changes cw

Author: marscher

notebooks/01-data-io-and-featurization.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "<a rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"><img alt=\"Creative Commons Licence\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by/4.0/88x31.png\" title='This work is licensed under a Creative Commons Attribution 4.0 International License.' align=\"right\"/></a>\n",
     "\n",
-    "In this notebook, we will cover how to load (and visualize) data with PyEMMA. Different features (collective variables) are extracted and compared how well these are suited for Markov state model building. The concept of streaming data is briefly introduced.\n",
+    "In this notebook, we will cover how to load (and visualize) data with PyEMMA. We are going to extract different features (collective variables) and compare how well these are suited for Markov state model building. Further we will introduce the concept of streaming data, which is mandatory to work with large data sets.\n",
     "\n",
     "As with the other notebooks, we employ multiple examples. The idea is, first, to highlight the fundamental ideas with a non-physical test system (diffusion in a 2D double-well potential) and, second, to demonstrate real-world applications with molecular dynamics data.\n",
     "\n",
@@ -195,7 +195,7 @@
    "source": [
     "Now we pass the featurizer to the load function to extract the Cartesian coordinates from the trajectory files into memory. For real world examples one would prefer the `source` function, because usually one has more data available than main memory in the workstation.\n",
     "\n",
-    "The warning about 'plain coordinates' is triggered, because these coordinates will include diffusion as a dynamical process, which might not be what one is interested in. If the molecule of interest has been aligned to a reference prior the analysis, it is fine to use these coordinates, but we will see that there are better choices. "
+    "The warning about **plain coordinates** is triggered, because these coordinates will include diffusion as a dynamical process, which might not be what one is interested in. If the molecule of interest has been aligned to a reference prior the analysis, it is fine to use these coordinates, but we will see that there are better choices. "
    ]
   },
   {
@@ -215,7 +215,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next, we start adding features which we want to extract from the simulation data. Here, we want to load the backbone torsions, because these angles are known to describe all flexibility in the system. Since this feature is two dimensional is also easier to visualize. Please note that in complex systems it is not trivial to visualize plain input features."
+    "Next, we start adding features which we want to extract from the simulation data. Here, we want to load the backbone torsions, because these angles are known to describe all flexibility in the system. Since this feature is two dimensional, it is also easier to visualize. Please note that in complex systems it is not trivial to visualize plain input features."
    ]
   },
   {
@@ -435,7 +435,7 @@
     "score_pair_heavy_atom_dists = pyemma.coordinates.vamp(data[:-1], dim=2).score(\n",
     "    test_data=data[-1],\n",
     "    score_method='VAMP2')\n",
-    "print('VAMP2-score: {:f}'.format(score_pair_dists_ca))"
+    "print('VAMP2-score: {:.2f}'.format(score_pair_heavy_atom_dists))"
    ]
   },
   {
@@ -544,7 +544,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "solution2": "shown"
+    "solution2": "hidden"
    },
    "outputs": [],
    "source": [