geometry
Type |
Status |
|---|---|
CML extraction template |
|
HTML5 representation |
|
Attribute |
Value |
|---|---|
source |
MOPAC log |
id |
geometry |
name |
Cartesian Coordinates |
pattern |
\s*CARTESIAN\sCOORDINATES.* |
endPattern |
\s*Empirical\s*Formula.* |
endPattern2 |
\s*$\s*$\s* |
repeat |
* |
xml:base |
job/atomiccoordinates.xml |
Input
CARTESIAN COORDINATES
1 C -4.374598305 2.688732629 1.251130091
2 C -5.092724453 3.683249302 0.425878871
3 C -6.471282903 3.691879674 0.356170876
4 C -7.330541146 2.837499652 1.233383342
5 C -6.546466024 1.752175053 2.134695421
6 C -5.058520354 1.736674464 1.980132375
7 C -3.146588734 2.345471392 0.555689153
8 C -2.967412654 3.247627856 -0.624015350
9 C -4.291530172 3.929989962 -0.760299282
...
Empirical Formula: C510 H498 N66 O172 = 1246 atoms
Input
CARTESIAN COORDINATES
NO. ATOM X Y Z
1 C -4.1918 2.5617 1.3518
2 C -4.8544 3.5730 0.5005
3 C -6.2295 3.6275 0.3952
4 C -7.1393 2.8094 1.2560
5 C -6.4160 1.7058 2.1856
6 C -4.9260 1.6393 2.0699
7 C -2.9585 2.1717 0.6912
8 C -2.7186 3.0577 -0.4900
9 C -4.0147 3.7838 -0.6656
...
Output text
1<comment class="example.output" id="geometry">
2 <module cmlx:templateRef="geometry">
3 <molecule id="molecule">
4 <atomArray>
5 <atom elementType="C" id="a1" x3="0.3745983" y3="2.68873263" z3="1.25113009">
6 <scalar dataType="xsd:integer" dictRef="cc:serial">1</scalar>
7 <scalar dataType="xsd:integer" dictRef="g:atomicType">-4</scalar>
8 </atom>
9 <atom elementType="C" id="a2" x3="0.09272445" y3="3.6832493" z3="0.42587887">
10 <scalar dataType="xsd:integer" dictRef="cc:serial">2</scalar>
11 <scalar dataType="xsd:integer" dictRef="g:atomicType">-5</scalar>
12 </atom>
13 <atom elementType="C" id="a3" x3="0.4712829" y3="3.69187967" z3="0.35617088">
14 <scalar dataType="xsd:integer" dictRef="cc:serial">3</scalar>
15 <scalar dataType="xsd:integer" dictRef="g:atomicType">-6</scalar>
16 </atom>
17 <atom elementType="C" id="a4" x3="0.33054115" y3="2.83749965" z3="1.23338334">
18 <scalar dataType="xsd:integer" dictRef="cc:serial">4</scalar>
19 <scalar dataType="xsd:integer" dictRef="g:atomicType">-7</scalar>
20 </atom>
21 <atom elementType="C" id="a5" x3="0.54646602" y3="1.75217505" z3="2.13469542">
22 <scalar dataType="xsd:integer" dictRef="cc:serial">5</scalar>
23 <scalar dataType="xsd:integer" dictRef="g:atomicType">-6</scalar>
24 </atom>
25 <atom elementType="C" id="a6" x3="0.05852035" y3="1.73667446" z3="1.98013238">
26 <scalar dataType="xsd:integer" dictRef="cc:serial">6</scalar>
27 <scalar dataType="xsd:integer" dictRef="g:atomicType">-5</scalar>
28 </atom>
29 <atom elementType="C" id="a7" x3="0.14658873" y3="2.34547139" z3="0.55568915">
30 <scalar dataType="xsd:integer" dictRef="cc:serial">7</scalar>
31 <scalar dataType="xsd:integer" dictRef="g:atomicType">-3</scalar>
32 </atom>
33 <atom elementType="C" id="a8" x3="0.96741265" y3="3.24762786" z3="-0.62401535">
34 <scalar dataType="xsd:integer" dictRef="cc:serial">8</scalar>
35 <scalar dataType="xsd:integer" dictRef="g:atomicType">-2</scalar>
36 </atom>
37 <atom elementType="C" id="a9" x3="0.29153017" y3="3.92998996" z3="-0.76029928">
38 <scalar dataType="xsd:integer" dictRef="cc:serial">9</scalar>
39 <scalar dataType="xsd:integer" dictRef="g:atomicType">-4</scalar>
40 </atom>
41 </atomArray>
42 </molecule>
43 </module>
44 </comment>
Template definition
1<record repeat="*">((?!\s*1).*)</record>
2<record name="molecule" repeat="*">{I,cc:serial}{A,cc:elementType}{F,cc:x3}\*?{F,cc:y3}\*?{F,cc:z3}</record>
3<transform process="delete" xpath="//cml:list[child::cml:scalar[@dictRef='cc:elementType' and text() = 'Tv']]" />
4<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:serial']" dictRef="cc:serial" dataType="xsd:integer" />
5<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:elementType']" dictRef="cc:elementType" dataType="xsd:string" />
6<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:x3']" dictRef="cc:x3" dataType="xsd:double" />
7<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:y3']" dictRef="cc:y3" dataType="xsd:double" />
8<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:z3']" dictRef="cc:z3" dataType="xsd:double" />
9<transform process="createMolecule" xpath=".//cml:list/cml:array" id="molecule" />
10<transform process="pullup" xpath=".//cml:molecule" repeat="2" />
11<transform process="delete" xpath=".//cml:list[count(*)=0]" />
12<transform process="delete" xpath=".//cml:list[count(*)=0]" />
13<transform process="delete" xpath=".//cml:molecule//cml:scalar[@dictRef='cc:serial']" />
14<transform process="delete" xpath=".//cml:molecule//cml:scalar[@dictRef='cc:atomicNumber']" />