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check_reaction_mapping.php
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check_reaction_mapping.php
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<?php
/*
Copyright 2006-2018 Felix Rudolphi and Lukas Goossen
open enventory is distributed under the terms of the GNU Affero General Public License, see COPYING for details. You can also find the license under http://www.gnu.org/licenses/agpl.txt
open enventory is a registered trademark of Felix Rudolphi and Lukas Goossen. Usage of the name "open enventory" or the logo requires prior written permission of the trademark holders.
This file is part of open enventory.
open enventory is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
open enventory is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with open enventory. If not, see <http://www.gnu.org/licenses/>.
*/
require_once "lib_global_funcs.php";
require_once "lib_molfile.php";
require_once "lib_reaction_mapping.php";
function getAtomInfoText(& $molecule,$atom_no) {
$atom=& $molecule["atoms"][$atom_no];
// Num, symbol, charge, isotope
$retval="";
if ($atom["iso"]) {
$retval.="<sup>".round($atom["m"])."</sup>";
}
$retval.=$atom["s"]."<sup>".getChargeText($atom["o_c"])."</sup>(".$atom_no.")";
return $retval;
}
function getAtomInfo(& $molecule,$atom_no) {
$atom=& $molecule["atoms"][$atom_no];
$retval=getAtomInfoText($molecule,$atom_no)."[";
// Neighbours (bond, num, symbol, charge, isotope)
$neighbour_info=array();
for ($a=0;$a<count($atom[NEIGHBOURS]);$a++) {
$neighbour_atom_no=$atom[NEIGHBOURS][$a];
$neighbour_info[]=SMaddBond($molecule["bondsFromNeighbours"][$atom_no][$neighbour_atom_no][ORIG_BOND_ORDER]).getAtomInfoText($molecule,$neighbour_atom_no);
}
$retval.=join(",",$neighbour_info)."]<br/>";
return $retval;
}
/*--------------------------------------------------------------------------------------------------
/ Function: checkReactionMapping
/
/ Purpose: applies comparison functions like similarity (=> fingerprints), substructure and identity (stereo and non-stereo) on molecules passed as data structures and compares with predefined results
/
/ Parameter:
/ & $reaction : reaction data structure to be mapped
/ $assignment_table : assignment should be like this
/ $paramHash
/
/ Return : no return value, direct output
/------------------------------------------------------------
/ History:
/ 2010-01-10 RUD01 Created
..--------------------------------------------------------------------------------------------------*/
function checkReactionMapping(& $reaction,$assignment_tables,$paramHash) {
if (isset($_REQUEST["identifier"])){
if ($_REQUEST["identifier"]!=$paramHash["identifier"]) {
return;
}
// return image
$paramHash["drawAssignment"]=true;
mapReaction($reaction,$paramHash);
header(getHeaderFromMime(getMimeFromExt("gif")));
echo getReactionGif($reaction,rxn_gif_x,rxn_gif_y,0,1,6);
return;
}
mapReaction($reaction,$paramHash);
if (!in_array($reaction["assignment_table"],$assignment_tables)) {
echo "Problem with ".$paramHash["identifier"].":".
"<img src=\"check_reaction_mapping.php?identifier=".$paramHash["identifier"]."&no_cache=".time()."\">".
"<br clear=\"all\">";
// costs twice the cpu time, but ok
// build $atom_map_inverted
$atom_map_inverted=array();
$idx=0;
for ($mol_reactant=0;$mol_reactant<$reaction["reactants"];$mol_reactant++) {
$reactant=& $reaction["molecules"][$mol_reactant];
for ($reac_atom_no=0;$reac_atom_no<count($reactant["atoms"]);$reac_atom_no++) {
$atom_map_inverted[$idx]=array($mol_reactant,$reac_atom_no);
$idx++;
}
}
// show differences
foreach ($assignment_tables[0] as $mol_product => $subtable) {
foreach ($subtable as $prod_atom_no => $matching_atom_no) {
$exp_match=$reaction["assignment_table"][$mol_product][$prod_atom_no];
if ($exp_match==$matching_atom_no) {
continue;
}
// Info on atom $prod_atom_no and $matching_atom_no
list($mol_reactant,$reac_atom_no)=$atom_map_inverted[$matching_atom_no];
$prod_atom_info=getAtomInfo($reaction["molecules"][ $mol_product+$reaction["reactants"] ],$prod_atom_no);
$true_atom_info=getAtomInfo($reaction["molecules"][$mol_reactant],$reac_atom_no);
if (empty($exp_match)) { // not matched
echo "Did not assign ".$prod_atom_info."Should have been ".$true_atom_info;
}
else { // matched wrong
list($wrong_mol_reactant,$wrong_reac_atom_no)=$atom_map_inverted[$exp_match];
echo $prod_atom_info." was matched (".$reaction["assignment_quality"][$mol_product][$prod_atom_no].") to ".getAtomInfo($reaction["molecules"][$wrong_mol_reactant],$wrong_reac_atom_no)."Should have been ".$true_atom_info;
}
}
}
echo "If this is false alarm (check image carefully), you can add <br/>";
var_export($reaction["assignment_table"]);
echo "<hr>";
}
else {
echo $paramHash["identifier"]." is correct<hr>";
}
}
if (isset($_REQUEST["identifier"])) {
pageHeader(true,false,true,false);
}
else {
pageHeader();
echo stylesheet."</head>
<body>".s("check_for_errors").":<br/>";
}
$malonate='$RXN
open enventory Fri, 12.06.2009 10:28:01
5 1
$MOL
Cc1cccc(C)c1Br
open enventory Sat, 24.05.2008 21:31:17
9 9 0 0 0 0 0 0 0 0999 V2000
5.2578 -2.6398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5435 -2.2290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2562 -3.4636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9778 -2.2226 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
3.8280 -3.4664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8277 -2.6379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5423 -3.8771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5450 -1.4010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9751 -3.8892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 2 0 0 0 0
3 1 1 0 0 0 0
4 1 1 0 0 0 0
5 7 1 0 0 0 0
6 2 1 0 0 0 0
7 3 2 0 0 0 0
8 2 1 0 0 0 0
9 3 1 0 0 0 0
5 6 2 0 0 0 0
M END
$MOL
CCOC(=O)CC(=O)OCC
open enventory Sat, 24.05.2008 21:32:31
11 10 0 0 0 0 0 0 0 0999 V2000
5.1292 -2.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4125 -2.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8417 -2.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4125 -1.1958 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.8417 -1.1958 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.5583 -2.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7000 -2.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.9833 -2.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2667 -2.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2725 -2.0245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.9873 -2.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 1 0 0 0 0
4 2 2 0 0 0 0
5 3 2 0 0 0 0
6 3 1 0 0 0 0
7 2 1 0 0 0 0
8 7 1 0 0 0 0
9 8 1 0 0 0 0
6 10 1 0 0 0 0
2 1 1 0 0 0 0
10 11 1 0 0 0 0
M END
$MOL
[Pd@@]234789([C@H](c1ccccc1)[C@@H]2C(=O)[C@H]3[C@@H]4c5ccccc5)[C@H](c6ccccc6)[C@@H]7C(=O)[C@H]8[C@@H]9c%10ccccc%10
open enventory Sat, 24.05.2008 21:31:33
37 46 0 0 0 0 0 0 0 0999 V2000
4.9042 -2.6167 0.0000 Pd 0 0 0 0 0 0 0 0 0 0 0 0
5.1542 -0.6917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1542 -0.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7542 -4.8375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5750 -4.5542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0167 -1.0125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7125 -0.5292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9250 -4.7417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9167 -4.1625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7292 -0.2917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0875 -5.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8667 0.2875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.9667 -5.4167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.3750 -0.8292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4625 -1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4375 -4.2542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5625 -3.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3167 -1.7292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2375 -1.3917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9292 -0.6542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0417 -0.7667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1000 -4.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6000 -3.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6792 -3.6542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8625 -4.1125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7625 -1.9042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6375 -1.7917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3542 -1.0542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4917 -0.9250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7750 -3.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3917 -3.6042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1125 -3.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3292 -3.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3292 -1.4792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2042 -1.6375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4792 -3.2292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.9125 -3.5875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 6 0 0 0
3 1 1 6 0 0 0
4 1 1 6 0 0 0
5 1 1 6 0 0 0
6 1 1 6 0 0 0
7 1 1 6 0 0 0
8 1 1 6 0 0 0
9 1 1 6 0 0 0
10 3 1 0 0 0 0
11 5 1 0 0 0 0
12 10 2 0 0 0 0
13 11 2 0 0 0 0
14 7 1 0 0 0 0
15 6 1 0 0 0 0
16 8 1 0 0 0 0
17 9 1 0 0 0 0
18 15 1 0 0 0 0
19 14 2 0 0 0 0
20 14 1 0 0 0 0
21 15 2 0 0 0 0
22 17 1 0 0 0 0
23 16 1 0 0 0 0
24 17 2 0 0 0 0
25 16 2 0 0 0 0
26 18 2 0 0 0 0
27 19 1 0 0 0 0
28 20 2 0 0 0 0
29 21 1 0 0 0 0
30 22 2 0 0 0 0
31 25 1 0 0 0 0
32 23 2 0 0 0 0
33 24 1 0 0 0 0
34 29 2 0 0 0 0
35 28 1 0 0 0 0
36 31 2 0 0 0 0
37 33 2 0 0 0 0
9 4 1 0 0 0 0
8 5 1 0 0 0 0
7 2 1 0 0 0 0
6 3 1 0 0 0 0
4 11 1 0 0 0 0
2 10 1 0 0 0 0
37 30 1 0 0 0 0
36 32 1 0 0 0 0
35 27 2 0 0 0 0
26 34 1 0 0 0 0
M END
$MOL
CC(C)(C)P(C(C)(C)C)C(C)(C)C
open enventory Sat, 24.05.2008 21:30:29
13 12 0 0 0 0 0 0 0 0999 V2000
5.1250 -2.8292 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
5.1250 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4125 -3.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8375 -3.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9958 -2.5208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8292 -3.9625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6917 -3.6583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2542 -2.5208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4208 -3.9625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5583 -3.6583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9500 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1250 -1.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 1 1 0 0 0 0
4 1 1 0 0 0 0
5 3 1 0 0 0 0
6 3 1 0 0 0 0
7 3 1 0 0 0 0
8 4 1 0 0 0 0
9 4 1 0 0 0 0
10 4 1 0 0 0 0
11 2 1 0 0 0 0
12 2 1 0 0 0 0
13 2 1 0 0 0 0
M END
$MOL
[K]OP(=O)(O[K])O[K]
Marvin 07210810312D
8 4 0 0 0 0 999 V2000
1.9012 -0.6135 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
1.1625 -0.9809 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
2.6399 -0.9809 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
1.9012 0.1252 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
1.9012 -1.3522 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7696 -0.4420 0.0000 K 0 3 0 0 0 0 0 0 0 0 0 0
1.0018 -0.4125 0.0000 K 0 3 0 0 0 0 0 0 0 0 0 0
1.8857 0.7366 0.0000 K 0 3 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 1 1 0 0 0 0
4 1 1 0 0 0 0
5 1 2 0 0 0 0
M CHG 6 2 -1 3 -1 4 -1 6 1 7 1 8 1
M END
$MOL
CCOC(=O)C(C(=O)OCC)c1c(C)cccc1C
open enventory Fri, 17.10.2008 11:18:41
19 19 0 0 0 0 0 0 0 0999 V2000
5.0972 0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3827 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3827 -1.0312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0972 -1.4438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8117 -1.0312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8117 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0972 1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8117 1.4438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3827 1.4438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8117 2.2688 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.5261 1.0313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.6683 1.0313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.3827 2.2688 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.9538 1.4438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2393 1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5261 0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2406 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6682 0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2242 0.5083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 2 0 0 0 0
1 7 1 0 0 0 0
2 3 2 0 0 0 0
2 18 1 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
6 19 1 0 0 0 0
7 8 1 0 0 0 0
7 9 1 0 0 0 0
8 10 2 0 0 0 0
8 11 1 0 0 0 0
9 12 1 0 0 0 0
9 13 2 0 0 0 0
11 16 1 0 0 0 0
12 14 1 0 0 0 0
14 15 1 0 0 0 0
16 17 1 0 0 0 0
M END';
$ass_malonate=array(
array( 0 => array( 10 => 14, 7 => 11, 6 => 9, 0 => 10, 9 => 13, 15 => 18, 16 => 19, 11 => 15, 13 => 16, 14 => 17, 2 => 45, 1 => 37, 3 => 53, 4 => 48, 5 => 40, 17 => 61, 18 => 62, 12 => 12, 8 => 10, ), ),
array( 0 => array( 13 => 16, 11 => 15, 8 => 10, 6 => 9, 7 => 11, 9 => 13, 10 => 14, 15 => 18, 16 => 19, 12 => 12, 14 => 17, 3 => 4, 2 => 6, 1 => 2, 0 => 0, 5 => 1, 4 => 5, 18 => 7, 17 => 8, ), ),
array( 0 => array( 13 => 16, 11 => 15, 8 => 10, 6 => 9, 7 => 11, 9 => 13, 10 => 14, 15 => 18, 16 => 19, 12 => 12, 14 => 17, 0 => 0, 1 => 1, 2 => 5, 3 => 4, 4 => 6, 5 => 2, 18 => 8, 17 => 7, ), ),
);
$rxn_malonate=readRxnfile($malonate);
$paramHash["identifier"]="Malonate";
checkReactionMapping($rxn_malonate,$ass_malonate,$paramHash);
$hydroamidation='$RXN
open enventory Mon, 15.06.2009 15:01:37
5 1
$MOL
O=C1CCCCCN1
open enventory Sat, 24.05.2008 21:30:32
8 8 0 0 0 0 0 0 0 0999 V2000
3.7958 -2.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4412 -2.1042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2449 -2.2875 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.5990 -3.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7958 -3.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2454 -3.7708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4412 -3.9542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4240 -3.0230 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
4 6 1 0 0 0 0
2 3 1 0 0 0 0
5 7 1 0 0 0 0
1 2 1 0 0 0 0
6 7 1 0 0 0 0
3 4 1 0 0 0 0
4 8 2 0 0 0 0
M END
$MOL
CCCCC#C
open enventory Sat, 24.05.2008 21:30:35
6 5 0 0 0 0 0 0 0 0999 V2000
6.5668 -3.9048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2897 -4.3230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8559 -3.4957 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1438 -3.9078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4287 -3.4946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7165 -3.9067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 3 0 0 0 0
3 1 1 0 0 0 0
4 3 1 0 0 0 0
5 4 1 0 0 0 0
6 5 1 0 0 0 0
M END
$MOL
[Cl-].[Cl-].[Cl-].[Ru+++]
Marvin 05280812482D
7 0 0 0 0 0 999 V2000
4.4500 -2.9750 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0
4.4500 -1.9750 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0
4.4500 -3.9750 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0
3.1875 -2.9625 0.0000 Ru 0 1 0 0 0 0 0 0 0 0 0 0
1.2964 -1.9446 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4437 -2.8580 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.6795 -3.7714 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
M CHG 4 1 -1 2 -1 3 -1 4 3
M END
$MOL
CCCCP(CCCC)CCCC
open enventory Sat, 24.05.2008 21:30:33
13 12 0 0 0 0 0 0 0 0999 V2000
0.0000 -1.4042 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
-1.1250 -1.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.2792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1250 -1.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2500 -1.4042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1250 0.2833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2458 -1.4042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3750 -1.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1250 1.4083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3750 -1.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.5000 -1.4042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2500 1.9708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5000 -1.4042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 1 1 0 0 0 0
4 1 1 0 0 0 0
5 2 1 0 0 0 0
6 3 1 0 0 0 0
7 4 1 0 0 0 0
8 5 1 0 0 0 0
9 6 1 0 0 0 0
10 7 1 0 0 0 0
11 8 1 0 0 0 0
12 9 1 0 0 0 0
13 10 1 0 0 0 0
M END
$MOL
CN(C)c1ccncc1
open enventory Sat, 24.05.2008 21:30:29
9 9 0 0 0 0 0 0 0 0999 V2000
5.1417 -1.8458 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.1417 -2.6708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1417 -4.3250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.8583 -3.0833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4292 -3.0833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4292 -3.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8583 -3.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4250 -1.4333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8542 -1.4333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 6 1 0 0 0 0
4 2 2 0 0 0 0
5 2 1 0 0 0 0
6 5 2 0 0 0 0
7 4 1 0 0 0 0
8 1 1 0 0 0 0
9 1 1 0 0 0 0
7 3 2 0 0 0 0
M END
$MOL
CCCC/C=C/N1CCCCCC1=O
open enventory Fri, 20.06.2008 12:23:56
14 14 0 0 0 0 0 0 0 0999 V2000
23.1680 -9.2890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.3818 -9.5358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.7013 -9.0778 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
21.6314 -8.2609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.4640 -8.5189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.2330 -7.6931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.0455 -7.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.8613 -7.9738 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
20.9927 -9.5018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.0054 -10.3281 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.2938 -10.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.3066 -11.5772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.5950 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.6077 -12.8262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
4 8 2 0 0 0 0
1 5 1 0 0 0 0
3 9 1 0 0 0 0
4 6 1 0 0 0 0
9 10 2 0 0 0 0
1 2 1 0 0 0 0
10 11 1 0 0 0 0
5 7 1 0 0 0 0
11 12 1 0 0 0 0
3 4 1 0 0 0 0
12 13 1 0 0 0 0
6 7 1 0 0 0 0
13 14 1 0 0 0 0
M END';
$ass_hydroamidation=array(
array( 0 => array( 7 => 7, 3 => 3, 5 => 5, 6 => 6, 4 => 4, 0 => 0, 1 => 1, 2 => 2, 10 => 10, 9 => 8, 8 => 9, 11 => 11, 12 => 12, 13 => 13, ), ),
);
$rxn_hydroamidation=readRxnfile($hydroamidation);
$paramHash["identifier"]="Hydroamidation";
checkReactionMapping($rxn_hydroamidation,$ass_hydroamidation,$paramHash);
$hydrolysis='$RXN
1 2
$MOL
imes v0.1 pre alpha
6 5 0 0 0 0 999 V2000
178.3495 -186.2968 0.0000 C 0 0 0 0 0 0 0
208.3495 -186.2968 0.0000 C 0 0 0 0 0 0 0
223.3495 -212.2776 0.0000 O 0 0 0 0 0 0 0
223.3495 -160.3161 0.0000 O 0 0 0 0 0 0 0
253.3495 -160.3160 0.0000 C 0 0 0 0 0 0 0
268.3495 -134.3353 0.0000 C 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
2 3 2 0 0 0 0
M END
$MOL
imes v0.1 pre alpha
3 2 0 0 0 0 999 V2000
384.3495 -162.8760 0.0000 C 0 0 0 0 0 0 0
414.2811 -160.8517 0.0000 C 0 0 0 0 0 0 0
431.0000 -185.7611 0.0000 O 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
M END
$MOL
imes v0.1 pre alpha
4 3 0 0 0 0 999 V2000
579.1149 -148.2483 0.0000 O 0 0 0 0 0 0 0
575.6324 -178.0455 0.0000 C 0 0 0 0 0 0 0
547.0000 -187.0000 0.0000 C 0 0 0 0 0 0 0
597.7035 -198.3646 0.0000 O 0 0 0 0 0 0 0
3 2 1 0 0 0 0
2 4 1 0 0 0 0
2 1 2 0 0 0 0
M END';
$ass_hydrolysis=array(
array( 1 => array( 1 => 1, 2 => 0, 0 => 3, 3 => 2, ), 0 => array( 1 => 4, 0 => 5, 2 => 3, ), ),
array( 1 => array( 1 => 1, 2 => 0, 0 => 2, 3 => 3, ), 0 => array( 1 => 4, 0 => 5, 2 => 3, ), ),
);
$rxn_hydrolysis=readRxnfile($hydrolysis);
$paramHash["identifier"]="Hydrolysis";
checkReactionMapping($rxn_hydrolysis,$ass_hydrolysis,$paramHash);
$elimination='$RXN
1 1
$MOL
imes v0.1 pre alpha
8 7 0 0 0 0 999 V2000
32.3077 -49.3732 0.0000 C 0 0 0 0 0 0 0
58.1163 -34.0791 0.0000 C 0 0 0 0 0 0 0
84.2658 -48.7829 0.0000 C 0 0 0 0 0 0 0
110.0744 -33.4886 0.0000 C 0 0 0 0 0 0 0
136.2240 -48.1925 0.0000 C 0 0 0 0 0 0 0
162.0326 -32.8982 0.0000 C 0 0 0 0 0 0 0
188.1821 -47.6020 0.0000 C 0 0 0 0 0 0 0
213.9907 -32.3077 0.0000 Br 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
M END
$MOL
imes v0.1 pre alpha
7 6 0 0 0 0 999 V2000
381.9489 -48.4877 0.0000 C 0 0 0 0 0 0 0
407.7575 -33.1934 0.0000 C 0 0 0 0 0 0 0
459.7157 -32.6029 0.0000 C 0 0 0 0 0 0 0
433.9070 -47.8971 0.0000 C 0 0 0 0 0 0 0
485.8651 -47.3068 0.0000 C 0 0 0 0 0 0 0
355.7992 -33.7837 0.0000 C 0 0 0 0 0 0 0
329.9907 -49.0780 0.0000 C 0 0 0 0 0 0 0
1 2 1 0 0 0 0
6 1 1 0 0 0 0
7 6 1 0 0 0 0
2 4 1 0 0 0 0
4 3 1 0 0 0 0
3 5 2 0 0 0 0
M END
';
$ass_elimination=array(
array( 0 => array( 0 => 2, 1 => 3, 3 => 4, 2 => 5, 4 => 6, 5 => 1, 6 => 0, ), ),
);
$rxn_elimination=readRxnfile($elimination);
$paramHash["identifier"]="Elimination";
checkReactionMapping($rxn_elimination,$ass_elimination,$paramHash);
$permethylation='$RXN
2 1
$MOL
imes v0.1 pre alpha
11 11 0 0 0 0 999 V2000
144.0000 -272.9519 0.0000 C 0 0 0 0 0 0 0
174.0000 -220.9904 0.0000 C 0 0 0 0 0 0 0
174.0000 -272.9519 0.0000 C 0 0 0 0 0 0 0
189.0000 -246.9712 0.0000 C 0 0 0 0 0 0 0
129.0000 -246.9712 0.0000 C 0 0 0 0 0 0 0
144.0000 -220.9904 0.0000 C 0 0 0 0 0 0 0
219.0000 -246.9712 0.0000 O 0 0 0 0 0 0 0
129.0000 -298.9326 0.0000 C 0 0 0 0 0 0 0
99.0000 -298.9327 0.0000 O 0 0 0 0 0 0 0
144.0000 -324.9134 0.0000 O 0 0 0 0 0 0 0
129.0000 -195.0096 0.0000 O 0 0 0 0 0 0 0
4 3 2 0 0 0 0
4 2 1 0 0 0 0
6 5 1 0 0 0 0
1 5 2 0 0 0 0
4 7 1 0 0 0 0
1 8 1 0 0 0 0
8 10 1 0 0 0 0
8 9 2 0 0 0 0
6 2 2 0 0 0 0
1 3 1 0 0 0 0
6 11 1 0 0 0 0
M END
$MOL
imes v0.1 pre alpha
2 1 0 0 0 0 999 V2000
335.0000 -259.9615 0.0000 C 0 0 0 0 0 0 0
365.0000 -259.9615 0.0000 I 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END
$MOL
imes v0.1 pre alpha
14 14 0 0 0 0 999 V2000
556.0000 -220.9903 0.0000 C 0 0 0 0 0 0 0
526.0000 -272.9518 0.0000 C 0 0 0 0 0 0 0
556.0000 -272.9518 0.0000 C 0 0 0 0 0 0 0
571.0000 -246.9712 0.0000 C 0 0 0 0 0 0 0
526.0000 -220.9903 0.0000 C 0 0 0 0 0 0 0
511.0000 -246.9712 0.0000 C 0 0 0 0 0 0 0
601.0001 -246.9712 0.0000 O 0 0 0 0 0 0 0
616.0001 -272.9519 0.0000 C 0 0 0 0 0 0 0
511.0000 -298.9326 0.0000 C 0 0 0 0 0 0 0
481.0000 -298.9326 0.0000 O 0 0 0 0 0 0 0
526.0000 -324.9134 0.0000 O 0 0 0 0 0 0 0
511.0000 -350.8942 0.0000 C 0 0 0 0 0 0 0
511.0000 -195.0096 0.0000 O 0 0 0 0 0 0 0
526.0000 -169.0288 0.0000 C 0 0 0 0 0 0 0
4 7 1 0 0 0 0
5 6 1 0 0 0 0
4 3 2 0 0 0 0
2 3 1 0 0 0 0
4 1 1 0 0 0 0
7 8 1 0 0 0 0
2 9 1 0 0 0 0
9 11 1 0 0 0 0
9 10 2 0 0 0 0
11 12 1 0 0 0 0
5 1 2 0 0 0 0
5 13 1 0 0 0 0
13 14 1 0 0 0 0
2 6 2 0 0 0 0
M END';
$ass_permethylation=array(
array ( 0 => array ( 0 => 1, 3 => 3, 6 => 6, 2 => 2, 1 => 0, 8 => 7, 10 => 9, 9 => 8, 5 => 4, 4 => 5, 12 => 10, 7 => 11, 11 => 11, 13 => 11, ), ),
array ( 0 => array ( 8 => 7, 1 => 0, 2 => 4, 3 => 5, 6 => 10, 0 => 1, 4 => 3, 5 => 2, 12 => 6, 10 => 9, 9 => 8, 7 => 11, 11 => 11, 13 => 11, ), ),
);
$rxn_permethylation=readRxnfile($permethylation);
$paramHash["identifier"]="Permethylation";
checkReactionMapping($rxn_permethylation,$ass_permethylation,$paramHash);
$benzylic_chlorination_with_challenge='$RXN
2 1
$MOL
imes v0.1 pre alpha
2 1 0 0 0 0 999 V2000
122.0000 -277.9615 0.0000 Cl 0 0 0 0 0 0 0
152.0000 -277.9615 0.0000 Cl 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END
$MOL
imes v0.1 pre alpha
9 9 0 0 0 0 999 V2000
313.0000 -290.9520 0.0000 C 0 0 0 0 0 0 0
268.0000 -264.9712 0.0000 C 0 0 0 0 0 0 0
328.0000 -264.9712 0.0000 C 0 0 0 0 0 0 0
283.0000 -290.9520 0.0000 C 0 0 0 0 0 0 0
313.0000 -238.9903 0.0000 C 0 0 0 0 0 0 0
283.0000 -238.9903 0.0000 N 0 0 0 0 0 0 0
328.0000 -213.0096 0.0000 C 0 0 0 0 0 0 0
328.0000 -316.9327 0.0000 C 0 0 0 0 0 0 0
313.0000 -342.9135 0.0000 Cl 0 0 0 0 0 0 0
4 2 2 0 0 0 0
3 5 1 0 0 0 0
5 7 1 0 0 0 0
6 5 2 0 0 0 0
6 2 1 0 0 0 0
4 1 1 0 0 0 0
3 1 2 0 0 0 0
1 8 1 0 0 0 0
8 9 1 0 0 0 0
M END
$MOL
imes v0.1 pre alpha
10 10 0 0 0 0 999 V2000
489.0000 -238.9904 0.0000 C 0 0 0 0 0 0 0
489.0000 -290.9519 0.0000 C 0 0 0 0 0 0 0
459.0000 -290.9519 0.0000 C 0 0 0 0 0 0 0
459.0000 -238.9904 0.0000 N 0 0 0 0 0 0 0
504.0000 -264.9713 0.0000 C 0 0 0 0 0 0 0
444.0000 -264.9713 0.0000 C 0 0 0 0 0 0 0
504.0000 -213.0097 0.0000 C 0 0 0 0 0 0 0
534.0000 -213.0097 0.0000 Cl 0 0 0 0 0 0 0
504.0000 -316.9327 0.0000 C 0 0 0 0 0 0 0
488.9999 -342.9134 0.0000 Cl 0 0 0 0 0 0 0
3 6 2 0 0 0 0
4 6 1 0 0 0 0
1 7 1 0 0 0 0
7 8 1 0 0 0 0
5 1 1 0 0 0 0
4 1 2 0 0 0 0
3 2 1 0 0 0 0
5 2 2 0 0 0 0
2 9 1 0 0 0 0
9 10 1 0 0 0 0
M END';
$ass_benzylic_chlorination_with_challenge=array(
array ( 0 => array ( 3 => 7, 5 => 3, 2 => 5, 1 => 2, 4 => 4, 0 => 6, 6 => 8, 8 => 9, 9 => 10, 7 => 0, ), ),
);
$rxn_benzylic_chlorination_with_challenge=readRxnfile($benzylic_chlorination_with_challenge);
$paramHash["identifier"]="Benzylic chlorination with challenge";
checkReactionMapping($rxn_benzylic_chlorination_with_challenge,$ass_benzylic_chlorination_with_challenge,$paramHash);
/* copy this for new ones
$hydrolysis='';
$ass_hydrolysis=array(
);
$rxn_hydrolysis=readRxnfile($hydrolysis);
$paramHash["identifier"]="Hydrolysis";
checkReactionMapping($rxn_hydrolysis,$ass_hydrolysis,$paramHash);
*/
if (!isset($_REQUEST["identifier"])) {
echo "<h2>".s("checks_complete").<<<END
</h2>
</body>
</html>
END;
}
completeDoc();
?>