Mercurial > repos > bgruening > align_it
changeset 0:1b8b6787dfbb draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
| author | bgruening |
|---|---|
| date | Mon, 22 May 2017 03:02:39 -0400 |
| parents | |
| children | 10c0df29e6d1 |
| files | 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 |
| diffstat | 10 files changed, 2372 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it.xml Mon May 22 03:02:39 2017 -0400 @@ -0,0 +1,245 @@ +<tool id="ctb_alignit" name="Pharmacophore Alignment" version="1.0.3.1"> + <description>and Optimization (Align-it)</description> + <requirements> + <requirement type="package" version="1.0.3">align_it</requirement> + </requirements> + <command detect_errors="aggressive"> +<![CDATA[ + align-it + #if str($database.ext).strip() == 'phar': + --dbType PHAR + #else: + --dbType '${database.ext}' + #end if + --dbase "$database" + + --reference "$reference" + #if str($reference.ext).strip() == 'phar': + --refType PHAR + #else: + --refType ${reference.ext} + #end if + ####################################### + #### output options + ####################################### + --pharmacophore $aligned_pharmacophores + + + --out '$aligned_structures' + --outType $oformat + + #if float( str($cutoff) ) > 0: + --cutOff $cutoff + #end if + #if int( str($best) ) > 0: + --best $best + #end if + --rankBy $rankBy + --scores '$score_result_file' + + ####################################### + #### Options + ####################################### + + #set $fgroups_combined = str( $fgroups ).strip() + --funcGroup $fgroups_combined + + --epsilon $epsilon + $merge + $noNormal + $noHybrid + $scoreOnly + $withExclusion +]]> + </command> + <inputs> + <param name="database" type="data" format='mol,mol2,sdf,smi,txt' label="Defines the database of molecules that will be used to screen"/> + <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference Molecule"/> + + <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment"> + <option value='AROM' selected="true">aromatic rings</option> + <option value='HDON' selected="true">hydrogen bond donors</option> + <option value='HACC' selected="true">hydrogen bond acceptors</option> + <option value='LIPO' selected="true">lipophilic spots</option> + <option value='CHARGE' selected="true">charge centers</option> + </param> + + + <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."> + <validator type="in_range" min="0" max="1" /> + </param> + <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' /> + <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."/> + <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."/> + <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." /> + <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue='' + label='No translational or rotational optimization will be performed' help=""/> + + <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format"> + <option value='smi'>SMILES</option> + <option value='inchi'>InChI</option> + <option value='sdf'>SD file</option> + </param> + + <param name="cutoff" type="float" value="0" label="Only structures with a score larger than this cutoff will be written to the files" + help="This value should be between 0 and 1."> + <validator type="in_range" min="0" max="1" /> + </param> + <param name="best" type="integer" value="0" label="With this option only a limited number of best scoring structures are written to the files" + help="0 means this option is deactivated"> + <validator type="in_range" min="0"/> + </param> + + <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme"> + <option value='TANIMOTO'>Tanimoto</option> + <option value='TVERSKY_REF'>TVERSKY_REF</option> + <option value='TVERSKY_DB'>TVERSKY_DB</option> + </param> + + </inputs> + <outputs> + <data name="aligned_pharmacophores" format="txt" label="${tool.name} on ${on_string} (aligned pharmacophores)"/> + <data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)"> + <change_format> + <when input="oformat" value="inchi" format="inchi"/> + <when input="oformat" value="sdf" format="sdf"/> + </change_format> + </data> + <data name="score_result_file" format="tabular" label="${tool.name} on ${on_string} (scores)"/> + </outputs> + <tests> + <test> + <param name="database" ftype="sdf" value="CID_2244.sdf"/> + <param name="reference" ftype="sdf" value="CID_2244.sdf"/> + <param name="oformat" value="sdf"/> + <output name="aligned_pharmacophores" file="align-it_Search_on_CID2244.phar" /> + <output name="aligned_structures" file="align-it_Search_on_CID2244.sdf" lines_diff="2" /> + <output name="score_result_file" file="aliginit_scores.tabular.tabular" /> + </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 +(use the tool **Pharmacophore generation** if you want to store these for further use). +Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting +score is calculated from the volume overlap resulting of the alignments. + +.. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html + +----- + +.. class:: infomark + +**Input** + +* Example:: + + - database + + 30 31 0 0 0 0 0 0 0999 V2000 + 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 + + - cutoff : 0.0 + +----- + +.. class:: infomark + +**Output** + +The format of the output file is shown in the table below: + ++--------+-----------------------------------------------------------------------+ +| Column | Content | ++========+=======================================================================+ +| 1 | Id of the reference structure | ++--------+-----------------------------------------------------------------------+ +| 2 | Maximum volume of the reference structure | ++--------+-----------------------------------------------------------------------+ +| 3 | Id of the database structure | ++--------+-----------------------------------------------------------------------+ +| 4 | Maximum volume of the database structure | ++--------+-----------------------------------------------------------------------+ +| 5 | Maximum volume overlap of the two structures | ++--------+-----------------------------------------------------------------------+ +| 6 | Overlap between pharmacophore and exclusion spheres in the reference | ++--------+-----------------------------------------------------------------------+ +| 7 | Corrected volume overlap between database pharmacophore and reference | ++--------+-----------------------------------------------------------------------+ +| 8 | Number of pharmacophore points in the processed pharmacophore | ++--------+-----------------------------------------------------------------------+ +| 9 | TANIMOTO score | ++--------+-----------------------------------------------------------------------+ +| 10 | TVERSKY_REF score | ++--------+-----------------------------------------------------------------------+ +| 11 | TVERSKY_DB score | ++--------+-----------------------------------------------------------------------+ + + +* Example:: + + - aligned Pharmacophores + + 3033 + HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0 + HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0 + HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827 + HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616 + HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767 + $$$$ + + +]]> + </help> + <citations> + <citation type="doi">10.1016/j.jmgm.2008.04.003</citation> + </citations> +</tool>
--- /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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<PUBCHEM_IUPAC_SYSTEMATIC_NAME> +methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxyphenyl)carbonyloxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +(1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylic acid methyl ester + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C33H40N2O9/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3/t18-,22+,24-,27-,28+,31+/m1/s1 + +> <PUBCHEM_IUPAC_INCHIKEY> +QEVHRUUCFGRFIF-MDEJGZGSSA-N + +> <PUBCHEM_XLOGP3_AA> +4 + +> <PUBCHEM_EXACT_MASS> +608.273381 + +> <PUBCHEM_MOLECULAR_FORMULA> +C33H40N2O9 + +> <PUBCHEM_MOLECULAR_WEIGHT> +608.6787 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +COC1C(CC2CN3CCC4=C(C3CC2C1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC + +> 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(1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_CAS_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-[oxo-(3,4,5-trimethoxyphenyl)methoxy]-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylic acid methyl ester + +> <PUBCHEM_IUPAC_NAME> +6-chloro-1,1-dioxo-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxybenzoyl)oxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +6-chloranyl-1,1-bis(oxidanylidene)-3,4-dihydro-2H-1$l^{6},2,4-benzothiadiazine-7-sulfonamide; methyl (1R,15S,17R,18R,19S,20S)-6,18-dimethoxy-17-(3,4,5-trimethoxyphenyl)carbonyloxy-1,3,11,12,14,15,16,17,18,19,20,21-dodecahydroyohimban-19-carboxylate + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> 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+InChI=1S/C29H26N4/c1-3-29(4-2)31-25-20-27-24(19-28(25)33(29)22-15-9-6-10-16-22)30-23-17-11-12-18-26(23)32(27)21-13-7-5-8-14-21/h5-20H,3-4H2,1-2H3 + +> <PUBCHEM_IUPAC_INCHIKEY> +UOOUPHIKFMZJEA-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3_AA> +6.5 + +> <PUBCHEM_EXACT_MASS> +430.215747 + +> <PUBCHEM_MOLECULAR_FORMULA> +C29H26N4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +430.54354 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)CC + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)CC + +> <PUBCHEM_CACTVS_TPSA> +31.2 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +430.215747 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +33 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> 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6.2781 -0.6891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3117 1.3932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.0781 0.3317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3107 -2.1506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9570 -2.6886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.0781 -0.7099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1605 1.8455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -3.1011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6464 -3.6392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0093 0.8887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0093 -1.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6678 -3.8454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.0207 2.3555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2887 2.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9530 0.3534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9530 -0.7316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.0091 3.3554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2772 3.3354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1374 3.8454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6112 0.5696 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9354 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0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7367 3.6392 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1302 4.4653 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 6 1 0 0 0 0 + 1 10 1 0 0 0 0 + 2 5 1 0 0 0 0 + 2 8 2 0 0 0 0 + 3 12 1 0 0 0 0 + 3 16 1 0 0 0 0 + 3 20 1 0 0 0 0 + 4 14 2 0 0 0 0 + 4 19 1 0 0 0 0 + 5 7 1 0 0 0 0 + 5 9 1 0 0 0 0 + 6 8 1 0 0 0 0 + 6 11 2 0 0 0 0 + 7 15 1 0 0 0 0 + 7 33 1 0 0 0 0 + 7 34 1 0 0 0 0 + 8 13 1 0 0 0 0 + 9 35 1 0 0 0 0 + 9 36 1 0 0 0 0 + 9 37 1 0 0 0 0 + 10 17 2 0 0 0 0 + 10 18 1 0 0 0 0 + 11 14 1 0 0 0 0 + 11 38 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 14 1 0 0 0 0 + 13 39 1 0 0 0 0 + 15 40 1 0 0 0 0 + 15 41 1 0 0 0 0 + 15 42 1 0 0 0 0 + 16 19 1 0 0 0 0 + 16 23 2 0 0 0 0 + 17 21 1 0 0 0 0 + 17 43 1 0 0 0 0 + 18 22 2 0 0 0 0 + 18 44 1 0 0 0 0 + 19 24 2 0 0 0 0 + 20 26 2 0 0 0 0 + 20 27 1 0 0 0 0 + 21 25 2 0 0 0 0 + 21 46 1 0 0 0 0 + 22 25 1 0 0 0 0 + 22 47 1 0 0 0 0 + 23 28 1 0 0 0 0 + 23 45 1 0 0 0 0 + 24 29 1 0 0 0 0 + 24 48 1 0 0 0 0 + 25 49 1 0 0 0 0 + 26 30 1 0 0 0 0 + 26 50 1 0 0 0 0 + 27 31 2 0 0 0 0 + 27 51 1 0 0 0 0 + 28 29 2 0 0 0 0 + 28 52 1 0 0 0 0 + 29 53 1 0 0 0 0 + 30 32 2 0 0 0 0 + 30 54 1 0 0 0 0 + 31 32 1 0 0 0 0 + 31 55 1 0 0 0 0 + 32 56 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +473726 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +855 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +0 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADceB7gAAAAAAAAAAAAAAAAAAAAQAAAAAwYMECAAAAAECBUAAAHAAAAAAACAiBEAAzwIMAAACgASRiRACCAAAhAgAIiAAQdJiIYGLAkZGUIAhggALIyCcQAAAAAAAAAAAAACAAAAAAAAAAQAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_CAS_NAME> +2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_NAME> +2-ethyl-2-methyl-1,5-diphenylimidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-ethyl-2-methyl-1,5-diphenyl-imidazo[4,5-b]phenazine + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C28H24N4/c1-3-28(2)30-24-19-26-23(18-27(24)32(28)21-14-8-5-9-15-21)29-22-16-10-11-17-25(22)31(26)20-12-6-4-7-13-20/h4-19H,3H2,1-2H3 + +> <PUBCHEM_IUPAC_INCHIKEY> +YQCDIJPZZOKCLA-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3_AA> +6 + +> <PUBCHEM_EXACT_MASS> +416.200097 + +> <PUBCHEM_MOLECULAR_FORMULA> +C28H24N4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +416.51696 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C + +> <PUBCHEM_CACTVS_TPSA> +31.2 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +416.200097 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +32 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +1 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +10 17 8 +10 18 8 +11 14 8 +12 13 8 +12 14 8 +16 19 8 +16 23 8 +17 21 8 +18 22 8 +19 24 8 +20 26 8 +20 27 8 +21 25 8 +22 25 8 +23 28 8 +24 29 8 +26 30 8 +27 31 8 +28 29 8 +30 32 8 +31 32 8 +5 9 3 +6 11 8 +6 8 8 +8 13 8 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244.sdf Mon May 22 03:02:39 2017 -0400 @@ -0,0 +1,155 @@ +2244 + -OEChem-05151212332D + + 21 21 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +$$$$ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aliginit_scores.tabular.tabular Mon May 22 03:02:39 2017 -0400 @@ -0,0 +1,1 @@ +2244 89.8904 2244 89.8904 89.8904 0 89.8904 5 1 1 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/align-it_Search_on_CID2244.phar Mon May 22 03:02:39 2017 -0400 @@ -0,0 +1,7 @@ +NAME +HYBL 5.63852 -1.334 0 0.7 0 -1.77636e-15 -2.22045e-16 0 +HYBH 6.3301 1.44 0 1 1 7.19612 1.94001 0 +HACC 3.732 -0.06 0 1 1 3.7319 0.94 0 +HACC 4.5981 1.44 0 1 1 3.73208 1.94001 0 +HACC 2.866 -1.56 0 1 1 2.866 -2.56 0 +$$$$
--- /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 @@ -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 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignit_Create_Phar_DB_6mol.phar Mon May 22 03:02:39 2017 -0400 @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignit_on_CID2244.phar Mon May 22 03:02:39 2017 -0400 @@ -0,0 +1,7 @@ +2244 +HYBL 5.63852 -1.334 0 0.7 0 0 0 0 +HYBH 6.3301 1.44 0 1 1 7.19612 1.94001 0 +HACC 3.732 -0.06 0 1 1 3.7319 0.94 0 +HACC 4.5981 1.44 0 1 1 3.73208 1.94001 0 +HACC 2.866 -1.56 0 1 1 2.866 -2.56 0 +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.phar Mon May 22 03:02:39 2017 -0400 @@ -0,0 +1,84 @@ +3639 +HYBL 5.135 0.2327 0 0.7 0 0 0 0 +HDON 7.801 -0.2881 0 1 1 8.66511 -0.791402 0 +HDON 6.895 1.2674 0 1 1 6.88356 2.26733 0 +HDON 2.5369 -1.2673 0 1 1 1.67086 -1.76727 0 +HACC 7.3849 -1.6737 0 1 1 7.87483 -2.54546 0 +HACC 6.385 -1.6622 0 1 1 5.87501 -2.52238 0 +HACC 3.903 -1.6333 0 1 1 4.40301 -2.49932 0 +HACC 2.903 0.0987 0 1 1 2.40299 0.964719 0 +$$$$ +3440 +HYBL 2.76694 -3.69567 0 0.7 0 0 0 0 +HYBL 3.73203 0.8644 0 0.7 0 0 0 0 +HYBH 6.3301 0.3644 0 1 1 7.19612 0.864411 0 +HDON 3.732 -1.1356 0 1 1 4.59802 -1.63561 0 +HDON 3.732 3.8644 0 1 1 3.732 4.8644 0 +HACC 3.675 -3.2234 0 1 1 4.62607 -2.91443 0 +HACC 4.732 2.8644 0 1 1 5.732 2.8644 0 +HACC 2.732 2.8644 0 1 1 1.732 2.8644 0 +HACC 5.4641 -1.1356 0 1 1 5.4641 -2.1356 0 +$$$$ +5770 +HYBL 6.16242 1.84504 0 0.7 0 0 0 0 +HYBL 4.62364 2.39911 0 0.7 0 0 0 0 +HYBL 14.9777 -0.177867 0 0.7 0 0 0 0 +HDON 6.1621 0.9988 0 1 1 6.1603 -0.00119838 0 +HACC 10.954 -2.0697 0 1 1 10.282 -2.81028 0 +HACC 12.3536 -0.5153 0 1 1 12.6664 -1.46512 0 +HACC 9.2094 -2.5737 0 1 1 10.1851 -2.79299 0 +HACC 7.9357 -1.3999 0 1 1 6.96002 -1.1807 0 +HACC 12.7071 1.1803 0 1 1 12.3944 2.13016 0 +HACC 2.6726 1.9031 0 1 1 2.36798 0.950627 0 +HACC 16.3102 1.3136 0 1 1 17.2892 1.10959 0 +HACC 15.6031 -2.0776 0 1 1 16.582 -2.28179 0 +HACC 16.9356 -0.5862 0 1 1 17.2483 -1.53604 0 +HACC 8.6152 2.1163 0 1 1 7.62744 1.96034 0 +HYBL 7.40226 2.93747 0 0.7 0 0 0 0 +$$$$ +24847843 +HYBL 4.6212 11.4143 0 0.7 0 0 0 0 +HYBL 8.19057 2.12 0 0.7 0 0 0 0 +HYBL 3.08244 11.9684 0 0.7 0 0 0 0 +HYBL 13.4365 9.39135 0 0.7 0 0 0 0 +HDON 4.6209 10.5681 0 1 1 4.6191 9.5681 0 +HDON 10.8566 1.5992 0 1 1 11.7207 1.09594 0 +HDON 9.9505 3.1547 0 1 1 9.93887 4.15463 0 +HDON 5.5925 0.62 0 1 1 4.72648 0.119989 0 +HACC 9.4128 7.4995 0 1 1 8.74088 6.75888 0 +HACC 10.8123 9.0539 0 1 1 11.1249 8.10401 0 +HACC 7.6682 6.9956 0 1 1 8.64388 6.7764 0 +HACC 6.3945 8.1694 0 1 1 5.41882 8.3886 0 +HACC 11.1659 10.7495 0 1 1 10.8532 11.6994 0 +HACC 1.1314 11.4723 0 1 1 0.826806 10.5198 0 +HACC 14.769 10.8828 0 1 1 15.7479 10.6786 0 +HACC 14.0618 7.4917 0 1 1 15.0408 7.28767 0 +HACC 15.3944 8.9831 0 1 1 15.7072 8.03328 0 +HACC 10.4405 0.2136 0 1 1 10.9305 -0.658117 0 +HACC 9.4405 0.2252 0 1 1 8.93047 -0.634955 0 +HACC 6.9585 0.254 0 1 1 7.45851 -0.612019 0 +HACC 5.9585 1.986 0 1 1 5.45849 2.85202 0 +HACC 7.0739 11.6855 0 1 1 6.08703 11.524 0 +HYBL 5.86105 12.5068 0 0.7 0 0 0 0 +$$$$ +473727 +HYBL 6.1184 -0.1891 0 0.7 0 0 0 0 +HYBL 7.8824 -0.189083 0 0.7 0 0 0 0 +HYBL 9.98896 -0.303677 0 0.7 0 0 0 0 +HYBL 3.64759 -3.15249 0 0.7 0 0 0 0 +HYBL 7.87839 3.11341 0 0.7 0 0 0 0 +HACC 4.3062 0.6156 0 1 1 3.99553 1.56612 0 +HACC 7.8784 -1.2237 0 1 1 7.86695 -2.22363 0 +HYBL 3.0181 1.3932 0 0.7 0 0 0 0 +HYBL 2 -0.3701 0 0.7 0 0 0 0 +$$$$ +473726 +HYBL 5.41207 -0.1891 0 0.7 0 0 0 0 +HYBL 7.17607 -0.189083 0 0.7 0 0 0 0 +HYBL 9.28261 -0.303677 0 0.7 0 0 0 0 +HYBL 2.92103 -3.14557 0 0.7 0 0 0 0 +HYBL 7.17208 3.11341 0 0.7 0 0 0 0 +HACC 3.5998 0.6156 0 1 1 3.28913 1.56612 0 +HACC 7.172 -1.2237 0 1 1 7.16036 -2.22363 0 +HYBL 2.3117 1.3932 0 0.7 0 0 0 0 +$$$$