Add ethylene, ethyne, and phosphate standard functional groups (#1557)

* Add ethylene, ethyne, and phosphate standard functional groups

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>

avogadro/qtplugins/templatetool/ligands/ethylene.cjson

@@ -0,0 +1,84 @@
+{
+  "chemicalJson": 1,
+  "atoms": {
+    "coords": {
+      "3d": [
+        -1.5534,
+        0.0749,
+        0.2664,
+        -1.1883,
+        0.1873,
+        1.3083,
+        -0.6202,
+        1.3071,
+        1.4603,
+        -1.4535,
+        -0.6764,
+        1.7673,
+        -0.1841,
+        1.6185,
+        2.4293,
+        -0.5234,
+        2.0418,
+        0.6403
+      ]
+    },
+    "elements": {
+      "number": [
+        0,
+        6,
+        6,
+        1,
+        1,
+        1
+      ]
+    },
+    "formalCharges": [
+      0,
+      0,
+      0,
+      0,
+      0,
+      0
+    ]
+  },
+  "partialCharges": {
+    "Gasteiger": [
+      0.0,
+      0.0,
+      0.0,
+      0.0,
+      0.0,
+      0.0
+    ]
+  },
+  "bonds": {
+    "connections": {
+      "index": [
+        0,
+        1,
+        1,
+        2,
+        1,
+        3,
+        2,
+        4,
+        2,
+        5
+      ]
+    },
+    "order": [
+      1,
+      2,
+      1,
+      1,
+      1
+    ]
+  },
+  "properties": {
+    "name": "",
+    "totalCharge": 0,
+    "totalSpinMultiplicity": 2,
+    "totalEnergy": 0.0
+  }
+}

avogadro/qtplugins/templatetool/ligands/ethyne.cjson

@@ -0,0 +1,66 @@
+{
+  "chemicalJson": 1,
+  "atoms": {
+    "coords": {
+      "3d": [
+        -2.6584,
+        -0.0146,
+        -0.0614,
+        -2.3373,
+        -0.3508,
+        0.7114,
+        -1.9233,
+        -0.7914,
+        1.7521,
+        -1.5732,
+        -1.1666,
+        2.6719
+      ]
+    },
+    "elements": {
+      "number": [
+        0,
+        6,
+        6,
+        1
+      ]
+    },
+    "formalCharges": [
+      0,
+      0,
+      0,
+      0
+    ]
+  },
+  "partialCharges": {
+    "Gasteiger": [
+      0.0,
+      0.0,
+      0.0,
+      0.0
+    ]
+  },
+  "bonds": {
+    "connections": {
+      "index": [
+        0,
+        1,
+        1,
+        2,
+        2,
+        3
+      ]
+    },
+    "order": [
+      1,
+      3,
+      1
+    ]
+  },
+  "properties": {
+    "name": "",
+    "totalCharge": 0,
+    "totalSpinMultiplicity": 2,
+    "totalEnergy": 0.0
+  }
+}

avogadro/qtplugins/templatetool/ligands/phosphate.cjson

@@ -0,0 +1,101 @@
+{
+  "chemicalJson": 1,
+  "atoms": {
+    "coords": {
+      "3d": [
+        -1.0432,
+        -3.0021,
+        -1.018,
+        -0.6229,
+        -2.4983,
+        -0.3244,
+        0.0053,
+        -1.1643,
+        -0.9673,
+        0.1276,
+        -1.2157,
+        -2.4175,
+        1.3655,
+        -0.9921,
+        -0.1479,
+        -0.8777,
+        0.0094,
+        -0.3854,
+        2.0864,
+        -1.3719,
+        -0.6453,
+        -0.8116,
+        0.0459,
+        0.5684
+      ]
+    },
+    "elements": {
+      "number": [
+        0,
+        8,
+        15,
+        8,
+        8,
+        8,
+        1,
+        1
+      ]
+    },
+    "formalCharges": [
+      0,
+      0,
+      0,
+      0,
+      0,
+      0,
+      0,
+      0
+    ]
+  },
+  "partialCharges": {
+    "Gasteiger": [
+      0.0,
+      0.0,
+      0.0,
+      0.0,
+      0.0,
+      0.0,
+      0.0,
+      0.0
+    ]
+  },
+  "bonds": {
+    "connections": {
+      "index": [
+        0,
+        1,
+        1,
+        2,
+        2,
+        3,
+        2,
+        4,
+        2,
+        5,
+        4,
+        6,
+        5,
+        7
+      ]
+    },
+    "order": [
+      1,
+      1,
+      2,
+      1,
+      1,
+      1,
+      1
+    ]
+  },
+  "properties": {
+    "name": "",
+    "totalCharge": 0,
+    "totalSpinMultiplicity": 2
+  }
+}

avogadro/qtplugins/templatetool/template.qrc

@@ -33,9 +33,12 @@
     <file>ligands/6-edta.png</file>
     <file>ligands/amide.png</file>
     <file>ligands/carboxylate.png</file>
+    <file>ligands/ethylene.png</file>
+    <file>ligands/ethyne.png</file>
     <file>ligands/ester.png</file>
     <file>ligands/nitro.png</file>
     <file>ligands/phenyl.png</file>
+    <file>ligands/phosphate.png</file>
     <file>ligands/sulfonate.png</file>
     <file>ligands/eta2-ethylene.png</file>
     <file>ligands/eta5-cyclopentyl.png</file>
@@ -78,8 +81,11 @@
     <file>ligands/amide.cjson</file>
     <file>ligands/carboxylate.cjson</file>
     <file>ligands/ester.cjson</file>
+    <file>ligands/ethylene.cjson</file>
+    <file>ligands/ethyne.cjson</file>
     <file>ligands/nitro.cjson</file>
     <file>ligands/phenyl.cjson</file>
+    <file>ligands/phosphate.cjson</file>
     <file>ligands/sulfonate.cjson</file>
     <file>ligands/eta2-ethylene.cjson</file>
     <file>ligands/eta5-cyclopentyl.cjson</file>

avogadro/qtplugins/templatetool/templatetool.cpp

@@ -377,8 +377,6 @@ void TemplateTool::atomLeftClick(QMouseEvent*)
     // - otherwise use the template
     Molecule templateMolecule;
 
-    qDebug() << "ligandString: " << m_toolWidget->ligandString();
-
     if (m_toolWidget->ligandString() == "Clipboard") {
       const QMimeData* mimeData(QApplication::clipboard()->mimeData());
 

avogadro/qtplugins/templatetool/templatetoolwidget.ui

@@ -481,6 +481,16 @@
              <string>ester</string>
             </property>
            </item>
+           <item>
+            <property name="text">
+             <string>ethylene</string>
+            </property>
+           </item>
+           <item>
+            <property name="text">
+             <string>ethyne</string>
+            </property>
+           </item>
            <item>
             <property name="text">
              <string>nitro</string>
@@ -491,6 +501,11 @@
              <string>phenyl</string>
             </property>
            </item>
+           <item>
+            <property name="text">
+             <string>phosphate</string>
+            </property>
+           </item>
            <item>
             <property name="text">
              <string>sulfonate</string>