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/wwwfiles/admin/editdata.php

https://github.com/annulen/MolDB
PHP | 2749 lines | 2429 code | 191 blank | 129 comment | 442 complexity | ca2d3d8ecb2b91b928e09ce230c18800 MD5 | raw file
    

  1. <?php
    2. 

  2. // admin/editdata.php    Norbert Haider, University of Vienna, 2009-2010
    3. 

  3. // part of MolDB5R       last change: 2010-06-14
    4. 

  4. 

  5. $myname = $_SERVER['PHP_SELF'];
    6. 

  6. @include("moldb5conf.php");    // if moldb5conf.php is in the PHP include path
    7. 

  7. @include("../moldb5conf.php"); // if moldb5conf.php is where it should *not* be...
    8. 

  8. require_once("../functions.php");
    9. 

  9. require_once("../rxnfunct.php");
    10. 

  10. require_once("dbfunct.php");
    11. 

  11. 

  12. $debug = 1;        // 0: remain silent, higher values: be more verbose
    13. 

  13.                    // odd numbers: output as HTML comments, 
    14. 

  14.                    // even numbers: output as clear-text messages
    15. 

  15. 

  16. if (config_quickcheck() > 0) { die(); }
    17. 

  17. 

  18. if (!isset($sitename) || ($sitename == "")) {
    19. 

  19.   $sitename = "MolDB5R demo";
    20. 

  20. }
    21. 

  21. 

  22. $db_id    = $_REQUEST['db'];
    23. 

  23. $datatype = $_REQUEST['datatype'];
    24. 

  24. $action   = $_REQUEST['action'];
    25. 

  25. $smiles   = $_POST['smiles'];
    26. 

  26. $jme      = $_POST['jme'];
    27. 

  27. $mol      = $_POST['mol'];
    28. 

  28. 

  29. $ostype = getostype();
    30. 

  30. 

  31. $link = mysql_pconnect($hostname,"$rw_user", "$rw_password")
    32. 

  32.   or die("Could not connect to database server!");
    33. 

  33. mysql_select_db($database)
    34. 

  34.   or die("Could not select database!");    
    35. 

  35. 

  36. $db_id = check_db($db_id);
    37. 

  37. if ($db_id < 0) {
    38. 

  38.   $db_id = $default_db;
    39. 

  39.   $db_id = check_db_all($db_id);
    40. 

  40.   if ($db_id < 0) {
    41. 

  41.     $db_id = get_lowestdbid();
    42. 

  42.   }
    43. 

  43. }
    44. 

  44. 

  45. $mydb = get_dbproperties($db_id);
    46. 

  46. $dbtype = $mydb['type'];
    47. 

  47. if (($dbtype == 1) && ($datatype != 1)) { $datatype = 1; }
    48. 

  48. if (($dbtype == 2) && ($datatype != 2)) { $datatype = 2; }
    49. 

  49. 

  50. $ip = $_SERVER['REMOTE_ADDR'];
    51. 

  51. $trusted = is_trustedIP($ip);
    52. 

  52. if ($trusted == false) {
    53. 

  53.   $trusted = is_db_trustedIP($db_id,$ip);   // try if IP is trusted for this db
    54. 

  54. }
    55. 

  55. 

  56. ?>
    57. 

  57. <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
    58. 

  58. <html>
    59. 

  59. <head>
    60. 

  60. <link href="../moldb.css" rel="stylesheet" type="text/css">
    61. 

  61. <meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
    62. 

  62. <meta name="author" content="Norbert Haider, University of Vienna">
    63. 

  63. <title><?php echo "$sitename (administration page)"; ?></title>
    64. 

  64. </head>
    65. 

  65. <body>
    66. 

  66. <?php
    67. 

  67. echo "<!-- MolDB5R, OS type $ostype --!>\n";
    68. 

  68. echo "<h1>$sitename: data input/editing</h1>\n";
    69. 

  69. echo "On this page, you can add new MolDB5R entries and erase or edit existing ones.<br />\n";
    70. 

  70. echo "<hr />\n";
    71. 

  71. echo "<small>selected data collection: $db_id</small><p />\n";
    72. 

  72. 

  73. $dbprefix      = $prefix . "db" . $db_id . "_";
    74. 

  74. $moldatatable  = $dbprefix . $moldatasuffix;
    75. 

  75. $molfgbtable   = $dbprefix . $molfgbsuffix;
    76. 

  76. $molstattable  = $dbprefix . $molstatsuffix;
    77. 

  77. $molstructable = $dbprefix . $molstrucsuffix;
    78. 

  78. $molcfptable   = $dbprefix . $molcfpsuffix;
    79. 

  79. $pic2dtable    = $dbprefix . $pic2dsuffix;
    80. 

  80. 

  81. $rxnstructable = $dbprefix . $rxnstrucsuffix;
    82. 

  82. $rxndatatable  = $dbprefix . $rxndatasuffix;
    83. 

  83. $rxnfgbtable   = $dbprefix . $rxnfgbsuffix;
    84. 

  84. $rxncfptable   = $dbprefix . $rxncfpsuffix;
    85. 

  85. 

  86. 

  87. $mydb = get_dbproperties($db_id);
    88. 

  88. $db     = $mydb['db_id'];
    89. 

  89. $access = $mydb['access'];
    90. 

  90. $usemem = $mydb['usemem'];
    91. 

  91. $dbtype = $mydb['type'];
    92. 

  92. 

  93. 

  94. if ($dbtype == 1) {
    95. 

  95.   $structable = $molstructable;
    96. 

  96.   $idname = "mol_id";
    97. 

  97.   $namename = "mol_name";
    98. 

  98. } elseif ($dbtype == 2) {
    99. 

  99.   $structable = $rxnstructable;
    100. 

  100.   $idname = "rxn_id";
    101. 

  101.   $namename = "rxn_name";
    102. 

  102. }
    103. 

  103. 

  104. if (($access < 2) && ($trusted == FALSE)) {
    105. 

  105.   echo "Your client IP is not authorized to perform the requested operation!<br />\n";
    106. 

  106.   //echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    107. 

  107.   echo "</body></html>\n";
    108. 

  108.   die();
    109. 

  109. }
    110. 

  110. 

  111. 

  112. if ($action == "addstruc1") {
    113. 

  113.   if ($dbtype == 1) { $what = "structure"; } elseif ($dbtype == 2) { $what = "reaction"; }
    114. 

  114.   echo "<h3>Add a new $what to data collection $db_id</h3>\n";
    115. 

  115. 

  116.   echo "<table>\n<tr>\n<td valign=\"top\">\n";
    117. 

  117. 

  118.   if ($dbtype == 1) {
    119. 

  119.     echo "<small>draw the molecule in the applet window....</small><br />\n";
    120. 

  120.     echo "<applet name=\"JME\" code=\"JME.class\" \n";
    121. 

  121.     echo "archive=\"../JME.jar\" width=\"350\" height=\"290\">\n";
    122. 

  122.     echo "<param name=\"jme\" value=\"$jme\">\n";
    123. 

  123.     //echo "<param name=\"options\" value=\"xbutton, query, hydrogens\">\n";
    124. 

  124.     echo "<param name=\"options\" value=\"xbutton, hydrogens, multipart\">\n";
    125. 

  125.     echo "You have to enable Java in your browser.\n";
    126. 

  126.     echo "</applet>\n";
    127. 

  127.   } elseif ($dbtype == 2) {
    128. 

  128.     
    129. 

  129.     echo "<small>draw the reaction in the applet window....</small><br />\n";
    130. 

  130.     echo "<applet name='JME' code='JME.class' \n";
    131. 

  131.     echo "archive='../JME.jar' width=450 height=288>\n";
    132. 

  132.     if (strlen($jme) > 0) {
    133. 

  133.       echo "<param name=\"jme\" value=\"$jme\">\n";
    134. 

  134.     }
    135. 

  135.     echo "<param name=\"options\" value=\"xbutton, hydrogens, reaction, multipart\">\n";
    136. 

  136.     echo "You have to enable Java in your browser.\n";
    137. 

  137.     echo "</applet>\n";
    138. 

  138.   }
    139. 

  139.   ?>
    140. 

  140.  
    141. 

  141. <script> 
    142. 

  142.   function check_ss() {
    143. 

  143.     var smiles = document.JME.smiles();
    144. 

  144.     var jme = document.JME.jmeFile(); 
    145. 

  145.     var mol = document.JME.molFile();
    146. 

  146.     if (smiles.length < 1) {
    147. 

  147.       alert("No molecule!");
    148. 

  148.     }
    149. 

  149.     else {
    150. 

  150.       document.form.smiles.value = smiles;
    151. 

  151.       document.form.jme.value = jme;
    152. 

  152.       document.form.mol.value = mol;
    153. 

  153.       document.form.submit();
    154. 

  154.     }
    155. 

  155.   }
    156. 

  156. </script>
    157. 

  157. 

  158. <p />
    159. 

  159. <form name="form" action="<?php echo $myname; ?>" method="post">
    160. 

  160. <input type="button" value="&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submit&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;" onClick="check_ss()">
    161. 

  161. <input type="hidden" name="smiles">
    162. 

  162. <input type="hidden" name="jme">
    163. 

  163. <input type="hidden" name="mol">
    164. 

  164. <input type="hidden" name="action" value="addstruc2">
    165. 

  165. <input type="hidden" name="db" value="<?php echo "$db_id";?>">
    166. 

  166. </form>
    167. 

  167. 

  168.   <?php
    169. 

  169.   
    170. 

  170.   echo "</td>\n<td valign=\"top\">\n";
    171. 

  171.   if ($dbtype == 1) {
    172. 

  172.     echo "<small>...or paste it in MDL (V2000) molfile format into the text window</small><br />\n";
    173. 

  173.   } elseif ($dbtype == 2) {
    174. 

  174.     echo "<small>...or paste it in MDL (V2000) rxnfile format into the text window</small><br />\n";
    175. 

  175.   }
    176. 

  176.   echo "<form name=\"form2\" action=\"$myname\" method=\"post\">\n";
    177. 

  177.   echo "<textarea name=\"mol\" cols=\"70\" rows=\"17\"></textarea>\n";
    178. 

  178.   echo "<input type=\"hidden\" name=\"action\" value=\"addstruc2\">\n";
    179. 

  179.   echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\"><p />\n";
    180. 

  180.   echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submit&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\">\n";
    181. 

  181.   echo "</form>\n";
    182. 

  182.   
    183. 

  183.   echo "</td></tr>\n</table>\n";
    184. 

  184.   
    185. 

  185.   echo "<p /><a href=\"$myname?db=$db_id\">Continue without saving</a>\n";
    186. 

  186.   echo "</body></html>\n";
    187. 

  187.   die();
    188. 

  188. }
    189. 

  189. 

  190. if ($action == "addstruc2") {
    191. 

  191.   if ($dbtype == 1) { 
    192. 

  192.     $what = "structure"; 
    193. 

  193.     $reserved_mol_id = get_next_mol_id($db_id);
    194. 

  194.   } elseif ($dbtype == 2) { 
    195. 

  195.     $what = "reaction"; 
    196. 

  196.     $reserved_mol_id = get_next_rxn_id($db_id);
    197. 

  197.   }
    198. 

  198.   // find out the next available mol_id
    199. 

  199.   // get next available mol_id 
    200. 

  200. 

  201. 

  202.   // check if we got a valid molfile (either from JME or from the text area)
    203. 

  203.   if (is_validmol($mol) == FALSE) {
    204. 

  204.     echo "<h3>ERROR: this is not a valid input MDL (V2000) molfile!</h3>\n";
    205. 

  205.     echo "<pre>$safemol </pre>\n";
    206. 

  206.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    207. 

  207.     echo "</body></html>\n";
    208. 

  208.     die();
    209. 

  209.   }
    210. 

  210.   // if in reaction mode, check if we have the rxn file header (if not, add it)
    211. 

  211.   if ($dbtype == 2) {
    212. 

  212.     if (strpos($mol, '$RXN') === FALSE) {
    213. 

  213.       $mol = "\$RXN\n\n\n\n  0  1\n\$MOL\n" . $mol;
    214. 

  214.     }
    215. 

  215.   }
    216. 

  216. 

  217.   echo "<h3>Do you really want to add this $what to data collection $db_id?</h3>\n";
    218. 

  218. 

  219.   // JME needs MDL molfiles with the "|" character instead of linebreaks
    220. 

  220.   $jmehitmol = strtr($mol,"\n","|");
    221. 

  221.       
    222. 

  222.   echo "<applet name=\"JME\" code=\"JME.class\" archive=\"../JME.jar\" \n";
    223. 

  223.   if ($dbtype == 1) {
    224. 

  224.     echo "width=\"250\" height=\"220\">";
    225. 

  225.   } elseif ($dbtype == 2) {
    226. 

  226.     echo "width=\"450\" height=\"220\">";
    227. 

  227.   }
    228. 

  228.   
    229. 

  229.   echo "<param name=\"options\" value=\"depict\"> \n";
    230. 

  230.   echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    231. 

  231.   echo "</applet>\n";
    232. 

  232. ?>
    233. 

  233. 

  234. <script> 
    235. 

  235.   function submit1_ss() {
    236. 

  236.     var smiles = document.JME.smiles();
    237. 

  237.     var jme = document.JME.jmeFile(); 
    238. 

  238.     var mol = document.JME.molFile();
    239. 

  239.     if (smiles.length < 1) {
    240. 

  240.       alert("No molecule!");
    241. 

  241.     }
    242. 

  242.     else {
    243. 

  243.       document.addstruc1.smiles.value = smiles;
    244. 

  244.       document.addstruc1.jme.value = jme;
    245. 

  245.       document.addstruc1.mol.value = mol;
    246. 

  246.       document.addstruc1.submit();
    247. 

  247.     }
    248. 

  248.   }
    249. 

  249. </script>
    250. 

  250. 

  251. <script> 
    252. 

  252.   function submit2_ss() {
    253. 

  253.     var smiles = document.JME.smiles();
    254. 

  254.     var jme = document.JME.jmeFile(); 
    255. 

  255.     var mol = document.JME.molFile();
    256. 

  256.     if (smiles.length < 1) {
    257. 

  257.       alert("No molecule!");
    258. 

  258.     }
    259. 

  259.     else {
    260. 

  260.       document.addstruc2.smiles.value = smiles;
    261. 

  261.       document.addstruc2.jme.value = jme;
    262. 

  262.       document.addstruc2.mol.value = mol;
    263. 

  263.       document.addstruc2.submit();
    264. 

  264.     }
    265. 

  265.   }
    266. 

  266. </script>
    267. 

  267. <?php
    268. 

  268. 

  269.   echo "<form name=\"addstruc1\" action=\"$myname\" method=\"post\">\n";
    270. 

  270.   echo "<input type=\"hidden\" name=\"action\" value=\"addstruc3\">\n";
    271. 

  271.   echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    272. 

  272.   echo "<input type=\"hidden\" name=\"nextid\" value=\"$reserved_mol_id\">\n";
    273. 

  273.   echo "<input type=\"hidden\" name=\"mol\" value=\"$mol\">\n";
    274. 

  274.   echo "<input type=\"hidden\" name=\"jme\" value=\"$jme\">\n";
    275. 

  275.   echo "<input type=\"hidden\" name=\"smiles\" value=\"$smiles\">\n";
    276. 

  276. //  echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;Yes, add new structure!\">\n";
    277. 

  277.   echo "<input type=\"button\" value=\"&nbsp;Yes, add new structure!\" onClick=\"submit1_ss()\">\n";
    278. 

  278. 

  279.   echo "</form><p />\n";
    280. 

  280. 

  281.   echo "<form name=\"addstruc2\" action=\"$myname\" method=\"post\">\n";
    282. 

  282.   echo "<input type=\"hidden\" name=\"action\" value=\"addstruc1\">\n";
    283. 

  283.   echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    284. 

  284.   echo "<input type=\"hidden\" name=\"mol\" value=\"$mol\">\n";
    285. 

  285.   echo "<input type=\"hidden\" name=\"jme\" value=\"$jme\">\n";
    286. 

  286.   echo "<input type=\"hidden\" name=\"smiles\" value=\"$smiles\">\n";
    287. 

  287. //  echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;No, edit again\">\n";
    288. 

  288.   echo "<input type=\"button\" value=\"&nbsp;No, edit again\" onClick=\"submit2_ss()\">\n";
    289. 

  289.   echo "</form><p />\n";
    290. 

  290. 

  291.   echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    292. 

  292.   echo "</body></html>\n";
    293. 

  293.   die();
    294. 

  294. }
    295. 

  295. 

  296. if (($action == "addstruc3") && ($dbtype == 1)) {    // structure input
    297. 

  297.   $errorcount = 0;
    298. 

  298.   $proposed_mol_id = $_POST['nextid'];
    299. 

  299.   if ($use_cmmmsrv == 'y') {
    300. 

  300.     /* create a TCP/IP socket */
    301. 

  301.     $socket = socket_create(AF_INET, SOCK_STREAM, SOL_TCP);
    302. 

  302.     if ($socket < 0) {
    303. 

  303.       //echo "socket_create() failed.\nreason: " . socket_strerror ($socket) . "\n";
    304. 

  304.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    305. 

  305.       $use_cmmmsrv = "n";
    306. 

  306.     }
    307. 

  307.     $sockresult = socket_connect ($socket, $cmmmsrv_addr, $cmmmsrv_port);
    308. 

  308.     if ($sockresult < 0) {
    309. 

  309.       //echo "socket_connect() failed.\nreason: ($sockresult) " . socket_strerror($sockresult) . "\n";
    310. 

  310.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    311. 

  311.       $use_cmmmsrv = "n";
    312. 

  312.     }
    313. 

  313.   }
    314. 

  314.   if ($use_cmmmsrv == 'y') {
    315. 

  315.     $a = socket_read($socket, 250, PHP_NORMAL_READ);
    316. 

  316.     //echo "$a\n";
    317. 

  317.     $pos = strpos($a,"READY");
    318. 

  318.     if ($pos === false) {
    319. 

  319.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    320. 

  320.       $use_cmmmsrv = "n";
    321. 

  321.     }
    322. 

  322.     $pos = 0;
    323. 

  323.   }
    324. 

  324. 

  325.   // remove CR if present (IE, Mozilla et al.) and add it again (for Opera)
    326. 

  326.   $mol = str_replace("\r\n","\n",$mol);
    327. 

  327.   $mol = str_replace("\n","\r\n",$mol);
    328. 

  328. 

  329.   //$safemol = escapeshellcmd($mol);
    330. 

  330.   $safemol = str_replace(";"," ",$mol);
    331. 

  331.   $safemol = str_replace("\""," ",$safemol);
    332. 

  332.   $safemol = str_replace("\'"," ",$safemol);
    333. 

  333.   $safemol = str_replace("\�"," ",$safemol);
    334. 

  334.   $safemol = str_replace("\`"," ",$safemol);
    335. 

  335.   $safemol = str_replace("\|"," ",$safemol);
    336. 

  336.   
    337. 

  337.   // first, tweak the molfile (if enabled in config file)
    338. 

  338.   if ($tweakmolfiles == "y") {
    339. 

  339.     if ($use_cmmmsrv == 'y') {
    340. 

  340.       $safemol = filterthroughcmmm($safemol,"#### checkmol:m");
    341. 

  341.     } else {
    342. 

  342.       if ($ostype == 1) {$safemol = filterthroughcmd($safemol,"$CHECKMOL -m - "); }
    343. 

  343.   	if ($ostype == 2) {$safemol = filterthroughcmd2($safemol,"$CHECKMOL -m - "); }
    344. 

  344.     }
    345. 

  345.   }
    346. 

  346.   // check if we (still) have a valid MDL molfile
    347. 

  347.   if (is_validmol($safemol) == FALSE) {
    348. 

  348.     echo "<h3>ERROR: this is not a valid input MDL (V2000) molfile!</h3>\n";
    349. 

  349.     echo "<pre>$safemol </pre>\n";
    350. 

  350.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    351. 

  351.     echo "</body></html>\n";
    352. 

  352.     die();
    353. 

  353.   }
    354. 

  354. 

  355.   // next step: get the molecular statistics of the input structure
    356. 

  356.   // by piping it through the checkmol program
    357. 

  357. 

  358.   //echo "adding this structure:\<br />\n<pre>$safemol</pre>\n";
    359. 

  359. 

  360.   // get next available mol_id 
    361. 

  361.   $result = mysql_query("SELECT COUNT(mol_id) AS molcount FROM $molstructable")
    362. 

  362.     or die("Query failed! (1c3)");
    363. 

  363.   $line = mysql_fetch_row($result);
    364. 

  364.   mysql_free_result($result);
    365. 

  365.   $molcount = $line[0];
    366. 

  366.   if ($molcount == 0) { 
    367. 

  367.     $next_mol_id = 1; 
    368. 

  368.   } else {
    369. 

  369.     $result = mysql_query("SELECT MAX(mol_id) AS molcount FROM $molstructable")
    370. 

  370.       or die("Query failed! (1c4)");
    371. 

  371.     $line = mysql_fetch_row($result);
    372. 

  372.     mysql_free_result($result);
    373. 

  373.     $molcount = $line[0];
    374. 

  374.     $next_mol_id = $molcount + 1;
    375. 

  375.   }
    376. 

  376.  if ($proposed_mol_id != $next_mol_id) {
    377. 

  377.    echo "This entry exists already!<br />\n";
    378. 

  378.    echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    379. 

  379.    echo "</body></html>\n";
    380. 

  380.    die();
    381. 

  381.  }
    382. 

  382. 

  383.   // add structure to molstruc
    384. 

  384.   $qstr = "INSERT INTO $molstructable (`mol_id`, `struc`) VALUES ($next_mol_id, \"$safemol\" )";
    385. 

  385. 

  386.   if ($debug > 0) { debug_output("adding structure as no. $next_mol_id to data collection $db_id <br />\n"); }
    387. 

  387. 

  388.   $result = mysql_query($qstr);
    389. 

  389.   $err = 0;
    390. 

  390.   $err = mysql_errno();
    391. 

  391.   if ($err != 0) { 
    392. 

  392.     echo "<br />Action failed (#1/$err: " . mysql_error() . ")<br />\n"; 
    393. 

  393.     $errorcount++;
    394. 

  394.   } #else { echo "."; }
    395. 

  395. 

  396.   if ($use_cmmmsrv == 'y') {
    397. 

  397.     $chkresult = filterthroughcmmm("$safemol", "#### checkmol:aXbH"); 
    398. 

  398.   } else {
    399. 

  399.     if ($ostype == 1) { $chkresult = filterthroughcmd("$safemol", "$CHECKMOL -aXbH - ");  }
    400. 

  400. 	if ($ostype == 2) { 
    401. 

  401.       $safemol = str_replace("\n","\r\n",$safemol);
    402. 

  402. 	  $chkresult = filterthroughcmd2("$safemol", "$CHECKMOL -aXbH - ");  
    403. 

  403. 	}
    404. 

  404.   }
    405. 

  405.   #echo "<pre>$chkresult</pre>\n";
    406. 

  406. 

  407.   if (strlen($chkresult) < 2) {
    408. 

  408.     echo "no response from checkmol (maybe a server configuration problem?)\n</body></html>\n";
    409. 

  409.     exit;
    410. 

  410.   }
    411. 

  411. 

  412.   $cr      = explode("\n", $chkresult);
    413. 

  413.   $molstat = trim($cr[0]);
    414. 

  414.   $molfgb  = trim($cr[1]);
    415. 

  415.   $molfgb  = str_replace(";",",",$molfgb);
    416. 

  416.   $molhfp  = trim($cr[2]);
    417. 

  417.   $molhfp  = str_replace(";",",",$molhfp);
    418. 

  418. 

  419.   $qstr = "INSERT INTO $molstattable VALUES ( $next_mol_id,$molstat )";
    420. 

  420.   $result = mysql_query($qstr);
    421. 

  421.   $err = 0;
    422. 

  422.   $err = mysql_errno();
    423. 

  423.   if ($err != 0) { 
    424. 

  424.     echo "<br />Action failed (#2/$err: " . mysql_error() . ")<br />\n"; 
    425. 

  425.     $errorcount++;
    426. 

  426.   } #else { echo "."; }
    427. 

  427. 

  428.   $qstr = "INSERT INTO $molfgbtable VALUES ($next_mol_id,$molfgb )";
    429. 

  429.   $result = mysql_query($qstr);
    430. 

  430.   $err = 0;
    431. 

  431.   $err = mysql_errno();
    432. 

  432.   if ($err != 0) { 
    433. 

  433.     echo "<br />Action failed (#3/$err: " . mysql_error() . ")<br />\n"; 
    434. 

  434.     $errorcount++;
    435. 

  435.   } #else { echo "."; }
    436. 

  436. 

  437.   // get the fingerprint dictionary
    438. 

  438.   $fpdefqstr = "SELECT fp_id, fpdef FROM $fpdeftable;";
    439. 

  439.   $fpdefresult = mysql_query($fpdefqstr)
    440. 

  440.       or die("Could not get fingerprint definition!"); 
    441. 

  441.   $i = -1;
    442. 

  442.   $n_dict = 0;
    443. 

  443.   $fpdef = array();
    444. 

  444.   while ($fpdefline = mysql_fetch_array($fpdefresult, MYSQL_ASSOC)) {
    445. 

  445.     $i++;
    446. 

  446.     $n_dict++;
    447. 

  447.     $fpdef[$i] = $fpdefline["fpdef"];
    448. 

  448.   } 
    449. 

  449.   mysql_free_result($fpdefresult);
    450. 

  450. 

  451.   //create the dictionary-based fingerprints
    452. 

  452.   $moldfp = "";
    453. 

  453.   for ($k = 0; $k < $n_dict; $k++) {
    454. 

  454.     $dict = $fpdef[$k];
    455. 

  455.     if ($ostype == 1) { $cand = $safemol . "\n" . '$$$$' ."\n" . $dict; }
    456. 

  456. 	if ($ostype == 2) {
    457. 

  457. 	  $dict = str_replace("\r","",$dict);
    458. 

  458. 	  $dict = str_replace("\n","\r\n",$dict);
    459. 

  459. 	  $cand = $safemol . "\r\n" . '$$$$' ."\r\n" . $dict;
    460. 

  460. 	}
    461. 

  461.     if ($use_cmmmsrv == 'y') {
    462. 

  462.       $dfpstr = filterthroughcmmm($cand,"#### MATCHMOL:F");
    463. 

  463.     } else {
    464. 

  464.       $cand   = str_replace("\$","\\\$",$cand);
    465. 

  465.       if ($ostype == 1) { $dfpstr = filterthroughcmd($cand,"$MATCHMOL -F - "); }
    466. 

  466. 	  if ($ostype == 2) { $dfpstr = filterthroughcmd2($cand,"$MATCHMOL -F - "); }
    467. 

  467.     }
    468. 

  468.     $dfpstr = trim($dfpstr);
    469. 

  469.     if ($k > 0) { $moldfp .= ","; }
    470. 

  470.     $moldfp .= " " . $dfpstr;
    471. 

  471.   }  // for..
    472. 

  472. 

  473.   //now insert dictionary-based and hash-based fingerprints into molcfptable
    474. 

  474.   $qstr = "INSERT INTO $molcfptable VALUES ($next_mol_id, $moldfp, $molhfp )";
    475. 

  475.   //echo "$qstr<br />\n";
    476. 

  476.   //echo "adding combined fingerprints for no. $next_mol_id to table $molcfptable.... ";
    477. 

  477.   $result = mysql_query($qstr);
    478. 

  478.   $err = 0;
    479. 

  479.   $err = mysql_errno();
    480. 

  480.   if ($err != 0) { 
    481. 

  481.     echo "<br />Action failed (#4i/$err: " . mysql_error() . ")<br />\n"; 
    482. 

  482.     $errorcount++;
    483. 

  483.   } #else { echo "."; }
    484. 

  484. 

  485.   // add new record to pic2dtable
    486. 

  486.   $qstr = "INSERT INTO $pic2dtable VALUES ($next_mol_id, \"1\", \"3\" )"; // 0 = does not exist, 1 = OK, 2 = OK, but do not show, 3 = to be created/updated, 4 = to be deleted
    487. 

  487.   //echo "$qstr<br />\n";
    488. 

  488.   //echo "adding 2D depiction information for no. $next_mol_id to table $pic2dtable.... ";
    489. 

  489.   $result = mysql_query($qstr);
    490. 

  490.   $err = 0;
    491. 

  491.   $err = mysql_errno();
    492. 

  492.   if ($err != 0) { 
    493. 

  493.     echo "<br />Action failed (#5/$err: " . mysql_error() . ")<br />\n"; 
    494. 

  494.     $errorcount++;
    495. 

  495.   } #else { echo "."; }
    496. 

  496. 

  497.   // add new record to moldatatable
    498. 

  498.   $qstr = "INSERT INTO $moldatatable (`mol_id`) VALUES (\"$next_mol_id\")";
    499. 

  499.   //echo "$qstr<br />\n";
    500. 

  500.   //echo "adding mol data for no. $next_mol_id to table $moldatatable.... ";
    501. 

  501.   $result = mysql_query($qstr);
    502. 

  502.   $err = 0;
    503. 

  503.   $err = mysql_errno();
    504. 

  504.   if ($err != 0) { 
    505. 

  505.     echo "<br />Action failed (#6/$err: " . mysql_error() . ")<br />\n"; 
    506. 

  506.     $errorcount++;
    507. 

  507.   } #else { echo "."; }
    508. 

  508. 

  509.   // MySQL syntax for table description, including comments:
    510. 

  510.   // SHOW FULL COLUMNS FROM db3_pic2d;
    511. 

  511. 

  512.   // MySQL syntax for changing just a comment:
    513. 

  513.   // ALTER TABLE `db3_pic2d` CHANGE `status` `status` TINYINT( 4 ) NOT NULL DEFAULT '0' 
    514. 

  514.   // COMMENT '0 = does not exist, 1 = OK, 2 = OK, but do not show, 3 = to be created/updated, 4 = to be deleted, 5 = in progress' 
    515. 

  515. 

  516.   // finished.....
    517. 

  517.   if ($use_cmmmsrv == 'y') {
    518. 

  518.     socket_write($socket,'#### bye');
    519. 

  519.     socket_close($socket);
    520. 

  520.   }
    521. 

  521. 

  522.   // for now, disable use of memory-based tables
    523. 

  523.   set_memstatus_dirty($db_id);
    524. 

  524. 

  525.   if ($debug > 0) { debug_output("Finished with $errorcount errors.<br />\n"); }
    526. 

  526. 

  527.   if ($err == 0) {
    528. 

  528.     
    529. 

  529.     // JME needs MDL molfiles with the "|" character instead of linebreaks
    530. 

  530.     $jmehitmol = strtr($safemol,"\n","|");
    531. 

  531.         
    532. 

  532.     echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    533. 

  533.     echo "width=\"250\" height=\"120\">";
    534. 

  534.     echo "<param name=\"options\" value=\"depict\"> \n";
    535. 

  535.     echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    536. 

  536.     echo "</applet>\n";
    537. 

  537. 

  538.     echo "<p />\n";
    539. 

  539.     mk_dataeditform($next_mol_id,1);
    540. 

  540.   } else {
    541. 

  541.     echo "something went wrong....<br />\n";
    542. 

  542.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    543. 

  543.   }
    544. 

  544.   echo "</body></html>\n";
    545. 

  545.   die();
    546. 

  546. }  // action=addstruc3
    547. 

  547. 

  548. if (($action == "addstruc3") && ($dbtype == 2)) {    // reaction input
    549. 

  549.   $errorcount = 0;
    550. 

  550.   $proposed_rxn_id = $_POST['nextid'];
    551. 

  551. 

  552.   if (strpos($mol,"\$RXN") === FALSE) {
    553. 

  553.     echo "this is not a valid reaction file!\n";
    554. 

  554.     echo "</body></html>\n";
    555. 

  555.     die();
    556. 

  556.   }
    557. 

  557.   $errorcount = 0;
    558. 

  558.   $proposed_rxn_id = $_POST['nextid'];
    559. 

  559.   if ($use_cmmmsrv == 'y') {
    560. 

  560.     /* create a TCP/IP socket */
    561. 

  561.     $socket = socket_create(AF_INET, SOCK_STREAM, SOL_TCP);
    562. 

  562.     if ($socket < 0) {
    563. 

  563.       //echo "socket_create() failed.\nreason: " . socket_strerror ($socket) . "\n";
    564. 

  564.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    565. 

  565.       $use_cmmmsrv = "n";
    566. 

  566.     }
    567. 

  567.     $sockresult = socket_connect ($socket, $cmmmsrv_addr, $cmmmsrv_port);
    568. 

  568.     if ($sockresult < 0) {
    569. 

  569.       //echo "socket_connect() failed.\nreason: ($sockresult) " . socket_strerror($sockresult) . "\n";
    570. 

  570.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    571. 

  571.       $use_cmmmsrv = "n";
    572. 

  572.     }
    573. 

  573.   }
    574. 

  574.   if ($use_cmmmsrv == 'y') {
    575. 

  575.     $a = socket_read($socket, 250, PHP_NORMAL_READ);
    576. 

  576.     //echo "$a\n";
    577. 

  577.     $pos = strpos($a,"READY");
    578. 

  578.     if ($pos === false) {
    579. 

  579.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    580. 

  580.       $use_cmmmsrv = "n";
    581. 

  581.     }
    582. 

  582.     $pos = 0;
    583. 

  583.   }
    584. 

  584. 

  585.   // remove CR if present (IE, Mozilla et al.) and add it again (for Opera)
    586. 

  586.   $mol = str_replace("\r\n","\n",$mol);
    587. 

  587.   $mol = str_replace("\n","\r\n",$mol);
    588. 

  588.   //$saferxn = escapeshellcmd($mol);
    589. 

  589.   $saferxn = str_replace(";"," ",$mol);
    590. 

  590.   $saferxn = str_replace("\""," ",$saferxn);
    591. 

  591.   $saferxn = str_replace("\'"," ",$saferxn);
    592. 

  592.   $saferxn = str_replace("\�"," ",$saferxn);
    593. 

  593.   $saferxn = str_replace("\`"," ",$saferxn);
    594. 

  594.   $saferxn = str_replace("\|"," ",$saferxn);
    595. 

  595.   $rxndescr = analyze_rxnfile($saferxn);
    596. 

  596.   $nrmol = get_nrmol($rxndescr);
    597. 

  597.   $npmol = get_npmol($rxndescr);
    598. 

  598.   //echo "there are $nrmol reactants and $npmol products<br>\n";
    599. 

  599.   if (($nrmol == 0) || ($npmol == 0)) {
    600. 

  600.     echo "incomplete reaction file!\n";
    601. 

  601.     echo "</body></html>\n";
    602. 

  602.     die();
    603. 

  603.   }
    604. 

  604.   $allmol = array();
    605. 

  605.   $rmol = array();
    606. 

  606.   $pmol = array();
    607. 

  607.   $label_list = array();
    608. 

  608.   $map_list = array();
    609. 

  609.   $n_labels = 0;
    610. 

  610.   $n_maps = 0;
    611. 

  611.   $mapstr = "";
    612. 

  612.   
    613. 

  613.   echo "<pre>\n";
    614. 

  614.   $allmol = explode("\$MOL\r\n",$saferxn);
    615. 

  615.   $header = $allmol[0];
    616. 

  616. 

  617.   // get the fingerprint dictionary
    618. 

  618.   $fpdefqstr = "SELECT fp_id, fpdef FROM $fpdeftable;";
    619. 

  619.   $fpdefresult = mysql_query($fpdefqstr)
    620. 

  620.       or die("Could not get fingerprint definition!"); 
    621. 

  621.   $i = -1;
    622. 

  622.   $n_dict = 0;
    623. 

  623.   $fpdef = array();
    624. 

  624.   while ($fpdefline = mysql_fetch_array($fpdefresult, MYSQL_ASSOC)) {
    625. 

  625.     $i++;
    626. 

  626.     $n_dict++;
    627. 

  627.     $fpdef[$i] = $fpdefline["fpdef"];
    628. 

  628.   } 
    629. 

  629.   mysql_free_result($fpdefresult);
    630. 

  630. 

  631.   // get next available rxn_id 
    632. 

  632.   $result = mysql_query("SELECT COUNT(rxn_id) AS molcount FROM $rxnstructable")
    633. 

  633.     or die("Query failed! (1c3a)");
    634. 

  634.   $line = mysql_fetch_row($result);
    635. 

  635.   mysql_free_result($result);
    636. 

  636.   $rxncount = $line[0];
    637. 

  637.   if ($rxncount == 0) { 
    638. 

  638.     $next_rxn_id = 1; 
    639. 

  639.   } else {
    640. 

  640.     $result = mysql_query("SELECT MAX(rxn_id) AS molcount FROM $rxnstructable")
    641. 

  641.       or die("Query failed! (1c4a)");
    642. 

  642.     $line = mysql_fetch_row($result);
    643. 

  643.     mysql_free_result($result);
    644. 

  644.     $rxncount = $line[0];
    645. 

  645.     $next_rxn_id = $rxncount + 1;
    646. 

  646.   }
    647. 

  647.   if ($proposed_rxn_id != $next_rxn_id) {
    648. 

  648.     echo "This entry exists already!<br />\n";
    649. 

  649.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    650. 

  650.     echo "</body></html>\n";
    651. 

  651.     die();
    652. 

  652.   }
    653. 

  653. 

  654.   $mapstr = get_maps($saferxn);
    655. 

  655. 

  656.   if ($nrmol > 0) {
    657. 

  657.     $moldfpsum = "";
    658. 

  658.     $molhfpsum = "";
    659. 

  659.     $molfgbsum = "";
    660. 

  660.     for ($i = 0; $i < $nrmol; $i++) {
    661. 

  661.       $rmol[$i] = $allmol[($i+1)];
    662. 

  662.       $mnum = $i + 1;
    663. 

  663.       //echo "processing reactant no. $mnum ...";
    664. 

  664.       $labels = get_atomlabels($rmol[$i]);
    665. 

  665.       $mid = "r" . $mnum;
    666. 

  666.       if (strlen($labels) > 0) {
    667. 

  667.         add_labels($mid,$labels);
    668. 

  668.       }
    669. 

  669.       $safemol = $rmol[$i];
    670. 

  670.       // now tweak each molecule
    671. 

  671.       if ($tweakmolfiles == "y") {
    672. 

  672.         if ($use_cmmmsrv == 'y') {
    673. 

  673.           $safemol = filterthroughcmmm($safemol,"#### checkmol:m");
    674. 

  674.         } else {
    675. 

  675.           if ($ostype == 1) { $safemol = filterthroughcmd($safemol,"$CHECKMOL -m - "); }
    676. 

  676.       	  if ($ostype == 2) { 
    677. 

  677.       	    $safemol = filterthroughcmd2($safemol,"$CHECKMOL -m - "); 
    678. 

  678.       	    $safemol = str_replace("\n","\r\n",$safemol);
    679. 

  679.           }
    680. 

  680.         }
    681. 

  681.         $rmol[$i] = $safemol;
    682. 

  682.       }  // end tweakmolefiles = y
    683. 

  683.       
    684. 

  684.       //create the dictionary-based fingerprints
    685. 

  685.       $moldfp = "";
    686. 

  686.       for ($k = 0; $k < $n_dict; $k++) {
    687. 

  687.         $dict = $fpdef[$k];
    688. 

  688.         if ($ostype == 1) { $cand = $safemol . "\n" . '$$$$' ."\n" . $dict; }
    689. 

  689.     	if ($ostype == 2) {
    690. 

  690.     	  $dict = str_replace("\r","",$dict);
    691. 

  691.     	  $dict = str_replace("\n","\r\n",$dict);
    692. 

  692.     	  $cand = $safemol . "\r\n" . '$$$$' ."\r\n" . $dict;
    693. 

  693.     	}
    694. 

  694.         if ($use_cmmmsrv == 'y') {
    695. 

  695.           $dfpstr = filterthroughcmmm($cand,"#### MATCHMOL:F");
    696. 

  696.         } else {
    697. 

  697.           $cand   = str_replace("\$","\\\$",$cand);
    698. 

  698.           if ($ostype == 1) { $dfpstr = filterthroughcmd($cand,"$MATCHMOL -F - "); }
    699. 

  699.     	  if ($ostype == 2) { $dfpstr = filterthroughcmd2($cand,"$MATCHMOL -F - "); }
    700. 

  700.         }
    701. 

  701.         $dfpstr = trim($dfpstr);
    702. 

  702.         if ($k > 0) { $moldfp .= ","; }
    703. 

  703.         $moldfp .= $dfpstr;
    704. 

  704.         //echo "dictionary-based fingerprints for reactant $i + dictionary $k\n$dfpstr\n";
    705. 

  705.       }  // for..
    706. 

  706.       //echo "moldfp: $moldfp\n";
    707. 

  707.       $moldfpsum = add_molfp($moldfpsum,$moldfp);
    708. 

  708.       
    709. 

  709.       // create the hash-based fingerprints
    710. 

  710.       if ($use_cmmmsrv == 'y') {
    711. 

  711.         $chkresult = filterthroughcmmm($safemol,"#### checkmol:bH");
    712. 

  712.       } else {
    713. 

  713.         if ($ostype == 1) {$chkresult = filterthroughcmd($safemol,"$CHECKMOL -bH - "); }
    714. 

  714.     	if ($ostype == 2) {$chkresult = filterthroughcmd2($safemol,"$CHECKMOL -bH - "); }
    715. 

  715.       }
    716. 

  716. 

  717.       if (strlen($chkresult) < 2) {
    718. 

  718.         echo "no response from checkmol (maybe a server configuration problem?)\n</body></html>\n";
    719. 

  719.         exit;
    720. 

  720.       }
    721. 

  721. 

  722.       $cr      = explode("\n", $chkresult);
    723. 

  723.       $molfgb  = trim($cr[0]);
    724. 

  724.       $fgbarr = explode(";",$molfgb);   // cut off the n1bits value
    725. 

  725.       $molfgb = $fgbarr[0];
    726. 

  726.       $molhfp  = trim($cr[1]);
    727. 

  727.       $hfparr = explode(";",$molhfp);   // cut off the n1bits value
    728. 

  728.       $molhfp = $hfparr[0];
    729. 

  729.       //echo "molhfp: $molhfp\n";
    730. 

  730.       $molhfpsum = add_molfp($molhfpsum,$molhfp);
    731. 

  731.       $molfgbsum = add_molfp($molfgbsum,$molfgb);
    732. 

  732.       
    733. 

  733.     }  // end for ($i = 0; $i < $nrmol; $i++) ...
    734. 

  734.     //echo "added moldfp: $moldfpsum\n";
    735. 

  735.     //echo "added molhfp: $molhfpsum\n";
    736. 

  736.     
    737. 

  737.     // insert combined reaction fingerprints for reactant(s)
    738. 

  738.     $qstr = "INSERT INTO $rxncfptable VALUES ($next_rxn_id,'R',$moldfpsum,$molhfpsum,0)";
    739. 

  739.     //echo "adding combined fingerprints for no. $next_rxn_id to table $rxncfptable.... ";
    740. 

  740.     $result = mysql_query($qstr);
    741. 

  741.     $err = 0;
    742. 

  742.     $err = mysql_errno();
    743. 

  743.     if ($err != 0) { 
    744. 

  744.       echo "<br />Action failed (#4a/$err: " . mysql_error() . ")<br />\n"; 
    745. 

  745.       $errorcount++;
    746. 

  746.     } // else { echo "done\n"; }
    747. 

  747. 

  748.     // insert combined functional group bitstring for reactant(s)
    749. 

  749.     $qstr = "INSERT INTO $rxnfgbtable VALUES ($next_rxn_id,'R',$molfgbsum,0)";
    750. 

  750.     //echo "adding combined reactant functional group codes for no. $next_rxn_id to table $rxncfptable.... ";
    751. 

  751.     $result = mysql_query($qstr);
    752. 

  752.     $err = 0;
    753. 

  753.     $err = mysql_errno();
    754. 

  754.     if ($err != 0) { 
    755. 

  755.       echo "<br />Action failed (#4b/$err: " . mysql_error() . ")<br />\n"; 
    756. 

  756.       $errorcount++;
    757. 

  757.     } // else { echo "done\n"; }
    758. 

  758.   }
    759. 

  759. 

  760.   if ($npmol > 0) {
    761. 

  761.     $moldfpsum = "";
    762. 

  762.     $molhfpsum = "";
    763. 

  763.     $molfgbsum = "";
    764. 

  764.     for ($i = 0; $i < $npmol; $i++) {
    765. 

  765.       $pmol[$i] = $allmol[($i+1+$nrmol)];
    766. 

  766.       $mnum = $i + 1;
    767. 

  767.       //echo "processing product no. $mnum ...";
    768. 

  768.       $labels = get_atomlabels($pmol[$i]);
    769. 

  769.       $mid = "p" . $mnum;
    770. 

  770.       if (strlen($labels) > 0) {
    771. 

  771.         add_labels($mid,$labels);
    772. 

  772.       }
    773. 

  773.       $safemol = $pmol[$i];
    774. 

  774.       // tweak the molfile
    775. 

  775.       if ($tweakmolfiles == "y") {
    776. 

  776.         if ($use_cmmmsrv == 'y') {
    777. 

  777.           $safemol = filterthroughcmmm($safemol,"#### checkmol:m");
    778. 

  778.         } else {
    779. 

  779.           if ($ostype == 1) { $safemol = filterthroughcmd($safemol,"$CHECKMOL -m - "); }
    780. 

  780.       	  if ($ostype == 2) { 
    781. 

  781.       	    $safemol = filterthroughcmd2($safemol,"$CHECKMOL -m - "); 
    782. 

  782.       	    $safemol = str_replace("\n","\r\n",$safemol);
    783. 

  783.           }
    784. 

  784.         }
    785. 

  785.         $pmol[$i] = $safemol;
    786. 

  786.       }  // end tweakmolefiles = y
    787. 

  787.       
    788. 

  788.       //create the dictionary-based fingerprints
    789. 

  789.       $moldfp = "";
    790. 

  790.       for ($k = 0; $k < $n_dict; $k++) {
    791. 

  791.         $dict = $fpdef[$k];
    792. 

  792.         if ($ostype == 1) { $cand = $safemol . "\n" . '$$$$' ."\n" . $dict; }
    793. 

  793.     	if ($ostype == 2) {
    794. 

  794.     	  $dict = str_replace("\r","",$dict);
    795. 

  795.     	  $dict = str_replace("\n","\r\n",$dict);
    796. 

  796.     	  $cand = $safemol . "\r\n" . '$$$$' ."\r\n" . $dict;
    797. 

  797.     	}
    798. 

  798.         if ($use_cmmmsrv == 'y') {
    799. 

  799.           $dfpstr = filterthroughcmmm($cand,"#### MATCHMOL:F");
    800. 

  800.         } else {
    801. 

  801.           $cand   = str_replace("\$","\\\$",$cand);
    802. 

  802.           if ($ostype == 1) { $dfpstr = filterthroughcmd($cand,"$MATCHMOL -F - "); }
    803. 

  803.     	  if ($ostype == 2) { $dfpstr = filterthroughcmd2($cand,"$MATCHMOL -F - "); }
    804. 

  804.         }
    805. 

  805.         $dfpstr = trim($dfpstr);
    806. 

  806.         if ($k > 0) { $moldfp .= ","; }
    807. 

  807.         $moldfp .= $dfpstr;
    808. 

  808.         //echo "dictionary-based fingerprints for product $i + dictionary $k\n$dfpstr\n";
    809. 

  809.       }  // for..
    810. 

  810.       //echo "moldfp: $moldfp\n";
    811. 

  811.       $moldfpsum = add_molfp($moldfpsum,$moldfp);
    812. 

  812.       
    813. 

  813.       // create the hash-based fingerprints
    814. 

  814.       if ($use_cmmmsrv == 'y') {
    815. 

  815.         $chkresult = filterthroughcmmm($safemol,"#### checkmol:bH");
    816. 

  816.       } else {
    817. 

  817.         if ($ostype == 1) {$chkresult = filterthroughcmd($safemol,"$CHECKMOL -bH - "); }
    818. 

  818.     	if ($ostype == 2) {$chkresult = filterthroughcmd2($safemol,"$CHECKMOL -bH - "); }
    819. 

  819.       }
    820. 

  820.       
    821. 

  821.       if (strlen($chkresult) < 2) {
    822. 

  822.         echo "no response from checkmol (maybe a server configuration problem?)\n</body></html>\n";
    823. 

  823.         exit;
    824. 

  824.       }
    825. 

  825.       
    826. 

  826.       $cr      = explode("\n", $chkresult);
    827. 

  827.       $molfgb  = trim($cr[0]);
    828. 

  828.       $fgbarr = explode(";",$molfgb);   // cut off the n1bits value
    829. 

  829.       $molfgb = $fgbarr[0];
    830. 

  830.       $molhfp  = trim($cr[1]);
    831. 

  831.       $hfparr = explode(";",$molhfp);   // cut off the n1bits value
    832. 

  832.       $molhfp = $hfparr[0];
    833. 

  833.       //echo "molhfp: $molhfp\n";
    834. 

  834.       $molhfpsum = add_molfp($molhfpsum,$molhfp);
    835. 

  835.       $molfgbsum = add_molfp($molfgbsum,$molfgb);
    836. 

  836.     }  // end for ($i = 0; $i < $npmol; $i++) ...
    837. 

  837.     //echo "added moldfp: $moldfpsum\n";
    838. 

  838.     //echo "added molhfp: $molhfpsum\n";
    839. 

  839.     
    840. 

  840.     // insert combined reaction fingerprints for product(s)
    841. 

  841.     $qstr = "INSERT INTO $rxncfptable VALUES ($next_rxn_id,'P',$moldfpsum,$molhfpsum,0)";
    842. 

  842.     //echo "adding combined fingerprints for no. $next_rxn_id to table $rxncfptable.... ";
    843. 

  843.     $result = mysql_query($qstr);
    844. 

  844.     $err = 0;
    845. 

  845.     $err = mysql_errno();
    846. 

  846.     if ($err != 0) { 
    847. 

  847.       echo "<br />Action failed (#4c/$err: " . mysql_error() . ")<br />\n"; 
    848. 

  848.       $errorcount++;
    849. 

  849.     } // else { echo "done"; }
    850. 

  850. 

  851.     // insert combined functional group bitstring for product(s)
    852. 

  852.     $qstr = "INSERT INTO $rxnfgbtable VALUES ($next_rxn_id,'P',$molfgbsum,0)";
    853. 

  853.     //echo "adding combined product functional group codes for no. $next_rxn_id to table $rxncfptable.... ";
    854. 

  854.     $result = mysql_query($qstr);
    855. 

  855.     $err = 0;
    856. 

  856.     $err = mysql_errno();
    857. 

  857.     if ($err != 0) { 
    858. 

  858.       echo "<br />Action failed (#4d/$err: " . mysql_error() . ")<br />\n"; 
    859. 

  859.       $errorcount++;
    860. 

  860.     } // else { echo "done\n"; }
    861. 

  861.   }
    862. 

  862. 

  863.   // re-apply the reaction maps after tweaking  (checkmol strips the atom labels)
    864. 

  864.   if ($tweakmolfiles == "y") {
    865. 

  865.     $saferxn = $header;
    866. 

  866.     for ($nm = 0; $nm < $nrmol; $nm++) {
    867. 

  867.       $saferxn .= "\$MOL\r\n" . $rmol[$nm];
    868. 

  868.     }
    869. 

  869.     for ($nm = 0; $nm < $npmol; $nm++) {
    870. 

  870.       $saferxn .= "\$MOL\r\n" . $pmol[$nm];
    871. 

  871.     }
    872. 

  872.     $saferxn = apply_maps($saferxn,$mapstr);
    873. 

  873.   }
    874. 

  874. 

  875.   $qstr = "INSERT INTO $rxnstructable (`rxn_id`, `struc`, `map`) VALUES ($next_rxn_id, \"$saferxn\", \"$mapstr\" )";
    876. 

  876.   //echo "adding reaction as no. $next_rxn_id to data collection $db_id ...";
    877. 

  877.   //echo "<pre>$qstr</pre>\n";
    878. 

  878.   $result = mysql_query($qstr);
    879. 

  879.   $err = 0;
    880. 

  880.   $err = mysql_errno();
    881. 

  881.   if ($err != 0) { 
    882. 

  882.     echo "<br />Action failed (#1/$err: " . mysql_error() . ")<br />\n"; 
    883. 

  883.     $errorcount++;
    884. 

  884.   } // else { echo "done\n"; }
    885. 

  885. 

  886.   // add new record to rxndatatable
    887. 

  887.   $qstr = "INSERT INTO $rxndatatable (`rxn_id`) VALUES (\"$next_rxn_id\")";
    888. 

  888.   //echo "adding reaction data for no. $next_rxn_id  ...";
    889. 

  889.   $result = mysql_query($qstr);
    890. 

  890.   $err = 0;
    891. 

  891.   $err = mysql_errno();
    892. 

  892.   if ($err != 0) { 
    893. 

  893.     echo "<br />Action failed (#6/$err: " . mysql_error() . ")<br />\n"; 
    894. 

  894.     $errorcount++;
    895. 

  895.   } // else { echo "done\n"; }
    896. 

  896.   echo "</pre>\n";
    897. 

  897. 

  898.   if ($debug > 0) { debug_output("Action finished with $errorcount errors.<br />\n"); }
    899. 

  899. 

  900.   if ($err == 0) {
    901. 

  901.     // JME needs MDL molfiles with the "|" character instead of linebreaks
    902. 

  902.     $jmehitmol = strtr($saferxn,"\n","|");
    903. 

  903.     echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    904. 

  904.     echo "width=\"250\" height=\"120\">";
    905. 

  905.     echo "<param name=\"options\" value=\"depict\"> \n";
    906. 

  906.     echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    907. 

  907.     echo "</applet>\n";
    908. 

  908.     echo "<p />\n";
    909. 

  909.     mk_dataeditform($next_rxn_id,2);
    910. 

  910.   } else {
    911. 

  911.     echo "something went wrong....<br />\n";
    912. 

  912.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    913. 

  913.   }
    914. 

  914.   echo "</body></html>\n";
    915. 

  915.   die();
    916. 

  916. }
    917. 

  917. 

  918. if ($action == "savedata") {
    919. 

  919.   global $db_id;
    920. 

  920.   global $datatype;
    921. 

  921.   global $moldatatable; 
    922. 

  922.   global $rxndatatable; 
    923. 

  923.   $item_id = $_POST["id"];
    924. 

  924.   if ($datatype == 2) {
    925. 

  925.     $idname = "rxn_id";
    926. 

  926.     $datatable = $rxndatatable;
    927. 

  927.   } else {
    928. 

  928.     $idname = "mol_id";
    929. 

  929.     $datatable = $moldatatable;
    930. 

  930.   }
    931. 

  931.   echo "<h3>Saving data for entry no. $item_id in data collection $db_id</h3>\n";
    932. 

  932.   echo "<table bgcolor=\"#eeeeee\">\n";
    933. 

  933.   echo "<tr align=\"left\"><th>Field:</th><th>Value:</th></tr>\n";
    934. 

  934.   $i = 0;
    935. 

  935.   $qstr = "SHOW FULL COLUMNS FROM $datatable";
    936. 

  936.   $result = mysql_query($qstr)
    937. 

  937.     or die("Query failed! (savedata)");
    938. 

  938.   $updstr = "UPDATE $datatable SET ";
    939. 

  939.   while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    940. 

  940.     $field   = $line["Field"];
    941. 

  941.     $type    = $line["Type"];
    942. 

  942.     $comment = $line["Comment"];
    943. 

  943.     if ($field != $idname) {
    944. 

  944.       $i++;
    945. 

  945.       $newval = "";   //preliminary....
    946. 

  946.       $f = "f" . $i;
    947. 

  947.       $newval = $_POST[$f];
    948. 

  948.       echo "<tr><td>$field</td><td>$newval</td></tr>\n";
    949. 

  949.       if ($i > 1) { $updstr .= ","; }
    950. 

  950.       $updstr .= " $field = \"$newval\"";
    951. 

  951.     }  // if...
    952. 

  952.   }  // while
    953. 

  953.   $updstr .= " WHERE $idname = $item_id";
    954. 

  954.   echo "</table>\n";
    955. 

  955.   $result = mysql_query($updstr)
    956. 

  956.     or die("Save data failed!");
    957. 

  957.   echo "<h3>Done.</h3>\n";
    958. 

  958.   echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    959. 

  959.   echo "</body></html>\n";
    960. 

  960.   die();
    961. 

  961. }  // action = savedata
    962. 

  962. 

  963. 

  964. if ($action == "duplcopy") {
    965. 

  965.   $item_id = $_REQUEST["id"];
    966. 

  966.   if ($datatype == 2) {
    967. 

  967.     $idname = "rxn_id";
    968. 

  968.     $datatable = $rxndatatable;
    969. 

  969.     $structable = $rxnstructable;
    970. 

  970.     $dtstr = "RD";
    971. 

  971.     $what = "reaction";
    972. 

  972.   } else {
    973. 

  973.     $idname = "mol_id";
    974. 

  974.     $datatable = $moldatatable;
    975. 

  975.     $structable = $molstructable;
    976. 

  976.     $dtstr = "SD";
    977. 

  977.     $what = "structure";
    978. 

  978.   }
    979. 

  979. 

  980.   // sanity checks...
    981. 

  981.   if (!is_numeric($item_id)) {
    982. 

  982.     echo "invalid input!</body></html>";
    983. 

  983.   } else { 
    984. 

  984.     $qstr = "SELECT COUNT($idname) AS itemcount FROM $structable WHERE $idname = $item_id";
    985. 

  985.     $result = mysql_query($qstr) or die("Query failed! (struc 1)");    
    986. 

  986.     while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    987. 

  987.       $itemcount = $line["itemcount"];
    988. 

  988.     }
    989. 

  989.     mysql_free_result($result);
    990. 

  990.     if ($itemcount < 1) {
    991. 

  991.       echo "<h2>Entry no. $item_id in data collection $db_id ($dtstr)</h2>\n<hr />\n";
    992. 

  992.       echo "This entry does not exist!<br />\n";
    993. 

  993.       echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    994. 

  994.       echo "</body></html>\n";
    995. 

  995.       die();
    996. 

  996.     }
    997. 

  997.     echo "<h2>Entry no. $item_id in data collection $db_id ($dtstr)</h2>\n<hr />\n";
    998. 

  998. 

  999.     $molstruc = "";   // can be MOL or RXN
    1000. 

  1000.     $qstr = "SELECT struc FROM $structable WHERE $idname = $item_id";
    1001. 

  1001.     $result = mysql_query($qstr) or die("Query failed! (struc 2)");    
    1002. 

  1002.     while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    1003. 

  1003.       $molstruc = $line["struc"];
    1004. 

  1004.     }
    1005. 

  1005.     mysql_free_result($result);
    1006. 

  1006. 

  1007.     if ($molstruc == "") {
    1008. 

  1008.       echo "empty structure<br />\n";
    1009. 

  1009.     } else {
    1010. 

  1010.       // JME needs MDL molfiles with the "|" character instead of linebreaks
    1011. 

  1011.       $jmehitmol = strtr($molstruc,"\n","|");
    1012. 

  1012.       if ($datatype == 1) { 
    1013. 

  1013.         $what1 = "Structure:";
    1014. 

  1014.         $what2 = "structure";
    1015. 

  1015.         $jmewidth = 250;
    1016. 

  1016.       } elseif ($datatype == 2) { 
    1017. 

  1017.         $what1 = "Reaction:";
    1018. 

  1018.         $what2 = "reaction";
    1019. 

  1019.         $jmewidth = 450;
    1020. 

  1020.       }
    1021. 

  1021.       echo "<h3>$what1</h3>\n";
    1022. 

  1022.       echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    1023. 

  1023.       echo "width=\"$jmewidth\" height=\"120\">";
    1024. 

  1024.       echo "<param name=\"options\" value=\"depict\"> \n";
    1025. 

  1025.       echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    1026. 

  1026.       echo "</applet>\n";
    1027. 

  1027.     }
    1028. 

  1028.     echo "<p />\n";
    1029. 

  1029.     
    1030. 

  1030.    // show data fields
    1031. 

  1031.    
    1032. 

  1032.     $result4 = mysql_query("SELECT * FROM $datatable WHERE $idname = $item_id")
    1033. 

  1033.       or die("Query failed! (duplcopy)");
    1034. 

  1034.     $y = mysql_num_fields($result4);
    1035. 

  1035.     echo "<table bgcolor=\"#eeeeee\">\n";
    1036. 

  1036.     while ($line4 = mysql_fetch_array($result4, MYSQL_BOTH)) {
    1037. 

  1037.       for ($x = 0; $x < $y; $x++) {
    1038. 

  1038.         $fieldname = mysql_field_name($result4, $x);
    1039. 

  1039.         //$fieldtype = mysql_field_type($result4, $x);
    1040. 

  1040.         if (($fieldname != $idname) && ($line4[$fieldname] != "")) {
    1041. 

  1041.           //echo  "<b>$fieldname:</b> \t$line4[$fieldname] <br />\n";
    1042. 

  1042.           echo "<tr>\n";
    1043. 

  1043.           echo "  <td><b>$fieldname</b></td><td>$line4[$fieldname]</td>\n";
    1044. 

  1044.           echo "</tr>\n";
    1045. 

  1045.         }
    1046. 

  1046.       }
    1047. 

  1047.       echo "<br />\n";
    1048. 

  1048.     }
    1049. 

  1049.     echo "</table>\n";
    1050. 

  1050.     echo "<p />\n<hr />\n";
    1051. 

  1051. 

  1052.     // and now the buttons for duplicate and copy
    1053. 

  1053.     echo "<form name=\"edform1\" action=\"$myname\" method=post>\n";
    1054. 

  1054.     echo "<input type=\"hidden\" name=\"action\" value=\"duplicate\">\n";
    1055. 

  1055.     echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    1056. 

  1056.     echo "<input type=\"hidden\" name=\"datatype\" value=\"$datatype\">\n";
    1057. 

  1057.     echo "<input type=\"hidden\" name=\"id\" value=\"$item_id\">\n";
    1058. 

  1058.     echo "<input type=\"Submit\" name=\"select\" value=\"Duplicate\"> this $what + all data fields in current data collection ($db_id)\n";
    1059. 

  1059.     echo "</form><p />\n";
    1060. 

  1060. 

  1061.     // now, get number of available data collections
    1062. 

  1062.     $db_list = array();
    1063. 

  1063.     $n_db = 0;
    1064. 

  1064.     $qstr5 = "SELECT db_id FROM $metatable WHERE (type = $datatype) AND (db_id != $db_id) ORDER BY db_id";
    1065. 

  1065.     $result5 = mysql_query($qstr5)
    1066. 

  1066.       or die("Query failed! (duplcopy 2)");
    1067. 

  1067.     while ($line5 = mysql_fetch_array($result5, MYSQL_BOTH)) {
    1068. 

  1068.       $db_list[$n_db] = $line5["db_id"];
    1069. 

  1069.       $n_db++;
    1070. 

  1070.     }
    1071. 

  1071.     if ($n_db > 0) {
    1072. 

  1072.       echo "<form name=\"edform1\" action=\"$myname\" method=post>\n";
    1073. 

  1073.       echo "<input type=\"hidden\" name=\"action\" value=\"copy\">\n";
    1074. 

  1074.       echo "<input type=\"hidden\" name=\"sourcedb\" value=\"$db_id\">\n";
    1075. 

  1075.       echo "<input type=\"hidden\" name=\"datatype\" value=\"$datatype\">\n";
    1076. 

  1076.       echo "<input type=\"hidden\" name=\"id\" value=\"$item_id\">\n";
    1077. 

  1077.       echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Copy&nbsp;&nbsp;&nbsp;\"> this $what + name to data collection ";
    1078. 

  1078.   
    1079. 

  1079.       echo "<select size=\"1\" name=\"db\">\n";
    1080. 

  1080.       for ($i = 0; $i < $n_db; $i++) {
    1081. 

  1081.         $db   = $db_list[$i];
    1082. 

  1082.         echo "<option value=\"$db\"";
    1083. 

  1083.         //if ($db == $db_id) { echo " selected"; }
    1084. 

  1084.         echo ">$db</option>\n";
    1085. 

  1085.       }
    1086. 

  1086.       echo "</select>\n";
    1087. 

  1087.       echo "</form><p />\n";
    1088. 

  1088.     } else { echo "no other data collections available for copying..."; }
    1089. 

  1089. 

  1090. 

  1091.   }  // end   if is_numeric(item_id)
    1092. 

  1092.   echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1093. 

  1093.   echo "</body></html>\n";
    1094. 

  1094.   die();
    1095. 

  1095. }
    1096. 

  1096. 

  1097. 

  1098. if (($action == "editdata") || ($action == "duplicate") || ($action == "copy")) {
    1099. 

  1099.   $item_id = $_REQUEST["id"];
    1100. 

  1100.   $sourcedb_id = $db_id;
    1101. 

  1101.   $targetdb_id = $db_id;
    1102. 

  1102.   if ($datatype == 2) {
    1103. 

  1103.     $idname = "rxn_id";
    1104. 

  1104.     $datatable = $rxndatatable;
    1105. 

  1105.     $datasuffix = $rxndatasuffix;
    1106. 

  1106.     $structable = $rxnstructable;
    1107. 

  1107.     $strucsuffix = $rxnstrucsuffix;
    1108. 

  1108.     $dtstr = "RD";
    1109. 

  1109.   } else {
    1110. 

  1110.     $idname = "mol_id";
    1111. 

  1111.     $datatable = $moldatatable;
    1112. 

  1112.     $datasuffix = $moldatasuffix;
    1113. 

  1113.     $structable = $molstructable;
    1114. 

  1114.     $strucsuffix = $molstrucsuffix;
    1115. 

  1115.     $dtstr = "SD";
    1116. 

  1116.   }
    1117. 

  1117. 

  1118.   // sanity checks...
    1119. 

  1119.   if (!is_numeric($item_id)) {
    1120. 

  1120.     echo "invalid input!</body></html>";
    1121. 

  1121.   } else { 
    1122. 

  1122. 

  1123.     if ($action == "copy") {
    1124. 

  1124.       $sourcedb_id = $_REQUEST['sourcedb'];
    1125. 

  1125.       $db_id = $sourcedb_id;
    1126. 

  1126.       //echo "db_id: $db_id<br>sourcedb_id: $sourcedb_id<br>targetdb_id: $targetdb_id<br>";
    1127. 

  1127.     }
    1128. 

  1128. 

  1129.     $structable = $prefix . "db" . $db_id . "_" . $strucsuffix;
    1130. 

  1130.     $qstr = "SELECT COUNT($idname) AS itemcount FROM $structable WHERE $idname = $item_id";
    1131. 

  1131.     $result = mysql_query($qstr) or die("Query failed! (struc 1)");    
    1132. 

  1132.     while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    1133. 

  1133.       $itemcount = $line["itemcount"];
    1134. 

  1134.     }
    1135. 

  1135.     mysql_free_result($result);
    1136. 

  1136.     if ($itemcount < 1) {
    1137. 

  1137.       echo "<h2>Entry no. $item_id in data collection $db_id ($dtstr)</h2>\n<hr />\n";
    1138. 

  1138.       echo "This entry does not exist!<br />\n";
    1139. 

  1139.       $db_id = $targetdb_id;
    1140. 

  1140.       echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1141. 

  1141.       echo "</body></html>\n";
    1142. 

  1142.       die();
    1143. 

  1143.     }
    1144. 

  1144.   
    1145. 

  1145.     if ($action == "duplicate") {
    1146. 

  1146.       if ($datatype == 1) {
    1147. 

  1147.         $new_item_id = copy_mol($db_id,$item_id,$db_id);
    1148. 

  1148.         $item_id = $new_item_id;
    1149. 

  1149.       } elseif ($datatype == 2) {
    1150. 

  1150.         $new_item_id = copy_rxn($db_id,$item_id,$db_id);
    1151. 

  1151.         $item_id = $new_item_id;
    1152. 

  1152.       }
    1153. 

  1153.     }
    1154. 

  1154.     if ($action == "copy") {
    1155. 

  1155.       if ($datatype == 1) {
    1156. 

  1156.         $new_item_id = copy_mol($db_id,$item_id,$targetdb_id);
    1157. 

  1157.         if ($new_item_id > 0) {
    1158. 

  1158.           $item_id = $new_item_id;
    1159. 

  1159.           $db_id = $targetdb_id;
    1160. 

  1160.         }
    1161. 

  1161.       } elseif ($datatype == 2) {
    1162. 

  1162.         $new_item_id = copy_rxn($db_id,$item_id,$targetdb_id);
    1163. 

  1163.         if ($new_item_id > 0) {
    1164. 

  1164.           $item_id = $new_item_id;
    1165. 

  1165.           $db_id = $targetdb_id;
    1166. 

  1166.         }
    1167. 

  1167.       }
    1168. 

  1168.       $structable = $prefix . "db" . $db_id . "_" . $strucsuffix;
    1169. 

  1169.     }
    1170. 

  1170. 

  1171.     echo "<h2>Entry no. $item_id in data collection $db_id ($dtstr)</h2>\n<hr />\n";
    1172. 

  1172. 

  1173.     $molstruc = "";   // can be MOL or RXN
    1174. 

  1174.     $qstr = "SELECT struc FROM $structable WHERE $idname = $item_id";
    1175. 

  1175.     $result = mysql_query($qstr) or die("Query failed! (struc 2)");    
    1176. 

  1176.     while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    1177. 

  1177.       $molstruc = $line["struc"];
    1178. 

  1178.     }
    1179. 

  1179.     mysql_free_result($result);
    1180. 

  1180. 

  1181.     if ($molstruc == "") {
    1182. 

  1182.       echo "empty structure<br />\n";
    1183. 

  1183.     } else {
    1184. 

  1184.       // JME needs MDL molfiles with the "|" character instead of linebreaks
    1185. 

  1185.       $jmehitmol = strtr($molstruc,"\n","|");
    1186. 

  1186.       if ($datatype == 1) { 
    1187. 

  1187.         $what1 = "Structure:";
    1188. 

  1188.         $what2 = "structure";
    1189. 

  1189.         $jmewidth = 250;
    1190. 

  1190.       } elseif ($datatype == 2) { 
    1191. 

  1191.         $what1 = "Reaction:";
    1192. 

  1192.         $what2 = "reaction";
    1193. 

  1193.         $jmewidth = 450;
    1194. 

  1194.       }
    1195. 

  1195.       echo "<h3>$what1</h3>\n";
    1196. 

  1196.       echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    1197. 

  1197.       echo "width=\"$jmewidth\" height=\"120\">";
    1198. 

  1198.       echo "<param name=\"options\" value=\"depict\"> \n";
    1199. 

  1199.       echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    1200. 

  1200.       echo "</applet>\n";
    1201. 

  1201.     }
    1202. 

  1202.     
    1203. 

  1203.     echo "<form name=\"strucform\" action=\"$myname\" method=\"post\">\n";
    1204. 

  1204.     echo "<input type=\"hidden\" name=\"action\" value=\"editstruc\">\n";
    1205. 

  1205.     echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    1206. 

  1206.     echo "<input type=\"hidden\" name=\"datatype\" value=\"$datatype\">\n";
    1207. 

  1207.     echo "<input type=\"hidden\" name=\"id\" value=\"$item_id\">\n";
    1208. 

  1208.     echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Edit $what2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\">\n";
    1209. 

  1209.     echo "</form>";
    1210. 

  1210.     if ($datatype == 2) {
    1211. 

  1211.       echo "<form name=\"strucform\" action=\"$myname\" method=\"post\">\n";
    1212. 

  1212.       echo "<input type=\"hidden\" name=\"action\" value=\"extract\">\n";
    1213. 

  1213.       echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    1214. 

  1214.       echo "<input type=\"hidden\" name=\"datatype\" value=\"$datatype\">\n";
    1215. 

  1215.       echo "<input type=\"hidden\" name=\"id\" value=\"$item_id\">\n";
    1216. 

  1216.       echo "<input type=\"Submit\" name=\"select\" value=\"Extract molecules\">\n";
    1217. 

  1217.       echo "</form>";
    1218. 

  1218.     }    
    1219. 

  1219.     
    1220. 

  1220.     if ($datatype == 1) {
    1221. 

  1221.       echo "&nbsp;&nbsp;<small><a href=\"../showmol.php?mol=${item_id}&db=${db_id}&mode=txt\"";
    1222. 

  1222.       echo " target=\"blank\">display molfile</a></small><p />\n";
    1223. 

  1223.     } elseif ($datatype == 2) {
    1224. 

  1224.       echo "&nbsp;&nbsp;<small><a href=\"../showmol.php?rxn=${item_id}&db=${db_id}&mode=txt\"";
    1225. 

  1225.       echo " target=\"blank\">display rxnfile</a></small><p />\n";
    1226. 

  1226.     }
    1227. 

  1227. 

  1228.     echo "<p />\n<hr />\n";
    1229. 

  1229.     mk_dataeditform($item_id,$datatype);
    1230. 

  1230. 

  1231.   }
    1232. 

  1232.   echo "<p /><a href=\"$myname?db=$sourcedb_id\">Continue without saving</a>\n";
    1233. 

  1233.   echo "</body></html>\n";
    1234. 

  1234.   die();
    1235. 

  1235. }
    1236. 

  1236. 

  1237. 

  1238. if (($action == "extract") && ($datatype == 2)) {
    1239. 

  1239.   $item_id = $_REQUEST["id"];
    1240. 

  1240.   $idname = "rxn_id";
    1241. 

  1241.   $datatable = $rxndatatable;
    1242. 

  1242.   $structable = $rxnstructable;
    1243. 

  1243.   $dtstr = "RD";
    1244. 

  1244. 

  1245.   // sanity checks...
    1246. 

  1246.   if (!is_numeric($item_id)) {
    1247. 

  1247.     echo "invalid input!</body></html>";
    1248. 

  1248.   } else { 
    1249. 

  1249. 

  1250.     $qstr = "SELECT COUNT($idname) AS itemcount FROM $structable WHERE $idname = $item_id";
    1251. 

  1251.     $result = mysql_query($qstr) or die("Query failed! (extract 1)");    
    1252. 

  1252.     while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    1253. 

  1253.       $itemcount = $line["itemcount"];
    1254. 

  1254.     }
    1255. 

  1255.     mysql_free_result($result);
    1256. 

  1256.     if ($itemcount < 1) {
    1257. 

  1257.       echo "<h2>Entry no. $item_id in data collection $db_id ($dtstr)</h2>\n<hr />\n";
    1258. 

  1258.       echo "This entry does not exist!<br />\n";
    1259. 

  1259.       echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1260. 

  1260.       echo "</body></html>\n";
    1261. 

  1261.       die();
    1262. 

  1262.     }
    1263. 

  1263.   
    1264. 

  1264.     echo "<h2>Entry no. $item_id in data collection $db_id ($dtstr)</h2>\n<hr />\n";
    1265. 

  1265. 

  1266.     $molstruc = "";   // can be MOL or RXN
    1267. 

  1267.     $qstr = "SELECT struc FROM $structable WHERE $idname = $item_id";
    1268. 

  1268.     $result = mysql_query($qstr) or die("Query failed! (extract 2)");    
    1269. 

  1269.     while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    1270. 

  1270.       $rxnstruc = $line["struc"];
    1271. 

  1271.     }
    1272. 

  1272.     mysql_free_result($result);
    1273. 

  1273. 

  1274.     if ($rxnstruc == "") {
    1275. 

  1275.       echo "empty reaction<br />\n";
    1276. 

  1276.     } else {
    1277. 

  1277.       // JME needs MDL molfiles with the "|" character instead of linebreaks
    1278. 

  1278.       $jmehitmol = strtr($rxnstruc,"\n","|");
    1279. 

  1279.       $what1 = "Reaction:";
    1280. 

  1280.       $what2 = "reaction";
    1281. 

  1281.       $jmewidth = 450;
    1282. 

  1282. 

  1283.       echo "<h3>$what1</h3>\n";
    1284. 

  1284.       echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    1285. 

  1285.       echo "width=\"$jmewidth\" height=\"120\">";
    1286. 

  1286.       echo "<param name=\"options\" value=\"depict\"> \n";
    1287. 

  1287.       echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    1288. 

  1288.       echo "</applet>\n";
    1289. 

  1289.     }
    1290. 

  1290. 

  1291.     echo "<hr />\n";
    1292. 

  1292. 

  1293.     // get a list of all structure databases
    1294. 

  1294.     $db_list = array();
    1295. 

  1295.     $result1 = mysql_query("SELECT db_id FROM $metatable WHERE (type = 1) ORDER BY db_id")
    1296. 

  1296.       or die("Query failed! (extract 3)");
    1297. 

  1297.     $ndb = mysql_num_rows($result1);
    1298. 

  1298.     $i = 0;
    1299. 

  1299.     while ($line = mysql_fetch_array($result1, MYSQL_ASSOC)) {
    1300. 

  1300.       $db   = $line["db_id"];
    1301. 

  1301.       $db_list[$i] = $db;
    1302. 

  1302.       $i++;
    1303. 

  1303.     }
    1304. 

  1304.     mysql_free_result($result1);
    1305. 

  1305.     
    1306. 

  1306.     // now split the rxnfile into pieces
    1307. 

  1307.     $rxnstruc = str_replace("\n","\r\n",$rxnstruc);
    1308. 

  1308.     $rxnstruc = str_replace("\r\r\n","\r\n",$rxnstruc);
    1309. 

  1309.     $rxnstruc = strip_labels($rxnstruc);
    1310. 

  1310.     $rxndescr = analyze_rxnfile($rxnstruc);
    1311. 

  1311.     $nrmol = get_nrmol($rxndescr);
    1312. 

  1312.     $npmol = get_npmol($rxndescr);
    1313. 

  1313.     $allmol = array();
    1314. 

  1314.     $allmol = explode("\$MOL\r\n",$rxnstruc);
    1315. 

  1315.     $header = $allmol[0];
    1316. 

  1316.     if ($nrmol > 0) {
    1317. 

  1317.       echo "<h3>Reactants:</h3>\n";
    1318. 

  1318.       for ($i = 0; $i < $nrmol; $i++) {
    1319. 

  1319.         $rmol[$i] = $allmol[($i+1)];
    1320. 

  1320.         $mnum = $i + 1;
    1321. 

  1321.         echo "  reactant no. $mnum<br>\n";
    1322. 

  1322.         $jmehitmol = strtr($rmol[$i],"\n","|");
    1323. 

  1323.         
    1324. 

  1324.         echo "<table cellpadding=\"2\" cellspacing=\"2\" border=\"0\" width=\"100%\">\n";
    1325. 

  1325.         echo "<tr align=\"left\">\n";
    1326. 

  1326.         echo "<td width=\"20%\">\n";
    1327. 

  1327.         
    1328. 

  1328.         echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    1329. 

  1329.         echo "width=\"250\" height=\"120\">";
    1330. 

  1330.         echo "<param name=\"options\" value=\"depict\"> \n";
    1331. 

  1331.         echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    1332. 

  1332.         echo "</applet>\n";
    1333. 

  1333.         
    1334. 

  1334.         echo "</td>\n<td align=\"left\">\n";
    1335. 

  1335.         echo "<br />\n";
    1336. 

  1336. 

  1337.         if ($ndb > 0) {
    1338. 

  1338.           echo "<form name=\"searchform\" action=\"../moldbsss.php\" method=\"post\">\n";
    1339. 

  1339.           echo "<input type=\"hidden\" name=\"mode\" value=\"1\">\n";
    1340. 

  1340.           echo "<input type=\"hidden\" name=\"mol\" value=\"$rmol[$i]\">\n";
    1341. 

  1341.           //echo "<input type=\"hidden\" name=\"db\" value=\"2\">\n";
    1342. 

  1342.           echo "<input type=\"Submit\" name=\"select\" value=\"Search\"> in data collection ";
    1343. 

  1343.           echo "<select size=\"1\" name=\"db\">\n";
    1344. 

  1344.           $j = 0;
    1345. 

  1345.           foreach ($db_list as $db) {
    1346. 

  1346.             echo "<option value=\"$db\"";
    1347. 

  1347.             if ($j == 0) { echo " selected"; }
    1348. 

  1348.             echo "> $db </option>\n";
    1349. 

  1349.             $j++;
    1350. 

  1350.           }
    1351. 

  1351.           echo "</select>\n";
    1352. 

  1352.           echo "</form>\n";
    1353. 

  1353.           //echo "<pre>$rmol[$i]</pre>";
    1354. 

  1354.           echo "<form name=\"copyform\" action=\"$myname\" method=\"post\">\n";
    1355. 

  1355.           echo "<input type=\"hidden\" name=\"action\" value=\"addstruc2\">\n";
    1356. 

  1356.           echo "<input type=\"hidden\" name=\"mol\" value=\"$rmol[$i]\">\n";
    1357. 

  1357.           //echo "<input type=\"hidden\" name=\"db\" value=\"2\">\n";
    1358. 

  1358.           echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;Copy&nbsp;&nbsp;\"> to data collection ";
    1359. 

  1359.           echo "<select size=\"1\" name=\"db\">\n";
    1360. 

  1360.           $i = 0;
    1361. 

  1361.           foreach ($db_list as $db) {
    1362. 

  1362.             echo "<option value=\"$db\"";
    1363. 

  1363.             if ($i == 0) { echo " selected"; }
    1364. 

  1364.             echo "> $db </option>\n";
    1365. 

  1365.             $i++;
    1366. 

  1366.           }
    1367. 

  1367.           echo "</select>\n";
    1368. 

  1368.           echo "</form><br /></td>";
    1369. 

  1369.         }  // end if ndb > 0
    1370. 

  1370.         echo "</tr>\n</table>\n";
    1371. 

  1371.       }
    1372. 

  1372.       echo "<hr />\n";
    1373. 

  1373.     }  // end if nrmol > 0
    1374. 

  1374.     
    1375. 

  1375.     if ($npmol > 0) {
    1376. 

  1376.       echo "<h3>Products:</h3>\n";
    1377. 

  1377.       for ($i = 0; $i < $npmol; $i++) {
    1378. 

  1378.         $pmol[$i] = $allmol[($i+1+$nrmol)];
    1379. 

  1379.         $mnum = $i + 1;
    1380. 

  1380.         echo "  product no. $mnum<br>\n";
    1381. 

  1381.         $jmehitmol = strtr($pmol[$i],"\n","|");
    1382. 

  1382.         
    1383. 

  1383.         echo "<table cellpadding=\"2\" cellspacing=\"2\" border=\"0\" width=\"100%\">\n";
    1384. 

  1384.         echo "<tr align=\"left\">\n";
    1385. 

  1385.         echo "<td width=\"20%\">\n";
    1386. 

  1386.         
    1387. 

  1387.         echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    1388. 

  1388.         echo "width=\"250\" height=\"120\">";
    1389. 

  1389.         echo "<param name=\"options\" value=\"depict\"> \n";
    1390. 

  1390.         echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    1391. 

  1391.         echo "</applet>\n";
    1392. 

  1392.         
    1393. 

  1393.         echo "</td>\n<td align=\"left\">\n";
    1394. 

  1394.         echo "<br />\n";
    1395. 

  1395. 

  1396.         if ($ndb > 0) {
    1397. 

  1397.           echo "<form name=\"searchform\" action=\"../moldbsss.php\" method=\"post\">\n";
    1398. 

  1398.           echo "<input type=\"hidden\" name=\"mode\" value=\"1\">\n";
    1399. 

  1399.           echo "<input type=\"hidden\" name=\"mol\" value=\"$pmol[$i]\">\n";
    1400. 

  1400.           //echo "<input type=\"hidden\" name=\"db\" value=\"2\">\n";
    1401. 

  1401.           echo "<input type=\"Submit\" name=\"select\" value=\"Search\"> in data collection ";
    1402. 

  1402.           echo "<select size=\"1\" name=\"db\">\n";
    1403. 

  1403.           $j = 0;
    1404. 

  1404.           foreach ($db_list as $db) {
    1405. 

  1405.             echo "<option value=\"$db\"";
    1406. 

  1406.             if ($j == 0) { echo " selected"; }
    1407. 

  1407.             echo "> $db </option>\n";
    1408. 

  1408.             $j++;
    1409. 

  1409.           }
    1410. 

  1410.           echo "</select>\n";
    1411. 

  1411.           echo "</form>\n";
    1412. 

  1412.           echo "<form name=\"copyform\" action=\"$myname\" method=\"post\">\n";
    1413. 

  1413.           echo "<input type=\"hidden\" name=\"action\" value=\"addstruc2\">\n";
    1414. 

  1414.           echo "<input type=\"hidden\" name=\"mol\" value=\"$pmol[$i]\">\n";
    1415. 

  1415.           //echo "<input type=\"hidden\" name=\"db\" value=\"2\">\n";
    1416. 

  1416.           echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;Copy&nbsp;&nbsp;\"> to data collection ";
    1417. 

  1417.           echo "<select size=\"1\" name=\"db\">\n";
    1418. 

  1418.           $i = 0;
    1419. 

  1419.           foreach ($db_list as $db) {
    1420. 

  1420.             echo "<option value=\"$db\"";
    1421. 

  1421.             if ($i == 0) { echo " selected"; }
    1422. 

  1422.             echo "> $db </option>\n";
    1423. 

  1423.             $i++;
    1424. 

  1424.           }
    1425. 

  1425.           echo "</select>\n";
    1426. 

  1426.           echo "</form><br /></td>";
    1427. 

  1427.         }
    1428. 

  1428.         echo "</tr>\n</table>\n";
    1429. 

  1429.       }
    1430. 

  1430.       echo "<hr />\n";
    1431. 

  1431.     }  // end if npmol > 0
    1432. 

  1432.   }
    1433. 

  1433.   echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1434. 

  1434.   echo "</body></html>\n";
    1435. 

  1435.   die();
    1436. 

  1436. }
    1437. 

  1437. 

  1438. 

  1439. if ($action == "editstruc") {
    1440. 

  1440.   $item_id = $_POST["id"];
    1441. 

  1441.   if ($datatype == 1) {
    1442. 

  1442.     $idname = "mol_id";
    1443. 

  1443.     $structable = $molstructable;
    1444. 

  1444.     $jmewidth = 350;
    1445. 

  1445.     $jmeheigth = 288;
    1446. 

  1446.     $jmeopt = "xbutton, hydrogens, multipart";
    1447. 

  1447.     $btnlabel = "Save structure";
    1448. 

  1448.   } elseif ($datatype == 2) {
    1449. 

  1449.     $idname = "rxn_id";
    1450. 

  1450.     $structable = $rxnstructable;
    1451. 

  1451.     $jmewidth = 640;
    1452. 

  1452.     $jmeheigth = 480;
    1453. 

  1453.     $jmeopt = "xbutton, hydrogens, reaction, multipart";
    1454. 

  1454.     $btnlabel = "Save reaction";
    1455. 

  1455.   }
    1456. 

  1456.   
    1457. 

  1457.   echo "<h2>Entry no. $item_id in data collection $db_id</h2>\n";
    1458. 

  1458. 

  1459.   // sanity checks...
    1460. 

  1460.   if (!is_numeric($item_id)) {
    1461. 

  1461.     echo "invalid input!";
    1462. 

  1462.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1463. 

  1463.     echo "</body></html>\n";
    1464. 

  1464.     die();
    1465. 

  1465.   } else { 
    1466. 

  1466. 

  1467.     $qstr = "SELECT COUNT($idname) AS itemcount FROM $structable WHERE $idname = $item_id";
    1468. 

  1468.     $result = mysql_query($qstr) or die("Query failed! (struc 3)");    
    1469. 

  1469.     while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    1470. 

  1470.       $itemcount = $line["itemcount"];
    1471. 

  1471.     }
    1472. 

  1472.     mysql_free_result($result);
    1473. 

  1473.     if ($itemcount < 1) {
    1474. 

  1474.       echo "This entry does not exist!<br />\n";
    1475. 

  1475.       echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1476. 

  1476.       echo "</body></html>\n";
    1477. 

  1477.       die();
    1478. 

  1478.     }
    1479. 

  1479. 

  1480.     $molstruc = "";
    1481. 

  1481.     $qstr = "SELECT struc FROM $structable WHERE $idname = $item_id";
    1482. 

  1482.     $result = mysql_query($qstr) or die("Query failed! (struc 4)");    
    1483. 

  1483.     while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    1484. 

  1484.       $molstruc = $line["struc"];
    1485. 

  1485.     }
    1486. 

  1486.     mysql_free_result($result);
    1487. 

  1487. 

  1488.     // JME needs MDL molfiles with the "|" character instead of linebreaks
    1489. 

  1489.     $jmehitmol = strtr($molstruc,"\n","|");
    1490. 

  1490.     echo "<applet name =\"JME\" code=\"JME.class\" archive=\"../JME.jar\" \n";
    1491. 

  1491.     echo "width=\"$jmewidth\" height=\"$jmeheigth\">\n";
    1492. 

  1492.     echo "<param name=\"options\" value=\"$jmeopt\"> \n";
    1493. 

  1493.     if ($molstruc != "") {
    1494. 

  1494.       echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    1495. 

  1495.     }
    1496. 

  1496.     echo "</applet>\n";
    1497. 

  1497. ?>
    1498. 

  1498. 

  1499. <script> 
    1500. 

  1500.   function check_ss() {
    1501. 

  1501.     var smiles = document.JME.smiles();
    1502. 

  1502.     var jme = document.JME.jmeFile(); 
    1503. 

  1503.     var mol = document.JME.molFile();
    1504. 

  1504.     if (smiles.length < 1) {
    1505. 

  1505.       alert("No molecule!");
    1506. 

  1506.     }
    1507. 

  1507.     else {
    1508. 

  1508.       document.form.smiles.value = smiles;
    1509. 

  1509.       document.form.jme.value = jme;
    1510. 

  1510.       document.form.mol.value = mol;
    1511. 

  1511.       document.form.submit();
    1512. 

  1512.     }
    1513. 

  1513.   }
    1514. 

  1514. </script>
    1515. 

  1515. <p />
    1516. 

  1516. <form name="form" action="<?php echo $myname; ?>" method="post">
    1517. 

  1517. <input type="button" value="&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<?php echo "$btnlabel"; ?>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;" onClick="check_ss()">
    1518. 

  1518. <input type="hidden" name="smiles">
    1519. 

  1519. <input type="hidden" name="jme">
    1520. 

  1520. <input type="hidden" name="mol">
    1521. 

  1521. <input type="hidden" name="action" value="savestruc">
    1522. 

  1522. <input type="hidden" name="db" value="<?php echo "$db_id";?>">
    1523. 

  1523. <input type="hidden" name="datatype" value="<?php echo "$datatype";?>">
    1524. 

  1524. <input type="hidden" name="id" value="<?php echo "$item_id";?>">
    1525. 

  1525. </form>
    1526. 

  1526. 

  1527. <form name="cancel" action="<?php echo "$myname"; ?>" method="post">
    1528. 

  1528. <input type="hidden" name="smiles">
    1529. 

  1529. <input type="hidden" name="jme">
    1530. 

  1530. <input type="hidden" name="mol">
    1531. 

  1531. <input type="hidden" name="action" value="editdata">
    1532. 

  1532. <input type="hidden" name="db" value="<?php echo "$db_id";?>">
    1533. 

  1533. <input type="hidden" name="datatype" value="<?php echo "$datatype";?>">
    1534. 

  1534. <input type="hidden" name="id" value="<?php echo "$item_id";?>">
    1535. 

  1535. <input type="Submit" name="select" value="&nbsp;&nbsp;&nbsp;&nbsp;Cancel&nbsp;&nbsp;&nbsp;&nbsp;">
    1536. 

  1536. </form>
    1537. 

  1537. 

  1538. <?php
    1539. 

  1539. 

  1540.     echo "<p />\n";
    1541. 

  1541.     echo "</body></html>\n";
    1542. 

  1542.     exit;
    1543. 

  1543.   }
    1544. 

  1544. }
    1545. 

  1545. 

  1546. 

  1547. if (($action == "savestruc") && ($datatype == 1)) {
    1548. 

  1548.   $errorcount = 0;
    1549. 

  1549.   $mol_id = $_POST['id'];
    1550. 

  1550.   if (!is_numeric($mol_id)) {
    1551. 

  1551.     echo "invalid input!";
    1552. 

  1552.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1553. 

  1553.     echo "</body></html>\n";
    1554. 

  1554.     die();
    1555. 

  1555.   }
    1556. 

  1556.   $qstr = "SELECT COUNT(mol_id) AS molcount FROM $molstructable WHERE mol_id = $mol_id";
    1557. 

  1557.   //echo "$qstr<br />\n";
    1558. 

  1558.   $result = mysql_query($qstr) or die("Query failed! (struc 5)");    
    1559. 

  1559.   while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    1560. 

  1560.     $molcount = $line["molcount"];
    1561. 

  1561.   }
    1562. 

  1562.   mysql_free_result($result);
    1563. 

  1563.   if ($molcount < 1) {
    1564. 

  1564.     echo "This entry does not exist!<br />\n";
    1565. 

  1565.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1566. 

  1566.     echo "</body></html>\n";
    1567. 

  1567.     die();
    1568. 

  1568.   }
    1569. 

  1569.   
    1570. 

  1570.   if ($mol == "") {
    1571. 

  1571.     echo "empty structure, nothing saved!<br />\n";
    1572. 

  1572.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1573. 

  1573.     echo "</body></html>\n";
    1574. 

  1574.     die();    
    1575. 

  1575.   }
    1576. 

  1576. 

  1577.   if ($use_cmmmsrv == 'y') {
    1578. 

  1578.     /* create a TCP/IP socket */
    1579. 

  1579.     $socket = socket_create(AF_INET, SOCK_STREAM, SOL_TCP);
    1580. 

  1580.     if ($socket < 0) {
    1581. 

  1581.       //echo "socket_create() failed.\nreason: " . socket_strerror ($socket) . "\n";
    1582. 

  1582.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    1583. 

  1583.       $use_cmmmsrv = "n";
    1584. 

  1584.     }
    1585. 

  1585.     $sockresult = socket_connect ($socket, $cmmmsrv_addr, $cmmmsrv_port);
    1586. 

  1586.     if ($sockresult < 0) {
    1587. 

  1587.       //echo "socket_connect() failed.\nreason: ($sockresult) " . socket_strerror($sockresult) . "\n";
    1588. 

  1588.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    1589. 

  1589.       $use_cmmmsrv = "n";
    1590. 

  1590.     }
    1591. 

  1591.   }
    1592. 

  1592.   if ($use_cmmmsrv == 'y') {
    1593. 

  1593.     $a = socket_read($socket, 250, PHP_NORMAL_READ);
    1594. 

  1594.     //echo "$a\n";
    1595. 

  1595.     $pos = strpos($a,"READY");
    1596. 

  1596.     if ($pos === false) {
    1597. 

  1597.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    1598. 

  1598.       $use_cmmmsrv = "n";
    1599. 

  1599.     }
    1600. 

  1600.     $pos = 0;
    1601. 

  1601.   }
    1602. 

  1602. 

  1603.   $safemol = str_replace(";"," ",$mol);
    1604. 

  1604.   $safemol = str_replace("\""," ",$safemol);
    1605. 

  1605.   $safemol = str_replace("\'"," ",$safemol);
    1606. 

  1606.   $safemol = str_replace("\�"," ",$safemol);
    1607. 

  1607.   $safemol = str_replace("\`"," ",$safemol);
    1608. 

  1608.   $safemol = str_replace("\|"," ",$safemol);
    1609. 

  1609.   
    1610. 

  1610.   // first, tweak the molfile
    1611. 

  1611.   if ($use_cmmmsrv == 'y') {
    1612. 

  1612.     $safemol = filterthroughcmmm($safemol,"#### checkmol:m");
    1613. 

  1613.   } else {
    1614. 

  1614.     if ($ostype == 1) { $safemol = filterthroughcmd($safemol,"$CHECKMOL -m - "); }
    1615. 

  1615. 	if ($ostype == 2) { 
    1616. 

  1616. 	  $safemol = filterthroughcmd2($safemol,"$CHECKMOL -m - "); 
    1617. 

  1617. 	  #$safemol = str_replace("\n","\r\n",$safemol);
    1618. 

  1618. 	}
    1619. 

  1619.   }
    1620. 

  1620. 

  1621.   // next step: get the molecular statistics of the input structure
    1622. 

  1622.   // by piping it through the checkmol program, then do a search
    1623. 

  1623.   // in molstat and the fingerprint table(s) ==> this gives a list of candidates
    1624. 

  1624. 

  1625.   // update structure in molstruc
    1626. 

  1626.   $qstr = "UPDATE $molstructable SET struc =\"$safemol\" WHERE mol_id = $mol_id";
    1627. 

  1627.   echo "<h2>Entry no. $mol_id in data collection $db_id</h2><hr />\n";
    1628. 

  1628.   
    1629. 

  1629.   //echo "<small>updating structure no. $mol_id in data collection $db_id ";
    1630. 

  1630.   $result = mysql_query($qstr);
    1631. 

  1631.   $err = 0;
    1632. 

  1632.   $err = mysql_errno();
    1633. 

  1633.   if ($err != 0) { 
    1634. 

  1634.     echo "<br />Action failed (#7/$err: " . mysql_error() . ")<br />\n"; 
    1635. 

  1635.     $errorcount++;
    1636. 

  1636.   } #else { echo "."; }
    1637. 

  1637. 

  1638.   if ($use_cmmmsrv == 'y') {
    1639. 

  1639.     $chkresult = filterthroughcmmm("$safemol", "#### checkmol:aXbH"); 
    1640. 

  1640.   } else {
    1641. 

  1641.     if ($ostype == 1) { $chkresult = filterthroughcmd("$safemol", "$CHECKMOL -aXbH - "); }
    1642. 

  1642.       if ($ostype == 2) { 
    1643. 

  1643.         $safemol = str_replace("\n","\r\n",$safemol);
    1644. 

  1644.         $chkresult = filterthroughcmd2("$safemol", "$CHECKMOL -aXbH - "); 
    1645. 

  1645.       }
    1646. 

  1646.   }
    1647. 

  1647.   //echo "<pre>$chkresult</pre>\n";
    1648. 

  1648.   
    1649. 

  1649.   if (strlen($chkresult) < 2) {
    1650. 

  1650.     echo "no response from checkmol (maybe a server configuration problem?)\n</body></html>\n";
    1651. 

  1651.     exit;
    1652. 

  1652.   }
    1653. 

  1653.   
    1654. 

  1654.   $cr = explode("\n", $chkresult);
    1655. 

  1655.   $molstat = trim($cr[0]);
    1656. 

  1656.   $molfgb  = trim($cr[1]);
    1657. 

  1657.   $molfgb  = str_replace(";",",",$molfgb);
    1658. 

  1658.   $molhfp  = trim($cr[2]);
    1659. 

  1659.   $molhfp  = str_replace(";",",",$molhfp);
    1660. 

  1660. 

  1661.   //echo "molstat ($next_mol_id): $molstat<br />\n";
    1662. 

  1662.   //echo "molfgb ($next_mol_id): $molfgb<br />\n";
    1663. 

  1663.   //echo "molhfp ($next_mol_id): $molhfp<br />\n";
    1664. 

  1664. 

  1665.   // delete old molstat record first
    1666. 

  1666.   $qstr = "DELETE FROM $molstattable WHERE mol_id = $mol_id";
    1667. 

  1667.   $result = mysql_query($qstr);
    1668. 

  1668.   $err = mysql_errno();
    1669. 

  1669.   if ($err != 0) { 
    1670. 

  1670.     echo "<br />Action failed (#8/$err: " . mysql_error() . ")<br />\n"; 
    1671. 

  1671.     $errorcount++;
    1672. 

  1672.   } #else { echo "."; }
    1673. 

  1673.   // add new molstat record
    1674. 

  1674.   $qstr = "INSERT INTO $molstattable VALUES ( $mol_id,$molstat )";
    1675. 

  1675.   $result = mysql_query($qstr);
    1676. 

  1676.   $err = mysql_errno();
    1677. 

  1677.   if ($err != 0) { 
    1678. 

  1678.     echo "<br />Action failed (#9/$err: " . mysql_error() . ")<br />\n"; 
    1679. 

  1679.     $errorcount++;
    1680. 

  1680.   } #else { echo "."; }
    1681. 

  1681. 

  1682.   // delete old molfgb record first
    1683. 

  1683.   $qstr = "DELETE FROM $molfgbtable WHERE mol_id = $mol_id";
    1684. 

  1684.   $result = mysql_query($qstr);
    1685. 

  1685.   $err = mysql_errno();
    1686. 

  1686.   if ($err != 0) { 
    1687. 

  1687.     echo "<br />Action failed (#10/$err: " . mysql_error() . ")<br />\n"; 
    1688. 

  1688.     $errorcount++;
    1689. 

  1689.   } #else { echo "."; }
    1690. 

  1690.   // add new molfgb record
    1691. 

  1691.   $qstr = "INSERT INTO $molfgbtable VALUES ($mol_id,$molfgb )";
    1692. 

  1692.   $result = mysql_query($qstr);
    1693. 

  1693.   $err = mysql_errno();
    1694. 

  1694.   if ($err != 0) { 
    1695. 

  1695.     echo "<br />Action failed (#11/$err: " . mysql_error() . ")<br />\n"; 
    1696. 

  1696.     $errorcount++;
    1697. 

  1697.   } #else { echo "."; }
    1698. 

  1698. 

  1699.   // delete old molcfp record first
    1700. 

  1700.   $qstr = "DELETE FROM $molcfptable WHERE mol_id = $mol_id";
    1701. 

  1701.   $result = mysql_query($qstr);
    1702. 

  1702.   $err = mysql_errno();
    1703. 

  1703.   if ($err != 0) { 
    1704. 

  1704.     echo "<br />Action failed (#12/$err: " . mysql_error() . ")<br />\n"; 
    1705. 

  1705.     $errorcount++;
    1706. 

  1706.   } #else { echo "."; }
    1707. 

  1707. 

  1708.   // add new molcfp record
    1709. 

  1709.   // get the fingerprint dictionary
    1710. 

  1710.   $fpdefqstr = "SELECT fp_id, fpdef FROM $fpdeftable;";
    1711. 

  1711.   $fpdefresult = mysql_query($fpdefqstr)
    1712. 

  1712.       or die("Could not get fingerprint definition!"); 
    1713. 

  1713.   $i = -1;
    1714. 

  1714.   $n_dict = 0;
    1715. 

  1715.   $fpdef = array();
    1716. 

  1716.   while ($fpdefline = mysql_fetch_array($fpdefresult, MYSQL_ASSOC)) {
    1717. 

  1717.     $i++;
    1718. 

  1718.     $n_dict++;
    1719. 

  1719.     $fpdef[$i] = $fpdefline["fpdef"];
    1720. 

  1720.   } 
    1721. 

  1721.   mysql_free_result($fpdefresult);
    1722. 

  1722. 

  1723.   //create the dictionary-based fingerprints
    1724. 

  1724.   $moldfp = "";
    1725. 

  1725.   for ($k = 0; $k < $n_dict; $k++) {
    1726. 

  1726.     $dict = $fpdef[$k];
    1727. 

  1727.     if ($ostype == 1) { $cand = $safemol . "\n" . '$$$$' ."\n" . $dict; }
    1728. 

  1728. 	if ($ostype == 2) {
    1729. 

  1729. 	  $dict = str_replace("\r","",$dict);
    1730. 

  1730. 	  $dict = str_replace("\n","\r\n",$dict);
    1731. 

  1731. 	  $cand = $safemol . "\r\n" . '$$$$' ."\r\n" . $dict;
    1732. 

  1732. 	}
    1733. 

  1733.     if ($use_cmmmsrv == 'y') {
    1734. 

  1734.       $dfpstr = filterthroughcmmm($cand,"#### MATCHMOL:F");
    1735. 

  1735.     } else {
    1736. 

  1736.       $cand   = str_replace("\$","\\\$",$cand);
    1737. 

  1737.       if ($ostype == 1) { $dfpstr = filterthroughcmd($cand,"$MATCHMOL -F - "); }
    1738. 

  1738. 	  if ($ostype == 2) { $dfpstr = filterthroughcmd2($cand,"$MATCHMOL -F - "); }
    1739. 

  1739.     }
    1740. 

  1740.     $dfpstr = trim($dfpstr);
    1741. 

  1741.     if ($k > 0) { $moldfp .= ","; }
    1742. 

  1742.     $moldfp .= " " . $dfpstr;
    1743. 

  1743.   }  // for..
    1744. 

  1744. 

  1745.   //now insert dictionary-based and hash-based fingerprints into molcfptable
    1746. 

  1746.   $qstr = "INSERT INTO $molcfptable VALUES ($mol_id, $moldfp, $molhfp )";
    1747. 

  1747.   //echo "adding combined fingerprints for no. $mol_id to table $molcfptable.... ";
    1748. 

  1748.   $result = mysql_query($qstr);
    1749. 

  1749.   $err = 0;
    1750. 

  1750.   $err = mysql_errno();
    1751. 

  1751.   if ($err != 0) { 
    1752. 

  1752.     echo "<br />Action failed (#13/$err: " . mysql_error() . ")<br />\n"; 
    1753. 

  1753.     $errorcount++;
    1754. 

  1754.   } #else { echo "."; }
    1755. 

  1755. 

  1756.   // update record in pic2dtable
    1757. 

  1757.   $qstr = "UPDATE $pic2dtable SET status = \"3\" WHERE mol_id = $mol_id"; // 0 = does not exist, 1 = OK, 2 = OK, but do not show, 3 = to be created/updated, 4 = to be deleted
    1758. 

  1758.   $result = mysql_query($qstr);
    1759. 

  1759.   $err = mysql_errno();
    1760. 

  1760.   if ($err != 0) { 
    1761. 

  1761.     echo "<br />Action failed (#14/$err: " . mysql_error() . ")<br />\n"; 
    1762. 

  1762.     $errorcount++;
    1763. 

  1763.   } #else { echo "."; }
    1764. 

  1764. 

  1765.   // finished.....
    1766. 

  1766. 

  1767.   if ($use_cmmmsrv == 'y') {
    1768. 

  1768.     socket_write($socket,'#### bye');
    1769. 

  1769.     socket_close($socket);
    1770. 

  1770.   }
    1771. 

  1771. 

  1772.   if ($debug > 0) { debug_output("Action finished with $errorcount errors.<br />\n"); }
    1773. 

  1773. 

  1774.   if ($err == 0) {
    1775. 

  1775.     echo "<h3>Structure:</h3>\n";
    1776. 

  1776.     // JME needs MDL molfiles with the "|" character instead of linebreaks
    1777. 

  1777. 	$jmehitmol = strtr($safemol,"\n","|");
    1778. 

  1778.         
    1779. 

  1779.     echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    1780. 

  1780.     echo "width=\"250\" height=\"120\">";
    1781. 

  1781.     echo "<param name=\"options\" value=\"depict\"> \n";
    1782. 

  1782.     echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    1783. 

  1783.     echo "</applet>\n";
    1784. 

  1784. 

  1785.     echo "<p />\n";
    1786. 

  1786.     echo "<form name=\"strucform\" action=\"$myname\" method=\"post\">\n";
    1787. 

  1787.     echo "<input type=\"hidden\" name=\"action\" value=\"editstruc\">\n";
    1788. 

  1788.     echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    1789. 

  1789.     echo "<input type=\"hidden\" name=\"datatype\" value=\"1\">\n";
    1790. 

  1790.     echo "<input type=\"hidden\" name=\"id\" value=\"$mol_id\">\n";
    1791. 

  1791.     echo "<input type=\"Submit\" name=\"select\" value=\"Edit structure\">\n";
    1792. 

  1792.     echo "</form><p />\n";
    1793. 

  1793. 

  1794.     echo "<p />\n<hr />\n";
    1795. 

  1795.     mk_dataeditform($mol_id,1);
    1796. 

  1796.   } else {
    1797. 

  1797.     echo "something went wrong....<br />\n";
    1798. 

  1798.   }
    1799. 

  1799.   set_memstatus_dirty($db_id);
    1800. 

  1800.   echo "<p /><a href=\"$myname?db=$db_id\">Continue without saving</a>\n";
    1801. 

  1801.   echo "</body></html>\n";
    1802. 

  1802.   die();
    1803. 

  1803. }
    1804. 

  1804. 

  1805. 

  1806. if (($action == "savestruc") && ($datatype == 2)) {
    1807. 

  1807.   $errorcount = 0;
    1808. 

  1808.   $rxn_id = $_POST['id'];
    1809. 

  1809.   if (!is_numeric($rxn_id)) {
    1810. 

  1810.     echo "invalid input!";
    1811. 

  1811.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1812. 

  1812.     echo "</body></html>\n";
    1813. 

  1813.     die();
    1814. 

  1814.   }
    1815. 

  1815.   $qstr = "SELECT COUNT(rxn_id) AS rxncount FROM $rxnstructable WHERE rxn_id = $rxn_id";
    1816. 

  1816.   $result = mysql_query($qstr) or die("Query failed! (struc 6)");    
    1817. 

  1817.   while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    1818. 

  1818.     $rxncount = $line["rxncount"];
    1819. 

  1819.   }
    1820. 

  1820.   mysql_free_result($result);
    1821. 

  1821.   if ($rxncount < 1) {
    1822. 

  1822.     echo "This entry does not exist!<br />\n";
    1823. 

  1823.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1824. 

  1824.     echo "</body></html>\n";
    1825. 

  1825.     die();
    1826. 

  1826.   }
    1827. 

  1827.   if ($mol == "") {
    1828. 

  1828.     echo "empty reaction, nothing saved!<br />\n";
    1829. 

  1829.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    1830. 

  1830.     echo "</body></html>\n";
    1831. 

  1831.     die();    
    1832. 

  1832.   }
    1833. 

  1833.   if (strpos($mol,"\$RXN") === FALSE) {
    1834. 

  1834.     echo "this is not a valid reaction file!\n";
    1835. 

  1835.     echo "</body></html>\n";
    1836. 

  1836.     die();
    1837. 

  1837.   }
    1838. 

  1838. 

  1839.   if ($use_cmmmsrv == 'y') {
    1840. 

  1840.     /* create a TCP/IP socket */
    1841. 

  1841.     $socket = socket_create(AF_INET, SOCK_STREAM, SOL_TCP);
    1842. 

  1842.     if ($socket < 0) {
    1843. 

  1843.       //echo "socket_create() failed.\nreason: " . socket_strerror ($socket) . "\n";
    1844. 

  1844.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    1845. 

  1845.       $use_cmmmsrv = "n";
    1846. 

  1846.     }
    1847. 

  1847.     $sockresult = socket_connect ($socket, $cmmmsrv_addr, $cmmmsrv_port);
    1848. 

  1848.     if ($sockresult < 0) {
    1849. 

  1849.       //echo "socket_connect() failed.\nreason: ($sockresult) " . socket_strerror($sockresult) . "\n";
    1850. 

  1850.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    1851. 

  1851.       $use_cmmmsrv = "n";
    1852. 

  1852.     }
    1853. 

  1853.   }
    1854. 

  1854.   if ($use_cmmmsrv == 'y') {
    1855. 

  1855.     $a = socket_read($socket, 250, PHP_NORMAL_READ);
    1856. 

  1856.     //echo "$a\n";
    1857. 

  1857.     $pos = strpos($a,"READY");
    1858. 

  1858.     if ($pos === false) {
    1859. 

  1859.       echo "<!-- could not connect to cmmmsrv - reverting to checkmol/matchmol --!>\n";
    1860. 

  1860.       $use_cmmmsrv = "n";
    1861. 

  1861.     }
    1862. 

  1862.     $pos = 0;
    1863. 

  1863.   }
    1864. 

  1864. 

  1865.   // remove CR if present (IE, Mozilla et al.) and add it again (for Opera)
    1866. 

  1866.   $mol = str_replace("\r\n","\n",$mol);
    1867. 

  1867.   $mol = str_replace("\n","\r\n",$mol);
    1868. 

  1868.   //$saferxn = escapeshellcmd($mol);
    1869. 

  1869.   $saferxn = str_replace(";"," ",$mol);
    1870. 

  1870.   $saferxn = str_replace("\""," ",$saferxn);
    1871. 

  1871.   $saferxn = str_replace("\'"," ",$saferxn);
    1872. 

  1872.   $saferxn = str_replace("\�"," ",$saferxn);
    1873. 

  1873.   $saferxn = str_replace("\`"," ",$saferxn);
    1874. 

  1874.   $saferxn = str_replace("\|"," ",$saferxn);
    1875. 

  1875.   $rxndescr = analyze_rxnfile($saferxn);
    1876. 

  1876.   $nrmol = get_nrmol($rxndescr);
    1877. 

  1877.   $npmol = get_npmol($rxndescr);
    1878. 

  1878.   //echo "there are $nrmol reactants and $npmol products<br>\n";
    1879. 

  1879.   if (($nrmol == 0) || ($npmol == 0)) {
    1880. 

  1880.     echo "incomplete reaction file!\n";
    1881. 

  1881.     echo "</body></html>\n";
    1882. 

  1882.     die();
    1883. 

  1883.   }
    1884. 

  1884.   $allmol = array();
    1885. 

  1885.   $rmol = array();
    1886. 

  1886.   $pmol = array();
    1887. 

  1887.   $label_list = array();
    1888. 

  1888.   $map_list = array();
    1889. 

  1889.   $n_labels = 0;
    1890. 

  1890.   $n_maps = 0;
    1891. 

  1891.   $mapstr = "";
    1892. 

  1892. 

  1893.   $allmol = explode("\$MOL\r\n",$saferxn);
    1894. 

  1894.   $header = $allmol[0];
    1895. 

  1895. 

  1896.   // get the fingerprint dictionary
    1897. 

  1897.   $fpdefqstr = "SELECT fp_id, fpdef FROM $fpdeftable;";
    1898. 

  1898.   $fpdefresult = mysql_query($fpdefqstr)
    1899. 

  1899.       or die("Could not get fingerprint definition!"); 
    1900. 

  1900.   $i = -1;
    1901. 

  1901.   $n_dict = 0;
    1902. 

  1902.   $fpdef = array();
    1903. 

  1903.   while ($fpdefline = mysql_fetch_array($fpdefresult, MYSQL_ASSOC)) {
    1904. 

  1904.     $i++;
    1905. 

  1905.     $n_dict++;
    1906. 

  1906.     $fpdef[$i] = $fpdefline["fpdef"];
    1907. 

  1907.   } 
    1908. 

  1908.   mysql_free_result($fpdefresult);
    1909. 

  1909. 

  1910.   $mapstr = get_maps($saferxn);
    1911. 

  1911.   
    1912. 

  1912.   // delete old rxnfgb record first
    1913. 

  1913.   $qstr = "DELETE FROM $rxnfgbtable WHERE rxn_id = $rxn_id";
    1914. 

  1914.   $result = mysql_query($qstr);
    1915. 

  1915.   $err = mysql_errno();
    1916. 

  1916.   if ($err != 0) { 
    1917. 

  1917.     echo "<br />Action failed (#11/$err: " . mysql_error() . ")<br />\n"; 
    1918. 

  1918.     $errorcount++;
    1919. 

  1919.   } #else { echo "."; }
    1920. 

  1920. 

  1921.   // delete old rxncfp record first
    1922. 

  1922.   $qstr = "DELETE FROM $rxncfptable WHERE rxn_id = $rxn_id";
    1923. 

  1923.   $result = mysql_query($qstr);
    1924. 

  1924.   $err = mysql_errno();
    1925. 

  1925.   if ($err != 0) { 
    1926. 

  1926.     echo "<br />Action failed (#12/$err: " . mysql_error() . ")<br />\n"; 
    1927. 

  1927.     $errorcount++;
    1928. 

  1928.   } #else { echo "done\n"; }
    1929. 

  1929. 

  1930.   if ($nrmol > 0) {
    1931. 

  1931.     $moldfpsum = "";
    1932. 

  1932.     $molhfpsum = "";
    1933. 

  1933.     $molfgbsum = "";
    1934. 

  1934.     for ($i = 0; $i < $nrmol; $i++) {
    1935. 

  1935.       $rmol[$i] = $allmol[($i+1)];
    1936. 

  1936.       $mnum = $i + 1;
    1937. 

  1937.       #echo "processing reactant no. $mnum ...";
    1938. 

  1938.       $labels = get_atomlabels($rmol[$i]);
    1939. 

  1939.       $mid = "r" . $mnum;
    1940. 

  1940.       if (strlen($labels) > 0) {
    1941. 

  1941.         add_labels($mid,$labels);
    1942. 

  1942.       }
    1943. 

  1943.       $safemol = $rmol[$i];
    1944. 

  1944.       // now tweak each molecule
    1945. 

  1945.       if ($tweakmolfiles == "y") {
    1946. 

  1946.         if ($use_cmmmsrv == 'y') {
    1947. 

  1947.           $safemol = filterthroughcmmm($safemol,"#### checkmol:m");
    1948. 

  1948.         } else {
    1949. 

  1949.           if ($ostype == 1) { $safemol = filterthroughcmd($safemol,"$CHECKMOL -m - "); }
    1950. 

  1950.       	  if ($ostype == 2) { 
    1951. 

  1951.       	    $safemol = filterthroughcmd2($safemol,"$CHECKMOL -m - "); 
    1952. 

  1952.       	    $safemol = str_replace("\n","\r\n",$safemol);
    1953. 

  1953.           }
    1954. 

  1954.         }
    1955. 

  1955.         $rmol[$i] = $safemol;
    1956. 

  1956.       }  // end tweakmolefiles = y
    1957. 

  1957.       
    1958. 

  1958.       //create the dictionary-based fingerprints
    1959. 

  1959.       $moldfp = "";
    1960. 

  1960.       for ($k = 0; $k < $n_dict; $k++) {
    1961. 

  1961.         $dict = $fpdef[$k];
    1962. 

  1962.         if ($ostype == 1) { $cand = $safemol . "\n" . '$$$$' ."\n" . $dict; }
    1963. 

  1963.     	if ($ostype == 2) {
    1964. 

  1964.     	  $dict = str_replace("\r","",$dict);
    1965. 

  1965.     	  $dict = str_replace("\n","\r\n",$dict);
    1966. 

  1966.     	  $cand = $safemol . "\r\n" . '$$$$' ."\r\n" . $dict;
    1967. 

  1967.     	}
    1968. 

  1968.         if ($use_cmmmsrv == 'y') {
    1969. 

  1969.           $dfpstr = filterthroughcmmm($cand,"#### MATCHMOL:F");
    1970. 

  1970.         } else {
    1971. 

  1971.           $cand   = str_replace("\$","\\\$",$cand);
    1972. 

  1972.           if ($ostype == 1) { $dfpstr = filterthroughcmd($cand,"$MATCHMOL -F - "); }
    1973. 

  1973.     	  if ($ostype == 2) { $dfpstr = filterthroughcmd2($cand,"$MATCHMOL -F - "); }
    1974. 

  1974.         }
    1975. 

  1975.         $dfpstr = trim($dfpstr);
    1976. 

  1976.         if ($k > 0) { $moldfp .= ","; }
    1977. 

  1977.         $moldfp .= $dfpstr;
    1978. 

  1978.         //echo "dictionary-based fingerprints for reactant $i + dictionary $k\n$dfpstr\n";
    1979. 

  1979.       }  // for..
    1980. 

  1980.       $moldfpsum = add_molfp($moldfpsum,$moldfp);
    1981. 

  1981.       
    1982. 

  1982.       // create the hash-based fingerprints
    1983. 

  1983.       if ($use_cmmmsrv == 'y') {
    1984. 

  1984.         $chkresult = filterthroughcmmm($safemol,"#### checkmol:bH");
    1985. 

  1985.       } else {
    1986. 

  1986.         if ($ostype == 1) {$chkresult = filterthroughcmd($safemol,"$CHECKMOL -bH - "); }
    1987. 

  1987.     	if ($ostype == 2) {$chkresult = filterthroughcmd2($safemol,"$CHECKMOL -bH - "); }
    1988. 

  1988.       }
    1989. 

  1989.       
    1990. 

  1990.       if (strlen($chkresult) < 2) {
    1991. 

  1991.         echo "no response from checkmol (maybe a server configuration problem?)\n</body></html>\n";
    1992. 

  1992.         exit;
    1993. 

  1993.       }
    1994. 

  1994.       
    1995. 

  1995.       $cr      = explode("\n", $chkresult);
    1996. 

  1996.       $molfgb  = trim($cr[0]);
    1997. 

  1997.       $fgbarr = explode(";",$molfgb);   // cut off the n1bits value
    1998. 

  1998.       $molfgb = $fgbarr[0];
    1999. 

  1999.       $molhfp  = trim($cr[1]);
    2000. 

  2000.       $hfparr = explode(";",$molhfp);   // cut off the n1bits value
    2001. 

  2001.       $molhfp = $hfparr[0];
    2002. 

  2002.       //echo "molhfp: $molhfp\n";
    2003. 

  2003.       $molhfpsum = add_molfp($molhfpsum,$molhfp);
    2004. 

  2004.       $molfgbsum = add_molfp($molfgbsum,$molfgb);
    2005. 

  2005.       
    2006. 

  2006.     }  // end for ($i = 0; $i < $nrmol; $i++) ...
    2007. 

  2007.     //echo "added moldfp: $moldfpsum\n";
    2008. 

  2008.     //echo "added molhfp: $molhfpsum\n";
    2009. 

  2009.     
    2010. 

  2010.     // insert combined reaction fingerprints for reactant(s)
    2011. 

  2011.     $qstr = "INSERT INTO $rxncfptable VALUES ($rxn_id,'R',$moldfpsum,$molhfpsum,0)";
    2012. 

  2012.     #echo "adding combined fingerprints (reactants) for no. $next_rxn_id to table $rxncfptable.... ";
    2013. 

  2013.     $result = mysql_query($qstr);
    2014. 

  2014.     $err = 0;
    2015. 

  2015.     $err = mysql_errno();
    2016. 

  2016.     if ($err != 0) { 
    2017. 

  2017.       echo "<br />Action failed (#4e/$err: " . mysql_error() . ")<br />\n"; 
    2018. 

  2018.       $errorcount++;
    2019. 

  2019.     } #else { echo "done\n"; }
    2020. 

  2020. 

  2021.     // insert combined functional group bitstring for reactant(s)
    2022. 

  2022.     $qstr = "INSERT INTO $rxnfgbtable VALUES ($rxn_id,'R',$molfgbsum,0)";
    2023. 

  2023.     #echo "adding combined reactant functional group codes for no. $next_rxn_id to table $rxncfptable.... ";
    2024. 

  2024.     $result = mysql_query($qstr);
    2025. 

  2025.     $err = 0;
    2026. 

  2026.     $err = mysql_errno();
    2027. 

  2027.     if ($err != 0) { 
    2028. 

  2028.       echo "<br />Action failed (#4f/$err: " . mysql_error() . ")<br />\n"; 
    2029. 

  2029.       $errorcount++;
    2030. 

  2030.     } #else { echo "done\n"; }
    2031. 

  2031.   }
    2032. 

  2032. 

  2033.   if ($npmol > 0) {
    2034. 

  2034.     $moldfpsum = "";
    2035. 

  2035.     $molhfpsum = "";
    2036. 

  2036.     $molfgbsum = "";
    2037. 

  2037.     for ($i = 0; $i < $npmol; $i++) {
    2038. 

  2038.       $pmol[$i] = $allmol[($i+1+$nrmol)];
    2039. 

  2039.       $mnum = $i + 1;
    2040. 

  2040.       #echo "processing product no. $mnum ...";
    2041. 

  2041.       $labels = get_atomlabels($pmol[$i]);
    2042. 

  2042.       $mid = "p" . $mnum;
    2043. 

  2043.       if (strlen($labels) > 0) {
    2044. 

  2044.         add_labels($mid,$labels);
    2045. 

  2045.       }
    2046. 

  2046.       $safemol = $pmol[$i];
    2047. 

  2047.       // tweak the molfile
    2048. 

  2048.       if ($tweakmolfiles == "y") {
    2049. 

  2049.         if ($use_cmmmsrv == 'y') {
    2050. 

  2050.           $safemol = filterthroughcmmm($safemol,"#### checkmol:m");
    2051. 

  2051.         } else {
    2052. 

  2052.           if ($ostype == 1) { $safemol = filterthroughcmd($safemol,"$CHECKMOL -m - "); }
    2053. 

  2053.       	  if ($ostype == 2) { 
    2054. 

  2054.       	    $safemol = filterthroughcmd2($safemol,"$CHECKMOL -m - "); 
    2055. 

  2055.       	    $safemol = str_replace("\n","\r\n",$safemol);
    2056. 

  2056.           }
    2057. 

  2057.         }
    2058. 

  2058.         $pmol[$i] = $safemol;
    2059. 

  2059.       }  // end tweakmolefiles = y
    2060. 

  2060.       
    2061. 

  2061.       //create the dictionary-based fingerprints
    2062. 

  2062.       $moldfp = "";
    2063. 

  2063.       for ($k = 0; $k < $n_dict; $k++) {
    2064. 

  2064.         $dict = $fpdef[$k];
    2065. 

  2065.         if ($ostype == 1) { $cand = $safemol . "\n" . '$$$$' ."\n" . $dict; }
    2066. 

  2066.     	if ($ostype == 2) {
    2067. 

  2067.     	  $dict = str_replace("\r","",$dict);
    2068. 

  2068.     	  $dict = str_replace("\n","\r\n",$dict);
    2069. 

  2069.     	  $cand = $safemol . "\r\n" . '$$$$' ."\r\n" . $dict;
    2070. 

  2070.     	}
    2071. 

  2071.         if ($use_cmmmsrv == 'y') {
    2072. 

  2072.           $dfpstr = filterthroughcmmm($cand,"#### MATCHMOL:F");
    2073. 

  2073.         } else {
    2074. 

  2074.           $cand   = str_replace("\$","\\\$",$cand);
    2075. 

  2075.           if ($ostype == 1) { $dfpstr = filterthroughcmd($cand,"$MATCHMOL -F - "); }
    2076. 

  2076.     	  if ($ostype == 2) { $dfpstr = filterthroughcmd2($cand,"$MATCHMOL -F - "); }
    2077. 

  2077.         }
    2078. 

  2078.         $dfpstr = trim($dfpstr);
    2079. 

  2079.         if ($k > 0) { $moldfp .= ","; }
    2080. 

  2080.         $moldfp .= $dfpstr;
    2081. 

  2081.         //echo "dictionary-based fingerprints for product $i + dictionary $k\n$dfpstr\n";
    2082. 

  2082.       }  // for..
    2083. 

  2083.       $moldfpsum = add_molfp($moldfpsum,$moldfp);
    2084. 

  2084.       
    2085. 

  2085.       // create the hash-based fingerprints
    2086. 

  2086.       if ($use_cmmmsrv == 'y') {
    2087. 

  2087.         $chkresult = filterthroughcmmm($safemol,"#### checkmol:bH");
    2088. 

  2088.       } else {
    2089. 

  2089.         if ($ostype == 1) {$chkresult = filterthroughcmd($safemol,"$CHECKMOL -bH - "); }
    2090. 

  2090.     	if ($ostype == 2) {$chkresult = filterthroughcmd2($safemol,"$CHECKMOL -bH - "); }
    2091. 

  2091.       }
    2092. 

  2092.       
    2093. 

  2093.       if (strlen($chkresult) < 2) {
    2094. 

  2094.         echo "no response from checkmol (maybe a server configuration problem?)\n</body></html>\n";
    2095. 

  2095.         exit;
    2096. 

  2096.       }
    2097. 

  2097.       
    2098. 

  2098.       $cr      = explode("\n", $chkresult);
    2099. 

  2099.       $molfgb  = trim($cr[0]);
    2100. 

  2100.       $fgbarr = explode(";",$molfgb);   // cut off the n1bits value
    2101. 

  2101.       $molfgb = $fgbarr[0];
    2102. 

  2102.       $molhfp  = trim($cr[1]);
    2103. 

  2103.       $hfparr = explode(";",$molhfp);   // cut off the n1bits value
    2104. 

  2104.       $molhfp = $hfparr[0];
    2105. 

  2105.       //echo "molhfp: $molhfp\n";
    2106. 

  2106.       $molhfpsum = add_molfp($molhfpsum,$molhfp);
    2107. 

  2107.       $molfgbsum = add_molfp($molfgbsum,$molfgb);
    2108. 

  2108. 

  2109.     }  // end for ($i = 0; $i < $npmol; $i++) ...
    2110. 

  2110.     //echo "added moldfp: $moldfpsum\n";
    2111. 

  2111.     //echo "added molhfp: $molhfpsum\n";
    2112. 

  2112.     
    2113. 

  2113.     // insert combined reaction fingerprints for product(s)
    2114. 

  2114.     $qstr = "INSERT INTO $rxncfptable VALUES ($rxn_id,'P',$moldfpsum,$molhfpsum,0)";
    2115. 

  2115.     //echo "adding combined fingerprints for no. $next_rxn_id to table $rxncfptable.... ";
    2116. 

  2116.     $result = mysql_query($qstr);
    2117. 

  2117.     $err = 0;
    2118. 

  2118.     $err = mysql_errno();
    2119. 

  2119.     if ($err != 0) { 
    2120. 

  2120.       echo "<br />Action failed (#4g/$err: " . mysql_error() . ")<br />\n"; 
    2121. 

  2121.       $errorcount++;
    2122. 

  2122.     } #else { echo "done"; }
    2123. 

  2123.     
    2124. 

  2124.     // insert combined functional group bitstring for product(s)
    2125. 

  2125.     $qstr = "INSERT INTO $rxnfgbtable VALUES ($rxn_id,'P',$molfgbsum,0)";
    2126. 

  2126.     //echo "adding combined product functional group codes for no. $next_rxn_id to table $rxncfptable.... ";
    2127. 

  2127.     $result = mysql_query($qstr);
    2128. 

  2128.     $err = 0;
    2129. 

  2129.     $err = mysql_errno();
    2130. 

  2130.     if ($err != 0) { 
    2131. 

  2131.       echo "<br />Action failed (#4h/$err: " . mysql_error() . ")<br />\n"; 
    2132. 

  2132.       $errorcount++;
    2133. 

  2133.     } #else { echo "done\n"; }
    2134. 

  2134.   }
    2135. 

  2135.   // re-apply the reaction maps after tweaking  (checkmol strips the atom labels)
    2136. 

  2136.   if ($tweakmolfiles == "y") {
    2137. 

  2137.     $saferxn = $header;
    2138. 

  2138.     for ($nm = 0; $nm < $nrmol; $nm++) {
    2139. 

  2139.       $saferxn .= "\$MOL\r\n" . $rmol[$nm];
    2140. 

  2140.     }
    2141. 

  2141.     for ($nm = 0; $nm < $npmol; $nm++) {
    2142. 

  2142.       $saferxn .= "\$MOL\r\n" . $pmol[$nm];
    2143. 

  2143.     }
    2144. 

  2144.     $saferxn = apply_maps($saferxn,$mapstr);
    2145. 

  2145.   }
    2146. 

  2146. 

  2147.   // update structure in rxnstruc
    2148. 

  2148.   $qstr = "UPDATE $rxnstructable SET struc =\"$saferxn\", map = \"$mapstr\"  WHERE rxn_id = $rxn_id";
    2149. 

  2149. 

  2150.   //echo "updating reaction no. $rxn_id in data collection $db_id ...";
    2151. 

  2151.   $result = mysql_query($qstr);
    2152. 

  2152.   $err = 0;
    2153. 

  2153.   $err = mysql_errno();
    2154. 

  2154.   if ($err != 0) { 
    2155. 

  2155.     echo "<br />Action failed (#1/$err: " . mysql_error() . ")<br />\n"; 
    2156. 

  2156.     $errorcount++;
    2157. 

  2157.   } #else { echo "done\n"; }
    2158. 

  2158. 

  2159.   // finished.....
    2160. 

  2160. 

  2161.   if ($use_cmmmsrv == 'y') {
    2162. 

  2162.     socket_write($socket,'#### bye');
    2163. 

  2163.     socket_close($socket);
    2164. 

  2164.   }
    2165. 

  2165. 

  2166.   if ($debug > 0) { debug_output("Action finished with $errorcount errors.<br />\n"); }
    2167. 

  2167. 

  2168.   if ($err == 0) {
    2169. 

  2169.     echo "<h3>Reaction:</h3>\n";
    2170. 

  2170.     // JME needs MDL molfiles with the "|" character instead of linebreaks
    2171. 

  2171. 	$jmehitmol = strtr($saferxn,"\n","|");
    2172. 

  2172.         
    2173. 

  2173.     echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    2174. 

  2174.     echo "width=\"350\" height=\"120\">";
    2175. 

  2175.     echo "<param name=\"options\" value=\"depict\"> \n";
    2176. 

  2176.     echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    2177. 

  2177.     echo "</applet>\n";
    2178. 

  2178. 

  2179.     echo "<p />\n";
    2180. 

  2180.     echo "<form name=\"strucform\" action=\"$myname\" method=\"post\">\n";
    2181. 

  2181.     echo "<input type=\"hidden\" name=\"action\" value=\"editstruc\">\n";
    2182. 

  2182.     echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    2183. 

  2183.     echo "<input type=\"hidden\" name=\"datatype\" value=\"2\">\n";
    2184. 

  2184.     echo "<input type=\"hidden\" name=\"id\" value=\"$rxn_id\">\n";
    2185. 

  2185.     echo "<input type=\"Submit\" name=\"select\" value=\"Edit reaction\">\n";
    2186. 

  2186.     echo "</form><p />\n";
    2187. 

  2187. 

  2188.     echo "<p />\n<hr />\n";
    2189. 

  2189.     mk_dataeditform($rxn_id,2);
    2190. 

  2190.   } else {
    2191. 

  2191.     echo "something went wrong....<br />\n";
    2192. 

  2192.   }
    2193. 

  2193.   echo "<p /><a href=\"$myname?db=$db_id\">Continue without saving</a>\n";
    2194. 

  2194.   echo "</body></html>\n";
    2195. 

  2195.   die();
    2196. 

  2196. 

  2197. }  // end action = savestruc && datatype = 2
    2198. 

  2198. 

  2199. 

  2200. if ($action == "eraserecord") {
    2201. 

  2201.   if ($datatype == 1) {
    2202. 

  2202.     $idname = "mol_id";
    2203. 

  2203.     $structable = $molstructable;
    2204. 

  2204.     $datatable = $moldatatable;
    2205. 

  2205.     $jmewidth = 250;
    2206. 

  2206.   } elseif ($datatype == 2) {
    2207. 

  2207.     $idname = "rxn_id";
    2208. 

  2208.     $structable = $rxnstructable;
    2209. 

  2209.     $datatable = $rxndatatable;
    2210. 

  2210.     $jmewidth = 350;
    2211. 

  2211.   }
    2212. 

  2212.   $item_id = $_POST['id'];
    2213. 

  2213.   if (!is_numeric($item_id)) {
    2214. 

  2214.     echo "invalid input!";
    2215. 

  2215.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    2216. 

  2216.     echo "</body></html>\n";
    2217. 

  2217.     die();
    2218. 

  2218.   }
    2219. 

  2219.   $qstr = "SELECT COUNT($idname) AS itemcount FROM $structable WHERE $idname = $item_id";
    2220. 

  2220.   $result = mysql_query($qstr) or die("Query failed! (struc 7)");    
    2221. 

  2221.   while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    2222. 

  2222.     $itemcount = $line["itemcount"];
    2223. 

  2223.   }
    2224. 

  2224.   mysql_free_result($result);
    2225. 

  2225.   if ($itemcount < 1) {
    2226. 

  2226.     echo "This entry does not exist!<br />\n";
    2227. 

  2227.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    2228. 

  2228.     echo "</body></html>\n";
    2229. 

  2229.     die();
    2230. 

  2230.   }
    2231. 

  2231.   $molstruc = "";
    2232. 

  2232.   $md5str = "";
    2233. 

  2233.   $qstr = "SELECT struc FROM $structable WHERE $idname = $item_id";
    2234. 

  2234.   $result = mysql_query($qstr) or die("Query failed! (struc 8)");    
    2235. 

  2235.   while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    2236. 

  2236.     $molstruc = $line["struc"];
    2237. 

  2237.   }
    2238. 

  2238.   mysql_free_result($result);
    2239. 

  2239. 

  2240.   if ($molstruc == "") {
    2241. 

  2241.     echo "empty structure<br />\n";
    2242. 

  2242.   } else {
    2243. 

  2243.     $md5str = md5($molstruc);
    2244. 

  2244.   }  
    2245. 

  2245.   echo "<h3>Do you really want to erase entry no. $item_id from data collection $db_id?</h3>\n";
    2246. 

  2246.   // JME needs MDL molfiles with the "|" character instead of linebreaks
    2247. 

  2247.   $jmehitmol = strtr($molstruc,"\n","|");
    2248. 

  2248.       
    2249. 

  2249.   echo "<applet code=\"JME.class\" archive=\"../JME.jar\" \n";
    2250. 

  2250.   echo "width=\"$jmewidth\" height=\"120\">";
    2251. 

  2251.   echo "<param name=\"options\" value=\"depict\"> \n";
    2252. 

  2252.   echo "<param name=\"mol\" value=\"$jmehitmol\">\n";
    2253. 

  2253.   echo "</applet>\n";
    2254. 

  2254. 

  2255.   // show data fields
    2256. 

  2256.   echo "<table bgcolor=\"#eeeeee\">\n";
    2257. 

  2257.   echo "<tr align=\"left\"><th>Field:</th><th>Value:</th></tr>\n";
    2258. 

  2258.   $i = 0;
    2259. 

  2259.   $qstr = "SHOW FULL COLUMNS FROM $datatable";
    2260. 

  2260.   $result = mysql_query($qstr)
    2261. 

  2261.     or die("Query failed! (1c5)");
    2262. 

  2262.   while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    2263. 

  2263.     $field   = $line["Field"];
    2264. 

  2264.     $type    = $line["Type"];
    2265. 

  2265.     $comment = $line["Comment"];
    2266. 

  2266.     if ($field != $idname) {
    2267. 

  2267.       $i++;
    2268. 

  2268.       $oldval = "";   //preliminary....
    2269. 

  2269.       $qstr2 = "SELECT $field FROM $datatable WHERE $idname = $item_id";
    2270. 

  2270.       $result2 = mysql_query($qstr2)
    2271. 

  2271.         or die("Query failed! (oldval)");
    2272. 

  2272.       $line2 = mysql_fetch_row($result2);
    2273. 

  2273.       mysql_free_result($result2);
    2274. 

  2274.       $oldval = $line2[0];
    2275. 

  2275.       echo "<tr><td>$field</td><td>$oldval</td></tr>\n"; 
    2276. 

  2276.     }  // if...
    2277. 

  2277. 

  2278.   }
    2279. 

  2279.   echo "</table><p />\n";
    2280. 

  2280.   
    2281. 

  2281.   // show yes/no buttons
    2282. 

  2282.   
    2283. 

  2283.   echo "<table>\n<tr>\n<td>\n";
    2284. 

  2284.   echo "<form name=\"erase\" action=\"$myname\" method=\"post\">\n";
    2285. 

  2285.   echo "<input type=\"hidden\" name=\"action\" value=\"eraseconfirm\">\n";
    2286. 

  2286.   echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    2287. 

  2287.   echo "<input type=\"hidden\" name=\"id\" value=\"$item_id\">\n";
    2288. 

  2288.   echo "<input type=\"hidden\" name=\"token\" value=\"$md5str\">\n";
    2289. 

  2289.   echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;Yes, erase it!\">\n";
    2290. 

  2290.   echo "</form><p />\n";
    2291. 

  2291. 

  2292.   echo "</td>\n<td>\n";
    2293. 

  2293. 

  2294.   echo "<form name=\"goback\" action=\"$myname\" method=\"post\">\n";
    2295. 

  2295.   echo "<input type=\"hidden\" name=\"action\" value=\"\">\n";
    2296. 

  2296.   echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    2297. 

  2297.   echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;No, keep it!\">\n";
    2298. 

  2298.   echo "</form><p />\n";
    2299. 

  2299.   echo "</td>\n</tr>\n</table>\n";
    2300. 

  2300. 

  2301.   echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    2302. 

  2302.   echo "</body></html>\n";
    2303. 

  2303.   die();
    2304. 

  2304. }
    2305. 

  2305. 

  2306. 

  2307. if ($action == "eraseconfirm") {
    2308. 

  2308.   if (($access < 3) && ($trusted == false)) {
    2309. 

  2309.     echo "Your client IP is not authorized to perform the requested operation!<br />\n";
    2310. 

  2310.     //echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    2311. 

  2311.     echo "</body></html>\n";
    2312. 

  2312.     die();
    2313. 

  2313.   }
    2314. 

  2314.   if ($datatype == 1) {
    2315. 

  2315.     $idname = "mol_id";
    2316. 

  2316.     $structable = $molstructable;
    2317. 

  2317.     $datatable = $moldatatable;
    2318. 

  2318.     $cfptable = $molcfptable;
    2319. 

  2319.     $fgbtable = $molfgbtable;
    2320. 

  2320.     $jmewidth = 250;
    2321. 

  2321.   } elseif ($datatype == 2) {
    2322. 

  2322.     $idname = "rxn_id";
    2323. 

  2323.     $structable = $rxnstructable;
    2324. 

  2324.     $datatable = $rxndatatable;
    2325. 

  2325.     $cfptable = $rxncfptable;
    2326. 

  2326.     $fgbtable = $rxnfgbtable;
    2327. 

  2327.     $jmewidth = 350;
    2328. 

  2328.   }
    2329. 

  2329.   $item_id = $_POST['id'];
    2330. 

  2330.   $md5str = $_POST['token'];
    2331. 

  2331.   if (!is_numeric($item_id)) {
    2332. 

  2332.     echo "invalid input!";
    2333. 

  2333.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    2334. 

  2334.     echo "</body></html>\n";
    2335. 

  2335.     die();
    2336. 

  2336.   }
    2337. 

  2337.   $qstr = "SELECT COUNT($idname) AS itemcount FROM $structable WHERE $idname = $item_id";
    2338. 

  2338.   $result = mysql_query($qstr) or die("Query failed! (struc 9)");    
    2339. 

  2339.   while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    2340. 

  2340.     $itemcount = $line["itemcount"];
    2341. 

  2341.   }
    2342. 

  2342.   mysql_free_result($result);
    2343. 

  2343.   if ($itemcount < 1) {
    2344. 

  2344.     echo "This entry does not exist!<br />\n";
    2345. 

  2345.     echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    2346. 

  2346.     echo "</body></html>\n";
    2347. 

  2347.     die();
    2348. 

  2348.   }
    2349. 

  2349.   $molstruc = "";
    2350. 

  2350.   $mymd5str = "";
    2351. 

  2351.   $qstr = "SELECT struc FROM $structable WHERE $idname = $item_id";
    2352. 

  2352.   $result = mysql_query($qstr) or die("Query failed! (struc 10)");    
    2353. 

  2353.   while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    2354. 

  2354.     $molstruc = $line["struc"];
    2355. 

  2355.   }
    2356. 

  2356.   mysql_free_result($result);
    2357. 

  2357. 

  2358.   if ($molstruc == "") {
    2359. 

  2359.     echo "empty structure<br />\n";
    2360. 

  2360.   } else {
    2361. 

  2361.     $mymd5str = md5($molstruc);
    2362. 

  2362.   }  
    2363. 

  2363.   
    2364. 

  2364.   echo "<h3>Erasing entry $item_id from data collection $db_id...</h3>\n";
    2365. 

  2365.   //echo "hash value (requested): $md5str<br />\n";
    2366. 

  2366.   //echo "hash value (calculated): $mymd5str<br />\n";
    2367. 

  2367.   
    2368. 

  2368.   if ($md5str == $mymd5str) {
    2369. 

  2369.     // erase everything
    2370. 

  2370.     // delete old molstruc record
    2371. 

  2371.     $qstr = "DELETE FROM $structable WHERE $idname = $item_id";
    2372. 

  2372.     $result = mysql_query($qstr);
    2373. 

  2373.     $err = mysql_errno();
    2374. 

  2374.     if ($err != 0) { $errorcount++; }
    2375. 

  2375.   
    2376. 

  2376.     // delete old moldata record
    2377. 

  2377.     $qstr = "DELETE FROM $datatable WHERE $idname = $item_id";
    2378. 

  2378.     $result = mysql_query($qstr);
    2379. 

  2379.     $err = mysql_errno();
    2380. 

  2380.     if ($err != 0) { $errorcount++; }
    2381. 

  2381. 

  2382.     // delete old molcfp record
    2383. 

  2383.     $qstr = "DELETE FROM $cfptable WHERE $idname = $item_id";
    2384. 

  2384.     $result = mysql_query($qstr);
    2385. 

  2385.     $err = mysql_errno();
    2386. 

  2386.     if ($err != 0) { $errorcount++; }
    2387. 

  2387. 

  2388.     // delete old molfgb record
    2389. 

  2389.     $qstr = "DELETE FROM $fgbtable WHERE $idname = $item_id";
    2390. 

  2390.     $result = mysql_query($qstr);
    2391. 

  2391.     $err = mysql_errno();
    2392. 

  2392.     if ($err != 0) { $errorcount++; }
    2393. 

  2393.   
    2394. 

  2394.     if ($datatype == 1) {
    2395. 

  2395.       // delete old molstat record
    2396. 

  2396.       $qstr = "DELETE FROM $molstattable WHERE mol_id = $item_id";
    2397. 

  2397.       $result = mysql_query($qstr);
    2398. 

  2398.       $err = mysql_errno();
    2399. 

  2399.       if ($err != 0) { $errorcount++; }
    2400. 

  2400.     
    2401. 

  2401.       // delete old pic2d record
    2402. 

  2402.       $qstr = "DELETE FROM $pic2dtable WHERE mol_id = $item_id";
    2403. 

  2403.       $result = mysql_query($qstr);
    2404. 

  2404.       $err = mysql_errno();
    2405. 

  2405.       if ($err != 0) { $errorcount++; }
    2406. 

  2406.     
    2407. 

  2407.       if ($usemem == 'T') {
    2408. 

  2408.         $molstattable  = str_replace($memsuffix, "", $molstattable);
    2409. 

  2409.         $molcfptable   = str_replace($memsuffix, "", $molcfptable);
    2410. 

  2410.       
    2411. 

  2411.         // delete old molststat record first
    2412. 

  2412.         $qstr = "DELETE FROM $molstattable WHERE mol_id = $item_id";
    2413. 

  2413.         $result = mysql_query($qstr);
    2414. 

  2414.         $err = mysql_errno();
    2415. 

  2415.         if ($err != 0) { $errorcount++; }
    2416. 

  2416.       
    2417. 

  2417.         // delete old molcfp record first
    2418. 

  2418.         $qstr = "DELETE FROM $molcfptable WHERE mol_id = $item_id";
    2419. 

  2419.         $result = mysql_query($qstr);
    2420. 

  2420.         $err = mysql_errno();
    2421. 

  2421.         if ($err != 0) { $errorcount++; }
    2422. 

  2422.       }
    2423. 

  2423.     }
    2424. 

  2424.   
    2425. 

  2425.     echo "<h3>Done.</h3>\n";
    2426. 

  2426.   }
    2427. 

  2427.   if ($debug > 0) { debug_output("Action finished with $errorcount errors.<br />\n"); }
    2428. 

  2428.   $errorcount = 0;
    2429. 

  2429. 

  2430.   echo "<p /><a href=\"$myname?db=$db_id\">Continue</a>\n";
    2431. 

  2431.   echo "</body></html>\n";
    2432. 

  2432.   die();
    2433. 

  2433. }
    2434. 

  2434. 

  2435. function mk_inputline($iname,$idefault) {
    2436. 

  2436.   echo "<input type=\"text\" name=\"$iname\" size=\"106\" value=\"$idefault\">";
    2437. 

  2437. }
    2438. 

  2438. 

  2439. function mk_inputarea($iname,$idefault) {
    2440. 

  2440.   echo "<textarea name=\"$iname\" cols=\"80\" rows=\"4\">$idefault</textarea>\n";
    2441. 

  2441. }
    2442. 

  2442. 

  2443. function mk_inputselect($iname,$itype,$idefault) {
    2444. 

  2444.   $lpos = strpos($itype,"(");
    2445. 

  2445.   $itype = substr($itype,($lpos+1));
    2446. 

  2446.   $rpos = strrpos($itype,")");
    2447. 

  2447.   $list1 = substr($itype,0,$rpos);
    2448. 

  2448.   $aitems = explode(",",$list1);
    2449. 

  2449.   echo "<select size=\"1\" name=\"$iname\">\n";
    2450. 

  2450.   foreach ($aitems as $item) {
    2451. 

  2451.     $ditem = str_replace("'","",$item);
    2452. 

  2452.     echo "<option value=\"$ditem\""; if ($idefault == $ditem) {echo " selected";} echo ">&nbsp;$ditem&nbsp;</option>\n";
    2453. 

  2453.   }  // foreach
    2454. 

  2454.   echo "</select>";
    2455. 

  2455. }
    2456. 

  2456. 

  2457. 

  2458. function mk_dataeditform($item_id,$formtype) {
    2459. 

  2459.   global $db_id;
    2460. 

  2460.   global $moldatatable; 
    2461. 

  2461.   global $rxndatatable; 
    2462. 

  2462.   global $myname;
    2463. 

  2463.   if ($formtype == 1) {
    2464. 

  2464.     $idname = "mol_id";
    2465. 

  2465.     $datatable = $moldatatable;
    2466. 

  2466.   } elseif ($formtype == 2) {
    2467. 

  2467.     $idname = "rxn_id";
    2468. 

  2468.     $datatable = $rxndatatable;
    2469. 

  2469.   }
    2470. 

  2470.   echo "<h3>Edit textual data for entry no. $item_id in data collection $db_id</h3>\n";
    2471. 

  2471.   echo "<form name=\"dataform\" action=\"$myname\" method=post>\n";
    2472. 

  2472.   echo "<table bgcolor=\"#eeeeee\">\n";
    2473. 

  2473.   echo "<tr align=\"left\"><th>Field:</th><th>Value:</th></tr>\n";
    2474. 

  2474.   $i = 0;
    2475. 

  2475.   $qstr = "SHOW FULL COLUMNS FROM $datatable";
    2476. 

  2476.   $result = mysql_query($qstr)
    2477. 

  2477.     or die("Query failed! (1c6)");
    2478. 

  2478.   while ($line = mysql_fetch_array($result, MYSQL_ASSOC)) {
    2479. 

  2479.     $field   = $line["Field"];
    2480. 

  2480.     $type    = $line["Type"];
    2481. 

  2481.     $comment = $line["Comment"];
    2482. 

  2482.     if ($field != $idname) {
    2483. 

  2483.       $i++;
    2484. 

  2484.       $oldval = "";   //preliminary....
    2485. 

  2485.       $qstr2 = "SELECT $field FROM $datatable WHERE $idname = $item_id";
    2486. 

  2486.       $result2 = mysql_query($qstr2)
    2487. 

  2487.         or die("Query failed! (oldval)");
    2488. 

  2488.       $line2 = mysql_fetch_row($result2);
    2489. 

  2489.       mysql_free_result($result2);
    2490. 

  2490.       $oldval = $line2[0];
    2491. 

  2491.       $ifmt = "line";
    2492. 

  2492.       if (strlen($comment)>4) {
    2493. 

  2493.         $pos = strpos($comment, ">>>>");
    2494. 

  2494.         if ($pos !== false) {
    2495. 

  2495.           if ($pos == 0) {
    2496. 

  2496.             $comment = str_replace(">>>>","",$comment);
    2497. 

  2497.             $acomment = explode("<",$comment);
    2498. 

  2498.             $label  = $acomment[0];
    2499. 

  2499.             $nformat = $acomment[1];
    2500. 

  2500.             if ($nformat == 0) { $ifmt = "line"; }
    2501. 

  2501.             if ($nformat == 1) { $ifmt = "line"; }
    2502. 

  2502.             if ($nformat == 2) { $ifmt = "text"; }
    2503. 

  2503.             if ($nformat == 3) { $ifmt = "line"; }
    2504. 

  2504.           }
    2505. 

  2505.         }
    2506. 

  2506.       }
    2507. 

  2507.       if(stristr($type, 'text') != FALSE) { $ifmt = "text"; }
    2508. 

  2508.       if(stristr($type, 'enum') != FALSE) { $ifmt = "select"; }
    2509. 

  2509.       if(stristr($type, 'set')  != FALSE) { $ifmt = "select"; }
    2510. 

  2510.       
    2511. 

  2511.       echo "<tr><td>$field</td><td>";
    2512. 

  2512.       if ($ifmt == "line")   { mk_inputline("f${i}",$oldval); }
    2513. 

  2513.       if ($ifmt == "text")   { mk_inputarea("f${i}",$oldval); }
    2514. 

  2514.       if ($ifmt == "select") { mk_inputselect("f${i}",$type,$oldval); }
    2515. 

  2515.       echo "</td></tr>\n";
    2516. 

  2516.     }  // if...
    2517. 

  2517.   }
    2518. 

  2518.   echo "</table><p />\n";
    2519. 

  2519.   echo "<input type=\"hidden\" name=\"action\" value=\"savedata\">\n";
    2520. 

  2520.   echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    2521. 

  2521.   echo "<input type=\"hidden\" name=\"datatype\" value=\"$formtype\">\n";
    2522. 

  2522.   echo "<input type=\"hidden\" name=\"id\" value=\"$item_id\">\n";
    2523. 

  2523.   echo "<input type=\"hidden\" name=\"nf\" value=\"$i\">\n";
    2524. 

  2524.   echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;Save data&nbsp;&nbsp;\">\n";
    2525. 

  2525.   echo "</form><p />\n";
    2526. 

  2526.   mysql_free_result($result);
    2527. 

  2527. }
    2528. 

  2528. 

  2529. function copy_mol($db_id,$mol_id,$targetdb_id) {
    2530. 

  2530.   global $prefix;
    2531. 

  2531.   global $molstrucsuffix;
    2532. 

  2532.   global $moldatasuffix;
    2533. 

  2533.   global $molfgbsuffix;
    2534. 

  2534.   global $molstatsuffix;
    2535. 

  2535.   global $molcfpsuffix;
    2536. 

  2536.   global $pic2dsuffix;
    2537. 

  2537.   global $memsuffix;
    2538. 

  2538.   global $metatable;
    2539. 

  2539. 

  2540.   $dbprefix = $prefix . "db" . $db_id . "_";
    2541. 

  2541.   $targetdbprefix = $prefix . "db" . $targetdb_id . "_";
    2542. 

  2542.   $moldatatable  = $dbprefix . $moldatasuffix;
    2543. 

  2543.   $molfgbtable   = $dbprefix . $molfgbsuffix;
    2544. 

  2544.   $molstattable  = $dbprefix . $molstatsuffix;
    2545. 

  2545.   $molstructable = $dbprefix . $molstrucsuffix;
    2546. 

  2546.   $molcfptable   = $dbprefix . $molcfpsuffix;
    2547. 

  2547.   $pic2dtable    = $dbprefix . $pic2dsuffix;
    2548. 

  2548. 

  2549.   $next_mol_id = get_next_mol_id($targetdb_id);
    2550. 

  2550. 

  2551.   if (intval($db_id) == intval($targetdb_id)) {
    2552. 

  2552.     $table_list = array($moldatatable,$molfgbtable,$molstattable,$molstructable,$molcfptable);
    2553. 

  2553.   } else {
    2554. 

  2554.     $table_list = array($molfgbtable,$molstattable,$molstructable,$molcfptable);
    2555. 

  2555.   }
    2556. 

  2556. 

  2557.   $field_name = array();
    2558. 

  2558.   $field_val = array();
    2559. 

  2559.   foreach ($table_list as $table) {
    2560. 

  2560.     $targettable = str_replace($dbprefix,$targetdbprefix,$table);
    2561. 

  2561.     $qstr1 = "DESCRIBE $table";
    2562. 

  2562.     $result1 = mysql_query($qstr1) or die("Query failed! (copy_mol #1)");
    2563. 

  2563.     $i = 0;
    2564. 

  2564.     while ($line1 = mysql_fetch_array($result1, MYSQL_ASSOC)) {
    2565. 

  2565.       $field_name[$i] = $line1["Field"];
    2566. 

  2566.       $i++;
    2567. 

  2567.     } 
    2568. 

  2568.     $n_fields = $i;
    2569. 

  2569.     #mysql_free_result($result1);
    2570. 

  2570.     $qstr2 = "SELECT * FROM $table WHERE mol_id = $mol_id";
    2571. 

  2571.     $result2 = mysql_query($qstr2) or die("Query failed! (copy_mol #2)");
    2572. 

  2572.     while ($line2 = mysql_fetch_array($result2, MYSQL_ASSOC)) {
    2573. 

  2573.       for ($i = 0; $i < $n_fields; $i++) {
    2574. 

  2574.         $field = $field_name[$i];
    2575. 

  2575.         $field_val[$i] = $line2[$field];
    2576. 

  2576.         if ($field == "mol_id") {
    2577. 

  2577.           $field_val[$i] = $next_mol_id;
    2578. 

  2578.         }
    2579. 

  2579.       }   // end for ...
    2580. 

  2580.     }   // end while ...
    2581. 

  2581.     $valstr = "";
    2582. 

  2582.     for ($i = 0; $i < $n_fields; $i++) {
    2583. 

  2583.       $val = $field_val[$i];
    2584. 

  2584.       if (strlen($valstr) > 0) { $valstr .= ","; }
    2585. 

  2585.       $valstr .= "\"" . $val . "\"";
    2586. 

  2586.     }
    2587. 

  2587.     $qstr3 = "INSERT INTO $targettable VALUES (" . $valstr . ")";
    2588. 

  2588.     $result3 = mysql_query($qstr3);
    2589. 

  2589.     $err = 0;
    2590. 

  2590.     $err = mysql_errno();
    2591. 

  2591.     if ($err != 0) { 
    2592. 

  2592.       echo "<br />Action failed (duplicate_mol #3/$err: " . mysql_error() . ")<br />\n"; 
    2593. 

  2593.     } #else { echo "."; }
    2594. 

  2594.   }  // end foreach table ...
    2595. 

  2595.   
    2596. 

  2596.   // if sourcedb and targetdb are different, copy only mol_name in moldatatable
    2597. 

  2597.   if (intval($db_id) != intval($targetdb_id)) {
    2598. 

  2598.     $qstr4 = "SELECT mol_name FROM $moldatatable WHERE mol_id = $mol_id";
    2599. 

  2599.     $result4 = mysql_query($qstr4) or die("Query failed! (copy_mol #4)");
    2600. 

  2600.     while ($line4 = mysql_fetch_array($result4, MYSQL_ASSOC)) {
    2601. 

  2601.       $mol_name = $line4["mol_name"];
    2602. 

  2602.     }
    2603. 

  2603.     $qstr5 = "INSERT INTO " . $targetdbprefix . $moldatasuffix . "(mol_id,mol_name) ";
    2604. 

  2604.     $qstr5 .= "VALUES (" . $next_mol_id . ",'" . $mol_name . "')";
    2605. 

  2605.     $result5 = mysql_query($qstr5);
    2606. 

  2606.     $err = 0;
    2607. 

  2607.     $err = mysql_errno();
    2608. 

  2608.     if ($err != 0) { 
    2609. 

  2609.       echo "<br />Action failed (copy_mol #5/$err: " . mysql_error() . ")<br />\n"; 
    2610. 

  2610.     } #else { echo "."; }
    2611. 

  2611.   }
    2612. 

  2612.   // handle pic2dtable separately...
    2613. 

  2613.   $qstr6 = "INSERT INTO " . $targetdbprefix . $pic2dsuffix . " VALUES ($next_mol_id, \"1\", \"3\" )"; // 0 = does not exist, 1 = OK, 2 = OK, but do not show, 3 = to be created/updated, 4 = to be deleted
    2614. 

  2614.   $result6 = mysql_query($qstr6);
    2615. 

  2615.   $err = 0;
    2616. 

  2616.   $err = mysql_errno();
    2617. 

  2617.   if ($err != 0) { 
    2618. 

  2618.     echo "<br />Action failed (copy_mol #6/$err: " . mysql_error() . ")<br />\n"; 
    2619. 

  2619.   } #else { echo "."; }
    2620. 

  2620.   set_memstatus_dirty($db_id);
    2621. 

  2621.   return($next_mol_id);
    2622. 

  2622. }
    2623. 

  2623. 

  2624. function copy_rxn($db_id,$rxn_id,$targetdb_id) {
    2625. 

  2625.   global $prefix;
    2626. 

  2626.   global $rxnstrucsuffix;
    2627. 

  2627.   global $rxndatasuffix;
    2628. 

  2628.   global $rxnfgbsuffix;
    2629. 

  2629.   global $rxncfpsuffix;
    2630. 

  2630. 

  2631.   $dbprefix = $prefix . "db" . $db_id . "_";
    2632. 

  2632.   $targetdbprefix = $prefix . "db" . $targetdb_id . "_";
    2633. 

  2633.   $rxndatatable  = $dbprefix . $rxndatasuffix;
    2634. 

  2634.   $rxnfgbtable   = $dbprefix . $rxnfgbsuffix;
    2635. 

  2635.   $rxnstructable = $dbprefix . $rxnstrucsuffix;
    2636. 

  2636.   $rxncfptable   = $dbprefix . $rxncfpsuffix;
    2637. 

  2637. 

  2638.   $next_rxn_id = get_next_rxn_id($targetdb_id);
    2639. 

  2639. 

  2640.   if (intval($db_id) == intval($targetdb_id)) {
    2641. 

  2641.     $table_list = array($rxndatatable,$rxnfgbtable,$rxnstructable,$rxncfptable);
    2642. 

  2642.   } else {
    2643. 

  2643.     $table_list = array($rxnfgbtable,$rxnstructable,$rxncfptable);
    2644. 

  2644.   }
    2645. 

  2645. 

  2646.   $field_name = array();
    2647. 

  2647.   $field_val = array();
    2648. 

  2648.   foreach ($table_list as $table) {
    2649. 

  2649.     $targettable = str_replace($dbprefix,$targetdbprefix,$table);
    2650. 

  2650.     $qstr1 = "DESCRIBE $table";
    2651. 

  2651.     $result1 = mysql_query($qstr1) or die("Query failed! (copy_rxn #1)");
    2652. 

  2652.     $i = 0;
    2653. 

  2653.     while ($line1 = mysql_fetch_array($result1, MYSQL_ASSOC)) {
    2654. 

  2654.       $field_name[$i] = $line1["Field"];
    2655. 

  2655.       $i++;
    2656. 

  2656.     } 
    2657. 

  2657.     $n_fields = $i;
    2658. 

  2658.     $qstr2 = "SELECT * FROM $table WHERE rxn_id = $rxn_id";
    2659. 

  2659.     $result2 = mysql_query($qstr2) or die("Query failed! (copy_rxn #2)");
    2660. 

  2660.     while ($line2 = mysql_fetch_array($result2, MYSQL_ASSOC)) {
    2661. 

  2661.       for ($i = 0; $i < $n_fields; $i++) {
    2662. 

  2662.         $field = $field_name[$i];
    2663. 

  2663.         $field_val[$i] = $line2[$field];
    2664. 

  2664.         if ($field == "rxn_id") {
    2665. 

  2665.           $field_val[$i] = $next_rxn_id;
    2666. 

  2666.         }
    2667. 

  2667.       }   // end for ...
    2668. 

  2668.     }   // end while ...
    2669. 

  2669.     $valstr = "";
    2670. 

  2670.     for ($i = 0; $i < $n_fields; $i++) {
    2671. 

  2671.       $val = $field_val[$i];
    2672. 

  2672.       if (strlen($valstr) > 0) { $valstr .= ","; }
    2673. 

  2673.       $valstr .= "\"" . $val . "\"";
    2674. 

  2674.     }
    2675. 

  2675.     $qstr3 = "INSERT INTO $targettable VALUES (" . $valstr . ")";
    2676. 

  2676.     $result3 = mysql_query($qstr3);
    2677. 

  2677.     $err = 0;
    2678. 

  2678.     $err = mysql_errno();
    2679. 

  2679.     if ($err != 0) { 
    2680. 

  2680.       echo "<br />Action failed (copy_rxn #3/$err: " . mysql_error() . ")<br />\n"; 
    2681. 

  2681.     } #else { echo "."; }
    2682. 

  2682.   }  // end foreach table ...
    2683. 

  2683.   if (intval($db_id) != intval($targetdb_id)) {
    2684. 

  2684.     $qstr4 = "SELECT rxn_name FROM $rxndatatable WHERE rxn_id = $rxn_id";
    2685. 

  2685.     $result4 = mysql_query($qstr4) or die("Query failed! (copy_rxn #4)");
    2686. 

  2686.     while ($line4 = mysql_fetch_array($result4, MYSQL_ASSOC)) {
    2687. 

  2687.       $rxn_name = $line4["rxn_name"];
    2688. 

  2688.     }
    2689. 

  2689.     $qstr5 = "INSERT INTO " . $targetdbprefix . $rxndatasuffix . "(rxn_id,rxn_name) ";
    2690. 

  2690.     $qstr5 .= "VALUES (" . $next_rxn_id . ",'" . $rxn_name . "')";
    2691. 

  2691.     $result5 = mysql_query($qstr5);
    2692. 

  2692.     $err = 0;
    2693. 

  2693.     $err = mysql_errno();
    2694. 

  2694.     if ($err != 0) { 
    2695. 

  2695.       echo "<br />Action failed (copy_rxn #5/$err: " . mysql_error() . ")<br />\n"; 
    2696. 

  2696.     } #else { echo "."; }
    2697. 

  2697.   }
    2698. 

  2698.   return($next_rxn_id);
    2699. 

  2699. }
    2700. 

  2700. 

  2701. 

  2702. $result = mysql_query("SELECT COUNT($idname) AS molcount, MAX($idname) AS max_mol_id FROM $structable")
    2703. 

  2703.   or die("Query failed! (1c7)");
    2704. 

  2704. $line = mysql_fetch_row($result);
    2705. 

  2705. mysql_free_result($result);
    2706. 

  2706. $molcount   = $line[0];
    2707. 

  2707. $max_mol_id = $line[1];
    2708. 

  2708. if ($molcount == 0) { $max_mol_id = 0; }
    2709. 

  2709. if ($molcount > 0) {
    2710. 

  2710.   echo "<p><small>current entries: $molcount, highest entry no.: $max_mol_id</small></p>\n";
    2711. 

  2711. 

  2712.   echo "<form name=\"edform1\" action=\"$myname\" method=post>\n";
    2713. 

  2713.   echo "<input type=\"hidden\" name=\"action\" value=\"editdata\">\n";
    2714. 

  2714.   echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    2715. 

  2715.   echo "<input type=\"hidden\" name=\"datatype\" value=\"$formtype\">\n";
    2716. 

  2716.   echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Edit entry no.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\">\n";
    2717. 

  2717.   echo "<input type=\"text\" name=\"id\" size=\"12\"><br />\n";
    2718. 

  2718.   echo "</form><p />\n";
    2719. 

  2719. 

  2720.   echo "<form name=\"edform1\" action=\"$myname\" method=post>\n";
    2721. 

  2721.   echo "<input type=\"hidden\" name=\"action\" value=\"duplcopy\">\n";
    2722. 

  2722.   echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    2723. 

  2723.   echo "<input type=\"hidden\" name=\"datatype\" value=\"$formtype\">\n";
    2724. 

  2724.   echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;&nbsp;&nbsp;Copy entry no.&nbsp;&nbsp;&nbsp;&nbsp;\">\n";
    2725. 

  2725.   echo "<input type=\"text\" name=\"id\" size=\"12\"><br />\n";
    2726. 

  2726.   echo "</form><p />\n";
    2727. 

  2727. 

  2728.   echo "<form name=\"edform1\" action=\"$myname\" method=post>\n";
    2729. 

  2729.   echo "<input type=\"hidden\" name=\"action\" value=\"eraserecord\">\n";
    2730. 

  2730.   echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    2731. 

  2731.   echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;&nbsp;&nbsp;Erase entry no.&nbsp;&nbsp;&nbsp;\">\n";
    2732. 

  2732.   echo "<input type=\"text\" name=\"id\" size=\"12\"><br />\n";
    2733. 

  2733.   echo "</form><p />\n";
    2734. 

  2734. 

  2735. }
    2736. 

  2736. echo "<form name=\"edform2\" action=\"$myname\" method=\"post\">\n";
    2737. 

  2737. echo "<input type=\"hidden\" name=\"action\" value=\"addstruc1\">\n";
    2738. 

  2738. echo "<input type=\"hidden\" name=\"db\" value=\"$db_id\">\n";
    2739. 

  2739. echo "<input type=\"Submit\" name=\"select\" value=\"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Add new entry&nbsp;&nbsp;&nbsp;&nbsp;\">\n";
    2740. 

  2740. echo "</form><p />\n";
    2741. 

  2741. 

  2742. echo "Back to <a href=\"./?db=$db_id\">database administration</a>\n";
    2743. 

  2743. ?>
    2744. 

  2744. 

  2745. <br />
    2746. 

  2746. <hr />
    2747. 

  2747. <br />
    2748. 

  2748. </body>
    2749. 

  2749. </html>
    2750. 

  2750.