update version strings from v0.4.0 to v0.5.0

README.md

@@ -1,7 +1,7 @@
 # Meeko: preparation of small molecules for AutoDock
 
 [![API stability](https://img.shields.io/badge/stable%20API-no-orange)](https://shields.io/)
-[![PyPI version fury.io](https://img.shields.io/badge/version-0.4.0-green.svg)](https://pypi.python.org/pypi/ansicolortags/)
+[![PyPI version fury.io](https://img.shields.io/badge/version-0.5.0-green.svg)](https://pypi.python.org/pypi/ansicolortags/)
 
 Meeko reads an RDKit molecule object and writes a PDBQT string (or file)
 for [AutoDock-Vina](https://github.com/ccsb-scripps/AutoDock-Vina)
@@ -30,7 +30,7 @@ and RDKit issues
 [917](https://github.com/rdkit/rdkit/issues/917).
 
 
-## Recent changes
+## API changes in v0.5
 
 Class `MoleculePreparation` no longer has method `write_pdbqt_string()`.
 Instead, `MoleculePreparation.prepare()` returns a list of `MoleculeSetup` objects
@@ -299,8 +299,11 @@ Reactive parameters can also be modified:
                         r_eq scaling for 1-4 interaction across reactive atoms
 ```
 
-We can't handle heteroatoms for the moment. Nor nucleic acids.
-phosphorilation, and a mechanism to support heteroatoms.
+Receptor preparation can't handle heteroatoms for the moment.
+Also nucleic acids, ions, and post-translational modifications (e.g.
+phosphorilation) are not supported. Only the 20 standard amino acids
+can be parsed, and it is required to have Amber atom names and
+hydrogens. No atoms can be missing.
 
 ### 3. Run autogrid
 

meeko/__init__.py

@@ -4,7 +4,7 @@
 # Meeko
 #
 
-__version__ = "0.4.0"
+__version__ = "0.5.0"
 
 try:
     import openbabel

setup.py

@@ -21,7 +21,7 @@ def find_files(directory):
 
 setup(
     name="meeko",
-    version='0.4.0',
+    version='0.5.0',
     author="Forli Lab",
     author_email="[email protected]",
     url="https://github.com/ccsb-scripps/meeko",