MultiMM 1.0.1__tar.gz → 1.0.3__tar.gz

{multimm-1.0.1 → multimm-1.0.3}/MultiMM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MultiMM
-Version: 1.0.1
+Version: 1.0.3
 Summary: A tool for chromatin modeling from nucleosomes to chromosomal territories.
 Home-page: https://github.com/SFGLab/MultiMM
 Author: Sebastian Korsak
@@ -25,10 +25,8 @@ Requires-Dist: typing-extensions
 Requires-Dist: pyBigWig
 Requires-Dist: hilbertcurve
 Requires-Dist: tqdm
-Provides-Extra: viz
-Requires-Dist: pyvista[all]; extra == "viz"
-Provides-Extra: simulations
-Requires-Dist: OpenMM; extra == "simulations"
+Requires-Dist: pyvista[all]
+Requires-Dist: OpenMM
 
 # MultiMM: An OpenMM-based software for whole genome 3D structure reconstruction
 

multimm-1.0.3/MultiMM.egg-info/SOURCES.txt

@@ -0,0 +1,17 @@
+LICENSE
+README.md
+setup.py
+MultiMM.egg-info/PKG-INFO
+MultiMM.egg-info/SOURCES.txt
+MultiMM.egg-info/dependency_links.txt
+MultiMM.egg-info/entry_points.txt
+MultiMM.egg-info/requires.txt
+MultiMM.egg-info/top_level.txt
+simulation/__init__.py
+simulation/args_definition.py
+simulation/initial_structure_tools.py
+simulation/nucleosome_interpolation.py
+simulation/plots.py
+simulation/run.py
+simulation/utils.py
+simulation/validation.py

{multimm-1.0.1 → multimm-1.0.3}/MultiMM.egg-info/requires.txt

@@ -11,9 +11,5 @@ typing-extensions
 pyBigWig
 hilbertcurve
 tqdm
-
-[simulations]
-OpenMM
-
-[viz]
 pyvista[all]
+OpenMM

multimm-1.0.3/MultiMM.egg-info/top_level.txt

@@ -0,0 +1 @@
+simulation

{multimm-1.0.1 → multimm-1.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MultiMM
-Version: 1.0.1
+Version: 1.0.3
 Summary: A tool for chromatin modeling from nucleosomes to chromosomal territories.
 Home-page: https://github.com/SFGLab/MultiMM
 Author: Sebastian Korsak
@@ -25,10 +25,8 @@ Requires-Dist: typing-extensions
 Requires-Dist: pyBigWig
 Requires-Dist: hilbertcurve
 Requires-Dist: tqdm
-Provides-Extra: viz
-Requires-Dist: pyvista[all]; extra == "viz"
-Provides-Extra: simulations
-Requires-Dist: OpenMM; extra == "simulations"
+Requires-Dist: pyvista[all]
+Requires-Dist: OpenMM
 
 # MultiMM: An OpenMM-based software for whole genome 3D structure reconstruction
 

{multimm-1.0.1 → multimm-1.0.3}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='MultiMM',  # Package name
-    version='1.0.1',  # Version of the software
+    version='1.0.3',  # 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',
@@ -29,11 +29,9 @@ setup(
         'pyBigWig',
         'hilbertcurve',
         'tqdm',
+        'pyvista[all]',
+        'OpenMM',
     ],
-    extras_require={  # Optional dependencies
-        'viz': ['pyvista[all]'],
-        'simulations': ['OpenMM'],
-    },
     entry_points={
         'console_scripts': [
             'MultiMM=simulation.run:main',  # MultiMM command points to run.py's main function

multimm-1.0.3/simulation/__init__.py

@@ -0,0 +1,4 @@
+# Importing specific functions or classes from submodules
+from .run import main
+
+__version__ = "1.0.0"

multimm-1.0.3/simulation/args_definition.py

@@ -0,0 +1,224 @@
+import datetime
+import re
+from dataclasses import dataclass
+from math import pi
+from typing import Union
+import argparse
+import openmm as mm
+from openmm.unit import Quantity
+
+@dataclass
+class Arg(object):
+    name: str
+    help: str
+    type: type
+    default: Union[str, float, int, bool, Quantity, None]
+    val: Union[str, float, int, bool, Quantity, None]
+
+# Define custom type to parse list from string
+def parse_list(s):
+    try:
+        return [int(x.strip()) for x in s.strip('[]').split(',')]
+    except ValueError:
+        raise argparse.ArgumentTypeError("Invalid list format. Must be a comma-separated list of integers.")
+
+class ListOfArgs(list):
+    quantity_regexp = re.compile(r'(?P<value>[-+]?\d+(?:\.\d+)?) ?(?P<unit>\w+)')
+
+    def get_arg(self, name: str) -> Arg:
+        """Stupid arg search in list of args"""
+        name = name.upper()
+        for i in self:
+            if i.name == name:
+                return i
+        raise ValueError(f"No such arg: {name}")
+
+    def __getattr__(self, item):
+        return self.get_arg(item).val
+
+    def parse_args(self):
+        parser = argparse.ArgumentParser()
+        for arg in self.arg_list:
+            parser.add_argument(arg['name'], help=arg['help'], type=arg.get('type', str), default=arg.get('default', ''), val=arg.get('val', ''))
+
+        args = parser.parse_args()
+        parsed_args = {arg['name']: getattr(args, arg['name']) for arg in self.arg_list}
+        return parsed_args
+
+    def parse_quantity(self, val: str) -> Union[Quantity, None]:
+        if val == '':
+            return None
+        match_obj = self.quantity_regexp.match(val)
+        value, unit = match_obj.groups()
+        try:
+            unit = getattr(mm.unit, unit)
+        except AttributeError:
+            raise ValueError(f"I Can't recognise unit {unit} in expression {val}. Example of valid quantity: 12.3 femtosecond.")
+        return Quantity(value=float(value), unit=unit)
+
+    def to_python(self):
+        """Casts string args to ints, floats, bool..."""
+        for i in self:
+            if i.val == '':
+                i.val = None
+            elif i.name == "HR_K_PARAM":  # Workaround for complex unit
+                i.val = Quantity(float(i.val), mm.unit.kilojoule_per_mole / mm.unit.nanometer ** 2)
+            elif i.type == str:
+                continue
+            elif i.type == int:
+                i.val = int(i.val)
+            elif i.type == float:
+                i.val = float(i.val)
+            elif i.type == bool:
+                if i.val.lower() in ['true', '1', 'y', 'yes']:
+                    i.val = True
+                elif i.val.lower() in ['false', '0', 'n', 'no']:
+                    i.val = False
+                else:
+                    raise ValueError(f"Can't convert {i.val} into bool type.")
+            elif i.type == Quantity:
+                try:
+                    i.val = self.parse_quantity(i.val)
+                except AttributeError:
+                    raise ValueError(f"Can't parse: {i.name} = {i.val}")
+            else:
+                raise ValueError(f"Can't parse: {i.name} = {i.val}")
+
+    def get_complete_config(self) -> str:
+        w = "####################\n"
+        w += "#   MultiMM Model   #\n"
+        w += "####################\n\n"
+        w += "# This is automatically generated config file.\n"
+        w += f"# Generated at: {datetime.datetime.now().isoformat()}\n\n"
+        w += "# Notes:\n"
+        w += "# Some fields require units. Units are represented as objects from mm.units module.\n"
+        w += "# Simple units are parsed directly. For example: \n"
+        w += "# HR_R0_PARAM = 0.2 nanometer\n"
+        w += "# But more complex units does not have any more sophisticated parser written, and will fail.'\n"
+        w += "# In such cases the unit is fixed (and noted in comment), so please convert complex units manually if needed.\n"
+        w += "# <float> and <int> types does not require any unit. Quantity require unit.\n\n"
+        w += "# Default values does not mean valid value. In many places it's only a empty field that need to be filled.\n\n"
+
+        w += '[Main]'
+        for i in self:
+            w += f'; {i.help}, type: {i.type.__name__}, default: {i.default}\n'
+            if i.val is None:
+                w += f'{i.name} = \n\n'
+            else:
+                if i.type == Quantity:
+                    # noinspection PyProtectedMember
+                    w += f'{i.name} = {i.val._value} {i.val.unit.get_name()}\n\n'
+                else:
+                    w += f'{i.name} = {i.val}\n\n'
+        w = w[:-2]
+        return w
+
+    def write_config_file(self):
+        auto_config_filename = 'config_auto.ini'
+        with open(auto_config_filename, 'w') as f:
+            f.write(self.get_complete_config())
+        print(f"Automatically generated config file saved in {auto_config_filename}")
+
+
+available_platforms = [mm.Platform.getPlatform(i).getName() for i in range(mm.Platform.getNumPlatforms())]
+
+args = ListOfArgs([
+    # Platform settings
+    Arg('PLATFORM', help=f"name of the platform. Available choices: {' '.join(available_platforms)}", type=str, default='', val=''),
+    Arg('DEVICE', help="device index for CUDA or OpenCL (count from 0)", type=str, default='', val=''),
+    
+    # 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('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=''),
+    Arg('ATACSEQ_PATH', help="A .bw or .BigWig file path with atacseq data. It is not required.", type=str, default='', val=''),
+    Arg('OUT_PATH', help="Output folder name.", type=str, default='results', val='results'),
+    Arg('LOC_START', help="Starting region coordinate.", type=int, default='', val=''),
+    Arg('LOC_END', help="Ending region coordinate.", type=int, default='', val=''),
+    Arg('CHROM', help="Chromosome that corresponds the the modelling region of interest (in case that you do not want to model the whole genome).", type=str, default='', val=''),
+    Arg('SHUFFLE_CHROMS', help="Shuffle the chromosomes.", type=bool, default='False', val='False'),
+    Arg('SHUFFLING_SEED', help="Shuffling random seed.", type=int, default='0', val='0'),
+    Arg('SAVE_PLOTS', help='Save plots.', type=bool, default='True', val='True'),
+    
+    # Basic Polymer Bond
+    Arg('POL_USE_HARMONIC_BOND', help="Use harmonic bond interaction.", type=bool, default='True', val='True'),
+    Arg('POL_HARMONIC_BOND_R0', help="harmonic bond distance equilibrium constant", type=float, default='0.1', val='0.1'),
+    Arg('POL_HARMONIC_BOND_K', help="harmonic bond force constant (fixed unit: kJ/mol/nm^2)", type=float, default='300000.0', val='300000.0'),
+
+    # Basic polymer stiffness
+    Arg('POL_USE_HARMONIC_ANGLE', help="Use harmonic angle interaction.", type=bool, default='True', val='True'),
+    Arg('POL_HARMONIC_ANGLE_R0', help="harmonic angle distance equilibrium constant", type=float, default=str(pi), val=str(pi)),
+    Arg('POL_HARMONIC_ANGLE_CONSTANT_K', help="harmonic angle force constant (fixed unit: kJ/mol/radian^2)", type=float, default='100.0', val='100.0'),
+
+    # Long-Range loop bonds
+    Arg('LE_USE_HARMONIC_BOND', help="Use harmonic bond interaction for long range loops.", type=bool, default='True', val='True'),
+    Arg('LE_FIXED_DISTANCES', help="For fixed distances between loops. False if you want to correlate with the hatmap strength.", type=bool, default='False', val='False'),
+    Arg('LE_HARMONIC_BOND_R0', help="harmonic bond distance equilibrium constant", type=float, default='0.1', val='0.1'),
+    Arg('LE_HARMONIC_BOND_K', help="harmonic bond force constant (fixed unit: kJ/mol/nm^2)", type=float, default='30000.0', val='30000.0'),
+
+    # Excluded Volume
+    Arg('EV_USE_EXCLUDED_VOLUME', help="Use excluded volume.", type=bool, default='True', val='True'),
+    Arg('EV_EPSILON', help="Epsilon parameter.", type=float, default='100.0', val='100.0'),
+    Arg('EV_R_SMALL', help="Add something small in denominator to make it not exploding all the time.", type=float, default='0.05', val='0.05'),
+    Arg('EV_POWER', help="Power in the exponent of EV potential.", type=float, default='3.0', val='3.0'),
+    
+    # Spherical container
+    Arg('SC_USE_SPHERICAL_CONTAINER', help='Use Spherical container', type=bool, default='False', val='False'),
+    Arg('SC_RADIUS1', help='Spherical container radius,', type=float, default='', val=''),
+    Arg('SC_RADIUS2', help='Spherical container radius,', type=float, default='', val=''),
+    Arg('SC_SCALE', help='Spherical container scaling factor', type=float, default='1000.0', val='1000.0'),
+
+    # Chromosomal Blocks
+    Arg('CHB_USE_CHROMOSOMAL_BLOCKS', help='Use Chromosomal Blocks.', type=bool, default='False', val='False'),
+    Arg('CHB_KC', help='Block copolymer width parameter.', type=float, default='0.3', val='0.3'),
+    Arg('CHB_DE', help='Energy factor for block copolymer chromosomal model.', type=float, default='1e-5', val='1e-5'),
+    
+    # Compartment Blocks
+    Arg('COB_USE_COMPARTMENT_BLOCKS', help='Use Compartment Blocks.', type=bool, default='False', val='False'),
+    Arg('COB_DISTANCE', help='Block copolymer equilibrium distance for chromosomal blocks.', type=float, default='', val=''),
+    Arg('COB_EA', help='Energy strength for A compartment.', type=float, default='1.0', val='1.0'),
+    Arg('COB_EB', help='Energy strength for B compartment.', type=float, default='2.0', val='2.0'),
+    
+    # Subcompartment Blocks
+    Arg('SCB_USE_SUBCOMPARTMENT_BLOCKS', help='Use Subcompartment Blocks.', type=bool, default='False', val='False'),
+    Arg('SCB_DISTANCE', help='Block copolymer equilibrium distance for chromosomal blocks.', type=float, default='', val=''),
+    Arg('SCB_EA1', help='Energy strength for A1 compartment.', type=float, default='1.0', val='1.0'),
+    Arg('SCB_EA2', help='Energy strength for A2 compartment.', type=float, default='1.33', val='1.33'),
+    Arg('SCB_EB1', help='Energy strength for B1 compartment.', type=float, default='1.66', val='1.66'),
+    Arg('SCB_EB2', help='Energy strength for B2 compartment.', type=float, default='2.0', val='2.0'),
+
+    # Interactions of B compartment with lamina
+    Arg('IBL_USE_B_LAMINA_INTERACTION', help='Interactions of B compartment with lamina.', type=bool, default='False', val='False'),
+    Arg('IBL_SCALE', help='Scaling factor for B comoartment interaction with lamina.', type=float, default='400.0', val='400.0'),
+    
+    # Central Force for Smaller Chromosomes Attraction to the Nucleolus
+    Arg('CF_USE_CENTRAL_FORCE', help='Attraction of smaller chromosomes.', type=bool, default='False', val='False'),
+    Arg('CF_STRENGTH', help='Strength of Interaction', type=float, default='100.0', val='100.0'),
+
+    # Nucleosome interpolation
+    Arg('NUC_DO_INTERPOLATION', help='Attraction of smaller chromosomes.', type=bool, default='False', val='False'),
+    Arg('MAX_NUCS_PER_BEAD', help='Maximum amount of nucleosomes per single bead.', type=int, default='4', val='4'),
+    Arg('NUC_RADIUS', help='The radius of the single nucleosome helix.', type=float, default='0.1', val='0.1'),
+    Arg('POINTS_PER_NUC', help='The number of points that consist a nucleosome helix.', type=int, default='20', val='20'),
+    Arg('PHI_NORM', help='Zig zag angle. ', type=float, default=str(pi/5), val=str(pi/5)),
+    
+    # Simulation parameters
+    Arg('SIM_RUN_MD', help='Do you want to run MD simulation?', type=bool, default='False', val='False'),
+    Arg('SIM_N_STEPS', help='Number of steps in MD simulation', type=int, default='', val=''),
+    Arg('SIM_ERROR_TOLERANCE', help='Error tolerance for variable MD simulation', type=float, default='0.01', val='0.01'),
+    Arg('SIM_AMD_ALPHA', help='Alpha of AMD simulation.', type=float, default='100.0', val='100.0'),
+    Arg('SIM_AMD_E', help='E (energy) of AMD simulation.', type=float, default='1000.0', val='1000.0'),
+    Arg('SIM_SAMPLING_STEP', help='It determines in t how many steps we save a structure.', type=int, default='100', val='100'),
+    Arg('SIM_INTEGRATOR_TYPE', help='Alternative: langevin, verlet', type=str, default='langevin', val='langevin'),
+    Arg('SIM_INTEGRATOR_STEP', help='The step of integrator.', type=Quantity, default='1 femtosecond', val='1 femtosecond'),
+    Arg('SIM_FRICTION_COEFF', help='Friction coefficient (Used only with langevin integrator)', type=float, default='0.5', val='0.5'),
+    Arg('SIM_SET_INITIAL_VELOCITIES', help='Sets initial velocities based on Boltzmann distribution', type=bool, default='False', val='False'),
+    Arg('SIM_TEMPERATURE', help='Simulation temperature', type=Quantity, default='310 kelvin', val='310 kelvin'),
+
+    # Trajectory settings
+    Arg('TRJ_FRAMES', help='Number of trajectory frames to save.', type=int, default='2000', val='2000'),
+])