From 0badd5b04b5f749f0941f83ce08cdbc206dcd665 Mon Sep 17 00:00:00 2001 From: diogom Date: Fri, 28 Jul 2023 16:42:08 -0700 Subject: [PATCH] update version strings from v0.4.0 to v0.5.0 --- README.md | 11 +++++++---- meeko/__init__.py | 2 +- setup.py | 2 +- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index dff9aa95..bbbb9de3 100644 --- a/README.md +++ b/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 diff --git a/meeko/__init__.py b/meeko/__init__.py index d97d5e03..abbec75c 100644 --- a/meeko/__init__.py +++ b/meeko/__init__.py @@ -4,7 +4,7 @@ # Meeko # -__version__ = "0.4.0" +__version__ = "0.5.0" try: import openbabel diff --git a/setup.py b/setup.py index 35ac525a..325f247d 100644 --- a/setup.py +++ b/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="forli@scripps.edu", url="https://github.com/ccsb-scripps/meeko",