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check_substruct.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";
$sub_time=0;
$sub_count=0;
/*--------------------------------------------------------------------------------------------------
/ Function: checkSubstructure
/
/ 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:
/ & $needle : molecule data structure to be found/not found in haystack, depending on the desired results defined in $correct
/ & $haystack : haystack data structure to be matched to needle
/ $correct : desired results, tests will only be performed if a certain desired result is set
/
/ Return : no return value, direct output
/------------------------------------------------------------
/ History:
/ 2009-07-17 RUD01 Created
..--------------------------------------------------------------------------------------------------*/
function checkSubstructure(& $needle,& $haystack,$correct=array()) {
global $sub_time,$sub_count;
// FP
if (isset($correct["FP"]) && getFPmatch($needle,$haystack)!=$correct["FP"]) {
echo "Problem with ".$correct["identifier"]." on FP.<table><tbody><tr><td><pre>";
print_r($haystack["fingerprints"]);
echo "</pre></td><td><pre>";
print_r($needle["fingerprints"]);
echo "</pre></td><td><pre>";
$test=array();
for ($a=0;$a<count($needle["fingerprints"]);$a++) {
$test[$a]=$haystack["fingerprints"][$a] & $needle["fingerprints"][$a];
}
print_r($test);
echo "</pre></td></tr></tbody></table><br/>";
}
// Sub
if (isset($correct["substruct"])) {
$start_time=microtime(true);
if (getSubstMatch($needle,$haystack,array("mode" => "test", ))!=$correct["substruct"]) { // mode => test prevents structures to pass due to identical SMILES
echo "Problem with ".$correct["identifier"]." on substruct.<br/>";
}
$sub_time+=microtime(true)-$start_time;
$sub_count++;
}
// SMILES
if (isset($correct["smiles_stereo"]) && ($needle["smiles_stereo"]==$haystack["smiles_stereo"])!=$correct["smiles_stereo"]) {
echo "Problem with ".$correct["identifier"]." on smiles_stereo (".$needle["smiles_stereo"]." vs. ".$haystack["smiles_stereo"].").<br/>";
}
// SMILES non-stereo
if (isset($correct["smiles"]) && ($needle["smiles"]==$haystack["smiles"])!=$correct["smiles"]) {
echo "Problem with ".$correct["identifier"]." on smiles (".$needle["smiles"]." vs. ".$haystack["smiles"].").<br/>";
}
}
pageHeader();
echo stylesheet."</head>
<body>".s("check_for_errors").":<br/>";
// Cp-Tests
$fe_metallacyc1=<<<END
Marvin 10140814332D
7 11 0 0 0 0 999 V2000
-1.7089 0.4955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3764 0.0106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1214 -0.7740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2964 -0.7740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0415 0.0106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6064 -1.4414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0281 1.1805 0.0000 Fe 0 3 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 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
3 6 1 0 0 0 0
1 7 1 0 0 0 0
5 7 1 0 0 0 0
2 7 1 0 0 0 0
7 4 1 0 0 0 0
7 3 1 0 0 0 0
M CHG 1 7 1
M END
END;
$fe_regioiso1=<<<END
Marvin 10140814352D
7 7 0 0 0 0 999 V2000
-1.2080 0.6134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8755 0.1285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 -0.6561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7955 -0.6561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5406 0.1285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2080 1.4384 0.0000 Fe 0 3 0 0 0 0 0 0 0 0 0 0
-2.1055 -1.3236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
1 6 1 0 0 0 0
3 7 1 0 0 0 0
M CHG 1 6 1
M END
END;
$fe_regioiso2=<<<END
Marvin 10140814352D
7 7 0 0 0 0 999 V2000
-1.2080 0.6134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8755 0.1285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 -0.6561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7955 -0.6561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5406 0.1285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2080 1.4384 0.0000 Fe 0 3 0 0 0 0 0 0 0 0 0 0
-2.6601 0.3834 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
1 6 1 0 0 0 0
2 7 1 0 0 0 0
M CHG 1 6 1
M END
END;
$mol_fe_metallacyc1=readMolfile($fe_metallacyc1,array("forStructureSearch" => true, ));
$mol_fe_regioiso1=readMolfile($fe_regioiso1,array("forStructureSearch" => true, ));
$mol_fe_regioiso2=readMolfile($fe_regioiso2,array("forStructureSearch" => true, ));
checkSubstructure($mol_fe_regioiso1,$mol_fe_metallacyc1,array("identifier" => "Fe1", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
checkSubstructure($mol_fe_regioiso2,$mol_fe_metallacyc1,array("identifier" => "Fe2", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
checkSubstructure($mol_fe_regioiso1,$mol_fe_regioiso2,array("identifier" => "Fe3", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
checkSubstructure($mol_fe_regioiso2,$mol_fe_regioiso1,array("identifier" => "Fe4", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
// Allyl-System
$ru_metallacyc=<<<END
CC12C[Ru]134568(C2)(CC3(C)C4)[C@H]7CC[C@@H]5[C@@H]6CC[C@@H]78
open enventory Sat, 24.05.2008 21:30:59
17 24 0 0 0 0 0 0 0 0 0 V2000
6.0750 -5.9167 0.0000 Ru 0 0 0 0 0 0 0 0 0 0 0 0
6.6375 -7.2125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8042 -4.8167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9292 -5.7792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9292 -5.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9292 -6.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9250 -6.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0667 -6.8417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9250 -5.4917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0875 -4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9292 -6.6625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3750 -6.2792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9542 -5.9875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9542 -6.6167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3750 -5.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7667 -7.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1667 -4.4542 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 0 0 0 0
1 9 1 6 0 0 0
10 1 1 0 0 0 0
1 11 1 1 0 0 0
12 6 1 0 0 0 0
13 4 1 0 0 0 0
14 7 1 0 0 0 0
15 5 1 0 0 0 0
16 2 1 0 0 0 0
17 3 1 0 0 0 0
11 2 1 0 0 0 0
3 10 1 0 0 0 0
9 3 1 0 0 0 0
2 8 1 0 0 0 0
7 6 1 0 0 0 0
4 5 1 0 0 0 0
14 13 1 0 0 0 0
12 15 1 0 0 0 0
M END
END;
$ru_covalent=<<<END
CC12C[Ru]134568(C2)(CC3(C)C4)[C@H]7CC[C@@H]5[C@@H]6CC[C@@H]78
Marvin 10140815362D
5 4 0 0 0 0 999 V2000
8.0450 -8.7419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3531 -8.2925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3985 -8.0753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.2016 -9.3328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.4545 -6.3348 0.0000 Ru 0 3 0 0 0 0 0 0 0 0 0 0
4 1 1 0 0 0 0
3 1 1 0 0 0 0
1 2 2 0 0 0 0
5 3 1 0 0 0 0
M CHG 1 5 1
M END
END;
$ru_ionic=<<<END
CC12C[Ru]134568(C2)(CC3(C)C4)[C@H]7CC[C@@H]5[C@@H]6CC[C@@H]78
Marvin 10140815352D
5 3 0 0 0 0 999 V2000
8.0450 -8.7419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3531 -8.2925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3985 -8.0753 0.0000 C 0 5 0 0 0 0 0 0 0 0 0 0
8.2016 -9.3328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.4545 -6.3348 0.0000 Ru 0 2 0 0 0 0 0 0 0 0 0 0
4 1 1 0 0 0 0
3 1 1 0 0 0 0
1 2 2 0 0 0 0
M CHG 2 3 -1 5 2
M END
END;
$mol_ru_metallacyc=readMolfile($ru_metallacyc,array("forStructureSearch" => true, ));
$mol_ru_covalent=readMolfile($ru_covalent,array("forStructureSearch" => true, ));
$mol_ru_ionic=readMolfile($ru_ionic,array("forStructureSearch" => true, ));
checkSubstructure($mol_ru_covalent,$mol_ru_metallacyc,array("identifier" => "Ru1", "FP" => true, "substruct" => true, "smiles_stereo" => false, "smiles" => false, ));
checkSubstructure($mol_ru_ionic,$mol_ru_metallacyc,array("identifier" => "Ru2", "FP" => true, "substruct" => true, "smiles_stereo" => false, "smiles" => false, ));
checkSubstructure($mol_ru_ionic,$mol_ru_covalent,array("identifier" => "Ru3", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
checkSubstructure($mol_ru_covalent,$mol_ru_ionic,array("identifier" => "Ru4", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
// acac
$pd_enol=<<<END
FC(F)(F)C(=O)/C=C(O[Pd]O/C(=C\C(=O)C(F)(F)F)C(F)(F)F)/C(F)(F)F
open enventory Sat, 24.05.2008 21:31:08
27 26 0 0 0 0 0 0 0 0 0 V2000
3.4560 4.9339 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.8543 2.5313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 5.7903 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
2.6299 6.7492 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.8792 7.4767 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
8.3103 1.6749 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
5.6919 0.7238 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
7.4426 0.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 1.6749 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.8792 0.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
2.6299 0.7238 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
7.4426 7.4767 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
5.6919 6.7492 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
8.3103 5.7903 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1.3528 3.7250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9538 3.7250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4560 2.5313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.8543 4.9339 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.1533 3.7250 0.0000 Pd 0 0 0 0 0 0 0 0 0 0 0 0
2.0690 4.9339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2527 2.5313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0690 2.5313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2527 4.9339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3528 6.1542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9538 1.3225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3528 1.3225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9538 6.1542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 20 2 0 0 0 0
2 21 2 0 0 0 0
3 24 1 0 0 0 0
4 24 1 0 0 0 0
5 24 1 0 0 0 0
6 25 1 0 0 0 0
7 25 1 0 0 0 0
8 25 1 0 0 0 0
9 26 1 0 0 0 0
10 26 1 0 0 0 0
11 26 1 0 0 0 0
12 27 1 0 0 0 0
13 27 1 0 0 0 0
14 27 1 0 0 0 0
15 20 1 0 0 0 0
15 22 2 0 0 0 0
16 21 1 0 0 0 0
16 23 2 0 0 0 0
17 19 1 0 0 0 0
17 22 1 0 0 0 0
18 19 1 0 0 0 0
18 23 1 0 0 0 0
20 24 1 0 0 0 0
21 25 1 0 0 0 0
22 26 1 0 0 0 0
23 27 1 0 0 0 0
M END
END;
$pd_alpha=<<<END
FC(F)(F)C(=O)/C=C(O[Pd]O/C(=C\C(=O)C(F)(F)F)C(F)(F)F)/C(F)(F)F
Marvin 10140814452D
27 26 0 0 0 0 999 V2000
2.0371 2.9082 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.8613 1.4920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 3.4130 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1.5502 3.9782 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.5182 4.4070 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
4.8984 0.9872 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
3.3550 0.4266 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
4.3869 0.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.9872 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.5182 0.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1.5502 0.4266 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
4.3869 4.4070 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
3.3550 3.9782 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
4.8984 3.4130 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.7974 2.1956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0988 2.1956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0371 1.4920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.8613 2.9082 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.4481 2.1956 0.0000 Pd 0 0 0 0 0 0 0 0 0 0 0 0
1.2195 2.9082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6856 1.4920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2195 1.4920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6856 2.9082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7974 3.6275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0988 0.7795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7974 0.7795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0988 3.6275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 20 2 0 0 0 0
2 21 2 0 0 0 0
3 24 1 0 0 0 0
4 24 1 0 0 0 0
5 24 1 0 0 0 0
6 25 1 0 0 0 0
7 25 1 0 0 0 0
8 25 1 0 0 0 0
9 26 1 0 0 0 0
10 26 1 0 0 0 0
11 26 1 0 0 0 0
12 27 1 0 0 0 0
13 27 1 0 0 0 0
14 27 1 0 0 0 0
15 20 1 0 0 0 0
15 22 1 0 0 0 0
16 21 1 0 0 0 0
16 23 1 0 0 0 0
17 22 2 0 0 0 0
18 23 2 0 0 0 0
20 24 1 0 0 0 0
21 25 1 0 0 0 0
22 26 1 0 0 0 0
23 27 1 0 0 0 0
19 16 1 0 0 0 0
19 15 1 0 0 0 0
M END
END;
$mol_pd_enol=readMolfile($pd_enol,array("forStructureSearch" => true, ));
$mol_pd_alpha=readMolfile($pd_alpha,array("forStructureSearch" => true, ));
checkSubstructure($mol_pd_enol,$mol_pd_alpha,array("identifier" => "Pd1", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
checkSubstructure($mol_pd_alpha,$mol_pd_enol,array("identifier" => "Pd2", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
// aromatisation of annelated rings
$me_anthracen=<<<END
Marvin 10140815082D
15 17 0 0 0 0 999 V2000
2.7107 3.3589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9963 3.7714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2817 3.3589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2817 2.5339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9963 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7107 2.5339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4252 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1397 2.5339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1397 3.3589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4252 3.7714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5673 3.7714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1472 3.3590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8617 3.7715 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1472 2.5340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5672 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 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
7 8 1 0 0 0 0
8 9 2 0 0 0 0
9 10 1 0 0 0 0
1 6 1 0 0 0 0
1 10 2 0 0 0 0
6 7 2 0 0 0 0
3 11 1 0 0 0 0
11 12 2 0 0 0 0
12 13 1 0 0 0 0
12 14 1 0 0 0 0
14 15 2 0 0 0 0
4 15 1 0 0 0 0
M END
END;
$tol=<<<END
Marvin 10140815092D
7 7 0 0 0 0 999 V2000
1.2817 3.3589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2817 2.5339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5673 3.7714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1472 3.3590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8617 3.7715 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1472 2.5340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5672 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
4 6 1 0 0 0 0
6 7 2 0 0 0 0
2 7 1 0 0 0 0
M END
END;
$mol_me_anthracen=readMolfile($me_anthracen,array("forStructureSearch" => true, ));
$mol_tol=readMolfile($tol,array("forStructureSearch" => true, ));
checkSubstructure($mol_tol,$mol_me_anthracen,array("identifier" => "Cyc1", "FP" => true, "substruct" => true, "smiles_stereo" => false, "smiles" => false, ));
$rh_carbonyl_triple=<<<END
Marvin 07170911072D
3 2 0 0 0 0 999 V2000
-1.5027 -0.2652 0.0000 Rh 0 0 0 0 0 0 0 0 0 0 0 0
-0.7058 -0.0517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0911 0.1619 0.0000 O 0 3 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 3 0 0 0 0
M CHG 1 3 1
M END
END;
$rh_carbonyl_cumulene=<<<END
Marvin 07170911122D
3 2 0 0 0 0 999 V2000
-1.5027 -0.2652 0.0000 Rh 0 3 0 0 0 0 0 0 0 0 0 0
-0.7058 -0.0517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0911 0.1619 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 2 0 0 0 0
M CHG 1 1 1
M END
END;
$rh_carbonyl_separate=<<<END
[Rh+].[C]=O
Marvin 07170911072D 5.58000
3 1 0 0 0 0 999 V2000
-0.7058 -0.0517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0911 0.1619 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.5634 -0.5893 0.0000 Rh 0 3 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
M CHG 1 3 1
M RAD 1 1 1
M END
END;
$mol_rh_carbonyl_triple=readMolfile($rh_carbonyl_triple,array("forStructureSearch" => true, ));
$mol_rh_carbonyl_cumulene=readMolfile($rh_carbonyl_cumulene,array("forStructureSearch" => true, ));
$mol_rh_carbonyl_separate=readMolfile($rh_carbonyl_separate,array("forStructureSearch" => true, ));
checkSubstructure($mol_rh_carbonyl_triple,$mol_rh_carbonyl_cumulene,array("identifier" => "Rh1", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
checkSubstructure($mol_rh_carbonyl_triple,$mol_rh_carbonyl_separate,array("identifier" => "Rh2", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
checkSubstructure($mol_rh_carbonyl_separate,$mol_rh_carbonyl_cumulene,array("identifier" => "Rh3", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
// Listen
// handling of protons
$am_acetate_ionic=<<<END
N.CC(=O)[O-].[H+]
Marvin 12050914112D 8.39000
5 3 0 0 0 0 999 V2000
-1.5027 0.6187 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
0.9134 -1.2154 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
2.1509 -0.5009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3259 -0.5009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9134 0.2136 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4 3 1 0 0 0 0
2 4 1 0 0 0 0
4 5 2 0 0 0 0
M CHG 2 1 1 2 -1
M END
END;
$am_acetate_separate=<<<END
Marvin 12050914112D
5 3 0 0 0 0 999 V2000
-1.5027 0.6187 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.9134 -1.2154 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.1509 -0.5009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3259 -0.5009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9134 0.2136 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4 3 1 0 0 0 0
2 4 1 0 0 0 0
4 5 2 0 0 0 0
M END
END;
// Proton intentionally moved into the middle
$am_acetate_w_proton=<<<END
N.CC(=O)[O-].[H+]
Marvin 12050914532D 8.39000
6 3 0 0 0 0 999 V2000
-1.5027 0.6187 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.9134 -1.2154 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
2.1509 -0.5009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0625 -1.5027 0.0000 H 0 3 0 0 0 0 0 0 0 0 0 0
1.3259 -0.5009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9134 0.2136 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5 3 1 0 0 0 0
2 5 1 0 0 0 0
6 5 2 0 0 0 0
M CHG 2 2 -1 4 1
M END
END;
$mol_am_acetate_ionic=readMolfile($am_acetate_ionic,array("forStructureSearch" => true, ));
$mol_am_acetate_separate=readMolfile($am_acetate_separate,array("forStructureSearch" => true, ));
$mol_am_acetate_w_proton=readMolfile($am_acetate_w_proton,array("forStructureSearch" => true, ));
checkSubstructure($mol_am_acetate_ionic,$mol_am_acetate_separate,array("identifier" => "Ammonium acetate1", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
checkSubstructure($mol_am_acetate_ionic,$mol_am_acetate_w_proton,array("identifier" => "Ammonium acetate2", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
checkSubstructure($mol_am_acetate_separate,$mol_am_acetate_w_proton,array("identifier" => "Ammonium acetate3", "FP" => true, "substruct" => true, "smiles_stereo" => true, "smiles" => true, ));
// Multiple parts in one part
$fe_cl2_dihyd=<<<END
Marvin 01031017302D 29.43000
5 0 0 0 0 0 999 V2000
0.3241 1.5321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3536 -0.6482 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.5911 0.2946 0.0000 Fe 0 2 0 0 0 0 0 0 0 0 0 0
3.0643 1.2670 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0
2.9170 -0.7366 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0
M CHG 3 3 2 4 -1 5 -1
M END
END;
$fe_cl2_dme=<<<END
Marvin 01031017302D
9 7 0 0 0 0 999 V2000
0.0589 0.6777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7734 1.0902 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0589 -0.1473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7734 -0.5598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7734 1.9152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7734 -1.3848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2964 0.1768 0.0000 Fe 0 0 0 0 0 0 0 0 0 0 0 0
1.8798 -0.4066 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
2.0109 0.5893 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
3 4 1 0 0 0 0
2 5 1 0 0 0 0
4 6 1 0 0 0 0
7 8 1 0 0 0 0
7 9 1 0 0 0 0
M END
END;
$mol_fe_cl2_dihyd=readMolfile($fe_cl2_dihyd,array("forStructureSearch" => true, ));
$mol_fe_cl2_dme=readMolfile($fe_cl2_dme,array("forStructureSearch" => true, ));
checkSubstructure($mol_fe_cl2_dihyd,$mol_fe_cl2_dme,array("identifier" => "FeCl2 multipart", "FP" => true, "substruct" => true, ));
// Chains and rings
$dimethylcyclohexane=<<<END
CC1CCC(C)CC1
open enventory Sat, 24.05.2008 21:43:30
8 8 0 0 0 0 0 0 0 0999 V2000
-0.3125 -1.5583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0958 -2.2708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9125 -2.2734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3270 -1.5652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9187 -0.8527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0958 -0.8484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1500 -1.5625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1375 -1.5542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 6 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
4 7 1 0 0 0 0
1 2 1 0 0 0 0
1 8 1 0 0 0 0
M END
END;
$camphor=<<<END
O=C1CC2CCC1(C)C2(C)C
open enventory Sat, 24.05.2008 21:30:26
11 12 0 0 0 0 0 0 0 0999 V2000
4.8833 -3.2083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8833 -1.7417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7083 -3.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.3333 -2.4708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1542 -2.6958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0958 -3.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5208 -2.6958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0167 -4.2167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.6083 -3.6917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.3708 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4083 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7 4 1 0 0 0 0
3 1 1 0 0 0 0
4 2 1 0 0 0 0
5 3 1 0 0 0 0
6 1 1 0 0 0 0
7 6 1 0 0 0 0
8 3 2 0 0 0 0
9 1 1 0 0 0 0
10 2 1 0 0 0 0
11 2 1 0 0 0 0
5 4 1 0 0 0 0
1 2 1 0 0 0 0
M END
END;
$octane=<<<END
CCCCCCCC
open enventory Sat, 24.05.2008 21:31:28
8 7 0 0 0 0 0 0 0 0999 V2000
-3.2167 0.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2125 -0.3208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9250 0.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9292 -0.3208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6458 0.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6417 -0.3208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.5000 -0.3208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5000 0.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
3 6 1 0 0 0 0
4 1 1 0 0 0 0
5 4 1 0 0 0 0
6 5 1 0 0 0 0
7 1 1 0 0 0 0
8 2 1 0 0 0 0
M END
END;
$nonane=<<<END
CCCCCCCCC
open enventory Sat, 24.05.2008 21:33:23
9 8 0 0 0 0 0 0 0 0999 V2000
1.2167 -4.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9292 -3.8625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6417 -4.2708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3542 -3.8583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0667 -4.2667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7792 -3.8542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4917 -4.2625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2042 -3.8500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9167 -4.2583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4 5 1 0 0 0 0
2 3 1 0 0 0 0
5 6 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
7 8 1 0 0 0 0
8 9 1 0 0 0 0
M END
END;
$mol_dimethylcyclohexane=readMolfile($dimethylcyclohexane,array("forStructureSearch" => true, ));
$mol_camphor=readMolfile($camphor,array("forStructureSearch" => true, ));
$mol_octane=readMolfile($octane,array("forStructureSearch" => true, ));
$mol_nonane=readMolfile($nonane,array("forStructureSearch" => true, ));
checkSubstructure($mol_octane,$mol_dimethylcyclohexane,array("identifier" => "Octane in 1,4-dimethylcyclohexane", "substruct" => false, ));
checkSubstructure($mol_octane,$mol_camphor,array("identifier" => "Octane in camphor", "substruct" => true, ));
checkSubstructure($mol_nonane,$mol_camphor,array("identifier" => "Nonane in camphor", "substruct" => false, ));
checkSubstructure($mol_dimethylcyclohexane,$mol_camphor,array("identifier" => "1,4-Dimethylcyclohexane in camphor", "substruct" => true, ));
// fingerprinting, single/double/aromatic
$vinyl_pyridine=<<<END
imes v0.1 pre alpha
8 8 0 0 0 0 999 V2000
129.0000 -139.9808 0.0000 C 0 0 0 0 0 0 0
84.0000 -165.9616 0.0000 C 0 0 0 0 0 0 0
69.0000 -139.9809 0.0000 C 0 0 0 0 0 0 0
114.0000 -114.0001 0.0000 N 0 0 0 0 0 0 0
83.9999 -114.0001 0.0000 C 0 0 0 0 0 0 0
114.0000 -165.9616 0.0000 C 0 0 0 0 0 0 0
159.0000 -139.9808 0.0000 C 0 0 0 0 0 0 0
174.0000 -165.9615 0.0000 C 0 0 0 0 0 0 0
1 7 1 0 0 0 0
8 7 2 0 0 0 0
4 1 1 0 0 0 0
6 1 2 0 0 0 0
6 2 1 0 0 0 0
3 2 2 0 0 0 0
3 5 1 0 0 0 0
4 5 2 0 0 0 0
M END
END;
$bipy=<<<END
imes v0.1 pre alpha
12 13 0 0 0 0 999 V2000
129.0000 -139.9808 0.0000 C 0 0 0 0 0 0 0
84.0000 -165.9616 0.0000 C 0 0 0 0 0 0 0
69.0000 -139.9809 0.0000 C 0 0 0 0 0 0 0
114.0000 -114.0001 0.0000 N 0 0 0 0 0 0 0
83.9999 -114.0001 0.0000 C 0 0 0 0 0 0 0
114.0000 -165.9616 0.0000 C 0 0 0 0 0 0 0
159.0000 -139.9808 0.0000 C 0 0 0 0 0 0 0
204.0000 -114.0000 0.0000 C 0 0 0 0 0 0 0
174.0000 -114.0000 0.0000 N 0 0 0 0 0 0 0
219.0000 -139.9808 0.0000 C 0 0 0 0 0 0 0
174.0000 -165.9615 0.0000 C 0 0 0 0 0 0 0
204.0000 -165.9615 0.0000 C 0 0 0 0 0 0 0
4 1 2 0 0 0 0
3 2 1 0 0 0 0
3 5 2 0 0 0 0
4 5 1 0 0 0 0
6 2 2 0 0 0 0
6 1 1 0 0 0 0
9 7 1 0 0 0 0
10 8 1 0 0 0 0
9 8 2 0 0 0 0
1 7 1 0 0 0 0
10 12 2 0 0 0 0
11 12 1 0 0 0 0
11 7 2 0 0 0 0
M END
END;
$phen=<<<END
imes v0.1 pre alpha
14 16 0 0 0 0 999 V2000
65.0000 -98.0000 0.0000 C 0 0 0 0 0 0 0
90.5072 -82.2081 0.0000 C 0 0 0 0 0 0 0
116.9370 -96.4019 0.0000 C 0 0 0 0 0 0 0
117.1110 -126.4014 0.0000 N 0 0 0 0 0 0 0
91.2177 -141.5519 0.0000 C 0 0 0 0 0 0 0
65.2369 -126.5519 0.0000 C 0 0 0 0 0 0 0
89.5845 -52.2223 0.0000 C 0 0 0 0 0 0 0
142.6392 -80.9295 0.0000 C 0 0 0 0 0 0 0
115.0917 -36.4303 0.0000 C 0 0 0 0 0 0 0
168.8898 -95.4521 0.0000 N 0 0 0 0 0 0 0
141.0724 -51.4303 0.0000 C 0 0 0 0 0 0 0
167.0532 -36.4303 0.0000 C 0 0 0 0 0 0 0
193.0339 -51.4303 0.0000 C 0 0 0 0 0 0 0
193.0339 -81.4303 0.0000 C 0 0 0 0 0 0 0
9 11 1 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
1 2 2 0 0 0 0
2 7 1 0 0 0 0
7 9 2 0 0 0 0
8 10 2 0 0 0 0
14 10 1 0 0 0 0
13 14 2 0 0 0 0
12 13 1 0 0 0 0
11 12 2 0 0 0 0
3 8 1 0 0 0 0
11 8 1 0 0 0 0
M END
END;
$semi_strange_phen=<<<END
imes v0.1 pre alpha
14 16 0 0 0 0 999 V2000
65.0000 -98.0000 0.0000 C 0 0 0 0 0 0 0
90.5072 -82.2081 0.0000 C 0 0 0 0 0 0 0
116.9370 -96.4019 0.0000 C 0 0 0 0 0 0 0
117.1110 -126.4014 0.0000 N 0 0 0 0 0 0 0
91.2177 -141.5519 0.0000 C 0 0 0 0 0 0 0
65.2369 -126.5519 0.0000 C 0 0 0 0 0 0 0
89.5845 -52.2223 0.0000 C 0 0 0 0 0 0 0
142.6392 -80.9295 0.0000 C 0 0 0 0 0 0 0
115.0917 -36.4303 0.0000 C 0 0 0 0 0 0 0
168.8898 -95.4521 0.0000 N 0 0 0 0 0 0 0
141.0724 -51.4303 0.0000 C 0 0 0 0 0 0 0
167.0532 -36.4303 0.0000 C 0 0 0 0 0 0 0
193.0339 -51.4303 0.0000 C 0 0 0 0 0 0 0
193.0339 -81.4303 0.0000 C 0 0 0 0 0 0 0
9 11 1 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
1 2 2 0 0 0 0
7 9 2 0 0 0 0
2 7 1 0 0 0 0
3 8 1 0 0 0 0
8 10 1 0 0 0 0
11 12 1 0 0 0 0
11 8 2 0 0 0 0
12 13 2 0 0 0 0
13 14 1 0 0 0 0
14 10 2 0 0 0 0
M END
END;
$strange_phen=<<<END
imes v0.1 pre alpha
14 16 0 0 0 0 999 V2000
337.7124 -441.9795 0.0000 N 0 0 0 0 0 0 0
337.6647 -472.3458 0.0000 C 0 0 0 0 0 0 0
363.7275 -487.5786 0.0000 C 0 0 0 0 0 0 0
390.0206 -472.3260 0.0000 C 0 0 0 0 0 0 0
363.6561 -426.9175 0.0000 C 0 0 0 0 0 0 0
389.7983 -441.8882 0.0000 C 0 0 0 0 0 0 0
415.6984 -426.8897 0.0000 C 0 0 0 0 0 0 0
415.6587 -396.7219 0.0000 C 0 0 0 0 0 0 0
363.5608 -396.9006 0.0000 C 0 0 0 0 0 0 0
389.3219 -382.0768 0.0000 C 0 0 0 0 0 0 0
389.2227 -352.2464 0.0000 C 0 0 0 0 0 0 0
363.3782 -337.5972 0.0000 C 0 0 0 0 0 0 0
337.5972 -352.7784 0.0000 C 0 0 0 0 0 0 0
337.7997 -382.1522 0.0000 N 0 0 0 0 0 0 0
4 6 1 0 0 0 0
7 8 1 0 0 0 0
8 10 2 0 0 0 0
9 5 2 0 0 0 0
5 1 1 0 0 0 0
2 3 1 0 0 0 0
9 10 1 0 0 0 0
1 2 2 0 0 0 0
10 11 1 0 0 0 0
5 6 1 0 0 0 0
11 12 2 0 0 0 0
3 4 2 0 0 0 0
12 13 1 0 0 0 0
6 7 2 0 0 0 0
13 14 2 0 0 0 0
14 9 1 0 0 0 0
M END
END;
$dime_py_dbl_betw_me=<<<END
imes v0.1 pre alpha
8 8 0 0 0 0 999 V2000
65.0000 -98.0000 0.0000 C 0 0 0 0 0 0 0
90.5072 -82.2081 0.0000 C 0 0 0 0 0 0 0
116.9370 -96.4019 0.0000 C 0 0 0 0 0 0 0
117.1110 -126.4014 0.0000 N 0 0 0 0 0 0 0
91.2177 -141.5519 0.0000 C 0 0 0 0 0 0 0
65.2369 -126.5519 0.0000 C 0 0 0 0 0 0 0
89.5845 -52.2223 0.0000 C 0 0 0 0 0 0 0
142.6392 -80.9295 0.0000 C 0 0 0 0 0 0 0
1 2 1 0 0 0 0
5 6 1 0 0 0 0
6 1 2 0 0 0 0
3 4 1 0 0 0 0
2 7 1 0 0 0 0
4 5 2 0 0 0 0
2 3 2 0 0 0 0
3 8 1 0 0 0 0
M END
END;
$dime_py_sng_betw_me=<<<END
imes v0.1 pre alpha
8 8 0 0 0 0 999 V2000
65.0000 -98.0000 0.0000 C 0 0 0 0 0 0 0
90.5072 -82.2081 0.0000 C 0 0 0 0 0 0 0
116.9370 -96.4019 0.0000 C 0 0 0 0 0 0 0
117.1110 -126.4014 0.0000 N 0 0 0 0 0 0 0
91.2177 -141.5519 0.0000 C 0 0 0 0 0 0 0
65.2369 -126.5519 0.0000 C 0 0 0 0 0 0 0
89.5845 -52.2223 0.0000 C 0 0 0 0 0 0 0
142.6392 -80.9295 0.0000 C 0 0 0 0 0 0 0
1 2 1 0 0 0 0
5 6 1 0 0 0 0
6 1 2 0 0 0 0
3 4 1 0 0 0 0
2 7 1 0 0 0 0
4 5 2 0 0 0 0
2 3 2 0 0 0 0
3 8 1 0 0 0 0
M END
END;
$butane=<<<END
imes v0.1 pre alpha
4 3 0 0 0 0 999 V2000
89.3388 -75.6380 0.0000 C 0 0 0 0 0 0 0
114.9461 -91.2670 0.0000 C 0 0 0 0 0 0 0
141.2849 -76.9049 0.0000 C 0 0 0 0 0 0 0
142.0163 -46.9138 0.0000 C 0 0 0 0 0 0 0
3 4 1 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
M END
END;
$sear_vinyl_pyridine=readMolfile($vinyl_pyridine,array("forStructureSearch" => true, ));
$sear_dime_py_dbl_betw_me=readMolfile($dime_py_dbl_betw_me,array("forStructureSearch" => true, ));
$sear_dime_py_sng_betw_me=readMolfile($dime_py_sng_betw_me,array("forStructureSearch" => true, ));
$sear_bipy=readMolfile($bipy,array("forStructureSearch" => true, ));
$sear_phen=readMolfile($phen,array("forStructureSearch" => true, ));
$sear_semi_strange_phen=readMolfile($semi_strange_phen,array("forStructureSearch" => true, ));
$sear_strange_phen=readMolfile($strange_phen,array("forStructureSearch" => true, ));
$sear_butane=readMolfile($butane,array("forStructureSearch" => true, ));