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Add AMBER testcase with CML output from JAMBER

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Files changed (9)

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">
+      <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>
+    </property>
+    <property dictRef="mjw:equilibriumHarmonicAngle">
+      <scalar dataType="xsd:double" units="units:degrees">122.03005235638598</scalar>
+    </property>
+    <property dictRef="mjw:HarmonicAnglePotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">9.380028504185615</scalar>
+    </property>
+  </angle>
+  <torsion atomRefs4="a2 a1 a6 a7">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">2.5</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">2.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.4073234105837767</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a2 a1 a6 a8">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">2.5</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">2.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">3.71913044606626</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a6 a1 a2 a3">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.0</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">2.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.0</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a2 a3">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.8</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">0.0</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.1505755257613113</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a2 a3">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.08</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">3.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.15824335171814283</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a6 a1 a2 a4">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.0</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">2.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.0</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a2 a4">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.8</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">0.0</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.12781097209959924</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a2 a4">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.08</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">3.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.06816877688804915</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a6 a1 a2 a5">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.0</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">2.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.0</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a2 a5">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.8</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">0.0</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.017975777950701</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a2 a5">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.08</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">3.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.13891981937297157</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a6 a7">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">2.0</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">0.0</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">2.837803959872224</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a6 a7">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">2.5</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">2.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">4.122603095314725</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a6 a8">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">2.0</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">0.0</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">3.963636738961668</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a6 a8">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">2.5</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">2.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.18016470141450858</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a1 a7 a6 a8">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.1</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">2.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.1056169794379673</scalar>
+    </property>
+  </torsion>
+  <torsion atomRefs4="a9 a1 a6 a2">
+    <property dictRef="mjw:barrierHeight">
+      <scalar dataType="xsd:double" units="units:kcal/mol">10.5</scalar>
+    </property>
+    <property dictRef="mjw:multiplicity">
+      <scalar dataType="xsd:double" units="units:none">1.0</scalar>
+    </property>
+    <property dictRef="mjw:periodicicity">
+      <scalar dataType="xsd:double" units="units:none">2.0</scalar>
+    </property>
+    <property dictRef="mjw:phase">
+      <scalar dataType="xsd:double" units="units:degrees">3.141594</scalar>
+    </property>
+    <property dictRef="mjw:TorsionPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">11.834422644999401</scalar>
+    </property>
+  </torsion>
+  <length atomRefs2="a3 a7">
+    <property dictRef="mjw:VDWPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-6.504532800537454E-4</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a3 a8">
+    <property dictRef="mjw:VDWPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-6.015539141014519E-4</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a4 a7">
+    <property dictRef="mjw:VDWPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-0.0014157353872324724</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a4 a8">
+    <property dictRef="mjw:VDWPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-0.001097719652187737</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a5 a7">
+    <property dictRef="mjw:VDWPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-9.569982384141979E-4</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a5 a8">
+    <property dictRef="mjw:VDWPotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-0.001514279893759916</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a2 a7">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-0.023832160091216036</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a2 a8">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-0.02477236152187442</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a6 a3">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-0.022097145429179982</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a9 a3">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.5114346783145297</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a6 a4">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.6398240810503197</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a9 a4">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.01538722259173661</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a6 a5">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.4129061597036091</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a9 a5">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">0.3039084188881567</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a9 a7">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-0.05729975525187451</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a9 a8">
+    <property dictRef="mjw:VDW14PotentialEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-0.057288017450822064</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a3 a7">
+    <property dictRef="mjw:EEPotentiaEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">2.073961713687628</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a3 a8">
+    <property dictRef="mjw:EEPotentiaEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.975484556069492</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a4 a7">
+    <property dictRef="mjw:EEPotentiaEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.7647641862587127</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a4 a8">
+    <property dictRef="mjw:EEPotentiaEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.6310578805401663</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a5 a7">
+    <property dictRef="mjw:EEPotentiaEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.6511281222248197</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a5 a8">
+    <property dictRef="mjw:EEPotentiaEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">1.7229294585184376</scalar>
+    </property>
+  </length>
+  <length atomRefs2="a2 a7">
+    <property dictRef="mjw:EE14PotentiaEnergy">
+      <scalar dataType="xsd:double" units="units:kcal/mol">-6.099552091234665</scalar>
+    </property>
+  </length>
+  <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>

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

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

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

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
+ /

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

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

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>

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
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