############################################################################
/**
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################
# MAIN - the beginning of execution for this page
############################################################################
// Security check on filename
$file = realpath($_REQUEST['file']);
if (!$file || !startsWith($file, realpath($_SESSION['dataDir']))) {
mpLog("security:Attempt to access '{$file}' as '{$_REQUEST['file']}'");
die("Security failure: illegal file request '{$_REQUEST['file']}'");
}
$tmp = mpTempfile('tmp_pdb_trim_');
reduceTrim($file, $tmp);
$name = basename($file);
if (preg_match('/H[0-9]*.pdb$/', $name)) {
// uses preg_split to split the name into an array with the H from the name missing.
$nameArray = preg_split('/H([0-9]*.pdb)$/', $name, -1, PREG_SPLIT_DELIM_CAPTURE);
$name = $nameArray[0] . $nameArray[1];
} elseif (preg_match('/H_reg[0-9]*.pdb$/', $name)) {
// uses preg_split to split the name into an array with the H from the name missing.
$nameArray = preg_split('/H_reg([0-9]*.pdb)$/', $name, -1, PREG_SPLIT_DELIM_CAPTURE);
$name = $nameArray[0] . $nameArray[1];
}
### FUNKY: This turns into a binary file download rather than an HTML page,
### and then calls die(), leaving the user on the original HTML page.
// These lines may be required by Internet Explorer
header("Pragma: public");
header("Cache-Control: must-revalidate, post-check=0, pre-check=0");
function onEditPDB()
{
$req = $_REQUEST;
//if($req['cmd'] == 'Cancel')
if ($req['cmd'] == 'Go back') {
pageGoto("editpdb_setup1.php");
return;
}
// Otherwise, moving forward:
$oldID = $req['modelID'];
$oldModel = $_SESSION['models'][$oldID];
$inpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $oldModel['pdb'];
$newModel = createModel($oldID . "_edit");
$newID = $newModel['id'];
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
$s = "";
if (is_array($req['removechain']) && count($req['removechain']) > 0) {
removeChains($inpath, $outpath, $req['removechain']);
$s .= "<p>You created {$newModel['pdb']} by removing chain(s) " . implode(', ', $req['removechain']) . " from {$oldModel['pdb']}.\n";
mpLog("editpdb:Removed chains from a PDB file");
} else {
copy($inpath, $outpath);
}
$resolu = $req['resolution'] + 0;
$oldRes = $oldModel['stats']['resolution'] + 0;
if ($resolu && ($oldRes == 0 || $oldRes != $resolu)) {
$remark2 = sprintf("REMARK 2 \nREMARK 2 RESOLUTION. %.2f ANGSTROMS. \n", $resolu);
replacePdbRemark($outpath, $remark2, 2);
$s .= "<p>You manually set the resolution for {$newModel['pdb']}.\n";
mpLog("editpdb:Changed/set resolution for a PDB file");
}
if ($req['removeHs']) {
$newModel = createModel($oldID . "_trimmed");
$newID = $newModel['id'];
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
reduceTrim($inpath, $outpath);
$s .= "<p>You created {$newModel['pdb']} by removing hydrogens from {$oldModel['pdb']}.\n";
mpLog("editpdb:Removed hydrogens from a PDB file");
}
$newModel['stats'] = pdbstat($outpath);
$newModel['history'] = "Edited {$oldModel['pdb']}";
$newModel['isUserSupplied'] = $oldModel['isUserSupplied'];
$_SESSION['models'][$newID] = $newModel;
$_SESSION['lastUsedModelID'] = $newID;
// this is now the current model
$details = describePdbStats($newModel['stats'], true);
$s .= "<ul>\n";
foreach ($details as $detail) {
$s .= "<li>{$detail}</li>\n";
}
$s .= "</ul>\n";
$entrynum = addLabbookEntry("Created PDB file {$newModel['pdb']}", $s, "{$oldID}|{$newID}", "auto", "scissors.png");
pageGoto("generic_done.php", array('labbookEntry' => $entrynum));
}
function removeHydrogens($inpath, $outpath)
{
$tasks = getProgressTasks();
$tasks['reducetrim'] = "Remove hydrogens to avoid possible conflict with hydrogen lengths";
$tmp1 = mpTempfile("tmp_pdb_");
setProgress($tasks, 'reducetrim');
reduceTrim($inpath, $tmp1);
copy($tmp1, $outpath);
// Clean up temp files
unlink($tmp1);
setProgress($tasks, null);
// all done
}
