README.md in rubabel-0.4.1 vs README.md in rubabel-0.4.2

- old
+ new

@@ -2,10 +2,12 @@ Ruby interface to the OpenBabel ruby bindings (or the openbabel gem). The interface attempts to be a ruby-ish analogue of [pybel](http://openbabel.org/docs/current/UseTheLibrary/Python_PybelAPI.html). Works with ruby 1.9 and 2.0. +**NOTE: Lipid fragmentation code has been moved to the [msplinter](https://github.com/princelab/msplinter).** + ## Examples The [Chemistry Toolkit Rosetta Wiki](http://ctr.wikia.com/wiki/Chemistry_Toolkit_Rosetta_Wiki) has a lot of examples you can check out. ### Creating a molecule @@ -21,16 +23,17 @@ serine = Rubabel::Molecule.from_string("C(C(C(=O)O)N)O") # also any other format openbabel supports, for example inchi serine = Rubabel["InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)", :inchi] -# from the internet: -mol = Rubabel[some_molecule, Rubabel.format_from_mime(some_mime_type)] +# from an InChI Key or other id (such as LipidMaps ID) [requires internet] +serine = Rubabel["MTCFGRXMJLQNBG-REOHCLBHSA-N", :inchikey] Find out all the formats Rubabel supports (hash is format key pointing to the description): hash = Rubabel.in_formats hash = Rubabel.out_formats +hash = Rubabel.id_formats # molecule retrieved by web-lookup ``` #### From a file Reading multiple entries from a file: