Updates after sroet's review

examples/contact_map.ipynb

@@ -30,7 +30,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from contact_map import ContactMap, ContactFrequency, ContactDifference"
+    "from contact_map import ContactFrequency, ContactDifference"
    ]
   },
   {
@@ -422,7 +422,7 @@
     "\n",
     "The `.most_common()` method gives a list of the contact pairs and the frequency, sorted by frequency. See also `collections.Counter.most_common()` in the standard Python `collections` module.\n",
     "\n",
-    "Here we do this with the `ContactDifference` we created, although it works the same for `ContactFrequency` and `ContactMap` (with the single-frame contact map, the ordering is a bit nonsensical, since every entry is either 0 or 1)."
+    "Here we do this with the `ContactDifference` we created, although it works the same for `ContactFrequency` (with the single-frame contact map, the ordering is a bit nonsensical, since every entry is either 0 or 1)."
    ]
   },
   {

examples/contact_map_without_atom_slice.ipynb

@@ -17,7 +17,7 @@
    "metadata": {},
    "source": [
     "## The worst case example\n",
-    "This is only adding a noticeable overhead for `ContactMap` in this case, but this could be worse for other systems"
+    "This is only adding a noticeable overhead for a single frame trajectory in this case, but this could be worse for other systems"
    ]
   },
   {
@@ -64,8 +64,27 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPU times: user 14.7 s, sys: 111 ms, total: 14.8 s\n",
-      "Wall time: 15.7 s\n"
+      "CPU times: user 251 ms, sys: 14.7 ms, total: 266 ms\n",
+      "Wall time: 293 ms\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%time\n",
+    "frame_contacts = ContactFrequency(traj[0], query=used_atoms, haystack=used_atoms)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CPU times: user 12.9 s, sys: 76.4 ms, total: 13 s\n",
+      "Wall time: 13.3 s\n"
      ]
     }
    ],
@@ -77,7 +96,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -86,7 +105,7 @@
        "True"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -107,7 +126,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -117,15 +136,34 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CPU times: user 150 ms, sys: 4.99 ms, total: 155 ms\n",
+      "Wall time: 171 ms\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%time\n",
+    "frame_contacts = ContactFrequency(traj[0], query=used_atoms, haystack=used_atoms)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPU times: user 15.8 s, sys: 88.7 ms, total: 15.9 s\n",
-      "Wall time: 16.3 s\n"
+      "CPU times: user 13.2 s, sys: 76 ms, total: 13.3 s\n",
+      "Wall time: 13.4 s\n"
      ]
     }
    ],
@@ -137,7 +175,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -146,7 +184,7 @@
        "False"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -166,7 +204,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -176,7 +214,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -187,15 +225,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPU times: user 122 ms, sys: 2.35 ms, total: 124 ms\n",
-      "Wall time: 132 ms\n"
+      "CPU times: user 112 ms, sys: 3.98 ms, total: 116 ms\n",
+      "Wall time: 124 ms\n"
      ]
     }
    ],
@@ -206,7 +244,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -217,15 +255,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPU times: user 2.08 s, sys: 10.8 ms, total: 2.09 s\n",
-      "Wall time: 2.12 s\n"
+      "CPU times: user 1.89 s, sys: 15.1 ms, total: 1.9 s\n",
+      "Wall time: 1.93 s\n"
      ]
     }
    ],