# HG changeset patch # User bgruening # Date 1376552040 14400 # Node ID bb92d30b4f52190fb787f795437a61b9417aa295 Uploaded diff -r 000000000000 -r bb92d30b4f52 align-it/align-it.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/align-it.xml Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,238 @@ + + and Optimization (Align-it) + + silicos_it + openbabel + + + align-it + #if str($database.ext).strip() == 'phar': + --dbType PHAR + #else: + --dbType ${database.ext} + #end if + --dbase $database + + --reference $reference + #if str($reference.ext).strip() == 'phar': + --refType PHAR + #else: + --refType ${reference.ext} + #end if + ####################################### + #### output options + ####################################### + --pharmacophore $aligned_pharmacophores + + + ##--out $aligned_structures + ##--outType $oformat + + #if float( str($cutoff) ) > 0: + --cutOff $cutoff + #end if + #if int( str($best) ) > 0: + --best $best + #end if + --rankBy $rankBy + --scores $score_result_file + + ####################################### + #### Options + ####################################### + + #set $fgroups_combined = str( $fgroups ).strip() + --funcGroup $fgroups_combined + + --epsilon $epsilon + $merge + $noNormal + $noHybrid + $scoreOnly + $withExclusion + + 2>&1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**What this tool does** + +Align-it_ is a tool to align molecules according to their pharmacophores. +A pharmacophore is an abstract concept based on the specific interactions +observed in drug-receptor interactions: hydrogen bonding, +charge transfer, electrostatic and hydrophobic interactions. +Molecular modeling and/or screening based on pharmacophore similarities +has been proven to be an important and useful method in drug discovery. + +The functionality of Align-it_ consists mainly of two parts. +The first functionality is the generation of pharmacophores from molecules +(use the tool **Pharmacophore generation** if you want to store these for further use). +Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting +score is calculated from the volume overlap resulting of the alignments. + +.. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html + +----- + +.. class:: infomark + +**Input** + +* Example:: + + - 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 + +----- + +.. class:: infomark + +**Output** + +The format of the output file is shown in the table below: + ++--------+-----------------------------------------------------------------------+ +| Column | Content | ++========+=======================================================================+ +| 1 | Id of the reference structure | ++--------+-----------------------------------------------------------------------+ +| 2 | Maximum volume of the reference structure | ++--------+-----------------------------------------------------------------------+ +| 3 | Id of the database structure | ++--------+-----------------------------------------------------------------------+ +| 4 | Maximum volume of the database structure | ++--------+-----------------------------------------------------------------------+ +| 5 | Maximum volume overlap of the two structures | ++--------+-----------------------------------------------------------------------+ +| 6 | Overlap between pharmacophore and exclusion spheres in the reference | ++--------+-----------------------------------------------------------------------+ +| 7 | Corrected volume overlap between database pharmacophore and reference | ++--------+-----------------------------------------------------------------------+ +| 8 | Number of pharmacophore points in the processed pharmacophore | ++--------+-----------------------------------------------------------------------+ +| 9 | TANIMOTO score | ++--------+-----------------------------------------------------------------------+ +| 10 | TVERSKY_REF score | ++--------+-----------------------------------------------------------------------+ +| 11 | TVERSKY_DB score | ++--------+-----------------------------------------------------------------------+ + + +* Example:: + + - 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 + $$$$ + +----- + +.. class:: infomark + +**Cite** + +`Silicos-it`_ - align-it + +.. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html + + + + diff -r 000000000000 -r bb92d30b4f52 align-it/align-it_create_db.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/align-it_create_db.xml Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,123 @@ + + generation (Align-it) + + silicos_it + openbabel + + + align-it + --dbType ${database.ext} + --dbase $database + --pharmacophore $pharmacophores + $merge + $noHybrid + + 2>&1 + + + + + + + + + + + + + + + +.. class:: infomark + +**What this tool does** + +Align-it_ is a tool to align molecules according to their pharmacophores. +A pharmacophore is an abstract concept based on the specific interactions +observed in drug-receptor interactions: hydrogen bonding, +charge transfer, electrostatic and hydrophobic interactions. +Molecular modeling and/or screening based on pharmacophore similarities +has been proven to be an important and useful method in drug discovery. + +The functionality of Align-it_ consists mainly of two parts. +The first functionality is the generation of pharmacophores from molecules +(the function of this tool). Secondly, pairs of pharmacophores +can be aligned (use the tool **Pharmacophore Alignment**). The resulting +score is calculated from the volume overlap resulting of the alignments. + +.. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html + +----- + +.. class:: infomark + +**Input** + +* Example:: + + - 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 + +----- + +.. class:: infomark + +**Output** + +* Example:: + + - 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 + $$$$ + +----- + +.. class:: infomark + +**Cite** + +`Silicos-it`_ - align-it + +.. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html + + + diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/6mol.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/6mol.sdf Thu Aug 15 03:34:00 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 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(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 + +> 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0 0 + 4.6634 -2.6886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.7844 0.3317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.7844 -0.7099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8668 1.8455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7063 -3.1011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.3527 -3.6392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.7156 0.8887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.3742 -3.8454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.7156 -1.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.7270 2.3555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9951 2.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.6594 0.3534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.6594 -0.7316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.7154 3.3554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9835 3.3354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.8437 3.8454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3176 0.5696 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6418 -0.1586 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5668 -1.2909 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.3595 -1.2076 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 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0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2772 3.3354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1374 3.8454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6112 0.5696 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9354 -0.1586 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8428 -0.2753 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7056 -1.1413 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5716 -1.2785 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4121 -1.8091 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4121 1.4309 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9283 1.3284 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3765 2.0098 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6951 1.4580 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8966 -1.6891 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5637 -2.5608 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0021 1.5086 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3933 -3.2289 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0604 -4.1006 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0021 -1.8868 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4752 -4.4347 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5612 2.0517 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7554 2.0193 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 10.4888 0.6655 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 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 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+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 + +> 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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 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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 +> +473726 + +> +1 + +> +855 + +> +4 + +> +0 + +> +3 + +> +AAADceB7gAAAAAAAAAAAAAAAAAAAAQAAAAAwYMECAAAAAECBUAAAHAAAAAAACAiBEAAzwIMAAACgASRiRACCAAAhAgAIiAAQdJiIYGLAkZGUIAhggALIyCcQAAAAAAAAAAAAACAAAAAAAAAAQAAAAAAAAA== + +> +2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> +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 + +$$$$ diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/alignit_Create_Phar_DB_6mol.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/alignit_Create_Phar_DB_6mol.phar Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$ diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/alignit_on_CID2244.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/alignit_on_CID2244.phar Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,7 @@ +2244 +HYBL 5.63852 -1.334 0 0.7 0 0 0 0 +HYBH 6.3301 1.44 0 1 1 7.19612 1.94001 0 +HACC 3.732 -0.06 0 1 1 3.7319 0.94 0 +HACC 4.5981 1.44 0 1 1 3.73208 1.94001 0 +HACC 2.866 -1.56 0 1 1 2.866 -2.56 0 +$$$$ diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/reference.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/reference.phar Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$ diff -r 000000000000 -r bb92d30b4f52 qed/errors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qed/errors.py Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,17 @@ +__all__ = ['SilicosItError', 'WrongArgument'] + +class SilicosItError(Exception): + """Base class for exceptions in Silicos-it code""" + pass + +class WrongArgument(SilicosItError): + """ + Exception raised when argument to function is not of correct type. + + Attributes: + function -- function in which error occurred + msg -- explanation of the error + """ + def __init__(self, function, msg): + self.function = function + self.msg = msg diff -r 000000000000 -r bb92d30b4f52 qed/qed.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qed/qed.py Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,414 @@ +#!/usr/bin/env python +__all__ = ['weights_max', 'weights_mean', 'weights_none', 'default'] + +# Silicos-it +from errors import WrongArgument + +# RDKit +from rdkit.Chem import Descriptors +from rdkit import Chem + +# General +from copy import deepcopy +from math import exp, log +import sys, os, re +import argparse + +def check_filetype(filepath): + mol = False + possible_inchi = True + for line_counter, line in enumerate(open(filepath)): + if line_counter > 10000: + break + if line.find('$$$$') != -1: + return 'sdf' + elif line.find('@MOLECULE') != -1: + return 'mol2' + elif line.find('ligand id') != -1: + return 'drf' + elif possible_inchi and re.findall('^InChI=', line): + return 'inchi' + elif re.findall('^M\s+END', line): + mol = True + # first line is not an InChI, so it can't be an InChI file + possible_inchi = False + + if mol: + # END can occures before $$$$, so and SDF file will + # be recognised as mol, if you not using this hack' + return 'mol' + return 'smi' + +AliphaticRings = Chem.MolFromSmarts('[$([A;R][!a])]') + +AcceptorSmarts = [ + '[oH0;X2]', + '[OH1;X2;v2]', + '[OH0;X2;v2]', + '[OH0;X1;v2]', + '[O-;X1]', + '[SH0;X2;v2]', + '[SH0;X1;v2]', + '[S-;X1]', + '[nH0;X2]', + '[NH0;X1;v3]', + '[$([N;+0;X3;v3]);!$(N[C,S]=O)]' + ] +Acceptors = [] +for hba in AcceptorSmarts: + Acceptors.append(Chem.MolFromSmarts(hba)) + +StructuralAlertSmarts = [ + '*1[O,S,N]*1', + '[S,C](=[O,S])[F,Br,Cl,I]', + '[CX4][Cl,Br,I]', + '[C,c]S(=O)(=O)O[C,c]', + '[$([CH]),$(CC)]#CC(=O)[C,c]', + '[$([CH]),$(CC)]#CC(=O)O[C,c]', + 'n[OH]', + '[$([CH]),$(CC)]#CS(=O)(=O)[C,c]', + 'C=C(C=O)C=O', + 'n1c([F,Cl,Br,I])cccc1', + '[CH1](=O)', + '[O,o][O,o]', + '[C;!R]=[N;!R]', + '[N!R]=[N!R]', + '[#6](=O)[#6](=O)', + '[S,s][S,s]', + '[N,n][NH2]', + 'C(=O)N[NH2]', + '[C,c]=S', + '[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]=[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]', + 'C1(=[O,N])C=CC(=[O,N])C=C1', + 'C1(=[O,N])C(=[O,N])C=CC=C1', + 'a21aa3a(aa1aaaa2)aaaa3', + 'a31a(a2a(aa1)aaaa2)aaaa3', + 'a1aa2a3a(a1)A=AA=A3=AA=A2', + 'c1cc([NH2])ccc1', + '[Hg,Fe,As,Sb,Zn,Se,se,Te,B,Si,Na,Ca,Ge,Ag,Mg,K,Ba,Sr,Be,Ti,Mo,Mn,Ru,Pd,Ni,Cu,Au,Cd,Al,Ga,Sn,Rh,Tl,Bi,Nb,Li,Pb,Hf,Ho]', + 'I', + 'OS(=O)(=O)[O-]', + '[N+](=O)[O-]', + 'C(=O)N[OH]', + 'C1NC(=O)NC(=O)1', + '[SH]', + '[S-]', + 'c1ccc([Cl,Br,I,F])c([Cl,Br,I,F])c1[Cl,Br,I,F]', + 'c1cc([Cl,Br,I,F])cc([Cl,Br,I,F])c1[Cl,Br,I,F]', + '[CR1]1[CR1][CR1][CR1][CR1][CR1][CR1]1', + '[CR1]1[CR1][CR1]cc[CR1][CR1]1', + '[CR2]1[CR2][CR2][CR2][CR2][CR2][CR2][CR2]1', + '[CR2]1[CR2][CR2]cc[CR2][CR2][CR2]1', + '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1', + '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1', + 'C#C', + '[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]', + '[$([N+R]),$([n+R]),$([N+]=C)][O-]', + '[C,c]=N[OH]', + '[C,c]=NOC=O', + '[C,c](=O)[CX4,CR0X3,O][C,c](=O)', + 'c1ccc2c(c1)ccc(=O)o2', + '[O+,o+,S+,s+]', + 'N=C=O', + '[NX3,NX4][F,Cl,Br,I]', + 'c1ccccc1OC(=O)[#6]', + '[CR0]=[CR0][CR0]=[CR0]', + '[C+,c+,C-,c-]', + 'N=[N+]=[N-]', + 'C12C(NC(N1)=O)CSC2', + 'c1c([OH])c([OH,NH2,NH])ccc1', + 'P', + '[N,O,S]C#N', + 'C=C=O', + '[Si][F,Cl,Br,I]', + '[SX2]O', + '[SiR0,CR0](c1ccccc1)(c2ccccc2)(c3ccccc3)', + 'O1CCCCC1OC2CCC3CCCCC3C2', + 'N=[CR0][N,n,O,S]', + '[cR2]1[cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2][cR2]1[cR2]2[cR2][cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2]2', + 'C=[C!r]C#N', + '[cR2]1[cR2]c([N+0X3R0,nX3R0])c([N+0X3R0,nX3R0])[cR2][cR2]1', + '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2]c([N+0X3R0,nX3R0])[cR2]1', + '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2][cR2]c1([N+0X3R0,nX3R0])', + '[OH]c1ccc([OH,NH2,NH])cc1', + 'c1ccccc1OC(=O)O', + '[SX2H0][N]', + 'c12ccccc1(SC(S)=N2)', + 'c12ccccc1(SC(=S)N2)', + 'c1nnnn1C=O', + 's1c(S)nnc1NC=O', + 'S1C=CSC1=S', + 'C(=O)Onnn', + 'OS(=O)(=O)C(F)(F)F', + 'N#CC[OH]', + 'N#CC(=O)', + 'S(=O)(=O)C#N', + 'N[CH2]C#N', + 'C1(=O)NCC1', + 'S(=O)(=O)[O-,OH]', + 'NC[F,Cl,Br,I]', + 'C=[C!r]O', + '[NX2+0]=[O+0]', + '[OR0,NR0][OR0,NR0]', + 'C(=O)O[C,H1].C(=O)O[C,H1].C(=O)O[C,H1]', + '[CX2R0][NX3R0]', + 'c1ccccc1[C;!R]=[C;!R]c2ccccc2', + '[NX3R0,NX4R0,OR0,SX2R0][CX4][NX3R0,NX4R0,OR0,SX2R0]', + '[s,S,c,C,n,N,o,O]~[n+,N+](~[s,S,c,C,n,N,o,O])(~[s,S,c,C,n,N,o,O])~[s,S,c,C,n,N,o,O]', + '[s,S,c,C,n,N,o,O]~[nX3+,NX3+](~[s,S,c,C,n,N])~[s,S,c,C,n,N]', + '[*]=[N+]=[*]', + '[SX3](=O)[O-,OH]', + 'N#N', + 'F.F.F.F', + '[R0;D2][R0;D2][R0;D2][R0;D2]', + '[cR,CR]~C(=O)NC(=O)~[cR,CR]', + 'C=!@CC=[O,S]', + '[#6,#8,#16][C,c](=O)O[C,c]', + 'c[C;R0](=[O,S])[C,c]', + 'c[SX2][C;!R]', + 'C=C=C', + 'c1nc([F,Cl,Br,I,S])ncc1', + 'c1ncnc([F,Cl,Br,I,S])c1', + 'c1nc(c2c(n1)nc(n2)[F,Cl,Br,I])', + '[C,c]S(=O)(=O)c1ccc(cc1)F', + '[15N]', + '[13C]', + '[18O]', + '[34S]' + ] + +StructuralAlerts = [] +for smarts in StructuralAlertSmarts: + StructuralAlerts.append(Chem.MolFromSmarts(smarts)) + + +# ADS parameters for the 8 molecular properties: [row][column] +# rows[8]: MW, ALOGP, HBA, HBD, PSA, ROTB, AROM, ALERTS +# columns[7]: A, B, C, D, E, F, DMAX +# ALOGP parameters from Gregory Gerebtzoff (2012, Roche) +pads1 = [ [2.817065973, 392.5754953, 290.7489764, 2.419764353, 49.22325677, 65.37051707, 104.9805561], + [0.486849448, 186.2293718, 2.066177165, 3.902720615, 1.027025453, 0.913012565, 145.4314800], + [2.948620388, 160.4605972, 3.615294657, 4.435986202, 0.290141953, 1.300669958, 148.7763046], + [1.618662227, 1010.051101, 0.985094388, 0.000000001, 0.713820843, 0.920922555, 258.1632616], + [1.876861559, 125.2232657, 62.90773554, 87.83366614, 12.01999824, 28.51324732, 104.5686167], + [0.010000000, 272.4121427, 2.558379970, 1.565547684, 1.271567166, 2.758063707, 105.4420403], + [3.217788970, 957.7374108, 2.274627939, 0.000000001, 1.317690384, 0.375760881, 312.3372610], + [0.010000000, 1199.094025, -0.09002883, 0.000000001, 0.185904477, 0.875193782, 417.7253140] ] +# ALOGP parameters from the original publication +pads2 = [ [2.817065973, 392.5754953, 290.7489764, 2.419764353, 49.22325677, 65.37051707, 104.9805561], + [3.172690585, 137.8624751, 2.534937431, 4.581497897, 0.822739154, 0.576295591, 131.3186604], + [2.948620388, 160.4605972, 3.615294657, 4.435986202, 0.290141953, 1.300669958, 148.7763046], + [1.618662227, 1010.051101, 0.985094388, 0.000000001, 0.713820843, 0.920922555, 258.1632616], + [1.876861559, 125.2232657, 62.90773554, 87.83366614, 12.01999824, 28.51324732, 104.5686167], + [0.010000000, 272.4121427, 2.558379970, 1.565547684, 1.271567166, 2.758063707, 105.4420403], + [3.217788970, 957.7374108, 2.274627939, 0.000000001, 1.317690384, 0.375760881, 312.3372610], + [0.010000000, 1199.094025, -0.09002883, 0.000000001, 0.185904477, 0.875193782, 417.7253140] ] + +def ads(x, a, b, c, d, e, f, dmax): + return ((a+(b/(1+exp(-1*(x-c+d/2)/e))*(1-1/(1+exp(-1*(x-c-d/2)/f))))) / dmax) + +def properties(mol): + """ + Calculates the properties that are required to calculate the QED descriptor. + """ + matches = [] + if (mol is None): + raise WrongArgument("properties(mol)", "mol argument is \'None\'") + x = [0] * 9 + x[0] = Descriptors.MolWt(mol) # MW + x[1] = Descriptors.MolLogP(mol) # ALOGP + for hba in Acceptors: # HBA + if (mol.HasSubstructMatch(hba)): + matches = mol.GetSubstructMatches(hba) + x[2] += len(matches) + x[3] = Descriptors.NumHDonors(mol) # HBD + x[4] = Descriptors.TPSA(mol) # PSA + x[5] = Descriptors.NumRotatableBonds(mol) # ROTB + x[6] = Chem.GetSSSR(Chem.DeleteSubstructs(deepcopy(mol), AliphaticRings)) # AROM + for alert in StructuralAlerts: # ALERTS + if (mol.HasSubstructMatch(alert)): x[7] += 1 + ro5_failed = 0 + if x[3] > 5: + ro5_failed += 1 #HBD + if x[2] > 10: + ro5_failed += 1 #HBA + if x[0] >= 500: + ro5_failed += 1 + if x[1] > 5: + ro5_failed += 1 + x[8] = ro5_failed + return x + + +def qed(w, p, gerebtzoff): + d = [0.00] * 8 + if gerebtzoff: + for i in range(0, 8): + d[i] = ads(p[i], pads1[i][0], pads1[i][1], pads1[i][2], pads1[i][3], pads1[i][4], pads1[i][5], pads1[i][6]) + else: + for i in range(0, 8): + d[i] = ads(p[i], pads2[i][0], pads2[i][1], pads2[i][2], pads2[i][3], pads2[i][4], pads2[i][5], pads2[i][6]) + t = 0.0 + for i in range(0, 8): + t += w[i] * log(d[i]) + return (exp(t / sum(w))) + + +def weights_max(mol, gerebtzoff = True, props = False): + """ + Calculates the QED descriptor using maximal descriptor weights. + If props is specified we skip the calculation step and use the props-list of properties. + """ + if not props: + props = properties(mol) + return qed([0.50, 0.25, 0.00, 0.50, 0.00, 0.50, 0.25, 1.00], props, gerebtzoff) + + +def weights_mean(mol, gerebtzoff = True, props = False): + """ + Calculates the QED descriptor using average descriptor weights. + If props is specified we skip the calculation step and use the props-list of properties. + """ + if not props: + props = properties(mol) + return qed([0.66, 0.46, 0.05, 0.61, 0.06, 0.65, 0.48, 0.95], props, gerebtzoff) + + +def weights_none(mol, gerebtzoff = True, props = False): + """ + Calculates the QED descriptor using unit weights. + If props is specified we skip the calculation step and use the props-list of properties. + """ + if not props: + props = properties(mol) + return qed([1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00], props, gerebtzoff) + + +def default(mol, gerebtzoff = True): + """ + Calculates the QED descriptor using average descriptor weights and Gregory Gerebtzoff parameters. + """ + return weights_mean(mol, gerebtzoff) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('-i', '--input', + required=True, + help='path to the input file name') + parser.add_argument("-m", "--method", + dest="method", + choices=['max', 'mean', 'unweighted'], + default="mean", + help="Specify the method you want to use.") + parser.add_argument("--iformat", + help="Input format. It must be supported by openbabel.") + parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), + default=sys.stdout, + help="path to the result file, default it sdtout") + parser.add_argument("--header", dest="header", action="store_true", + default=False, + help="Write header line.") + + + args = parser.parse_args() + + # Elucidate filetype and open supplier + ifile = os.path.abspath(args.input) + if not os.path.isfile(ifile): + print "Error: ", ifile, " is not a file or cannot be found." + sys.exit(1) + if not os.path.exists(ifile): + print "Error: ", ifile, " does not exist or cannot be found." + sys.exit(1) + if not os.access(ifile, os.R_OK): + print "Error: ", ifile, " is not readable." + sys.exit(1) + + if not args.iformat: + # try to guess the filetype + filetype = check_filetype( ifile ) + else: + filetype = args.iformat # sdf or smi + + + """ + We want to store the original SMILES in the output. So in case of a SMILES file iterate over the file and convert each line separate. + """ + if filetype == 'sdf': + supplier = Chem.SDMolSupplier( ifile ) + # Process file + if args.header: + args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n") + count = 0 + for mol in supplier: + count += 1 + if mol is None: + print "Warning: skipping molecule ", count, " and continuing with next." + continue + props = properties(mol) + + if args.method == 'max': + calc_qed = weights_max(mol, True, props) + elif args.method == 'unweighted': + calc_qed = weights_none(mol, True, props) + else: + calc_qed = weights_mean(mol, True, props) + + args.outfile.write( "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\n" % ( + props[0], + props[1], + props[2], + props[3], + props[4], + props[5], + props[6], + props[7], + props[8], + calc_qed, + mol.GetProp("_Name"), + )) + elif filetype == 'smi': + supplier = Chem.SmilesMolSupplier( ifile, " \t", 0, 1, False, True ) + + # Process file + if args.header: + args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\tSMILES\n") + count = 0 + for line in open(ifile): + tokens = line.strip().split('\t') + if len(tokens) > 1: + smiles, title = tokens + else: + smiles = tokens[0] + title = '' + mol = Chem.MolFromSmiles(smiles) + count += 1 + if mol is None: + print "Warning: skipping molecule ", count, " and continuing with next." + continue + props = properties(mol) + + if args.method == 'max': + calc_qed = weights_max(mol, True, props) + elif args.method == 'unweighted': + calc_qed = weights_none(mol, True, props) + else: + calc_qed = weights_mean(mol, True, props) + + args.outfile.write( "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\t%s\n" % ( + props[0], + props[1], + props[2], + props[3], + props[4], + props[5], + props[6], + props[7], + props[8], + calc_qed, + title, + smiles + )) + else: + sys.exit("Error: unknown file-type: ", filetype) diff -r 000000000000 -r bb92d30b4f52 qed/silicos_qed.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qed/silicos_qed.xml Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,121 @@ + + quantitative estimation (QED) + + + silicos_it + rdkit + numpy + + + qed.py -i "${infile}" + --method "${method}" + --iformat ${infile.ext} + -o "${outfile}" $header 2>&1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**What this tool does** + +Estimates the drug-likeness of molecules and reports a score. Comes with three applicable varieties (QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\ , QED\ :sub:`w,u` ). + +----- + +.. class:: warningmark + +**HINT** + +- All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item. + +- QED\ :sub:`w,max` using the set of weights that give maximal information content + +- QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content + +- QED\ :sub:`w,u` with all weights as unity, hence unweighted. + +----- + +.. class:: infomark + +**Input** + + +| - `SD-Format`_ +| - `SMILES Format`_ + +.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification + +----- + +.. class:: infomark + +**Output** + ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| MW | ALOGP | HBA | HBD | PSA | ROTB | AROM | ALERTS | QED | NAME | Ro5 | ++========+=======+=====+=====+========+======+======+========+=======+================+=====+ +| 286.34 | 1.092 | 6 | 3 | 101.88 | 4 | 2 | 1 | 0.737 | Abacavir | 0 | ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| 181.21 | 0.481 | 4 | 2 | 83.47 | 5 | 0 | 2 | 0.487 | Acamprosate | 0 | ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| 336.43 | 2.365 | 5 | 3 | 87.66 | 11 | 1 | 1 | 0.540 | Acebutolol | 0 | ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| 151.16 | 1.351 | 2 | 2 | 49.33 | 2 | 1 | 1 | 0.633 | Acetaminophen | 0 | ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| 222.25 | 0.225 | 5 | 2 | 115.04 | 3 | 1 | 1 | 0.727 | Acetazolamide | 0 | ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| 324.40 | 3.291 | 4 | 2 | 92.34 | 6 | 1 | 1 | 0.772 | Acetohexamide | 0 | ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| 411.57 | 3.492 | 6 | 1 | 47.02 | 7 | 2 | 1 | 0.688 | Acetophenazine | 0 | ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| 329.37 | 3.327 | 4 | 1 | 39.72 | 4 | 2 | 0 | 0.917 | Paroxetine | 0 | ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| 270.21 | 3.146 | 3 | 1 | 55.13 | 4 | 2 | 0 | 0.915 | Leflunomide | 0 | ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ + +----- + +.. class:: infomark + +**Cite** + +Bickerton et al. - `Quantifying the chemical beauty of drugs`_ + +.. _Quantifying the chemical beauty of drugs: http://www.nature.com/nchem/journal/v4/n2/full/nchem.1243.html + + + diff -r 000000000000 -r bb92d30b4f52 qed/tool-data/qed_test.smi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qed/tool-data/qed_test.smi Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,25 @@ +Nc1nc(NC2CC2)c2ncn([C@@H]3C[C@H](CO)C=C3)c2n1 Abacavir +CC(=O)NCCCS(O)(=O)=O Acamprosate +CCCC(=O)Nc1ccc(OCC(O)CNC(C)C)c(c1)C(C)=O Acebutolol +CC(=O)Nc1ccc(O)cc1 Acetaminophen +CC(=O)Nc1nnc(s1)S(N)(=O)=O Acetazolamide +CC(=O)c1ccc(cc1)S(=O)(=O)NC(=O)NC1CCCCC1 Acetohexamide +CC(=O)c1ccc2Sc3ccccc3N(CCCN3CCN(CCO)CC3)c2c1 Acetophenazine +Fc4ccc(C1CCNCC1COc3ccc2OCOc2c3)cc4 Paroxetine +Cc1oncc1C(=O)Nc2ccc(C(F)(F)F)cc2 Leflunomide +CN1C4CCCC1CC(NC(=O)c2nn(C)c3ccccc23)C4 Granisetron +CCCN2CC(CSC)CC1c3cccc4[nH]cc(CC12)c34 Pergolide +CCc3c(C)[nH]c2CCC(CN1CCOCC1)C(=O)c23 Molindone +CCCCCCCCCCCCCCCC(=O)OCC(NC(=O)C(Cl)Cl)C(O)c1ccc([N+]([O-])=O)cc1 ChloramphenicalPalmitate +CCCCCCCCCCCCCCCOC(=O)C2C(O)C(O)C(C(NC(=O)C1CC(CCC)CN1C)C(C)Cl)OC2SC ClindamycinPalmitate +CCOc3nc2cccc(C(=O)OC(C)OC(=O)OC1CCCCC1)c2n3Cc6ccc(c4ccccc4c5nn[nH]n5)cc6 CandesartanCilexetil +CN(C)CCC=c2c1ccccc1sc3ccc(Cl)cc23 Chlorprothixene +O=c3c(O)c(C2CCC(c1ccc(Cl)cc1)CC2)c(=O)c4ccccc34 Atovaquone +CN(C)CCCN3c1ccccc1CCc2ccc(Cl)cc23 Clomipramine +CN4CCCC(CC3c1ccccc1Sc2ccccc23)C4 Methixene +CCN(CC)C(C)Cn3c1ccccc1sc2ccccc23 Ethopropazine +N=C(CCSCc1csc(N=C(N)N)n1)NS(N)(=O)=O Famotidine +CNC(=NCCSCc1nc[nH]c1C)NC#N Cimetidine +CCCCCNC(=N)NN=Cc1c[nH]c2ccc(CO)cc12 Tegaserod +C=CC3=C(C(=O)O)N2C(=O)C(NC(=O)C(=NO)c1csc(N)n1)C2SC3 Cefdinir +CC5(C)SC4C(NC(=O)C(C(=O)Oc2ccc1CCCc1c2)c3ccccc3)C(=O)N4C5C(=O)O CarbenicillinIndanyl diff -r 000000000000 -r bb92d30b4f52 qed/tool-data/qed_test_max.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qed/tool-data/qed_test_max.tab Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,26 @@ +MW ALOGP HBA HBD PSA ROTB AROM ALERTS QED NAME +286.34 1.092 6 3 101.88 4 2 1 0.715 Abacavir +181.21 0.481 4 2 83.47 5 0 2 0.446 Acamprosate +336.43 2.365 5 3 87.66 11 1 1 0.520 Acebutolol +151.16 1.351 2 2 49.33 2 1 1 0.615 Acetaminophen +222.25 0.225 5 2 115.04 3 1 1 0.722 Acetazolamide +324.40 3.291 4 2 92.34 6 1 1 0.753 Acetohexamide +411.57 3.492 6 1 47.02 7 2 1 0.674 Acetophenazine +329.37 3.327 4 1 39.72 4 2 0 0.913 Paroxetine +270.21 3.146 3 1 55.13 4 2 0 0.908 Leflunomide +312.42 2.318 3 1 50.16 3 2 0 0.935 Granisetron +314.50 3.789 2 1 19.03 4 2 0 0.905 Pergolide +276.38 1.481 3 1 45.33 3 1 0 0.913 Molindone +561.55 6.476 6 2 118.77 23 1 5 0.038 ChloramphenicalPalmitate +663.41 6.279 8 3 108.33 24 0 3 0.057 ClindamycinPalmitate +610.67 5.837 10 1 143.34 13 5 2 0.148 CandesartanCilexetil +315.87 5.079 2 0 3.24 3 3 0 0.698 Chlorprothixene +366.84 5.505 3 1 54.37 2 2 0 0.771 Atovaquone +314.86 4.528 2 0 6.48 4 2 0 0.802 Clomipramine +309.48 5.015 2 0 3.24 2 2 0 0.765 Methixene +312.48 5.020 3 0 6.48 5 2 0 0.761 Ethopropazine +337.46 0.371 6 5 173.33 8 1 3 0.217 Famotidine +252.35 -0.036 5 3 88.89 7 1 5 0.142 Cimetidine +301.39 1.664 3 5 96.29 9 2 4 0.149 Tegaserod +395.42 -0.172 8 4 158.21 6 1 4 0.175 Cefdinir +494.57 2.496 7 2 113.01 8 2 4 0.185 CarbenicillinIndanyl diff -r 000000000000 -r bb92d30b4f52 qed/tool-data/qed_test_mean.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qed/tool-data/qed_test_mean.tab Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,26 @@ +MW ALOGP HBA HBD PSA ROTB AROM ALERTS QED NAME +286.34 1.092 6 3 101.88 4 2 1 0.737 Abacavir +181.21 0.481 4 2 83.47 5 0 2 0.487 Acamprosate +336.43 2.365 5 3 87.66 11 1 1 0.540 Acebutolol +151.16 1.351 2 2 49.33 2 1 1 0.633 Acetaminophen +222.25 0.225 5 2 115.04 3 1 1 0.727 Acetazolamide +324.40 3.291 4 2 92.34 6 1 1 0.772 Acetohexamide +411.57 3.492 6 1 47.02 7 2 1 0.688 Acetophenazine +329.37 3.327 4 1 39.72 4 2 0 0.917 Paroxetine +270.21 3.146 3 1 55.13 4 2 0 0.915 Leflunomide +312.42 2.318 3 1 50.16 3 2 0 0.947 Granisetron +314.50 3.789 2 1 19.03 4 2 0 0.898 Pergolide +276.38 1.481 3 1 45.33 3 1 0 0.918 Molindone +561.55 6.476 6 2 118.77 23 1 5 0.052 ChloramphenicalPalmitate +663.41 6.279 8 3 108.33 24 0 3 0.063 ClindamycinPalmitate +610.67 5.837 10 1 143.34 13 5 2 0.126 CandesartanCilexetil +315.87 5.079 2 0 3.24 3 3 0 0.636 Chlorprothixene +366.84 5.505 3 1 54.37 2 2 0 0.741 Atovaquone +314.86 4.528 2 0 6.48 4 2 0 0.782 Clomipramine +309.48 5.015 2 0 3.24 2 2 0 0.735 Methixene +312.48 5.020 3 0 6.48 5 2 0 0.734 Ethopropazine +337.46 0.371 6 5 173.33 8 1 3 0.266 Famotidine +252.35 -0.036 5 3 88.89 7 1 5 0.214 Cimetidine +301.39 1.664 3 5 96.29 9 2 4 0.213 Tegaserod +395.42 -0.172 8 4 158.21 6 1 4 0.231 Cefdinir +494.57 2.496 7 2 113.01 8 2 4 0.251 CarbenicillinIndanyl diff -r 000000000000 -r bb92d30b4f52 qed/tool-data/qed_test_unweighted.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qed/tool-data/qed_test_unweighted.tab Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,26 @@ +MW ALOGP HBA HBD PSA ROTB AROM ALERTS QED NAME +286.34 1.092 6 3 101.88 4 2 1 0.713 Abacavir +181.21 0.481 4 2 83.47 5 0 2 0.589 Acamprosate +336.43 2.365 5 3 87.66 11 1 1 0.599 Acebutolol +151.16 1.351 2 2 49.33 2 1 1 0.716 Acetaminophen +222.25 0.225 5 2 115.04 3 1 1 0.708 Acetazolamide +324.40 3.291 4 2 92.34 6 1 1 0.796 Acetohexamide +411.57 3.492 6 1 47.02 7 2 1 0.711 Acetophenazine +329.37 3.327 4 1 39.72 4 2 0 0.919 Paroxetine +270.21 3.146 3 1 55.13 4 2 0 0.937 Leflunomide +312.42 2.318 3 1 50.16 3 2 0 0.965 Granisetron +314.50 3.789 2 1 19.03 4 2 0 0.857 Pergolide +276.38 1.481 3 1 45.33 3 1 0 0.936 Molindone +561.55 6.476 6 2 118.77 23 1 5 0.111 ChloramphenicalPalmitate +663.41 6.279 8 3 108.33 24 0 3 0.101 ClindamycinPalmitate +610.67 5.837 10 1 143.34 13 5 2 0.116 CandesartanCilexetil +315.87 5.079 2 0 3.24 3 3 0 0.559 Chlorprothixene +366.84 5.505 3 1 54.37 2 2 0 0.759 Atovaquone +314.86 4.528 2 0 6.48 4 2 0 0.707 Clomipramine +309.48 5.015 2 0 3.24 2 2 0 0.651 Methixene +312.48 5.020 3 0 6.48 5 2 0 0.669 Ethopropazine +337.46 0.371 6 5 173.33 8 1 3 0.299 Famotidine +252.35 -0.036 5 3 88.89 7 1 5 0.375 Cimetidine +301.39 1.664 3 5 96.29 9 2 4 0.360 Tegaserod +395.42 -0.172 8 4 158.21 6 1 4 0.267 Cefdinir +494.57 2.496 7 2 113.01 8 2 4 0.357 CarbenicillinIndanyl diff -r 000000000000 -r bb92d30b4f52 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,4 @@ + + + + diff -r 000000000000 -r bb92d30b4f52 shape-it/shape-it.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shape-it/shape-it.xml Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,236 @@ + + against a database of molecules (Shape-it) + + silicos_it + openbabel + + + shape-it + --format ${database.ext} + --dbase $database + --reference $reference + --addIterations $addIterations + #if int($best) > 0: + --best $best + #end if + --cutoff $cutoff + #if $scores == 'yes': + --scores $output_scores + #end if + --rankBy $rankBy + $noref + --out $output 2>&1 + + + + + + + + + + + + + + + + + + + + + scores == "yes" + + + + + + + + + + + + + + + +.. class:: infomark + +**What this tool does** + +Shape-it_ is a tool that aligns a reference molecule against a set of database +molecules using the shape of the molecules as the align criterion. +It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as it was introduced by Grant and Pickup. + +The program expects one reference molecule with +its three-dimensional coordinates and one database files containing one +or more molecules in three dimensions. The results are either the alignment +of all database molecules and their respective scores or the N best +scoring molecules of the complete database. + +.. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016 +.. _Shape-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html + +----- + +.. class:: infomark + +**Input** + + +| - `formates recognized by OpenBabel`_ + +.. _formates recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats + +* Example:: + + - database + 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 + 5 7 1 0 0 0 0 + ..... + + - reference + + 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 + 1 14 1 0 0 0 0 + 2 15 1 0 0 0 0 + 3 16 1 0 0 0 0 + 3 30 1 0 0 0 0 + 4 16 2 0 0 0 0 + 5 7 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 22 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + ...... + + - cutoff : 0.0 + +----- + +.. class:: infomark + +**Output** + +* Example:: + + 27 28 0 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 + 5 7 1 0 0 0 0 + 5 18 1 0 0 0 0 + 5 19 1 0 0 0 0 + 6 8 2 0 0 0 0 + ...... + +----- + +.. class:: infomark + +**Cite** + +`Silicos-it`_ - shape-it + +.. _Silicos-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html + + + + diff -r 000000000000 -r bb92d30b4f52 shape-it/test_data/CID_3033.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shape-it/test_data/CID_3033.sdf Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,271 @@ +3033 + -OEChem-08231107463D + + 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 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1 17240202131864233360 +6992083 37 18058168521433072460 +7615 1 18201433675414973908 +77492 1 18272651289913926852 +81228 2 17968373550240022809 +9709674 26 17896035610527288590 + +> +378.03 +7.01 +2.75 +1.77 +0.78 +1.58 +0.3 +0.41 +1.94 +-1.08 +1.9 +-8.69 +11.04 +2.58 + +> +790.335 + +> +214.7 + +> +2 +5 +255 + +$$$$ + diff -r 000000000000 -r bb92d30b4f52 shape-it/test_data/CID_3037.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shape-it/test_data/CID_3037.sdf Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,220 @@ +3037 + -OEChem-08231108593D + + 27 28 0 0 0 0 0 0 0999 V2000 + -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2565 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51 18340768233908588503 +15207287 21 15719111361650760302 +15375358 24 15647053767618106914 +15775835 57 18272650117329930317 +16945 1 17906452130063974618 +17834072 14 15936410035134206066 +18186145 218 17132117918276567720 +19422 9 18271525295227750719 +20279233 1 15719389529571237654 +20645476 183 18339080393619327415 +23402539 116 18186809105365620101 +23402655 69 18342736308283284156 +23559900 14 17603590712323212176 +25 1 17561083592297532664 +26918003 58 6266902359448424189 +296302 2 15213020427345972082 +3082319 5 18338798905472319583 +34934 24 18341891845236497020 +633830 44 17703790310130762689 +74978 22 18266740181857992718 +7832392 63 18340206284835898173 +81228 2 15720767252053392762 +9981440 41 17403743242177431832 + +> +341.85 +8.38 +1.9 +1.1 +0.02 +0 +-1.15 +1.94 +-0.01 +0 +-0.39 +-4.15 +0.01 +0 + +> +722.787 + +> +193 + +> +2 +5 +255 + +> +0.606434 + +> +0.721775 + +> +0.791445 + +$$$$ diff -r 000000000000 -r bb92d30b4f52 strip-it/strip-it.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/strip-it/strip-it.xml Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,90 @@ + + extracts predefined scaffolds from molecules + + + openbabel + silicos_it + + + strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog --noHeader 2>&1 + + + + + + + + + + + + + + + + +.. class:: infomark + +**What this tool does** + +Strip-it is a program that extracts predefined scaffolds from organic small +molecules. + +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 + - `molecular frameworks and the reduced molecular frameworks`_ as + described by Ansgar Schuffenhauer and coworkers + - `scaffold topologies`_ as described by Sara Pollock and coworkers + +.. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122 +.. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf +.. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680 + +----- + +.. class:: infomark + + +**Input** + +| - `SD-Format`_ +| - `SMILES Format`_ +| - `MOL2 Format`_ + +.. _SD-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 + + +----- + +.. class:: infomark + +**Output** + ++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+ +| NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... | ++=============+================================+======================+========================+======================+=====+ +| Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1 | c1ccc(cc1)Nc1ccccc1 | C1CCC(CC1)CC1CCCCC1 | ... | ++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+ +| Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... | ++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+ +| ... | ... | ... | ... | ... | ... | ++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+ + +----- + +.. class:: infomark + +**Cite** + +`Silicos-it`_ - strip-it + +.. _Silicos-it: http://silicos-it.com/software/strip-it/1.0.2/strip-it.html + + + + diff -r 000000000000 -r bb92d30b4f52 strip-it/test-data/CID_3037.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/strip-it/test-data/CID_3037.sdf Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,220 @@ +3037 + -OEChem-08231108593D + + 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 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tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,61 @@ + + + + + + + + + + + + + + + https://github.com/bgruening/silicos-it_store/raw/master/strip-it/strip-it-1.0.2.tar.gz + + + + + + + + + + + cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/strip-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && + make && + make install + + $INSTALL_DIR/strip-it/bin + + + + wget https://github.com/bgruening/silicos-it_store/raw/master/align-it/align-it-1.0.3.tar.gz + tar xfvz align-it-1.0.3.tar.gz && + cd align-it-1.0.3 && + cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/align-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && + make && + make install + + $INSTALL_DIR/align-it/bin + + + + wget https://github.com/bgruening/silicos-it_store/raw/master/shape-it/shape-it-1.0.1.tar.gz + tar xfvz shape-it-1.0.1.tar.gz && + cd shape-it-1.0.1 && + cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/shape-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && + make && + make install + + $INSTALL_DIR/shape-it/bin + + + + + Compiling silicos-it requires g++ and CMake 2.4+. + +