pyVLMP 1.0.2__tar.gz → 1.0.4__tar.gz

{pyVLMP-1.0.2/pyVLMP.egg-info → pyVLMP-1.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyVLMP
-Version: 1.0.2
+Version: 1.0.4
 Summary: Virtual Laboratory for the simulation of Macromolecular Properties
 Home-page: https://github.com/PabloIbannez/pyGrained
 Author-email: Pablo Ibáñez-Freire <p.ibanez.fre@gmail.com>

{pyVLMP-1.0.2 → pyVLMP-1.0.4}/VLMP/__init__.py

@@ -49,6 +49,12 @@ logger.addHandler(clogger)
 
 #################################################
 
-from .VLMP  import VLMP
-from .utils import *
+if "-m" not in sys.argv:
+    #This done to avoid the error when running the program with -m option.
+    #When running with -m option a large number of libraries imported by VLMP
+    #are not needed.
 
+    logger.info("Starting VLMP...")
+
+    from .VLMP  import VLMP
+    from .utils import *

{pyVLMP-1.0.2 → pyVLMP-1.0.4}/VLMP/components/models/HELIX.py

@@ -4,6 +4,7 @@ import itertools
 import logging
 
 from . import modelBase
+from ...utils.utils import getEx
 
 import random
 
@@ -33,35 +34,22 @@ class HELIX(modelBase):
     def __computeKdst(self,var,Eb,rc):
         init = 1.0
         Kdst = root(lambda K: var - (self.kT/Eb)*((rc*rc)/(np.pi*np.pi))*((1.0-np.exp(-2.0*K))/K),init)
+        varTheo = (self.kT/Eb)*((rc*rc)/(np.pi*np.pi))*((1.0-np.exp(-2.0*Kdst["x"][0]))/Kdst["x"][0])
+        if np.abs(varTheo-var) > 1e-6:
+            self.logger.error(f"[HELIX] Error computing Kdst")
+            raise Exception("Error computing Kdst")
         return Kdst["x"][0]
 
     def __computeKangle(self,var,Eb):
         init = (1.0-0.5*var*(Eb/self.kT))/2.0
         Kangle = root(lambda K: var - (self.kT/Eb)*((1.0-np.exp(-2.0*K))/K),init)
+        varTheo = (self.kT/Eb)*((1.0-np.exp(-2.0*Kangle["x"][0]))/Kangle["x"][0])
+        if np.abs(varTheo-var) > 1e-6:
+            self.logger.error(f"[HELIX] Error computing Kangle")
+            raise Exception("Error computing Kangle")
         return Kangle["x"][0]
 
 
-    def __getEx(self,q):
-        """ Given a quaternion, q, the function returns the z vector of the local basis"""
-
-        q0,q1,q2,q3 = q
-
-        return 2.0*np.asarray([q0*q0+q1*q1-0.5,q1*q2+q0*q3,q1*q3-q0*q2])
-
-    def __getEy(self,q):
-        """ Given a quaternion, q, the function returns the z vector of the local basis"""
-
-        q0,q1,q2,q3 = q
-
-        return 2.0*np.asarray([q1*q2-q0*q3,q0*q0+q2*q2-0.5,q2*q3+q0*q1])
-
-    def __getEz(self,q):
-        """ Given a quaternion, q, the function returns the z vector of the local basis"""
-
-        q0,q1,q2,q3 = q
-
-        return 2.0*np.asarray([q1*q3+q0*q2,q2*q3-q0*q1,q0*q0+q3*q3-0.5])
-
     def __generateRandomPositions(self):
         monomersPositions    = []
         monomersOrientations = []
@@ -171,7 +159,7 @@ class HELIX(modelBase):
                 q1,q2,q3,q0 = r_init.as_quat()
 
             else:
-                x,y,z = monomersPositions[-1]+sigma*self.__getEx(monomersOrientations[-1])
+                x,y,z = monomersPositions[-1]+sigma*getEx(monomersOrientations[-1])
 
                 q0,q1,q2,q3 = monomersOrientations[-1]
                 r_prev    = R.from_quat([q1,q2,q3,q0])
@@ -199,8 +187,8 @@ class HELIX(modelBase):
         return np.asarray(monomersPositions),np.asarray(monomersOrientations)
 
     def __getMonomerConnections(self,position,orientation):
-        connectionStart = position-self.monomerRadius*self.__getEx(orientation)
-        connectionEnd   = position+self.monomerRadius*self.__getEx(orientation)
+        connectionStart = position-self.monomerRadius*getEx(orientation)
+        connectionEnd   = position+self.monomerRadius*getEx(orientation)
 
         return connectionStart,connectionEnd
 
@@ -302,6 +290,10 @@ class HELIX(modelBase):
         self.logger.info(f"[HELIX] K theta computed {self.Ka} for variance {varTheta}")
         self.logger.info(f"[HELIX] K phi computed {self.Kd} for variance {varPhi}")
 
+        if self.Kb < 0 or self.Ka < 0 or self.Kd < 0:
+            self.logger.error(f"[HELIX] Negative spring constant: Kb {self.Kb} Ka {self.Ka} Kd {self.Kd}")
+            raise Exception("Negative spring constant")
+
         ##############################################
 
         self.logger.info(f"[HELIX] Generating HELIX model with {self.nMonomers} monomers")

{pyVLMP-1.0.2 → pyVLMP-1.0.4}/VLMP/utils/utils.py

@@ -13,6 +13,20 @@ def picosecond2KcalMol_A_time():
 
 #Geometry utils
 
+def getEx(q):
+    """ Given a quaternion, q, the function returns the z vector of the local basis"""
+
+    q0,q1,q2,q3 = q
+
+    return 2.0*np.asarray([q0*q0+q1*q1-0.5,q1*q2+q0*q3,q1*q3-q0*q2])
+
+def getEy(q):
+    """ Given a quaternion, q, the function returns the z vector of the local basis"""
+
+    q0,q1,q2,q3 = q
+
+    return 2.0*np.asarray([q1*q2-q0*q3,q0*q0+q2*q2-0.5,q2*q3+q0*q1])
+
 def getEz(q):
     """ Given a quaternion, q, the function returns the z vector of the local basis"""
 
@@ -20,6 +34,7 @@ def getEz(q):
 
     return 2.0*np.asarray([q1*q3+q0*q2,q2*q3-q0*q1,q0*q0+q3*q3-0.5])
 
+
 def quaternionFromVectors(vec1, vec2):
     """ Given two vector the function returns the rotation that transform one into another.
         The rotation is codified as a quaternion"""

{pyVLMP-1.0.2 → pyVLMP-1.0.4/pyVLMP.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyVLMP
-Version: 1.0.2
+Version: 1.0.4
 Summary: Virtual Laboratory for the simulation of Macromolecular Properties
 Home-page: https://github.com/PabloIbannez/pyGrained
 Author-email: Pablo Ibáñez-Freire <p.ibanez.fre@gmail.com>

{pyVLMP-1.0.2 → pyVLMP-1.0.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name="pyVLMP"
-version="1.0.2"
+version="1.0.4"
 authors = [
     {name = "Pablo Ibáñez-Freire", email = "p.ibanez.fre@gmail.com"},
 ]