rerun

openNucleome/utils/final_frame.py

@@ -39,7 +39,7 @@ def final_frame(traj_data, type_final, output_config, n_chrom = 46, n_nuc = 300,
     """
 
     traj = mda.coordinates.LAMMPS.DCDReader(traj_data)
-    chr_info = np.loadtxt(os.path.join(config_path, 'chromatin_info.txt'))
+    chr_info = np.loadtxt(os.path.join(config_path, 'chromatin_info.txt'), dtype=int)
     X, zero = 'X', 0
     type_final = np.loadtxt(type_final, dtype=int)
     coor = traj.trajectory[-1].positions

openNucleome/whole_nucleus_model.py

@@ -311,14 +311,18 @@ def load_default_settings(self):
         self.add_nucleolus_potential(dict_nuc_ff, chr_nuc_param)
         self.add_lamina_potential(dict_lam_ff, chr_lam_param)
 
-    def load_customized_settings(self, force_field, k = 1.0):
+    def load_customized_settings(self, force_field, param_folder, k = 1.0):
         '''
         Load customized force field settings
 
         Parameters
         ----------
         force_field (Pandas Dataframe, required):
             Store the flag of all the potentials and the parameter file names
+
+        param_folder (string, required):
+            Save the customized parameters used in the simulations
+
         k (float, required):
             The strength of force squeezing the nucleus (Default: 1.0)
         '''
@@ -328,22 +332,22 @@ def load_customized_settings(self, force_field, k = 1.0):
         dict_lam_ff = {'lam-chrom':force_field.loc['lamina']['lam-chrom'], 'hard-wall':force_field.loc['lamina']['hard-wall'], 'lam-lam':self.flag_membrane, 'squeeze_nucleus':self.flag_membrane, 'strength': k}
         ideal_param_file = force_field.loc['chromosome']['ideal_param_file']
         if ideal_param_file:
-            ideal_param_file = os.path.join('.', 'parameters', ideal_param_file)
+            ideal_param_file = os.path.join('.', param_folder, ideal_param_file)
         compt_param_file = force_field.loc['chromosome']['compt_param_file']
         if compt_param_file:
-            compt_param_file = os.path.join('.', 'parameters', compt_param_file)
+            compt_param_file = os.path.join('.', param_folder, compt_param_file)
         interchr_param_file = force_field.loc['chromosome']['interchr_param_file']
         if interchr_param_file:
-            interchr_param_file = os.path.join('.', 'parameters', interchr_param_file)
+            interchr_param_file = os.path.join('.', param_folder, interchr_param_file)
         chr_nuc_param = force_field.loc['nucleolus']['chr_nuc_param']
         if chr_nuc_param:
-            chr_nuc_param = os.path.join('.', 'parameters', chr_nuc_param)
+            chr_nuc_param = os.path.join('.', param_folder, chr_nuc_param)
         chr_spec_param = force_field.loc['speckle']['chr_spec_param']
         if chr_spec_param:
-            chr_spec_param = os.path.join('.', 'parameters', chr_spec_param)
+            chr_spec_param = os.path.join('.', param_folder, chr_spec_param)
         chr_lam_param = force_field.loc['lamina']['chr_lam_param']
         if chr_lam_param:
-            chr_lam_param = os.path.join('.', 'parameters', chr_lam_param)
+            chr_lam_param = os.path.join('.', param_folder, chr_lam_param)
         self.add_chromosome_potential(dict_chrom_ff, ideal_param_file, compt_param_file, interchr_param_file)
         self.add_speckle_potential(dict_spec_ff, chr_spec_param)
         self.add_nucleolus_potential(dict_nuc_ff, chr_nuc_param)

tutorials/HFF_100KB/NuclearDeformation/NuclearDeformation.ipynb

@@ -311,7 +311,7 @@
     "force_field = pd.read_csv('input.csv', sep=' ', header=0, index_col=0)\n",
     "model.load_customized_settings(force_field, k = 1.0)\n",
     "\n",
-    "index_spec_spec_potential = 6\n",
+    "index_spec_spec_potential = 6 #The 6-th potential is speckle-speckle interaction in the default settings\n",
     "start_spec_index = model.N_chr_nuc+1\n",
     "end_spec_index = model.N_chr_nuc_spec+1\n",
     "N_spec = end_spec_index-start_spec_index\n",
@@ -430,14 +430,14 @@
     "        model.chr_system.getForce(index_spec_spec_potential).setParticleParameters(m, [model.compart_type[m]])\n",
     "    model.chr_system.getForce(index_spec_spec_potential).updateParametersInContext(simulation.context)\n",
     "\n",
-    "# Keep the final result of spec types in case constructing the configuration for the continuous simulation.\n",
+    "# Keep the final result of bead types in case constructing the configuration for the continuous simulation.\n",
     "np.savetxt('compt_final_frame.txt', (np.array(model.compart_type)+1).reshape((-1,1)), fmt='%d')"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -451,7 +451,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.8.15"
   }
  },
  "nbformat": 4,