Mercurial > repos > bgruening > silicos_it
changeset 5:987524196f3e
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 11 May 2013 17:14:14 -0400 |
| parents | b5abf2862e97 |
| children | a3dfd1432e43 |
| files | align-it/align-it.xml align-it/alignit_create_db.xml align-it/test_data/6mol.sdf align-it/test_data/CID_2244.sdf align-it/test_data/aliginit_scores.tabular.tabular align-it/test_data/align-it_Search_on_CID2244.phar align-it/test_data/align-it_Search_on_CID2244.sdf align-it/test_data/alignit_Create_Phar_DB_6mol.phar align-it/test_data/alignit_on_CID2244.phar align-it/test_data/reference.phar qed/qed.py qed/silicos_qed.xml repository_dependencies.xml strip-it/strip-it.xml tool_dependencies.xml |
| diffstat | 14 files changed, 3657 insertions(+), 53 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/align-it.xml Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,100 @@ +<tool id="ctb_alignit" name="Pharmacophore Alignment"> + <description>and Optimization (Align-it)</description> + <requirements> + <requirement type="package" version="1.0.0">silicos_it</requirement> + </requirements> + <command> + align-it --format ${database.ext} --dbase $database --pharmacophore $alignedPharmacophores --dbType 'MOL' --scores $result --epsilon $0epsilon $merge $noHybrid $withExclusion 2>&1 + </command> + <inputs> + <param name="database" type="data" format='mol,mol2,sdf,smi' label="database"/> + <param name="epsilon" type="float" label='change the tolerance for points to be matched' value="0.5" /> + <param name='merge' type='boolean' truevalue='--merge' falsvalue='' label='merge pharmacophore points' /> + <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsvalue='' label='disable the use of hybrid pharmacophore points' /> + <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsvalue='' label='add exclusion spheres into the optimization process instead of processing them afterwards' /> + </inputs> + <outputs> + <data name="alignedPharmacophores" format="phar" /> + <data name="result" format="tabular" /> + </outputs> + <tests> + <test> + <param name="database" ftype='sdf' value='CID_2244.sdf'/> + <param name="epsilon" value="0.5" /> + <param name='merge' value='' /> + <param name='noHybrid' value='' /> + <param name='withExclusion' value='' /> + <output name="alignedPharmacophores" ftype="phar" file="alignit_on_CID2244.phar" /> + <output name="result" file="aliginit_scores.tabular" /> + </test> + </tests> + <help> + +**What it does** + +Align-it is a tool to align molecules according their pharmacophores. A +pharmacophore is an abstract concept based on the specific interactions +that have been observed in drug-receptor interactions: hydrogen bonding, +charge transfer, electrostatic and hydrophobic interactions. Molecular +modeling and/or screening using pharmacophores have proven to be an +important and useful method in drug discovery. + + +----- + +**Example** + +* input:: + + - database + + 30 31 0 0 0 0 0 0 0999 V2000 + 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 + + - cutoff : 0.0 + +* output:: + + - aligned Pharmacophores + + 3033 + HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0 + HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0 + HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827 + HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616 + HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767 + $$$$ + + + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/alignit_create_db.xml Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,90 @@ +<tool id="ctb_alignit_create_db" name="Pharmacophore"> + <description>database building (Align-it)</description> + <requirements> + <requirement type="package" version="1.0.0">silicos_it</requirement> + </requirements> + <command > + align-it --format ${database.ext} -d $database -p $Pharmacophores --dbType MOL 2>&1 + </command> + <inputs> + <param name="database" type="data" format='sdf,mol,mol2,inchi,smi' label="database"/> + </inputs> + <outputs> + <data name="Pharmacophores" format="phar" /> + </outputs> + <tests> + <test> + <param name="database" ftype='sdf' value='6mol.sdf'/> + <data name="Pharmacophores" ftype="phar" file='alignit_create_db_on_6mol.phar' /> + </test> + </tests> + <help> + +**What it does** + +Pharao is an acronym for Pharmacophore Alignment and Optimization. A +pharmacophore is an abstract concept based on the specific interactions +that have been observed in drug-receptor interactions: hydrogen bonding, +charge transfer, electrostatic and hydrophobic interactions. Molecular +modeling and/or screening using pharmacophores have proven to be an +important and useful method in drug discovery. + + +----- + +**Example** + +* input:: + + - database + + 30 31 0 0 0 0 0 0 0999 V2000 + 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 + + - cutoff : 0.0 + +* output:: + + - aligned Pharmacophores + + 3033 + HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0 + HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0 + HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827 + HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616 + HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767 + $$$$ + + + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/6mol.sdf Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,1502 @@ +3639 + -OEChem-06261205352D + + 25 26 0 0 0 0 0 0 0999 V2000 + 3.4030 1.2327 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8950 -0.8020 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4030 -0.7673 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3849 -1.6737 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3850 -1.6622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9030 -1.6333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9030 0.0987 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8010 -0.2881 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8950 1.2674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5369 -1.2673 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0010 -0.2673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0010 0.7327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8010 0.7535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1350 -0.7673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2690 -0.2673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1350 1.2327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2690 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(1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxyphenyl)carbonyloxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +(1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylic acid methyl ester + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C33H40N2O9/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3/t18-,22+,24-,27-,28+,31+/m1/s1 + +> <PUBCHEM_IUPAC_INCHIKEY> +QEVHRUUCFGRFIF-MDEJGZGSSA-N + +> <PUBCHEM_XLOGP3_AA> +4 + +> <PUBCHEM_EXACT_MASS> +608.273381 + +> <PUBCHEM_MOLECULAR_FORMULA> +C33H40N2O9 + +> 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<PUBCHEM_IUPAC_OPENEYE_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_CAS_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-[oxo-(3,4,5-trimethoxyphenyl)methoxy]-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylic acid methyl ester + +> <PUBCHEM_IUPAC_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +6-chloranyl-1,1-bis(oxidanylidene)-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxyphenyl)carbonyloxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +6-chloro-1,1-diketo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylic acid methyl ester + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C33H40N2O9.C7H8ClN3O4S2/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19;8-4-1-5-7(2-6(4)16(9,12)13)17(14,15)11-3-10-5/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3;1-2,10-11H,3H2,(H2,9,12,13)/t18-,22+,24-,27-,28+,31+;/m1./s1 + +> <PUBCHEM_IUPAC_INCHIKEY> +NJKRHQRIYAWMRO-BQTSRIDJSA-N + +> <PUBCHEM_EXACT_MASS> +905.237856 + +> <PUBCHEM_MOLECULAR_FORMULA> +C40H48ClN5O13S2 + +> <PUBCHEM_MOLECULAR_WEIGHT> +906.41782 + +> 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0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8365 4.4653 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 8 1 0 0 0 0 + 1 10 1 0 0 0 0 + 2 5 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 13 1 0 0 0 0 + 3 19 1 0 0 0 0 + 3 21 1 0 0 0 0 + 4 16 2 0 0 0 0 + 4 20 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 1 0 0 0 0 + 6 15 1 0 0 0 0 + 6 34 1 0 0 0 0 + 6 35 1 0 0 0 0 + 7 14 1 0 0 0 0 + 7 36 1 0 0 0 0 + 7 37 1 0 0 0 0 + 8 9 1 0 0 0 0 + 8 11 2 0 0 0 0 + 9 12 1 0 0 0 0 + 10 17 2 0 0 0 0 + 10 18 1 0 0 0 0 + 11 16 1 0 0 0 0 + 11 38 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 39 1 0 0 0 0 + 13 16 1 0 0 0 0 + 14 40 1 0 0 0 0 + 14 41 1 0 0 0 0 + 14 42 1 0 0 0 0 + 15 43 1 0 0 0 0 + 15 44 1 0 0 0 0 + 15 45 1 0 0 0 0 + 17 22 1 0 0 0 0 + 17 46 1 0 0 0 0 + 18 23 2 0 0 0 0 + 18 47 1 0 0 0 0 + 19 20 1 0 0 0 0 + 19 24 2 0 0 0 0 + 20 26 2 0 0 0 0 + 21 27 2 0 0 0 0 + 21 28 1 0 0 0 0 + 22 25 2 0 0 0 0 + 22 48 1 0 0 0 0 + 23 25 1 0 0 0 0 + 23 49 1 0 0 0 0 + 24 29 1 0 0 0 0 + 24 50 1 0 0 0 0 + 25 51 1 0 0 0 0 + 26 30 1 0 0 0 0 + 26 52 1 0 0 0 0 + 27 31 1 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+2,2-diethyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C29H26N4/c1-3-29(4-2)31-25-20-27-24(19-28(25)33(29)22-15-9-6-10-16-22)30-23-17-11-12-18-26(23)32(27)21-13-7-5-8-14-21/h5-20H,3-4H2,1-2H3 + +> <PUBCHEM_IUPAC_INCHIKEY> +UOOUPHIKFMZJEA-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3_AA> +6.5 + +> <PUBCHEM_EXACT_MASS> +430.215747 + +> <PUBCHEM_MOLECULAR_FORMULA> +C29H26N4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +430.54354 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)CC + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)CC + +> <PUBCHEM_CACTVS_TPSA> +31.2 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +430.215747 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +33 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +10 17 8 +10 18 8 +11 16 8 +12 13 8 +13 16 8 +17 22 8 +18 23 8 +19 20 8 +19 24 8 +20 26 8 +21 27 8 +21 28 8 +22 25 8 +23 25 8 +24 29 8 +26 30 8 +27 31 8 +28 32 8 +29 30 8 +31 33 8 +32 33 8 +8 11 8 +8 9 8 +9 12 8 + +$$$$ +473726 + -OEChem-06261205352D + + 56 61 0 1 0 0 0 0 0999 V2000 + 3.5998 -0.9938 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5998 0.6156 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1720 0.8456 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1720 -1.2237 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0162 -0.1891 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 4.5460 -0.6891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.2072 0.3987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5460 0.3109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.2072 -0.7769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.2892 -1.9443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4121 -1.1891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2781 0.3109 0.0000 C 0 0 0 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10.4888 -1.0436 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5424 3.6716 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7367 3.6392 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1302 4.4653 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 6 1 0 0 0 0 + 1 10 1 0 0 0 0 + 2 5 1 0 0 0 0 + 2 8 2 0 0 0 0 + 3 12 1 0 0 0 0 + 3 16 1 0 0 0 0 + 3 20 1 0 0 0 0 + 4 14 2 0 0 0 0 + 4 19 1 0 0 0 0 + 5 7 1 0 0 0 0 + 5 9 1 0 0 0 0 + 6 8 1 0 0 0 0 + 6 11 2 0 0 0 0 + 7 15 1 0 0 0 0 + 7 33 1 0 0 0 0 + 7 34 1 0 0 0 0 + 8 13 1 0 0 0 0 + 9 35 1 0 0 0 0 + 9 36 1 0 0 0 0 + 9 37 1 0 0 0 0 + 10 17 2 0 0 0 0 + 10 18 1 0 0 0 0 + 11 14 1 0 0 0 0 + 11 38 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 14 1 0 0 0 0 + 13 39 1 0 0 0 0 + 15 40 1 0 0 0 0 + 15 41 1 0 0 0 0 + 15 42 1 0 0 0 0 + 16 19 1 0 0 0 0 + 16 23 2 0 0 0 0 + 17 21 1 0 0 0 0 + 17 43 1 0 0 0 0 + 18 22 2 0 0 0 0 + 18 44 1 0 0 0 0 + 19 24 2 0 0 0 0 + 20 26 2 0 0 0 0 + 20 27 1 0 0 0 0 + 21 25 2 0 0 0 0 + 21 46 1 0 0 0 0 + 22 25 1 0 0 0 0 + 22 47 1 0 0 0 0 + 23 28 1 0 0 0 0 + 23 45 1 0 0 0 0 + 24 29 1 0 0 0 0 + 24 48 1 0 0 0 0 + 25 49 1 0 0 0 0 + 26 30 1 0 0 0 0 + 26 50 1 0 0 0 0 + 27 31 2 0 0 0 0 + 27 51 1 0 0 0 0 + 28 29 2 0 0 0 0 + 28 52 1 0 0 0 0 + 29 53 1 0 0 0 0 + 30 32 2 0 0 0 0 + 30 54 1 0 0 0 0 + 31 32 1 0 0 0 0 + 31 55 1 0 0 0 0 + 32 56 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +473726 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +855 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +0 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADceB7gAAAAAAAAAAAAAAAAAAAAQAAAAAwYMECAAAAAECBUAAAHAAAAAAACAiBEAAzwIMAAACgASRiRACCAAAhAgAIiAAQdJiIYGLAkZGUIAhggALIyCcQAAAAAAAAAAAAACAAAAAAAAAAQAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_CAS_NAME> +2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_NAME> +2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C28H24N4/c1-3-28(2)30-24-19-26-23(18-27(24)32(28)21-14-8-5-9-15-21)29-22-16-10-11-17-25(22)31(26)20-12-6-4-7-13-20/h4-19H,3H2,1-2H3 + +> <PUBCHEM_IUPAC_INCHIKEY> +YQCDIJPZZOKCLA-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3_AA> +6 + +> <PUBCHEM_EXACT_MASS> +416.200097 + +> <PUBCHEM_MOLECULAR_FORMULA> +C28H24N4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +416.51696 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C + +> <PUBCHEM_CACTVS_TPSA> +31.2 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +416.200097 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +32 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +1 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +10 17 8 +10 18 8 +11 14 8 +12 13 8 +12 14 8 +16 19 8 +16 23 8 +17 21 8 +18 22 8 +19 24 8 +20 26 8 +20 27 8 +21 25 8 +22 25 8 +23 28 8 +24 29 8 +26 30 8 +27 31 8 +28 29 8 +30 32 8 +31 32 8 +5 9 3 +6 11 8 +6 8 8 +8 13 8 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/CID_2244.sdf Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,155 @@ +2244 + -OEChem-05151212332D + + 21 21 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +$$$$ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/align-it_Search_on_CID2244.phar Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,44 @@ +NAME +HYBL 5.135 0.2327 0 0.7 0 -2.66454e-15 -2.77556e-17 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +NAME +HYBL 5.07563 0.248657 0 0.7 0 4.00384 3.9265 0 +HDON 6.81996 1.22708 0 1 1 7.67971 0.716361 0 +HDON 2.45909 -1.2189 0 1 1 1.58692 -1.7081 0 +HYBH 6.78268 -1.77271 0 1 1 6.77024 -2.77263 0 +HACC 3.82046 -1.60188 0 1 1 4.30966 -2.47405 0 +HACC 2.84207 0.142469 0 1 1 2.35288 1.01464 0 +$$$$ +NAME +HYBL 5.03878 0.168252 0 0.7 0 8.92097 14.6352 0 +HACC 6.15373 -1.49215 0 1 1 5.71359 -2.39008 0 +HACC 4.15822 -1.6275 0 1 1 3.16052 -1.69523 0 +HACC 3.04334 0.0328893 0 1 1 2.60305 -0.864963 0 +$$$$ +NAME +HYBL 5.13502 0.232688 0 0.7 0 -3.05555 -1.88732 0 +HDON 7.80105 -0.28811 0 1 1 8.66519 -0.79137 0 +HDON 6.89495 1.26739 0 1 1 6.88332 2.26732 0 +HDON 2.53695 -1.26731 0 1 1 1.67093 -1.76732 0 +HACC 7.38495 -1.67371 0 1 1 7.87496 -2.54543 0 +HACC 6.38495 -1.66211 0 1 1 5.87492 -2.52227 0 +HACC 3.90295 -1.63331 0 1 1 4.40296 -2.49933 0 +HACC 2.90295 0.0986875 0 1 1 2.40294 0.964706 0 +$$$$ +NAME +HYBL 4.88436 -0.25257 0 0.7 0 -1.23357 -0.0488526 0 +HACC 6.64188 -1.29137 0 1 1 6.62805 -2.29128 0 +HACC 3.07408 0.556457 0 1 1 2.76569 1.50771 0 +$$$$ +NAME +HYBL 4.88439 -0.252571 0 0.7 0 -0.527205 -0.0505055 0 +HACC 6.64184 -1.29138 0 1 1 6.62781 -2.29129 0 +HACC 3.07406 0.556469 0 1 1 2.76567 1.50773 0 +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/align-it_Search_on_CID2244.sdf Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,1556 @@ +3639 + OpenBabel07171214472D + + 25 26 0 0 0 0 0 0 0 0999 V2000 + 3.4030 1.2327 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8950 -0.8020 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4030 -0.7673 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3849 -1.6737 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3850 -1.6622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9030 -1.6333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9030 0.0987 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8010 -0.2881 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8950 1.2674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5369 -1.2673 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0010 -0.2673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0010 0.7327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8010 0.7535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1350 -0.7673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2690 -0.2673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1350 1.2327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2690 0.7327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4119 0.6474 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.0101 1.3372 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1350 -1.3873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.3368 -0.6002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8878 1.8873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1350 1.8527 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.9573 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5369 -1.8873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 17 1 0 0 0 0 + 2 4 2 0 0 0 0 + 2 5 2 0 0 0 0 + 2 8 1 0 0 0 0 + 2 11 1 0 0 0 0 + 3 6 2 0 0 0 0 + 3 7 2 0 0 0 0 + 3 10 1 0 0 0 0 + 3 15 1 0 0 0 0 + 8 13 1 0 0 0 0 + 8 21 1 0 0 0 0 + 9 12 1 0 0 0 0 + 9 13 1 0 0 0 0 + 9 22 1 0 0 0 0 + 10 24 1 0 0 0 0 + 10 25 1 0 0 0 0 + 11 12 1 0 0 0 0 + 11 14 2 0 0 0 0 + 12 16 2 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 14 15 1 0 0 0 0 + 14 20 1 0 0 0 0 + 15 17 2 0 0 0 0 + 16 17 1 0 0 0 0 + 16 23 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3639 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +494 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +7 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +3 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +1 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBjOABkAAAAAAAAAAAAAAAAAAAAAAA8QAAAAAAAAACxAAAAHAYQQAAACAqBUCQxwYLAAAKAACRCQHDCABAhBwAAiJwIZoiIICLBkpGEIAhgkAJIyCcQAAAAAAYAAEIAAYAADAAAhAADAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide + +> <PUBCHEM_IUPAC_CAS_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide + +> <PUBCHEM_IUPAC_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +6-chloranyl-1,1-bis(oxidanylidene)-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +6-chloro-1,1-diketo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C7H8ClN3O4S2/c8-4-1-5-7(2-6(4)16(9,12)13)17(14,15)11-3-10-5/h1-2,10-11H,3H2,(H2,9,12,13) + +> <PUBCHEM_IUPAC_INCHIKEY> +JZUFKLXOESDKRF-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +-0.1 + +> <PUBCHEM_EXACT_MASS> +296.964475 + +> <PUBCHEM_MOLECULAR_FORMULA> +C7H8ClN3O4S2 + +> <PUBCHEM_MOLECULAR_WEIGHT> +297.73912 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl + +> <PUBCHEM_OPENEYE_ISO_SMILES> +C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl + +> <PUBCHEM_CACTVS_TPSA> +135 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +296.964475 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +17 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +11 12 8 +11 14 8 +12 16 8 +14 15 8 +15 17 8 +16 17 8 + +> <PHARAO_TANIMOTO> +1 + +> <PHARAO_TVERSKY_REF> +1 + +> <PHARAO_TVERSKY_DB> +1 + +$$$$ +3440 + OpenBabel07171214472D + + 32 33 0 0 0 0 0 0 0 0999 V2000 + 3.3562 1.2701 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 3.3313 -0.7297 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 8.6130 2.2981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8205 -1.6019 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8421 0.1425 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7827 -1.7727 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.6673 -0.2836 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8200 1.2271 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4591 -1.2189 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9478 0.7379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2034 -0.2405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9354 -0.2621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0632 -0.7513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8324 2.2270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0881 1.2486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2159 0.7594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.7046 2.7162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7951 -0.7728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8215 3.7093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.8021 3.9050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.2913 3.0329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0555 -1.3712 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2206 2.1269 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6275 2.8122 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3530 0.9104 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0958 1.8685 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3659 4.1298 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4514 -1.8389 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9261 -0.9023 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0613 4.4682 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9070 2.9604 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3158 -2.0894 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 16 1 0 0 0 0 + 2 4 2 0 0 0 0 + 2 5 2 0 0 0 0 + 2 9 1 0 0 0 0 + 2 11 1 0 0 0 0 + 3 17 1 0 0 0 0 + 3 21 1 0 0 0 0 + 6 18 1 0 0 0 0 + 6 32 1 0 0 0 0 + 7 18 2 0 0 0 0 + 8 10 1 0 0 0 0 + 8 14 1 0 0 0 0 + 8 25 1 0 0 0 0 + 9 28 1 0 0 0 0 + 9 29 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 15 2 0 0 0 0 + 11 13 1 0 0 0 0 + 11 16 2 0 0 0 0 + 12 13 2 0 0 0 0 + 12 18 1 0 0 0 0 + 13 22 1 0 0 0 0 + 14 17 1 0 0 0 0 + 14 23 1 0 0 0 0 + 14 24 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 26 1 0 0 0 0 + 17 19 2 0 0 0 0 + 19 20 1 0 0 0 0 + 19 27 1 0 0 0 0 + 20 21 2 0 0 0 0 + 20 30 1 0 0 0 0 + 21 31 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3440 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +481 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +7 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +3 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +5 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBzOABEAAAAAAAAAAAAAAAAASAAAAAwAAAAAAAAAAABwAAAHgYQSAAADA7h2CYwzYLABkKIAqzSyHDCCBAlJwAIiJmObsgOJjrFt7uHeajm0BHY+ceY2SKOBAQAgAICAIAICAEABAQBAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +4-chloro-2-(2-furylmethylamino)-5-sulfamoyl-benzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +4-chloro-2-(2-furanylmethylamino)-5-sulfamoylbenzoic acid + +> <PUBCHEM_IUPAC_NAME> +4-chloro-2-(furan-2-ylmethylamino)-5-sulfamoylbenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +4-chloranyl-2-(furan-2-ylmethylamino)-5-sulfamoyl-benzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +4-chloro-2-(2-furfurylamino)-5-sulfamoyl-benzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C12H11ClN2O5S/c13-9-5-10(15-6-7-2-1-3-20-7)8(12(16)17)4-11(9)21(14,18)19/h1-5,15H,6H2,(H,16,17)(H2,14,18,19) + +> <PUBCHEM_IUPAC_INCHIKEY> +ZZUFCTLCJUWOSV-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +2 + +> <PUBCHEM_EXACT_MASS> +330.00772 + +> <PUBCHEM_MOLECULAR_FORMULA> +C12H11ClN2O5S + +> <PUBCHEM_MOLECULAR_WEIGHT> +330.74414 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +C1=COC(=C1)CNC2=CC(=C(C=C2C(=O)O)S(=O)(=O)N)Cl + +> <PUBCHEM_OPENEYE_ISO_SMILES> +C1=COC(=C1)CNC2=CC(=C(C=C2C(=O)O)S(=O)(=O)N)Cl + +> <PUBCHEM_CACTVS_TPSA> +131 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +330.00772 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +21 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +4 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +10 12 8 +10 15 8 +11 13 8 +11 16 8 +12 13 8 +15 16 8 +17 19 8 +19 20 8 +20 21 8 +3 17 8 +3 21 8 + +> <PHARAO_TANIMOTO> +0.525032 + +> <PHARAO_TVERSKY_REF> +0.756062 + +> <PHARAO_TVERSKY_DB> +0.63211 + +$$$$ +5770 + OpenBabel07171214472D + + 84 89 0 0 1 0 0 0 0 0999 V2000 + 4.2025 4.5352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3618 2.7942 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1464 6.3502 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5991 7.2935 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9170 2.0317 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 10.1028 11.5745 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1537 -1.4922 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0433 0.0329 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1582 -1.6275 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.8374 5.7642 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0 0 + 37 72 1 0 0 0 0 + 38 41 1 0 0 0 0 + 39 41 2 0 0 0 0 + 40 73 1 0 0 0 0 + 40 74 1 0 0 0 0 + 40 75 1 0 0 0 0 + 42 76 1 0 0 0 0 + 42 77 1 0 0 0 0 + 42 78 1 0 0 0 0 + 43 79 1 0 0 0 0 + 43 80 1 0 0 0 0 + 43 81 1 0 0 0 0 + 44 82 1 0 0 0 0 + 44 83 1 0 0 0 0 + 44 84 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +5770 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +1000 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +10 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +10 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADcfB/PAAAAAAAAAAAAAAAAAAAAWAAAAA8eMECAAAAAFix9AAAHgAQAAAADTzhngYyzvPJlACoAyTyTACCiCAlIiAImSE+7NgNZ/bEtZuWMSpn8B3K6Yf6/f/eoAABCgACQABAAAYUADSAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_CAS_NAME> +(1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-[oxo-(3,4,5-trimethoxyphenyl)methoxy]-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylic acid methyl ester + +> <PUBCHEM_IUPAC_NAME> +methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxyphenyl)carbonyloxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +(1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylic acid methyl ester + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C33H40N2O9/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3/t18-,22+,24-,27-,28+,31+/m1/s1 + +> <PUBCHEM_IUPAC_INCHIKEY> +QEVHRUUCFGRFIF-MDEJGZGSSA-N + +> <PUBCHEM_XLOGP3_AA> +4 + +> <PUBCHEM_EXACT_MASS> +608.273381 + +> <PUBCHEM_MOLECULAR_FORMULA> +C33H40N2O9 + +> <PUBCHEM_MOLECULAR_WEIGHT> +608.6787 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +COC1C(CC2CN3CCC4=C(C3CC2C1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CO[C@H]1[C@@H](C[C@@H]2CN3CCC4=C([C@H]3C[C@@H]2[C@@H]1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC + +> <PUBCHEM_CACTVS_TPSA> +118 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +608.273381 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +44 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +6 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> 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59 61 2 0 0 0 0 + 60 61 1 0 0 0 0 + 60107 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +24847843 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +1500 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +17 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +4 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +11 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADcfB/vABkAAAAAAAAAAAAAAAAAWAAAAA8ePGCAAAAAFix9AAAHgYQQAAADT7h3iYzz/PJlAKoAyTyTHDCiDAlJyAImb0+7tiNZ/bFt5uWMSpn8B/K6af6/f/eoAYBCkICQYBADAYUhDSDAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_CAS_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-[oxo-(3,4,5-trimethoxyphenyl)methoxy]-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylic acid methyl ester + +> <PUBCHEM_IUPAC_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +6-chloranyl-1,1-bis(oxidanylidene)-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxyphenyl)carbonyloxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +6-chloro-1,1-diketo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylic acid methyl ester + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C33H40N2O9.C7H8ClN3O4S2/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19;8-4-1-5-7(2-6(4)16(9,12)13)17(14,15)11-3-10-5/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3;1-2,10-11H,3H2,(H2,9,12,13)/t18-,22+,24-,27-,28+,31+;/m1./s1 + +> <PUBCHEM_IUPAC_INCHIKEY> +NJKRHQRIYAWMRO-BQTSRIDJSA-N + +> <PUBCHEM_EXACT_MASS> +905.237856 + +> <PUBCHEM_MOLECULAR_FORMULA> +C40H48ClN5O13S2 + +> <PUBCHEM_MOLECULAR_WEIGHT> +906.41782 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +COC1C(CC2CN3CCC4=C(C3CC2C1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC.C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CO[C@H]1[C@@H](C[C@@H]2CN3CCC4=C([C@H]3C[C@@H]2[C@@H]1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC.C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl + +> <PUBCHEM_CACTVS_TPSA> +253 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +905.237856 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +61 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +6 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +2 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +18 31 8 +18 37 8 +22 62 6 +23 63 6 +25 35 5 +26 67 5 +31 34 8 +34 36 8 +36 37 8 +36 39 8 +37 41 8 +39 42 8 +29 4 6 +41 43 8 +42 43 8 +45 46 8 +45 47 8 +46 49 8 +47 48 8 +48 51 8 +49 51 8 +30 5 5 +55 56 8 +55 58 8 +56 60 8 +58 59 8 +59 61 8 +60 61 8 + +> <PHARAO_TANIMOTO> +0.328121 + +> <PHARAO_TVERSKY_REF> +1 + +> <PHARAO_TVERSKY_DB> +0.328121 + +$$$$ +473727 + OpenBabel07171214472D + + 59 64 0 0 0 0 0 0 0 0999 V2000 + 3.0702 -1.0529 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0741 0.5565 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6468 0.7779 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6419 -1.2914 0.0000 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<PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +0 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +4 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADceB7gAAAAAAAAAAAAAAAAAAAAQAAAAAwYMECAAAAAECBUAAAHAAAAAAACAiBEAAzwIMAAACgASRiRACCAAAhAgAIiAAQdJiIYGLAkZGUIAhggALIyCcQAAAAAAAAAAAAACAAAAAAAAAAQAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2,2-diethyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_CAS_NAME> +2,2-diethyl-1,5-diphenylimidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_NAME> +2,2-diethyl-1,5-diphenylimidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2,2-diethyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2,2-diethyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C29H26N4/c1-3-29(4-2)31-25-20-27-24(19-28(25)33(29)22-15-9-6-10-16-22)30-23-17-11-12-18-26(23)32(27)21-13-7-5-8-14-21/h5-20H,3-4H2,1-2H3 + +> <PUBCHEM_IUPAC_INCHIKEY> +UOOUPHIKFMZJEA-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3_AA> +6.5 + +> 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+InChI=1S/C28H24N4/c1-3-28(2)30-24-19-26-23(18-27(24)32(28)21-14-8-5-9-15-21)29-22-16-10-11-17-25(22)31(26)20-12-6-4-7-13-20/h4-19H,3H2,1-2H3 + +> <PUBCHEM_IUPAC_INCHIKEY> +YQCDIJPZZOKCLA-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3_AA> +6 + +> <PUBCHEM_EXACT_MASS> +416.200097 + +> <PUBCHEM_MOLECULAR_FORMULA> +C28H24N4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +416.51696 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C + +> <PUBCHEM_CACTVS_TPSA> +31.2 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +416.200097 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +32 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +1 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +10 17 8 +10 18 8 +11 14 8 +12 13 8 +12 14 8 +16 19 8 +16 23 8 +17 21 8 +18 22 8 +19 24 8 +20 26 8 +20 27 8 +21 25 8 +22 25 8 +23 28 8 +24 29 8 +26 30 8 +27 31 8 +28 29 8 +30 32 8 +31 32 8 +5 9 3 +6 11 8 +6 8 8 +8 13 8 + +> <PHARAO_TANIMOTO> +0.188319 + +> <PHARAO_TVERSKY_REF> +0.38133 + +> <PHARAO_TVERSKY_DB> +0.27117 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/alignit_Create_Phar_DB_6mol.phar Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/alignit_on_CID2244.phar Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,7 @@ +2244 +HYBL 5.63852 -1.334 0 0.7 0 0 0 0 +HYBH 6.3301 1.44 0 1 1 7.19612 1.94001 0 +HACC 3.732 -0.06 0 1 1 3.7319 0.94 0 +HACC 4.5981 1.44 0 1 1 3.73208 1.94001 0 +HACC 2.866 -1.56 0 1 1 2.866 -2.56 0 +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/reference.phar Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$
--- a/qed/qed.py Fri Apr 26 11:10:33 2013 -0400 +++ b/qed/qed.py Sat May 11 17:14:14 2013 -0400 @@ -1,3 +1,4 @@ +#!/usr/bin/env python __all__ = ['weights_max', 'weights_mean', 'weights_none', 'default'] # Silicos-it
--- a/qed/silicos_qed.xml Fri Apr 26 11:10:33 2013 -0400 +++ b/qed/silicos_qed.xml Sat May 11 17:14:14 2013 -0400 @@ -4,7 +4,7 @@ <requirements> <requirement type="package" version="1.0.0">silicos_it</requirement> </requirements> - <command interpreter="python">qed.py -i "${infile}" --method "${method}" -o "${outfile}" 2>&1</command> + <command interpreter="python">qed.py -i "${infile}" --method "${method}" -o "${outfile}" $header 2>&1</command> <inputs> <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/> <param name="method" type="select" label="Method"> @@ -12,6 +12,7 @@ <option value="mean">Mean weight (QEDw,mo)</option> <option value="unweighted">unweighted (QEDw,u)</option> </param> + <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" /> </inputs> <outputs> <data format="tabular" name="outfile" />
--- a/repository_dependencies.xml Fri Apr 26 11:10:33 2013 -0400 +++ b/repository_dependencies.xml Sat May 11 17:14:14 2013 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="e533de975501" /> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="1a070566e9c6" /> </repositories>
--- a/strip-it/strip-it.xml Fri Apr 26 11:10:33 2013 -0400 +++ b/strip-it/strip-it.xml Sat May 11 17:14:14 2013 -0400 @@ -1,10 +1,10 @@ -<tool id="stripit" name="Strip-it"> +<tool id="stripit" name="Strip-it" version="1.0.0"> <description> extracts predefined scaffolds from molecules</description> <requirements> <requirement type="package" version="1.0.0">silicos_it</requirement> </requirements> - <command > - strip-it --inputFormat ${infile.ext} --input $infile --output $outfile 2>&1 + <command> + strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog </command> <inputs> <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" /> @@ -28,61 +28,41 @@ The program comes with a number of predefined molecular scaffolds for extraction. These scaffolds include, amongst others - - Molecular frameworks as originally described by Bemis and - Murcko;1 - - Molecular frameworks and the reduced molecular frameworks as - described by Ansgar Schuffenhauer and coworkers;2 - - Scaffold topologies as described by Sara Pollock and coworkers.3 + - Molecular frameworks as originally described by Bemis and + Murcko;1 + - Molecular frameworks and the reduced molecular frameworks as + described by Ansgar Schuffenhauer and coworkers;2 + - Scaffold topologies as described by Sara Pollock and coworkers.3 + + +http://silicos-it.com/software/strip-it/1.0.1/strip-it.html ----- -**Example** +Example +------- -* input :: +**input** - - input - 27 28 0 0 0 0 0 0 0999 V2000 - -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 - 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 - -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 - -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 - -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 - -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 - -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 - -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 - 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 - -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 - -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 - -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 - 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 - 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 - 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 14 1 0 0 0 0 - 2 15 1 0 0 0 0 - 3 8 1 0 0 0 0 - 3 26 1 0 0 0 0 - 4 9 1 0 0 0 0 - 4 27 1 0 0 0 0 - 5 6 1 0 0 0 0 +- `SDF Format`_ +- `SMILES Format`_ +- `MOL2 Format`_ + +.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES FORMAT: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification +.. _MOL2 FORMAT: http://www.tripos.com/data/support/mol2.pdf +**output** -* output :: +TODO: - NAME MOLECULE RINGS_WITH_LINKERS_1 RINGS_WITH_LINKERS_2 MURCKO_1 MURCKO_2 OPREA_1 OPREA_2 OPREA_3 SCHUFFENHAUER_1 SCHUFFENHAUER_2 SCHUFFENHAUER_3 SCHUFFENHAUER_4 SCHUFFENHAUER_5 - 3037 Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl c1ccc(cc1)Cc1ccccc1 c1ccc(cc1)Cc1ccccc1 C1CCC(CC1)CC1CCCCC1 C1CCC(CC1)C1CCCCC1 C1CC1C1CC1 C1CC1C1CC1 C1CC1C1CC1 c1ccccc1 + ==== =========================== ==================== ==================== =================== ================== ========== ========== ========== + NAME MOLECULE RINGS_WITH_LINKERS_1 RINGS_WITH_LINKERS_2 MURCKO_1 MURCKO_2 OPREA_1 OPREA_2 OPREA_3 + ==== =========================== ==================== ==================== =================== ================== ========== ========== ========== + 3037 Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl c1ccc(cc1)Cc1ccccc1 c1ccc(cc1)Cc1ccccc1 C1CCC(CC1)CC1CCCCC1 C1CCC(CC1)C1CCCCC1 C1CC1C1CC1 C1CC1C1CC1 C1CC1C1CC1 + 3037 Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl c1ccc(cc1)Cc1ccccc1 c1ccc(cc1)Cc1ccccc1 C1CCC(CC1)CC1CCCCC1 C1CCC(CC1)C1CCCCC1 C1CC1C1CC1 C1CC1C1CC1 C1CC1C1CC1 + ==== =========================== ==================== ==================== =================== ================== ========== ========== ========== </help> </tool>
--- a/tool_dependencies.xml Fri Apr 26 11:10:33 2013 -0400 +++ b/tool_dependencies.xml Sat May 11 17:14:14 2013 -0400 @@ -1,12 +1,12 @@ <tool_dependency> <package name="numpy" version="1.7.1"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="c3041382815c" prior_installation_required="True" /> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="ec80bba4bccb" prior_installation_required="True" /> </package> <package name="openbabel" version="2.3.2"> <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="13d2ea9436b3" prior_installation_required="True" /> </package> <package name="rdkit" version="2012_12_1"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_rdkit_2012_12" owner="bgruening" changeset_revision="0adc830e7d71" prior_installation_required="True" /> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_rdkit_2012_12" owner="bgruening" changeset_revision="158956be0623" prior_installation_required="True" /> </package> <package name="silicos_it" version="1.0.0"> <install version="1.0">