#!/usr/bin/env php
<?php # (jEdit options) :folding=explicit:collapseFolds=1:
/*****************************************************************************
    Processes a directory full of PDB files non-recursively and outputs
    a list of all the Ramachanadran scores
    
 -> We assume all files already have H's added! <-

INPUTS (via $_SERVER['argv']):
    the path to a directory; *.pdb will be processed

OUTPUTS:

*****************************************************************************/
// EVERY *top-level* page must start this way:
// 1. Define it's relationship to the root of the MolProbity installation.
// Pages in subdirectories of lib/ or public_html/ will need more "/.." 's.
    if(!defined('MP_BASE_DIR')) define('MP_BASE_DIR', realpath(dirname(__FILE__).'/..'));
// 2. Include core functionality - defines constants, etc.
    require_once(MP_BASE_DIR.'/lib/core.php');
    require_once(MP_BASE_DIR.'/lib/model.php');
    require_once(MP_BASE_DIR.'/lib/analyze.php');
    require_once(MP_BASE_DIR.'/lib/visualize.php');
// 3. Restore session data. If you don't want to access the session
// data for some reason, you must call mpInitEnvirons() instead.
    mpInitEnvirons();       // use std PATH, etc.
    //mpStartSession(true);   // create session dir
// 5. Set up reasonable values to emulate CLI behavior if we're CGI
    set_time_limit(0); // don't want to bail after 30 sec!

#{{{ a_function_definition - sumary_statement_goes_here
############################################################################
/**
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################

# MAIN - the beginning of execution for this page
############################################################################
// First argument is the name of this script...
if(is_array($_SERVER['argv'])) foreach(array_slice($_SERVER['argv'], 1) as $arg)
{
    if(!isset($inDir))
        $inDir = $arg;
    else
        die("Too many or unrecognized arguments: '$arg'\n");
}

if(! isset($inDir))
    die("No input directory specified.\n");
elseif(! is_dir($inDir))
    die("Input directory '$inDir' does not exist or is not a directory.\n");

echo "#filename:chain:resType:resNum+iCode:phi:psi:score%:eval:type\n";

// Loop through all PDBs in the provided directory
$h = opendir($inDir);
while(($infile = readdir($h)) !== false)
{
    $infile = "$inDir/$infile";
    if(is_file($infile) && endsWith($infile, ".pdb"))
    {
        $filename = basename($infile);
        $tmp = mpTempfile();
        
        // Run analysis; load data
        runRamachandran($infile, $tmp);
        $rama = loadRamachandran($tmp);
        unlink($tmp);
        
        foreach($rama as $r)
            echo "$filename:$r[chainID]:$r[resType]:".trim($r['resNum'].$r['insCode']).":$r[phi]:$r[psi]:$r[scorePct]:$r[eval]:$r[type]\n";
    }
}
closedir($h);

############################################################################
// Clean up and go home
?>
