Created using Colaboratory

pablo-arantes · Aug 12, 2021 · 328feb0 · 328feb0
1 parent 331577f
commit 328feb0
Showing 1 changed file with 10 additions and 9 deletions.
diff --git a/AlphaFold2+MD.ipynb b/AlphaFold2+MD.ipynb
@@ -1613,7 +1613,7 @@
         "#@markdown **Attention:** A high number of frames can explode the memory on Colab. You should be fine with 5000 frames or less.\n",
         "\n",
         "simulation_time_analysis = stride_time_ps*nstride\n",
-        "simulation_ns = int(Stride_Time)*int(Number_of_strides)\n",
+        "simulation_ns = float(Stride_Time)*int(Number_of_strides)\n",
         "number_frames = int(simulation_time_analysis)/int(Write_the_trajectory)\n",
         "number_frames_analysis = number_frames/int(stride_traj)\n",
         "\n",
@@ -1655,6 +1655,7 @@
         "\n",
         "import warnings\n",
         "warnings.filterwarnings('ignore')\n",
+        "!rm *.pdb 2> /dev/null\n",
         "\n",
         "#py3dmol functions\n",
         "class Atom(dict):\n",
@@ -1928,10 +1929,10 @@
         "last_frame = len(time_array)\n",
         "\n",
         "stride_ticks_f = (last_frame)/5\n",
-        "ticks_frame = np.arange(0,(len(time_array) + int(stride_ticks_f)), int(stride_ticks_f))\n",
+        "ticks_frame = np.arange(0,(len(time_array) + float(stride_ticks_f)), float(stride_ticks_f))\n",
         "a = ticks_frame.astype(float)\n",
         "stride_ticks_t = (simulation_ns)/5\n",
-        "tick_time = np.arange(0,(int(simulation_ns) + int(stride_ticks_t)), int(stride_ticks_t))\n",
+        "tick_time = np.arange(0,(float(simulation_ns) + float(stride_ticks_t)), float(stride_ticks_t))\n",
         "b = tick_time.astype(float)\n",
         "\n",
         "mat1 = pt.pairwise_rmsd(traj_load, mask=\"@CA\", frame_indices=range(int(number_frames_analysis)))\n",
@@ -1943,8 +1944,8 @@
         "plt.ylabel('Time (ns)', fontsize = 14, fontweight = 'bold')\n",
         "# plt.xticks(fontsize = 12)\n",
         "# plt.yticks(fontsize = 12)\n",
-        "plt.xticks(a, b, fontsize = 12)\n",
-        "plt.yticks(a, b, fontsize = 12)\n",
+        "plt.xticks(a, b.round(decimals=3), fontsize = 12)\n",
+        "plt.yticks(a, b.round(decimals=3), fontsize = 12)\n",
         "# plt.xlim(0, a[-1])\n",
         "# plt.ylim(0, a[-1])\n",
         "\n",
@@ -1978,11 +1979,11 @@
         "last_frame = len(time_array)\n",
         "\n",
         "stride_ticks_f = (last_frame)/5\n",
-        "ticks_frame = np.arange(0,(len(time_array) + int(stride_ticks_f)), int(stride_ticks_f))\n",
-        "a = ticks_frame.astype(int)\n",
+        "ticks_frame = np.arange(0,(len(time_array) + float(stride_ticks_f)), float(stride_ticks_f))\n",
+        "a = ticks_frame.astype(float)\n",
         "a2 = a.tolist()\n",
         "stride_ticks_t = (simulation_ns)/5\n",
-        "tick_time = np.arange(0,(int(simulation_ns) + int(stride_ticks_t)), int(stride_ticks_t))\n",
+        "tick_time = np.arange(0,(float(simulation_ns) + float(stride_ticks_t)), float(stride_ticks_t))\n",
         "b = tick_time.astype(float)\n",
         "\n",
         "#@markdown **Provide output file names below:** \n",
@@ -2011,7 +2012,7 @@
         "cbar1 = plt.colorbar(a, orientation=\"vertical\")\n",
         "cbar1.set_label('Time(ns)', fontsize = 14, fontweight = 'bold')\n",
         "cbar1.set_ticks(a2)\n",
-        "cbar1.set_ticklabels(b)\n",
+        "cbar1.set_ticklabels(b.round(decimals=3))\n",
         "\n",
         "plt.savefig(os.path.join(workDir, Output_name + \".png\"), dpi=600, bbox_inches='tight')\n",
         "\n",