Delete codvid. i

old commit

.vscode/launch.json

@@ -4,6 +4,7 @@
     // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
     "version": "0.2.0",
     "configurations": [
+
         {
             "name": "Python: Current File",
             "type": "python",

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.pythonPath": "C:\\Users\\bicke\\anaconda3\\envs\\csi\\python.exe"
+}

src/identify_dihedrals.py

@@ -0,0 +1,24 @@
+import sys
+import MDAnalysis as mda
+from MDAnalysis.topology.guessers import guess_bonds, guess_angles, guess_dihedrals
+
+if len(sys.argv) != 2:
+    print("Usage: python identify_dihedrals.py <topology>")
+    sys.exit(1)
+else:
+    u = mda.Universe(sys.argv[1])
+
+    n_bonds = len(u.bonds)
+    print(f'{len(u.bonds)} bonds specified in original file')
+
+    u.add_TopologyAttr('bonds', guess_bonds(u.atoms, u.atoms.positions))  # add additional bonds using same bond guessing algoritm as VMD
+    print(f'{len(u.bonds) - n_bonds} additional bonds guessed')
+    u.add_TopologyAttr('angles', guess_angles(u.bonds))  # add angles in order to be able to calculate dihedrals
+    u.add_TopologyAttr('dihedrals', guess_dihedrals(u.angles))  # add dihedrals
+
+    print(f'{len(u.dihedrals)} dihedrals found. Outputting atom IDs:')
+
+    # print id of all atoms in every dihedral
+    for i, dihedral in enumerate(u.dihedrals):
+        ids = [str(a.id) for a in dihedral]
+        print('  ' + ' '.join(ids))

src/main.py

@@ -6,17 +6,18 @@
 
 
 # ================= User Input ================= #
-topology = 'inputs/pkA_run3.psf'
-trajectory = 'inputs/pkA_run3.dcd'
+topology = 'inputs/new/step3_input.psf'
+trajectory = 'inputs/new/pkka_run6_skip2.dcd'
 
-residue_list = ['ALA', 'DGLU', 'DLYS']  # list of ammino acids to be CoarseGrained
+residue_list = ['ALA', 'DALA', 'LYS', 'DGLU', 'GLU', 'DLYS']  # list of ammino acids to be CoarseGrained
 # residue_list = ['ALA']
 # residue_list = ['DA', 'DT', 'DG', 'DC', 'PHOSPHATE', 'RIBOSE']
 
 
 # ================= Execution ================= #
 u = generate_universe(topology, trajectory)
 sim_name = get_file_name(topology)
+
 u_cg = coarse_grain(u, residue_list, simulation_name=sim_name, export=True)
 measurement_dict = parametize(u_cg, export=True)
 startup_manual_refining(measurement_dict, u_cg)