pyLoopSage 1.0.2__tar.gz → 1.0.3__tar.gz

{pyloopsage-1.0.2 → pyloopsage-1.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.2
+Version: 1.0.3
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak
@@ -137,7 +137,7 @@ where the last two columns represent the probabilites for left and right anchor
 
 Then, we define the main parameters of the simulation `N_beads,N_coh,kappa,f,b` or we can choose the default ones (take care because it might be the case that they are not the appropriate ones and they need to be changed), the parameters of Monte Carlo `N_steps, MC_step, burnin, T`, and we initialize the class `LoopSage()`. The command `sim.run_energy_minimization()` corresponds to the stochastic Monte Carlo simulation, and it produces a set of cohesin constraints as a result (`Ms, Ns`). Note that the stochastic simulation has two modes: `Annealing` and `Metropolis`. We feed cohesin constraints to the molecular simulation part of and we run `MD_LE()` or `MD_EM()` simulation which produces a trajectory of 3d-structures, and the average heatmap. `MD_LE()` function can produce an actual trajectory and a `.dcd` video of how simulation changes over time. However, the implementation needs a high amount of memory since we need to define a bond for each time step, and it may not work for large systems. `EM_LE()` is suggested for large simulations, because it does not require so big amount of memory.
 
-### Command-line command
+### Running LoopSage from command-line
 To run LoopSage from command-line, you only need to type a command
 
 ```bash
@@ -147,24 +147,57 @@ loopsage -c config.ini
 With this command the model will run with parameters specified in `config.ini` file. An example of a `config.ini` file would be the following,
 
 ```txt
-# Definition of Monte Carlo parameters
-N_steps, MC_step, burnin, T, T_min = int(4e4), int(5e2), 1000, 2.5, 1.0
-mode = 'Metropolis'
+[Main]
+
+; Input Data and Information
+BEDPE_PATH = /home/skorsak/Data/HiChIP/Maps/hg00731_smc1_maps_2.bedpe
+REGION_START = 15550000
+REGION_END = 16850000
+CHROM = chr6
+OUT_PATH = ../HiChIP_Annealing_T15_MD_region
+
+; Simulation Parameters
+N_BEADS = 1000
+N_STEPS = 40000
+MC_STEP = 500
+BURNIN = 1000
+T_INIT = 1.5
+T_FINAL = 0.01
+METHOD = Metropolis
+
+; Molecular Dynamics
+PLATFORM = CUDA
+INITIAL_STRUCTURE_TYPE = rw
+SIMULATION_TYPE = EM 
+TOLERANCE = 1.0
+``` 
 
-# Simulation Strengths
-f, b, kappa = 1.0, 1.0, 1.0
+### Visualization with PyVista
 
-# Definition of region
-region, chrom = [15550000,16850000], 'chr6'
+There are many tools for visualization of polymer structures. A very good one is UCSF chimera: https://www.cgl.ucsf.edu/chimera/. Usually these visualization tools work well for proteins, but we can use them for chromatin as well.
 
-# Definition of data
-output_name='../HiChIP_Annealing_T1_MD_region'
-bedpe_file = '/home/skorsak/Data/HiChIP/Maps/hg00731_smc1_maps_2.bedpe'
+LoopSage offers its own visualization which relies in the `pyvista` python library. To visualize a structure, you can run some very simple commands, which call LoopSage functions,
 
-sim = StochasticSimulation(region,chrom,bedpe_file,out_dir=output_name,N_beads=1000)
-Es, Ms, Ns, Bs, Ks, Fs, ufs = sim.run_energy_minimization(N_steps,MC_step,burnin,T,T_min,mode=mode,viz=True,save=True)
-sim.run_MD('CUDA')
-``` 
+```python
+import loopsage.vizualization_tools as vz
+import loopsage.utils as uts
+
+V = uts.get_coordinates_cif('/home/skorsak/Projects/mine/LoopSage/HiChIP_Annealing_T15_EM_region/ensemble/EMLE_1.cif')
+vz.viz_structure(V)
+```
+
+The output should be something like that,
+
+![image](https://github.com/user-attachments/assets/457d2b1f-e037-4ff1-8cec-c9eef7de789d)
+
+
+In case that you would like to create a continuous video from the enseble of structures, you can use the following command, which would generate an interactive video in gif format which would show how the structure changes in 3D. The command includes quaternion Kabsch aligment as well.
+
+```python
+import loopsage.vizualization_tools as vz
+
+vz.interactive_plot('/home/skorsak/Projects/mine/LoopSage/HiChIP_Annealing_T15_EM_region/ensemble')
+```
 
 ### Output Files
 In the output files, simulation produces one folder with 4 subfolders. In subfolder `plots`, you can find plots that are the diagnostics of the algorithm. One of the most basic results you should see is the trajectories of cohesins (LEFs). this diagram should look like that,

{pyloopsage-1.0.2 → pyloopsage-1.0.3}/README.md

@@ -103,7 +103,7 @@ where the last two columns represent the probabilites for left and right anchor
 
 Then, we define the main parameters of the simulation `N_beads,N_coh,kappa,f,b` or we can choose the default ones (take care because it might be the case that they are not the appropriate ones and they need to be changed), the parameters of Monte Carlo `N_steps, MC_step, burnin, T`, and we initialize the class `LoopSage()`. The command `sim.run_energy_minimization()` corresponds to the stochastic Monte Carlo simulation, and it produces a set of cohesin constraints as a result (`Ms, Ns`). Note that the stochastic simulation has two modes: `Annealing` and `Metropolis`. We feed cohesin constraints to the molecular simulation part of and we run `MD_LE()` or `MD_EM()` simulation which produces a trajectory of 3d-structures, and the average heatmap. `MD_LE()` function can produce an actual trajectory and a `.dcd` video of how simulation changes over time. However, the implementation needs a high amount of memory since we need to define a bond for each time step, and it may not work for large systems. `EM_LE()` is suggested for large simulations, because it does not require so big amount of memory.
 
-### Command-line command
+### Running LoopSage from command-line
 To run LoopSage from command-line, you only need to type a command
 
 ```bash
@@ -113,24 +113,57 @@ loopsage -c config.ini
 With this command the model will run with parameters specified in `config.ini` file. An example of a `config.ini` file would be the following,
 
 ```txt
-# Definition of Monte Carlo parameters
-N_steps, MC_step, burnin, T, T_min = int(4e4), int(5e2), 1000, 2.5, 1.0
-mode = 'Metropolis'
+[Main]
+
+; Input Data and Information
+BEDPE_PATH = /home/skorsak/Data/HiChIP/Maps/hg00731_smc1_maps_2.bedpe
+REGION_START = 15550000
+REGION_END = 16850000
+CHROM = chr6
+OUT_PATH = ../HiChIP_Annealing_T15_MD_region
+
+; Simulation Parameters
+N_BEADS = 1000
+N_STEPS = 40000
+MC_STEP = 500
+BURNIN = 1000
+T_INIT = 1.5
+T_FINAL = 0.01
+METHOD = Metropolis
+
+; Molecular Dynamics
+PLATFORM = CUDA
+INITIAL_STRUCTURE_TYPE = rw
+SIMULATION_TYPE = EM 
+TOLERANCE = 1.0
+``` 
 
-# Simulation Strengths
-f, b, kappa = 1.0, 1.0, 1.0
+### Visualization with PyVista
 
-# Definition of region
-region, chrom = [15550000,16850000], 'chr6'
+There are many tools for visualization of polymer structures. A very good one is UCSF chimera: https://www.cgl.ucsf.edu/chimera/. Usually these visualization tools work well for proteins, but we can use them for chromatin as well.
 
-# Definition of data
-output_name='../HiChIP_Annealing_T1_MD_region'
-bedpe_file = '/home/skorsak/Data/HiChIP/Maps/hg00731_smc1_maps_2.bedpe'
+LoopSage offers its own visualization which relies in the `pyvista` python library. To visualize a structure, you can run some very simple commands, which call LoopSage functions,
 
-sim = StochasticSimulation(region,chrom,bedpe_file,out_dir=output_name,N_beads=1000)
-Es, Ms, Ns, Bs, Ks, Fs, ufs = sim.run_energy_minimization(N_steps,MC_step,burnin,T,T_min,mode=mode,viz=True,save=True)
-sim.run_MD('CUDA')
-``` 
+```python
+import loopsage.vizualization_tools as vz
+import loopsage.utils as uts
+
+V = uts.get_coordinates_cif('/home/skorsak/Projects/mine/LoopSage/HiChIP_Annealing_T15_EM_region/ensemble/EMLE_1.cif')
+vz.viz_structure(V)
+```
+
+The output should be something like that,
+
+![image](https://github.com/user-attachments/assets/457d2b1f-e037-4ff1-8cec-c9eef7de789d)
+
+
+In case that you would like to create a continuous video from the enseble of structures, you can use the following command, which would generate an interactive video in gif format which would show how the structure changes in 3D. The command includes quaternion Kabsch aligment as well.
+
+```python
+import loopsage.vizualization_tools as vz
+
+vz.interactive_plot('/home/skorsak/Projects/mine/LoopSage/HiChIP_Annealing_T15_EM_region/ensemble')
+```
 
 ### Output Files
 In the output files, simulation produces one folder with 4 subfolders. In subfolder `plots`, you can find plots that are the diagnostics of the algorithm. One of the most basic results you should see is the trajectories of cohesins (LEFs). this diagram should look like that,

{pyloopsage-1.0.2 → pyloopsage-1.0.3}/loopsage/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.0.2"
+__version__ = "1.0.3"

{pyloopsage-1.0.2 → pyloopsage-1.0.3}/pyLoopSage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyLoopSage
-Version: 1.0.2
+Version: 1.0.3
 Summary: An energy-based stochastic model of loop extrusion in chromatin.
 Home-page: https://github.com/SFGLab/pyLoopSage
 Author: Sebastian Korsak
@@ -137,7 +137,7 @@ where the last two columns represent the probabilites for left and right anchor
 
 Then, we define the main parameters of the simulation `N_beads,N_coh,kappa,f,b` or we can choose the default ones (take care because it might be the case that they are not the appropriate ones and they need to be changed), the parameters of Monte Carlo `N_steps, MC_step, burnin, T`, and we initialize the class `LoopSage()`. The command `sim.run_energy_minimization()` corresponds to the stochastic Monte Carlo simulation, and it produces a set of cohesin constraints as a result (`Ms, Ns`). Note that the stochastic simulation has two modes: `Annealing` and `Metropolis`. We feed cohesin constraints to the molecular simulation part of and we run `MD_LE()` or `MD_EM()` simulation which produces a trajectory of 3d-structures, and the average heatmap. `MD_LE()` function can produce an actual trajectory and a `.dcd` video of how simulation changes over time. However, the implementation needs a high amount of memory since we need to define a bond for each time step, and it may not work for large systems. `EM_LE()` is suggested for large simulations, because it does not require so big amount of memory.
 
-### Command-line command
+### Running LoopSage from command-line
 To run LoopSage from command-line, you only need to type a command
 
 ```bash
@@ -147,24 +147,57 @@ loopsage -c config.ini
 With this command the model will run with parameters specified in `config.ini` file. An example of a `config.ini` file would be the following,
 
 ```txt
-# Definition of Monte Carlo parameters
-N_steps, MC_step, burnin, T, T_min = int(4e4), int(5e2), 1000, 2.5, 1.0
-mode = 'Metropolis'
+[Main]
+
+; Input Data and Information
+BEDPE_PATH = /home/skorsak/Data/HiChIP/Maps/hg00731_smc1_maps_2.bedpe
+REGION_START = 15550000
+REGION_END = 16850000
+CHROM = chr6
+OUT_PATH = ../HiChIP_Annealing_T15_MD_region
+
+; Simulation Parameters
+N_BEADS = 1000
+N_STEPS = 40000
+MC_STEP = 500
+BURNIN = 1000
+T_INIT = 1.5
+T_FINAL = 0.01
+METHOD = Metropolis
+
+; Molecular Dynamics
+PLATFORM = CUDA
+INITIAL_STRUCTURE_TYPE = rw
+SIMULATION_TYPE = EM 
+TOLERANCE = 1.0
+``` 
 
-# Simulation Strengths
-f, b, kappa = 1.0, 1.0, 1.0
+### Visualization with PyVista
 
-# Definition of region
-region, chrom = [15550000,16850000], 'chr6'
+There are many tools for visualization of polymer structures. A very good one is UCSF chimera: https://www.cgl.ucsf.edu/chimera/. Usually these visualization tools work well for proteins, but we can use them for chromatin as well.
 
-# Definition of data
-output_name='../HiChIP_Annealing_T1_MD_region'
-bedpe_file = '/home/skorsak/Data/HiChIP/Maps/hg00731_smc1_maps_2.bedpe'
+LoopSage offers its own visualization which relies in the `pyvista` python library. To visualize a structure, you can run some very simple commands, which call LoopSage functions,
 
-sim = StochasticSimulation(region,chrom,bedpe_file,out_dir=output_name,N_beads=1000)
-Es, Ms, Ns, Bs, Ks, Fs, ufs = sim.run_energy_minimization(N_steps,MC_step,burnin,T,T_min,mode=mode,viz=True,save=True)
-sim.run_MD('CUDA')
-``` 
+```python
+import loopsage.vizualization_tools as vz
+import loopsage.utils as uts
+
+V = uts.get_coordinates_cif('/home/skorsak/Projects/mine/LoopSage/HiChIP_Annealing_T15_EM_region/ensemble/EMLE_1.cif')
+vz.viz_structure(V)
+```
+
+The output should be something like that,
+
+![image](https://github.com/user-attachments/assets/457d2b1f-e037-4ff1-8cec-c9eef7de789d)
+
+
+In case that you would like to create a continuous video from the enseble of structures, you can use the following command, which would generate an interactive video in gif format which would show how the structure changes in 3D. The command includes quaternion Kabsch aligment as well.
+
+```python
+import loopsage.vizualization_tools as vz
+
+vz.interactive_plot('/home/skorsak/Projects/mine/LoopSage/HiChIP_Annealing_T15_EM_region/ensemble')
+```
 
 ### Output Files
 In the output files, simulation produces one folder with 4 subfolders. In subfolder `plots`, you can find plots that are the diagnostics of the algorithm. One of the most basic results you should see is the trajectories of cohesins (LEFs). this diagram should look like that,

{pyloopsage-1.0.2 → pyloopsage-1.0.3}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='pyLoopSage',  # Package name
-    version='1.0.2',  # Version of the software
+    version='1.0.3',  # 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',