pyLoopSage 1.0.4__tar.gz → 1.0.5__tar.gz

{pyloopsage-1.0.4 → pyloopsage-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.4
+Version: 1.0.5
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.4 → pyloopsage-1.0.5}/loopsage/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.0.4"
+__version__ = "1.0.5"

{pyloopsage-1.0.4 → pyloopsage-1.0.5}/loopsage/args_definition.py

@@ -153,8 +153,8 @@ args = ListOfArgs([
     Arg('FORCEFIELD_PATH', help="Path to XML file with forcefield.", type=str, default='forcefield/classic_sm_ff.xml', val='forcefield/classic_sm_ff.xml'),
     Arg('ANGLE_FF_STRENGTH', help="Angle force strength.", type=float, default='200.0', val='200.0'),
     Arg('LE_FF_LENGTH', help="Equillibrium distance of loop forces.", type=float, default='0.0', val='0.0'),
-    Arg('LE_FF_STRENGTH', help="Equillibrium distance of loop forces.", type=float, default='300000.0', val='300000.0'),
+    Arg('LE_FF_STRENGTH', help="Equillibrium distance of loop forces.", type=float, default='30000.0', val='30000.0'),
     Arg('EV_FF_STRENGTH', help="Excluded-volume strength.", type=float, default='10.0', val='10.0'),
     Arg('TOLERANCE', help="Tolerance that works as stopping condition for energy minimization.", type=float, default='0.001', val='0.001'),
     Arg('SIM_STEP', help="This is the amount of simulation steps that are perform each time that we change the loop forces. If this number is too high, the simulation is slow, if is too low it may not have enough time to adapt the structure to the new constraints.", type=int, default='100', val='100'),
-])
+])

{pyloopsage-1.0.4 → pyloopsage-1.0.5}/loopsage/md.py

@@ -16,7 +16,7 @@ from .utils import *
 from .initial_structures import *
 
 class MD_LE:
-    def __init__(self,M,N,N_beads,burnin,MC_step,path,platform,angle_ff_strength=200,le_distance=0.1,le_ff_strength=300000.0,ev_ff_strength=10.0,tolerance=0.001):
+    def __init__(self,M,N,N_beads,burnin,MC_step,path,platform,angle_ff_strength=200,le_distance=0.1,le_ff_strength=30000.0,ev_ff_strength=10.0,tolerance=0.001):
         '''
         M, N (np arrays): Position matrix of two legs of cohesin m,n. 
                           Rows represent  loops/cohesins and columns represent time
@@ -117,7 +117,7 @@ class MD_LE:
 
     def add_evforce(self):
         'Leonard-Jones potential for excluded volume'
-        self.ev_force = mm.CustomNonbondedForce('epsilon*((sigma1+sigma2)/(r+r_small))^6')
+        self.ev_force = mm.CustomNonbondedForce('epsilon*(sigma1+sigma2)/(r+r_small)')
         self.ev_force.addGlobalParameter('epsilon', defaultValue=self.ev_ff_strength)
         self.ev_force.addGlobalParameter('r_small', defaultValue=0.01)
         self.ev_force.addPerParticleParameter('sigma')

{pyloopsage-1.0.4 → pyloopsage-1.0.5}/pyLoopSage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.4
+Version: 1.0.5
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.4 → pyloopsage-1.0.5}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='pyLoopSage',  # Package name
-    version='1.0.4',  # Version of the software
+    version='1.0.5',  # Version of the software
     description='An energy-based stochastic model of loop extrusion in chromatin.',
     long_description=long_description,
     long_description_content_type='text/markdown',