| Next changeset 1:10c0df29e6d1 (2019-05-07) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7 |
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added:
align-it.xml align-it_create_db.xml test-data/6mol.sdf test-data/CID_2244.sdf test-data/aliginit_scores.tabular.tabular test-data/align-it_Search_on_CID2244.phar test-data/align-it_Search_on_CID2244.sdf test-data/alignit_Create_Phar_DB_6mol.phar test-data/alignit_on_CID2244.phar test-data/reference.phar |
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| diff -r 000000000000 -r 1b8b6787dfbb align-it.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it.xml Mon May 22 03:02:39 2017 -0400 |
| [ |
| b'@@ -0,0 +1,245 @@\n+<tool id="ctb_alignit" name="Pharmacophore Alignment" version="1.0.3.1">\n+ <description>and Optimization (Align-it)</description>\n+ <requirements>\n+ <requirement type="package" version="1.0.3">align_it</requirement>\n+ </requirements>\n+ <command detect_errors="aggressive">\n+<![CDATA[\n+ align-it\n+ #if str($database.ext).strip() == \'phar\':\n+ --dbType PHAR\n+ #else:\n+ --dbType \'${database.ext}\'\n+ #end if\n+ --dbase "$database"\n+\n+ --reference "$reference"\n+ #if str($reference.ext).strip() == \'phar\':\n+ --refType PHAR\n+ #else:\n+ --refType ${reference.ext}\n+ #end if\n+ #######################################\n+ #### output options\n+ #######################################\n+ --pharmacophore $aligned_pharmacophores\n+\n+\n+ --out \'$aligned_structures\'\n+ --outType $oformat\n+\n+ #if float( str($cutoff) ) > 0:\n+ --cutOff $cutoff\n+ #end if\n+ #if int( str($best) ) > 0:\n+ --best $best\n+ #end if\n+ --rankBy $rankBy\n+ --scores \'$score_result_file\'\n+\n+ #######################################\n+ #### Options\n+ #######################################\n+\n+ #set $fgroups_combined = str( $fgroups ).strip()\n+ --funcGroup $fgroups_combined\n+\n+ --epsilon $epsilon\n+ $merge\n+ $noNormal\n+ $noHybrid\n+ $scoreOnly\n+ $withExclusion\n+]]>\n+ </command>\n+ <inputs>\n+ <param name="database" type="data" format=\'mol,mol2,sdf,smi,txt\' label="Defines the database of molecules that will be used to screen"/>\n+ <param name="reference" type="data" format=\'mol,mol2,sdf,smi,txt\' label="Reference Molecule"/>\n+\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">\n+ <option value=\'AROM\' selected="true">aromatic rings</option>\n+ <option value=\'HDON\' selected="true">hydrogen bond donors</option>\n+ <option value=\'HACC\' selected="true">hydrogen bond acceptors</option>\n+ <option value=\'LIPO\' selected="true">lipophilic spots</option>\n+ <option value=\'CHARGE\' selected="true">charge centers</option>\n+ </param>\n+\n+\n+ <param name="epsilon" type="float" value="0.5" label=\'Change the tolerance for points to be matched in the alignment phase\'\n+ help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned.">\n+ <validator type="in_range" min="0" max="1" />\n+ </param>\n+ <param name=\'merge\' type=\'boolean\' truevalue=\'--merge\' falsevalue=\'\' label=\'Merge pharmacophore points\' />\n+ <param name=\'noNormal\' type=\'boolean\' truevalue=\'--noNormal\' falsevalue=\'\' \n+ label=\'No normal information is included during the alignment\'\n+ help="Using this flag makes the pharmacophore models less specific but also less conformation-dependent."/>\n+ <param name=\'noHybrid\' type=\'boolean\' truevalue=\'--noHybrid\' falsevalue=\'\'\n+ label=\'Disable the use of hybrid pharmacophore points\' help="Using this flag will increase the number of pharmacophore points."/>\n+ <param name=\'withExclusion\' type=\'boolean\' truevalue=\'--withExclusion\' falsevalue=\'\'\n+ label=\'Add exclusion spheres into the optimization process instead of processing them afterwards\'\n+ help="When this flag is set, the exclusion spheres have also an impact on the optimization procedure." />\n+ <param name=\'scoreOnly\' type=\'boolean\' truevalue=\'--scoreOnly\' falsevalue=\'\'\n+ label=\'No translational or rotational opti'..b'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+\n+ - cutoff : 0.0\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Output**\n+\n+The format of the output file is shown in the table below:\n+\n++--------+-----------------------------------------------------------------------+\n+| Column | Content |\n++========+=======================================================================+\n+| 1 | Id of the reference structure |\n++--------+-----------------------------------------------------------------------+\n+| 2 | Maximum volume of the reference structure |\n++--------+-----------------------------------------------------------------------+\n+| 3 | Id of the database structure |\n++--------+-----------------------------------------------------------------------+\n+| 4 | Maximum volume of the database structure |\n++--------+-----------------------------------------------------------------------+\n+| 5 | Maximum volume overlap of the two structures |\n++--------+-----------------------------------------------------------------------+\n+| 6 | Overlap between pharmacophore and exclusion spheres in the reference |\n++--------+-----------------------------------------------------------------------+\n+| 7 | Corrected volume overlap between database pharmacophore and reference |\n++--------+-----------------------------------------------------------------------+\n+| 8 | Number of pharmacophore points in the processed pharmacophore |\n++--------+-----------------------------------------------------------------------+\n+| 9 | TANIMOTO score |\n++--------+-----------------------------------------------------------------------+\n+| 10 | TVERSKY_REF score |\n++--------+-----------------------------------------------------------------------+\n+| 11 | TVERSKY_DB score |\n++--------+-----------------------------------------------------------------------+\n+\n+\n+* Example::\n+\n+ - aligned Pharmacophores\n+\n+ 3033\n+ HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0\n+ HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0\n+ HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827\n+ HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616\n+ HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767\n+ $$$$\n+\n+\n+]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1016/j.jmgm.2008.04.003</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 1b8b6787dfbb align-it_create_db.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it_create_db.xml Mon May 22 03:02:39 2017 -0400 |
| [ |
| @@ -0,0 +1,124 @@ +<tool id="ctb_alignit_create_db" name="Pharmacophore" version="0.1"> + <description>generation (Align-it)</description> + <requirements> + <requirement type="package" version="1.0.3">align_it</requirement> + </requirements> + <command detect_errors="aggressive"> +<![CDATA[ + align-it + --dbType '${database.ext}' + --dbase '$database' + --pharmacophore '$pharmacophores' + $merge + $noHybrid +]]> + </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="txt" label="${tool.name} on ${on_string} (scores)"/> + </outputs> + <tests> + <test> + <param name="database" ftype="sdf" value="6mol.sdf"/> + <output name="pharmacophores" file="alignit_Create_Phar_DB_6mol.phar" /> + </test> + </tests> + <help> +<![CDATA[ + +.. 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 + $$$$ + + +]]> + </help> + <citations> + <citation type="doi">10.1016/j.jmgm.2008.04.003</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 1b8b6787dfbb test-data/6mol.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6mol.sdf Mon May 22 03:02:39 2017 -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 1b8b6787dfbb test-data/CID_2244.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244.sdf Mon May 22 03:02:39 2017 -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 + +$$$$ + |
| b |
| diff -r 000000000000 -r 1b8b6787dfbb test-data/aliginit_scores.tabular.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aliginit_scores.tabular.tabular Mon May 22 03:02:39 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +2244 89.8904 2244 89.8904 89.8904 0 89.8904 5 1 1 1 |
| b |
| diff -r 000000000000 -r 1b8b6787dfbb test-data/align-it_Search_on_CID2244.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/align-it_Search_on_CID2244.phar Mon May 22 03:02:39 2017 -0400 |
| b |
| @@ -0,0 +1,7 @@ +NAME +HYBL 5.63852 -1.334 0 0.7 0 -1.77636e-15 -2.22045e-16 0 +HYBH 6.3301 1.44 0 1 1 7.19612 1.94001 0 +HACC 3.732 -0.06 0 1 1 3.7319 0.94 0 +HACC 4.5981 1.44 0 1 1 3.73208 1.94001 0 +HACC 2.866 -1.56 0 1 1 2.866 -2.56 0 +$$$$ |
| b |
| diff -r 000000000000 -r 1b8b6787dfbb test-data/align-it_Search_on_CID2244.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/align-it_Search_on_CID2244.sdf Mon May 22 03:02:39 2017 -0400 |
| b |
| @@ -0,0 +1,163 @@ +2244 + OpenBabel05221700322D + + 21 21 0 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 + +> <PHARAO_TANIMOTO> +1 + +> <PHARAO_TVERSKY_REF> +1 + +> <PHARAO_TVERSKY_DB> +1 + +$$$$ |
| b |
| diff -r 000000000000 -r 1b8b6787dfbb test-data/alignit_Create_Phar_DB_6mol.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignit_Create_Phar_DB_6mol.phar Mon May 22 03:02:39 2017 -0400 |
| b |
| @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$ |
| b |
| diff -r 000000000000 -r 1b8b6787dfbb test-data/alignit_on_CID2244.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignit_on_CID2244.phar Mon May 22 03:02:39 2017 -0400 |
| b |
| @@ -0,0 +1,7 @@ +2244 +HYBL 5.63852 -1.334 0 0.7 0 0 0 0 +HYBH 6.3301 1.44 0 1 1 7.19612 1.94001 0 +HACC 3.732 -0.06 0 1 1 3.7319 0.94 0 +HACC 4.5981 1.44 0 1 1 3.73208 1.94001 0 +HACC 2.866 -1.56 0 1 1 2.866 -2.56 0 +$$$$ |
| b |
| diff -r 000000000000 -r 1b8b6787dfbb test-data/reference.phar --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.phar Mon May 22 03:02:39 2017 -0400 |
| b |
| @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$ |