pyLoopSage 1.0.9__tar.gz → 1.0.10__tar.gz

{pyloopsage-1.0.9 → pyloopsage-1.0.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.9
+Version: 1.0.10
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.9 → pyloopsage-1.0.10}/loopsage/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.0.9"
+__version__ = "1.0.10"

{pyloopsage-1.0.9 → pyloopsage-1.0.10}/loopsage/args_definition.py

@@ -136,12 +136,12 @@ args = ListOfArgs([
     
     # Stochastic Simulation parameters
     Arg('LEF_RW', help="True in case that you would like to make cohesins slide as random walk, instead of sliding only in one direction.", type=bool, default='True', val='True'),
-    Arg('N_STEPS', help="Number of Monte Carlo steps.", type=int, default='', val=''),
+    Arg('N_STEPS', help="Number of Monte Carlo steps.", type=int, default='40000', val='40000'),
     Arg('N_LEF', help="Number of loop extrusion factors (condensins and cohesins).", type=int, default='', val=''),
-    Arg('MC_STEP', help="Monte Carlo frequency. It should be hundreds of steps, except if you would like to include molecular dynamics (MD) and in this case it should be ideally 1.", type=int, default='200', val='200'),
+    Arg('MC_STEP', help="Monte Carlo frequency. It should be hundreds of steps so as to avoid autocorrelated ensembles.", type=int, default='200', val='200'),
     Arg('BURNIN', help="Burnin-period (steps that are considered before equillibrium).", type=int, default='1000', val='1000'),
-    Arg('T_INIT', help="Initial Temperature of the Stochastic Model.", type=float, default='1.8', val='1.8'),
-    Arg('T_FINAL', help="Final Temperature of the Stochastic Model.", type=float, default='0.01', val='0.01'),
+    Arg('T_INIT', help="Initial Temperature of the Stochastic Model.", type=float, default='2.0', val='2.0'),
+    Arg('T_FINAL', help="Final Temperature of the Stochastic Model.", type=float, default='1.0', val='1.0'),
     Arg('METHOD', help="Stochastic modelling method. It can be Metropolis or Simulated Annealing.", type=str, default='Annealing', val='Annealing'),
     Arg('FOLDING_COEFF', help="Folding coefficient.", type=float, default='1.0', val='1.0'),
     Arg('CROSS_COEFF', help="LEF crossing coefficient.", type=float, default='1.0', val='1.0'),
@@ -152,15 +152,15 @@ args = ListOfArgs([
     # Molecular Dynamic Properties
     Arg('INITIAL_STRUCTURE_TYPE', help="you can choose between: rw, confined_rw, self_avoiding_rw, helix, circle, spiral, sphere.", type=str, default='rw', val='rw'),
     Arg('SIMULATION_TYPE', help="It can be either EM (multiple energy minimizations) or MD (one energy minimization and then run molecular dynamics).", type=str, default='', val=''),
-    Arg('INTEGRATOR_STEP', help="The step of the integrator.", type=Quantity, default='5 femtosecond', val='5 femtosecond'),
+    Arg('INTEGRATOR_STEP', help="The step of the integrator.", type=Quantity, default='100 femtosecond', val='100 femtosecond'),
     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='0.1', val='0.1'),
-    Arg('LE_FF_STRENGTH', help="Interaction Strength of loop forces.", type=float, default='3000.0', val='3000.0'),
+    Arg('LE_FF_STRENGTH', help="Interaction Strength of loop forces.", type=float, default='50000.0', val='50000.0'),
     Arg('EV_FF_STRENGTH', help="Excluded-volume strength.", type=float, default='10.0', val='10.0'),
     Arg('FRICTION',help='Friction coefficient of the Langevin integrator.',type=float, default='0.1', val='0.1'),
     Arg('TOLERANCE', help="Tolerance that works as stopping condition for energy minimization.", type=float, default='0.001', val='0.001'),
     Arg('VIZ_HEATS', help="Visualize the output average heatmap.", type=bool, default='True', val='True'),
     Arg('SIM_TEMP', help="The temperature of the 3D simulation (EM or MD).", type=Quantity, default='310 kelvin', val='310 kelvin'),
-    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='10', val='10'),
+    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='1000', val='1000'),
 ])

{pyloopsage-1.0.9 → pyloopsage-1.0.10}/pyLoopSage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.9
+Version: 1.0.10
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak

{pyloopsage-1.0.9 → pyloopsage-1.0.10}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='pyLoopSage',  # Package name
-    version='1.0.9',  # Version of the software
+    version='1.0.10',  # 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',