Modified available_to_bind to allowed_to_bind. Added to Example 1-02.

KarrLab · May 11, 2018 · d8b3a63 · d8b3a63
1 parent a1bae8e
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diff --git a/examples/Example 1-02 Bonds.ipynb b/examples/Example 1-02 Bonds.ipynb
@@ -24,9 +24,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from wc_rules.chem2 import Molecule,Site,Bond"
@@ -35,9 +33,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "class Rec(Molecule):pass\n",
@@ -62,9 +58,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "rec1 = Lig1.get_sites(id='rec1')[0]\n",
@@ -167,9 +161,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "class TetramerBond(Bond):\n",
@@ -238,6 +230,51 @@
     "except:\n",
     "    print('Not allowed.')"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "To **disallow a site type from binding**, one can set the `allowed_to_bind` attribute during subclassing. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Allowed.\n",
+      "Not allowed.\n"
+     ]
+    }
+   ],
+   "source": [
+    "class Site1(Site):\n",
+    "    pass\n",
+    "class Site2(Site):\n",
+    "    allowed_to_bind = False\n",
+    "    \n",
+    "x1 = Site1()\n",
+    "x2 = Site2()\n",
+    "bnd = Bond().add_targets(x1,x2)\n",
+    "for site in [x1,x2]:\n",
+    "    try:\n",
+    "        site.verify_allowed_to_bind()\n",
+    "        print('Allowed.')\n",
+    "    except:\n",
+    "        print('Not allowed.')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/wc_rules/chem2.py b/wc_rules/chem2.py
@@ -28,7 +28,7 @@ def remove_sites(self,*args):
 class Site(entity.Entity):
     molecule = core.ManyToOneAttribute(Molecule,related_name='sites')
     allowed_molecule_types = None
-    available_to_bind = True
+    allowed_to_bind = True
 
     # Setters
     def set_molecule(self,molecule):
@@ -84,8 +84,10 @@ def verify_maximum_allowed_relations_as_a_target(self):
                     raise utils.ValidateError('Maximum number of relations of the same type allowed for this target site exceeded.')
         return
 
-    def verify_available_to_bind(self):
-        return self.available_to_bind
+    def verify_allowed_to_bind(self):
+        if not self.allowed_to_bind:
+            raise utils.ValidateError('This site is not allowed to have a bond.')
+        return
 
 class SiteRelation(entity.Entity):
     sources = core.ManyToManyAttribute(Site,related_name='site_relations_sources')