Stable release v1.0

docs/conf.py

@@ -23,14 +23,14 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u'HPS-Urry'
+project = u'HPS'
 copyright = u'2021, Quyen Vu'
 author = u'Quyen Vu'
 
 # The short X.Y version
 version = '2021.0'
 # The full version, including alpha/beta/rc tags
-release = 'alpha'
+release = 'v1.0'
 
 # -- General configuration ---------------------------------------------------
 

docs/index.rst

@@ -3,7 +3,7 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to HPS-Urry's documentation!
+Welcome to HPS's documentation!
 ====================================
 
 .. toctree::
@@ -12,15 +12,15 @@ Welcome to HPS-Urry's documentation!
 
    modules
 
-HPS-Urry Documentation
+HPS Documentation
 #######################
 
 Introduction
 ************
 
 .. include:: sections/introduction.rst
 
-HPS-Urry Models
+HPS Models
 **********
 
 .. include:: sections/models.rst

docs/modules.rst

@@ -1,7 +1,7 @@
-hps_urry
+HPS
 ========
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 2
 
    hps

docs/sections/introduction.rst

@@ -1,19 +1,19 @@
-Hydropathy Scale-Urryl (hps-urry) are representations of protein systems based on simplifications made over classical Molecular Dynamics (MD) force fields. 
+Hydropathy Scale are the model of protein systems based on simplifications made over classical Molecular Dynamics (MD) force fields.
 
-The hps-urry model is a Python library that offers flexibility to set up coarse-grained simulation of IDP using the MD framework of OpenMM toolkit.
-The codebase is based on hps-urry.
-It automates the creation of openmm.system classes that contain the necessary force field parameters to run molecular dynamics simulations using a protein structure as the only necessary inputs.
+The hps model is a Python library that offers flexibility to set up coarse-grained simulation of IDP using the MD framework of OpenMM toolkit.
+The codebase is based on sbmOpenMM scripts.
+It automates the creation of :code:`openmm.system` classes that contain the necessary force field parameters to run molecular dynamics simulations using a protein structure as the only necessary inputs.
 
-hps-urry is divided in three main classes:
+hps is divided in three main classes:
 
-1. geometry
-2. models
-3. system
+1. :code:`geometry`
+2. :code:`models`
+3. :code:`system`
 
-The first class, geometry, contains methods to calculate the geometrical parameters from the input structures. 
+The first class, :code:`geometry`, contains methods to calculate the geometrical parameters from the input structures.
 It's not useful in current need of simulation method.
-The second class, models, allows to easily set up CG models.
-The third class, system, is the main class that holds all the methods to define, modify and create CG system to be simulated with OpenMM.
+The second class, :code:`models`, allows to easily set up CG models.
+The third class, :code:`system`, is the main class that holds all the methods to define, modify and create CG system to be simulated with OpenMM.
 
 The library is open-source and offers flexibility to simulate IDPs.
-We test on RTX 2060 with the timestep of 30fs, we can get upto :math:`80\mu s/day`.
+

docs/sections/models.rst

@@ -1,14 +1,16 @@
-The models class of sbmOpenMM contains three methods for automatic setting up predefined SBM potentials. It works by initializing a system class with the necessary force field parameters, derived from the input files, to set up one of the possible models which are detailed next:
+The models class contains three methods for automatic setting up predefined potentials.
+It works by initializing a system class with the necessary force field parameters.
 
 Coarse grained, alpha-carbon (CA), model
 ++++++++++++++++++++++++++++++++++++++++
 
 The coarse grained method represents the protein system as beads centered at the alpha carbons of each residue in the protein. It uses harmonic potentials to hold the covalent connectivity and geometry of the beads. Torsional geometries are modeled with a periodic torsion potential. Native contacts are represented through the use of Lennard-Jones potentials that allow to form and break non-bonded interactions, permitting complete and local unfolding of the structures.
 
 To create a CA model, call:
-:code:`hps.models.getCAModel(pdb_file)`
+:code:`hps.models.getCAModel(pdb_file, hps_scale)`
 
 Here, pdb_file is the path to the PDB format structure of the protein.
+hps_scale is hydropathy scale that are going to be used. :code:`urry` or :code:`kr`
 
 The force field equations are:
 
@@ -20,7 +22,7 @@ The Bonded potential:
 .. math::
         V_{bond} = \frac{k_b}{2}(r-r_0)^2
 
-Here the default values are :math:`k_b=20 kCal/(mol \times A^2), r_0=3.82 A^2`
+Here the default values are :math:`k_b= 8368 kJ/(mol \times nm^2), r_0=0.382 nm`
 
 The Pairwise potential:
 +++++++++++++++++++++++
@@ -45,7 +47,8 @@ where, :math:`\sigma_{i,j}=\frac{\sigma_i+\sigma_j}{2}`: is the vdW radius inter
 
 In the current implementation, hydropathy scales are taken from Urry model, :math:`(\mu, \Delta) = (1, 0.08)`
 
-* Note that two atoms are in bonded interaction do not interact via pair-wise potential.
+Nonbonded exclusion rule is :code:`1-2`.
+Cutoff distance for Electrostatics interactions: :math:`3.5 nm`, for Lennard-Jone potential: :math:`2.0 nm`
 
 The Debye-Huckle potential has following form:
 ++++++++++++++++++++++++++++++++++++++++++++++
@@ -57,7 +60,9 @@ where, :math:`q_i, q_j` are charge of residues :math:`i, j`
 :math:`\epsilon_0`: Vacuum permitivity. For convenient, we precalculated the electric conversion factor
 :math:`\frac{1}{4\pi\epsilon_0}= 138.935 485(9) kJ \times mol^{−1} \times nm \times e^{−2}`.
 
-:math:`D`: dielectric constant, at 100mM monovalent salt (NaCl), it takes values of 80
+:math:`D`: dielectric constant, at 100mM mono-valence salt (NaCl), it takes values of 80.
+The dielectric constant here is fixed, but it can be temperature dependent as the function:
+:math:`\frac{5321}{T}+233.76-0.9297T+0.1417\times 10^{-2}\times T^2 - 0.8292\times 10^{-6}\times T^3`
 
 :math:`\kappa`: inverse Debye length, at 100mM NaCl has values of :math:`1 nm^{-1}`