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===<center>Welcome to Chemistry Toolkit Rosetta Wiki</center>===
 
===<center>Welcome to Chemistry Toolkit Rosetta Wiki</center>===
 
The Chemistry Toolkit Rosetta is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks. The main focus is on chemical informatics, with toolkits that handle molecular structures, depiction, databases, property analysis, nomenclature, and the like. This includes 3D structure visualization especially as applied to docking and small molecule conformation generation, but the visualization should support bond types. In the future we may add other chemistry tasks, like MMFF energy evaluation, molecular dynamics, spectra analysis, x-ray crystallography, quantum mechanics and more, but don't hold your breath unless you want to help define and evaluate the tasks!
 
The Chemistry Toolkit Rosetta is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks. The main focus is on chemical informatics, with toolkits that handle molecular structures, depiction, databases, property analysis, nomenclature, and the like. This includes 3D structure visualization especially as applied to docking and small molecule conformation generation, but the visualization should support bond types. In the future we may add other chemistry tasks, like MMFF energy evaluation, molecular dynamics, spectra analysis, x-ray crystallography, quantum mechanics and more, but don't hold your breath unless you want to help define and evaluate the tasks!
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==What's it all about?==
 
==What's it all about?==
   
Chemical informatics toolkits share many core functions, but often use different approaches. The goal of this project is to help people be able to compare and contrast toolkit functionality. You might know how to use RDKit and what to see how CDK does something, or you have the choice between OpenBabel or OEChem and you want to see which is easier to use or better fits your needs. Perhaps you are a Pipeline Pilot user and want to show how to implement something graphically.
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Chemical informatics toolkits share many core functions, but often use different approaches. The goal of this project is to help people be able to compare and contrast toolkit functionality. You might know how to use RDKit and want to see how CDK does something, or you have the choice between OpenBabel or OEChem and you want to see which is easier to use or better fits your needs. Perhaps you are a Pipeline Pilot user and want to show how to implement via a graphical workflow vs. using a text program.
   
 
You should feel free to contribute code solutions using any toolkit, or set of toolkits, which solves the problem. Please include comments if a given entry is designed for simplicity, performance, maintainability, or some other criteria.
 
You should feel free to contribute code solutions using any toolkit, or set of toolkits, which solves the problem. Please include comments if a given entry is designed for simplicity, performance, maintainability, or some other criteria.
   
This inspiration for this wiki comes from [http://rosettacode.org/ Rosetta Code] and [http://pleac.sourceforge.net/ PLEAC], and the term "Rosetta" in term comes from the [http://en.wikipedia.org/wiki/Rosetta_Stone Rosetta Stone].
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This is not meant as a cookbook site for any one toolkit. For example, a page on how to generate OpenBabel FP3 fingerprints isn't going to be that useful to users of other toolkits, or that fair of a comparison since it's not a widely used fingerprint and OpenBabel is the only one which has it as a built-in feature.
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This inspiration for this wiki comes from [http://rosettacode.org/ Rosetta Code] and [http://pleac.sourceforge.net/ PLEAC], and the term "Rosetta" in term comes from the [http://en.wikipedia.org/wiki/Rosetta_Stone Rosetta Stone]. Many of the initial examples and code are based on Noel O'Boyle's work, like where he shows [[http://www.redbrick.dcu.ie/~noel/parseSD.html different ways to manipulate SD files with Open Source tools]] and his [[http://code.google.com/p/cinfony/ Cinfony package]] which "presents a common API to ... OpenBabel, RDKit and the CDK."
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==The Code==
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* [http://ctr.wikia.com/wiki/Heavy_atom_counts_from_an_SD_file Read an SD file and list the heavy atom counts]
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* [http://ctr.wikia.com/wiki/Ring_counts_in_a_SMILES_file Read a SMILES file and list the number of rings]
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* [http://ctr.wikia.com/wiki/Convert_a_SMILES_string_to_canonical_SMILES Convert a SMILES string to canonical SMILES]
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* [http://ctr.wikia.com/wiki/Working_with_SD_tag_data Working with SD tag data]
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* [http://ctr.wikia.com/wiki/Detect_and_report_SMILES_and_SDF_parsing_errors Detect and report SMILES and SDF parsing errors]
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* [http://ctr.wikia.com/wiki/Report_how_many_SD_file_records_are_within_a_certain_molecular_weight_range Report how many SD file records are within a certain molecular weight range]
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* [http://ctr.wikia.com/wiki/Convert_SMILES_file_to_SD_file Convert SMILES file to SD file]
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* [http://ctr.wikia.com/wiki/Report_the_similarity_between_two_structures Report the similarity between two structures]
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* [http://ctr.wikia.com/wiki/Find_the_10_nearest_neighbors_in_a_data_set Find the 10 nearest neighbors in a data set]
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* [http://ctr.wikia.com/wiki/Depict_a_compound_as_an_image Depict a compound as an image]
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* [http://ctr.wikia.com/wiki/Highlight_a_substructure_in_the_depiction Highlight a substructure in the depiction]
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* [http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructure Align the depiction using a fixed substructure]
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* [http://ctr.wikia.com/wiki/Unique_SMARTS_matches_against_a_SMILES_string Unique SMARTS matches against a SMILES string]
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* [http://ctr.wikia.com/wiki/Calculate_TPSA Calculate TPSA]
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* [http://ctr.wikia.com/wiki/Find_the_graph_diameter Find the graph diameter]
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* [http://ctr.wikia.com/wiki/Break_rotatable_bonds_and_report_the_fragments Break rotatable bonds and report the fragments]
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* [http://ctr.wikia.com/wiki/Perform_a_substructure_search_on_SDF_file_and_report_the_number_of_false_positives Perform a substructure search on SDF file and report the number of false positives]
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* [http://ctr.wikia.com/wiki/Change_stereochemistry_of_certain_atoms_in_SMILES_file Change stereochemistry of certain atoms in SMILES file]
   
 
==Latest activity==
 
==Latest activity==

Latest revision as of 22:05, June 1, 2011

Welcome to Chemistry Toolkit Rosetta Wiki
Edit

The Chemistry Toolkit Rosetta is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks. The main focus is on chemical informatics, with toolkits that handle molecular structures, depiction, databases, property analysis, nomenclature, and the like. This includes 3D structure visualization especially as applied to docking and small molecule conformation generation, but the visualization should support bond types. In the future we may add other chemistry tasks, like MMFF energy evaluation, molecular dynamics, spectra analysis, x-ray crystallography, quantum mechanics and more, but don't hold your breath unless you want to help define and evaluate the tasks!

What's it all about?Edit

Chemical informatics toolkits share many core functions, but often use different approaches. The goal of this project is to help people be able to compare and contrast toolkit functionality. You might know how to use RDKit and want to see how CDK does something, or you have the choice between OpenBabel or OEChem and you want to see which is easier to use or better fits your needs. Perhaps you are a Pipeline Pilot user and want to show how to implement via a graphical workflow vs. using a text program.

You should feel free to contribute code solutions using any toolkit, or set of toolkits, which solves the problem. Please include comments if a given entry is designed for simplicity, performance, maintainability, or some other criteria.

This is not meant as a cookbook site for any one toolkit. For example, a page on how to generate OpenBabel FP3 fingerprints isn't going to be that useful to users of other toolkits, or that fair of a comparison since it's not a widely used fingerprint and OpenBabel is the only one which has it as a built-in feature.

This inspiration for this wiki comes from Rosetta Code and PLEAC, and the term "Rosetta" in term comes from the Rosetta Stone. Many of the initial examples and code are based on Noel O'Boyle's work, like where he shows [different ways to manipulate SD files with Open Source tools] and his [Cinfony package] which "presents a common API to ... OpenBabel, RDKit and the CDK."

The CodeEdit

Latest activityEdit

Community content is available under CC-BY-SA unless otherwise noted.