MultiMM 1.0.7__tar.gz → 1.0.9__tar.gz

{multimm-1.0.7 → multimm-1.0.9}/MultiMM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: MultiMM
-Version: 1.0.7
+Version: 1.0.9
 Summary: A tool for chromatin modeling from nucleosomes to chromosomal territories.
 Home-page: https://github.com/SFGLab/MultiMM
 Author: Sebastian Korsak
@@ -27,6 +27,16 @@ Requires-Dist: hilbertcurve
 Requires-Dist: tqdm
 Requires-Dist: pyvista[all]
 Requires-Dist: OpenMM
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # MultiMM: An OpenMM-based software for whole genome 3D structure reconstruction
 
@@ -176,6 +186,8 @@ This version should now be more precise and polished. Let me know if you'd like
 | INITIAL_STRUCTURE_PATH       | str          | None        | None          | Path to CIF file. |
 | BUILD_INITIAL_STRUCTURE      | bool         | True        | None          | To build a new initial structure. |
 | INITIAL_STRUCTURE_TYPE       | str          | hilbert     | None          | you can choose between: hilbert, circle, rw, confined_rw, self_avoiding_rw, helix, spiral, sphere, knot. |
+| GENERATE_ENSEMBLE      | bool         | False        | False          | True if you need to create an ensemble of structures. |
+| N_ENSEMBLE      | int         | None        | None          | Number of samples that you would like to create. |
 | FORCEFIELD_PATH              | str          | None        | None          | Path to XML file with forcefield. |
 | N_BEADS                      | int          | 50000       | None          | Number of Simulation Beads. |
 | COMPARTMENT_PATH             | str          | None        | None          | It should be  a `.bed` file with subcompartments from Calder. |

{multimm-1.0.7 → multimm-1.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: MultiMM
-Version: 1.0.7
+Version: 1.0.9
 Summary: A tool for chromatin modeling from nucleosomes to chromosomal territories.
 Home-page: https://github.com/SFGLab/MultiMM
 Author: Sebastian Korsak
@@ -27,6 +27,16 @@ Requires-Dist: hilbertcurve
 Requires-Dist: tqdm
 Requires-Dist: pyvista[all]
 Requires-Dist: OpenMM
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # MultiMM: An OpenMM-based software for whole genome 3D structure reconstruction
 
@@ -176,6 +186,8 @@ This version should now be more precise and polished. Let me know if you'd like
 | INITIAL_STRUCTURE_PATH       | str          | None        | None          | Path to CIF file. |
 | BUILD_INITIAL_STRUCTURE      | bool         | True        | None          | To build a new initial structure. |
 | INITIAL_STRUCTURE_TYPE       | str          | hilbert     | None          | you can choose between: hilbert, circle, rw, confined_rw, self_avoiding_rw, helix, spiral, sphere, knot. |
+| GENERATE_ENSEMBLE      | bool         | False        | False          | True if you need to create an ensemble of structures. |
+| N_ENSEMBLE      | int         | None        | None          | Number of samples that you would like to create. |
 | FORCEFIELD_PATH              | str          | None        | None          | Path to XML file with forcefield. |
 | N_BEADS                      | int          | 50000       | None          | Number of Simulation Beads. |
 | COMPARTMENT_PATH             | str          | None        | None          | It should be  a `.bed` file with subcompartments from Calder. |

{multimm-1.0.7 → multimm-1.0.9}/README.md

@@ -146,6 +146,8 @@ This version should now be more precise and polished. Let me know if you'd like
 | INITIAL_STRUCTURE_PATH       | str          | None        | None          | Path to CIF file. |
 | BUILD_INITIAL_STRUCTURE      | bool         | True        | None          | To build a new initial structure. |
 | INITIAL_STRUCTURE_TYPE       | str          | hilbert     | None          | you can choose between: hilbert, circle, rw, confined_rw, self_avoiding_rw, helix, spiral, sphere, knot. |
+| GENERATE_ENSEMBLE      | bool         | False        | False          | True if you need to create an ensemble of structures. |
+| N_ENSEMBLE      | int         | None        | None          | Number of samples that you would like to create. |
 | FORCEFIELD_PATH              | str          | None        | None          | Path to XML file with forcefield. |
 | N_BEADS                      | int          | 50000       | None          | Number of Simulation Beads. |
 | COMPARTMENT_PATH             | str          | None        | None          | It should be  a `.bed` file with subcompartments from Calder. |

{multimm-1.0.7 → multimm-1.0.9}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='MultiMM',  # Package name
-    version='1.0.7',  # Version of the software
+    version='1.0.9',  # Version of the software
     description='A tool for chromatin modeling from nucleosomes to chromosomal territories.',
     long_description=long_description,
     long_description_content_type='text/markdown',

{multimm-1.0.7 → multimm-1.0.9}/simulation/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.0.7"
+__version__ = "1.0.9"

{multimm-1.0.7 → multimm-1.0.9}/simulation/args_definition.py

@@ -4,9 +4,18 @@ from dataclasses import dataclass
 from math import pi
 from typing import Union
 import argparse
+import importlib.resources
 import openmm as mm
 from openmm.unit import Quantity
 
+# Dynamically set the default path to the XML file in the package
+try:
+    with importlib.resources.path('loopsage.forcefields', 'classic_sm_ff.xml') as default_xml_path:
+        default_xml_path = str(default_xml_path)
+except FileNotFoundError:
+    # If running in a development setup without the resource installed, fallback to a relative path
+    default_xml_path = 'simulation/forcefields/ff.xml'
+
 @dataclass
 class Arg(object):
     name: str
@@ -130,8 +139,10 @@ args = ListOfArgs([
     # Input data
     Arg('INITIAL_STRUCTURE_PATH', help="Path to CIF file.", type=str, default='', val=''),
     Arg('BUILD_INITIAL_STRUCTURE', help="To build a new initial structure.", type=bool, default='True', val='True'),
-    Arg('INITIAL_STRUCTURE_TYPE', help="you can choose between: hilbert, circle.", type=str, default='hilbert', val='hilbert'),
-    Arg('FORCEFIELD_PATH', help="Path to XML file with forcefield.", type=str, default='', val=''),
+    Arg('INITIAL_STRUCTURE_TYPE', help="you can choose between: hilbert, circle, rw, confined_rw, knot, self_avoiding_rw, spiral, sphere.", type=str, default='hilbert', val='hilbert'),
+    Arg('GENERATE_ENSEMBLE', help="Default value: false. True in case that you would like to have an ensemble of structures instead of one. Better to disable it for large simulations that require long computational time. Moreover it is better to start random walk initial structure in case of true value.", type=bool, default='False', val='False'),
+    Arg('N_ENSEMBLE', help="Number of samples of structures that you would like to calculate.", type=int, default='', val=''),
+    Arg('FORCEFIELD_PATH', help="Path to XML file with forcefield.", type=str, default=default_xml_path, val=default_xml_path),
     Arg('N_BEADS', help="Number of Simulation Beads.", type=int, default='50000', val='50000'),
     Arg('COMPARTMENT_PATH', help="It can be either .bed file with subcompartments from Calder or .BigWig signal.", type=str, default='', val=''),
     Arg('LOOPS_PATH', help="A .bedpe file path with loops. It is required.", type=str, default='', val=''),

{multimm-1.0.7 → multimm-1.0.9}/simulation/run.py

@@ -378,14 +378,19 @@ class MultiMM:
         if self.args.NUC_DO_INTERPOLATION and args.ATACSEQ_PATH!=None:
             self.nuc_interpolation()
             
-
 def main():
     # Input data
     args = get_config()
     
     # Run simulation
-    md = MultiMM(args)
-    md.run()
+    if args.GENERATE_ENSEMBLE:
+        for i in range(args.N_ENSEMBLE):
+            args.OUT_PATH = args.OUOUT_PATHT_PATH+f'_{i+1}'
+            md = MultiMM(args)
+            md.run()
+    else:
+        md = MultiMM(args)
+        md.run()
 
 if __name__=='__main__':
     main()