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l101.zmat ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceGaussian log
idl101.zmat
repeat*
pattern.*Symbolic Z\-matrix.*$\s*Charge.*Multiplicity.*$\s*\S+\s+\S+\s+\S+\s+\S+\s*
endPattern\s*
xml:basel101/l101.zmat.xml

Input ​

 Symbolic Z-matrix:
 Charge =  0 Multiplicity = 1
 H                     2.67317  -0.69436   1.17604 
 C                     1.98961  -0.3388    0.40746 
 H                     0.63164   1.77722  -0.58197

Input ​

 Symbolic Z-matrix:
 Charge =  0 Multiplicity = 1
 1                    -4.02766   0.28369   0.
 1                    -4.62766   0.28369   0.

Output text ​

xml
<comment class="example.output" id="l1.zmat">
    <module cmlx:templateRef="l101.zmat">
      <molecule id="zmat" formalCharge="0" spinMultiplicity="1" cmlx:templateRef="mol">
        <atomArray>
          <atom id="a1" elementType="H" x3="2.67317" y3="-0.69436" z3="1.17604">
            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
          </atom>
          <atom id="a2" elementType="C" x3="1.98961" y3="-0.3388" z3="0.40746">
            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
          </atom>
          <atom id="a3" elementType="H" x3="0.63164" y3="1.77722" z3="-0.58197">
            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
          </atom>
        </atomArray>
        <formula formalCharge="0" concise="C 1 H 2">
          <atomArray elementType="C H" count="1.0 2.0" />
        </formula>
        <bondArray>
          <bond atomRefs2="a1 a2" id="a1_a2" order="S" />
        </bondArray>
        <property dictRef="cml:molmass">
          <scalar dataType="xsd:double" units="unit:dalton">13.01864</scalar>
        </property>
      </molecule>
    </module>
  </comment>

Output text ​

xml
<comment class="example.output" id="l101.zmat2">
    <module cmlx:templateRef="l101.zmat">
        <molecule cmlx:templateRef="mol" formalCharge="0" id="zmat" spinMultiplicity="1">
            <atomArray>
              <atom elementType="H" id="a1" x3="-4.02766" y3="0.28369" z3="0.0000" />
              <atom elementType="H" id="a2" x3="-4.62766" y3="0.28369" z3="0.0000" />
           </atomArray>
           <bondArray />
           <formula concise="H2" />
           <property dictRef="cml:molmass">
              <scalar units="unit:dalton">0.0</scalar>
           </property>
           <list cmlx:templateRef="charge">
              <list>
                 <scalar dataType="xsd:integer" dictRef="g:charge">0</scalar>
                 <scalar dataType="xsd:integer" dictRef="g:mult">1</scalar>
              </list>
           </list>
        </molecule>
    </module>
  </comment>

Template definition ​

xml
<record />
<record id="charge">.*Charge =&#123;I,g:charge&#125; Multiplicity =&#123;I,g:mult&#125;</record>
<record id="mol" repeat="*" makeArray="true">&#123;I,gau:elementType&#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; &#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="zmat" xpath=".//cml:array" />
<transform process="move" to=".//cml:molecule" xpath="./cml:list[@cmlx:templateRef='charge']" />
<transform process="addAttribute" xpath=".//cml:molecule[@id='zmat']" name="formalCharge" value="$string(.//cml:scalar[@dictRef='g:charge'])" />
<transform process="addAttribute" xpath=".//cml:molecule[@id='zmat']" name="spinMultiplicity" value="$string(.//cml:scalar[@dictRef='g:mult'])" />
<transform process="delete" xpath="./cml:list[@cmlx:templateRef='charge']" />
<transform process="pullupSingleton" xpath="./cml:list" />