#!/usr/bin/env php
<?php # (jEdit options) :folding=explicit:collapseFolds=1:
/*****************************************************************************
INPUTS / SWITCHES (via $_SERVER['argv']):
    inDir           the a directory of files ending in ".pdb"
    outDir          a place to put the output files
    -q              quiet mode (no progress messages)

OUTPUTS / RESULTS:
    Renames Ser and Ile H's to PDB standard.
    Needed for C. Dobson's ubiquitin models.

*****************************************************************************/
// 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');
// 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() {}
#}}}########################################################################

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

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

#{{{ renameHydrogens - rename Ser OG and Ile CD hydrogens to PDB std.
############################################################################
/**
* Documentation for this function.
*/
function renameHydrogens($infile, $outfile)
{
    $in = fopen($infile, 'rb');
    $out = fopen($outfile, 'wb');
    while(!feof($in))
    {
        $s = fgets($in, 1024);
        $s = preg_replace('/^(ATOM.{8}) HG1(.SER.*)$/', '${1} HG $2', $s);
        $s = preg_replace('/^(ATOM.{8}) HD([123])(.ILE.*)$/', '${1}${2}HD1${3}', $s);
        fwrite($out, $s);
    }
    fclose($out);
    fclose($in);
}
#}}}########################################################################

# MAIN - the beginning of execution for this page
############################################################################
// Default options
$optVerbose = true;

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

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

if($optVerbose)
{
    echo "INPUT   : ".realpath($inDir)."\n";
    echo "OUTPUT  : ".realpath($outDir)."\n";
}

foreach(listDir($inDir) as $inFile) if(endsWith($inFile, ".pdb"))
{
    if($optVerbose) echo "Renaming Hs for $inFile\n";
    renameHydrogens($inDir.'/'.$inFile, $outDir.'/'.$inFile);
}

############################################################################
// Clean up and go home
//mpDestroySession(); // only call this if we created one
?>
