Chromo: Physics-based Simulator of Chromatin Architecture¶
- Chromo
- chromo.fields
FieldBaseNullFieldReconstructorUniformDensityFieldUniformDensityField._field_descriptorsUniformDensityField.width_xyzUniformDensityField.dxyzUniformDensityField.n_binsUniformDensityField.vol_binUniformDensityField.bin_indexUniformDensityField.nbr_indices_with_trialUniformDensityField.nbr_indsUniformDensityField.index_xyz_with_trialUniformDensityField.index_xyzUniformDensityField.wt_vec_with_trialUniformDensityField.wt_vecUniformDensityField.xyz_with_trialUniformDensityField.xyzUniformDensityField.weight_xyz_with_trialUniformDensityField.weight_xyzUniformDensityField.num_bindersUniformDensityField.confine_typeUniformDensityField.confine_lengthUniformDensityField.access_volsUniformDensityField.chiUniformDensityField.dict_UniformDensityField.binder_dictUniformDensityField.half_width_xyzUniformDensityField.half_step_xyzUniformDensityField.n_xyz_m1UniformDensityField.inds_xyz_to_superUniformDensityField.vf_limitUniformDensityField.fast_fieldUniformDensityField.n_pointsUniformDensityField.compute_E()UniformDensityField.from_file()UniformDensityField.get_accessible_volumes()UniformDensityField.get_dict()UniformDensityField.init_field_energy_prefactors()UniformDensityField.init_grid()UniformDensityField.nonspecific_interact_E()UniformDensityField.to_file()UniformDensityField.update_all_densities()UniformDensityField.update_all_densities_for_all_polymers()
assign_beads_to_bins()get_blocks()get_neighboring_bins()get_neighbors_at_ind()super_ind_to_inds()
- chromo.mixtures
- chromo.polymers
ChromatinDetailedChromatinDetailedChromatin2DetailedChromatinWithStericsDetailedChromatinWithSterics.check_steric_clashes()DetailedChromatinWithSterics.compute_E()DetailedChromatinWithSterics.compute_E_detailed()DetailedChromatinWithSterics.compute_E_detailed_reverse()DetailedChromatinWithSterics.compute_dE()DetailedChromatinWithSterics.eval_E_steric_clashes()DetailedChromatinWithSterics.eval_delta_steric_clashes()DetailedChromatinWithSterics.evaluate_binder_interactions()DetailedChromatinWithSterics.get_E_bind()DetailedChromatinWithSterics.get_delta_distances()DetailedChromatinWithSterics.get_distances()DetailedChromatinWithSterics.is_field_active()
LoopedSSTWLCPolymerBasePolymerBase.namePolymerBase.log_pathPolymerBase.beadsPolymerBase.num_beadsPolymerBase.configuration_trackerPolymerBase.lpPolymerBase.num_bindersPolymerBase.n_binders_p1PolymerBase.binder_namesPolymerBase.all_indsPolymerBase.statesPolymerBase.states_trialPolymerBase.chemical_modsPolymerBase.chemical_mod_namesPolymerBase.directionPolymerBase.pointPolymerBase.last_amp_movePolymerBase.last_amp_beadPolymerBase.densities_tempPolymerBase.max_bindersPolymerBase.check_attrs()PolymerBase.fill_missing_arguments()PolymerBase.from_csv()PolymerBase.from_dataframe()PolymerBase.from_file()PolymerBase.get_all()PolymerBase.get_num_beads()PolymerBase.get_num_binders()PolymerBase.get_prop()PolymerBase.is_field_active()PolymerBase.load_seqs()PolymerBase.to_csv()PolymerBase.to_dataframe()PolymerBase.to_file()PolymerBase.update_log_path()PolymerBase.update_prop()
RouseSSTWLCSSWLCTransformedObjectcompute_twist_angle_omega()helix_parametric_x()helix_parametric_y()helix_parametric_z()sin_func()
- chromo.beads
- chromo.binders
- chromo.__init__
- chromo.fields
- Chromo MC
- Chromo Utils
- chromo.util.linalg
- chromo.util.reproducibility
- chromo.util.__init__
- chromo.util.poly_paths
confined_gaussian_walk()confined_uniform_random_walk()coordinates_in_x_y()coordinates_in_x_y_z()estimate_tangents_from_coordinates()gaussian_walk()get_tangent_vals_x_y()get_tangent_vals_x_y_z()in_confinement()in_cubical_confinement()in_spherical_confinement()looped_confined_gaussian_walk()numerical_derivative()
- chromo.util.bead_selection
- chromo.util.poly_stat
- chromo.util.mc_stat
- chromo.util.gjk