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changeset 13:f34eb613e2ed

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Fri, 19 Jul 2013 16:28:38 +0200
parents 0ab075fb42f9
children 96d549a152c4
files force_pre-commit_hook_temp_file rdkit_descriptors.xml
diffstat 1 files changed, 108 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/rdkit_descriptors.xml	Fri May 31 22:32:52 2013 +0200
+++ b/rdkit_descriptors.xml	Fri Jul 19 16:28:38 2013 +0200
@@ -18,31 +18,125 @@
 
 .. 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** 
+
+| RDKit is an open source toolkit for cheminformatics and machine learning.
+| This implementation focuses on descriptor calculation, though, RDKit offers a vast number of other functions.
+| 
+| The table below shows a brief overview of the descriptors.
+| 
+
++-----------------------------------+------------+
+|    Descriptor/Descriptor Family   |  Language  | 
++===================================+============+ 
+| Gasteiger/Marsili Partial Charges |     C++    |
++-----------------------------------+------------+
+|            BalabanJ               |   Python   |
++-----------------------------------+------------+
+|             BertzCT               |   Python   |
++-----------------------------------+------------+
+|               Ipc                 |   Python   |
++-----------------------------------+------------+
+|          HallKierAlpha            |   Python   |
++-----------------------------------+------------+
+|         Kappa1 - Kappa3           |   Python   |
++-----------------------------------+------------+
+|            Chi0, Chi1             |   Python   |
++-----------------------------------+------------+
+|           Chi0n - Chi4n           |   Python   |
++-----------------------------------+------------+
+|           Chi0v - Chi4v           |   Python   |
++-----------------------------------+------------+
+|              MolLogP              |     C++    |
++-----------------------------------+------------+
+|               MolMR               |     C++    |
++-----------------------------------+------------+
+|               MolWt               |     C++    |
++-----------------------------------+------------+
+|           HeavyAtomCount          |   Python   |
++-----------------------------------+------------+
+|           HeavyAtomMolWt          |   Python   |
++-----------------------------------+------------+
+|             NHOHCount             |     C++    |
++-----------------------------------+------------+
+|              NOCount              |     C++    |
++-----------------------------------+------------+
+|            NumHAcceptors          |     C++    |
++-----------------------------------+------------+
+|             NumHDonors            |     C++    |
++-----------------------------------+------------+
+|            NumHeteroatoms         |     C++    |
++-----------------------------------+------------+
+|          NumRotatableBonds        |     C++    |
++-----------------------------------+------------+
+|         NumValenceElectrons       |   Python   |
++-----------------------------------+------------+
+|              RingCount            |     C++    |
++-----------------------------------+------------+
+|                 TPSA              |     C++    |
++-----------------------------------+------------+
+|              LabuteASA            |     C++    |
++-----------------------------------+------------+
+|       PEOE_VSA1 - PEOE_VSA14      | Python/C++ |
++-----------------------------------+------------+
+|         SMR_VSA1 - SMR_VSA10      | Python/C++ |
++-----------------------------------+------------+
+|      SlogP_VSA1 - SlogP_VSA12     | Python/C++ |
++-----------------------------------+------------+
+|     EState_VSA1 - EState_VSA11    |   Python   |
++-----------------------------------+------------+
+|     VSA_EState1 - VSA_EState10    |   Python   |
++-----------------------------------+------------+
+|           Topliss fragments       |   Python   |
++-----------------------------------+------------+
+
+| 
+| A full list of the descriptors can be obtained here_.
+
+.. _here: https://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit
 
 -----
 
-**Example**
-
-- Input file::
-
-    - SD-Format (http://en.wikipedia.org/wiki/Chemical_table_file)
-    - SMILES Format (http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification)
+.. class:: warningmark
 
-- Result::
-
+**HINT**
 
-http://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit
-http://rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html
-
+Use the **cut columns from a table** tool to select just the desired descriptors.
 
 -----
 
+.. class:: infomark
+
+**Input**
+
+| - `SD-Format`_
+| - `SMILES Format`_
+| - TDT_
+| - SLN
+| - `Corina MOL2`_
+
+.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+.. _TDT: https://earray.chem.agilent.com/earray/helppages/index.htm#tdt_format_files.htm
+.. _Corina MOL2: http://www.molecular-networks.com/products/corina
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+Tabularfile, where each descriptor (value) is shown in a seperate column.
+
+-----
+
+.. class:: informark
 
 **Cite**
 
-Greg Landrum
-[1] RDKit: Open-source cheminformatics; http://www.rdkit.org
+Greg Landrum - RDKit_: Open-source cheminformatics
+
+.. _RDKit: http://www.rdkit.org
 
 
     </help>