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: