.cutoff_Ashbaugh_Hatch)
 
         if isinstance(self.rf_sigma, float):
             for atom in self.atoms:
-                self.pairWiseForce.addParticle((self.rf_sigma,))
+                self.ashbaugh_HatchForce.addParticle((self.rf_sigma,))
 
         # in the case each atoms have different sigma para.
         elif isinstance(self.rf_sigma, list):
             assert self.n_atoms == len(self.rf_sigma) and self.n_atoms == len(self.particles_hps)
             for i, atom in enumerate(self.atoms):
-                self.pairWiseForce.addParticle((self.rf_sigma[i], self.particles_hps[i],))
+                self.ashbaugh_HatchForce.addParticle((self.rf_sigma[i], self.particles_hps[i],))
 
         # set exclusions rule
         bonded_exclusions = [(b[0].index, b[1].index) for b in list(self.topology.bonds())]
-        self.pairWiseForce.createExclusionsFromBonds(bonded_exclusions, self.bonded_exclusions_index)
+        self.ashbaugh_HatchForce.createExclusionsFromBonds(bonded_exclusions, self.bonded_exclusions_index)
 
     """ Functions for creating OpenMM system object """
     def createSystemObject(self, check_bond_distances=True, minimize=False, check_large_forces=True,
@@ -809,9 +809,9 @@ def addSystemForces(self):
             self.system.addForce(self.yukawaForce)
             self.forceGroups['Yukawa Energy'] = self.yukawaForce
 
-        if self.pairWiseForce is not None:
-            self.system.addForce(self.pairWiseForce)
-            self.forceGroups['PairWise Energy'] = self.pairWiseForce
+        if self.ashbaugh_HatchForce is not None:
+            self.system.addForce(self.ashbaugh_HatchForce)
+            self.forceGroups['PairWise Energy'] = self.ashbaugh_HatchForce
 
     def dumpStructure(self, output_file):
         """

hps/parameters/ca_parameters.py

@@ -43,8 +43,10 @@
              'SER': 0.595, 'THR': 0.676, 'TRP': 0.946,
              'TYR': 0.865, 'VAL': 0.892}
 """
-Hydropathy scale (Urry scale)
-Here we use muy=1 and delta = 0.08. Directly scale the hps.
+Hydropathy scale.
+There are two options to select when running simulation by specify hps_scale='kr'/'urry'
+In the case of Urry, we implicitly use muy=1 and delta = 0.08 to move equation in two scales to be the same.
+
 Regy, R. M., Thompson, J., Kim, Y. C., & Mittal, J. (2021). 
 Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins. 
 Protein Science, 30(7), 1371–1379. https://doi.org/10.1002/pro.4094
@@ -58,6 +60,8 @@
              'SER': 0.0, 'THR': 0.0, 'TRP': 0.0,
              'TYR': 0.0, 'VAL': 0.0}
 """
+* Kapcha-Rossy and Urry model different in charge of HIS, in Urry, HIS has charge of 0, while in KR, HIS=0.5
+We switch in set CA Charge function.
 Charge of the coarse-grain beads, assigns to it alpha-carbon atoms.
 Charges are determined at neutral pH (pH=7).
 Setting to the values from, where ARG, LYS =1 and ASP, GLU = -1,