FANDOM


(Added a new category)
(Links to the code pages)
Line 12: Line 12:
   
 
==The Code==
 
==The Code==
  +
  +
* [[http://ctr.wikia.com/wiki/Read_an_SD_file_and_list_the_atom_counts Read an SD file and list the atom counts]]
  +
* [[http://ctr.wikia.com/wiki/Read_a_SMILES_file_and_list_the_number_of_cycles Read a SMILES file and list the number of cycles]]
  +
* [[http://ctr.wikia.com/wiki/Convert_a_SMILES_string_to_canonical_SMILES Convert a SMILES string to canonical SMILES]]
  +
* [[http://ctr.wikia.com/wiki/Add_SMILES_tag_to_SD_file_records Add SMILES tag to SD file records]]
  +
* [[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]]
  +
* [[http://ctr.wikia.com/wiki/Convert_SMILES_file_to_SD_file Convert SMILES file to SD file]]
  +
* [[http://ctr.wikia.com/wiki/Report_the_similarity_between_two_structures Report the similarity between two structures]]
  +
* [[http://ctr.wikia.com/wiki/Find_the_most_similar_compound_in_a_data_set Find the most similar compound in a data set]]
  +
* [[http://ctr.wikia.com/wiki/Find_the_10_nearest_neighbors_in_a_data_set Find the 10 nearest neighbors in a data set]]
  +
* [[http://ctr.wikia.com/wiki/Depict_a_compound_as_an_image Depict a compound as an image]]
  +
* [[http://ctr.wikia.com/wiki/Highlight_a_substructure_in_the_depiction Highlight a substructure in the depiction]]
  +
* [[http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructure Align the depiction using a fixed substructure]]
  +
* [[http://ctr.wikia.com/wiki/Unique_SMARTS_matches_against_a_SMILES_string Unique SMARTS matches against a SMILES string]]
  +
* [[http://ctr.wikia.com/wiki/Calculate_TPSA Calculate TPSA]]
  +
* [[http://ctr.wikia.com/wiki/Find_the_longest_linear_chain_of_carbon_atoms Find the longest linear chain of carbon atoms]]
  +
* [[http://ctr.wikia.com/wiki/Break_rotatable_bonds_and_report_the_fragments Break rotatable bonds and report the fragments]]
   
 
==Latest activity==
 
==Latest activity==

Revision as of 23:42, December 19, 2009

Welcome to Chemistry Toolkit Rosetta Wiki

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?

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.

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 Rosetta Code and PLEAC, and the term "Rosetta" in term comes from the Rosetta Stone.

The Code

Latest activity

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