coordinates ​
Implementation level ​
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
Template attributes ​
| Attribute | Value |
|---|---|
| source | MOLCAS log |
| id | coordinates |
| name | Cartesian coordinates |
| pattern | \s+\*{20,}\s*$\s+\*\*\*\*\s+Cartesian\sCoordinates\s\/\sBohr,\sAngstrom.* |
| pattern2 | \s*Cartesian\scoordinates\sin\sAngstrom:\s* |
| endPattern | .*[0-9]\s*$\s* |
| endPattern2 | .*[0-9]\s*$\s*-{20,}\s* |
| endOffset | 1 |
| repeat | * |
| xml:base | modules/coordinates.xml |
Input ​
************************************************
**** Cartesian Coordinates / Bohr, Angstrom ****
************************************************
Center Label x y z x y z
1 N1 -0.000329 0.000000 -8.480849 -0.000174 0.000000 -4.487872
2 C2 0.000056 0.000000 1.868456 0.000030 0.000000 0.988744
3 C3 0.000079 2.304225 0.461974 0.000042 1.219344 0.244466
4 C4 0.000093 2.296046 -2.173609 0.000049 1.215015 -1.150224
5 C5 0.000078 -2.304225 0.461974 0.000041 -1.219344 0.244466
6 C6 0.000095 -2.296046 -2.173609 0.000050 -1.215015 -1.150224
7 C7 0.000061 0.000000 -3.552689 0.000032 0.000000 -1.880002
8 C8 -0.000120 0.000000 -6.258363 -0.000064 0.000000 -3.311783
9 H9 0.000105 4.105435 -3.202743 0.000056 2.172503 -1.694818
10 H10 0.000042 4.135857 1.440732 0.000022 2.188601 0.762403
11 H11 0.000115 -4.105435 -3.202743 0.000061 -2.172503 -1.694818
12 H12 0.000032 -4.135857 1.440732 0.000017 -2.188601 0.762403
13 N13 0.000007 0.000000 4.892017 0.000004 0.000000 2.588744
14 C14 1.309504 -2.268145 5.818004 0.692960 -1.200251 3.078755
15 H15 1.669031 -2.077449 7.798631 0.883213 -1.099338 4.126858
16 H16 0.150759 -3.893763 5.496772 0.079778 -2.060490 2.908767
17 H17 3.061892 -2.484185 4.832624 1.620284 -1.314574 2.557314
18 C18 1.309506 2.268143 5.818004 0.692961 1.200250 3.078755
19 H19 0.179321 3.901209 5.438146 0.094893 2.064431 2.877743
20 H20 1.611150 2.105902 7.810791 0.852584 1.114395 4.133292
21 H21 3.091220 2.448281 4.879091 1.635803 1.295574 2.581904
Input ​
Cartesian coordinates in Angstrom:
-----------------------------------------------------
No. Label X Y Z
-----------------------------------------------------
1 N1 -0.00017425 0.00000000 -4.48787180
2 C2 0.00002955 0.00000000 0.98874410
3 C3 0.00004205 1.21934360 0.24446610
4 C4 0.00004915 1.21501530 -1.15022430
5 C5 0.00004115 -1.21934360 0.24446610
6 C6 0.00005015 -1.21501530 -1.15022430
7 C7 0.00003235 0.00000000 -1.88000200
8 C8 -0.00006365 0.00000000 -3.31178300
9 H9 0.00005565 2.17250290 -1.69481840
10 H10 0.00002205 2.18860110 0.76240260
11 H11 0.00006095 -2.17250290 -1.69481840
12 H12 0.00001705 -2.18860110 0.76240260
13 N13 0.00000365 0.00000000 2.58874410
14 C14 0.69295969 -1.20025054 3.07875488
15 H15 0.88321339 -1.09933846 4.12685806
16 H16 0.07977834 -2.06049040 2.90876657
17 H17 1.62028373 -1.31457415 2.55731434
18 C18 0.69296088 1.20024985 3.07875488
19 H19 0.09489284 2.06443086 2.87774294
20 H20 0.85258368 1.11439520 4.13329248
21 H21 1.63580339 1.29557437 2.58190356
-----------------------------------------------------
Output text ​
xml
<comment class="example.output" id="coordinates">
<module cmlx:templateRef="coordinates">
<list id="coordinates">
<scalar dataType="xsd:string" dictRef="x:label">N1</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C2</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C3</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C4</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C5</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C6</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C7</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C8</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H9</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H10</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H11</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H12</scalar>
<scalar dataType="xsd:string" dictRef="x:label">N13</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C14</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H15</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H16</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H17</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C18</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H19</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H20</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H21</scalar>
<array dataType="xsd:double" dictRef="cc:x3" size="21">-0.000174 0.000030 0.000042 0.000049 0.000041 0.000050 0.000032 -0.000064 0.000056 0.000022 0.000061 0.000017 0.000004 0.692960 0.883213 0.079778 1.620284 0.692961 0.094893 0.852584 1.635803</array>
<array dataType="xsd:double" dictRef="cc:y3" size="21">0.000000 0.000000 1.219344 1.215015 -1.219344 -1.215015 0.000000 0.000000 2.172503 2.188601 -2.172503 -2.188601 0.000000 -1.200251 -1.099338 -2.060490 -1.314574 1.200250 2.064431 1.114395 1.295574</array>
<array dataType="xsd:double" dictRef="cc:z3" size="21">-4.487872 0.988744 0.244466 -1.150224 0.244466 -1.150224 -1.880002 -3.311783 -1.694818 0.762403 -1.694818 0.762403 2.588744 3.078755 4.126858 2.908767 2.557314 3.078755 2.877743 4.133292 2.581904</array>
</list>
</module>
</comment>Output text ​
xml
<comment class="example.output" id="coordinates2">
<module cmlx:templateRef="coordinates">
<list id="coordinates">
<scalar dataType="xsd:string" dictRef="x:label">N1</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C2</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C3</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C4</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C5</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C6</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C7</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C8</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H9</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H10</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H11</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H12</scalar>
<scalar dataType="xsd:string" dictRef="x:label">N13</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C14</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H15</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H16</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H17</scalar>
<scalar dataType="xsd:string" dictRef="x:label">C18</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H19</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H20</scalar>
<scalar dataType="xsd:string" dictRef="x:label">H21</scalar>
<array dataType="xsd:double" dictRef="cc:x3" size="21">-0.00017425 0.00002955 0.00004205 0.00004915 0.00004115 0.00005015 0.00003235 -0.00006365 0.00005565 0.00002205 0.00006095 0.00001705 0.00000365 0.69295969 0.88321339 0.07977834 1.62028373 0.69296088 0.09489284 0.85258368 1.63580339</array>
<array dataType="xsd:double" dictRef="cc:y3" size="21">0.00000000 0.00000000 1.21934360 1.21501530 -1.21934360 -1.21501530 0.00000000 0.00000000 2.17250290 2.18860110 -2.17250290 -2.18860110 0.00000000 -1.20025054 -1.09933846 -2.06049040 -1.31457415 1.20024985 2.06443086 1.11439520 1.29557437</array>
<array dataType="xsd:double" dictRef="cc:z3" size="21">-4.48787180 0.98874410 0.24446610 -1.15022430 0.24446610 -1.15022430 -1.88000200 -3.31178300 -1.69481840 0.76240260 -1.69481840 0.76240260 2.58874410 3.07875488 4.12685806 2.90876657 2.55731434 3.07875488 2.87774294 4.13329248 2.58190356</array>
</list>
</module>
</comment>Template definition ​
xml
<templateList> <template pattern="\s+\*{20,}\s*$\s+\*\*\*\*\s+Cartesian\sCoordinates\s\/\sBohr,\sAngstrom.*" endPattern="~"> <record repeat="5" /> <record repeat="*">{A,cc:serial}{A,x:label}\s+\S+\s+\S+\s+\S+\s+{F,cc:x3}{F,cc:y3}{F,cc:z3}</record>
</template> <template pattern="\s*Cartesian\scoordinates\sin\sAngstrom:\s*" endPattern="~"> <record repeat="4" /> <record repeat="*">{I,cc:serial}{A,x:label}{F,cc:x3}{F,cc:y3}{F,cc:z3}</record>
</template>
</templateList>
<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:x3']" />
<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:y3']" />
<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:z3']" />
<transform process="delete" xpath=".//cml:scalar[@dictRef='cc:serial']" />
<transform process="addChild" xpath="." elementName="cml:list" id="coordinates" />
<transform process="move" xpath=".//cml:scalar" to=".//cml:list[@id='coordinates']" />
<transform process="move" xpath=".//cml:array" to=".//cml:list[@id='coordinates']" />
<transform process="delete" xpath=".//cml:list[count(*) = 0]" />
<transform process="delete" xpath=".//cml:list[count(*) = 0]" />
<transform process="delete" xpath=".//cml:module[count(*) = 0]" />