Mercurial > repos > bgruening > silicos_it
changeset 20:9d1a5ff8c04f
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Mon, 22 Jul 2013 17:29:07 +0200 |
| parents | 588e3ff42c28 |
| children | c1e74b30da3f |
| files | align-it/align-it.xml align-it/align-it_create_db.xml qed/silicos_qed.xml repository_dependencies.xml shape-it/shape-it.xml strip-it/strip-it.xml tool_dependencies.xml |
| diffstat | 7 files changed, 245 insertions(+), 136 deletions(-) [+] |
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--- a/align-it/align-it.xml Sun Jun 02 19:54:27 2013 +0200 +++ b/align-it/align-it.xml Mon Jul 22 17:29:07 2013 +0200 @@ -1,7 +1,7 @@ <tool id="ctb_alignit" name="Pharmacophore Alignment" version="0.1"> <description>and Optimization (Align-it)</description> <requirements> - <requirement type="package" version="1.0.0">silicos_it</requirement> + <requirement type="package" version="1.0.1">silicos_it</requirement> <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command> @@ -113,29 +113,32 @@ </tests> <help> -**What it does** +.. class:: infomark + +**What this tool does** -Align-it_ is a tool to align molecules according their pharmacophores. +Align-it_ is a tool to align molecules according to their pharmacophores. A pharmacophore is an abstract concept based on the specific interactions -that have been observed in drug-receptor interactions: hydrogen bonding, +observed in drug-receptor interactions: hydrogen bonding, charge transfer, electrostatic and hydrophobic interactions. Molecular modeling and/or screening based on pharmacophore similarities -have proven to be an important and useful method in drug discovery. +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 consists of the generation of pharmacophores from molecules -(use the tool *Pharmacophore generation* if you want to store these for later use). -Second, pairs of **pharmacophores can be aligned** and the resulting -score is calculated from the volume overlap resulting from the alignments. - +The first functionality is the generation of pharmacophores from molecules +(use the tool **Pharmacophore generation** if you want to store these for further use). +Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting +score is calculated from the volume overlap resulting of the alignments. .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html ----- -**Example** +.. class:: infomark -* input:: +**Input** + +* Example:: - database @@ -173,7 +176,42 @@ - cutoff : 0.0 -* output:: +----- + +.. 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 @@ -185,25 +223,15 @@ HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767 $$$$ +----- -The format of this scores output file is as follows: +.. class:: infomark -====== ===================================================================== -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 -====== ===================================================================== +**Cite** +`Silicos-it`_ - align-it + +.. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html </help>
--- a/align-it/align-it_create_db.xml Sun Jun 02 19:54:27 2013 +0200 +++ b/align-it/align-it_create_db.xml Mon Jul 22 17:29:07 2013 +0200 @@ -28,30 +28,32 @@ </tests> <help> -**What it does** +.. class:: infomark + +**What this tool does** -Align-it_ is a tool to align molecules according their pharmacophores. +Align-it_ is a tool to align molecules according to their pharmacophores. A pharmacophore is an abstract concept based on the specific interactions -that have been observed in drug-receptor interactions: hydrogen bonding, +observed in drug-receptor interactions: hydrogen bonding, charge transfer, electrostatic and hydrophobic interactions. Molecular modeling and/or screening based on pharmacophore similarities -have proven to be an important and useful method in drug discovery. +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 consists of the **generation of pharmacophores from molecules** -(the function of this tool). Second, pairs of pharmacophores -can be aligned (use the tool *Pharmacophore Alignment*) and the resulting -score is calculated from the volume overlap resulting from the alignments. - +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 - ----- -**Example** +.. class:: infomark -* input:: +**Input** + +* Example:: - database @@ -89,7 +91,13 @@ - cutoff : 0.0 -* output:: +----- + +.. class:: infomark + +**Output** + +* Example:: - aligned Pharmacophores @@ -101,7 +109,15 @@ 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>
--- a/qed/silicos_qed.xml Sun Jun 02 19:54:27 2013 +0200 +++ b/qed/silicos_qed.xml Mon Jul 22 17:29:07 2013 +0200 @@ -2,7 +2,7 @@ <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="1.0.0">silicos_it</requirement> + <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> @@ -48,59 +48,74 @@ .. class:: infomark -**TIP:** If your data is not in SD- or SMILES format, use the pencil icon on your dataset to convert your data +**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` ). ----- -**Syntax** +.. 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 -The QED function comes in three flavors, each differing in the relative weight that is imposed on the underlying molecular descriptors (see [1]). -These three flavors correspond to the three different QED measures that were described in the original publication: +- 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** -- All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item. - -- **QEDw,max** using the set of weights that give maximal information content.: +| - `SD-Format`_ +| - `SMILES Format`_ -- **QEDw,mo** using the mean weights of the optimal 1,000 weight combinations that give the highest information content. - -- **QEDw,u** with all weights as unity, hence unweighted. - +.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification ----- -**Example** - -- Input file:: +.. class:: infomark - - SD-Format (http://en.wikipedia.org/wiki/Chemical_table_file) - - SMILES Format (http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification) - -- Result:: +**Output** - ====== ===== === === ====== ==== ==== ====== ===== ============== - 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 - ====== ===== === === ====== ==== ==== ====== ===== ============== - ++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ +| 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** -[1] Bickerton, G.R.; Paolini, G.V.; Besnard, J.; Muresan, S.; Hopkins, A.L. (2012) ‘Quantifying the chemical beauty of drugs’, Nature Chemistry, 4, 90-98 +Bickerton et al. - `Quantifying the chemical beauty of drugs`_ -http://dx.doi.org/10.1038/nchem.1243 +.. _Quantifying the chemical beauty of drugs: http://www.nature.com/nchem/journal/v4/n2/full/nchem.1243.html + </help> </tool>
--- a/repository_dependencies.xml Sun Jun 02 19:54:27 2013 +0200 +++ b/repository_dependencies.xml Mon Jul 22 17:29:07 2013 +0200 @@ -1,4 +1,4 @@ <?xml version='1.0' encoding='utf-8'?> <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository changeset_revision="a1474892287e" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="e6493849afd3" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </repositories> \ No newline at end of file
--- a/shape-it/shape-it.xml Sun Jun 02 19:54:27 2013 +0200 +++ b/shape-it/shape-it.xml Mon Jul 22 17:29:07 2013 +0200 @@ -1,7 +1,7 @@ <tool id="ctb_shapeit" name="Shape alignment" version="0.1"> <description>against a database of molecules (Shape-it)</description> <requirements> - <requirement type="package" version="1.0.0">silicos_it</requirement> + <requirement type="package" version="1.0.1">silicos_it</requirement> <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command > @@ -10,7 +10,9 @@ --dbase $database --reference $reference --addIterations $addIterations - --best $best + #if int($best) > 0: + --best $best + #end if --cutoff $cutoff #if $scores == 'yes': --scores $output_scores @@ -20,13 +22,13 @@ --out $output 2>&1 </command> <inputs> - <param name="reference" type="data" format='sdf,mol,mol2,smi' label="Refrence molecule" /> - <param name="database" type="data" format='sdf,mol,mol2' label="Database of Molecules (needs 3D coordinates)" /> - <param name="cutoff" type="float" value="0.0"> + <param name="reference" type="data" format='sdf,mol,mol2' label="Refrence molecule (with 3D coordinates)" /> + <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (with 3D coordinates)" /> + <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."> <validator type="in_range" min="0.0" /> </param> - <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure' /> - <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' /> + <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."/> + <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' help="0 means all molecules are reported"/> <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a Tab-delimited text file with the scores of molecules' checked="false" /> <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='The reference molecule is not written into the output files' checked="false" /> <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme"> @@ -53,31 +55,39 @@ </tests> <help> -**What it does** + +.. class:: infomark + +**What this tool does** Shape-it_ is a tool that aligns a reference molecule against a set of database molecules using the shape of the molecules as the align criterion. -It is based on the use of Gaussian volumes as descriptor for molecular -shape as it was introduced by `Grant and Pickup`_. +It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as it was introduced by Grant and Pickup. The program expects one reference molecule with its three-dimensional coordinates and one database files containing one or more molecules in three dimensions. The results are either the alignment of all database molecules and their respective scores or the N best -scoring molecules from the complete database. - +scoring molecules of the complete database. +.. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016 .. _Shape-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html -.. _`Grant and Pickup`: http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(19961115)17:14%3C1653::AID-JCC7%3E3.0.CO;2-K/abstract ----- -**Example** +.. class:: infomark + +**Input** + -* input:: +| - `formates recognized by OpenBabel`_ + +.. _formates recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats + +* Example:: - database - 27 28 0 0 0 0 0 0 0999 V2000 + 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 @@ -117,7 +127,7 @@ - reference - 30 31 0 0 0 0 0 0 0999 V2000 + 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 @@ -162,7 +172,13 @@ - cutoff : 0.0 -* output:: +----- + +.. class:: infomark + +**Output** + +* Example:: 27 28 0 0 0 0 0 0 0 0999 V2000 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 @@ -205,5 +221,16 @@ 6 8 2 0 0 0 0 ...... +----- + +.. class:: infomark + +**Cite** + +`Silicos-it`_ - shape-it + +.. _Silicos-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html + + </help> </tool>
--- a/strip-it/strip-it.xml Sun Jun 02 19:54:27 2013 +0200 +++ b/strip-it/strip-it.xml Mon Jul 22 17:29:07 2013 +0200 @@ -1,11 +1,12 @@ -<tool id="ctb_stripit" name="Strip-it" version="1.0.0"> +<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="1.0.0">silicos_it</requirement> + <requirement type="package" version="1.0.1">silicos_it</requirement> </requirements> <command> - strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog 2>&1 + 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" /> @@ -21,49 +22,71 @@ </tests> <help> -**What it does** + +.. class:: infomark -Strip-it is a program that extracts predefined scaffolds from organic -molecules +**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;1 - - Molecular frameworks and the reduced molecular frameworks as - described by Ansgar Schuffenhauer and coworkers;2 - - Scaffold topologies as described by Sara Pollock and coworkers.3 + - `molecular frameworks`_ as originally described by Bemis and + Murcko + - `molecular frameworks and the reduced molecular frameworks`_ as + described by Ansgar Schuffenhauer and coworkers + - `scaffold topologies`_ as described by Sara Pollock and coworkers - -http://silicos-it.com/software/strip-it/1.0.1/strip-it.html +.. _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 ----- -Example -------- +.. class:: infomark + +<<<<<<< HEAD +http://www.silicos-it.com/software/strip-it/1.0.2/strip-it.html +======= +**Input** -**input** +| - `SD-Format`_ +| - `SMILES Format`_ +| - `MOL2 Format`_ -- `SDF 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 +>>>>>>> 67ce87e8ccf30f81f72248a7fde0896c5e9ae953 + +----- + +.. class:: infomark -.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file -.. _SMILES FORMAT: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification -.. _MOL2 FORMAT: http://www.tripos.com/data/support/mol2.pdf - - -**output** +**Output** -TODO: ++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+ +| NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... | ++=============+================================+======================+========================+======================+=====+ +| 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 | ... | ++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+ +| ... | ... | ... | ... | ... | ... | ++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+ - ==== =========================== ==================== ==================== =================== ================== ========== ========== ========== - NAME MOLECULE RINGS_WITH_LINKERS_1 RINGS_WITH_LINKERS_2 MURCKO_1 MURCKO_2 OPREA_1 OPREA_2 OPREA_3 - ==== =========================== ==================== ==================== =================== ================== ========== ========== ========== - 3037 Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl c1ccc(cc1)Cc1ccccc1 c1ccc(cc1)Cc1ccccc1 C1CCC(CC1)CC1CCCCC1 C1CCC(CC1)C1CCCCC1 C1CC1C1CC1 C1CC1C1CC1 C1CC1C1CC1 - 3037 Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl c1ccc(cc1)Cc1ccccc1 c1ccc(cc1)Cc1ccccc1 C1CCC(CC1)CC1CCCCC1 C1CCC(CC1)C1CCCCC1 C1CC1C1CC1 C1CC1C1CC1 C1CC1C1CC1 - ==== =========================== ==================== ==================== =================== ================== ========== ========== ========== +----- + +.. class:: infomark + +**Cite** + +`Silicos-it`_ - strip-it + +.. _Silicos-it: http://silicos-it.com/software/strip-it/1.0.2/strip-it.html + </help> </tool>
--- a/tool_dependencies.xml Sun Jun 02 19:54:27 2013 +0200 +++ b/tool_dependencies.xml Mon Jul 22 17:29:07 2013 +0200 @@ -1,18 +1,18 @@ <?xml version='1.0' encoding='utf-8'?> <tool_dependency> <package name="numpy" version="1.7.1"> - <repository changeset_revision="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="62fda117ad4a" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="openbabel" version="2.3.2"> <repository changeset_revision="3a993ff17df5" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="rdkit" version="2012_12_1"> - <repository changeset_revision="5b30ea84ba25" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="2560d8a02782" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> - <package name="silicos_it" version="1.0.0"> + <package name="silicos_it" version="1.0.1"> <install version="1.0"> <actions> - <action type="download_by_url">http://www.silicos-it.com/_php/download.php?file=strip-it-1.0.1.tar.gz</action> + <action type="download_by_url">https://github.com/bgruening/silicos-it_store/blob/master/strip-it/strip-it-1.0.2.tar.gz</action> <!-- populate the environment variables from the dependend repos $OPENBABEL_INCLUDE_DIR and $OPENBABEL_LIB_DIR @@ -34,8 +34,8 @@ </action> <!-- compiling align-it --> - <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=align-it-1.0.3.tar.gz</action> - <action type="shell_command">tar xfvz download.php?file=align-it-1.0.3.tar.gz && + <action type="shell_command">wget https://github.com/bgruening/silicos-it_store/raw/master/align-it/align-it-1.0.3.tar.gz</action> + <action type="shell_command">tar xfvz align-it-1.0.3.tar.gz && cd align-it-1.0.3 && cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/align-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && make && @@ -45,8 +45,8 @@ </action> <!-- compiling shape-it --> - <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=shape-it-1.0.1.tar.gz</action> - <action type="shell_command">tar xfvz download.php?file=shape-it-1.0.1.tar.gz && + <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 &&