| Next changeset 1:fdc038522974 (2013-08-24) |
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align-it/align-it.xml align-it/align-it_create_db.xml align-it/test_data/6mol.sdf align-it/test_data/CID_2244.sdf align-it/test_data/aliginit_scores.tabular.tabular align-it/test_data/align-it_Search_on_CID2244.phar align-it/test_data/align-it_Search_on_CID2244.sdf align-it/test_data/alignit_Create_Phar_DB_6mol.phar align-it/test_data/alignit_on_CID2244.phar align-it/test_data/reference.phar qed/errors.py qed/qed.py qed/silicos_qed.xml qed/tool-data/qed_test.smi qed/tool-data/qed_test_max.tab qed/tool-data/qed_test_mean.tab qed/tool-data/qed_test_unweighted.tab repository_dependencies.xml shape-it/shape-it.xml shape-it/test_data/CID_3033.sdf shape-it/test_data/CID_3037.sdf shape-it/test_data/shapeit_on_CID30333_and_CID3037.sdf strip-it/strip-it.xml strip-it/test-data/CID_3037.sdf strip-it/test-data/Strip-it_on_CID3037.tabular tool_dependencies.xml |
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| 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 |
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| b'@@ -0,0 +1,238 @@\n+<tool id="ctb_alignit" name="Pharmacophore Alignment" version="0.1">\r\n+ <description>and Optimization (Align-it)</description>\r\n+ <requirements>\r\n+ <requirement type="package" version="1.0.1">silicos_it</requirement>\r\n+ <requirement type="package" version="2.3.2">openbabel</requirement>\r\n+ </requirements>\r\n+ <command>\r\n+ align-it \r\n+ #if str($database.ext).strip() == \'phar\':\r\n+ --dbType PHAR\r\n+ #else:\r\n+ --dbType ${database.ext}\r\n+ #end if\r\n+ --dbase $database\r\n+\r\n+ --reference $reference\r\n+ #if str($reference.ext).strip() == \'phar\':\r\n+ --refType PHAR\r\n+ #else:\r\n+ --refType ${reference.ext}\r\n+ #end if\r\n+ #######################################\r\n+ #### output options\r\n+ #######################################\r\n+ --pharmacophore $aligned_pharmacophores\r\n+ \r\n+ \r\n+ ##--out $aligned_structures\r\n+ ##--outType $oformat\r\n+ \r\n+ #if float( str($cutoff) ) > 0:\r\n+ --cutOff $cutoff\r\n+ #end if\r\n+ #if int( str($best) ) > 0:\r\n+ --best $best\r\n+ #end if\r\n+ --rankBy $rankBy\r\n+ --scores $score_result_file\r\n+\r\n+ #######################################\r\n+ #### Options\r\n+ #######################################\r\n+\r\n+ #set $fgroups_combined = str( $fgroups ).strip()\r\n+ --funcGroup $fgroups_combined\r\n+\r\n+ --epsilon $epsilon \r\n+ $merge \r\n+ $noNormal\r\n+ $noHybrid \r\n+ $scoreOnly\r\n+ $withExclusion \r\n+\r\n+ 2>&1\r\n+ </command>\r\n+ <inputs>\r\n+ <param name="database" type="data" format=\'mol,mol2,sdf,smi,phar\' label="Defines the database of molecules that will be used to screen"/>\r\n+ <param name="reference" type="data" format=\'mol,mol2,sdf,smi,phar\' label="Reference Molecule"/>\r\n+\r\n+ <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment">\r\n+ <option value=\'AROM\' selected="true">aromatic rings</option>\r\n+ <option value=\'HDON\' selected="true">hydrogen bond donors</option>\r\n+ <option value=\'HACC\' selected="true">hydrogen bond acceptors</option>\r\n+ <option value=\'LIPO\' selected="true">lipophilic spots</option>\r\n+ <option value=\'CHARGE\' selected="true">charge centers</option>\r\n+ </param>\r\n+\r\n+\r\n+ <param name="epsilon" type="float" value="0.5" label=\'Change the tolerance for points to be matched in the alignment phase\' help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned.">\r\n+ <validator type="in_range" min="0" max="1" />\r\n+ </param>\r\n+ <param name=\'merge\' type=\'boolean\' truevalue=\'--merge\' falsevalue=\'\' label=\'Merge pharmacophore points\' />\r\n+ <param name=\'noNormal\' type=\'boolean\' truevalue=\'--noNormal\' falsevalue=\'\' label=\'No normal information is included during the alignment\' help="Using this flag makes the pharmacophore models less specific but also less conformation-dependent."/>\r\n+ <param name=\'noHybrid\' type=\'boolean\' truevalue=\'--noHybrid\' falsevalue=\'\' label=\'Disable the use of hybrid pharmacophore points\' help="Using this flag will increase the number of pharmacophore points."/>\r\n+ <param name=\'withExclusion\' type=\'boolean\' truevalue=\'--withExclusion\' falsevalue=\'\' label=\'Add exclusion spheres into the optimization process instead of processing them afterwards\' help="When this flag is set, the exclusion spheres have also an impact on the optimization procedure." />\r\n+ <param name=\'scoreOnly\' type=\'boolean\' true'..b' 0 0 0 0 0 0\r\n+ 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+ -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0\r\n+\r\n+ - cutoff : 0.0\r\n+\r\n+-----\r\n+\r\n+.. class:: infomark\r\n+\r\n+**Output**\r\n+\r\n+The format of the output file is shown in the table below:\r\n+\r\n++--------+-----------------------------------------------------------------------+\r\n+| Column | Content |\r\n++========+=======================================================================+\r\n+| 1 | Id of the reference structure |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 2 | Maximum volume of the reference structure |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 3 | Id of the database structure |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 4 | Maximum volume of the database structure |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 5 | Maximum volume overlap of the two structures |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 6 | Overlap between pharmacophore and exclusion spheres in the reference |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 7 | Corrected volume overlap between database pharmacophore and reference |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 8 | Number of pharmacophore points in the processed pharmacophore |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 9 | TANIMOTO score |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 10 | TVERSKY_REF score |\r\n++--------+-----------------------------------------------------------------------+\r\n+| 11 | TVERSKY_DB score |\r\n++--------+-----------------------------------------------------------------------+\r\n+\r\n+\r\n+* Example::\r\n+ \r\n+ - aligned Pharmacophores \r\n+\r\n+ 3033\r\n+ HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0\r\n+ HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0\r\n+ HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827\r\n+ HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616\r\n+ HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767\r\n+ $$$$ \r\n+\r\n+-----\r\n+\r\n+.. class:: infomark\r\n+\r\n+**Cite**\r\n+\r\n+`Silicos-it`_ - align-it\r\n+\r\n+.. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html\r\n+\r\n+\r\n+ </help>\r\n+</tool>\r\n' |
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| 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 |
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| @@ -0,0 +1,123 @@ +<tool id="ctb_alignit_create_db" name="Pharmacophore" version="0.1"> + <description>generation (Align-it)</description> + <requirements> + <requirement type="package" version="1.0.0">silicos_it</requirement> + <requirement type="package" version="2.3.2">openbabel</requirement> + </requirements> + <command> + align-it + --dbType ${database.ext} + --dbase $database + --pharmacophore $pharmacophores + $merge + $noHybrid + + 2>&1 + </command> + <inputs> + <param name="database" type="data" format='mol,mol2,sdf,smi' label="Defines the database of molecules that will be converted to pharmacophores" /> + <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' /> + <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/> + </inputs> + <outputs> + <data name="pharmacophores" format="phar" label="${tool.name} on ${on_string} (scores)"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> + +.. 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 + + </help> +</tool> |
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| 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 |
| [ |
| b'@@ -0,0 +1,1502 @@\n+3639\n+ -OEChem-06261205352D\n+\n+ 25 26 0 0 0 0 0 0 0999 V2000\n+ 3.4030 1.2327 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8950 -0.8020 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.4030 -0.7673 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.3849 -1.6737 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3850 -1.6622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.9030 -1.6333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.9030 0.0987 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.8010 -0.2881 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8950 1.2674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5369 -1.2673 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0010 -0.2673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0010 0.7327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.8010 0.7535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1350 -0.7673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.2690 -0.2673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1350 1.2327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.2690 0.7327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4119 0.6474 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.0101 1.3372 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1350 -1.3873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.3368 -0.6002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8878 1.8873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1350 1.8527 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.0000 -0.9573 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5369 -1.8873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 17 1 0 0 0 0\n+ 2 4 2 0 0 0 0\n+ 2 5 2 0 0 0 0\n+ 2 8 1 0 0 0 0\n+ 2 11 1 0 0 0 0\n+ 3 6 2 0 0 0 0\n+ 3 7 2 0 0 0 0\n+ 3 10 1 0 0 0 0\n+ 3 15 1 0 0 0 0\n+ 8 13 1 0 0 0 0\n+ 8 21 1 0 0 0 0\n+ 9 12 1 0 0 0 0\n+ 9 13 1 0 0 0 0\n+ 9 22 1 0 0 0 0\n+ 10 24 1 0 0 0 0\n+ 10 25 1 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 11 14 2 0 0 0 0\n+ 12 16 2 0 0 0 0\n+ 13 18 1 0 0 0 0\n+ 13 19 1 0 0 0 0\n+ 14 15 1 0 0 0 0\n+ 14 20 1 0 0 0 0\n+ 15 17 2 0 0 0 0\n+ 16 17 1 0 0 0 0\n+ 16 23 1 0 0 0 0\n+M END\n+> <PUBCHEM_COMPOUND_CID>\n+3639\n+\n+> <PUBCHEM_COMPOUND_CANONICALIZED>\n+1\n+\n+> <PUBCHEM_CACTVS_COMPLEXITY>\n+494\n+\n+> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>\n+7\n+\n+> <PUBCHEM_CACTVS_HBOND_DONOR>\n+3\n+\n+> <PUBCHEM_CACTVS_ROTATABLE_BOND>\n+1\n+\n+> <PUBCHEM_CACTVS_SUBSKEYS>\n+AAADccBjOABkAAAAAAAAAAAAAAAAAAAAAAA8QAAAAAAAAACxAAAAHAYQQAAACAqBUCQxwYLAAAKAACRCQHDCABAhBwAAiJwIZoiIICLBkpGEIAhgkAJIyCcQAAAAAAYAAEIAAYAADAAAhAADAAAAAAAAAA==\n+\n+> <PUBCHEM_IUPAC_OPENEYE_NAME>\n+6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_CAS_NAME>\n+6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_NAME>\n+6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>\n+6-chloranyl-1,1-bis(oxidanylidene)-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_TRADITIONAL_NAME>\n+6-chloro-1,1-diketo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_INCHI>\n+InChI=1S/C7H8ClN3O4S2/c8-4-1-5-7(2-6(4)16(9,12)13)17(14,15)11-3-10-5/h1-2,10-11H,3H2,(H2,9,12,13)\n+\n+> <PUBCHEM_IUPAC_INCHIKEY>\n+JZUFKLXOESDKRF-UHFFFAOYSA-N\n+\n+> <PUBCHEM_XLOGP3>\n+-0.1\n+\n+> <PUBCHEM_EXACT_MASS>\n+296.964475\n+\n+> <PUBCHEM_MOLECULAR_FORMULA>\n+C7H8ClN3O4S2\n+\n+> <PUBCHEM_MOLECULAR_WEIGHT>\n+297.73912\n+\n+> <PUBCHEM_OPENEYE_CAN_SMILES>\n+C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl\n+\n+> <PUBCHEM_OPENEYE_ISO_SMILES>\n+C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl\n+\n+> <PUBCHEM_CACTVS_TPSA>\n+135\n+\n+> <PUBC'..b' 0 0 0 0 0 0 0 0 0 0 0\n+ 10.4888 0.6655 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.4888 -1.0436 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.5424 3.6716 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7367 3.6392 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.1302 4.4653 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 5 1 0 0 0 0\n+ 1 6 1 0 0 0 0\n+ 1 10 1 0 0 0 0\n+ 2 5 1 0 0 0 0\n+ 2 8 2 0 0 0 0\n+ 3 12 1 0 0 0 0\n+ 3 16 1 0 0 0 0\n+ 3 20 1 0 0 0 0\n+ 4 14 2 0 0 0 0\n+ 4 19 1 0 0 0 0\n+ 5 7 1 0 0 0 0\n+ 5 9 1 0 0 0 0\n+ 6 8 1 0 0 0 0\n+ 6 11 2 0 0 0 0\n+ 7 15 1 0 0 0 0\n+ 7 33 1 0 0 0 0\n+ 7 34 1 0 0 0 0\n+ 8 13 1 0 0 0 0\n+ 9 35 1 0 0 0 0\n+ 9 36 1 0 0 0 0\n+ 9 37 1 0 0 0 0\n+ 10 17 2 0 0 0 0\n+ 10 18 1 0 0 0 0\n+ 11 14 1 0 0 0 0\n+ 11 38 1 0 0 0 0\n+ 12 13 2 0 0 0 0\n+ 12 14 1 0 0 0 0\n+ 13 39 1 0 0 0 0\n+ 15 40 1 0 0 0 0\n+ 15 41 1 0 0 0 0\n+ 15 42 1 0 0 0 0\n+ 16 19 1 0 0 0 0\n+ 16 23 2 0 0 0 0\n+ 17 21 1 0 0 0 0\n+ 17 43 1 0 0 0 0\n+ 18 22 2 0 0 0 0\n+ 18 44 1 0 0 0 0\n+ 19 24 2 0 0 0 0\n+ 20 26 2 0 0 0 0\n+ 20 27 1 0 0 0 0\n+ 21 25 2 0 0 0 0\n+ 21 46 1 0 0 0 0\n+ 22 25 1 0 0 0 0\n+ 22 47 1 0 0 0 0\n+ 23 28 1 0 0 0 0\n+ 23 45 1 0 0 0 0\n+ 24 29 1 0 0 0 0\n+ 24 48 1 0 0 0 0\n+ 25 49 1 0 0 0 0\n+ 26 30 1 0 0 0 0\n+ 26 50 1 0 0 0 0\n+ 27 31 2 0 0 0 0\n+ 27 51 1 0 0 0 0\n+ 28 29 2 0 0 0 0\n+ 28 52 1 0 0 0 0\n+ 29 53 1 0 0 0 0\n+ 30 32 2 0 0 0 0\n+ 30 54 1 0 0 0 0\n+ 31 32 1 0 0 0 0\n+ 31 55 1 0 0 0 0\n+ 32 56 1 0 0 0 0\n+M END\n+> <PUBCHEM_COMPOUND_CID>\n+473726\n+\n+> <PUBCHEM_COMPOUND_CANONICALIZED>\n+1\n+\n+> <PUBCHEM_CACTVS_COMPLEXITY>\n+855\n+\n+> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>\n+4\n+\n+> <PUBCHEM_CACTVS_HBOND_DONOR>\n+0\n+\n+> <PUBCHEM_CACTVS_ROTATABLE_BOND>\n+3\n+\n+> <PUBCHEM_CACTVS_SUBSKEYS>\n+AAADceB7gAAAAAAAAAAAAAAAAAAAAQAAAAAwYMECAAAAAECBUAAAHAAAAAAACAiBEAAzwIMAAACgASRiRACCAAAhAgAIiAAQdJiIYGLAkZGUIAhggALIyCcQAAAAAAAAAAAAACAAAAAAAAAAQAAAAAAAAA==\n+\n+> <PUBCHEM_IUPAC_OPENEYE_NAME>\n+2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_CAS_NAME>\n+2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_NAME>\n+2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>\n+2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_TRADITIONAL_NAME>\n+2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_INCHI>\n+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\n+\n+> <PUBCHEM_IUPAC_INCHIKEY>\n+YQCDIJPZZOKCLA-UHFFFAOYSA-N\n+\n+> <PUBCHEM_XLOGP3_AA>\n+6\n+\n+> <PUBCHEM_EXACT_MASS>\n+416.200097\n+\n+> <PUBCHEM_MOLECULAR_FORMULA>\n+C28H24N4\n+\n+> <PUBCHEM_MOLECULAR_WEIGHT>\n+416.51696\n+\n+> <PUBCHEM_OPENEYE_CAN_SMILES>\n+CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C\n+\n+> <PUBCHEM_OPENEYE_ISO_SMILES>\n+CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C\n+\n+> <PUBCHEM_CACTVS_TPSA>\n+31.2\n+\n+> <PUBCHEM_MONOISOTOPIC_WEIGHT>\n+416.200097\n+\n+> <PUBCHEM_TOTAL_CHARGE>\n+0\n+\n+> <PUBCHEM_HEAVY_ATOM_COUNT>\n+32\n+\n+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n+1\n+\n+> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n+0\n+\n+> <PUBCHEM_COMPONENT_COUNT>\n+1\n+\n+> <PUBCHEM_CACTVS_TAUTO_COUNT>\n+1\n+\n+> <PUBCHEM_COORDINATE_TYPE>\n+1\n+5\n+255\n+\n+> <PUBCHEM_BONDANNOTATIONS>\n+10 17 8\n+10 18 8\n+11 14 8\n+12 13 8\n+12 14 8\n+16 19 8\n+16 23 8\n+17 21 8\n+18 22 8\n+19 24 8\n+20 26 8\n+20 27 8\n+21 25 8\n+22 25 8\n+23 28 8\n+24 29 8\n+26 30 8\n+27 31 8\n+28 29 8\n+30 32 8\n+31 32 8\n+5 9 3\n+6 11 8\n+6 8 8\n+8 13 8\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/CID_2244.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/CID_2244.sdf Thu Aug 15 03:34:00 2013 -0400 |
| b |
| @@ -0,0 +1,155 @@ +2244 + -OEChem-05151212332D + + 21 21 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +$$$$ + |
| b |
| diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/align-it_Search_on_CID2244.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/align-it_Search_on_CID2244.phar Thu Aug 15 03:34:00 2013 -0400 |
| b |
| @@ -0,0 +1,44 @@ +NAME +HYBL 5.135 0.2327 0 0.7 0 -2.66454e-15 -2.77556e-17 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +NAME +HYBL 5.07563 0.248657 0 0.7 0 4.00384 3.9265 0 +HDON 6.81996 1.22708 0 1 1 7.67971 0.716361 0 +HDON 2.45909 -1.2189 0 1 1 1.58692 -1.7081 0 +HYBH 6.78268 -1.77271 0 1 1 6.77024 -2.77263 0 +HACC 3.82046 -1.60188 0 1 1 4.30966 -2.47405 0 +HACC 2.84207 0.142469 0 1 1 2.35288 1.01464 0 +$$$$ +NAME +HYBL 5.03878 0.168252 0 0.7 0 8.92097 14.6352 0 +HACC 6.15373 -1.49215 0 1 1 5.71359 -2.39008 0 +HACC 4.15822 -1.6275 0 1 1 3.16052 -1.69523 0 +HACC 3.04334 0.0328893 0 1 1 2.60305 -0.864963 0 +$$$$ +NAME +HYBL 5.13502 0.232688 0 0.7 0 -3.05555 -1.88732 0 +HDON 7.80105 -0.28811 0 1 1 8.66519 -0.79137 0 +HDON 6.89495 1.26739 0 1 1 6.88332 2.26732 0 +HDON 2.53695 -1.26731 0 1 1 1.67093 -1.76732 0 +HACC 7.38495 -1.67371 0 1 1 7.87496 -2.54543 0 +HACC 6.38495 -1.66211 0 1 1 5.87492 -2.52227 0 +HACC 3.90295 -1.63331 0 1 1 4.40296 -2.49933 0 +HACC 2.90295 0.0986875 0 1 1 2.40294 0.964706 0 +$$$$ +NAME +HYBL 4.88436 -0.25257 0 0.7 0 -1.23357 -0.0488526 0 +HACC 6.64188 -1.29137 0 1 1 6.62805 -2.29128 0 +HACC 3.07408 0.556457 0 1 1 2.76569 1.50771 0 +$$$$ +NAME +HYBL 4.88439 -0.252571 0 0.7 0 -0.527205 -0.0505055 0 +HACC 6.64184 -1.29138 0 1 1 6.62781 -2.29129 0 +HACC 3.07406 0.556469 0 1 1 2.76567 1.50773 0 +$$$$ |
| b |
| diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/align-it_Search_on_CID2244.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/align-it_Search_on_CID2244.sdf Thu Aug 15 03:34:00 2013 -0400 |
| [ |
| b'@@ -0,0 +1,1556 @@\n+3639\n+ OpenBabel07171214472D\n+\n+ 25 26 0 0 0 0 0 0 0 0999 V2000\n+ 3.4030 1.2327 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8950 -0.8020 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.4030 -0.7673 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.3849 -1.6737 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3850 -1.6622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.9030 -1.6333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.9030 0.0987 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.8010 -0.2881 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8950 1.2674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5369 -1.2673 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0010 -0.2673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0010 0.7327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.8010 0.7535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1350 -0.7673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.2690 -0.2673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1350 1.2327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.2690 0.7327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4119 0.6474 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.0101 1.3372 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1350 -1.3873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.3368 -0.6002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8878 1.8873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1350 1.8527 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.0000 -0.9573 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5369 -1.8873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 17 1 0 0 0 0\n+ 2 4 2 0 0 0 0\n+ 2 5 2 0 0 0 0\n+ 2 8 1 0 0 0 0\n+ 2 11 1 0 0 0 0\n+ 3 6 2 0 0 0 0\n+ 3 7 2 0 0 0 0\n+ 3 10 1 0 0 0 0\n+ 3 15 1 0 0 0 0\n+ 8 13 1 0 0 0 0\n+ 8 21 1 0 0 0 0\n+ 9 12 1 0 0 0 0\n+ 9 13 1 0 0 0 0\n+ 9 22 1 0 0 0 0\n+ 10 24 1 0 0 0 0\n+ 10 25 1 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 11 14 2 0 0 0 0\n+ 12 16 2 0 0 0 0\n+ 13 18 1 0 0 0 0\n+ 13 19 1 0 0 0 0\n+ 14 15 1 0 0 0 0\n+ 14 20 1 0 0 0 0\n+ 15 17 2 0 0 0 0\n+ 16 17 1 0 0 0 0\n+ 16 23 1 0 0 0 0\n+M END\n+> <PUBCHEM_COMPOUND_CID>\n+3639\n+\n+> <PUBCHEM_COMPOUND_CANONICALIZED>\n+1\n+\n+> <PUBCHEM_CACTVS_COMPLEXITY>\n+494\n+\n+> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>\n+7\n+\n+> <PUBCHEM_CACTVS_HBOND_DONOR>\n+3\n+\n+> <PUBCHEM_CACTVS_ROTATABLE_BOND>\n+1\n+\n+> <PUBCHEM_CACTVS_SUBSKEYS>\n+AAADccBjOABkAAAAAAAAAAAAAAAAAAAAAAA8QAAAAAAAAACxAAAAHAYQQAAACAqBUCQxwYLAAAKAACRCQHDCABAhBwAAiJwIZoiIICLBkpGEIAhgkAJIyCcQAAAAAAYAAEIAAYAADAAAhAADAAAAAAAAAA==\n+\n+> <PUBCHEM_IUPAC_OPENEYE_NAME>\n+6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_CAS_NAME>\n+6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_NAME>\n+6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>\n+6-chloranyl-1,1-bis(oxidanylidene)-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_TRADITIONAL_NAME>\n+6-chloro-1,1-diketo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide\n+\n+> <PUBCHEM_IUPAC_INCHI>\n+InChI=1S/C7H8ClN3O4S2/c8-4-1-5-7(2-6(4)16(9,12)13)17(14,15)11-3-10-5/h1-2,10-11H,3H2,(H2,9,12,13)\n+\n+> <PUBCHEM_IUPAC_INCHIKEY>\n+JZUFKLXOESDKRF-UHFFFAOYSA-N\n+\n+> <PUBCHEM_XLOGP3>\n+-0.1\n+\n+> <PUBCHEM_EXACT_MASS>\n+296.964475\n+\n+> <PUBCHEM_MOLECULAR_FORMULA>\n+C7H8ClN3O4S2\n+\n+> <PUBCHEM_MOLECULAR_WEIGHT>\n+297.73912\n+\n+> <PUBCHEM_OPENEYE_CAN_SMILES>\n+C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl\n+\n+> <PUBCHEM_OPENEYE_ISO_SMILES>\n+C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl\n+\n+> <PUBCHEM_CACTVS_'..b' 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.0240 3.6006 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.2182 3.5749 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.6137 4.3977 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 5 1 0 0 0 0\n+ 1 6 1 0 0 0 0\n+ 1 10 1 0 0 0 0\n+ 2 5 1 0 0 0 0\n+ 2 8 2 0 0 0 0\n+ 3 12 1 0 0 0 0\n+ 3 16 1 0 0 0 0\n+ 3 20 1 0 0 0 0\n+ 4 14 2 0 0 0 0\n+ 4 19 1 0 0 0 0\n+ 5 7 1 0 0 0 0\n+ 5 9 1 0 0 0 0\n+ 6 8 1 0 0 0 0\n+ 6 11 2 0 0 0 0\n+ 7 15 1 0 0 0 0\n+ 7 33 1 0 0 0 0\n+ 7 34 1 0 0 0 0\n+ 8 13 1 0 0 0 0\n+ 9 35 1 0 0 0 0\n+ 9 36 1 0 0 0 0\n+ 9 37 1 0 0 0 0\n+ 10 17 2 0 0 0 0\n+ 10 18 1 0 0 0 0\n+ 11 14 1 0 0 0 0\n+ 11 38 1 0 0 0 0\n+ 12 13 2 0 0 0 0\n+ 12 14 1 0 0 0 0\n+ 13 39 1 0 0 0 0\n+ 15 40 1 0 0 0 0\n+ 15 41 1 0 0 0 0\n+ 15 42 1 0 0 0 0\n+ 16 19 1 0 0 0 0\n+ 16 23 2 0 0 0 0\n+ 17 21 1 0 0 0 0\n+ 17 43 1 0 0 0 0\n+ 18 22 2 0 0 0 0\n+ 18 44 1 0 0 0 0\n+ 19 24 2 0 0 0 0\n+ 20 26 2 0 0 0 0\n+ 20 27 1 0 0 0 0\n+ 21 25 2 0 0 0 0\n+ 21 46 1 0 0 0 0\n+ 22 25 1 0 0 0 0\n+ 22 47 1 0 0 0 0\n+ 23 28 1 0 0 0 0\n+ 23 45 1 0 0 0 0\n+ 24 29 1 0 0 0 0\n+ 24 48 1 0 0 0 0\n+ 25 49 1 0 0 0 0\n+ 26 30 1 0 0 0 0\n+ 26 50 1 0 0 0 0\n+ 27 31 2 0 0 0 0\n+ 27 51 1 0 0 0 0\n+ 28 29 2 0 0 0 0\n+ 28 52 1 0 0 0 0\n+ 29 53 1 0 0 0 0\n+ 30 32 2 0 0 0 0\n+ 30 54 1 0 0 0 0\n+ 31 32 1 0 0 0 0\n+ 31 55 1 0 0 0 0\n+ 32 56 1 0 0 0 0\n+M END\n+> <PUBCHEM_COMPOUND_CID>\n+473726\n+\n+> <PUBCHEM_COMPOUND_CANONICALIZED>\n+1\n+\n+> <PUBCHEM_CACTVS_COMPLEXITY>\n+855\n+\n+> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>\n+4\n+\n+> <PUBCHEM_CACTVS_HBOND_DONOR>\n+0\n+\n+> <PUBCHEM_CACTVS_ROTATABLE_BOND>\n+3\n+\n+> <PUBCHEM_CACTVS_SUBSKEYS>\n+AAADceB7gAAAAAAAAAAAAAAAAAAAAQAAAAAwYMECAAAAAECBUAAAHAAAAAAACAiBEAAzwIMAAACgASRiRACCAAAhAgAIiAAQdJiIYGLAkZGUIAhggALIyCcQAAAAAAAAAAAAACAAAAAAAAAAQAAAAAAAAA==\n+\n+> <PUBCHEM_IUPAC_OPENEYE_NAME>\n+2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_CAS_NAME>\n+2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_NAME>\n+2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>\n+2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_TRADITIONAL_NAME>\n+2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine\n+\n+> <PUBCHEM_IUPAC_INCHI>\n+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\n+\n+> <PUBCHEM_IUPAC_INCHIKEY>\n+YQCDIJPZZOKCLA-UHFFFAOYSA-N\n+\n+> <PUBCHEM_XLOGP3_AA>\n+6\n+\n+> <PUBCHEM_EXACT_MASS>\n+416.200097\n+\n+> <PUBCHEM_MOLECULAR_FORMULA>\n+C28H24N4\n+\n+> <PUBCHEM_MOLECULAR_WEIGHT>\n+416.51696\n+\n+> <PUBCHEM_OPENEYE_CAN_SMILES>\n+CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C\n+\n+> <PUBCHEM_OPENEYE_ISO_SMILES>\n+CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C\n+\n+> <PUBCHEM_CACTVS_TPSA>\n+31.2\n+\n+> <PUBCHEM_MONOISOTOPIC_WEIGHT>\n+416.200097\n+\n+> <PUBCHEM_TOTAL_CHARGE>\n+0\n+\n+> <PUBCHEM_HEAVY_ATOM_COUNT>\n+32\n+\n+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n+1\n+\n+> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n+0\n+\n+> <PUBCHEM_COMPONENT_COUNT>\n+1\n+\n+> <PUBCHEM_CACTVS_TAUTO_COUNT>\n+1\n+\n+> <PUBCHEM_COORDINATE_TYPE>\n+1\n+5\n+255\n+\n+> <PUBCHEM_BONDANNOTATIONS>\n+10 17 8\n+10 18 8\n+11 14 8\n+12 13 8\n+12 14 8\n+16 19 8\n+16 23 8\n+17 21 8\n+18 22 8\n+19 24 8\n+20 26 8\n+20 27 8\n+21 25 8\n+22 25 8\n+23 28 8\n+24 29 8\n+26 30 8\n+27 31 8\n+28 29 8\n+30 32 8\n+31 32 8\n+5 9 3\n+6 11 8\n+6 8 8\n+8 13 8\n+\n+> <PHARAO_TANIMOTO>\n+0.188319\n+\n+> <PHARAO_TVERSKY_REF>\n+0.38133\n+\n+> <PHARAO_TVERSKY_DB>\n+0.27117\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/alignit_Create_Phar_DB_6mol.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/alignit_Create_Phar_DB_6mol.phar Thu Aug 15 03:34:00 2013 -0400 |
| b |
| @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$ |
| b |
| diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/alignit_on_CID2244.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/alignit_on_CID2244.phar Thu Aug 15 03:34:00 2013 -0400 |
| b |
| @@ -0,0 +1,7 @@ +2244 +HYBL 5.63852 -1.334 0 0.7 0 0 0 0 +HYBH 6.3301 1.44 0 1 1 7.19612 1.94001 0 +HACC 3.732 -0.06 0 1 1 3.7319 0.94 0 +HACC 4.5981 1.44 0 1 1 3.73208 1.94001 0 +HACC 2.866 -1.56 0 1 1 2.866 -2.56 0 +$$$$ |
| b |
| diff -r 000000000000 -r bb92d30b4f52 align-it/test_data/reference.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/test_data/reference.phar Thu Aug 15 03:34:00 2013 -0400 |
| b |
| @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$ |
| b |
| diff -r 000000000000 -r bb92d30b4f52 qed/errors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qed/errors.py Thu Aug 15 03:34:00 2013 -0400 |
| [ |
| @@ -0,0 +1,17 @@ +__all__ = ['SilicosItError', 'WrongArgument'] + +class SilicosItError(Exception): + """Base class for exceptions in Silicos-it code""" + pass + +class WrongArgument(SilicosItError): + """ + Exception raised when argument to function is not of correct type. + + Attributes: + function -- function in which error occurred + msg -- explanation of the error + """ + def __init__(self, function, msg): + self.function = function + self.msg = msg |
| b |
| diff -r 000000000000 -r bb92d30b4f52 qed/qed.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qed/qed.py Thu Aug 15 03:34:00 2013 -0400 |
| [ |
| b"@@ -0,0 +1,414 @@\n+#!/usr/bin/env python\n+__all__ = ['weights_max', 'weights_mean', 'weights_none', 'default']\n+\n+# Silicos-it\n+from errors import WrongArgument\n+\n+# RDKit\n+from rdkit.Chem import Descriptors\n+from rdkit import Chem\n+\n+# General\n+from copy import deepcopy\n+from math import exp, log\n+import sys, os, re\n+import argparse\n+\n+def check_filetype(filepath):\n+ mol = False\n+ possible_inchi = True\n+ for line_counter, line in enumerate(open(filepath)):\n+ if line_counter > 10000:\n+ break\n+ if line.find('$$$$') != -1:\n+ return 'sdf'\n+ elif line.find('@<TRIPOS>MOLECULE') != -1:\n+ return 'mol2'\n+ elif line.find('ligand id') != -1:\n+ return 'drf'\n+ elif possible_inchi and re.findall('^InChI=', line):\n+ return 'inchi'\n+ elif re.findall('^M\\s+END', line):\n+ mol = True\n+ # first line is not an InChI, so it can't be an InChI file\n+ possible_inchi = False\n+\n+ if mol:\n+ # END can occures before $$$$, so and SDF file will \n+ # be recognised as mol, if you not using this hack'\n+ return 'mol'\n+ return 'smi'\n+\n+AliphaticRings = Chem.MolFromSmarts('[$([A;R][!a])]')\n+\n+AcceptorSmarts = [\n+ '[oH0;X2]',\n+ '[OH1;X2;v2]',\n+ '[OH0;X2;v2]',\n+ '[OH0;X1;v2]',\n+ '[O-;X1]',\n+ '[SH0;X2;v2]',\n+ '[SH0;X1;v2]',\n+ '[S-;X1]',\n+ '[nH0;X2]',\n+ '[NH0;X1;v3]',\n+ '[$([N;+0;X3;v3]);!$(N[C,S]=O)]'\n+ ]\n+Acceptors = []\n+for hba in AcceptorSmarts:\n+ Acceptors.append(Chem.MolFromSmarts(hba))\n+\n+StructuralAlertSmarts = [\n+ '*1[O,S,N]*1',\n+ '[S,C](=[O,S])[F,Br,Cl,I]',\n+ '[CX4][Cl,Br,I]',\n+ '[C,c]S(=O)(=O)O[C,c]',\n+ '[$([CH]),$(CC)]#CC(=O)[C,c]',\n+ '[$([CH]),$(CC)]#CC(=O)O[C,c]',\n+ 'n[OH]',\n+ '[$([CH]),$(CC)]#CS(=O)(=O)[C,c]',\n+ 'C=C(C=O)C=O',\n+ 'n1c([F,Cl,Br,I])cccc1',\n+ '[CH1](=O)',\n+ '[O,o][O,o]',\n+ '[C;!R]=[N;!R]',\n+ '[N!R]=[N!R]',\n+ '[#6](=O)[#6](=O)',\n+ '[S,s][S,s]',\n+ '[N,n][NH2]',\n+ 'C(=O)N[NH2]',\n+ '[C,c]=S',\n+ '[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]=[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]',\n+ 'C1(=[O,N])C=CC(=[O,N])C=C1',\n+ 'C1(=[O,N])C(=[O,N])C=CC=C1',\n+ 'a21aa3a(aa1aaaa2)aaaa3',\n+ 'a31a(a2a(aa1)aaaa2)aaaa3',\n+ 'a1aa2a3a(a1)A=AA=A3=AA=A2',\n+ 'c1cc([NH2])ccc1',\n+ '[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]',\n+ 'I',\n+ 'OS(=O)(=O)[O-]',\n+ '[N+](=O)[O-]',\n+ 'C(=O)N[OH]',\n+ 'C1NC(=O)NC(=O)1',\n+ '[SH]',\n+ '[S-]',\n+ 'c1ccc([Cl,Br,I,F])c([Cl,Br,I,F])c1[Cl,Br,I,F]',\n+ 'c1cc([Cl,Br,I,F])cc([Cl,Br,I,F])c1[Cl,Br,I,F]',\n+ '[CR1]1[CR1][CR1][CR1][CR1][CR1][CR1]1',\n+ '[CR1]1[CR1][CR1]cc[CR1][CR1]1',\n+ '[CR2]1[CR2][CR2][CR2][CR2][CR2][CR2][CR2]1',\n+ '[CR2]1[CR2][CR2]cc[CR2][CR2][CR2]1',\n+ '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1',\n+ '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1',\n+ 'C#C',\n+ '[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]',\n+ '[$([N+R]),$([n+R]),$([N+]=C)][O-]',\n+ '[C,c]=N[OH]',\n+ '[C,c]=NOC=O',\n+ '[C,c](=O)[CX4,CR0X3,O][C,c](=O)',\n+ 'c1ccc2c(c1)ccc(=O)o2',\n+ '[O+,o+,S+,s+]',\n+ 'N=C=O',\n+ '[NX3,NX4][F,Cl,Br,I]',\n+ 'c1ccccc1OC(=O)[#6]',\n+ '[CR0]=[CR0][CR0]=[CR0]',\n+ '[C+,c+,C-,c-]',\n+ 'N=[N+]=[N-]',\n+ 'C12C(NC(N1)=O)CSC2',\n+ 'c1c([OH])c([OH,NH2,NH])ccc1',\n+ 'P',\n+ '[N,O,S]C#N',\n+ 'C=C=O',\n+ '[Si][F,Cl,Br,I]',\n+ '[SX2]O',\n+ '[SiR0,CR0](c1ccccc1)(c2ccccc2)(c3ccccc3)',\n+ 'O1CCCCC1OC2CCC3CCCCC3C2',\n+ 'N=[CR0][N,n,O,S]',\n+ '[cR2]1[cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2][cR2]1[cR2]2[cR2][cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2]2',\n+ 'C=[C!r]C#N',\n+ '[cR2]1[cR2]c([N+0X3R0,nX3R0])c([N+0X3R0,nX3R0])[cR2][cR2]1',\n+ '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2]c([N+0X3R0,nX3R0])[cR2]1',\n+ '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2][cR2]c1([N+0X3R0,nX3R0])',\n+ '[OH]c1ccc([OH,NH2,NH])cc1',\n+ 'c1"..b'nt("--iformat",\n+ help="Input format. It must be supported by openbabel.")\n+ parser.add_argument(\'-o\', \'--outfile\', type=argparse.FileType(\'w+\'), \n+ default=sys.stdout, \n+ help="path to the result file, default it sdtout")\n+ parser.add_argument("--header", dest="header", action="store_true",\n+ default=False,\n+ help="Write header line.")\n+\n+\n+ args = parser.parse_args()\n+\n+ # Elucidate filetype and open supplier\n+ ifile = os.path.abspath(args.input)\n+ if not os.path.isfile(ifile):\n+ print "Error: ", ifile, " is not a file or cannot be found."\n+ sys.exit(1)\n+ if not os.path.exists(ifile):\n+ print "Error: ", ifile, " does not exist or cannot be found."\n+ sys.exit(1)\n+ if not os.access(ifile, os.R_OK):\n+ print "Error: ", ifile, " is not readable."\n+ sys.exit(1)\n+\n+ if not args.iformat:\n+ # try to guess the filetype\n+ filetype = check_filetype( ifile )\n+ else:\n+ filetype = args.iformat # sdf or smi\n+\n+\n+ """\n+ 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.\n+ """\n+ if filetype == \'sdf\':\n+ supplier = Chem.SDMolSupplier( ifile )\n+ # Process file\n+ if args.header:\n+ args.outfile.write("MW\\tALOGP\\tHBA\\tHBD\\tPSA\\tROTB\\tAROM\\tALERTS\\tLRo5\\tQED\\tNAME\\n")\n+ count = 0\n+ for mol in supplier:\n+ count += 1\n+ if mol is None:\n+ print "Warning: skipping molecule ", count, " and continuing with next."\n+ continue\n+ props = properties(mol)\n+\n+ if args.method == \'max\':\n+ calc_qed = weights_max(mol, True, props)\n+ elif args.method == \'unweighted\':\n+ calc_qed = weights_none(mol, True, props)\n+ else:\n+ calc_qed = weights_mean(mol, True, props)\n+\n+ 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" % (\n+ props[0], \n+ props[1], \n+ props[2], \n+ props[3], \n+ props[4], \n+ props[5], \n+ props[6], \n+ props[7],\n+ props[8],\n+ calc_qed,\n+ mol.GetProp("_Name"),\n+ ))\n+ elif filetype == \'smi\':\n+ supplier = Chem.SmilesMolSupplier( ifile, " \\t", 0, 1, False, True )\n+\n+ # Process file\n+ if args.header:\n+ args.outfile.write("MW\\tALOGP\\tHBA\\tHBD\\tPSA\\tROTB\\tAROM\\tALERTS\\tLRo5\\tQED\\tNAME\\tSMILES\\n")\n+ count = 0\n+ for line in open(ifile):\n+ tokens = line.strip().split(\'\\t\')\n+ if len(tokens) > 1:\n+ smiles, title = tokens\n+ else:\n+ smiles = tokens[0]\n+ title = \'\'\n+ mol = Chem.MolFromSmiles(smiles)\n+ count += 1\n+ if mol is None:\n+ print "Warning: skipping molecule ", count, " and continuing with next."\n+ continue\n+ props = properties(mol)\n+\n+ if args.method == \'max\':\n+ calc_qed = weights_max(mol, True, props)\n+ elif args.method == \'unweighted\':\n+ calc_qed = weights_none(mol, True, props)\n+ else:\n+ calc_qed = weights_mean(mol, True, props)\n+\n+ 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" % (\n+ props[0], \n+ props[1], \n+ props[2], \n+ props[3], \n+ props[4], \n+ props[5], \n+ props[6], \n+ props[7],\n+ props[8],\n+ calc_qed,\n+ title,\n+ smiles\n+ ))\n+ else:\n+ sys.exit("Error: unknown file-type: ", filetype)\n' |
| b |
| 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 |
| b |
| @@ -0,0 +1,121 @@ +<tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1"> + <description>quantitative estimation (QED)</description> + <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> + <requirements> + <requirement type="package" version="1.0.1">silicos_it</requirement> + <requirement type="package" version="2012_12_1">rdkit</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + </requirements> + <command interpreter="python"> + qed.py -i "${infile}" + --method "${method}" + --iformat ${infile.ext} + -o "${outfile}" $header 2>&1 + </command> + <inputs> + <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/> + <param name="method" type="select" label="Method"> + <option value="max">Max weight (QEDw,max)</option> + <option value="mean">Mean weight (QEDw,mo)</option> + <option value="unweighted">unweighted (QEDw,u)</option> + </param> + <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" /> + </inputs> + <outputs> + <data format="tabular" name="outfile" /> + </outputs> + <tests> + <!-- + Test a tabular input with the first line being a comment without a # character to start + --> + <test> + <param name="infile" value="qed_test.smi"/> + <param name="method" value="max"/> + <output name="outfile" file="qed_test_max.tab"/> + </test> + <test> + <param name="infile" value="qed_test.smi"/> + <param name="method" value="mean"/> + <output name="outfile" file="qed_test_mean.tab"/> + </test> + <test> + <param name="infile" value="qed_test.smi"/> + <param name="method" value="unweighted"/> + <output name="outfile" file="qed_test_unweighted.tab"/> + </test> + </tests> + <help> + +.. 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 + + </help> +</tool> |
| b |
| 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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> + <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> +</repositories> |
| b |
| 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 |
| b |
| b'@@ -0,0 +1,236 @@\n+<tool id="ctb_shapeit" name="Shape alignment" version="0.1">\n+ <description>against a database of molecules (Shape-it)</description>\n+ <requirements>\n+ <requirement type="package" version="1.0.1">silicos_it</requirement>\n+ <requirement type="package" version="2.3.2">openbabel</requirement>\n+ </requirements>\n+ <command >\n+ shape-it \n+ --format ${database.ext}\n+ --dbase $database\n+ --reference $reference\n+ --addIterations $addIterations\n+ #if int($best) > 0:\n+ --best $best\n+ #end if\n+ --cutoff $cutoff\n+ #if $scores == \'yes\':\n+ --scores $output_scores\n+ #end if\n+ --rankBy $rankBy\n+ $noref\n+ --out $output 2>&1\n+ </command>\n+ <inputs>\n+ <param name="reference" type="data" format=\'sdf,mol,mol2\' label="Refrence molecule (with 3D coordinates)" />\n+ <param name="database" type="data" format=\'sdf,mol,mol2\' label="Database of molecules (with 3D coordinates)" />\n+ <param name="cutoff" type="float" value="0.0" label="Only molecules with a score higher than the cutoff are reported." help="The scoring function is defined by the scoring scheme.">\n+ <validator type="in_range" min="0.0" />\n+ </param>\n+ <param name=\'addIterations\' type=\'integer\' value=\'0\' label=\'Perform N additional optimization steps with the simulated annealing procedure\' help="The default value is set to 0, which refers to only a local gradient ascent."/>\n+ <param name=\'best\' type=\'integer\' value=\'0\' label=\'The N best scoring molecules are reported\' help="0 means all molecules are reported"/>\n+ <param name=\'scores\' type=\'boolean\' truevalue=\'yes\' falsevalue=\'\' label=\'Output a Tab-delimited text file with the scores of molecules\' checked="false" />\n+ <param name=\'noref\' type=\'boolean\' truevalue=\'--noRef\' falsevalue=\'\' label=\'The reference molecule is not written into the output files\' checked="false" />\n+ <param name=\'rankBy\' type=\'select\' format=\'text\' label="This option defines the used scoring scheme">\n+ <option value=\'TANIMOTO\'>Tanimoto</option>\n+ <option value=\'TVERSKY_REF\'>TVERSKY_REF</option>\n+ <option value=\'TVERSKY_DB\'>TVERSKY_DB</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="output" format_source=\'database\' />\n+ <data name="output_scores" format="tabular">\n+ <filter>scores == "yes"</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="database" ftype=\'sdf\' value="CID_3033.sdf" />\n+ <param name="reference" type="sdf" value=\'CID_3037.sdf\' />\n+ <param name="cutoff" value="0.0" />\n+ <param name=\'addIterations\' value=\'0\' />\n+ <param name=\'best\' value=\'0\' />\n+ <output name="output" ftype=\'sdf\' file="shapeit_on_CID3033_and_CID3037.sdf" />\n+ </test>\n+ </tests>\n+ <help>\n+\n+\n+.. class:: infomark\n+\n+**What this tool does**\n+\n+Shape-it_ is a tool that aligns a reference molecule against a set of database\n+molecules using the shape of the molecules as the align criterion. \n+It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as it was introduced by Grant and Pickup.\n+\n+The program expects one reference molecule with\n+its three-dimensional coordinates and one database files containing one\n+or more molecules in three dimensions. The results are either the alignment\n+of all database molecules and their respective scores or the N best\n+scoring molecules of the complete database.\n+\n+.. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016\n+.. _Shape-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+\n+| - `formates recognized by OpenBabel`_\n+\n+.. _formates recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats'..b' 0\n+\t 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 1 14 1 0 0 0 0\n+\t 2 15 1 0 0 0 0\n+\t 3 16 1 0 0 0 0\n+\t 3 30 1 0 0 0 0\n+\t 4 16 2 0 0 0 0\n+\t 5 7 1 0 0 0 0\n+\t 5 9 1 0 0 0 0\n+\t 5 22 1 0 0 0 0\n+\t 6 7 1 0 0 0 0\n+\t 6 8 1 0 0 0 0\n+\t ......\t\n+\n+\t- cutoff : 0.0\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Output**\n+\n+* Example::\n+\n+\t 27 28 0 0 0 0 0 0 0 0999 V2000\n+\t -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0\n+\t 1 14 1 0 0 0 0\n+\t 2 15 1 0 0 0 0\n+\t 3 8 1 0 0 0 0\n+\t 3 26 1 0 0 0 0\n+\t 4 9 1 0 0 0 0\n+\t 4 27 1 0 0 0 0\n+\t 5 6 1 0 0 0 0\n+\t 5 7 1 0 0 0 0\n+\t 5 18 1 0 0 0 0\n+\t 5 19 1 0 0 0 0\n+\t 6 8 2 0 0 0 0\n+\t ......\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Cite**\n+\n+`Silicos-it`_ - shape-it\n+\n+.. _Silicos-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html\n+\n+\n+ </help>\n+</tool>\n' |
| b |
| 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 |
| b |
| @@ -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 -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 + 6 10 2 0 0 0 0 + 7 11 2 0 0 0 0 + 8 16 1 0 0 0 0 + 8 20 1 0 0 0 0 + 8 21 1 0 0 0 0 + 9 14 2 0 0 0 0 + 9 15 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 23 1 0 0 0 0 + 11 13 1 0 0 0 0 + 11 24 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 25 1 0 0 0 0 + 13 26 1 0 0 0 0 + 14 17 1 0 0 0 0 + 15 18 2 0 0 0 0 + 17 19 2 0 0 0 0 + 17 27 1 0 0 0 0 + 18 19 1 0 0 0 0 + 18 28 1 0 0 0 0 + 19 29 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3033 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +1 +20 +18 +39 +29 +42 +38 +35 +30 +25 +33 +28 +32 +36 +26 +24 +40 +11 +27 +37 +7 +41 +10 +19 +43 +8 +6 +16 +44 +23 +34 +14 +15 +31 +9 +13 +17 +21 +22 +5 +12 +2 +3 +4 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +28 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 0.66 +17 -0.15 +18 -0.15 +19 -0.15 +2 -0.18 +22 0.4 +23 0.15 +24 0.15 +25 0.15 +26 0.15 +27 0.15 +28 0.15 +29 0.15 +3 -0.65 +30 0.5 +4 -0.57 +5 -0.6 +6 -0.14 +7 0.1 +8 0.2 +9 0.1 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +4 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +7 +1 3 acceptor +1 4 acceptor +1 5 cation +1 5 donor +3 3 4 16 anion +6 6 7 10 11 12 13 rings +6 9 14 15 17 18 19 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +19 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_CONFORMER_ID> +00000BD900000001 + +> <PUBCHEM_MMFF94_ENERGY> +65.6362 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +35.578 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10366900 7 17386020514759110480 +114674 6 16903282898360328323 +11578080 2 17913245089295617604 +11582403 64 14544541357940910356 +11640471 11 18127963303313961600 +12236239 1 18272088352834916308 +12363563 72 18042978579496277287 +12553582 1 18190740839094073615 +12596599 1 18201439237582433270 +12788726 201 18410285909464206003 +13032168 30 18201440238019390274 +13140716 1 18187086113919468457 +13538477 17 18339642338307470464 +13583140 156 17241914119188522922 +13764800 53 17895191172601517065 +13965767 371 17259888045752176376 +14115302 16 18342181093776810149 +14787075 74 17907866106787333628 +15279307 12 18198622322777022915 +15375462 189 18270674264943931347 +15669948 3 18336550511731321249 +16752209 62 18336841852664817743 +16945 1 18188484791351783177 +19433438 48 18059583550169763352 +200 152 18130792217719576158 +20645476 183 18270115859187436189 +20905425 154 17970632883131290416 +21452121 199 18046637711133085653 +21639500 275 16988270998321974524 +22112679 90 18342446063036096292 +23419403 2 17835564502519425292 +23493267 7 18115023138028600728 +23526113 38 16660924516543134566 +23557571 272 17821721762863303772 +23559900 14 17896315990920094510 +23598288 3 18411412925846384519 +23598291 2 18059009613384180254 +238 59 16343141308025475526 +4340502 62 17273677940604857177 +6049 1 17240202131864233360 +6992083 37 18058168521433072460 +7615 1 18201433675414973908 +77492 1 18272651289913926852 +81228 2 17968373550240022809 +9709674 26 17896035610527288590 + +> <PUBCHEM_SHAPE_MULTIPOLES> +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 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +790.335 + +> <PUBCHEM_SHAPE_VOLUME> +214.7 + +> <PUBCHEM_COORDINATE_TYPE> +2 +5 +255 + +$$$$ + |
| b |
| 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 |
| b |
| @@ -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 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 + 6 10 1 0 0 0 0 + 7 9 2 0 0 0 0 + 7 11 1 0 0 0 0 + 8 12 1 0 0 0 0 + 9 13 1 0 0 0 0 + 10 14 2 0 0 0 0 + 10 20 1 0 0 0 0 + 11 15 2 0 0 0 0 + 11 21 1 0 0 0 0 + 12 16 2 0 0 0 0 + 12 22 1 0 0 0 0 + 13 17 2 0 0 0 0 + 13 23 1 0 0 0 0 + 14 16 1 0 0 0 0 + 15 17 1 0 0 0 0 + 16 24 1 0 0 0 0 + 17 25 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3037 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +8 +10 +12 +1 +7 +5 +11 +3 +6 +9 +4 +2 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +25 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 -0.15 +17 -0.15 +2 -0.18 +20 0.15 +21 0.15 +22 0.15 +23 0.15 +24 0.15 +25 0.15 +26 0.45 +27 0.45 +3 -0.53 +4 -0.53 +5 0.29 +6 -0.14 +7 -0.14 +8 0.08 +9 0.08 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +2 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +4 +1 3 donor +1 4 donor +6 6 8 10 12 14 16 rings +6 7 9 11 13 15 17 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +17 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +5 + +> <PUBCHEM_CONFORMER_ID> +00000BDD00000008 + +> <PUBCHEM_MMFF94_ENERGY> +44.6858 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +20.297 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10062212 137 18261117369936506423 +104564 63 17986963035811110412 +11458722 120 18339359768245870841 +11471102 22 5472872458301843344 +11578080 2 18190204380446433792 +116883 192 18265608969609498196 +12236239 1 18410856576819659107 +12592029 89 18338223951597366363 +13549 16 18410575084668353682 +13693222 15 6555421915516066822 +13764800 53 14189033175566991199 +14115302 16 18186237320680093898 +14341114 328 10087642619424135543 +14787075 74 9511159855286719151 +14993402 34 18410855451538227223 +15099037 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 + +> <PUBCHEM_SHAPE_MULTIPOLES> +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 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +722.787 + +> <PUBCHEM_SHAPE_VOLUME> +193 + +> <PUBCHEM_COORDINATE_TYPE> +2 +5 +255 + +$$$$ + |
| b |
| diff -r 000000000000 -r bb92d30b4f52 shape-it/test_data/shapeit_on_CID30333_and_CID3037.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shape-it/test_data/shapeit_on_CID30333_and_CID3037.sdf Thu Aug 15 03:34:00 2013 -0400 |
| b |
| b'@@ -0,0 +1,498 @@\n+3033\n+ OpenBabel06221213273D\n+\n+ 30 31 0 0 0 0 0 0 0 0999 V2000\n+ 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 14 1 0 0 0 0\n+ 2 15 1 0 0 0 0\n+ 3 16 1 0 0 0 0\n+ 3 30 1 0 0 0 0\n+ 4 16 2 0 0 0 0\n+ 5 7 1 0 0 0 0\n+ 5 9 1 0 0 0 0\n+ 5 22 1 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 6 8 1 0 0 0 0\n+ 6 10 2 0 0 0 0\n+ 7 11 2 0 0 0 0\n+ 8 16 1 0 0 0 0\n+ 8 20 1 0 0 0 0\n+ 8 21 1 0 0 0 0\n+ 9 14 2 0 0 0 0\n+ 9 15 1 0 0 0 0\n+ 10 12 1 0 0 0 0\n+ 10 23 1 0 0 0 0\n+ 11 13 1 0 0 0 0\n+ 11 24 1 0 0 0 0\n+ 12 13 2 0 0 0 0\n+ 12 25 1 0 0 0 0\n+ 13 26 1 0 0 0 0\n+ 14 17 1 0 0 0 0\n+ 15 18 2 0 0 0 0\n+ 17 19 2 0 0 0 0\n+ 17 27 1 0 0 0 0\n+ 18 19 1 0 0 0 0\n+ 18 28 1 0 0 0 0\n+ 19 29 1 0 0 0 0\n+M END\n+> <PUBCHEM_COMPOUND_CID>\n+3033\n+\n+> <PUBCHEM_CONFORMER_RMSD>\n+0.6\n+\n+> <PUBCHEM_CONFORMER_DIVERSEORDER>\n+1\n+20\n+18\n+39\n+29\n+42\n+38\n+35\n+30\n+25\n+33\n+28\n+32\n+36\n+26\n+24\n+40\n+11\n+27\n+37\n+7\n+41\n+10\n+19\n+43\n+8\n+6\n+16\n+44\n+23\n+34\n+14\n+15\n+31\n+9\n+13\n+17\n+21\n+22\n+5\n+12\n+2\n+3\n+4\n+\n+> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n+28\n+1 -0.18\n+10 -0.15\n+11 -0.15\n+12 -0.15\n+13 -0.15\n+14 0.18\n+15 0.18\n+16 0.66\n+17 -0.15\n+18 -0.15\n+19 -0.15\n+2 -0.18\n+22 0.4\n+23 0.15\n+24 0.15\n+25 0.15\n+26 0.15\n+27 0.15\n+28 0.15\n+29 0.15\n+3 -0.65\n+30 0.5\n+4 -0.57\n+5 -0.6\n+6 -0.14\n+7 0.1\n+8 0.2\n+9 0.1\n+\n+> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n+4\n+\n+> <PUBCHEM_PHARMACOPHORE_FEATURES>\n+7\n+1 3 acceptor\n+1 4 acceptor\n+1 5 cation\n+1 5 donor\n+3 3 4 16 anion\n+6 6 7 10 11 12 13 rings\n+6 9 14 15 17 18 19 rings\n+\n+> <PUBCHEM_HEAVY_ATOM_COUNT>\n+19\n+\n+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n+0\n+\n+> <PUBCHEM_COMPONENT_COUNT>\n+1\n+\n+> <PUBC'..b' 1.0134 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2183 0.8049 2.1749 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0727 2.1943 0.0848 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.3073 -0.1842 2.1352 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5356 -2.7462 0.2209 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.7192 0.5473 -2.7566 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.3771 -1.3662 -0.6554 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.5580 -0.5122 -1.5211 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2289 -1.3586 1.8240 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.7059 1.4288 -2.6511 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 14 1 0 0 0 0\n+ 2 15 1 0 0 0 0\n+ 3 8 1 0 0 0 0\n+ 3 26 1 0 0 0 0\n+ 4 9 1 0 0 0 0\n+ 4 27 1 0 0 0 0\n+ 5 6 1 0 0 0 0\n+ 5 7 1 0 0 0 0\n+ 5 18 1 0 0 0 0\n+ 5 19 1 0 0 0 0\n+ 6 8 2 0 0 0 0\n+ 6 10 1 0 0 0 0\n+ 7 9 2 0 0 0 0\n+ 7 11 1 0 0 0 0\n+ 8 12 1 0 0 0 0\n+ 9 13 1 0 0 0 0\n+ 10 14 2 0 0 0 0\n+ 10 20 1 0 0 0 0\n+ 11 15 2 0 0 0 0\n+ 11 21 1 0 0 0 0\n+ 12 16 2 0 0 0 0\n+ 12 22 1 0 0 0 0\n+ 13 17 2 0 0 0 0\n+ 13 23 1 0 0 0 0\n+ 14 16 1 0 0 0 0\n+ 15 17 1 0 0 0 0\n+ 16 24 1 0 0 0 0\n+ 17 25 1 0 0 0 0\n+M END\n+> <PUBCHEM_COMPOUND_CID>\n+3037\n+\n+> <PUBCHEM_CONFORMER_RMSD>\n+0.6\n+\n+> <PUBCHEM_CONFORMER_DIVERSEORDER>\n+8\n+10\n+12\n+1\n+7\n+5\n+11\n+3\n+6\n+9\n+4\n+2\n+\n+> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n+25\n+1 -0.18\n+10 -0.15\n+11 -0.15\n+12 -0.15\n+13 -0.15\n+14 0.18\n+15 0.18\n+16 -0.15\n+17 -0.15\n+2 -0.18\n+20 0.15\n+21 0.15\n+22 0.15\n+23 0.15\n+24 0.15\n+25 0.15\n+26 0.45\n+27 0.45\n+3 -0.53\n+4 -0.53\n+5 0.29\n+6 -0.14\n+7 -0.14\n+8 0.08\n+9 0.08\n+\n+> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n+2\n+\n+> <PUBCHEM_PHARMACOPHORE_FEATURES>\n+4\n+1 3 donor\n+1 4 donor\n+6 6 8 10 12 14 16 rings\n+6 7 9 11 13 15 17 rings\n+\n+> <PUBCHEM_HEAVY_ATOM_COUNT>\n+17\n+\n+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n+0\n+\n+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n+0\n+\n+> <PUBCHEM_COMPONENT_COUNT>\n+1\n+\n+> <PUBCHEM_CACTVS_TAUTO_COUNT>\n+5\n+\n+> <PUBCHEM_CONFORMER_ID>\n+00000BDD00000008\n+\n+> <PUBCHEM_MMFF94_ENERGY>\n+44.6858\n+\n+> <PUBCHEM_FEATURE_SELFOVERLAP>\n+20.297\n+\n+> <PUBCHEM_SHAPE_FINGERPRINT>\n+10062212 137 18261117369936506423\n+104564 63 17986963035811110412\n+11458722 120 18339359768245870841\n+11471102 22 5472872458301843344\n+11578080 2 18190204380446433792\n+116883 192 18265608969609498196\n+12236239 1 18410856576819659107\n+12592029 89 18338223951597366363\n+13549 16 18410575084668353682\n+13693222 15 6555421915516066822\n+13764800 53 14189033175566991199\n+14115302 16 18186237320680093898\n+14341114 328 10087642619424135543\n+14787075 74 9511159855286719151\n+14993402 34 18410855451538227223\n+15099037 51 18340768233908588503\n+15207287 21 15719111361650760302\n+15375358 24 15647053767618106914\n+15775835 57 18272650117329930317\n+16945 1 17906452130063974618\n+17834072 14 15936410035134206066\n+18186145 218 17132117918276567720\n+19422 9 18271525295227750719\n+20279233 1 15719389529571237654\n+20645476 183 18339080393619327415\n+23402539 116 18186809105365620101\n+23402655 69 18342736308283284156\n+23559900 14 17603590712323212176\n+25 1 17561083592297532664\n+26918003 58 6266902359448424189\n+296302 2 15213020427345972082\n+3082319 5 18338798905472319583\n+34934 24 18341891845236497020\n+633830 44 17703790310130762689\n+74978 22 18266740181857992718\n+7832392 63 18340206284835898173\n+81228 2 15720767252053392762\n+9981440 41 17403743242177431832\n+\n+> <PUBCHEM_SHAPE_MULTIPOLES>\n+341.85\n+8.38\n+1.9\n+1.1\n+0.02\n+0\n+-1.15\n+1.94\n+-0.01\n+0\n+-0.39\n+-4.15\n+0.01\n+0\n+\n+> <PUBCHEM_SHAPE_SELFOVERLAP>\n+722.787\n+\n+> <PUBCHEM_SHAPE_VOLUME>\n+193\n+\n+> <PUBCHEM_COORDINATE_TYPE>\n+2\n+5\n+255\n+\n+> <Shape-it::Tanimoto>\n+0.606434\n+\n+> <Shape-it::Tversky_Ref>\n+0.721775\n+\n+> <Shape-it::Tversky_Db>\n+0.791445\n+\n+$$$$\n' |
| b |
| 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 |
| b |
| @@ -0,0 +1,90 @@ +<tool id="ctb_stripit" name="Strip-it" version="1.0.1"> + <description> extracts predefined scaffolds from molecules</description> + <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism> + <requirements> + <requirement type="package" version="2.3.2">openbabel</requirement> + <requirement type="package" version="1.0.1">silicos_it</requirement> + </requirements> + <command> + strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog --noHeader 2>&1 + </command> + <inputs> + <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" /> + </inputs> + <outputs> + <data name="outfile" format="tabular" /> + </outputs> + <tests> + <test> + <param name="infile" type='sdf' value="CID_3037.sdf"/> + <data name="output" type="tabular" file="Strip-it_on_CID3037.tabular" /> + </test> + </tests> + <help> + + +.. 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 + + + </help> +</tool> |
| b |
| 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 |
| b |
| @@ -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 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 + 6 10 1 0 0 0 0 + 7 9 2 0 0 0 0 + 7 11 1 0 0 0 0 + 8 12 1 0 0 0 0 + 9 13 1 0 0 0 0 + 10 14 2 0 0 0 0 + 10 20 1 0 0 0 0 + 11 15 2 0 0 0 0 + 11 21 1 0 0 0 0 + 12 16 2 0 0 0 0 + 12 22 1 0 0 0 0 + 13 17 2 0 0 0 0 + 13 23 1 0 0 0 0 + 14 16 1 0 0 0 0 + 15 17 1 0 0 0 0 + 16 24 1 0 0 0 0 + 17 25 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3037 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +8 +10 +12 +1 +7 +5 +11 +3 +6 +9 +4 +2 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +25 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 -0.15 +17 -0.15 +2 -0.18 +20 0.15 +21 0.15 +22 0.15 +23 0.15 +24 0.15 +25 0.15 +26 0.45 +27 0.45 +3 -0.53 +4 -0.53 +5 0.29 +6 -0.14 +7 -0.14 +8 0.08 +9 0.08 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +2 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +4 +1 3 donor +1 4 donor +6 6 8 10 12 14 16 rings +6 7 9 11 13 15 17 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +17 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +5 + +> <PUBCHEM_CONFORMER_ID> +00000BDD00000008 + +> <PUBCHEM_MMFF94_ENERGY> +44.6858 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +20.297 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10062212 137 18261117369936506423 +104564 63 17986963035811110412 +11458722 120 18339359768245870841 +11471102 22 5472872458301843344 +11578080 2 18190204380446433792 +116883 192 18265608969609498196 +12236239 1 18410856576819659107 +12592029 89 18338223951597366363 +13549 16 18410575084668353682 +13693222 15 6555421915516066822 +13764800 53 14189033175566991199 +14115302 16 18186237320680093898 +14341114 328 10087642619424135543 +14787075 74 9511159855286719151 +14993402 34 18410855451538227223 +15099037 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 + +> <PUBCHEM_SHAPE_MULTIPOLES> +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 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +722.787 + +> <PUBCHEM_SHAPE_VOLUME> +193 + +> <PUBCHEM_COORDINATE_TYPE> +2 +5 +255 + +$$$$ + |
| b |
| diff -r 000000000000 -r bb92d30b4f52 strip-it/test-data/Strip-it_on_CID3037.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/strip-it/test-data/Strip-it_on_CID3037.tabular Thu Aug 15 03:34:00 2013 -0400 |
| b |
| @@ -0,0 +1,2 @@ +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 c1ccc(cc1)Cc1ccccc1 c1ccc(cc1)Cc1ccccc1 c1ccc(cc1)Cc1ccccc1 c1ccc(cc1)Cc1ccccc1 |
| b |
| diff -r 000000000000 -r bb92d30b4f52 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 |
| b |
| @@ -0,0 +1,61 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="openbabel" version="2.3.2"> + <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="rdkit" version="2012_12_1"> + <repository changeset_revision="7c60f011c70c" name="package_rdkit_2012_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="silicos_it" version="1.0.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://github.com/bgruening/silicos-it_store/raw/master/strip-it/strip-it-1.0.2.tar.gz</action> + + <!-- populate the environment variables from the dependend repos + $OPENBABEL_INCLUDE_DIR and $OPENBABEL_LIB_DIR + --> + <action type="set_environment_for_install"> + <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="openbabel" version="2.3.2" /> + </repository> + </action> + + <!--compiling strip-it --> + <action type="shell_command"> + cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/strip-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && + make && + make install</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/strip-it/bin</environment_variable> + </action> + + <!-- compiling align-it --> + <action type="shell_command">wget https://github.com/bgruening/silicos-it_store/raw/master/align-it/align-it-1.0.3.tar.gz</action> + <action type="shell_command">tar xfvz align-it-1.0.3.tar.gz && + cd align-it-1.0.3 && + cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/align-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && + make && + make install</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/align-it/bin</environment_variable> + </action> + + <!-- compiling shape-it --> + <action type="shell_command">wget https://github.com/bgruening/silicos-it_store/raw/master/shape-it/shape-it-1.0.1.tar.gz</action> + <action type="shell_command">tar xfvz shape-it-1.0.1.tar.gz && + cd shape-it-1.0.1 && + cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/shape-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && + make && + make install</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/shape-it/bin</environment_variable> + </action> + + </actions> + </install> + <readme>Compiling silicos-it requires g++ and CMake 2.4+.</readme> + </package> +</tool_dependency> |