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l101.zmatvariables ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceGaussian log
idl101.zmatvariables
pattern\s*Symbolic.*$\s+Charge.*Multiplicity.*$[^\.]+
endPattern\s*
repeat*
xml:basel101/l101.zmatvariables.xml

Input ​

 Symbolic Z-matrix:
 Charge =  0 Multiplicity = 1
 C
 H                    1    B1
 H                    1    B2       2    A1
 H                    1    B3       2    A2       3    D1       0
 H                    1    B4       2    A3       3    D2       0
       Variables:
  B1                    1.113                    
  B2                    1.113                    
  B3                    1.113                    
  B4                    1.113                    
  A1                  109.47124                  
  A2                  109.47119                  
  D1                  120.                       
  A3                  109.47123                  
  D2                 -120.

Output text ​

xml
<comment class="example.output" id="l101.zmatvariables">
    <module cmlx:templateRef="l101.zmatvariables">
      <map id="variableMap">
        <link from="B1" to="1.113" />
        <link from="B2" to="1.113" />
        <link from="B3" to="1.113" />
        <link from="B4" to="1.113" />
        <link from="A1" to="109.47124" />
        <link from="A2" to="109.47119" />
        <link from="D1" to="120.0" />
        <link from="A3" to="109.47123" />
        <link from="D2" to="-120.0" />
      </map>
      <molecule id="zinitial" spinMultiplicity="1" formalCharge="0">
        <zMatrix>
          <length atomRefs2="a1 a2">1.113</length>
          <length atomRefs2="a1 a3">1.113</length>
          <angle atomRefs3="a2 a1 a3">109.47124</angle>
          <length atomRefs2="a1 a4">1.113</length>
          <angle atomRefs3="a2 a1 a4">109.47119</angle>
          <torsion atomRefs4="a3 a2 a1 a4">120.0</torsion>
          <length atomRefs2="a1 a5">1.113</length>
          <angle atomRefs3="a2 a1 a5">109.47123</angle>
          <torsion atomRefs4="a3 a2 a1 a5">-120.0</torsion>
        </zMatrix>
        <atomArray>
          <atom elementType="C" id="a1" x3="1.113" y3="0.0" z3="0.0" />
          <atom elementType="H" id="a2" x3="0.0" y3="0.0" z3="0.0" />
          <atom elementType="H" id="a3" x3="1.4840003546705822" y3="1.0493463378857821" z3="0.0" />
          <atom elementType="H" id="a4" x3="1.4839994389430116" y3="-0.524673330822134" z3="0.9087608663603304" />
          <atom elementType="H" id="a5" x3="1.484000171525091" y3="-0.5246732013187714" z3="-0.9087606420539267" />
        </atomArray>
      </molecule>
    </module>
  </comment>

Template definition ​

xml
<record />
<record id="chargemult">\s*Charge\s*=&#123;I,x:formalCharge&#125;\s*Multiplicity\s*=&#123;I,x:multiplicity&#125;\s*</record>
<record id="atom1">\s*&#123;A,cc:elementType&#125;\s*</record>
<record id="atom2">\s*&#123;A,cc:elementType&#125;\s&#123;I,x:junk&#125;\s&#123;A,cc:name&#125;\s*</record>
<record id="atom3">\s*&#123;A,cc:elementType&#125;\s&#123;I,x:junk&#125;\s&#123;A,cc:name&#125;\s&#123;I,x:junk&#125;\s&#123;A,cc:name&#125;\s*</record>
<record id="atom4" repeat="*">\s*&#123;A,cc:elementType&#125;\s&#123;I,x:junk&#125;\s&#123;A,cc:name&#125;\s&#123;I,x:junk&#125;\s&#123;A,cc:name&#125;\s&#123;I,x:junk&#125;\s&#123;A,cc:name&#125;\s&#123;I,g:unknown&#125;\s*</record>
<record />
<record id="variable" repeat="*">\s*&#123;A,x:name&#125;\s&#123;F,x:value&#125;\s*</record>
<transform process="addMap" xpath="." id="variableMap" from=".//cml:scalar[@dictRef='x:name']" to=".//cml:scalar[@dictRef='x:value']" />
<transform process="delete" xpath="./cml:list[@cmlx:templateRef='variable']" />
<transform process="createAtom" xpath=".//cml:scalar[@dictRef='cc:elementType']" />
<transform process="setValue" xpath=".//cml:list/cml:scalar[2] |            .//cml:list/cml:scalar[4] |            .//cml:list/cml:scalar[6]" map="//cml:map[@id='variableMap']" value="$string(.)" />
<transform process="createLength" xpath=".//cml:list/cml:list[cml:atom]" atomRefs="$string(cml:scalar[1]) $string(cml:atom/@id)" value="$string(cml:scalar[2])" />
<transform process="createAngle" xpath=".//cml:list/cml:list[cml:atom]" atomRefs="$string(cml:scalar[3]) $string(cml:scalar[1]) $string(cml:atom/@id)" value="$string(cml:scalar[4])" />
<transform process="createTorsion" xpath=".//cml:list/cml:list[cml:atom]" atomRefs="$string(cml:scalar[5]) $string(cml:scalar[3]) $string(cml:scalar[1]) $string(cml:atom/@id)" value="$string(cml:scalar[6])" />
<transform process="createZMatrix" xpath="." id="zinitial" />
<transform process="addAttribute" xpath=".//cml:molecule" name="spinMultiplicity" value="$string(..//cml:scalar[@dictRef='x:multiplicity'])" />
<transform process="addAttribute" xpath=".//cml:molecule" name="formalCharge" value="$string(..//cml:scalar[@dictRef='x:formalCharge'])" />
<transform process="delete" xpath="./cml:list" />