public function action_add()
{
$community = $this->request->param('id');
if (!$community) {
$this->request->redirect(URL::base() . 'tournament');
}
$view = View::factory('tournament_add');
$view->community = com_from_id($community);
$view->available_maps = get_maps();
/*
$view->refs = '';
$view->maps = '';
*/
$view->description = '';
$view->exclusive = '';
if ($_POST) {
$refs = array();
$refCount = $_POST['refCount'];
for ($i = 1; $i <= $refCount; $i++) {
array_push($refs, $_POST['ref' . $i]);
}
$ref_ids = array();
foreach ($refs as $ref) {
if (!id_from_name($ref)) {
array_push($this->template->errors, "Could not find user: "******"You are not the admin of this community.");
}
if (empty($this->template->errors)) {
//DB::insert('tournies', array('community','admin','description','exclusive'))->values(array($community,$this->user,$description,$exclusive))->execute();
$this->request->redirect("/tournament?success");
} else {
$view->description = $description;
$view->exclusive = $exclusive;
}
}
$this->template->content = $view;
}
/**
* Cache all of the MAP's
*/
function cache_maps(&$cache, &$request)
{
$cache['maps'] = get_maps($request['dba']);
}
$mapstr = "";
$allmol = explode("\$MOL\r\n", $saferxn);
$header = $allmol[0];
// get the fingerprint dictionary
$fpdefqstr = "SELECT fp_id, fpdef FROM {$fpdeftable};";
$fpdefresult = mysql_query($fpdefqstr) or die("Could not get fingerprint definition!");
$i = -1;
$n_dict = 0;
$fpdef = array();
while ($fpdefline = mysql_fetch_array($fpdefresult, MYSQL_ASSOC)) {
$i++;
$n_dict++;
$fpdef[$i] = $fpdefline["fpdef"];
}
mysql_free_result($fpdefresult);
$mapstr = get_maps($saferxn);
// delete old rxnfgb record first
$qstr = "DELETE FROM {$rxnfgbtable} WHERE rxn_id = {$rxn_id}";
$result = mysql_query($qstr);
$err = mysql_errno();
if ($err != 0) {
echo "<br />Action failed (#11/{$err}: " . mysql_error() . ")<br />\n";
$errorcount++;
}
#else { echo "."; }
// delete old rxncfp record first
$qstr = "DELETE FROM {$rxncfptable} WHERE rxn_id = {$rxn_id}";
$result = mysql_query($qstr);
$err = mysql_errno();
if ($err != 0) {
echo "<br />Action failed (#12/{$err}: " . mysql_error() . ")<br />\n";
* Get ALL of the custom user profile fields
*/
$cache[PROFILEFIELDS] = array();
$result =& $_DBA->executeQuery("SELECT * FROM " . PROFILEFIELDS);
while ($result->next()) {
$temp = $result->current();
$cache[PROFILEFIELDS][$temp['name']] = $temp;
$cache[PROFILEFIELDS][$temp['name']]['html'] = format_profilefield($temp);
/* Add the extra values onto the end of the userinfo query params variable */
$query_params['userinfo'] .= ', ui.' . $temp['name'] . ' AS ' . $temp['name'];
}
$result->freeResult();
/* Memory saving */
unset($result);
/* Get the MAP's */
$cache[MAPS] = get_maps();
/* Create the cache file */
DBCache::createCache($cache, CACHE_FILE);
} else {
/* Include the cache file */
include_once CACHE_FILE;
if (!isset($cache) || !is_array($cache) || empty($cache)) {
compile_error('The cache array does not exist or it is empty.', __FILE__, __LINE__);
}
/* Add the extra values onto the end of the userinfo query params variable */
foreach ($cache[PROFILEFIELDS] as $field) {
$query_params['userinfo'] .= ', ui.' . $field['name'] . ' AS ' . $field['name'];
}
}
/**
* Should we rewrite the email cache file?
function admin_games_maps()
{
$tpl = new smarty();
$tpl->assign('games', get_games_form());
$tpl->assign('maps', get_maps());
ob_start();
$tpl->display(DESIGN . '/tpl/admin/maps.html');
$content = ob_get_contents();
ob_end_clean();
main_content(MAPS, $content, '', 1);
}
function matchrxn($qrxn, $crxn, $cmaps, $options)
{
global $use_cmmmsrv;
global $ostype;
global $MATCHMOL;
global $n_labels;
global $n_maps;
global $map_list;
global $debug;
$result = TRUE;
$rxndescr = analyze_rxnfile($qrxn);
$nqrmol = get_nrmol($rxndescr);
$nqpmol = get_npmol($rxndescr);
$rxndescr = analyze_rxnfile($crxn);
$ncrmol = get_nrmol($rxndescr);
$ncpmol = get_npmol($rxndescr);
$optstr = $options;
if ($nqrmol == 0 && $ncpmol == 0) {
$result = FALSE;
}
// some initial check
if ($nqpmol == 0 && $ncrmol == 0) {
$result = FALSE;
}
if ($result == TRUE) {
if ($use_cmmmsrv == "y") {
$separator = "\$\$\$\$";
$lf = "\n";
} else {
$separator = "\\\$\\\$\\\$\\\$";
if ($ostype == 1) {
$lf = "\n";
}
// Linux
if ($ostype == 2) {
$lf = "\r\n";
}
// Windows
}
$allmol = array();
$qrmol = array();
$qpmol = array();
$crmol = array();
$cpmol = array();
$allmol = explode("\$MOL\r\n", $qrxn);
$header = $allmol[0];
$label_list = array();
$map_list = array();
$n_labels = 0;
$n_maps = 0;
$n_qmaps = 0;
$n_cmaps = 0;
$qmap_list = array();
$cmap_list = array();
if ($nqrmol > 0) {
for ($i = 0; $i < $nqrmol; $i++) {
$qrmol[$i] = $allmol[$i + 1];
$mnum = $i + 1;
if ($debug > 2) {
debug_output("query reactant no. {$mnum}:\n{$qrmol[$i]}\n");
}
}
}
if ($nqpmol > 0) {
for ($i = 0; $i < $nqpmol; $i++) {
$qpmol[$i] = $allmol[$i + 1 + $nqrmol];
$mnum = $i + 1;
if ($debug > 2) {
debug_output("query product no. {$mnum}:\n{$qpmol[$i]}\n");
}
}
}
$qmaps = get_maps($qrxn);
$qmap_list = explode(",", $qmaps);
$n_qmaps = count($qmap_list);
if (strlen($qmaps) < 8) {
$n_qmaps = 0;
}
$allmol = "";
$allmol = explode("\$MOL\r\n", $crxn);
$header = $allmol[0];
// reset labels and maps
$n_maps = 0;
$map_list = "";
$n_labels = 0;
$label_list = "";
if ($ncrmol > 0) {
for ($i = 0; $i < $ncrmol; $i++) {
$crmol[$i] = $allmol[$i + 1];
$mnum = $i + 1;
if ($debug > 2) {
debug_output("candidate reactant no. {$mnum}:\n{$crmol[$i]}\n");
}
}
}
if ($ncpmol > 0) {
for ($i = 0; $i < $ncpmol; $i++) {
$cpmol[$i] = $allmol[$i + 1 + $ncrmol];
$mnum = $i + 1;
if ($debug > 2) {
debug_output("candidate product no. {$mnum}:\n{$cpmol[$i]}\n)");
}
}
}
//echo "<pre>$qrmol[0]\n$qpmol[0]\n\n$crmol[0]\n$cpmol[0]</pre>";
//$cmaps = get_maps($crxn); // this is now retrieved from rxnstructable
$cmap_list = explode(",", $cmaps);
$n_cmaps = count($cmap_list);
if (strlen($cmaps) < 8) {
$n_cmaps = 0;
}
// set up and initialize the two match matrices (reactant and product)
$rmm = array();
for ($iq = 0; $iq < $nqrmol; $iq++) {
for ($ic = 0; $ic < $ncrmol; $ic++) {
$rmm[$iq][$ic] = "0";
}
}
$pmm = array();
for ($iq = 0; $iq < $nqpmol; $iq++) {
for ($ic = 0; $ic < $ncpmol; $ic++) {
$pmm[$iq][$ic] = "0";
}
}
if ($n_qmaps > 0 && $n_cmaps > 0) {
$optstr .= "n";
}
$mmcmd = "{$MATCHMOL} {$optstr} -";
//============ first match the reactants, if there are any
if ($nqrmol > 0 && $ncrmol > 0) {
// assemble the SDF files to be passed to matchmol
for ($iq = 0; $iq < $nqrmol; $iq++) {
$qmol = rtrim($qrmol[$iq]);
$sdf = $qmol . $lf . $separator . $lf;
for ($ic = 0; $ic < $ncrmol; $ic++) {
$cmol = rtrim($crmol[$ic]);
$sdf .= $cmol . $lf . $separator . $lf;
}
// end for ($ic ...
//echo "<pre>reactant query for query reactant no. $iq:\n$sdf\n</pre>";
// now do the match
if ($use_cmmmsrv == "y") {
$matchresult = filterthroughcmmm("{$sdf}", "#### matchmol:{$optstr}");
} else {
if ($ostype == 1) {
$matchresult = filterthroughcmd("{$sdf} ", "{$mmcmd}");
}
if ($ostype == 2) {
$sdf = str_replace("\r", "", $sdf);
// for Windows
$sdf = str_replace("\n", "\r\n", $sdf);
// for Windows
$matchresult = filterthroughcmd2("{$sdf} ", "{$mmcmd}");
}
}
//echo "<pre>match result for for query reactant no. $iq:\n$matchresult\n</pre>";
$br = explode("\n", $matchresult);
$nr = count($br);
for ($ir = 0; $ir < $nr; $ir++) {
if (strpos($br[$ir], ":T") !== FALSE) {
$rmm[$iq][$ir] = $br[$ir];
}
}
}
// end for ($iq ....
// we have to clean up the matrix to remove multiple hits of one query mol
if ($nqrmol > 1) {
$rmm = cleanup_matrix($rmm);
}
}
// end if ($nqrmol > 0)
//============ now match the products, if there are any
if ($nqpmol > 0 && $ncpmol > 0) {
// assemble the SDF files to be passed to matchmol
for ($iq = 0; $iq < $nqpmol; $iq++) {
$qmol = rtrim($qpmol[$iq]);
$sdf = $qmol . $lf . $separator . $lf;
for ($ic = 0; $ic < $ncpmol; $ic++) {
$cmol = rtrim($cpmol[$ic]);
$sdf .= $cmol . $lf . $separator . $lf;
}
// end for ($ic ...
//echo "<pre>product query for query product no. $iq:\n$sdf\n</pre>";
// now do the match
//$sdf = str_replace("\r","",$sdf);
if ($use_cmmmsrv == "y") {
$matchresult = filterthroughcmmm("{$sdf}", "#### matchmol:{$optstr}");
} else {
if ($ostype == 1) {
$matchresult = filterthroughcmd("{$sdf} ", "{$mmcmd}");
}
if ($ostype == 2) {
$sdf = str_replace("\r", "", $sdf);
// for Windows
$sdf = str_replace("\n", "\r\n", $sdf);
// for Windows
$matchresult = filterthroughcmd2("{$sdf} ", "{$mmcmd}");
}
}
//echo "<pre>match result for for query product no. $iq:\n$matchresult\n</pre>";
$br = explode("\n", $matchresult);
$nr = count($br);
for ($ir = 0; $ir < $nr; $ir++) {
if (strpos($br[$ir], ":T") !== FALSE) {
$pmm[$iq][$ir] = $br[$ir];
}
}
}
// end for ($iq ....
// we have to clean up the matrix to remove multiple hits of one query mol
if ($nqpmol > 1) {
$pmm = cleanup_matrix($pmm);
}
}
// end if ($nqpmol > 0)
//echo "<pre>\n";
if ($debug == 4 || $debug == 6) {
echo "<pre>now the reactant match matrix looks like this:\n";
print_matrix($rmm);
echo "and the product match matrix looks like this:\n";
print_matrix($pmm);
echo "</pre>";
}
// and finally we check if every query structure matches a candidate structure
// first check: reactants
$foundallreactants = TRUE;
for ($iq = 0; $iq < $nqrmol; $iq++) {
$foundthisreactant = FALSE;
for ($ic = 0; $ic < $ncrmol; $ic++) {
if (strpos($rmm[$iq][$ic], ":T") !== FALSE) {
$foundthisreactant = TRUE;
}
}
if ($foundthisreactant == FALSE) {
$foundallreactants = FALSE;
}
}
// second check: products
$foundallproducts = TRUE;
for ($iq = 0; $iq < $nqpmol; $iq++) {
$foundthisproduct = FALSE;
for ($ic = 0; $ic < $ncpmol; $ic++) {
if (strpos($pmm[$iq][$ic], ":T") !== FALSE) {
$foundthisproduct = TRUE;
}
}
if ($foundthisproduct == FALSE) {
$foundallproducts = FALSE;
}
}
// now let's draw the conclusion:
if ($foundallreactants == FALSE || $foundallproducts == FALSE) {
$result = FALSE;
} else {
// now we should consider atom mappings, if present
if ($n_qmaps > 0 && $n_cmaps > 0) {
$allmapsconfirmed = TRUE;
for ($iqm = 0; $iqm < $n_qmaps; $iqm++) {
$thismapconfirmed = FALSE;
if ($debug > 2) {
debug_output("now checking query map no. {$iqm}: {$qmap_list[$iqm]}\n");
}
// split map into reactant and product part
$qmarr = explode("=", $qmap_list[$iqm]);
$qrpart = $qmarr[0];
$qppart = $qmarr[1];
if ($debug > 2) {
debug_output("query reactant: {$qrpart} query product: {$qppart}\n");
}
// extract mol id and atom id
$qrarr = explode(":", $qrpart);
$qrmid = $qrarr[0];
$qrmidn = str_replace("r", "", $qrmid);
$qrmidn = intval($qrmidn) - 1;
$qraid = $qrarr[1];
$qparr = explode(":", $qppart);
$qpmid = $qparr[0];
$qpmidn = str_replace("p", "", $qpmid);
$qpmidn = intval($qpmidn) - 1;
$qpaid = $qparr[1];
// now look up in the reactant match matrix which candidate reactant(s)
// match with this query reactant
if ($debug > 2) {
debug_output(" checking reactant match matrix for query reactant {$qrmid} ({$qrmidn})\n");
}
for ($irmm = 0; $irmm < $ncrmol; $irmm++) {
if ($rmm[$qrmidn][$irmm] !== "0") {
// assemble the id string
$crmidn = $irmm;
$crmid = $crmidn + 1;
$crmid = "r" . $crmid . ":";
if ($debug > 2) {
debug_output(" ---- there is a matching candidate reactant: {$crmid} ({$crmidn})\n");
}
// now check if there is a suitable counterpart on the product side
if ($debug > 2) {
debug_output(" checking product match matrix for query product {$qpmid} ({$qpmidn})\n");
}
for ($ipmm = 0; $ipmm < $ncpmol; $ipmm++) {
if ($pmm[$qpmidn][$ipmm] !== "0") {
// assemble the id string
$cpmidn = $ipmm;
$cpmid = $cpmidn + 1;
$cpmid = "p" . $cpmid . ":";
if ($debug > 2) {
debug_output(" ---- there is a matching candidate product: {$cpmid} ({$cpmidn})\n");
}
// now we can check the atom mappings....
// first, go through the list of candidate maps and look for a map
for ($icm = 0; $icm < $n_cmaps; $icm++) {
$cmarr = explode("=", $cmap_list[$icm]);
$crpart = $cmarr[0];
$cppart = $cmarr[1];
if ($debug > 2) {
debug_output(" checking query map {$iqm} against candidate map {$icm}\n");
}
if ($debug > 2) {
debug_output(" ==== candidate reactant: {$crpart} candidate product: {$cppart}\n");
}
// extract mol id and atom id
$crarr = explode(":", $crpart);
$crmid2 = $crarr[0];
$crmid2n = str_replace("r", "", $crmid2);
$crmid2n = intval($crmid2n) - 1;
$craid2 = trim($crarr[1]);
$cparr = explode(":", $cppart);
$cpmid2 = $cparr[0];
$cpmid2n = str_replace("p", "", $cpmid2);
$cpmid2n = intval($cpmid2n) - 1;
$cpaid2 = trim($cparr[1]);
// check for presence of both mol identifiers
if (strpos($crpart, $crmid) !== FALSE && strpos($cppart, $cpmid) !== FALSE) {
if ($debug > 2) {
debug_output(" **** found a map: {$cmap_list[$icm]}\n");
}
// now do some atom-number translation...
// first, get the atom match matrix for this pair of reactants
$rmmitem = $rmm[$qrmidn][$irmm];
$rmmitemarr = explode(":T ", $rmmitem);
$rmmitem = $rmmitemarr[1];
// next, get the atom match matrix for this pair of products
$pmmitem = $pmm[$qpmidn][$ipmm];
$pmmitemarr = explode(":T ", $pmmitem);
$pmmitem = $pmmitemarr[1];
if ($debug > 2) {
debug_output(" reactant atom map: {$rmmitem}\n");
debug_output(" product atom map: {$pmmitem}\n");
}
// now extract all possible orientations from the atom maps
$ror = explode(".", $rmmitem);
$n_ror = count($ror);
$por = explode(".", $pmmitem);
$n_por = count($por);
for ($i_ror = 0; $i_ror < $n_ror; $i_ror++) {
if ($debug > 4) {
debug_output(" trying reactant orientation no. {$i_ror}: {$ror[$i_ror]}\n");
}
$ratom = $ror[$i_ror];
$ratomarr = explode(";", $ratom);
foreach ($ratomarr as $ra) {
//echo " reactant atom pair: $ra\n";
$ra2arr = explode("=", $ra);
$rqa = $ra2arr[0];
$rcalist = "";
$rcalist = $ra2arr[1];
if ($debug > 4) {
debug_output(" query reactant atom {$rqa} corresponds to candidate reactant atom(s): {$rcalist}\n");
}
if ($qraid == $rqa) {
if ($debug > 4) {
debug_output(" .... this is interesting! (rqa = {$rqa})\n");
}
// get all sub-orientations
$rca2arr = explode(",", $rcalist);
foreach ($rca2arr as $rca) {
$rca = trim($rca);
// this is important!
if ($debug > 4) {
debug_output(" labelled query reactant atom {$rqa} corresponds to candidate reactant atom: {$rca}\n");
debug_output(" craid2 = {$craid2} rca = {$rca} rqa = {$rqa}\n");
}
if ($rca == $craid2) {
if ($debug > 4) {
debug_output(" found a label counterpart for {$qraid}: {$craid2}!!\n");
debug_output(" who is the counterpart of query product atom {$qpaid}? is it {$cpaid2}?\n");
}
// now look up the product end...
// check all possible reactant orientations....
for ($i_por = 0; $i_por < $n_por; $i_por++) {
if ($debug > 4) {
debug_output(" trying product orientation no. {$i_por}: {$por[$i_por]}\n");
}
$patom = $por[$i_por];
$patomarr = explode(";", $patom);
foreach ($patomarr as $pa) {
//echo " product atom pair: $pa\n";
$pa2arr = explode("=", $pa);
$pqa = trim($pa2arr[0]);
$pcalist = "";
$pcalist = $pa2arr[1];
if ($debug > 6) {
debug_output(" query product atom {$pqa} corresponds to candidate product atom(s): {$pcalist}\n");
}
if ($qpaid == $pqa) {
if ($debug > 6) {
debug_output(" NOW IT BECOMES INTERESTING!\n");
}
// again, get all sub-orientations
$pca2arr = explode(",", $pcalist);
foreach ($pca2arr as $pca) {
$pca = trim($pca);
// this is important!
if ($debug > 6) {
debug_output(" query product atom {$qpaid} corresponds to candidate product atom: {$pca}\n");
}
if ($cpaid2 == $pca) {
$thismapconfirmed = TRUE;
if ($debug > 2) {
debug_output("BINGO!!!! confirmed query map no. {$iqm}\n");
}
break 7;
// immediately stop looping (7 depth levels!)
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
if ($thismapconfirmed == FALSE) {
$allmapsconfirmed = FALSE;
if ($debug > 2) {
debug_output("==== could not confirm query map no. {$iqm}\n");
}
}
}
if ($allmapsconfirmed == FALSE) {
$result = FALSE;
}
}
// end of "if we have both maps..."
}
}
// end if ($result == TRUE) from initial check
return $result;
}
