# HG changeset patch # User bgruening # Date 1368306854 14400 # Node ID 987524196f3e648b7379063af960895bad249b18 # Parent b5abf2862e9732b0b2e66e93d3e74af1649abfbd Uploaded diff -r b5abf2862e97 -r 987524196f3e align-it/align-it.xml --- /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 @@ + + and Optimization (Align-it) + + silicos_it + + + align-it --format ${database.ext} --dbase $database --pharmacophore $alignedPharmacophores --dbType 'MOL' --scores $result --epsilon $0epsilon $merge $noHybrid $withExclusion 2>&1 + + + + + + + + + + + + + + + + + + + + + + + + + +**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 + $$$$ + + + + + diff -r b5abf2862e97 -r 987524196f3e align-it/alignit_create_db.xml --- /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 @@ + + database building (Align-it) + + silicos_it + + + align-it --format ${database.ext} -d $database -p $Pharmacophores --dbType MOL 2>&1 + + + + + + + + + + + + + + + +**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 + $$$$ + + + + + diff -r b5abf2862e97 -r 987524196f3e align-it/test_data/6mol.sdf --- /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 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 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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-carboxylic acid methyl ester + +> +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 + +> +QEVHRUUCFGRFIF-MDEJGZGSSA-N + +> +4 + +> +608.273381 + +> +C33H40N2O9 + +> +608.6787 + +> +COC1C(CC2CN3CCC4=C(C3CC2C1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC + +> +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 + +> +118 + +> +608.273381 + +> +0 + +> +44 + +> +6 + +> +0 + +> +0 + +> +0 + +> +0 + +> +1 + +> +1 + +> +1 +5 +255 + +> +19 1 6 +11 21 8 +11 27 8 +12 45 6 +13 46 6 +15 25 5 +16 50 5 +20 2 5 +21 23 8 +23 26 8 +26 27 8 +26 29 8 +27 31 8 +29 32 8 +31 33 8 +32 33 8 +35 36 8 +35 37 8 +36 39 8 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0 0 + 44 85 1 0 0 0 0 + 44 86 1 0 0 0 0 + 44 87 1 0 0 0 0 + 45 46 2 0 0 0 0 + 45 47 1 0 0 0 0 + 46 49 1 0 0 0 0 + 46 88 1 0 0 0 0 + 47 48 2 0 0 0 0 + 47 89 1 0 0 0 0 + 48 51 1 0 0 0 0 + 49 51 2 0 0 0 0 + 50 90 1 0 0 0 0 + 50 91 1 0 0 0 0 + 50 92 1 0 0 0 0 + 52 93 1 0 0 0 0 + 52 94 1 0 0 0 0 + 52 95 1 0 0 0 0 + 53 96 1 0 0 0 0 + 53 97 1 0 0 0 0 + 53 98 1 0 0 0 0 + 54 99 1 0 0 0 0 + 54100 1 0 0 0 0 + 54101 1 0 0 0 0 + 55 56 1 0 0 0 0 + 55 58 2 0 0 0 0 + 56 60 2 0 0 0 0 + 57102 1 0 0 0 0 + 57103 1 0 0 0 0 + 58 59 1 0 0 0 0 + 58106 1 0 0 0 0 + 59 61 2 0 0 0 0 + 60 61 1 0 0 0 0 + 60107 1 0 0 0 0 +M END +> +24847843 + +> +1 + +> +1500 + +> +17 + +> +4 + +> +11 + +> +AAADcfB/vABkAAAAAAAAAAAAAAAAAWAAAAA8ePGCAAAAAFix9AAAHgYQQAAADT7h3iYzz/PJlAKoAyTyTHDCiDAlJyAImb0+7tiNZ/bFt5uWMSpn8B/K6af6/f/eoAYBCkICQYBADAYUhDSDAAAAAAAAAA== + +> +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 + +> +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 + +> +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 + +> +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 + +> +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 + +> +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 + +> +NJKRHQRIYAWMRO-BQTSRIDJSA-N + +> +905.237856 + +> +C40H48ClN5O13S2 + +> +906.41782 + +> +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 + +> +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 + +> +253 + +> +905.237856 + +> +0 + +> +61 + +> +6 + +> +0 + +> +0 + +> +0 + +> +0 + +> +2 + +> +1 + +> +1 +5 +255 + +> +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 + +> +0.328121 + +> +1 + +> +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 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4886 -0.2468 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6810 0.3429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6782 -0.8327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0172 -0.7505 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0196 0.2495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7573 -2.0027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8820 -1.2526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8867 0.7474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7515 0.2454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7655 -0.4237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7878 1.3371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7492 -0.7546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7783 -2.2067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4234 -2.7486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5516 0.2619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5491 -0.7797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6376 1.7778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4653 -3.1564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.1104 -3.6984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4841 0.8166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1314 -3.9023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4790 -1.3389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4990 2.2858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7671 2.2699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.4266 0.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.4240 -0.8059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4898 3.2857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7579 3.2699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6193 3.7778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0854 0.5152 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4078 -0.2138 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3301 -1.3459 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1230 -1.2645 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8805 -1.8726 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8882 1.3674 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0191 0.1421 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1997 -0.1703 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5120 -0.9895 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4043 1.2709 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8541 1.9536 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1714 1.4034 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3653 -1.7442 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0303 -2.6222 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8584 -3.2828 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5234 -4.1608 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4784 1.4365 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9374 -4.4911 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4703 -1.9588 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.0388 1.9807 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2330 1.9550 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9631 0.5899 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9590 -1.1192 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.0240 3.6006 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2181 3.5749 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6136 4.3977 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 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+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 + +> +UOOUPHIKFMZJEA-UHFFFAOYSA-N + +> +6.5 + +> +430.215747 + +> +C29H26N4 + +> +430.54354 + +> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)CC + +> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)CC + +> +31.2 + +> +430.215747 + +> +0 + +> +33 + +> +0 + +> +0 + +> +0 + +> +0 + +> +0 + +> +1 + +> +1 + +> +1 +5 +255 + +> +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 + +> +0.171691 + +> +0.381328 + +> +0.237983 + +$$$$ +473726 + OpenBabel07171214472D + + 56 61 0 0 1 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 + 6.6418 -1.2914 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4885 -0.2468 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 4.0171 -0.7505 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6809 0.3429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0195 0.2495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6781 -0.8327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7573 -2.0027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8820 -1.2526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7516 0.2454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8868 0.7474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7492 -0.7546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7878 1.3372 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5517 0.2618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7783 -2.2066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4233 -2.7486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5492 -0.7798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6377 1.7778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4654 -3.1564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.1105 -3.6984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4842 0.8166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4790 -1.3389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1314 -3.9023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4991 2.2858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7671 2.2699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.4266 0.2790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.4240 -0.8059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4899 3.2857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7580 3.2698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6194 3.7778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0854 0.5152 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4078 -0.2137 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3149 -0.3302 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1757 -1.1959 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0413 -1.3352 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8805 -1.8726 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8883 1.3674 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4043 1.2709 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8541 1.9536 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1714 1.4034 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3653 -1.7441 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0303 -2.6222 0.0000 H 0 0 0 0 0 0 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+2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine + +> +2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine + +> +2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> +2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> +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 + +> +YQCDIJPZZOKCLA-UHFFFAOYSA-N + +> +6 + +> +416.200097 + +> +C28H24N4 + +> +416.51696 + +> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C + +> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C + +> +31.2 + +> +416.200097 + +> +0 + +> +32 + +> +0 + +> +1 + +> +0 + +> +0 + +> +0 + +> +1 + +> +1 + +> +1 +5 +255 + +> +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 + +> +0.188319 + +> +0.38133 + +> +0.27117 + +$$$$ diff -r b5abf2862e97 -r 987524196f3e align-it/test_data/alignit_Create_Phar_DB_6mol.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/alignit_Create_Phar_DB_6mol.phar Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$ diff -r b5abf2862e97 -r 987524196f3e align-it/test_data/alignit_on_CID2244.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/alignit_on_CID2244.phar Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,7 @@ +2244 +HYBL 5.63852 -1.334 0 0.7 0 0 0 0 +HYBH 6.3301 1.44 0 1 1 7.19612 1.94001 0 +HACC 3.732 -0.06 0 1 1 3.7319 0.94 0 +HACC 4.5981 1.44 0 1 1 3.73208 1.94001 0 +HACC 2.866 -1.56 0 1 1 2.866 -2.56 0 +$$$$ diff -r b5abf2862e97 -r 987524196f3e align-it/test_data/reference.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/reference.phar Sat May 11 17:14:14 2013 -0400 @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$ diff -r b5abf2862e97 -r 987524196f3e qed/qed.py --- 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 diff -r b5abf2862e97 -r 987524196f3e qed/silicos_qed.xml --- 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 @@ silicos_it - qed.py -i "${infile}" --method "${method}" -o "${outfile}" 2>&1 + qed.py -i "${infile}" --method "${method}" -o "${outfile}" $header 2>&1 @@ -12,6 +12,7 @@ + diff -r b5abf2862e97 -r 987524196f3e repository_dependencies.xml --- 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 @@ - + diff -r b5abf2862e97 -r 987524196f3e strip-it/strip-it.xml --- 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 @@ - + extracts predefined scaffolds from molecules silicos_it - - strip-it --inputFormat ${infile.ext} --input $infile --output $outfile 2>&1 + + strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog @@ -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 + ==== =========================== ==================== ==================== =================== ================== ========== ========== ========== diff -r b5abf2862e97 -r 987524196f3e tool_dependencies.xml --- 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 @@ - + - +