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Anonymous committed a820c56

renamed amber example and added svg

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  • Parent commits 26ce83c

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Files changed (23)

+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg">
+ <text x="100.0" y="210.0" style=" fill : blue; stroke : none;" font-size="10.0">0</text>
+ <circle cx="100.0" cy="210.0" r="1.5" style=" fill : green; stroke : black; stroke-width : 0.5;"/>
+ <text x="110.0" y="180.0" style=" fill : blue; stroke : none;" font-size="10.0">1</text>
+ <circle cx="110.0" cy="180.0" r="1.5" style=" fill : green; stroke : black; stroke-width : 0.5;"/>
+ <text x="120.0" y="190.0" style=" fill : blue; stroke : none;" font-size="10.0">2</text>
+ <circle cx="120.0" cy="190.0" r="1.5" style=" fill : green; stroke : black; stroke-width : 0.5;"/>
+ <text x="130.0" y="230.0" style=" fill : blue; stroke : none;" font-size="10.0">3</text>
+ <circle cx="130.0" cy="230.0" r="1.5" style=" fill : green; stroke : black; stroke-width : 0.5;"/>
+ <text x="140.0" y="200.0" style=" fill : blue; stroke : none;" font-size="10.0">4</text>
+ <circle cx="140.0" cy="200.0" r="1.5" style=" fill : green; stroke : black; stroke-width : 0.5;"/>
+ <text x="150.0" y="220.0" style=" fill : blue; stroke : none;" font-size="10.0">5</text>
+ <circle cx="150.0" cy="220.0" r="1.5" style=" fill : green; stroke : black; stroke-width : 0.5;"/>
+ <text x="160.0" y="280.0" style=" fill : blue; stroke : none;" font-size="10.0">6</text>
+ <circle cx="160.0" cy="280.0" r="1.5" style=" fill : green; stroke : black; stroke-width : 0.5;"/>
+ <text x="170.0" y="240.0" style=" fill : blue; stroke : none;" font-size="10.0">7</text>
+ <circle cx="170.0" cy="240.0" r="1.5" style=" fill : green; stroke : black; stroke-width : 0.5;"/>
+ <line x1="100.0" y1="210.0" x2="103.3" y2="200.1" style=" stroke : red; stroke-width : 1.0;"/>
+ <line style=" stroke : black; stroke-width : 1.0;" x1="110.0" y1="180.0" x2="102.6209756742507" y2="187.3790243257493"/>
+ <line x1="110.0" y1="180.0" x2="113.3" y2="176.7" style=" stroke : red; stroke-width : 1.0;"/>
+ <line style=" stroke : black; stroke-width : 1.0;" x1="120.0" y1="190.0" x2="118.26675508625166" y2="185.66688771562914"/>
+ <line x1="120.0" y1="190.0" x2="125.05323385702593" y2="202.63308464256482" style=" stroke : red; stroke-width : 1.0;"/>
+ <line style=" stroke : black; stroke-width : 1.0;" x1="130.0" y1="230.0" x2="117.83020131637339" y2="223.9151006581867"/>
+ <line x1="130.0" y1="230.0" x2="139.33380951166242" y2="234.6669047558312" style=" stroke : red; stroke-width : 1.0;"/>
+ <line style=" stroke : black; stroke-width : 1.0;" x1="140.0" y1="200.0" x2="130.66619048833758" y2="204.6669047558312"/>
+ <line x1="140.0" y1="200.0" x2="146.6" y2="196.7" style=" stroke : red; stroke-width : 1.0;"/>
+ <line style=" stroke : black; stroke-width : 1.0;" x1="150.0" y1="220.0" x2="148.2103237229961" y2="212.84129489198435"/>
+ <line x1="150.0" y1="220.0" x2="154.86844582037043" y2="239.47378328148173" style=" stroke : red; stroke-width : 1.0;"/>
+ <line style=" stroke : black; stroke-width : 1.0;" x1="160.0" y1="280.0" x2="145.80616330937966" y2="265.80616330937966"/>
+ <line x1="160.0" y1="280.0" x2="169.62107062649474" y2="289.62107062649477" style=" stroke : red; stroke-width : 1.0;"/>
+ <line style=" stroke : black; stroke-width : 1.0;" x1="170.0" y1="240.0" x2="166.7" y2="253.2"/>
+ <path style=" fill : none; stroke : black; stroke-width : 0.5;" d="M100.0 210.0 C103.3 200.1 102.62 187.379 110.0 180.0 C113.3 176.7 118.266 185.666 120.0 190.0 C125.053 202.633 117.83 223.915 130.0 230.0 C139.333 234.666 130.666 204.666 140.0 200.0 C146.6 196.7 148.21 212.841 150.0 220.0 C154.868 239.473 145.806 265.806 160.0 280.0 C169.621 289.621 166.7 253.2 170.0 240.0 "/>
+</svg>

File src/test/java/org/xmlcml/svg/SvgVisitorTest.java

 package org.xmlcml.svg;
 
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
 import nu.xom.Element;
 
 import org.junit.Test;
+import org.xmlcml.cml.base.CMLUtil;
+import org.xmlcml.cml.graphics.CurvePrimitive;
+import org.xmlcml.cml.graphics.MovePrimitive;
+import org.xmlcml.cml.graphics.SVGCircle;
+import org.xmlcml.cml.graphics.SVGLine;
+import org.xmlcml.cml.graphics.SVGPath;
+import org.xmlcml.cml.graphics.SVGPathPrimitive;
+import org.xmlcml.cml.graphics.SVGSVG;
+import org.xmlcml.cml.graphics.SVGText;
 import org.xmlcml.cml.testutil.JumboTestUtils;
+import org.xmlcml.euclid.Real2;
+import org.xmlcml.euclid.Real2Array;
+import org.xmlcml.euclid.Vector2;
 import org.xmlcml.semantic.NodeUtils;
 
 public class SvgVisitorTest {
+	private SVGSVG svg;
+
 	@Test
 	public void testArray2() {
 		
 				newElement, true, 0.0001);		
 	}
 	
+	@Test
+	public void testBezier() throws FileNotFoundException, IOException {
+		Real2Array real2Array = new Real2Array();
+		real2Array.add(new Real2(100, 210));
+		real2Array.add(new Real2(110, 180));
+		real2Array.add(new Real2(120, 190));
+		real2Array.add(new Real2(130, 230));
+		real2Array.add(new Real2(140, 200));
+		real2Array.add(new Real2(150, 220));
+		real2Array.add(new Real2(160, 280));
+		real2Array.add(new Real2(170, 240));
+		double factor = 0.33;
+		
+		svg = new SVGSVG();
+		for (int i = 0; i < real2Array.size(); i++) {
+			Real2 r2 = real2Array.get(i);
+			SVGText text = new SVGText(r2, ""+i);
+			text.setFill("blue");
+			text.setFontSize(10.0);
+			svg.appendChild(text);
+			SVGCircle circle = new SVGCircle(r2, 1.5);
+			circle.setFill("green");
+			svg.appendChild(circle);
+		}
+		List<SVGPathPrimitive> primitiveList = new ArrayList<SVGPathPrimitive>();
+		primitiveList.add(new MovePrimitive(real2Array.get(0)));
+		for(int i = 0; i < real2Array.size()-1; i++) {
+			// create path 12
+			Real2 p0 = (i == 0) ? null : real2Array.get(i-1);
+			Real2 p1 = real2Array.get(i);
+			Real2 p2 = real2Array.get(i+1);
+			Real2 p3 = (i == real2Array.size()-2) ? null : real2Array.get(i+2);
+			Real2Array coordArray = plotSegment(factor, p0, p1, p2, p3);
+			SVGPathPrimitive primitive = new CurvePrimitive(coordArray);
+			primitiveList.add(primitive);
+		}
+		String d = SVGPath.constructDString(primitiveList);
+		SVGPath path1 = new SVGPath(d);
+		svg.appendChild(path1);
+		CMLUtil.debug(svg, new FileOutputStream("junk.svg"), 1);
+	}
+
+	
+	/**
+	 * 
+	 * @param factor to scale control points by
+	 * @param p0 previous point (null at start)
+	 * @param p1 start of segment
+	 * @param p2 end of segment
+	 * @param p3 following point (null at end)
+	 * @return
+	 */
+	private Real2Array plotSegment(double factor, Real2 p0, Real2 p1, Real2 p2, Real2 p3) {
+		// create p1-p2 curve
+		double len12 = p1.getDistance(p2) * factor;
+		Vector2 vStart = (p0 == null) ? new Vector2(p2.subtract(p1)) : new Vector2(p2.subtract(p0));
+		vStart = new Vector2(vStart.getUnitVector().multiplyBy(len12));
+		Vector2 vEnd = (p3 == null) ?  new Vector2(p2.subtract(p1)) : new Vector2(p3.subtract(p1));
+		vEnd = new Vector2(vEnd.getUnitVector().multiplyBy(len12));
+		Real2Array coordArray = new Real2Array();
+		Real2 controlStart = p1.plus(vStart);
+		coordArray.add(controlStart);
+		Real2 controlEnd = p2.subtract(vEnd);
+		coordArray.add(controlEnd);
+		coordArray.add(p2);
+		// plot controls
+		SVGLine line12 = new SVGLine(p1, controlStart); 
+		line12.setStroke("red");
+		svg.appendChild(line12);
+		SVGLine line21 = new SVGLine(p2, controlEnd); 
+		svg.appendChild(line21);
+		return coordArray;
+	}
 	
 }
 

File src/test/resources/molecules/1_aminoethan_1_one/1_aminoethan_1_one_MM.cml

-<?xml version="1.0" encoding="UTF-8"?>
-<molecule xmlns="http://www.xml-cml.org/schema">
-  <atomArray>
-    <atom id="a1" x3="-6.001" y3="-0.499" z3="0.111" elementType="C">
-      <name>C</name>
-      <property dictRef="mjw:radius6_12VDW">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.9079999997313366</scalar>
-      </property>
-      <property dictRef="mjw:wellDepth6_12VDW">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.08600000012835884</scalar>
-      </property>
-      <property dictRef="mjw:AMBERCharge">
-        <scalar dataType="xsd:double" units="units:none">0.6560999983536655</scalar>
-      </property>
-    </atom>
-    <atom id="a2" x3="-4.94" y3="-0.214" z3="0.057" elementType="C">
-      <name>C1</name>
-      <property dictRef="mjw:radius6_12VDW">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.9080000000152688</scalar>
-      </property>
-      <property dictRef="mjw:wellDepth6_12VDW">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.10939999991572773</scalar>
-      </property>
-      <property dictRef="mjw:AMBERCharge">
-        <scalar dataType="xsd:double" units="units:none">-0.1741</scalar>
-      </property>
-    </atom>
-    <atom id="a3" x3="-4.395" y3="0.689" z3="0.37" elementType="H">
-      <name>H</name>
-      <property dictRef="mjw:radius6_12VDW">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.4869999997254757</scalar>
-      </property>
-      <property dictRef="mjw:wellDepth6_12VDW">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.01570000002623629</scalar>
-      </property>
-      <property dictRef="mjw:AMBERCharge">
-        <scalar dataType="xsd:double" units="units:none">0.0787</scalar>
-      </property>
-    </atom>
-    <atom id="a4" x3="-4.673" y3="0.412" z3="-0.807" elementType="H">
-      <name>H1</name>
-      <property dictRef="mjw:radius6_12VDW">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.4869999997254757</scalar>
-      </property>
-      <property dictRef="mjw:wellDepth6_12VDW">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.01570000002623629</scalar>
-      </property>
-      <property dictRef="mjw:AMBERCharge">
-        <scalar dataType="xsd:double" units="units:none">0.058699999999999995</scalar>
-      </property>
-    </atom>
-    <atom id="a5" x3="-3.993" y3="-0.743" z3="0.239" elementType="H">
-      <name>H2</name>
-      <property dictRef="mjw:radius6_12VDW">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.4869999997254757</scalar>
-      </property>
-      <property dictRef="mjw:wellDepth6_12VDW">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.01570000002623629</scalar>
-      </property>
-      <property dictRef="mjw:AMBERCharge">
-        <scalar dataType="xsd:double" units="units:none">0.058699999999999995</scalar>
-      </property>
-    </atom>
-    <atom id="a6" x3="-6.47" y3="-1.364" z3="-0.382" elementType="N">
-      <name>N</name>
-      <property dictRef="mjw:radius6_12VDW">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.8240000001431576</scalar>
-      </property>
-      <property dictRef="mjw:wellDepth6_12VDW">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.169999999917667</scalar>
-      </property>
-      <property dictRef="mjw:AMBERCharge">
-        <scalar dataType="xsd:double" units="units:none">-0.6829999999999999</scalar>
-      </property>
-    </atom>
-    <atom id="a7" x3="-7.536" y3="-1.56" z3="-0.568" elementType="H">
-      <name>H3</name>
-      <property dictRef="mjw:radius6_12VDW">
-        <scalar dataType="xsd:double" units="units:Angstrom">0.5999999999731258</scalar>
-      </property>
-      <property dictRef="mjw:wellDepth6_12VDW">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.015700000004219245</scalar>
-      </property>
-      <property dictRef="mjw:AMBERCharge">
-        <scalar dataType="xsd:double" units="units:none">0.3155</scalar>
-      </property>
-    </atom>
-    <atom id="a8" x3="-7.032" y3="-2.297" z3="-0.226" elementType="H">
-      <name>H4</name>
-      <property dictRef="mjw:radius6_12VDW">
-        <scalar dataType="xsd:double" units="units:Angstrom">0.5999999999731258</scalar>
-      </property>
-      <property dictRef="mjw:wellDepth6_12VDW">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.015700000004219245</scalar>
-      </property>
-      <property dictRef="mjw:AMBERCharge">
-        <scalar dataType="xsd:double" units="units:none">0.3045</scalar>
-      </property>
-    </atom>
-    <atom id="a9" x3="-6.378" y3="-0.593" z3="1.14" elementType="O">
-      <name>O</name>
-      <property dictRef="mjw:radius6_12VDW">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.661200000277935</scalar>
-      </property>
-      <property dictRef="mjw:wellDepth6_12VDW">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.20999999984182244</scalar>
-      </property>
-      <property dictRef="mjw:AMBERCharge">
-        <scalar dataType="xsd:double" units="units:none">-0.6130999983536656</scalar>
-      </property>
-    </atom>
-  </atomArray>
-  <bondArray>
-    <bond atomRefs2="a2 a3" id="a2_a3">
-      <property dictRef="mjw:equilbriumHarmonicBondLength">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.092</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondForceConstant">
-        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">337.3</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondPotentialEnergy">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.022587029747386758</scalar>
-      </property>
-    </bond>
-    <bond atomRefs2="a2 a4" id="a2_a4">
-      <property dictRef="mjw:equilbriumHarmonicBondLength">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.092</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondForceConstant">
-        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">337.3</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondPotentialEnergy">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.02076355390353283</scalar>
-      </property>
-    </bond>
-    <bond atomRefs2="a2 a5" id="a2_a5">
-      <property dictRef="mjw:equilbriumHarmonicBondLength">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.092</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondForceConstant">
-        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">337.3</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondPotentialEnergy">
-        <scalar dataType="xsd:double" units="units:kcal/mol">0.021036335388040006</scalar>
-      </property>
-    </bond>
-    <bond atomRefs2="a6 a7" id="a6_a7">
-      <property dictRef="mjw:equilbriumHarmonicBondLength">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.009</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondForceConstant">
-        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">410.20000000000005</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondPotentialEnergy">
-        <scalar dataType="xsd:double" units="units:kcal/mol">3.375450512000459</scalar>
-      </property>
-    </bond>
-    <bond atomRefs2="a6 a8" id="a6_a8">
-      <property dictRef="mjw:equilbriumHarmonicBondLength">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.009</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondForceConstant">
-        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">410.20000000000005</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondPotentialEnergy">
-        <scalar dataType="xsd:double" units="units:kcal/mol">3.419603316661956</scalar>
-      </property>
-    </bond>
-    <bond atomRefs2="a1 a2" id="a1_a2">
-      <property dictRef="mjw:equilbriumHarmonicBondLength">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.508</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondForceConstant">
-        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">328.3</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondPotentialEnergy">
-        <scalar dataType="xsd:double" units="units:kcal/mol">54.66693715572138</scalar>
-      </property>
-    </bond>
-    <bond atomRefs2="a1 a6" id="a1_a6">
-      <property dictRef="mjw:equilbriumHarmonicBondLength">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.345</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondForceConstant">
-        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">478.2</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondPotentialEnergy">
-        <scalar dataType="xsd:double" units="units:kcal/mol">28.5726015600637</scalar>
-      </property>
-    </bond>
-    <bond atomRefs2="a1 a9" id="a1_a9">
-      <property dictRef="mjw:equilbriumHarmonicBondLength">
-        <scalar dataType="xsd:double" units="units:Angstrom">1.214</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondForceConstant">
-        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">648.0</scalar>
-      </property>
-      <property dictRef="mjw:HarmonicBondPotentialEnergy">
-        <scalar dataType="xsd:double" units="units:kcal/mol">8.434441896070846</scalar>
-      </property>
-    </bond>
-  </bondArray>
-  <angle atomRefs3="a1 a2 a3">
-    <property dictRef="mjw:harmonicAngleForceConstant">
-      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">47.199999999999996</scalar>
-    </property>
-    <property dictRef="mjw:equilibriumHarmonicAngle">
-      <scalar dataType="xsd:double" units="units:degrees">109.68004677699744</scalar>
-    </property>
-    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">7.535647043871006</scalar>
-    </property>
-  </angle>
-  <angle atomRefs3="a1 a2 a4">
-    <property dictRef="mjw:harmonicAngleForceConstant">
-      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">47.199999999999996</scalar>
-    </property>
-    <property dictRef="mjw:equilibriumHarmonicAngle">
-      <scalar dataType="xsd:double" units="units:degrees">109.68004677699744</scalar>
-    </property>
-    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">0.38397270900951946</scalar>
-    </property>
-  </angle>
-  <angle atomRefs3="a1 a2 a5">
-    <property dictRef="mjw:harmonicAngleForceConstant">
-      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">47.199999999999996</scalar>
-    </property>
-    <property dictRef="mjw:equilibriumHarmonicAngle">
-      <scalar dataType="xsd:double" units="units:degrees">109.68004677699744</scalar>
-    </property>
-    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">8.678524397688578</scalar>
-    </property>
-  </angle>
-  <angle atomRefs3="a1 a6 a7">
-    <property dictRef="mjw:harmonicAngleForceConstant">
-      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">49.21</scalar>
-    </property>
-    <property dictRef="mjw:equilibriumHarmonicAngle">
-      <scalar dataType="xsd:double" units="units:degrees">118.46005088366657</scalar>
-    </property>
-    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">1.6561394641544045</scalar>
-    </property>
-  </angle>
-  <angle atomRefs3="a1 a6 a8">
-    <property dictRef="mjw:harmonicAngleForceConstant">
-      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">49.21</scalar>
-    </property>
-    <property dictRef="mjw:equilibriumHarmonicAngle">
-      <scalar dataType="xsd:double" units="units:degrees">118.46005088366657</scalar>
-    </property>
-    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">10.674774404140791</scalar>
-    </property>
-  </angle>
-  <angle atomRefs3="a3 a2 a4">
-    <property dictRef="mjw:harmonicAngleForceConstant">
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-  <length atomRefs2="a2 a8">
-    <property dictRef="mjw:EE14PotentiaEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">-5.93558622352549</scalar>
-    </property>
-  </length>
-  <length atomRefs2="a6 a3">
-    <property dictRef="mjw:EE14PotentiaEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">-5.921298243774533</scalar>
-    </property>
-  </length>
-  <length atomRefs2="a9 a3">
-    <property dictRef="mjw:EE14PotentiaEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">-6.450823351212268</scalar>
-    </property>
-  </length>
-  <length atomRefs2="a6 a4">
-    <property dictRef="mjw:EE14PotentiaEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">-5.196136754603651</scalar>
-    </property>
-  </length>
-  <length atomRefs2="a9 a4">
-    <property dictRef="mjw:EE14PotentiaEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">-4.304363302268246</scalar>
-    </property>
-  </length>
-  <length atomRefs2="a6 a5">
-    <property dictRef="mjw:EE14PotentiaEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">-5.065547633187609</scalar>
-    </property>
-  </length>
-  <length atomRefs2="a9 a5">
-    <property dictRef="mjw:EE14PotentiaEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">-4.679159952154912</scalar>
-    </property>
-  </length>
-  <length atomRefs2="a9 a7">
-    <property dictRef="mjw:EE14PotentiaEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">-28.184779841741587</scalar>
-    </property>
-  </length>
-  <length atomRefs2="a9 a8">
-    <property dictRef="mjw:EE14PotentiaEnergy">
-      <scalar dataType="xsd:double" units="units:kcal/mol">-27.191715325989055</scalar>
-    </property>
-  </length>
-</molecule>

File src/test/resources/molecules/1_aminoethan_1_one/Makefile

-# Generate a set of GAFF parameters using AnteChamber
-AMBERHOME=/home/mw529/code/AMBER/amber11
-
-mdout: prmtop
-	$(AMBERHOME)/bin/sander -O
-
-
-prmtop: 1_aminoethan_1_one.mol2
-	rm -f leap.log ; \
-	$(AMBERHOME)/bin/tleap -f leap.bat 
-
-1_aminoethan_1_one.mol2: ./raw/1_aminoethan_1_one.mol2
-	$(AMBERHOME)/bin/antechamber -i ./raw/1_aminoethan_1_one.mol2 -fi mol2 -c bcc -o 1_aminoethan_1_one.mol2 -fo mol2 -rn AEO
-
-
-
-
-
-clean:
-	rm -f ANTECHAMBER* sqm* *.mol2 ATOMTYPE.INF
-	rm -f prmtop inpcrd leap.log
-	rm -f mdinfo mdout restrt snap.pdb

File src/test/resources/molecules/1_aminoethan_1_one/inpcrd

-AEO
-     9
-  -6.0010000  -0.4990000   0.1110000  -4.9400000  -0.2140000   0.0570000
-  -4.3950000   0.6890000   0.3700000  -4.6730000   0.4120000  -0.8070000
-  -3.9930000  -0.7430000   0.2390000  -6.4700000  -1.3640000  -0.3820000
-  -7.5360000  -1.5600000  -0.5680000  -7.0320000  -2.2970000  -0.2260000
-  -6.3780000  -0.5930000   1.1400000

File src/test/resources/molecules/1_aminoethan_1_one/leap.bat

-# Load GAFF 
-source leaprc.gaff
-
-# Load the preparsed PDB
-AEO = loadMol2 1_aminoethan_1_one.mol2
-
-# Save a pdb for convenience of debugging
-savepdb AEO snap.pdb
-
-# Generate the AMBER parameter and coordinate files
-saveamberparm AEO prmtop inpcrd
-
-quit

File src/test/resources/molecules/1_aminoethan_1_one/mdin

-Title
- &cntrl
-   imin=1,
-   irest=0,
-   maxcyc=0,
-   ncyc=0,
-   ntpr=1,
-   ntb=0,
-   cut=999.0,
-   igb=5
- /

File src/test/resources/molecules/1_aminoethan_1_one/mdout

-
-          -------------------------------------------------------
-          Amber 11 SANDER                              2010
-          -------------------------------------------------------
-
-| Run on 01/18/2013 at 00:09:28
-  [-O]verwriting output
-
-File Assignments:
-|  MDIN: mdin                                                                  
-| MDOUT: mdout                                                                 
-|INPCRD: inpcrd                                                                
-|  PARM: prmtop                                                                
-|RESTRT: restrt                                                                
-|  REFC: refc                                                                  
-| MDVEL: mdvel                                                                 
-|  MDEN: mden                                                                  
-| MDCRD: mdcrd                                                                 
-|MDINFO: mdinfo                                                                
-|  MTMD: mtmd                                                                  
-|INPDIP: inpdip                                                                
-|RSTDIP: rstdip                                                                
-
-|INPTRA: inptraj                                                               
-|
-
- Here is the input file:
-
-Title                                                                          
- &cntrl                                                                        
-   imin=1,                                                                     
-   irest=0,                                                                    
-   maxcyc=0,                                                                   
-   ncyc=0,                                                                     
-   ntpr=1,                                                                     
-   ntb=0,                                                                      
-   cut=999.0,                                                                  
-   igb=5                                                                       
- /                                                                             
-
---------------------------------------------------------------------------------
-   1.  RESOURCE   USE: 
---------------------------------------------------------------------------------
-
-| Flags:                                                                        
-| New format PARM file being parsed.
-| Version =    1.000 Date = 01/18/13 Time = 00:09:28
- NATOM  =       9 NTYPES =       6 NBONH =       5 MBONA  =       3
- NTHETH =       9 MTHETA =       3 NPHIH =      16 MPHIA  =       1
- NHPARM =       0 NPARM  =       0 NNB   =      31 NRES   =       1
- NBONA  =       3 NTHETA =       3 NPHIA =       1 NUMBND =       5
- NUMANG =       7 NPTRA  =       7 NATYP =       6 NPHB   =       0
- IFBOX  =       0 NMXRS  =       9 IFCAP =       0 NEXTRA =       0
- NCOPY  =       0
-
- Implicit solvent radii are modified Bondi radii (mbondi)                                                   
-
-|     Memory Use     Allocated
-|     Real                 773
-|     Hollerith             30
-|     Integer            20358
-|     Max Pairs              1
-|     nblistReal             0
-|     nblist Int             0
-|       Total               85 kbytes
-
-| Note: 1-4 EEL scale factors are being read from the topology file.
-
-| Note: 1-4 VDW scale factors are being read from the topology file.
-| Duplicated    0 dihedrals
-| Duplicated    0 dihedrals
-
---------------------------------------------------------------------------------
-   2.  CONTROL  DATA  FOR  THE  RUN
---------------------------------------------------------------------------------
-
-AEO                                                                             
-
-General flags:
-     imin    =       1, nmropt  =       0
-
-Nature and format of input:
-     ntx     =       1, irest   =       0, ntrx    =       1
-
-Nature and format of output:
-     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =     500
-     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
-     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0
-
-Potential function:
-     ntf     =       1, ntb     =       0, igb     =       5, nsnb    =      25
-     ipol    =       0, gbsa    =       0, iesp    =       0
-     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
-     saltcon =   0.00000, offset  =   0.09000, gbalpha=    1.00000
-     gbbeta  =   0.80000, gbgamma =   4.85100, surften =   0.00500
-     rdt     =   0.00000, rgbmax  =  25.00000  extdiel =  78.50000
-     alpb  =        0
-
-Frozen or restrained atoms:
-     ibelly  =       0, ntr     =       0
-
-Energy minimization:
-     maxcyc  =       0, ncyc    =       0, ntmin   =       1
-     dx0     =   0.01000, drms    =   0.00010
-|  INFO: Old style inpcrd file read
-
-
---------------------------------------------------------------------------------
-   3.  ATOMIC COORDINATES AND VELOCITIES
---------------------------------------------------------------------------------
-
-AEO                                                                             
- begin time read from input coords =     0.000 ps
-
- Number of triangulated 3-point waters found:        0
-
---------------------------------------------------------------------------------
-   4.  RESULTS
---------------------------------------------------------------------------------
-
-
-
-   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
-      1       1.6856E+02     1.3490E+02     3.9037E+02     C1          2
-
- BOND    =       98.5334  ANGLE   =      121.8808  DIHED      =       30.8324
- VDWAALS =       -0.0062  EEL     =       10.8193  EGB        =      -11.8286
- 1-4 VDW =        0.8491  1-4 EEL =      -82.5241  RESTRAINT  =        0.0000
-
-
-  Maximum number of minimization cycles reached.
-
-
-                    FINAL RESULTS
-
-
-
-   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
-      1       1.6856E+02     1.3490E+02     3.9037E+02     C1          2
-
- BOND    =       98.5334  ANGLE   =      121.8808  DIHED      =       30.8324
- VDWAALS =       -0.0062  EEL     =       10.8193  EGB        =      -11.8286
- 1-4 VDW =        0.8491  1-4 EEL =      -82.5241  RESTRAINT  =        0.0000
-
---------------------------------------------------------------------------------
-   5.  TIMINGS
---------------------------------------------------------------------------------
-
-|    Read coords time           0.00 ( 6.52% of Total)
-|    Fast Water setup           0.00 ( 0.27% of Total)
-|          Nonbond force              0.00 (52.95% of Force)
-|          Bond/Angle/Dihedral        0.00 (33.52% of Force)
-|          Other                      0.00 (13.53% of Force)
-|       Force time                 0.00 (100.0% of Runmd)
-|    Runmd Time                 0.00 ( 9.01% of Total)
-|    Other                      0.00 (84.20% of Total)
-| Total time                 0.00 (97.87% of ALL  )
-
-| Highest rstack allocated:          0
-| Highest istack allocated:          0
-|           Job began  at 00:09:28.163  on 01/18/2013
-|           Setup done at 00:09:28.165  on 01/18/2013
-|           Run   done at 00:09:28.165  on 01/18/2013
-|     wallclock() was called      45 times

File src/test/resources/molecules/1_aminoethan_1_one/prmtop

-%VERSION  VERSION_STAMP = V0001.000  DATE = 01/18/13  00:09:28                  
-%FLAG TITLE                                                                     
-%FORMAT(20a4)                                                                   
-AEO                                                                             
-%FLAG POINTERS                                                                  
-%FORMAT(10I8)                                                                   
-       9       6       5       3       9       3      16       1       0       0
-      31       1       3       3       1       5       7       7       6       0
-       0       0       0       0       0       0       0       0       9       0
-       0
-%FLAG ATOM_NAME                                                                 
-%FORMAT(20a4)                                                                   
-C   C1  H   H1  H2  N   H3  H4  O   
-%FLAG CHARGE                                                                    
-%FORMAT(5E16.8)                                                                 
-  1.19556510E+01 -3.17250243E+00  1.43409501E+00  1.06964901E+00  1.06964901E+00
- -1.24458309E+01  5.74913565E+00  5.54869035E+00 -1.11720921E+01
-%FLAG MASS                                                                      
-%FORMAT(5E16.8)                                                                 
-  1.20100000E+01  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.00800000E+00
-  1.40100000E+01  1.00800000E+00  1.00800000E+00  1.60000000E+01
-%FLAG ATOM_TYPE_INDEX                                                           
-%FORMAT(10I8)                                                                   
-       1       2       3       3       3       4       5       5       6
-%FLAG NUMBER_EXCLUDED_ATOMS                                                     
-%FORMAT(10I8)                                                                   
-       8       7       4       3       2       3       2       1       1
-%FLAG NONBONDED_PARM_INDEX                                                      
-%FORMAT(10I8)                                                                   
-       1       2       4       7      11      16       2       3       5       8
-      12      17       4       5       6       9      13      18       7       8
-       9      10      14      19      11      12      13      14      15      20
-      16      17      18      19      20      21
-%FLAG RESIDUE_LABEL                                                             
-%FORMAT(20a4)                                                                   
-AEO 
-%FLAG RESIDUE_POINTER                                                           
-%FORMAT(10I8)                                                                   
-       1
-%FLAG BOND_FORCE_CONSTANT                                                       
-%FORMAT(5E16.8)                                                                 
-  3.28300000E+02  4.78200000E+02  6.48000000E+02  3.37300000E+02  4.10200000E+02
-%FLAG BOND_EQUIL_VALUE                                                          
-%FORMAT(5E16.8)                                                                 
-  1.50800000E+00  1.34500000E+00  1.21400000E+00  1.09200000E+00  1.00900000E+00
-%FLAG ANGLE_FORCE_CONSTANT                                                      
-%FORMAT(5E16.8)                                                                 
-  4.72000000E+01  4.92100000E+01  6.78600000E+01  6.80300000E+01  3.94300000E+01
-  7.58300000E+01  3.97300000E+01
-%FLAG ANGLE_EQUIL_VALUE                                                         
-%FORMAT(5E16.8)                                                                 
-  1.91427794E+00  2.06751792E+00  2.00974750E+00  2.14867576E+00  1.89106506E+00
-  2.12982620E+00  2.05687140E+00
-%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
-%FORMAT(5E16.8)                                                                 
-  2.50000000E+00  0.00000000E+00  8.00000000E-01  8.00000000E-02  2.00000000E+00
-  1.05000000E+01  1.10000000E+00
-%FLAG DIHEDRAL_PERIODICITY                                                      
-%FORMAT(5E16.8)                                                                 
-  2.00000000E+00  2.00000000E+00  1.00000000E+00  3.00000000E+00  1.00000000E+00
-  2.00000000E+00  2.00000000E+00
-%FLAG DIHEDRAL_PHASE                                                            
-%FORMAT(5E16.8)                                                                 
-  3.14159400E+00  3.14159400E+00  0.00000000E+00  3.14159400E+00  0.00000000E+00
-  3.14159400E+00  3.14159400E+00
-%FLAG SOLTY                                                                     
-%FORMAT(5E16.8)                                                                 
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00
-%FLAG LENNARD_JONES_ACOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  8.19971662E+05  9.24822270E+05  1.04308023E+06  8.61541883E+04  9.71708117E+04
-  7.51607703E+03  8.82619071E+05  9.95480466E+05  8.96776989E+04  9.44293233E+05
-  2.27577561E+03  2.56678134E+03  1.07193646E+02  2.12601181E+03  1.39982777E-01
-  5.74393458E+05  6.47841731E+05  5.44261042E+04  6.06829342E+05  1.02595236E+03
-  3.79876399E+05
-%FLAG LENNARD_JONES_BCOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  5.31102864E+02  5.99015525E+02  6.75612247E+02  1.12529845E+02  1.26919150E+02
-  2.17257828E+01  6.53361429E+02  7.36907417E+02  1.36131731E+02  8.01323529E+02
-  1.82891803E+01  2.06278363E+01  2.59456373E+00  2.09604198E+01  9.37598976E-02
-  5.55666448E+02  6.26720080E+02  1.11805549E+02  6.77220874E+02  1.53505284E+01
-  5.64885984E+02
-%FLAG BONDS_INC_HYDROGEN                                                        
-%FORMAT(10I8)                                                                   
-       3       6       4       3       9       4       3      12       4      15
-      18       5      15      21       5
-%FLAG BONDS_WITHOUT_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-       0       3       1       0      15       2       0      24       3
-%FLAG ANGLES_INC_HYDROGEN                                                       
-%FORMAT(10I8)                                                                   
-       0       3       6       1       0       3       9       1       0       3
-      12       1       0      15      18       2       0      15      21       2
-       6       3       9       5       6       3      12       5       9       3
-      12       5      18      15      21       7
-%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
-%FORMAT(10I8)                                                                   
-       3       0      15       3       3       0      24       4      15       0
-      24       6
-%FLAG DIHEDRALS_INC_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-       3       0      15      18       1       3       0      15      21       1
-      15       0       3       6       2      24       0       3       6       3
-      24       0      -3       6       4      15       0       3       9       2
-      24       0       3       9       3      24       0      -3       9       4
-      15       0       3      12       2      24       0       3      12       3
-      24       0      -3      12       4      24       0      15      18       5
-      24       0     -15      18       1      24       0      15      21       5
-      24       0     -15      21       1       0      18     -15     -21       7
-%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
-%FORMAT(10I8)                                                                   
-      24       0     -15      -3       6
-%FLAG EXCLUDED_ATOMS_LIST                                                       
-%FORMAT(10I8)                                                                   
-       2       3       4       5       6       7       8       9       3       4
-       5       6       7       8       9       4       5       6       9       5
-       6       9       6       9       7       8       9       8       9       9
-       0
-%FLAG HBOND_ACOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBOND_BCOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBCUT                                                                     
-%FORMAT(5E16.8)                                                                 
-
-%FLAG AMBER_ATOM_TYPE                                                           
-%FORMAT(20a4)                                                                   
-c   c3  hc  hc  hc  n   hn  hn  o   
-%FLAG TREE_CHAIN_CLASSIFICATION                                                 
-%FORMAT(20a4)                                                                   
-BLA BLA BLA BLA BLA BLA BLA BLA BLA 
-%FLAG JOIN_ARRAY                                                                
-%FORMAT(10I8)                                                                   
-       0       0       0       0       0       0       0       0       0
-%FLAG IROTAT                                                                    
-%FORMAT(10I8)                                                                   
-       0       0       0       0       0       0       0       0       0
-%FLAG RADIUS_SET                                                                
-%FORMAT(1a80)                                                                   
-modified Bondi radii (mbondi)                                                   
-%FLAG RADII                                                                     
-%FORMAT(5E16.8)                                                                 
-  1.70000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
-  1.55000000E+00  1.30000000E+00  1.30000000E+00  1.50000000E+00
-%FLAG SCREEN                                                                    
-%FORMAT(5E16.8)                                                                 
-  7.20000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
-  7.90000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01

File src/test/resources/molecules/1_aminoethan_1_one/raw/1_aminoethan_1_one.cml

-<molecule>
- <atomArray>
-  <atom id="a1" elementType="C" x3="-6.000639" y3="-0.499217" z3="0.110616"/>
-  <atom id="a2" elementType="C" x3="-4.939647" y3="-0.213890" z3="0.056596"/>
-  <atom id="a3" elementType="H" x3="-4.394621" y3="0.688693" z3="0.370180"/>
-  <atom id="a4" elementType="H" x3="-4.672464" y3="0.412270" z3="-0.807372"/>
-  <atom id="a5" elementType="H" x3="-3.992843" y3="-0.743164" z3="0.239437"/>
-  <atom id="a6" elementType="N" x3="-6.469849" y3="-1.363825" z3="-0.381603"/>
-  <atom id="a7" elementType="H" x3="-7.536225" y3="-1.560282" z3="-0.567692"/>
-  <atom id="a8" elementType="H" x3="-7.031605" y3="-2.296937" z3="-0.226391"/>
-  <atom id="a9" elementType="O" x3="-6.377525" y3="-0.592461" z3="1.139773"/>
- </atomArray>
- <bondArray>
-  <bond atomRefs2="a1 a2" order="1"/>
-  <bond atomRefs2="a2 a3" order="1"/>
-  <bond atomRefs2="a2 a4" order="1"/>
-  <bond atomRefs2="a2 a5" order="1"/>
-  <bond atomRefs2="a1 a6" order="1"/>
-  <bond atomRefs2="a6 a7" order="1"/>
-  <bond atomRefs2="a6 a8" order="1"/>
-  <bond atomRefs2="a1 a9" order="1"/>
- </bondArray>
-</molecule>

File src/test/resources/molecules/1_aminoethan_1_one/raw/1_aminoethan_1_one.mol2

-@<TRIPOS>MOLECULE
-*****
- 9 8 0 0 0
-SMALL
-GASTEIGER
-
-@<TRIPOS>ATOM
-      1 C          -6.0006   -0.4992    0.1106 C.3     1  LIG1        0.1950
-      2 C          -4.9396   -0.2139    0.0566 C.3     1  LIG1       -0.0151
-      3 H          -4.3946    0.6887    0.3702 H       1  LIG1        0.0273
-      4 H          -4.6725    0.4123   -0.8074 H       1  LIG1        0.0273
-      5 H          -3.9928   -0.7432    0.2394 H       1  LIG1        0.0273
-      6 N          -6.4698   -1.3638   -0.3816 N.3     1  LIG1       -0.2975
-      7 H          -7.5362   -1.5603   -0.5677 H       1  LIG1        0.1210
-      8 H          -7.0316   -2.2969   -0.2264 H       1  LIG1        0.1210
-      9 O          -6.3775   -0.5925    1.1398 O.3     1  LIG1       -0.2065
-@<TRIPOS>BOND
-     1     1     2    1
-     2     2     3    1
-     3     2     4    1
-     4     2     5    1
-     5     1     6    1
-     6     6     7    1
-     7     6     8    1
-     8     1     9    1

File src/test/resources/molecules/acetamide/Makefile

+# Generate a set of GAFF parameters using AnteChamber
+AMBERHOME=/home/mw529/code/AMBER/amber11
+
+mdout: prmtop
+	$(AMBERHOME)/bin/sander -O
+
+
+prmtop: 1_aminoethan_1_one.mol2
+	rm -f leap.log ; \
+	$(AMBERHOME)/bin/tleap -f leap.bat 
+
+1_aminoethan_1_one.mol2: ./raw/1_aminoethan_1_one.mol2
+	$(AMBERHOME)/bin/antechamber -i ./raw/1_aminoethan_1_one.mol2 -fi mol2 -c bcc -o 1_aminoethan_1_one.mol2 -fo mol2 -rn AEO
+
+
+
+
+
+clean:
+	rm -f ANTECHAMBER* sqm* *.mol2 ATOMTYPE.INF
+	rm -f prmtop inpcrd leap.log
+	rm -f mdinfo mdout restrt snap.pdb

File src/test/resources/molecules/acetamide/acetamide_MM.cml

+<?xml version="1.0" encoding="UTF-8"?>
+<molecule xmlns="http://www.xml-cml.org/schema">
+  <atomArray>
+    <atom id="a1" x3="-6.001" y3="-0.499" z3="0.111" elementType="C">
+      <name>C</name>
+      <property dictRef="mjw:radius6_12VDW">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.9079999997313366</scalar>
+      </property>
+      <property dictRef="mjw:wellDepth6_12VDW">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.08600000012835884</scalar>
+      </property>
+      <property dictRef="mjw:AMBERCharge">
+        <scalar dataType="xsd:double" units="units:none">0.6560999983536655</scalar>
+      </property>
+    </atom>
+    <atom id="a2" x3="-4.94" y3="-0.214" z3="0.057" elementType="C">
+      <name>C1</name>
+      <property dictRef="mjw:radius6_12VDW">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.9080000000152688</scalar>
+      </property>
+      <property dictRef="mjw:wellDepth6_12VDW">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.10939999991572773</scalar>
+      </property>
+      <property dictRef="mjw:AMBERCharge">
+        <scalar dataType="xsd:double" units="units:none">-0.1741</scalar>
+      </property>
+    </atom>
+    <atom id="a3" x3="-4.395" y3="0.689" z3="0.37" elementType="H">
+      <name>H</name>
+      <property dictRef="mjw:radius6_12VDW">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.4869999997254757</scalar>
+      </property>
+      <property dictRef="mjw:wellDepth6_12VDW">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.01570000002623629</scalar>
+      </property>
+      <property dictRef="mjw:AMBERCharge">
+        <scalar dataType="xsd:double" units="units:none">0.0787</scalar>
+      </property>
+    </atom>
+    <atom id="a4" x3="-4.673" y3="0.412" z3="-0.807" elementType="H">
+      <name>H1</name>
+      <property dictRef="mjw:radius6_12VDW">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.4869999997254757</scalar>
+      </property>
+      <property dictRef="mjw:wellDepth6_12VDW">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.01570000002623629</scalar>
+      </property>
+      <property dictRef="mjw:AMBERCharge">
+        <scalar dataType="xsd:double" units="units:none">0.058699999999999995</scalar>
+      </property>
+    </atom>
+    <atom id="a5" x3="-3.993" y3="-0.743" z3="0.239" elementType="H">
+      <name>H2</name>
+      <property dictRef="mjw:radius6_12VDW">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.4869999997254757</scalar>
+      </property>
+      <property dictRef="mjw:wellDepth6_12VDW">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.01570000002623629</scalar>
+      </property>
+      <property dictRef="mjw:AMBERCharge">
+        <scalar dataType="xsd:double" units="units:none">0.058699999999999995</scalar>
+      </property>
+    </atom>
+    <atom id="a6" x3="-6.47" y3="-1.364" z3="-0.382" elementType="N">
+      <name>N</name>
+      <property dictRef="mjw:radius6_12VDW">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.8240000001431576</scalar>
+      </property>
+      <property dictRef="mjw:wellDepth6_12VDW">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.169999999917667</scalar>
+      </property>
+      <property dictRef="mjw:AMBERCharge">
+        <scalar dataType="xsd:double" units="units:none">-0.6829999999999999</scalar>
+      </property>
+    </atom>
+    <atom id="a7" x3="-7.536" y3="-1.56" z3="-0.568" elementType="H">
+      <name>H3</name>
+      <property dictRef="mjw:radius6_12VDW">
+        <scalar dataType="xsd:double" units="units:Angstrom">0.5999999999731258</scalar>
+      </property>
+      <property dictRef="mjw:wellDepth6_12VDW">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.015700000004219245</scalar>
+      </property>
+      <property dictRef="mjw:AMBERCharge">
+        <scalar dataType="xsd:double" units="units:none">0.3155</scalar>
+      </property>
+    </atom>
+    <atom id="a8" x3="-7.032" y3="-2.297" z3="-0.226" elementType="H">
+      <name>H4</name>
+      <property dictRef="mjw:radius6_12VDW">
+        <scalar dataType="xsd:double" units="units:Angstrom">0.5999999999731258</scalar>
+      </property>
+      <property dictRef="mjw:wellDepth6_12VDW">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.015700000004219245</scalar>
+      </property>
+      <property dictRef="mjw:AMBERCharge">
+        <scalar dataType="xsd:double" units="units:none">0.3045</scalar>
+      </property>
+    </atom>
+    <atom id="a9" x3="-6.378" y3="-0.593" z3="1.14" elementType="O">
+      <name>O</name>
+      <property dictRef="mjw:radius6_12VDW">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.661200000277935</scalar>
+      </property>
+      <property dictRef="mjw:wellDepth6_12VDW">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.20999999984182244</scalar>
+      </property>
+      <property dictRef="mjw:AMBERCharge">
+        <scalar dataType="xsd:double" units="units:none">-0.6130999983536656</scalar>
+      </property>
+    </atom>
+  </atomArray>
+  <bondArray>
+    <bond atomRefs2="a2 a3" id="a2_a3">
+      <property dictRef="mjw:equilbriumHarmonicBondLength">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.092</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondForceConstant">
+        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">337.3</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondPotentialEnergy">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.022587029747386758</scalar>
+      </property>
+    </bond>
+    <bond atomRefs2="a2 a4" id="a2_a4">
+      <property dictRef="mjw:equilbriumHarmonicBondLength">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.092</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondForceConstant">
+        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">337.3</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondPotentialEnergy">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.02076355390353283</scalar>
+      </property>
+    </bond>
+    <bond atomRefs2="a2 a5" id="a2_a5">
+      <property dictRef="mjw:equilbriumHarmonicBondLength">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.092</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondForceConstant">
+        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">337.3</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondPotentialEnergy">
+        <scalar dataType="xsd:double" units="units:kcal/mol">0.021036335388040006</scalar>
+      </property>
+    </bond>
+    <bond atomRefs2="a6 a7" id="a6_a7">
+      <property dictRef="mjw:equilbriumHarmonicBondLength">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.009</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondForceConstant">
+        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">410.20000000000005</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondPotentialEnergy">
+        <scalar dataType="xsd:double" units="units:kcal/mol">3.375450512000459</scalar>
+      </property>
+    </bond>
+    <bond atomRefs2="a6 a8" id="a6_a8">
+      <property dictRef="mjw:equilbriumHarmonicBondLength">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.009</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondForceConstant">
+        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">410.20000000000005</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondPotentialEnergy">
+        <scalar dataType="xsd:double" units="units:kcal/mol">3.419603316661956</scalar>
+      </property>
+    </bond>
+    <bond atomRefs2="a1 a2" id="a1_a2">
+      <property dictRef="mjw:equilbriumHarmonicBondLength">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.508</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondForceConstant">
+        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">328.3</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondPotentialEnergy">
+        <scalar dataType="xsd:double" units="units:kcal/mol">54.66693715572138</scalar>
+      </property>
+    </bond>
+    <bond atomRefs2="a1 a6" id="a1_a6">
+      <property dictRef="mjw:equilbriumHarmonicBondLength">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.345</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondForceConstant">
+        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">478.2</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondPotentialEnergy">
+        <scalar dataType="xsd:double" units="units:kcal/mol">28.5726015600637</scalar>
+      </property>
+    </bond>
+    <bond atomRefs2="a1 a9" id="a1_a9">
+      <property dictRef="mjw:equilbriumHarmonicBondLength">
+        <scalar dataType="xsd:double" units="units:Angstrom">1.214</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondForceConstant">
+        <scalar dataType="xsd:double" units="units:kcal/mol/(Angstrom**2)">648.0</scalar>
+      </property>
+      <property dictRef="mjw:HarmonicBondPotentialEnergy">
+        <scalar dataType="xsd:double" units="units:kcal/mol">8.434441896070846</scalar>
+      </property>
+    </bond>
+  </bondArray>
+  <angle atomRefs3="a1 a2 a3">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">47.199999999999996</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">109.68004677699744</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">7.535647043871006</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a1 a2 a4">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">47.199999999999996</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">109.68004677699744</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.38397270900951946</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a1 a2 a5">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">47.199999999999996</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">109.68004677699744</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">8.678524397688578</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a1 a6 a7">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">49.21</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">118.46005088366657</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.6561394641544045</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a1 a6 a8">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">49.21</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">118.46005088366657</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">10.674774404140791</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a3 a2 a4">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">39.43</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">108.3500467226538</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">18.922407543107553</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a3 a2 a5">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">39.43</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">108.3500467226538</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">6.28305067103265</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a4 a2 a5">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">39.43</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">108.3500467226538</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.6092073785787424</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a7 a6 a8">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">39.73</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">117.85005022116495</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">53.24884309240649</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a2 a1 a6">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">67.86</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">115.15004963696842</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">2.5929988615940744</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a2 a1 a9">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">68.03</scalar>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">123.1100525900646</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.9152269461442228</scalar>
+    </property>
+  </angle>
+  <angle atomRefs3="a6 a1 a9">
+    <property dictRef="mjw:harmonicAngleForceConstant">
+      <scalar dataType="xsd:double" units="units:kcal/mol/(radian**2)">75.83</scalar>