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quild.coord-d3e5107.rst

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quild.coord

Implementation level
Type Status
CML extraction template image1
HTML5 representation image2
Template attributes
Attribute Value
source ADF log
id quild.coord
name Quild module initial coordinates
pattern \s*Atomic\scoordinates\s*
endPattern .\d+\s$\s*
endOffset 1
repeat *
xml:base quild/quild.coord.xml

Input

Atomic coordinates

atom nr x (Bohrs) y (Bohrs) z (Bohrs) x (angs) y (angs) z (angs)

-------------------------------------------------------------------------------------------- C 1 -4.35644 -4.32382 2.48365 -2.30533 -2.28807 1.31429

C 2 -5.56237 -5.32601 0.18408 -2.94348 -2.81840 0.09741 C 3 -7.06088 -2.91568 -0.71245 -3.73646 -1.54291 -0.37701 C 4 -7.55061 -1.29962 1.88992 -3.99561 -0.68773 1.00010 C 5 -5.22954 -2.06590 3.35741 -2.76735 -1.09323 1.77667 C 6 -1.87045 -5.13748 2.85502 -0.98980 -2.71864 1.51081 C 7 -1.04042 -6.39232 0.64033 -0.55057 -3.38267 0.33885 C 8 -3.14831 -6.30129 -1.37538 -1.66601 -3.33450 -0.72782

Output text

<comment class="example.output" id="quild.coord">
         <module cmlx:lineCount="80" cmlx:templateRef="quild.coord">
            <molecule id="quild.coord">
             <atomArray>
              <atom id="a1" elementType="C" x3="-2.30533" y3="-2.28807" z3="1.31429">
               <scalar dataType="xsd:integer" dictRef="cc:serial">1</scalar>
               <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
              </atom>
              <atom id="a2" elementType="C" x3="-2.94348" y3="-2.8184" z3="0.09741">
               <scalar dataType="xsd:integer" dictRef="cc:serial">2</scalar>
               <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
              </atom>
              <atom id="a3" elementType="C" x3="-3.73646" y3="-1.54291" z3="-0.37701">
               <scalar dataType="xsd:integer" dictRef="cc:serial">3</scalar>
               <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
              </atom>
              <atom id="a4" elementType="C" x3="-3.99561" y3="-0.68773" z3="1.0001">
               <scalar dataType="xsd:integer" dictRef="cc:serial">4</scalar>
               <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
              </atom>
              <atom id="a5" elementType="C" x3="-2.76735" y3="-1.09323" z3="1.77667">
               <scalar dataType="xsd:integer" dictRef="cc:serial">5</scalar>
               <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
              </atom>
              <atom id="a6" elementType="C" x3="-0.9898" y3="-2.71864" z3="1.51081">
               <scalar dataType="xsd:integer" dictRef="cc:serial">6</scalar>
               <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
              </atom>
              <atom id="a7" elementType="C" x3="-0.55057" y3="-3.38267" z3="0.33885">
               <scalar dataType="xsd:integer" dictRef="cc:serial">7</scalar>
               <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
              </atom>
              <atom id="a8" elementType="C" x3="-1.66601" y3="-3.3345" z3="-0.72782">
               <scalar dataType="xsd:integer" dictRef="cc:serial">8</scalar>
               <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
              </atom>
             </atomArray>
             <formula formalCharge="0" concise="C 8">
              <atomArray elementType="C" count="8.0" />
             </formula>
             <bondArray>
              <bond atomRefs2="a1 a2" id="a1_a2" order="S" />
              <bond atomRefs2="a1 a5" id="a1_a5" order="S" />
              <bond atomRefs2="a1 a6" id="a1_a6" order="S" />
              <bond atomRefs2="a2 a3" id="a2_a3" order="S" />
              <bond atomRefs2="a2 a8" id="a2_a8" order="S" />           
             </bondArray>
             <property dictRef="cml:molmass">
              <scalar dataType="xsd:double" units="unit:dalton">1241.0054</scalar>
             </property>
            </molecule>
           </module>


    </comment>

Template definition

<record repeat="4" />
<record id="atom" repeat="*" makeArray="true">{A,cc:elementType}{I,cc:serial}\s+\S+\s+\S+\s+\S+\s+{F,cc:x3}{F,cc:y3}{F,cc:z3}</record>
<transform process="createMolecule" id="quild.coord" xpath=".//cml:list[@cmlx:templateRef='atom']/cml:array" />
<transform process="pullup" xpath=".//cml:molecule" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:molecule[count(*)=0]" />