From 40871fcfdfeefe502c9ed69d5d7dec7d83500d05 Mon Sep 17 00:00:00 2001
From: diogom <diogom@scripps.edu>
Date: Thu, 30 Nov 2023 10:04:27 -0800
Subject: [PATCH] minor fixes to mk_prepare_receptor.py

---
 README.md                      | 4 ++--
 meeko/__init__.py              | 2 +-
 meeko/linked_rdkit_chorizo.py  | 6 +++---
 scripts/mk_prepare_receptor.py | 6 +++---
 setup.py                       | 2 +-
 5 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index ab2bf809..9ba6a7e3 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-0.6.0--alpha.1-green.svg)](https://pypi.python.org/pypi/ansicolortags/)
+[![PyPI version fury.io](https://img.shields.io/badge/version-0.6.0--alpha.2-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)
@@ -35,7 +35,7 @@ For example, reading Mol2 files from ZINC
 [led to incorrect net charge of some molecules.](https://github.com/forlilab/Meeko/issues/63)
 
 
-## v0.6.0-alpha.1
+## v0.6.0-alpha.2
 
 This release aims to distribute an enhanced `mk_prepare_receptor.py`.
 Some features are still being developed, hence the `-alpha` suffix in the version.
diff --git a/meeko/__init__.py b/meeko/__init__.py
index 5ede08fc..5178d1de 100644
--- a/meeko/__init__.py
+++ b/meeko/__init__.py
@@ -4,7 +4,7 @@
 # Meeko
 #
 
-__version__ = "0.6.0-alpha.1"
+__version__ = "0.6.0-alpha.2"
 
 try:
     import openbabel
diff --git a/meeko/linked_rdkit_chorizo.py b/meeko/linked_rdkit_chorizo.py
index 9b537e19..a5066430 100644
--- a/meeko/linked_rdkit_chorizo.py
+++ b/meeko/linked_rdkit_chorizo.py
@@ -650,9 +650,9 @@ def parameterize_residues(self, termini, ambiguous):
             resmol = best_resmol
             n_atoms = best_n_atoms
             resn = best_resn
-            if len(possible_resn) > 1:
-                print("%9s" % res, "-->", resn, "...out of", possible_resn)
-                ambiguous_chosen[res] = f"{chain}:{resn}:{resnum}"
+            #if len(possible_resn) > 1:
+            #    print("%9s" % res, "-->", resn, "...out of", possible_resn)
+            #    ambiguous_chosen[res] = f"{chain}:{resn}:{resnum}"
 
             resmol = self.build_resmol(res, resn)
             if resmol is None:
diff --git a/scripts/mk_prepare_receptor.py b/scripts/mk_prepare_receptor.py
index 3e0ddaa9..b0bdeac1 100755
--- a/scripts/mk_prepare_receptor.py
+++ b/scripts/mk_prepare_receptor.py
@@ -224,9 +224,9 @@ def get_args():
 ###         print(err, file=sys.stderr)
 ###         sys.exit(2)
 
-### reactive_flexres = {}
-### all_ok = True
-### all_err = ""
+reactive_flexres = {}
+all_ok = True
+all_err = ""
 ### for resid_string in args.reactive_flexres:
 ###     res_id, ok, err = parse_residue_string(resid_string)
 ###     if ok:
diff --git a/setup.py b/setup.py
index 8a4dc47d..0e895ad1 100644
--- a/setup.py
+++ b/setup.py
@@ -21,7 +21,7 @@ def find_files(directory):
 
 setup(
     name="meeko",
-    version='0.6.0-alpha.1',
+    version='0.6.0-alpha.2',
     author="Forli Lab",
     author_email="forli@scripps.edu",
     url="https://github.com/ccsb-scripps/meeko",