Gecko [ www.utparral.edu.mx ]

Name	Size	Permission
1hca.pdb	174.18 KB	-rw-r--r--
his.pdb	1.02 KB	-rw-r--r--
his.xyz	513 B	-rw-r--r--
lys.pdb	648 B	-rw-r--r--
lys.xyz	418 B	-rw-r--r--
pdb2xyz.php	550 B	-rw-r--r--
Science_Chemistry_PDBFileTest.php	123.46 KB	-rw-r--r--
Science_ChemistryTest.php	6.26 KB	-rw-r--r--
small.pdb	61.46 KB	-rw-r--r--
water.cml	2.23 KB	-rw-r--r--
xyz2cml.php	3.08 KB	-rw-r--r--

Code Editor : Science_Chemistry_PDBFileTest.php

<?php
require_once "PHPUnit/Framework/TestCase.php";
require_once "Science/Chemistry/PDBFile.php";

class Science_Chemistry_PDBFileTest extends PHPUnit_Framework_TestCase {

public function test() {
        $file = new Science_Chemistry_PDBFile(dirname(__FILE__) . "/small.pdb");
        //$file = new Science_Chemistry_PDBFile("1hca.pdb");

ob_start();
        for ($j=0; $j < $file->num_macromolecules; $j++) {
	        $mol =& $file->macromolecules[$j];
    	    echo $mol->toCML("model", ($j + 1));
        }
        $result = ob_get_clean();

ob_start();
?>
<molecule title="model" id="1">
<list title="molecules">
 <molecule title="TRP" id="1">
  <string title="name">TRP</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">8.5330 -0.7480 10.8820</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">7.6610 -1.6750 11.6200</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">6.7920 -2.5000 10.6650</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">6.5450 -2.1380 9.5060</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">6.8140 -0.9310 12.6200</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">5.7170 -0.0530 12.1650</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">CD1</string>
    <coordinate3 builtin="xyz3">5.7830 1.2690 11.8130</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">4.3280 -0.4210 12.0540</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">NE1</string>
    <coordinate3 builtin="xyz3">4.5360 1.7430 11.4810</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">CE2</string>
    <coordinate3 builtin="xyz3">3.6270 0.7250 11.6160</coordinate3>
   </atom>
   <atom title="atom" id="11">
    <string title="name">CE3</string>
    <coordinate3 builtin="xyz3">3.6340 -1.6010 12.2870</coordinate3>
   </atom>
   <atom title="atom" id="12">
    <string title="name">CZ2</string>
    <coordinate3 builtin="xyz3">2.2600 0.7160 11.4150</coordinate3>
   </atom>
   <atom title="atom" id="13">
    <string title="name">CZ3</string>
    <coordinate3 builtin="xyz3">2.2750 -1.6190 12.0690</coordinate3>
   </atom>
   <atom title="atom" id="14">
    <string title="name">CH2</string>
    <coordinate3 builtin="xyz3">1.5880 -0.4820 11.6460</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="GLY" id="2">
  <string title="name">GLY</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">6.3390 -3.5990 11.2240</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">5.4780 -4.5660 10.5170</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">5.1210 -5.6460 11.5470</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">5.1390 -5.3410 12.7470</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="TYR" id="3">
  <string title="name">TYR</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">4.8570 -6.8240 11.0400</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">4.4720 -7.9780 11.8470</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">5.3130 -9.1920 11.4790</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">5.0030 -10.3160 11.8730</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">2.9650 -8.2950 11.6580</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">2.0900 -7.1220 12.0340</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">CD1</string>
    <coordinate3 builtin="xyz3">1.6570 -6.9940 13.3560</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">1.7160 -6.1390 11.1130</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">CE1</string>
    <coordinate3 builtin="xyz3">0.8560 -5.9310 13.7480</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">CE2</string>
    <coordinate3 builtin="xyz3">0.9330 -5.0580 11.4960</coordinate3>
   </atom>
   <atom title="atom" id="11">
    <string title="name">CZ</string>
    <coordinate3 builtin="xyz3">0.4960 -4.9620 12.8230</coordinate3>
   </atom>
   <atom title="atom" id="12">
    <string title="name">OH</string>
    <coordinate3 builtin="xyz3">-0.2890 -3.9360 13.2630</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="GLY" id="4">
  <string title="name">GLY</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">6.3490 -8.9070 10.7260</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">7.3120 -9.9020 10.2420</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">8.3160 -10.2150 11.3480</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">8.2990 -9.6010 12.4280</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="LYS" id="5">
  <string title="name">LYS</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">9.1750 -11.1570 11.0440</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">10.2020 -11.6530 11.9550</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">11.1880 -10.6400 12.4740</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">11.5620 -10.7470 13.6630</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">10.9750 -12.7980 11.2490</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">11.9300 -13.5300 12.2100</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">CD</string>
    <coordinate3 builtin="xyz3">11.1470 -14.0260 13.4150</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CE</string>
    <coordinate3 builtin="xyz3">11.9850 -14.8510 14.3760</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">NZ</string>
    <coordinate3 builtin="xyz3">11.1060 -15.3590 15.4740</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="HIS" id="6">
  <string title="name">HIS</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">11.6200 -9.7070 11.6430</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">12.6170 -8.7040 12.0260</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">12.1040 -7.3050 12.2730</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">12.9290 -6.4050 12.5540</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">13.7340 -8.5610 10.9240</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">14.5460 -9.8200 10.8390</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">ND1</string>
    <coordinate3 builtin="xyz3">14.2870 -10.8480 9.9840</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">15.6250 -10.1840 11.5690</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">CE1</string>
    <coordinate3 builtin="xyz3">15.1760 -11.8080 10.1800</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">NE2</string>
    <coordinate3 builtin="xyz3">16.0140 -11.4260 11.1350</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="ASN" id="7">
  <string title="name">ASN</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">10.8120 -7.1240 12.1510</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">10.1840 -5.8070 12.3290</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">8.8950 -5.9450 13.1330</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">8.1700 -4.9510 13.3110</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">10.0010 -5.1360 10.9700</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">9.1570 -5.8760 9.9790</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">OD1</string>
    <coordinate3 builtin="xyz3">8.7930 -7.0530 10.1230</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">ND2</string>
    <coordinate3 builtin="xyz3">8.8170 -5.1700 8.8970</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="GLY" id="8">
  <string title="name">GLY</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">8.6660 -7.1560 13.5870</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">7.5040 -7.5030 14.3930</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">7.3750 -6.6530 15.6570</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">8.2700 -5.8720 16.0060</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="PRO" id="9">
  <string title="name">PRO</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">6.2430 -6.8380 16.3260</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">5.9270 -6.1210 17.5590</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">7.0210 -6.1330 18.6110</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">7.1110 -5.2030 19.4540</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">4.6420 -6.7820 18.0680</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">3.9990 -7.3930 16.8400</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">CD</string>
    <coordinate3 builtin="xyz3">5.1550 -7.7610 15.9290</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="GLU" id="10">
  <string title="name">GLU</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">7.8390 -7.1620 18.5910</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">8.9380 -7.3270 19.5590</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">10.0770 -6.3540 19.3220</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">10.9770 -6.2480 20.1790</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">9.4770 -8.7430 19.5670</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">10.0170 -9.4110 18.3400</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">CD</string>
    <coordinate3 builtin="xyz3">9.1470 -10.0270 17.2980</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">OE1</string>
    <coordinate3 builtin="xyz3">7.9290 -10.1590 17.5700</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">OE2</string>
    <coordinate3 builtin="xyz3">9.6310 -10.4110 16.2220</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="HIS" id="11">
  <string title="name">HIS</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">10.0560 -5.6370 18.2240</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">11.0760 -4.6660 17.8480</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">10.5470 -3.2360 17.9010</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">11.3680 -2.2960 17.7840</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">11.6180 -4.8710 16.4120</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">12.4870 -6.0590 16.1770</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">ND1</string>
    <coordinate3 builtin="xyz3">13.8610 -6.0070 16.0740</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">12.1620 -7.3700 16.0310</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">CE1</string>
    <coordinate3 builtin="xyz3">14.3330 -7.2240 15.8780</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">NE2</string>
    <coordinate3 builtin="xyz3">13.3320 -8.0660 15.8490</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="TRP" id="12">
  <string title="name">TRP</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">9.2440 -3.0790 18.0400</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">8.6740 -1.7090 18.0220</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">9.2930 -0.7830 19.0570</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">9.3680 0.4290 18.7680</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">7.1480 -1.6930 18.0670</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">6.4900 -2.4340 16.9490</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">CD1</string>
    <coordinate3 builtin="xyz3">7.0660 -2.8980 15.8010</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">5.0860 -2.7250 16.8370</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">NE1</string>
    <coordinate3 builtin="xyz3">6.1250 -3.5120 15.0170</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">CE2</string>
    <coordinate3 builtin="xyz3">4.9030 -3.4100 15.6170</coordinate3>
   </atom>
   <atom title="atom" id="11">
    <string title="name">CE3</string>
    <coordinate3 builtin="xyz3">3.9900 -2.4850 17.6610</coordinate3>
   </atom>
   <atom title="atom" id="12">
    <string title="name">CZ2</string>
    <coordinate3 builtin="xyz3">3.6560 -3.8570 15.1950</coordinate3>
   </atom>
   <atom title="atom" id="13">
    <string title="name">CZ3</string>
    <coordinate3 builtin="xyz3">2.7510 -2.9350 17.2490</coordinate3>
   </atom>
   <atom title="atom" id="14">
    <string title="name">CH2</string>
    <coordinate3 builtin="xyz3">2.5850 -3.6010 16.0440</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="HIS" id="13">
  <string title="name">HIS</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">9.7190 -1.3060 20.1810</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">10.3100 -0.5070 21.2570</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">11.4690 0.3820 20.8260</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">11.6090 1.4680 21.4350</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">10.7600 -1.3620 22.4620</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">11.9300 -2.2680 22.3060</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">ND1</string>
    <coordinate3 builtin="xyz3">13.1940 -1.9830 22.7790</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">12.0270 -3.4990 21.7360</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">CE1</string>
    <coordinate3 builtin="xyz3">13.9980 -3.0030 22.5030</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">NE2</string>
    <coordinate3 builtin="xyz3">13.3200 -3.9300 21.8690</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="LYS" id="14">
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 </molecule>
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  <string title="name">ASP</string>
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 </molecule>
 <molecule title="PHE" id="16">
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 </molecule>
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 </molecule>
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    <string title="name">CG1</string>
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 </molecule>
 <molecule title="ALA" id="19">
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 </molecule>
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 </molecule>
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 </molecule>
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 </molecule>
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 </molecule>
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 </molecule>
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 </molecule>
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 </molecule>
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 </molecule>
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 </molecule>
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 </molecule>
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    <coordinate3 builtin="xyz3">-15.0560 -1.2820 8.2810</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">CE2</string>
    <coordinate3 builtin="xyz3">-16.6810 0.4750 8.6460</coordinate3>
   </atom>
   <atom title="atom" id="11">
    <string title="name">CZ</string>
    <coordinate3 builtin="xyz3">-16.2340 -0.6630 7.9230</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="HIS" id="90">
  <string title="name">HIS</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">-11.0920 -0.4650 11.0180</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">-10.1300 -1.4090 10.4160</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">-10.2510 -2.7290 11.1620</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">-11.0020 -2.8370 12.1340</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">-8.6520 -0.9770 10.3960</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">-8.2510 -0.3270 11.6760</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">ND1</string>
    <coordinate3 builtin="xyz3">-8.4140 1.0250 11.9400</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">-7.6840 -0.8730 12.7790</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">CE1</string>
    <coordinate3 builtin="xyz3">-7.9680 1.2780 13.1530</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">NE2</string>
    <coordinate3 builtin="xyz3">-7.5190 0.1680 13.6870</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="PHE" id="91">
  <string title="name">PHE</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">-9.4790 -3.6980 10.7030</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">-9.5050 -5.0340 11.3280</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">-8.0680 -5.4930 11.5360</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">-7.1160 -4.9120 10.9960</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">-10.3150 -5.9910 10.4800</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">-11.7510 -5.7390 10.1640</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">CD1</string>
    <coordinate3 builtin="xyz3">-12.1210 -4.9080 9.0990</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">-12.7570 -6.3390 10.9210</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">CE1</string>
    <coordinate3 builtin="xyz3">-13.4500 -4.6760 8.7890</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">CE2</string>
    <coordinate3 builtin="xyz3">-14.1110 -6.1320 10.6200</coordinate3>
   </atom>
   <atom title="atom" id="11">
    <string title="name">CZ</string>
    <coordinate3 builtin="xyz3">-14.4480 -5.2940 9.5370</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="HIS" id="92">
  <string title="name">HIS</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">-7.9740 -6.5310 12.3300</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">-6.8210 -7.2970 12.7310</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">-7.3200 -8.7480 12.5790</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">-8.3300 -9.0370 13.2410</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">-6.2840 -7.1700 14.1790</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">-5.9210 -5.7340 14.3970</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">ND1</string>
    <coordinate3 builtin="xyz3">-4.6780 -5.2150 14.1450</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">-6.6910 -4.7090 14.8130</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">CE1</string>
    <coordinate3 builtin="xyz3">-4.7050 -3.9190 14.4050</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">NE2</string>
    <coordinate3 builtin="xyz3">-5.9070 -3.6030 14.8110</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="TRP" id="93">
  <string title="name">TRP</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">-6.6580 -9.4940 11.7510</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">-7.1170 -10.9030 11.5250</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">-5.9200 -11.8090 11.5990</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">-4.7850 -11.2890 11.6070</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">-7.9080 -10.9340 10.2090</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">CG</string>
    <coordinate3 builtin="xyz3">-7.2150 -10.4030 9.0130</coordinate3>
   </atom>
   <atom title="atom" id="7">
    <string title="name">CD1</string>
    <coordinate3 builtin="xyz3">-6.4650 -11.1170 8.1010</coordinate3>
   </atom>
   <atom title="atom" id="8">
    <string title="name">CD2</string>
    <coordinate3 builtin="xyz3">-7.1640 -9.0430 8.5700</coordinate3>
   </atom>
   <atom title="atom" id="9">
    <string title="name">NE1</string>
    <coordinate3 builtin="xyz3">-5.9580 -10.2660 7.1330</coordinate3>
   </atom>
   <atom title="atom" id="10">
    <string title="name">CE2</string>
    <coordinate3 builtin="xyz3">-6.3730 -9.0020 7.4000</coordinate3>
   </atom>
   <atom title="atom" id="11">
    <string title="name">CE3</string>
    <coordinate3 builtin="xyz3">-7.7360 -7.8600 9.0510</coordinate3>
   </atom>
   <atom title="atom" id="12">
    <string title="name">CZ2</string>
    <coordinate3 builtin="xyz3">-6.1520 -7.8250 6.7080</coordinate3>
   </atom>
   <atom title="atom" id="13">
    <string title="name">CZ3</string>
    <coordinate3 builtin="xyz3">-7.4920 -6.6900 8.3540</coordinate3>
   </atom>
   <atom title="atom" id="14">
    <string title="name">CH2</string>
    <coordinate3 builtin="xyz3">-6.7190 -6.6640 7.2150</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="GLY" id="94">
  <string title="name">GLY</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">-6.1280 -13.0980 11.6530</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">-5.0500 -14.0970 11.7300</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">-4.8750 -14.8860 10.4440</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">-5.6500 -14.7020 9.4970</coordinate3>
   </atom>
  </list>
 </molecule>
 <molecule title="SER" id="95">
  <string title="name">SER</string>
  <list title="atoms">
   <atom title="atom" id="1">
    <string title="name">N</string>
    <coordinate3 builtin="xyz3">-3.8820 -15.7530 10.4210</coordinate3>
   </atom>
   <atom title="atom" id="2">
    <string title="name">CA</string>
    <coordinate3 builtin="xyz3">-3.6020 -16.5980 9.2540</coordinate3>
   </atom>
   <atom title="atom" id="3">
    <string title="name">C</string>
    <coordinate3 builtin="xyz3">-4.5600 -17.7880 9.3050</coordinate3>
   </atom>
   <atom title="atom" id="4">
    <string title="name">O</string>
    <coordinate3 builtin="xyz3">-4.9460 -18.2990 8.2480</coordinate3>
   </atom>
   <atom title="atom" id="5">
    <string title="name">CB</string>
    <coordinate3 builtin="xyz3">-2.1780 -17.0670 9.1450</coordinate3>
   </atom>
   <atom title="atom" id="6">
    <string title="name">OG</string>
    <coordinate3 builtin="xyz3">-1.6470 -17.4660 10.3720</coordinate3>
   </atom>
  </list>
 </molecule>
</list>
</molecule>
<?php
        $expected = ob_get_clean();

$this->assertSame($expected, $result);

$this->markTestIncomplete("We should probably make a less fragile test here");
    }

}

${this.title}

Code Editor : Science_Chemistry_PDBFileTest.php