quild.coord

Implementation level
Type Status
CML extraction template image0
HTML5 representation image1
Template attributes
Attribute Value
source ADF log
id quild.coord
name Quild module initial coordinates
pattern \s*Atomicscoordinatess*
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]" />