} elseif (!isset($ChartKin)) {
die("No output file specified. \n");
}
//Iterate through the current directory for .pdb files to use
$ending = ".pdb";
$dirHandle = opendir($inpdbdir);
while (($file = readdir($dirHandle)) !== false) {
//make filename include designated directory + name
$file = $inpdbdir . "/" . $file;
if (is_file($file) && $ending == substr($file, -strlen($ending))) {
$pdbname[] = $file;
}
}
closedir($dirHandle);
print_r($pdbname);
makeChartKin($pdbname, $ChartKin);
/*
Multigraph:
Plotting in multiple ways the data outputs from MolProbity Validation web-service.
In the X, Y plane:
(+)X direction: linearly validated quality measures
- crystallographic resolution
- NMR constrains / residue
(+)Y direction: MolProbity global measures evaluated over an entire model
- clashscore
- mainchain H-bond score
- % rotamer outliers or raw number
- % rama outliers or raw number
$labbookEntry .= "<br>" . linkKinemage("{$ensemble['prefix']}multi.kin", "Multi-criterion kinemage");
$labbookEntry .= "</p>\n";
}
if ($opts['doRamaPDF']) {
setProgress($tasks, 'ramapdf');
// updates the progress display if running as a background job
$outfile = "{$chartDir}/{$ensemble['prefix']}rama.pdf";
makeRamachandranPDF($infile, $outfile);
$labbookEntry .= "<h3>Multi-model Ramachandran plot</h3>\n";
$labbookEntry .= "<p>" . linkAnyFile("{$ensemble['prefix']}rama.pdf", "Ramachandran plot PDF") . "</p>\n";
}
if ($opts['doMultiGraph']) {
setProgress($tasks, 'multigraph');
// updates the progress display if running as a background job
$outfile = "{$kinDir}/{$ensemble['prefix']}multigraph.kin";
makeChartKin($infiles, $outfile);
$labbookEntry .= "<div class='alert'>\n<center><h3>ALPHA TEST</h3></center>\n";
$labbookEntry .= "Not suitable for use by the general public: " . linkKinemage("{$ensemble['prefix']}multigraph.kin", "Multi-criterion graph");
$labbookEntry .= "</div>\n";
}
if ($opts['doMultiModelChart']) {
setProgress($tasks, 'multichart');
// updates the progress display if running as a background job
$outfile = "{$kinDir}/{$ensemble['prefix']}mmmcc.kin";
// Multi-Model Multi-Criterion Chart
writeMultimodelChart($infiles, $outfile);
$labbookEntry .= "<div class='alert'>\n<center><h3>ALPHA TEST</h3></center>\n";
$labbookEntry .= "Not suitable for use by the general public: " . linkKinemage("{$ensemble['prefix']}mmmcc.kin", "Multi-chart mockup");
$labbookEntry .= "</div>\n";
}
setProgress($tasks, null);