From c0dec352c6e4477f9d58403b29ca521b0e6a31ab Mon Sep 17 00:00:00 2001
From: diogom <diogom@scripps.edu>
Date: Wed, 20 Oct 2021 14:16:26 -0700
Subject: [PATCH] minor changes to release v0.2

---
 README.md | 41 ++++++++++++++++++++++++++++++-----------
 setup.py  |  2 +-
 2 files changed, 31 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 83c97663..0c467147 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,8 @@
 # Meeko: preparation of small molecules for AutoDock
 
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
-[![PyPI version fury.io](https://img.shields.io/badge/version-0.1-green.svg)](https://pypi.python.org/pypi/ansicolortags/)
+[![API stability](https://img.shields.io/badge/stable%20API-no-orange)](https://shields.io/)
+[![PyPI version fury.io](https://img.shields.io/badge/version-0.2-green.svg)](https://pypi.python.org/pypi/ansicolortags/)
 
 Meeko reads a chemoinformatics molecule object (currently Open Babel) and writes a string (or file)
 in PDBQT format for use with [AutoDock-Vina](https://github.com/ccsb-scripps/AutoDock-Vina)
@@ -17,12 +18,6 @@ Meeko is developed by the [Forli lab](https://forlilab.org/) at the
 [Center for Computational Structural Biology (CCSB)](https://ccsb.scripps.edu)
 at [Scripps Research](https://www.scripps.edu/).
 
-## Examples using the command line script
-```console
-mk_prepare_ligand.py -i molecule.sdf -o molecule.pdbqt
-mk_prepare_ligand.py -i multi_mol.sdf --multimol_outdir folder_for_pdbqt_files
-```
-
 ## Dependencies
 
 * Python (>=3.5)
@@ -30,6 +25,11 @@ mk_prepare_ligand.py -i multi_mol.sdf --multimol_outdir folder_for_pdbqt_files
 * Openbabel (>=3)
 * RDKit
 
+## Installation (from PyPI)
+```bash
+$ pip install meeko
+```
+
 ## Installation (from source)
 
 ```bash
@@ -38,15 +38,28 @@ $ cd Meeko
 $ pip install .
 ```
 
+Optionally include `--editable`. Changes in the original package location
+take effect immediately without the need to run `pip install .` again.
+```bash
+$ pip install --editable .
+```
+
+## Examples using the command line scripts
+```console
+mk_prepare_ligand.py -i molecule.sdf -o molecule.pdbqt
+mk_prepare_ligand.py -i multi_mol.sdf --multimol_outdir folder_for_pdbqt_files
+mk_copy_coords.py vina_results.pdbqt -o vina_results.sdf
+mk_copy_coords.py adgpu_results.dlg -o adgpu_results.sdf
+```
+
 ## Quick Python tutorial
 
-##### 1. flexible macrocycle with attached waters
+#### 1. flexible macrocycle with attached waters
 
 ```python
 from meeko import MoleculePreparation
 from meeko import obutils
 
-
 input_molecule_file = 'example/BACE_macrocycle/BACE_4.mol2'
 mol = obutils.load_molecule_from_file(input_molecule_file)
 
@@ -58,14 +71,20 @@ output_pdbqt_file = "test_macrocycle_hydrate.pdbqt"
 preparator.write_pdbqt_file(output_pdbqt_file)
 ```
 
-##### 2. RDKit molecule from docking results
-
+#### 2. RDKit molecule from docking results
 
 Assuming that 'docked.dlg' was written by AutoDock-GPU and that Meeko prepared the input ligands.
+
 ```python
 from meeko import PDBQTMolecule
 
+with open("docked.dlg") as f:
+    dlg_string = f.read()
+pdbqt_mol = PDBQTMolecule(dlg_string, is_dlg=True)
+
+# alternatively, read the .dlg file directly
 pdbqt_mol = PDBQTMolecule.from_file("docked.dlg", is_dlg=True)
+
 for pose in pdbqt_mol:
     rdkit_mol = pose.export_rdkit_mol()
 ```
diff --git a/setup.py b/setup.py
index eb36e330..ec49b9d5 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@ def find_files(directory):
 
 setup(
     name="meeko",
-    version='0.1.dev3',
+    version='0.2',
     author="Stefano Forli",
     author_email="forli@scripps.edu",
     url="https://github.com/ccsb-scripps/meeko",