Updating Tutorial

README.md

@@ -1,9 +1,8 @@
 # IMP spatiotemporal tutorial
-NOTE: This tutorial is still in progress of being completed. Please do not use yet. In the meantime, see https://github.com/salilab/imp/tree/develop/modules/spatiotemporal/examples/toy for a worked demonstration of the spatiotemporal module
 
 Tutorial for computing spatiotemporal integrative models in IMP. For more information please check out the related publications:
 * Latham bioRxiv, 2024, https://doi.org/10.1101/2024.08.06.606842.
-* Rožič et al. in preparation. (tutorial paper)
+* Latham et al. in preparation. (tutorial paper)
 
 ### This tutorial explores scripts that:
 * Generates snapshot models at various timepoints along a dynamic process

modeling/Snapshots/Snapshots_Assessment/README.md

@@ -1,3 +1,3 @@
 ### This directory contains the code necessary for analyzing static snapshot models
 
-See https://integrativemodeling.org/tutorials/spatiotemporal/snapshot_assess.html
+See https://integrativemodeling.org/tutorials/spatiotemporal/snapshots.html

modeling/Snapshots/Snapshots_Modeling/README.md

@@ -1,3 +1,3 @@
 ### This directory contains the code necessary for generating static snapshot models
 
-See https://integrativemodeling.org/tutorials/spatiotemporal/snapshot1.html
+See https://integrativemodeling.org/tutorials/spatiotemporal/snapshots.html

modeling/Trajectories/Trajectories_Assessment/README.md

@@ -1,3 +1,3 @@
 ### This directory contains the code necessary for analyzing trajectory models
 
-See https://integrativemodeling.org/tutorials/spatiotemporal/trajectory_assess.html
+See https://integrativemodeling.org/tutorials/spatiotemporal/trajectories.html

modeling/Trajectories/Trajectories_Assessment/trajectories_assessment.py

@@ -524,8 +524,11 @@ def process_foxs(state_dict, custom_dat_file = None):
                 command6 = f"gnuplot snapshot1_{time}_{time}_exp.plt"
                 os.system(command6)
 
-                command7 = f"mv snapshot1_{time}_{time}_exp.plt {time}_FoXS.png"
+                command7 = f"mv snapshot1_{time}_{time}_exp.plt {time}_FoXS.plt"
                 os.system(command7)
+
+                command8 = f"mv snapshot1_{time}_{time}_exp.png {time}_FoXS.png"
+                os.system(command8)
             else:
                 print(f"There is no states in this timepoint. Check stat_dict.")
 
@@ -638,7 +641,7 @@ def append_rmf_coordinates(coord_list, rmf_hierarchy, rmf_fh):
     return coord_list
 
 
-def RMSD(pdb_path, custom_n_plot=None, custom_output_directory=None, custom_base_path=None):
+def RMSD(pdb_path, custom_n_plot=None, custom_output_directory=None, custom_base_path=None, custom_heterogeneity_path=None):
     """
     This function reads a .config file generated by the imp sampcon exhaust function
     for each state to determine which chains from the pdb  file should be included in the calculation.
@@ -658,6 +661,7 @@ def RMSD(pdb_path, custom_n_plot=None, custom_output_directory=None, custom_base
     :param custom_output_directory (optional - str): If desired, different name of output directory (where plots and .txt
     files are saved) can be set. Default name: "RMSD_calculation_output"
     :param custom_base_path (optional - str): Custom path to the directory where snapshot{state}_{time} created with start_sim.py are.
+    :param custom_heterogeneity_path (optional - str): Custom path to the directory where .config files are
     """
     # create output directory where all RMSD output is gathered
     if custom_output_directory:
@@ -670,18 +674,23 @@ def RMSD(pdb_path, custom_n_plot=None, custom_output_directory=None, custom_base
     for time in state_dict.keys():
         for state in range(1, state_dict[time] + 1):
             # Construct directory path
-            # Base path is path to the directory where all the snapshot{state}_{time} are saved and .config files (both created with start_sim.py)
+            # Base path is path to the directory where all the snapshot{state}_{time} are saved (both created with start_sim.py)
             if custom_base_path:
                 base_path = custom_base_path
             else:
                 base_path = "../../Snapshots/Snapshots_Modeling"
+            # heterogeneity_path is the directory where .config files are
+            if custom_heterogeneity_path:
+                heterogeneity_path = custom_heterogeneity_path
+            else:
+                heterogeneity_path = "../../Heterogeneity/Heterogeneity_Modeling"
             snapshot = f"snapshot{state}_{time}"  # directory snapshot{state}_{time} is created with start_sim.py
             print(f"Now we are extracting from {snapshot}")
 
             directory_path = os.path.join(base_path, snapshot)
 
             # Read the configuration file created with start_sim.py
-            config_path = os.path.join(base_path,
+            config_path = os.path.join(heterogeneity_path,
                                        f"{state}_{time}.config")
             if not os.path.exists(config_path):
                 print(f"Configuration file {config_path} not found. Check base path and output")

modeling/Trajectories/Trajectories_Modeling/README.md

@@ -1,3 +1,3 @@
 ### This directory contains the code necessary for generating trajectory models
 
-See https://integrativemodeling.org/tutorials/spatiotemporal/trajectory1.html
+See https://integrativemodeling.org/tutorials/spatiotemporal/trajectories.html

modeling_empty/Heterogeneity/Heterogeneity_Assessment/README.md

@@ -0,0 +1,3 @@
+### This directory contains the code necessary for assessing heterogeneity models
+
+See https://integrativemodeling.org/tutorials/spatiotemporal/heterogeneity.html

modeling_empty/Heterogeneity/Heterogeneity_Modeling/README.md

@@ -0,0 +1,3 @@
+### This directory contains the code necessary for generating heterogeneity models
+
+See https://integrativemodeling.org/tutorials/spatiotemporal/heterogeneity.html

modeling_empty/Heterogeneity/README.md

@@ -0,0 +1 @@
+### This directory contains the code necessary for generating and analyzing heterogeneity models

modeling_empty/Snapshots/Snapshots_Assessment/README.md

@@ -1,3 +1,3 @@
 ### This directory contains the code necessary for analyzing static snapshot models
 
-See https://integrativemodeling.org/tutorials/spatiotemporal/snapshot_assess.html
+See https://integrativemodeling.org/tutorials/spatiotemporal/snapshots.html

modeling_empty/Snapshots/Snapshots_Modeling/README.md

@@ -1,3 +1,3 @@
 ### This directory contains the code necessary for generating static snapshot models
 
-See https://integrativemodeling.org/tutorials/spatiotemporal/snapshot1.html
+See https://integrativemodeling.org/tutorials/spatiotemporal/snapshots.html

modeling_empty/Trajectories/Trajectories_Assessment/README.md

@@ -1,3 +1,3 @@
 ### This directory contains the code necessary for analyzing trajectory models
 
-See https://integrativemodeling.org/tutorials/spatiotemporal/trajectory_assess.html
+See https://integrativemodeling.org/tutorials/spatiotemporal/trajectories.html

modeling_empty/Trajectories/Trajectories_Assessment/trajectories_assessment.py

@@ -33,24 +33,29 @@
 -analysis (from IMP.spatiotemporal)
 """
 # 1 - copy_files_for_data (copy all relevant files into 'data' directory)
-def copy_files_for_data(state_dict, custom_source_dir1 = None, custom_source_dir2 = None):
+def copy_files_for_data(state_dict, custom_source_dir1 = None, custom_source_dir2 = None, custom_source_dir3 = None):
     """
-    Copies three types of files important to generate two independent trajectory models (A and B):
+    Copies three types of files important to generate trajectory models:
     -.config files created with start_sim.py in Snapshot_Modeling (source_dir1)
     -time-dependent stoichiometry data for each timepoint. Data should be presented in .csv file. With this function all
     csv file in source_dir2 will be copied. These .csv files will be used in the exp_comp dictionary in create_DAG
     function
     -scoresA and scoresB for each snapshot created with imp sampcon exhaust
-    (source_dir1 + snapshot + good_scoring_models)
+    (source_dir1 + snapshot + good_scoring_models) are merged into total score .txt using merge_scores helper function.
+    All copied files are gathered in newly created './data/' directory, where everything is prepared for create_DAG
+    function.
+
 
     :param state_dict (dict): state_dict: dictionary that defines the spatiotemporal model.
            The keys are strings that correspond to each time point in the
            stepwise temporal process. Keys should be ordered according to the
            steps in the spatiotemporal process. The values are integers that
            correspond to the number of possible states at that timepoint.
-    :param custom_source_dir1 (optional - str): Custom path to snapshot modeling dir (start_sim.py), to copy .config
-    files and scoresA/scoresB (custom_source_dir1 + snapshot{state}_{time} + 'good_scoring_models')
+    :param custom_source_dir1 (optional - str): Custom path to heterogeneity modeling dir (heterogeneity_modeling.py),
+    to copy .config files
     :param custom_source_dir2 (optional - str): Custom path to stoichiometry data dir
+    :param custom_source_dir3 (optional - str): Custom path to snapshot modeling dir (start_sim.py), to copy .config
+    files and to access scoresA/scoresB (custom_source_dir3 + snapshot{state}_{time} + 'good_scoring_models')
     """
     # Create the destination directory for all the data copied in this function
     destination_dir = './data/'
@@ -60,14 +65,20 @@ def copy_files_for_data(state_dict, custom_source_dir1 = None, custom_source_dir
     if custom_source_dir1:
         source_dir1 = custom_source_dir1
     else:
-        source_dir1 = '../../Snapshots/Snapshots_Modeling/'
+        source_dir1 = '../../Heterogeneity/Heterogeneity_Modeling/'
 
     # path to stoichiometry data dir
     if custom_source_dir2:
         source_dir2 = custom_source_dir1
     else:
         source_dir2 = '../../Input_Information/gen_FCS/'
 
+    # path to snapshot modeling dir
+    if custom_source_dir3:
+        source_dir3 = custom_source_dir3
+    else:
+        source_dir3 = '../../Snapshots/Snapshots_Modeling/'
+
     # Copy all .config files from the first source directory to the destination directory
     try:
         for file_name in os.listdir(source_dir1):
@@ -94,7 +105,7 @@ def copy_files_for_data(state_dict, custom_source_dir1 = None, custom_source_dir
     try:
         for time in state_dict.keys():
             for state in range(1, state_dict[time] + 1):
-                snapshot_dir = os.path.join(source_dir1, f'snapshot{state}_{time}')
+                snapshot_dir = os.path.join(source_dir3, f'snapshot{state}_{time}')
                 good_scoring_models_dir = os.path.join(snapshot_dir, 'good_scoring_models')
                 if os.path.isdir(good_scoring_models_dir):
                     for score_file in ['scoresA.txt', 'scoresB.txt']:
@@ -513,8 +524,11 @@ def process_foxs(state_dict, custom_dat_file = None):
                 command6 = f"gnuplot snapshot1_{time}_{time}_exp.plt"
                 os.system(command6)
 
-                command7 = f"mv snapshot1_{time}_{time}_exp.plt {time}_FoXS.png"
+                command7 = f"mv snapshot1_{time}_{time}_exp.plt {time}_FoXS.plt"
                 os.system(command7)
+
+                command8 = f"mv snapshot1_{time}_{time}_exp.png {time}_FoXS.png"
+                os.system(command8)
             else:
                 print(f"There is no states in this timepoint. Check stat_dict.")
 
@@ -627,7 +641,7 @@ def append_rmf_coordinates(coord_list, rmf_hierarchy, rmf_fh):
     return coord_list
 
 
-def RMSD(pdb_path, custom_n_plot=None, custom_output_directory=None, custom_base_path=None):
+def RMSD(pdb_path, custom_n_plot=None, custom_output_directory=None, custom_base_path=None, custom_heterogeneity_path=None):
     """
     This function reads a .config file generated by the imp sampcon exhaust function
     for each state to determine which chains from the pdb  file should be included in the calculation.
@@ -647,6 +661,7 @@ def RMSD(pdb_path, custom_n_plot=None, custom_output_directory=None, custom_base
     :param custom_output_directory (optional - str): If desired, different name of output directory (where plots and .txt
     files are saved) can be set. Default name: "RMSD_calculation_output"
     :param custom_base_path (optional - str): Custom path to the directory where snapshot{state}_{time} created with start_sim.py are.
+    :param custom_heterogeneity_path (optional - str): Custom path to the directory where .config files are
     """
     # create output directory where all RMSD output is gathered
     if custom_output_directory:
@@ -659,18 +674,23 @@ def RMSD(pdb_path, custom_n_plot=None, custom_output_directory=None, custom_base
     for time in state_dict.keys():
         for state in range(1, state_dict[time] + 1):
             # Construct directory path
-            # Base path is path to the directory where all the snapshot{state}_{time} are saved and .config files (both created with start_sim.py)
+            # Base path is path to the directory where all the snapshot{state}_{time} are saved (both created with start_sim.py)
             if custom_base_path:
                 base_path = custom_base_path
             else:
                 base_path = "../../Snapshots/Snapshots_Modeling"
+            # heterogeneity_path is the directory where .config files are
+            if custom_heterogeneity_path:
+                heterogeneity_path = custom_heterogeneity_path
+            else:
+                heterogeneity_path = "../../Heterogeneity/Heterogeneity_Modeling"
             snapshot = f"snapshot{state}_{time}"  # directory snapshot{state}_{time} is created with start_sim.py
             print(f"Now we are extracting from {snapshot}")
 
             directory_path = os.path.join(base_path, snapshot)
 
             # Read the configuration file created with start_sim.py
-            config_path = os.path.join(base_path,
+            config_path = os.path.join(heterogeneity_path,
                                        f"{state}_{time}.config")
             if not os.path.exists(config_path):
                 print(f"Configuration file {config_path} not found. Check base path and output")

modeling_empty/Trajectories/Trajectories_Modeling/README.md

@@ -1,3 +1,3 @@
 ### This directory contains the code necessary for generating trajectory models
 
-See https://integrativemodeling.org/tutorials/spatiotemporal/trajectory1.html
+See https://integrativemodeling.org/tutorials/spatiotemporal/trajectories.html