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l101.zmatfragment ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceGaussian log
idl101.zmatfragment
repeat*
pattern.*Symbolic\sZ\-matrix.*$\s*Charge.*Multiplicity.*in\ssupermolecule\s*$\s*Charge.*Multiplicity.*in\sfragment.*
endPattern\s*
xml:basel101/l101.zmatfragment.xml

Input ​

 Symbolic Z-matrix:
 Charge =  0 Multiplicity = 1 in supermolecule
 Charge =  0 Multiplicity = 1 in fragment      1.
 Charge =  0 Multiplicity = 1 in fragment      2.
 H(Fragment=1)         10.95684   0.52181   5.17636 
 N(Fragment=1)         10.78265  -0.14558   6.33644 
 H(Fragment=1)         11.65274  -0.43711   6.75966 
 C(Fragment=1)         9.545    -0.78436   6.74173
 H(Fragment=2)         19.67428  -3.80756  -5.09505 
 H(Fragment=2)         18.43108  -7.54832  -1.03918

Output text ​

xml
<comment class="example.output" id="l101.zmatfragment">
    <module cmlx:templateRef="l101.zmatfragment">
        <list cmlx:templateRef="chargefragment">
           <array dataType="xsd:integer" dictRef="g:charge" size="2">0 0</array>
           <array dataType="xsd:integer" dictRef="g:mult" size="2">1 1</array>
           <array dataType="xsd:integer" dictRef="g:fragment" size="2">1 2</array>
        </list>
        <molecule cmlx:templateRef="mol" formalCharge="0" id="zmatfragment" spinMultiplicity="1">
            <atomArray>
               <atom elementType="H" id="a1" x3="10.95684" y3="0.52181" z3="5.17636">
                  <scalar dataType="xsd:integer" dictRef="g:fragment">1</scalar>
                  <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
               </atom>
               <atom elementType="N" id="a2" x3="10.78265" y3="-0.14558" z3="6.33644">
                  <scalar dataType="xsd:integer" dictRef="g:fragment">1</scalar>
                  <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">7</scalar>
               </atom>
               <atom elementType="H" id="a3" x3="11.65274" y3="-0.43711" z3="6.75966">
                  <scalar dataType="xsd:integer" dictRef="g:fragment">1</scalar>
                  <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
               </atom>
               <atom elementType="C" id="a4" x3="9.5450" y3="-0.78436" z3="6.74173">
                  <scalar dataType="xsd:integer" dictRef="g:fragment">1</scalar>
                  <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                </atom>
                <atom elementType="H" id="a203" x3="19.67428" y3="-3.80756" z3="-5.09505">
                    <scalar dataType="xsd:integer" dictRef="g:fragment">2</scalar>
                    <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                 </atom>
                 <atom elementType="H" id="a204" x3="18.43108" y3="-7.54832" z3="-1.03918">
                    <scalar dataType="xsd:integer" dictRef="g:fragment">2</scalar>
                    <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                 </atom>
            </atomArray>
            <bondArray>
                 <bond atomRefs2="a1 a2" order="S" />
                 <bond atomRefs2="a2 a4" order="S" />
                 <bond atomRefs2="a2 a3" order="S" />
                 <bond atomRefs2="a4 a17" order="S" />
            </bondArray>
            <formula concise="C84H90N14O14Zn2">
               <atomArray count="84 90 14 14 2" elementType="C H N O Zn" />
            </formula>
            <property dictRef="cml:molmass">
               <scalar units="unit:dalton">1559.8022000000024</scalar>
            </property>
        </molecule>
    </module>
  </comment>

Template definition ​

xml
<record />
<record id="charge">.*Charge =&#123;I,g:charge&#125; Multiplicity =&#123;I,g:mult&#125;\s*in\s*supermolecule</record>
<record id="chargefragment" repeat="*">.*Charge =&#123;I,g:charge&#125; Multiplicity =&#123;I,g:mult&#125;\sin\sfragment&#123;I,g:fragment&#125;\.\s*</record>
<record id="mol" repeat="*" makeArray="true">&#123;I,gau:elementType&#125;\(Fragment=&#123;I,g:fragment&#125;\)&#123;F,gau:x3,unit:angstrom&#125;&#123;F,gau:y3,unit:angstrom&#125;&#123;F,gau:z3,unit:angstrom&#125;</record>
<record id="mol" repeat="*" makeArray="true">&#123;A,gau:elementType&#125;\(Fragment=&#123;I,g:fragment&#125;\)&#123;F,gau:x3,unit:angstrom&#125;&#123;F,gau:y3,unit:angstrom&#125;&#123;F,gau:z3,unit:angstrom&#125;</record>
<transform process="createMolecule" id="zmatfragment" xpath=".//cml:array" />
<transform process="move" xpath="./cml:list[@cmlx:templateRef='charge']" to=".//cml:molecule" />
<transform process="addAttribute" xpath=".//cml:molecule[@id='zmatfragment']" name="formalCharge" value="$string(.//cml:scalar[@dictRef='g:charge'])" />
<transform process="addAttribute" xpath=".//cml:molecule[@id='zmatfragment']" name="spinMultiplicity" value="$string(.//cml:scalar[@dictRef='g:mult'])" />
<transform process="delete" xpath="./cml:list[@cmlx:templateRef='charge']" />
<transform process="createArray" xpath="." from="./cml:list[@cmlx:templateRef='chargefragment']//cml:scalar[@dictRef='g:charge']" />
<transform process="createArray" xpath="./cml:list[@cmlx:templateRef='chargefragment']" from=".//cml:scalar[@dictRef='g:mult']" />
<transform process="createArray" xpath="./cml:list[@cmlx:templateRef='chargefragment']" from=".//cml:scalar[@dictRef='g:fragment']" />
<transform process="pullupSingleton" xpath="./cml:list" />
<transform process="pullup" xpath=".//cml:list/cml:array" />
<transform process="delete" xpath=".//cml:list[@cmlx:templateRef='charge']" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />