atomcoord¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
| Attribute | Value |
|---|---|
| source | Turbomole log |
| repeat | * |
| id | atomcoord |
| name | Atomic coordinate, charge and isotop information |
| pattern | \s*\+\-+\+\s*$\s*\|\sAtomic coordinate, charge and isotop information\s\|\s*$\s*\+\-+\+\s*.*$\s* |
| endPattern | \s*center\sof\snuclear\scharge.* |
| endOffset | 1 |
| xml:base | atomcoord.xml |
Input
+--------------------------------------------------+
| Atomic coordinate, charge and isotop information |
+--------------------------------------------------+
atomic coordinates atom shells charge pseudo isotop
0.00783626 0.00005587 -0.14130773 n 7 7.000 0 0
2.70822787 2.70686248 -0.21748978 sc 15 21.000 0 0
1.04906177 -3.67570357 -0.06247923 sc 15 21.000 0 0
-3.69812652 0.97687983 -0.15811704 sc 15 21.000 0 0
-4.32169744 -4.97395025 -4.12476803 c 7 6.000 0 0
-2.03854015 -4.99235967 -5.60986553 c 7 6.000 0 0
-1.94573473 -2.68088110 -7.04449314 c 7 6.000 0 0
-4.16352418 -1.24380528 -6.45186689 c 7 6.000 0 0
-5.63978287 -2.65384028 -4.64807236 c 7 6.000 0 0
-7.10154380 -1.42802936 -2.73405978 c 7 6.000 0 0
-7.26393056 -2.63622666 -0.32420300 c 7 6.000 0 0
-5.94610521 -4.94964950 0.19813003 c 7 6.000 0 0
-4.39333236 -6.08095417 -1.68502336 c 7 6.000 0 0
-2.13479494 -7.32641516 -0.81742441 c 7 6.000 0 0
0.13112892 -7.47940581 -2.30472823 c 7 6.000 0 0
0.21937163 -6.13015070 -4.68713150 c 7 6.000 0 0
2.56075737 -4.97919278 -5.35330149 c 7 6.000 0 0
2.66696571 -2.68725575 -6.78968876 c 7 6.000 0 0
0.39522556 -1.44886610 -7.57372926 c 7 6.000 0 0
0.40821253 1.24551885 -7.67603204 c 7 6.000 0 0
-1.81344383 2.68257415 -7.06270204 c 7 6.000 0 0
-4.08771056 1.43989993 -6.35905933 c 7 6.000 0 0
-5.64383747 2.64894299 -4.47962405 c 7 6.000 0 0
-7.27838951 1.29799191 -2.76435689 c 7 6.000 0 0
-7.52176644 2.79214670 -0.43837130 c 7 6.000 0 0
-7.49492669 1.52167501 2.01462690 c 7 6.000 0 0
-7.41842688 -1.19395406 2.00155451 c 7 6.000 0 0
-6.15143656 -2.64516823 3.94271427 c 7 6.000 0 0
-5.26525934 -4.95190956 2.83002118 c 7 6.000 0 0
-2.97664829 -6.08927609 3.68137768 c 7 6.000 0 0
-1.44707676 -7.35406114 1.80941346 c 7 6.000 0 0
1.26467695 -7.56224823 1.98644747 c 7 6.000 0 0
2.29015552 -7.68438215 -0.59255010 c 7 6.000 0 0
4.56247098 -6.26241852 -1.20937045 c 7 6.000 0 0
4.66499577 -5.00078185 -3.60569803 c 7 6.000 0 0
6.06211699 -2.69353288 -3.98432827 c 7 6.000 0 0
4.82287758 -1.27280864 -5.94105106 c 7 6.000 0 0
4.74770803 1.41739769 -5.88012718 c 7 6.000 0 0
2.56986315 2.65551757 -6.83796893 c 7 6.000 0 0
1.69052419 4.97770157 -5.70969303 c 7 6.000 0 0
-1.02540903 4.98873319 -5.85050220 c 7 6.000 0 0
-2.48682291 6.12051178 -3.91027922 c 7 6.000 0 0
-4.84065343 4.93039919 -3.27573889 c 7 6.000 0 0
-5.91477922 5.00124179 -0.77666451 c 7 6.000 0 0
4.29242220 4.96190676 4.12561670 c 7 6.000 0 0
2.01721951 4.97230597 5.63006458 c 7 6.000 0 0
1.93760651 2.67308065 7.06861042 c 7 6.000 0 0
4.15962429 1.23022423 6.48650423 c 7 6.000 0 0
5.60576479 2.62366881 4.66844700 c 7 6.000 0 0
7.06482187 1.40790286 2.77113366 c 7 6.000 0 0
7.29768288 2.69868603 0.37141200 c 7 6.000 0 0
6.17474606 5.15427149 -0.15752410 c 7 6.000 0 0
4.50756815 6.25096736 1.74934256 c 7 6.000 0 0
2.20949456 7.40133430 0.86921373 c 7 6.000 0 0
-0.09098797 7.39253403 2.33855245 c 7 6.000 0 0
-0.23470596 6.12281285 4.71441331 c 7 6.000 0 0
-2.59115553 5.00890637 5.41328109 c 7 6.000 0 0
-2.67896314 2.68444250 6.81863136 c 7 6.000 0 0
-0.40955882 1.44689696 7.60472952 c 7 6.000 0 0
1.80409305 -2.68809133 7.09663384 c 7 6.000 0 0
4.09804739 -1.46689843 6.40295198 c 7 6.000 0 0
5.66883341 -2.69046837 4.58235132 c 7 6.000 0 0
7.14844087 -1.28547587 2.78980582 c 7 6.000 0 0
7.25300004 -2.70452414 0.47472749 c 7 6.000 0 0
7.27822407 -1.48890765 -1.91783204 c 7 6.000 0 0
7.29724074 1.22575094 -1.91095589 c 7 6.000 0 0
6.08015868 2.65846532 -3.85406309 c 7 6.000 0 0
5.36702160 5.07741168 -2.81840065 c 7 6.000 0 0
2.98831813 6.14564835 -3.64938938 c 7 6.000 0 0
1.48860064 7.39486984 -1.78055883 c 7 6.000 0 0
-1.21907174 7.41409962 -1.92137065 c 7 6.000 0 0
-2.18836818 7.41757235 0.61812127 c 7 6.000 0 0
-4.48300482 6.14614658 1.24576191 c 7 6.000 0 0
-4.66174699 5.00574728 3.67117440 c 7 6.000 0 0
-6.07311840 2.68405960 4.01123906 c 7 6.000 0 0
-4.82236915 1.26209301 5.97631540 c 7 6.000 0 0
-4.77323702 -1.43206109 5.91987268 c 7 6.000 0 0
-2.58860640 -2.67232259 6.88952988 c 7 6.000 0 0
-1.70570245 -4.98120195 5.76488552 c 7 6.000 0 0
1.01741866 -5.00181406 5.90246289 c 7 6.000 0 0
2.51231412 -6.16356675 3.98540450 c 7 6.000 0 0
4.85939953 -4.97984086 3.37586440 c 7 6.000 0 0
5.84155625 -5.00730695 0.82534781 c 7 6.000 0 0
-0.42107636 -1.24820715 7.69035721 c 7 6.000 0 0
center of nuclear mass : 0.00000000 0.00000000 0.00000000
center of nuclear charge: -0.00015670 -0.00002130 0.00115983
Input
+--------------------------------------------------+
| Atomic coordinate, charge and isotop information |
+--------------------------------------------------+
atomic coordinates atom charge isotop
-1.79267786 1.79292956 0.21711881 c 6.000 0
-4.64203010 1.72468295 0.02453055 c 6.000 0
-0.72232011 -0.24797201 -0.93360778 o 8.000 0
-0.54455624 3.43404491 1.23097559 o 8.000 0
-5.21620927 1.96641451 -1.97654605 h 1.000 0
-5.37835338 -0.13077601 0.65353692 h 1.000 0
-5.45824156 3.26101743 1.17396391 h 1.000 0
1.10943076 -0.01816375 -0.73154500 h 1.000 0
center of nuclear mass : -1.87534367 1.63763387 0.11277683
center of nuclear charge: -1.99020725 1.61477345 0.09213276
Output text
<comment class="example.output" id="geometry.cycle">
<module cmlx:lineCount="95" cmlx:templateRef="atomcoord">
<molecule id="atomcoord">
<atomArray>
<atom id="a1" x3="0.00783626" y3="5.587E-5" z3="-0.14130773" elementType="N" />
<atom id="a2" x3="2.70822787" y3="2.70686248" z3="-0.21748978" elementType="Sc" />
<atom id="a3" x3="1.04906177" y3="-3.67570357" z3="-0.06247923" elementType="Sc" />
<atom id="a4" x3="-3.69812652" y3="0.97687983" z3="-0.15811704" elementType="Sc" />
<atom id="a5" x3="-4.32169744" y3="-4.97395025" z3="-4.12476803" elementType="C" />
<atom id="a6" x3="-2.03854015" y3="-4.99235967" z3="-5.60986553" elementType="C" />
<atom id="a7" x3="-1.94573473" y3="-2.6808811" z3="-7.04449314" elementType="C" />
<atom id="a8" x3="-4.16352418" y3="-1.24380528" z3="-6.45186689" elementType="C" />
<atom id="a9" x3="-5.63978287" y3="-2.65384028" z3="-4.64807236" elementType="C" />
<atom id="a10" x3="-7.1015438" y3="-1.42802936" z3="-2.73405978" elementType="C" />
<atom id="a11" x3="-7.26393056" y3="-2.63622666" z3="-0.324203" elementType="C" />
<atom id="a12" x3="-5.94610521" y3="-4.9496495" z3="0.19813003" elementType="C" />
<atom id="a13" x3="-4.39333236" y3="-6.08095417" z3="-1.68502336" elementType="C" />
<atom id="a14" x3="-2.13479494" y3="-7.32641516" z3="-0.81742441" elementType="C" />
<atom id="a15" x3="0.13112892" y3="-7.47940581" z3="-2.30472823" elementType="C" />
<atom id="a16" x3="0.21937163" y3="-6.1301507" z3="-4.6871315" elementType="C" />
<atom id="a17" x3="2.56075737" y3="-4.97919278" z3="-5.35330149" elementType="C" />
<atom id="a18" x3="2.66696571" y3="-2.68725575" z3="-6.78968876" elementType="C" />
<atom id="a19" x3="0.39522556" y3="-1.4488661" z3="-7.57372926" elementType="C" />
<atom id="a20" x3="0.40821253" y3="1.24551885" z3="-7.67603204" elementType="C" />
<atom id="a21" x3="-1.81344383" y3="2.68257415" z3="-7.06270204" elementType="C" />
<atom id="a22" x3="-4.08771056" y3="1.43989993" z3="-6.35905933" elementType="C" />
<atom id="a23" x3="-5.64383747" y3="2.64894299" z3="-4.47962405" elementType="C" />
<atom id="a24" x3="-7.27838951" y3="1.29799191" z3="-2.76435689" elementType="C" />
<atom id="a25" x3="-7.52176644" y3="2.7921467" z3="-0.4383713" elementType="C" />
<atom id="a26" x3="-7.49492669" y3="1.52167501" z3="2.0146269" elementType="C" />
<atom id="a27" x3="-7.41842688" y3="-1.19395406" z3="2.00155451" elementType="C" />
<atom id="a28" x3="-6.15143656" y3="-2.64516823" z3="3.94271427" elementType="C" />
<atom id="a29" x3="-5.26525934" y3="-4.95190956" z3="2.83002118" elementType="C" />
<atom id="a30" x3="-2.97664829" y3="-6.08927609" z3="3.68137768" elementType="C" />
<atom id="a31" x3="-1.44707676" y3="-7.35406114" z3="1.80941346" elementType="C" />
<atom id="a32" x3="1.26467695" y3="-7.56224823" z3="1.98644747" elementType="C" />
<atom id="a33" x3="2.29015552" y3="-7.68438215" z3="-0.5925501" elementType="C" />
<atom id="a34" x3="4.56247098" y3="-6.26241852" z3="-1.20937045" elementType="C" />
<atom id="a35" x3="4.66499577" y3="-5.00078185" z3="-3.60569803" elementType="C" />
<atom id="a36" x3="6.06211699" y3="-2.69353288" z3="-3.98432827" elementType="C" />
<atom id="a37" x3="4.82287758" y3="-1.27280864" z3="-5.94105106" elementType="C" />
<atom id="a38" x3="4.74770803" y3="1.41739769" z3="-5.88012718" elementType="C" />
<atom id="a39" x3="2.56986315" y3="2.65551757" z3="-6.83796893" elementType="C" />
<atom id="a40" x3="1.69052419" y3="4.97770157" z3="-5.70969303" elementType="C" />
<atom id="a41" x3="-1.02540903" y3="4.98873319" z3="-5.8505022" elementType="C" />
<atom id="a42" x3="-2.48682291" y3="6.12051178" z3="-3.91027922" elementType="C" />
<atom id="a43" x3="-4.84065343" y3="4.93039919" z3="-3.27573889" elementType="C" />
<atom id="a44" x3="-5.91477922" y3="5.00124179" z3="-0.77666451" elementType="C" />
<atom id="a45" x3="4.2924222" y3="4.96190676" z3="4.1256167" elementType="C" />
<atom id="a46" x3="2.01721951" y3="4.97230597" z3="5.63006458" elementType="C" />
<atom id="a47" x3="1.93760651" y3="2.67308065" z3="7.06861042" elementType="C" />
<atom id="a48" x3="4.15962429" y3="1.23022423" z3="6.48650423" elementType="C" />
<atom id="a49" x3="5.60576479" y3="2.62366881" z3="4.668447" elementType="C" />
<atom id="a50" x3="7.06482187" y3="1.40790286" z3="2.77113366" elementType="C" />
<atom id="a51" x3="7.29768288" y3="2.69868603" z3="0.371412" elementType="C" />
<atom id="a52" x3="6.17474606" y3="5.15427149" z3="-0.1575241" elementType="C" />
<atom id="a53" x3="4.50756815" y3="6.25096736" z3="1.74934256" elementType="C" />
<atom id="a54" x3="2.20949456" y3="7.4013343" z3="0.86921373" elementType="C" />
<atom id="a55" x3="-0.09098797" y3="7.39253403" z3="2.33855245" elementType="C" />
<atom id="a56" x3="-0.23470596" y3="6.12281285" z3="4.71441331" elementType="C" />
<atom id="a57" x3="-2.59115553" y3="5.00890637" z3="5.41328109" elementType="C" />
<atom id="a58" x3="-2.67896314" y3="2.6844425" z3="6.81863136" elementType="C" />
<atom id="a59" x3="-0.40955882" y3="1.44689696" z3="7.60472952" elementType="C" />
<atom id="a60" x3="1.80409305" y3="-2.68809133" z3="7.09663384" elementType="C" />
<atom id="a61" x3="4.09804739" y3="-1.46689843" z3="6.40295198" elementType="C" />
<atom id="a62" x3="5.66883341" y3="-2.69046837" z3="4.58235132" elementType="C" />
<atom id="a63" x3="7.14844087" y3="-1.28547587" z3="2.78980582" elementType="C" />
<atom id="a64" x3="7.25300004" y3="-2.70452414" z3="0.47472749" elementType="C" />
<atom id="a65" x3="7.27822407" y3="-1.48890765" z3="-1.91783204" elementType="C" />
<atom id="a66" x3="7.29724074" y3="1.22575094" z3="-1.91095589" elementType="C" />
<atom id="a67" x3="6.08015868" y3="2.65846532" z3="-3.85406309" elementType="C" />
<atom id="a68" x3="5.3670216" y3="5.07741168" z3="-2.81840065" elementType="C" />
<atom id="a69" x3="2.98831813" y3="6.14564835" z3="-3.64938938" elementType="C" />
<atom id="a70" x3="1.48860064" y3="7.39486984" z3="-1.78055883" elementType="C" />
<atom id="a71" x3="-1.21907174" y3="7.41409962" z3="-1.92137065" elementType="C" />
<atom id="a72" x3="-2.18836818" y3="7.41757235" z3="0.61812127" elementType="C" />
<atom id="a73" x3="-4.48300482" y3="6.14614658" z3="1.24576191" elementType="C" />
<atom id="a74" x3="-4.66174699" y3="5.00574728" z3="3.6711744" elementType="C" />
<atom id="a75" x3="-6.0731184" y3="2.6840596" z3="4.01123906" elementType="C" />
<atom id="a76" x3="-4.82236915" y3="1.26209301" z3="5.9763154" elementType="C" />
<atom id="a77" x3="-4.77323702" y3="-1.43206109" z3="5.91987268" elementType="C" />
<atom id="a78" x3="-2.5886064" y3="-2.67232259" z3="6.88952988" elementType="C" />
<atom id="a79" x3="-1.70570245" y3="-4.98120195" z3="5.76488552" elementType="C" />
<atom id="a80" x3="1.01741866" y3="-5.00181406" z3="5.90246289" elementType="C" />
<atom id="a81" x3="2.51231412" y3="-6.16356675" z3="3.9854045" elementType="C" />
<atom id="a82" x3="4.85939953" y3="-4.97984086" z3="3.3758644" elementType="C" />
<atom id="a83" x3="5.84155625" y3="-5.00730695" z3="0.82534781" elementType="C" />
<atom id="a84" x3="-0.42107636" y3="-1.24820715" z3="7.69035721" elementType="C" />
</atomArray>
<formula formalCharge="0" concise="C 80 N 1 Sc 3">
<atomArray elementType="C N Sc" count="80.0 1.0 3.0" />
</formula>
<property dictRef="cml:molmass">
<scalar dataType="xsd:double" units="unit:dalton">1109.73043</scalar>
</property>
</molecule>
<list cmlx:templateRef="centnuclmass">
<scalar dataType="xsd:double" dictRef="cc:x3">0.0</scalar>
<scalar dataType="xsd:double" dictRef="cc:y3">0.0</scalar>
<scalar dataType="xsd:double" dictRef="cc:z3">0.0</scalar>
</list>
<list cmlx:templateRef="centnuclcharge">
<scalar dataType="xsd:double" dictRef="cc:x3">-1.567E-4</scalar>
<scalar dataType="xsd:double" dictRef="cc:y3">-2.13E-5</scalar>
<scalar dataType="xsd:double" dictRef="cc:z3">0.00115983</scalar>
</list>
</module>
</comment>
Output text
<comment class="example.output" id="geometry.cycle2">
<module cmlx:lineCount="16" cmlx:templateRef="atomcoord">
<module cmlx:templateRef="atomcoord">
<molecule id="atomcoord">
<atomArray>
<atom elementType="C" id="a1" x3="-1.79267786" y3="1.79292956" z3="0.21711881" />
<atom elementType="C" id="a2" x3="-4.6420301" y3="1.72468295" z3="0.02453055" />
<atom elementType="O" id="a3" x3="-0.72232011" y3="-0.24797201" z3="-0.93360778" />
<atom elementType="O" id="a4" x3="-0.54455624" y3="3.43404491" z3="1.23097559" />
<atom elementType="H" id="a5" x3="-5.21620927" y3="1.96641451" z3="-1.97654605" />
<atom elementType="H" id="a6" x3="-5.37835338" y3="-0.13077601" z3="0.65353692" />
<atom elementType="H" id="a7" x3="-5.45824156" y3="3.26101743" z3="1.17396391" />
<atom elementType="H" id="a8" x3="1.10943076" y3="-0.01816375" z3="-0.731545" />
</atomArray>
<formula concise="C 2 H 4 O 2">
<atomArray count="2 4 2" elementType="C H O" />
</formula>
<property dictRef="cml:molmass">
<scalar units="unit:dalton">56.0202</scalar>
</property>
</molecule>
<list cmlx:templateRef="centnuclmass">
<scalar dataType="xsd:double" dictRef="cc:x3">-1.87534367</scalar>
<scalar dataType="xsd:double" dictRef="cc:y3">1.63763387</scalar>
<scalar dataType="xsd:double" dictRef="cc:z3">0.11277683</scalar>
</list>
<list cmlx:templateRef="centnuclcharge">
<scalar dataType="xsd:double" dictRef="cc:x3">-1.99020725</scalar>
<scalar dataType="xsd:double" dictRef="cc:y3">1.61477345</scalar>
<scalar dataType="xsd:double" dictRef="cc:z3">0.09213276</scalar>
</list>
</module>
</module>
</comment>
Template definition
<templateList> <template id="withshells" pattern="\s*atomic\s*coordinates\s*atom\s*shells\s*charge\s*pseudo\s*isotop.*" endPattern="~"> <record repeat="1" /> <record id="atom" makeArray="true" repeat="*">{F,cc:x3}{F,cc:y3}{F,cc:z3}{A,cc:atomLabel}{I,t:shells}{F,cc:elementType}{I,t:pseudo}{I,t:isotop}</record> <record repeat="2" /> <record id="centnuclmass">\s*center of nuclear mass\s*:\s*{F,cc:x3}{F,cc:y3}{F,cc:z3}</record> <record /> <record id="centnuclcharge">\s*center of nuclear charge:\s*{F,cc:x3}{F,cc:y3}{F,cc:z3}</record> <transform process="operateArray" xpath=".//cml:array[@dictRef='cc:x3']" args="operator=multiply operand=0.529177" /> <transform process="operateArray" xpath=".//cml:array[@dictRef='cc:y3']" args="operator=multiply operand=0.529177" /> <transform process="operateArray" xpath=".//cml:array[@dictRef='cc:z3']" args="operator=multiply operand=0.529177" /> <transform process="createMolecule" xpath=".//cml:list[@cmlx:templateRef='atom']/cml:array" id="atomcoord" /> <transform process="pullup" xpath=".//cml:list/cml:list/cml:scalar" /> <transform process="pullup" xpath=".//cml:molecule" /> <transform process="delete" xpath=".//cml:atom/cml:scalar" /> <transform process="delete" xpath=".//cml:list[count(*)=0]" /> <transform process="delete" xpath=".//cml:list[count(*)=0]" />
</template> <template id="noshells" pattern="\s*atomic\s*coordinates\s*atom\s*charge\s*isotop.*" endPattern="~"> <record repeat="1" /> <record id="atom" makeArray="true" repeat="*">{F,cc:x3}{F,cc:y3}{F,cc:z3}{A,cc:atomLabel}{F,cc:elementType}{I,t:isotop}</record> <record repeat="1" /> <record id="centnuclmass">\s*center of nuclear mass\s*:\s*{F,cc:x3}{F,cc:y3}{F,cc:z3}</record> <record id="centnuclcharge">\s*center of nuclear charge:\s*{F,cc:x3}{F,cc:y3}{F,cc:z3}</record> <transform process="operateArray" xpath=".//cml:array[@dictRef='cc:x3']" args="operator=multiply operand=0.529177" /> <transform process="operateArray" xpath=".//cml:array[@dictRef='cc:y3']" args="operator=multiply operand=0.529177" /> <transform process="operateArray" xpath=".//cml:array[@dictRef='cc:z3']" args="operator=multiply operand=0.529177" /> <transform process="createMolecule" xpath=".//cml:list[@cmlx:templateRef='atom']/cml:array" id="atomcoord" /> <transform process="pullup" xpath=".//cml:list/cml:list/cml:scalar" /> <transform process="pullup" xpath=".//cml:molecule" /> <transform process="delete" xpath=".//cml:atom/cml:scalar" /> <transform process="delete" xpath=".//cml:list[count(*)=0]" /> <transform process="delete" xpath=".//cml:list[count(*)=0]" />
</template>
</templateList>
<transform process="pullup" xpath=".//cml:molecule" />
<transform process="pullup" xpath=".//cml:module/cml:list" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />