Mercurial > repos > bgruening > openbabel
changeset 16:3d3e7c1d0f49
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Fri, 19 Jul 2013 16:27:52 +0200 |
| parents | ec87a42dccec |
| children | 8cf36be96f1b |
| files | convert/ob_convert.xml filter/multi_obgrep.xml filter/ob_filter.xml filter/ob_grep.xml filter/ob_remDuplicates.xml filter/ob_remIons.xml filter/ob_remSmall.xml force_pre-commit_hook_temp_file modify/change_title_to_metadata_value.xml modify/ob_addh.xml modify/ob_genProp.xml modify/remove_protonation_state.xml search/ob_spectrophore_search.xml subsearch/subsearch.xml visualisation/ob_depiction_svg.xml |
| diffstat | 14 files changed, 390 insertions(+), 125 deletions(-) [+] |
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--- a/convert/ob_convert.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/convert/ob_convert.xml Fri Jul 19 16:27:52 2013 +0200 @@ -425,18 +425,33 @@ </outputs> <help> -**What it does** +.. class:: infomark + +**What this tool does** + +The compound converter joins several `Open Babel command prompt converters`_ in an easy to use tool. It converts various chemistry and moleculare modeling data files. The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state & pH) others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI). -Interconvert between many file formats used in molecular modeling and computational chemistry and related areas. A few output filetypes provides additional parameters. -If you are missing some options please contact your administrator or the ChemicalToolBoX team. +----- + +.. class:: infomark +**Output** + +Can be specified manually. -**References** +----- + +.. class:: infomark + +**Cite** -N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_ -The Open Babel Package http://openbabel.sourceforge.net/ +N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ + +.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 -.. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33 +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page </help>
--- a/filter/multi_obgrep.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/filter/multi_obgrep.xml Fri Jul 19 16:27:52 2013 +0200 @@ -36,21 +36,49 @@ </tests> <help> +.. class:: infomark -**What it does** +**What this tool does** -Providing a query file with SMARTS pattern in each line. These tool will run obgreg_ in parallel and merges the results. +Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files. It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_. - -.. _obgrep: http://openbabel.org/wiki/Obgrep +.. _Obgrep: http://openbabel.org/wiki/Obgrep .. _here: http://openbabel.org/wiki/SMARTS ----- -**Example** +.. class:: infomark + +**Input** + +| - `SD-Format`_ +| - `SMILES Format`_ + +.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification + +----- + +.. class:: infomark + +**Output** +Same as input format. +----- + +.. class:: infomark + +**Cite** + +N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ + +.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 + +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page </help> </tool>
--- a/filter/ob_filter.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/filter/ob_filter.xml Fri Jul 19 16:27:52 2013 +0200 @@ -138,25 +138,30 @@ <help> -**What does this tool do?** +.. class:: infomark + +**What this tool does** + +Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. + +----- - This tool filters a library of compounds provided by the user, based on a set of physico-chemical user-defined parameters. Multiple parameters can be selected for more specific queries. +.. class:: warningmark + +**Hint** + +| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file. +| +| For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value). +| +| Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds). ----- .. class:: infomark -**Tip:** If your input file is in SDF format you can use the 'Compute physico-chemical properties' tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but its bigger than a SMILES file. - -**Tip:** for exact matchings please use the target value for both the minimum and maximum parameters (e.g. a selection of EXACTLY 4 rotatable bonds can be performed by selecting 4 minimum and 4 maximum as values for the property). - -**Tip:** selecting multiple times the same property with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds). +**Definition of the pre-defined filtering rules** ------ - -.. class:: infomark - -**Definition of the pre-defined filtering rules:** **# Lipinski's Rule of Five:** =< 5 Hydrogen-bond donor groups @@ -195,15 +200,41 @@ .. class:: infomark -**Output:** the output formats included in this implementation are: +**Input** - # sdf formatted coordinates of the molecules, with selected properties stored as meta-data for each compound. +| - `SD-Format`_ +| - `SMILES Format`_ - # SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound. +.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification ----- -**This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5. +.. class:: infomark + +**Output** + +| SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound. +| +| SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound. + +----- + +.. class:: infomark + +**Cite** + +N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ + +.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://journal.chemistrycentral.com/content/2/1/5 + +N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ + +.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 + +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page </help> </tool>
--- a/filter/ob_grep.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/filter/ob_grep.xml Fri Jul 19 16:27:52 2013 +0200 @@ -48,28 +48,51 @@ </test> </tests> <help> -.. class:: warningmark + +.. class:: infomark -**What it does** +**What this tool does** -The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files. +Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files. It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_. -.. _obgrep: http://openbabel.org/wiki/Obgrep +.. _Obgrep: http://openbabel.org/wiki/Obgrep .. _here: http://openbabel.org/wiki/SMARTS ----- -**Output format** +.. class:: infomark + +**Input** + +| - `SD-Format`_ +| - `SMILES Format`_ +.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification -**References** +----- + +.. class:: infomark + +**Output** -N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_ -The Open Babel Package http://openbabel.sourceforge.net/ +Same as input format. + +----- + +.. class:: infomark + +**Cite** -.. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33 +N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ + +.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 + +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page </help> </tool>
--- a/filter/ob_remDuplicates.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/filter/ob_remDuplicates.xml Fri Jul 19 16:27:52 2013 +0200 @@ -36,25 +36,51 @@ .. class:: infomark -**What does this tool do?** +**What this tool does** - This tool filters a library of compounds and removes duplicated molecules. +Filters a library of compounds and removes duplicated molecules. ----- .. class:: warningmark -**Tip:** comparison based on Canonical SMILES without stereochemistry may be useful in cases where this information is not crucial for library preparation. Several VS tools will automatically generate stereoisomeric forms. +**Hint** + +Comparison based on Canonical SMILES without stereochemistry may be useful in cases where this information is not crucial for library preparation. Several VS tools will automatically generate stereoisomeric forms. + +----- + +.. class:: infomark + +**Input** + +| - `InChI`_ +| - `SMILES Format`_ + +.. _InChI: http://www.iupac.org/home/publications/e-resources/inchi.html +.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification ----- .. class:: infomark -**Output format:** is the same as the input file format. +**Output** + +Same as input format. ----- -**This tool uses OpenBabel:** The Open Babel Package, version 2.3.0 http://openbabel.sourceforge.net/ +.. class:: infomark + +**Cite** + +N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ + +.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 + +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page </help> </tool>
--- a/filter/ob_remIons.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/filter/ob_remIons.xml Fri Jul 19 16:27:52 2013 +0200 @@ -26,21 +26,37 @@ .. class:: infomark -**What does this tool do?** +**What this tool does** + +Parses a multiple molecules file and deletes any present counterions or fragments. + +----- - This tool parses a multiple molecules file and deletes any counter ion or fragment present in the file. +.. class:: warningmark + +**Hint** + +| Only the **largest fragment** on every molecule is extracted. +| +| Only molecules with more than 5 heavy atoms are parsed. ----- .. class:: infomark - ... Only the **largest fragment** on every molecule is extracted. +**Cite** - ... Only molecules with more than 5 heavy atoms are parsed. +N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ + +.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://journal.chemistrycentral.com/content/2/1/5 ------ +N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ + +.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 -**This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5. +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page </help> </tool>
--- a/filter/ob_remSmall.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/filter/ob_remSmall.xml Fri Jul 19 16:27:52 2013 +0200 @@ -32,25 +32,39 @@ .. class:: infomark -**What does this tool do?** +**What this tool does** - This tool filters a library of compounds and removes small molecules. +Filters a library of compounds and removes small molecules below a predefined input number of atoms. ----- .. class:: warningmark -**Tip:** some libraries may contain molecules without 1D/3D descriptor. These molecules may provoke the crashing of any other tool. As a general rule, the user is strongly adviced to run this tool before proceeding to any further step. +**Hint** + +Some libraries may contain molecules without a 1D/3D descriptor. These molecules may provoke crashes of any other tool. It is strongly adviced to run this tool before proceeding to any further steps. ----- .. class:: infomark -**Output format:** is the same as the input file format. +**Output** + +Same as input format. ----- -**This tool uses OpenBabel:** The Open Babel Package, version 2.3.0 http://openbabel.sourceforge.net/ +.. class:: infomark + +**Cite** + +N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ + +.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 + +`Open Babel`_ + +.. _`Open Babel`: http://openbabel.org/wiki/Main_Page </help> </tool>
--- a/modify/change_title_to_metadata_value.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/modify/change_title_to_metadata_value.xml Fri Jul 19 16:27:52 2013 +0200 @@ -28,28 +28,37 @@ .. class:: infomark -**Hint** +**What this tool does** - To convert the output, use the pencil icon next to the history entry. +Changes the title of a molecule file to a metadata value of a given ID in the same molecule file. + +----- ------- +.. class:: infomark + +**Input** -**What it does** +`SD-file`_ with metadata including the given ID. -Change the title from a molecule file to metadata value of a given-id of the same molecule file. +.. _SD-file: http://en.wikipedia.org/wiki/Chemical_table_file ----- -**Input format** +.. class:: infomark -SDF with metadata including the given key. - -**Output format** +**Output** Same as input with changed title tag. -**References** +----- + +.. class:: infomark +**Cite** + +`Open Babel`_ + +.. _Open Babel: http://openbabel.org/wiki/Main_Page </help> </tool>
--- a/modify/ob_addh.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/modify/ob_addh.xml Fri Jul 19 16:27:52 2013 +0200 @@ -32,31 +32,54 @@ .. class:: infomark -**What does this tool do?** +**What this tool does** + +Parses a molecular file and adds hydrogen atoms at a user-defined pH value. - This tool parses a molecular file and adds hydrogen atoms at a certain pH value. +* Protocol:: + + 1. The hydrogen atoms included in the input molecule are deleted. + 2. Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly. ----- .. class:: infomark -**Protocol:** +**Input** - **1.** The hydrogen atoms included in the input molecule are deleted. +3D format files are required, e.g. SDF_ + +.. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file - **2.** Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly. +----- + +.. class:: warningmark - **Hint:** to avoid possible crashes, only molecules with >5 heavy atoms are parsed. +**Hint** + +To avoid possible crashes, only molecules with more than five heavy atoms are parsed. ----- .. class:: infomark - **Output:** the output format is the same as the input format. 3D format files are required for this tool. +**Output** + +Same output format as the input format. ----- -**This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5. +.. class:: infomark + +**Cite** + +`Open Babel`_ + +.. _Open Babel: http://openbabel.org/wiki/Main_Page + +N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ + +.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf </help> </tool>
--- a/modify/ob_genProp.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/modify/ob_genProp.xml Fri Jul 19 16:27:52 2013 +0200 @@ -54,59 +54,82 @@ .. class:: infomark -**What does this tool do?** +**What this tool does** - This tool computes several physico-chemical properties for a set of molecules. +Computes several physico-chemical properties for a set of molecules. + +The following physico-chemical properties and descriptors are computed for each molecule: ------ + - number of hydrogen-bond donor and acceptor groups + + - number of rotatable bonds -.. class:: warningmark + - logP + + - number of rings -**Tip:** the generation of Spectrophores(TM) requires the previous addition of explicit hydrogen atoms and the proper definition of 3D coordinates. The user is directed towards the corresponding tools if accurate Spectrophores(TM) descriptors are required. + - number of heavy atoms + + - molecular weight ------ + - total Polar Surface Area + + - molecular refractivity -.. class:: infomark + - Canonical SMILES + + - InChI string -**Input:** molecular file in sdf or mol2 format files. The input file may contain multiple molecules. 3D coordinates of the files have to be provided. + - InChI-Key -**Output:** this program generates an sdf file containing several computed physico-chemical properties stored as meta-data, or a tabular formatted file with the meta-data stored in columns. + - Spectrophores(TM) ----- .. class:: infomark -The following **physico-chemical properties and descriptors** are computed for each molecule: - - # number of hydrogen-bond donor and acceptor groups - - # number of rotatable bonds +**Input** - # logP +- SDF_ +- MOL2_ - # number of rings - - # number of heavy atoms +.. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file +.. _MOL2: http://www.tripos.com/index.php?family=modules,SimplePage,Mol2_File_Format2009 - # molecular weight +3D coordinates of the molecules have to be provided. - # total Polar Surface Area - - # molecular refractivity +----- - # Canonical SMILES - - # InChI string +.. class:: warningmark - # InChI-Key - - # Spectrophores(TM) +**Hint** the generation of Spectrophores(TM) requires the previous addition of explicit hydrogen atoms and the proper definition of 3D coordinates. The user is directed towards the corresponding tools if accurate Spectrophores(TM) descriptors are required. ----- -**This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5. +.. class:: infomark + +**Output** + +Either a SD-file containing several computed physico-chemical properties stored as metadata or a tabular file with the metadata stored in columns. + +----- + +.. class:: infomark + +**Cite** -**Spectrophores(TM)** is a registered tool implemented in the open-source OpenBabel. Copyright (C) 2005-2010 by Silicos NV. +N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ + +Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel. + +.. |Spectrophores (TM)| unicode:: Spectrophores U+2122 + +`Open Babel`_ + +.. _Open Babel: http://openbabel.org/wiki/Main_Page +.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf +.. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html + </help> </tool>
--- a/modify/remove_protonation_state.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/modify/remove_protonation_state.xml Fri Jul 19 16:27:52 2013 +0200 @@ -23,11 +23,21 @@ </tests> <help> +.. class:: infomark -**What it does** -Remove protonation state of every atom. +**What this tool does** + +Removes the protonation state of every atom. ----- +.. class:: infomark + +**Cite** + +`Open Babel`_ + +.. _Open Babel: http://openbabel.org/wiki/Main_Page + </help> </tool>
--- a/search/ob_spectrophore_search.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/search/ob_spectrophore_search.xml Fri Jul 19 16:27:52 2013 +0200 @@ -33,40 +33,56 @@ **What does this tool do?** - This tool computes the Euclidean distance between the Spectrophores(TM) descriptors of the target to each molecule stored in the library. +This tool computes the Euclidean distance between the Spectrophores(TM) descriptors of the target to each molecule stored in the library. + +|Spectrophores (TM)| search + |Spectrophores (TM)| is a screening technology by Silicos_ which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation is independent of the position and orientation of a molecule and allows an easy comparison of |Spectrophores (TM)| of different molecules. + + Molecules with similar three-dimensional properties and shape, and therefore also similar biological activities, always have similar |Spectrophores (TM)|. As a result this technique is a very powerful tool to investigate the similarity of molecules and can be applied as a screening tool for molecular databases, virtual screening, and database characterisations. + +*Advantages:* + +- |Spectrophores (TM)| can realistically compute ligand-protein interactions based on aforementioned molecular descriptors +- |Spectrophores (TM)| can be applied in both a ligand- or target-based setting +- |Spectrophores (TM)| can distinguish, if needed, between the different enantiomers of stereo-selective compounds +- |Spectrophores (TM)| can be computed fast + +.. |Spectrophores (TM)| unicode:: Spectrophores U+2122 ----- .. class:: warningmark -**Tip:** this tool is useful to select compounds with similar chemical features to a target, but accounting for the discovery of diverse scaffolds. This is in contrast to the results expected in a similarity search based on atom connectivity. - -**Hint:** the target molecule MUST BE an sdf formatted file with the Spectrophores(TM) descriptors stored as meta-data. Such file can be generated using the "Compute physico-chemical properties" tool. - -**Hint:** the library of compounds is a tabular formatted file with 1 line / compound. One column contains the Spectrophores(TM) descriptors. +**Hint** this tool is useful to select compounds with similar chemical features to a target, but accounting for the discovery of diverse scaffolds. This is in contrast to the results expected in a similarity search based on atom connectivity. ----- .. class:: infomark -**Spectrophores(TM)** are Silicos' screening technology which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation of Spectrophores(TM) is independent of the position and orientation of a molecule and this allows to easily compare Spectrophores(TM) of different molecules. +**Input** -Molecules with similar three-dimensional properties and shape, and therefore also similar biological activities, always have similar Spectrophores(TM), and as a result this technique is very powerful as a tool to investigate the similarity of molecules and can be applied as a screening tool for molecular databases, virtual screening, and databse characterisations. +The target molecule must be a SD formatted file with the |Spectrophores (TM)| descriptors stored as metadata. Such files can be generated using the *Compute physico-chemical properties* tool. -**Advantages:** +----- - * Spectrophores(TM) can realistically compute ligand-protein interactions based on aforementioned molecular descriptors. - * Spectrophores(TM) can be applied in both a ligand- or target-based setting. - * Spectrophores(TM) can distinguish, if needed, between the different enantiomers of stereo-selective compounds. - * Spectrophores(TM) can be computed fast. +.. class:: infomark -Information extracted from the Silico's website: http://www.silicos.be/technologies/spectrophore +**Output** + +The library of compounds is a tabular file with one line per compound. One column contains the |Spectrophores (TM)| descriptors. ----- -**This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5. +.. class:: infomark + +**Cite** -**Spectrophores(TM)** is a registered tool implemented in the open-source OpenBabel. Copyright (C) 2005-2011 by Silicos NV. +N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ + +Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel. + +.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf +.. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html </help> </tool>
--- a/subsearch/subsearch.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/subsearch/subsearch.xml Fri Jul 19 16:27:52 2013 +0200 @@ -43,16 +43,31 @@ </tests> <help> +.. class:: infomark -**What it does** +**What this tool does** -Substructure search in a Open Babel Fastsearch Index. You can search with SMILES or SMARTS pattern, SD- and InChI files will be converted to SMILES. +Substructure search in based on Open Babel FastSearch_ Index. It uses molecular fingerprints to prepare and search an index of a multi-molecule datafile. + +.. _FastSearch: http://openbabel.org/wiki/FastSearch ----- -**Example** +.. class:: infomark + +**Input** + +SMILES or SMARTS patterns are possible. SD- and InChI files are converted to SMILES. + +----- +.. class:: infomark +**Cite** + +`Open Babel`_ + +.. _Open Babel: http://openbabel.org/wiki/Main_Page </help> </tool>
--- a/visualisation/ob_depiction_svg.xml Sat Jun 01 20:02:50 2013 +0200 +++ b/visualisation/ob_depiction_svg.xml Fri Jul 19 16:27:52 2013 +0200 @@ -96,16 +96,32 @@ </tests> <help> -**What it does** +.. class:: infomark + +**What this tool does** + +Creates an .svg or .png image of a small set of molecules (few hundreds). Based on Open Babel PNG_/SVG_ 2D depiction. -Creates a SVG image from a small library of molecules. +.. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html +.. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html + +----- + +.. class:: warningmark + +**Hint** + +Use only libraries with at most a few hundred molecules. ----- .. class:: infomark -Please use only libraries with at most a few hundrets of molecules. +**Cite** +`Open Babel`_ + +.. _Open Babel: http://openbabel.org/wiki/Main_Page </help> </tool>