MultiMM 1.0.7__tar.gz → 1.0.8__tar.gz

{multimm-1.0.7 → multimm-1.0.8}/MultiMM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: MultiMM
-Version: 1.0.7
+Version: 1.0.8
 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
 

{multimm-1.0.7 → multimm-1.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: MultiMM
-Version: 1.0.7
+Version: 1.0.8
 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
 

{multimm-1.0.7 → multimm-1.0.8}/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='1.0.8',  # 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-1.0.8}/simulation/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.0.7"
+__version__ = "1.0.8"

{multimm-1.0.7 → multimm-1.0.8}/simulation/args_definition.py

@@ -7,6 +7,14 @@ import argparse
 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
@@ -131,7 +139,7 @@ args = ListOfArgs([
     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('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=''),