l101.zmat

Implementation level

Type

Status

CML extraction template

image1

HTML5 representation

image2
Template attributes

Attribute

Value

source

Gaussian log

id

l101.zmat

repeat

*

pattern

.*Symbolic Z\-matrix.*$\s*Charge.*Multiplicity.*$\s*\S+\s+\S+\s+\S+\s+\S+\s*

endPattern

\s*

xml:base

l101/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

 1<comment class="example.output" id="l1.zmat">
 2    <module cmlx:templateRef="l101.zmat">
 3      <molecule id="zmat" formalCharge="0" spinMultiplicity="1" cmlx:templateRef="mol">
 4        <atomArray>
 5          <atom id="a1" elementType="H" x3="2.67317" y3="-0.69436" z3="1.17604">
 6            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
 7          </atom>
 8          <atom id="a2" elementType="C" x3="1.98961" y3="-0.3388" z3="0.40746">
 9            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
10          </atom>
11          <atom id="a3" elementType="H" x3="0.63164" y3="1.77722" z3="-0.58197">
12            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
13          </atom>
14        </atomArray>
15        <formula formalCharge="0" concise="C 1 H 2">
16          <atomArray elementType="C H" count="1.0 2.0" />
17        </formula>
18        <bondArray>
19          <bond atomRefs2="a1 a2" id="a1_a2" order="S" />
20        </bondArray>
21        <property dictRef="cml:molmass">
22          <scalar dataType="xsd:double" units="unit:dalton">13.01864</scalar>
23        </property>
24      </molecule>
25    </module>
26  </comment>

Output text

 1<comment class="example.output" id="l101.zmat2">
 2    <module cmlx:templateRef="l101.zmat">
 3        <molecule cmlx:templateRef="mol" formalCharge="0" id="zmat" spinMultiplicity="1">
 4            <atomArray>
 5              <atom elementType="H" id="a1" x3="-4.02766" y3="0.28369" z3="0.0000" />
 6              <atom elementType="H" id="a2" x3="-4.62766" y3="0.28369" z3="0.0000" />
 7           </atomArray>
 8           <bondArray />
 9           <formula concise="H2" />
10           <property dictRef="cml:molmass">
11              <scalar units="unit:dalton">0.0</scalar>
12           </property>
13           <list cmlx:templateRef="charge">
14              <list>
15                 <scalar dataType="xsd:integer" dictRef="g:charge">0</scalar>
16                 <scalar dataType="xsd:integer" dictRef="g:mult">1</scalar>
17              </list>
18           </list>
19        </molecule>
20    </module>
21  </comment>

Template definition

 1<record />
 2<record id="charge">.*Charge ={I,g:charge} Multiplicity ={I,g:mult}</record>
 3<record id="mol" repeat="*" makeArray="true">{I,gau:elementType} {F,gau:x3,unit:angstrom}  {F,gau:y3,unit:angstrom} {F,gau:z3,unit:angstrom}</record>
 4<record id="mol" repeat="*" makeArray="true">{A,gau:elementType} {F,gau:x3,unit:angstrom}  {F,gau:y3,unit:angstrom} {F,gau:z3,unit:angstrom}</record>
 5<transform process="createMolecule" id="zmat" xpath=".//cml:array" />
 6<transform process="move" to=".//cml:molecule" xpath="./cml:list[@cmlx:templateRef='charge']" />
 7<transform process="addAttribute" xpath=".//cml:molecule[@id='zmat']" name="formalCharge" value="$string(.//cml:scalar[@dictRef='g:charge'])" />
 8<transform process="addAttribute" xpath=".//cml:molecule[@id='zmat']" name="spinMultiplicity" value="$string(.//cml:scalar[@dictRef='g:mult'])" />
 9<transform process="delete" xpath="./cml:list[@cmlx:templateRef='charge']" />
10<transform process="pullupSingleton" xpath="./cml:list" />