From ce5db3e6617a1181ebe3d10a5925ae1dc7c6a298 Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Sat, 27 Nov 2021 20:39:09 +0000
Subject: [PATCH 01/15] Case if babel is not installed

---
 acpype_lib/parser_args.py |  1 +
 acpype_lib/topol.py       | 18 ++++++++++--------
 acpype_lib/utils.py       | 24 +++++++++++++++---------
 tests/test_acpype.py      |  2 +-
 tests/test_acs_api.py     |  3 ++-
 5 files changed, 29 insertions(+), 19 deletions(-)

diff --git a/acpype_lib/parser_args.py b/acpype_lib/parser_args.py
index c748ae08..eeab4b3d 100644
--- a/acpype_lib/parser_args.py
+++ b/acpype_lib/parser_args.py
@@ -3,6 +3,7 @@
 
 
 def get_option_parser():
+    # not used yet: -e -l -r
     parser = argparse.ArgumentParser(usage=usage + epilog)
     group = parser.add_mutually_exclusive_group()
     parser.add_argument(
diff --git a/acpype_lib/topol.py b/acpype_lib/topol.py
index d8c87e98..02fae7a8 100644
--- a/acpype_lib/topol.py
+++ b/acpype_lib/topol.py
@@ -1,3 +1,4 @@
+import re
 import signal
 import math
 import os
@@ -3053,14 +3054,15 @@ def __init__(
         self.inputFile = os.path.basename(inputFile)
         self.rootDir = os.path.abspath(".")
         self.absInputFile = os.path.abspath(inputFile)
-        if not os.path.exists(self.absInputFile) and checkSmiles(inputFile):
-            self.is_smiles = True
-            self.smiles = inputFile
-            if not basename:
-                self.inputFile = "smiles_molecule.mol2"
-            else:
-                self.inputFile = f"{basename}.mol2"
-            self.absInputFile = os.path.abspath(self.inputFile)
+        if not os.path.exists(self.absInputFile) and not re.search(r"\.mol2$|\.mdl$|\.pdb$", self.inputFile):
+            if checkSmiles(inputFile):
+                self.is_smiles = True
+                self.smiles = inputFile
+                if not basename:
+                    self.inputFile = "smiles_molecule.mol2"
+                else:
+                    self.inputFile = f"{basename}.mol2"
+                self.absInputFile = os.path.abspath(self.inputFile)
         elif not os.path.exists(self.absInputFile):
             raise Exception(f"Input file {inputFile} DOES NOT EXIST")
         baseOriginal, ext = os.path.splitext(self.inputFile)
diff --git a/acpype_lib/utils.py b/acpype_lib/utils.py
index 415cf324..a26c8c5c 100644
--- a/acpype_lib/utils.py
+++ b/acpype_lib/utils.py
@@ -16,25 +16,31 @@ def checkOpenBabelVersion():
 
 def checkSmiles(smiles):
 
-    if checkOpenBabelVersion() >= 300:
-        from openbabel import openbabel as ob
-        from openbabel import pybel
+    try:
+        if checkOpenBabelVersion() >= 300:
+            from openbabel import openbabel as ob
+            from openbabel import pybel
 
-        ob.cvar.obErrorLog.StopLogging()
-    elif checkOpenBabelVersion() >= 200 and checkOpenBabelVersion() < 300:
-        import openbabel as ob
-        import pybel  # type: ignore
+            ob.cvar.obErrorLog.StopLogging()
 
-        ob.cvar.obErrorLog.StopLogging()
+        elif checkOpenBabelVersion() >= 200 and checkOpenBabelVersion() < 300:
+            import openbabel as ob
+            import pybel  # type: ignore
 
-    " Check if input is a smiles string "
+            ob.cvar.obErrorLog.StopLogging()
+    except AttributeError:
+        print("WARNING: your input may be a SMILES but")
+        print("         without OpenBabel, this functionality won't work")
+        return False
 
+    # Check if input is a smiles string
     try:
         ob.obErrorLog.SetOutputLevel(0)
         pybel.readstring("smi", smiles)
         return True
     except Exception:
         ob.obErrorLog.SetOutputLevel(0)
+
         return False
 
 
diff --git a/tests/test_acpype.py b/tests/test_acpype.py
index 1ea4997d..70bc8d21 100644
--- a/tests/test_acpype.py
+++ b/tests/test_acpype.py
@@ -254,7 +254,7 @@ def test_inputs(capsys, argv):
         (None, 2, " error: "),  # NOTE: None -> sys.argv from pystest
         (["-v"], 0, version),
         ([], 2, "error: missing input files"),
-        (["-di", " 123"], 19, "ACPYPE FAILED: Input file  123 DOES NOT EXIST"),
+        (["-di", " 123"], 19, "ACPYPE FAILED: [Errno 2] No such file or directory"),
         (["-di", " 123", "-x", "abc"], 2, "either '-i' or ('-p', '-x'), but not both"),
         (["-di", " 123", "-u"], 2, "option -u is only meaningful in 'amb2gmx' mode (args '-p' and '-x')"),
     ],
diff --git a/tests/test_acs_api.py b/tests/test_acs_api.py
index 8865b575..560ba0ed 100644
--- a/tests/test_acs_api.py
+++ b/tests/test_acs_api.py
@@ -48,7 +48,8 @@ def test_json_simple():
 def test_json_failed():
     os.chdir(os.path.dirname(os.path.abspath(__file__)))
     jj = json.loads(acpype_api(inputFile="_fake_", debug=True))
-    assert jj.get("file_name") == "ERROR: Input file _fake_ DOES NOT EXIST"
+    assert "ERROR: [Errno 2] No such file or directory" in jj.get("file_name")
+    assert "tests/_fake_" in jj.get("file_name")
 
 
 def get_json():

From d87eba26f6cc2e1620bfe31045212bdf242bb6e8 Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Sun, 28 Nov 2021 18:36:09 +0000
Subject: [PATCH 02/15] Important changes: binaries dict in

---
 acpype_lib/__init__.py |  2 +-
 acpype_lib/acpype.py   | 43 ++++++++++++++++++++++++++----------------
 acpype_lib/params.py   |  2 ++
 acpype_lib/topol.py    | 29 +++++++++++++++-------------
 acpype_lib/utils.py    | 15 +++------------
 tests/test_acpype.py   | 13 +++++++++----
 6 files changed, 58 insertions(+), 46 deletions(-)

diff --git a/acpype_lib/__init__.py b/acpype_lib/__init__.py
index 05d4d6c6..99f6808d 100644
--- a/acpype_lib/__init__.py
+++ b/acpype_lib/__init__.py
@@ -1,3 +1,3 @@
 # from https://packaging.python.org/guides/single-sourcing-package-version/
 # using option 2
-__version__ = "2021.11.27"
+__version__ = "2021.11.28"
diff --git a/acpype_lib/acpype.py b/acpype_lib/acpype.py
index 87accab0..7a894052 100755
--- a/acpype_lib/acpype.py
+++ b/acpype_lib/acpype.py
@@ -65,30 +65,40 @@
 from acpype_lib.parser_args import get_option_parser
 from acpype_lib.utils import while_replace
 from acpype_lib.utils import checkSmiles, elapsedTime
+from acpype_lib.params import binaries
 
-# For pip package
-if which("antechamber") is None:
-    LOCAL_PATH = sysconfig.get_paths()["purelib"]
-    if sys.platform == "linux":
-        os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_linux/bin:" + LOCAL_PATH + "/amber21-11_linux/dat/"
-        os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_linux/"
-        os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_linux/bin/"
-        os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_linux/lib/"
-    elif sys.platform == "darwin":
-        os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_os/bin:" + LOCAL_PATH + "/amber21-11_os/dat/"
-        os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_os/"
-        os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_os/bin/"
-        os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
 
-if sys.version_info < (3, 6):
-    raise Exception("Sorry, you need python 3.6 or higher")
+def set_for_pip():
+    # For pip package
+    if which(binaries["ac_bin"]) is None:
+        LOCAL_PATH = sysconfig.get_paths()["purelib"]
+        if sys.platform == "linux":
+            os.environ["PATH"] += (
+                os.pathsep + LOCAL_PATH + "/amber21-11_linux/bin:" + LOCAL_PATH + "/amber21-11_linux/dat/"
+            )
+            os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_linux/"
+            os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_linux/bin/"
+            os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_linux/lib/"
+        elif sys.platform == "darwin":
+            os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_os/bin:" + LOCAL_PATH + "/amber21-11_os/dat/"
+            os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_os/"
+            os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_os/bin/"
+            os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
+            os.environ["DYLD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
+
+
+def chk_py_ver():
+    if sys.version_info < (3, 6):
+        raise Exception("Sorry, you need python 3.6 or higher")
 
 
-def init_main(argv=None):
+def init_main(binaries=binaries, argv=None):
 
     """
     Main function, to satisfy Conda
     """
+    chk_py_ver()
+    set_for_pip()
     if argv is None:
         argv = sys.argv[1:]
 
@@ -141,6 +151,7 @@ def init_main(argv=None):
         else:
             molecule = ACTopol(
                 args.input,
+                binaries=binaries,
                 chargeType=args.charge_method,
                 chargeVal=args.net_charge,
                 debug=args.debug,
diff --git a/acpype_lib/params.py b/acpype_lib/params.py
index 80bea120..de515203 100644
--- a/acpype_lib/params.py
+++ b/acpype_lib/params.py
@@ -1,3 +1,5 @@
+binaries = {"ac_bin": "antechamber", "obabel_bin": "obabel"}
+
 MAXTIME = 3 * 3600
 cal = 4.184
 Pi = 3.141593
diff --git a/acpype_lib/topol.py b/acpype_lib/topol.py
index 02fae7a8..ed43b777 100644
--- a/acpype_lib/topol.py
+++ b/acpype_lib/topol.py
@@ -11,7 +11,7 @@
 from acpype_lib.mol import Atom, Angle, AtomType, Bond, Dihedral
 from acpype_lib import __version__ as version
 from acpype_lib.params import minDist, minDist2, maxDist, maxDist2, MAXTIME, TLEAP_TEMPLATE, leapAmberFile
-from acpype_lib.params import ionOrSolResNameList, radPi, cal, outTopols, qDict, qConv, diffTol
+from acpype_lib.params import binaries, ionOrSolResNameList, radPi, cal, outTopols, qDict, qConv, diffTol
 from acpype_lib.params import dictAtomTypeAmb2OplsGmxCode, dictAtomTypeGaff2OplsGmxCode, oplsCode2AtomTypeDict
 from acpype_lib.utils import _getoutput, while_replace, distanceAA, job_pids_family, checkOpenBabelVersion
 from acpype_lib.utils import checkSmiles, find_antechamber, elapsedTime, imprDihAngle, parmMerge
@@ -3022,6 +3022,7 @@ class ACTopol(AbstractTopol):
     def __init__(
         self,
         inputFile,
+        binaries=binaries,
         chargeType="bcc",
         chargeVal=None,
         multiplicity="1",
@@ -3051,6 +3052,18 @@ def __init__(
         self.direct = direct
         self.sorted = is_sorted
         self.chiral = chiral
+        self.acExe = find_antechamber(binaries["ac_bin"])
+        if not os.path.exists(self.acExe):
+            self.printError("no 'antechamber' executable... aborting! ")
+            hint1 = "HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?"
+            hint2 = (
+                "HINT2: is 'antechamber' in your $PATH?"
+                + "\n    What 'which antechamber' in your terminal says?"
+                + "\n    'alias' doesn't work for ACPYPE."
+            )
+            self.printMess(hint1)
+            self.printMess(hint2)
+            raise Exception("Missing ANTECHAMBER")
         self.inputFile = os.path.basename(inputFile)
         self.rootDir = os.path.abspath(".")
         self.absInputFile = os.path.abspath(inputFile)
@@ -3063,6 +3076,8 @@ def __init__(
                 else:
                     self.inputFile = f"{basename}.mol2"
                 self.absInputFile = os.path.abspath(self.inputFile)
+            else:
+                self.is_smiles = False
         elif not os.path.exists(self.absInputFile):
             raise Exception(f"Input file {inputFile} DOES NOT EXIST")
         baseOriginal, ext = os.path.splitext(self.inputFile)
@@ -3099,18 +3114,6 @@ def __init__(
             self.gaffDatfile = "gaff2.dat"
         self.force = force
         self.allhdg = allhdg
-        self.acExe = find_antechamber()
-        if not os.path.exists(self.acExe):
-            self.printError("no 'antechamber' executable... aborting ! ")
-            hint1 = "HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?"
-            hint2 = (
-                "HINT2: is 'antechamber' in your $PATH?"
-                + "\n    What 'which antechamber' in your terminal says?"
-                + "\n    'alias' doesn't work for ACPYPE."
-            )
-            self.printMess(hint1)
-            self.printMess(hint2)
-            raise Exception("Missing ANTECHAMBER")
         self.tleapExe = which("tleap") or ""
         self.parmchkExe = which("parmchk2") or ""
         acBase = base + "_AC"
diff --git a/acpype_lib/utils.py b/acpype_lib/utils.py
index a26c8c5c..b7f9d24e 100644
--- a/acpype_lib/utils.py
+++ b/acpype_lib/utils.py
@@ -28,7 +28,7 @@ def checkSmiles(smiles):
             import pybel  # type: ignore
 
             ob.cvar.obErrorLog.StopLogging()
-    except AttributeError:
+    except Exception:
         print("WARNING: your input may be a SMILES but")
         print("         without OpenBabel, this functionality won't work")
         return False
@@ -281,15 +281,6 @@ def while_replace(string):
     return string
 
 
-def find_antechamber():
-    acExe = ""
-    dirAmber = os.getenv("AMBERHOME", os.getenv("ACHOME"))
-    if dirAmber:
-        for ac_bin in ["bin", "exe"]:
-            ac_path = os.path.join(dirAmber, ac_bin, "antechamber")
-            if os.path.exists(ac_path):
-                acExe = ac_path
-                break
-    if not acExe:
-        acExe = which("antechamber") or ""
+def find_antechamber(abin):
+    acExe = which(abin) or ""
     return acExe
diff --git a/tests/test_acpype.py b/tests/test_acpype.py
index 70bc8d21..9dc4b6da 100644
--- a/tests/test_acpype.py
+++ b/tests/test_acpype.py
@@ -132,13 +132,17 @@ def test_ildn_gmx4_fail():
     shutil.rmtree(molecule.absHomeDir)
 
 
-def test_smiles():
+@pytest.mark.parametrize(
+    ("base", "msg"), [(None, "smiles_molecule.mol2"), ("thalidomide_smiles", "thalidomide_smiles.mol2")],
+)
+def test_smiles(base, msg):
     os.chdir(os.path.dirname(os.path.abspath(__file__)))
     smiles = "c1ccc2c(c1)C(=O)N(C2=O)C3CCC(=NC3=O)O"
-    molecule = ACTopol(smiles, basename="thalidomide_smiles", chargeType="gas", debug=True)
+    molecule = ACTopol(smiles, basename=base, chargeType="gas", debug=True)
     molecule.createACTopol()
     molecule.createMolTopol()
     assert molecule
+    assert molecule.inputFile == msg
     assert len(molecule.molTopol.atoms) == 29
     shutil.rmtree(molecule.absHomeDir)
     os.remove(molecule.absInputFile)
@@ -241,7 +245,7 @@ def test_charge_user():
 def test_inputs(capsys, argv):
     os.chdir(os.path.dirname(os.path.abspath(__file__)))
     temp_base = "vir_temp"
-    init_main(argv + ["-b", temp_base])
+    init_main(argv=argv + ["-b", temp_base])
     captured = capsys.readouterr()
     assert "Total time of execution:" in captured.out
     os.chdir(os.path.dirname(os.path.abspath(__file__)))
@@ -254,6 +258,7 @@ def test_inputs(capsys, argv):
         (None, 2, " error: "),  # NOTE: None -> sys.argv from pystest
         (["-v"], 0, version),
         ([], 2, "error: missing input files"),
+        (["-di", "AAAx.mol2"], 19, "ACPYPE FAILED: Input file AAAx.mol2 DOES NOT EXIST"),
         (["-di", " 123"], 19, "ACPYPE FAILED: [Errno 2] No such file or directory"),
         (["-di", " 123", "-x", "abc"], 2, "either '-i' or ('-p', '-x'), but not both"),
         (["-di", " 123", "-u"], 2, "option -u is only meaningful in 'amb2gmx' mode (args '-p' and '-x')"),
@@ -261,7 +266,7 @@ def test_inputs(capsys, argv):
 )
 def test_args_wrong_inputs(capsys, argv, code, msg):
     with pytest.raises(SystemExit) as e_info:
-        init_main(argv)
+        init_main(argv=argv)
     captured = capsys.readouterr()
     assert msg in captured.err + captured.out
     assert e_info.typename == "SystemExit"

From 3d53821fef354a5264bf922bd8ee0a25d7b12c5f Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Sun, 28 Nov 2021 20:39:26 +0000
Subject: [PATCH 03/15] Refactored checkSmiles

---
 acpype_lib/acpype.py | 11 +++---
 acpype_lib/topol.py  | 89 ++++++++++++++++++++++++++++++--------------
 acpype_lib/utils.py  | 39 ++-----------------
 3 files changed, 70 insertions(+), 69 deletions(-)

diff --git a/acpype_lib/acpype.py b/acpype_lib/acpype.py
index 7a894052..465c6415 100755
--- a/acpype_lib/acpype.py
+++ b/acpype_lib/acpype.py
@@ -63,8 +63,7 @@
 from shutil import rmtree, which
 from acpype_lib.topol import MolTopol, ACTopol, header
 from acpype_lib.parser_args import get_option_parser
-from acpype_lib.utils import while_replace
-from acpype_lib.utils import checkSmiles, elapsedTime
+from acpype_lib.utils import while_replace, elapsedTime
 from acpype_lib.params import binaries
 
 
@@ -77,12 +76,12 @@ def set_for_pip():
                 os.pathsep + LOCAL_PATH + "/amber21-11_linux/bin:" + LOCAL_PATH + "/amber21-11_linux/dat/"
             )
             os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_linux/"
-            os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_linux/bin/"
+            # os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_linux/bin/"
             os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_linux/lib/"
         elif sys.platform == "darwin":
             os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_os/bin:" + LOCAL_PATH + "/amber21-11_os/dat/"
             os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_os/"
-            os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_os/bin/"
+            # os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_os/bin/"
             os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
             os.environ["DYLD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
 
@@ -207,8 +206,8 @@ def init_main(binaries=binaries, argv=None):
     except Exception:
         pass
 
-    if not amb2gmxF and molecule.babelExe:
-        if checkSmiles(args.input):
+    if not amb2gmxF and molecule.obabelExe:
+        if molecule.checkSmiles():
             afile = "smiles_molecule.mol2"
             if os.path.exists(afile):
                 os.remove(afile)
diff --git a/acpype_lib/topol.py b/acpype_lib/topol.py
index ed43b777..3391ff56 100644
--- a/acpype_lib/topol.py
+++ b/acpype_lib/topol.py
@@ -14,7 +14,7 @@
 from acpype_lib.params import binaries, ionOrSolResNameList, radPi, cal, outTopols, qDict, qConv, diffTol
 from acpype_lib.params import dictAtomTypeAmb2OplsGmxCode, dictAtomTypeGaff2OplsGmxCode, oplsCode2AtomTypeDict
 from acpype_lib.utils import _getoutput, while_replace, distanceAA, job_pids_family, checkOpenBabelVersion
-from acpype_lib.utils import checkSmiles, find_antechamber, elapsedTime, imprDihAngle, parmMerge
+from acpype_lib.utils import find_bin, elapsedTime, imprDihAngle, parmMerge
 
 year = datetime.today().year
 tag = version
@@ -210,7 +210,7 @@ def __init__(self):
         self.tmpDir = None
         self.absInputFile = None
         self.chargeType = None
-        self.babelExe = None
+        self.obabelExe = None
         self.baseName = None
         self.acExe = None
         self.force = None
@@ -251,7 +251,7 @@ def __init__(self):
         self.tleapLog = None
         self.parmchkLog = None
         self.inputFile = None
-        self.babelLog = None
+        self.obabelLog = None
         self.absHomeDir = None
         self.molTopol = None
         self.topFileData = None
@@ -316,6 +316,35 @@ def search(self, name=None, alist=False):
             ll = ll[0]
         return ll
 
+    def checkSmiles(self):
+
+        if find_bin(self.binaries["obabel_bin"]):
+            if checkOpenBabelVersion() >= 300:
+                from openbabel import openbabel as ob
+                from openbabel import pybel
+
+                ob.cvar.obErrorLog.StopLogging()
+
+            elif checkOpenBabelVersion() >= 200 and checkOpenBabelVersion() < 300:
+                import openbabel as ob
+                import pybel  # type: ignore
+
+                ob.cvar.obErrorLog.StopLogging()
+        else:
+            print("WARNING: your input may be a SMILES but")
+            print("         without OpenBabel, this functionality won't work")
+            return False
+
+        # Check if input is a smiles string
+        try:
+            ob.obErrorLog.SetOutputLevel(0)
+            pybel.readstring("smi", self.smiles)
+            return True
+        except Exception:
+            ob.obErrorLog.SetOutputLevel(0)
+
+            return False
+
     def guessCharge(self):
         """
         Guess the charge of a system based on antechamber
@@ -344,7 +373,7 @@ def guessCharge(self):
             self.printWarn("no charge value given, trying to guess one...")
             mol2FileForGuessCharge = self.inputFile
             if self.ext == ".pdb":
-                cmd = f"{self.babelExe} -ipdb {self.inputFile} -omol2 -O {self.baseName}.mol2"
+                cmd = f"{self.obabelExe} -ipdb {self.inputFile} -omol2 -O {self.baseName}.mol2"
                 self.printDebug(f"guessCharge: {cmd}")
                 out = _getoutput(cmd)
                 self.printDebug(out)
@@ -955,23 +984,24 @@ def checkFrcmod(self):
         return check
 
     def convertPdbToMol2(self):
-        """Convert PDB to MOL2 by using babel"""
+        """Convert PDB to MOL2 by using obabel"""
         if self.ext == ".pdb":
-            if self.execBabel():
-                self.printError("convert pdb to mol2 via babel failed")
+            if self.execObabel():
+                self.printError(f"convert pdb to mol2 via {binaries['obabel_bin']} failed")
                 return True
         return False
 
     def convertSmilesToMol2(self):
-        if not self.babelExe:
-            raise Exception("SMILES needs openbabel python module")
+        """Convert Smiles to MOL2 by using obabel"""
+
+        if not self.obabelExe:
+            raise Exception("SMILES needs OpenBabel python module")
         if checkOpenBabelVersion() >= 300:
             from openbabel import pybel
 
         elif checkOpenBabelVersion() >= 200 and checkOpenBabelVersion() < 300:
             import pybel  # type: ignore
 
-        """Convert Smiles to MOL2 by using babel"""
         try:
             mymol = pybel.readstring("smi", str(self.smiles))
             mymol.addh()
@@ -981,20 +1011,20 @@ def convertSmilesToMol2(self):
         except Exception:
             return False
 
-    def execBabel(self):
-        """Execute babel"""
+    def execObabel(self):
+        """Execute obabel"""
         self.makeDir()
 
-        cmd = f"{self.babelExe} -ipdb {self.inputFile} -omol2 -O {self.baseName}.mol2"
+        cmd = f"{self.obabelExe} -ipdb {self.inputFile} -omol2 -O {self.baseName}.mol2"
         self.printDebug(cmd)
-        self.babelLog = _getoutput(cmd)
+        self.obabelLog = _getoutput(cmd)
         self.ext = ".mol2"
         self.inputFile = self.baseName + self.ext
         self.acParDict["ext"] = "mol2"
         if os.path.exists(self.inputFile):
             self.printMess("* Babel OK *")
         else:
-            self.printQuoted(self.babelLog)
+            self.printQuoted(self.obabelLog)
             return True
         return False
 
@@ -1352,7 +1382,7 @@ def getChirals(self):
         Get chiral atoms, its 4 neighbours and improper dihedral angle
         to store non-planar improper dihedrals for CNS (and CNS only!)
         """
-        if not self._parent.babelExe:
+        if not self._parent.obabelExe:
             self.printWarn("No Openbabel python module, no chiral groups")
             self.chiralGroups = []
             return
@@ -3044,6 +3074,7 @@ def __init__(
         amb2gmx=False,
     ):
         super().__init__()
+        self.binaries = binaries
         self.amb2gmx = amb2gmx
         self.debug = debug
         self.verbose = verbose
@@ -3052,13 +3083,13 @@ def __init__(
         self.direct = direct
         self.sorted = is_sorted
         self.chiral = chiral
-        self.acExe = find_antechamber(binaries["ac_bin"])
+        self.acExe = find_bin(binaries["ac_bin"])
         if not os.path.exists(self.acExe):
-            self.printError("no 'antechamber' executable... aborting! ")
-            hint1 = "HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?"
+            self.printError(f"no '{binaries['ac_bin']}' executable... aborting! ")
+            hint1 = "HINT1: is 'AMBERHOME' environment variable set?"
             hint2 = (
-                "HINT2: is 'antechamber' in your $PATH?"
-                + "\n    What 'which antechamber' in your terminal says?"
+                f"HINT2: is '{binaries['ac_bin']}' in your $PATH?"
+                + f"\n    What 'which {binaries['ac_bin']}' in your terminal says?"
                 + "\n    'alias' doesn't work for ACPYPE."
             )
             self.printMess(hint1)
@@ -3067,10 +3098,11 @@ def __init__(
         self.inputFile = os.path.basename(inputFile)
         self.rootDir = os.path.abspath(".")
         self.absInputFile = os.path.abspath(inputFile)
+
         if not os.path.exists(self.absInputFile) and not re.search(r"\.mol2$|\.mdl$|\.pdb$", self.inputFile):
-            if checkSmiles(inputFile):
+            self.smiles = inputFile
+            if self.checkSmiles():
                 self.is_smiles = True
-                self.smiles = inputFile
                 if not basename:
                     self.inputFile = "smiles_molecule.mol2"
                 else:
@@ -3078,6 +3110,7 @@ def __init__(
                 self.absInputFile = os.path.abspath(self.inputFile)
             else:
                 self.is_smiles = False
+                self.smiles = None
         elif not os.path.exists(self.absInputFile):
             raise Exception(f"Input file {inputFile} DOES NOT EXIST")
         baseOriginal, ext = os.path.splitext(self.inputFile)
@@ -3085,14 +3118,14 @@ def __init__(
         self.baseOriginal = baseOriginal
         self.ext = ext
         self.baseName = base  # name of the input file without ext.
-        self.babelExe = which("obabel") or ""
-        if not os.path.exists(self.babelExe):
+        self.obabelExe = find_bin(binaries["obabel_bin"])
+        if not os.path.exists(self.obabelExe):
             if self.ext != ".mol2" and self.ext != ".mdl":
-                self.printError("no 'babel' executable; you need it if input is PDB or SMILES")
+                self.printError(f"no '{binaries['obabel_bin']}' executable; you need it if input is PDB or SMILES")
                 self.printError("otherwise use only MOL2 or MDL file as input ... aborting!")
-                raise Exception("Missing BABEL")
+                raise Exception("Missing OBABEL")
             else:
-                self.printWarn("no 'babel' executable, no PDB file as input can be used!")
+                self.printWarn(f"no '{binaries['obabel_bin']}' executable, no PDB file can be used as input!")
         if self.is_smiles:
             self.convertSmilesToMol2()
         self.timeTol = timeTol
diff --git a/acpype_lib/utils.py b/acpype_lib/utils.py
index b7f9d24e..bf88662b 100644
--- a/acpype_lib/utils.py
+++ b/acpype_lib/utils.py
@@ -5,6 +5,10 @@
 from acpype_lib.params import Pi
 
 
+def find_bin(abin):
+    return which(abin) or ""
+
+
 def checkOpenBabelVersion():
     "check openbabel version"
     import openbabel as obl
@@ -14,36 +18,6 @@ def checkOpenBabelVersion():
     return int(obl.OBReleaseVersion().replace(".", ""))
 
 
-def checkSmiles(smiles):
-
-    try:
-        if checkOpenBabelVersion() >= 300:
-            from openbabel import openbabel as ob
-            from openbabel import pybel
-
-            ob.cvar.obErrorLog.StopLogging()
-
-        elif checkOpenBabelVersion() >= 200 and checkOpenBabelVersion() < 300:
-            import openbabel as ob
-            import pybel  # type: ignore
-
-            ob.cvar.obErrorLog.StopLogging()
-    except Exception:
-        print("WARNING: your input may be a SMILES but")
-        print("         without OpenBabel, this functionality won't work")
-        return False
-
-    # Check if input is a smiles string
-    try:
-        ob.obErrorLog.SetOutputLevel(0)
-        pybel.readstring("smi", smiles)
-        return True
-    except Exception:
-        ob.obErrorLog.SetOutputLevel(0)
-
-        return False
-
-
 def dotproduct(aa, bb):
     """scalar product"""
     return sum((a * b) for a, b in zip(aa, bb))
@@ -279,8 +253,3 @@ def while_replace(string):
     while "  " in string:
         string = string.replace("  ", " ")
     return string
-
-
-def find_antechamber(abin):
-    acExe = which(abin) or ""
-    return acExe

From eb8ded651218a2c528869ebab05c953fe641eb5e Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Sun, 28 Nov 2021 20:42:56 +0000
Subject: [PATCH 04/15] New tests for user's scenarios

---
 tests/test_scenarios.py | 51 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 tests/test_scenarios.py

diff --git a/tests/test_scenarios.py b/tests/test_scenarios.py
new file mode 100644
index 00000000..1c4de1e0
--- /dev/null
+++ b/tests/test_scenarios.py
@@ -0,0 +1,51 @@
+import os
+import pytest
+from acpype_lib.acpype import init_main
+from acpype_lib.utils import _getoutput
+
+
+def test_no_ac(capsys):
+    binaries = {"ac_bin": "no_ac", "obabel_bin": "obabel"}
+    msg = f"ERROR: no '{binaries['ac_bin']}' executable... aborting!"
+    inp = "AAA.mol2"
+    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+    with pytest.raises(SystemExit) as e_info:
+        init_main(argv=["-di", inp, "-c", "gas"], binaries=binaries)
+    captured = capsys.readouterr()
+    assert msg in captured.out
+    assert e_info.typename == "SystemExit"
+    assert e_info.value.code == 19
+
+
+def test_only_ac(capsys):
+    binaries = {"ac_bin": "antechamber", "obabel_bin": "no_obabel"}
+    msg1 = f"WARNING: no '{binaries['obabel_bin']}' executable, no PDB file can be used as input!"
+    msg2 = "Total time of execution:"
+    msg3 = "WARNING: No Openbabel python module, no chiral groups"
+    inp = "AAA.mol2"
+    temp_base = "vir_temp"
+    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+    init_main(argv=["-di", inp, "-c", "gas", "-b", temp_base], binaries=binaries)
+    captured = capsys.readouterr()
+    assert msg1 in captured.out
+    assert msg2 in captured.out
+    assert msg3 in captured.out
+    _getoutput(f"rm -fr {temp_base}*")
+
+
+@pytest.mark.parametrize(
+    ("inp", "msg"),
+    [
+        ("AAA.pdb", "ERROR: no 'no_obabel' executable; you need it if input is PDB or SMILES"),
+        ("cccc", "WARNING: your input may be a SMILES but"),
+    ],
+)
+def test_no_obabel(capsys, inp, msg):
+    binaries = {"ac_bin": "antechamber", "obabel_bin": "no_obabel"}
+    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+    with pytest.raises(SystemExit) as e_info:
+        init_main(argv=["-di", inp, "-c", "gas"], binaries=binaries)
+    captured = capsys.readouterr()
+    assert msg in captured.out
+    assert e_info.typename == "SystemExit"
+    assert e_info.value.code == 19

From 32407d94f339b866f1c43b2fffc1c976ea828712 Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Sun, 28 Nov 2021 20:54:07 +0000
Subject: [PATCH 05/15] Added test_amb2gmx_no_bins

---
 tests/test_scenarios.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/tests/test_scenarios.py b/tests/test_scenarios.py
index 1c4de1e0..9a2ed52d 100644
--- a/tests/test_scenarios.py
+++ b/tests/test_scenarios.py
@@ -49,3 +49,15 @@ def test_no_obabel(capsys, inp, msg):
     assert msg in captured.out
     assert e_info.typename == "SystemExit"
     assert e_info.value.code == 19
+
+
+def test_amb2gmx_no_bins(capsys):
+    binaries = {"ac_bin": "no_ac", "obabel_bin": "no_obabel"}
+    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+    argv = ["-x", "Base.inpcrd", "-p", "Base.prmtop"]
+    temp_base = "vir_temp"
+    init_main(argv=argv + ["-b", temp_base], binaries=binaries)
+    captured = capsys.readouterr()
+    assert "Total time of execution:" in captured.out
+    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+    _getoutput(f"rm -fr {temp_base}*")

From 4af778b477a2cb46272689d509385877dd9da13c Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Sun, 28 Nov 2021 23:11:28 +0000
Subject: [PATCH 06/15] Bash script to simplify acpype docker usage

---
 Dockerfile       | 4 +++-
 acpype_docker.sh | 3 +++
 2 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100755 acpype_docker.sh

diff --git a/Dockerfile b/Dockerfile
index 4476a734..3228512b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -29,9 +29,11 @@ RUN apt-get update && apt-get install -y \
     python3-openbabel \
     libgfortran5 \
     libarpack++2-dev \
+    python3-ipython \
     && apt-get autoremove -y && apt-get autoclean -y && apt-get clean -y \
     && rm -rf /var/lib/apt/lists/*
 
 COPY run_acpype.py /home
 COPY acpype_lib /home/acpype_lib
-RUN ln -s /home/run_acpype.py /usr/local/bin/acpype
\ No newline at end of file
+RUN ln -s /home/run_acpype.py /usr/local/bin/acpype
+ENV PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/amber21/bin" 
\ No newline at end of file
diff --git a/acpype_docker.sh b/acpype_docker.sh
new file mode 100755
index 00000000..f8827b85
--- /dev/null
+++ b/acpype_docker.sh
@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+docker run -i -t -v "${PWD}":/wdir -w /wdir acpype/acpype acpype "$@"

From abf38dd646d5abfa77fbf76926aa3571f361ce2e Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Sun, 28 Nov 2021 23:21:39 +0000
Subject: [PATCH 07/15] Update README for acpype_docker usage

---
 README.md | 23 +++++++++--------------
 1 file changed, 9 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index 27679390..86c22d7d 100644
--- a/README.md
+++ b/README.md
@@ -110,23 +110,18 @@ There are several ways of obtaining `acpype`:
 
 4. Via **[Docker](https://hub.docker.com/repository/docker/acpype/acpype/)**:
 
-   If you have Docker installed, you can run `acpype` by:
-  
-   ```bash
-   docker pull acpype/acpype:latest
-   ```
+   If you have Docker installed, you can run `acpype_docker.sh` by:
+
+   NOTE: first time may take some time as it pulls the `acpype` docker image.
 
-   Then, on Linux / MacOS choose a folder where to work (e.g. contains your PDB, MOL2 or inpcrd/prmtop files) and do:
+   On Linux / MacOS:
 
    ```bash
+   ln -fsv "$PWD/acpype_docker.sh" /usr/local/bin/acpype_docker
+
+   acpype_docker -i CCCC
    
-   # it opens a terminal inside docker with access to your working folder
-   docker run -i -t --rm -v ${PWD}:/wdir -w /wdir acpype/acpype bash
-   
-   # use acpype 
-   acpype -i CCCC
-   acpype -i DDD.pdb -c gas # if you have a DDD.pdb file there in "wdir" ($PWD)
-   exit # and your output files will be at your working directory ($PWD)
+   acpype_docker -i tests/DDD.pdb -c gas
    ```
 
    On Windows:
@@ -174,7 +169,7 @@ To get help and more information, type:
 At folder `acpype/`, type:
 
 ```bash
-  ln -s $PWD/run_acpype.py /usr/local/bin/acpype
+  ln -fsv "$PWD/run_acpype.py" /usr/local/bin/acpype
 ```
 
 Then re-login or start another shell session.

From 10c7548a5ed775d44b73f23f251341c27780b353 Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Mon, 29 Nov 2021 10:59:33 +0000
Subject: [PATCH 08/15] Script for releasing in pip and docker

---
 release.sh | 80 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100755 release.sh

diff --git a/release.sh b/release.sh
new file mode 100755
index 00000000..74ce1966
--- /dev/null
+++ b/release.sh
@@ -0,0 +1,80 @@
+#!/usr/bin/env bash
+
+# Create releases for pip or docker or both
+
+set -euo pipefail
+
+function usage() {
+    echo "syntax: $0 < [-p, -d] | -a > to create a release for pip or docker or both"
+    echo " -p : for pip, create wheel and upload to https://pypi.org/project/acpype/ (if you have permission)"
+    echo " -d : for docker, create images and upload to https://hub.docker.com/u/acpype (if you have permission)"
+    echo " -a : do both above"
+    echo " -v : verbose mode, print all commands"
+    echo " -h : prints this message"
+    exit 1
+}
+
+function run_pip() {
+    echo ">>> Creating pip package"
+    python3 -m build
+    python3 -m twine upload --repository testpypi dist/*"$today"* # TestPyPI
+    python3 -m twine upload --repository acpype dist/*"$today"*   # official release
+    rm -vfr dist/*"$today"*
+}
+
+function run_docker() {
+    echo ">>> Creating docker images"
+    docker build -t acpype/acpype:latest -t acpype/acpype:"$today" .
+
+    echo ">>> Pushing docker images"
+    docker push acpype/acpype --all-tags
+    docker image rm acpype/acpype:"$today"
+}
+
+function run_both() {
+    run_docker
+    run_pip
+}
+
+do_pip=false
+do_doc=false
+do_all=false
+verb=false
+no_args=true
+
+while getopts "adpvh" optionName; do
+    case "$optionName" in
+    a) do_all=true ;;
+    d) do_doc=true ;;
+    p) do_pip=true ;;
+    v) verb=true ;;
+    h) usage ;;
+    ?) usage ;;
+    *) usage ;;
+    esac
+    no_args=false
+done
+
+if "${no_args}"; then
+    usage
+elif $do_all && ($do_doc || $do_pip); then
+    usage
+fi
+
+if ${verb}; then
+    set -x
+fi
+
+today="$(date +%Y.%m.%d)"
+
+if $do_pip; then
+    run_pip
+fi
+
+if $do_doc; then
+    run_docker
+fi
+
+if $do_all; then
+    run_both
+fi

From 00f0a7e0429fbdab34912c8bef02159048ca7a60 Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Mon, 29 Nov 2021 14:01:14 +0000
Subject: [PATCH 09/15] Use verson instead of today

---
 release.sh | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/release.sh b/release.sh
index 74ce1966..c38d434c 100755
--- a/release.sh
+++ b/release.sh
@@ -4,6 +4,8 @@
 
 set -euo pipefail
 
+version="$(grep -o '[0-9]\{4\}\.[0-9]\{2\}\.[0-9]\{2\}' acpype_lib/__init__.py)"
+
 function usage() {
     echo "syntax: $0 < [-p, -d] | -a > to create a release for pip or docker or both"
     echo " -p : for pip, create wheel and upload to https://pypi.org/project/acpype/ (if you have permission)"
@@ -17,18 +19,17 @@ function usage() {
 function run_pip() {
     echo ">>> Creating pip package"
     python3 -m build
-    python3 -m twine upload --repository testpypi dist/*"$today"* # TestPyPI
-    python3 -m twine upload --repository acpype dist/*"$today"*   # official release
-    rm -vfr dist/*"$today"*
+    python3 -m twine upload --repository testpypi dist/*"$version"* # TestPyPI
+    python3 -m twine upload --repository pypi dist/*"$version"*     # official release
+    rm -vfr dist/*"$version"*
 }
 
 function run_docker() {
     echo ">>> Creating docker images"
-    docker build -t acpype/acpype:latest -t acpype/acpype:"$today" .
-
+    docker build -t acpype/acpype:latest -t acpype/acpype:"$version" .
     echo ">>> Pushing docker images"
     docker push acpype/acpype --all-tags
-    docker image rm acpype/acpype:"$today"
+    docker image rm acpype/acpype:"$version"
 }
 
 function run_both() {
@@ -65,8 +66,6 @@ if ${verb}; then
     set -x
 fi
 
-today="$(date +%Y.%m.%d)"
-
 if $do_pip; then
     run_pip
 fi

From aecc53973d02618a6c9d78cd20b8b6115a738041 Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Mon, 29 Nov 2021 14:12:21 +0000
Subject: [PATCH 10/15] Simplified set_for_pip()

---
 acpype_lib/acpype.py | 28 +++++++++++++---------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/acpype_lib/acpype.py b/acpype_lib/acpype.py
index 465c6415..aa949568 100755
--- a/acpype_lib/acpype.py
+++ b/acpype_lib/acpype.py
@@ -59,7 +59,6 @@
 import time
 import os
 import sys
-import sysconfig
 from shutil import rmtree, which
 from acpype_lib.topol import MolTopol, ACTopol, header
 from acpype_lib.parser_args import get_option_parser
@@ -70,20 +69,19 @@
 def set_for_pip():
     # For pip package
     if which(binaries["ac_bin"]) is None:
-        LOCAL_PATH = sysconfig.get_paths()["purelib"]
-        if sys.platform == "linux":
-            os.environ["PATH"] += (
-                os.pathsep + LOCAL_PATH + "/amber21-11_linux/bin:" + LOCAL_PATH + "/amber21-11_linux/dat/"
-            )
-            os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_linux/"
-            # os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_linux/bin/"
-            os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_linux/lib/"
-        elif sys.platform == "darwin":
-            os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_os/bin:" + LOCAL_PATH + "/amber21-11_os/dat/"
-            os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_os/"
-            # os.environ["ACHOME"] = LOCAL_PATH + "/amber21-11_os/bin/"
-            os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
-            os.environ["DYLD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
+        try:
+            LOCAL_PATH = os.path.dirname(os.path.dirname(__file__))
+            if sys.platform == "linux":
+                os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_linux/bin"
+                os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_linux/"
+                os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_linux/lib/"
+            elif sys.platform == "darwin":
+                os.environ["PATH"] += os.pathsep + LOCAL_PATH + "/amber21-11_os/bin"
+                os.environ["AMBERHOME"] = LOCAL_PATH + "/amber21-11_os/"
+                os.environ["LD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
+                os.environ["DYLD_LIBRARY_PATH"] = LOCAL_PATH + "/amber21-11_os/lib/"
+        except Exception:
+            print("ERROR: AmberTools NOT FOUND")
 
 
 def chk_py_ver():

From 69f38eafc69ca8b124202f66643d36e8e3606e7f Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Mon, 29 Nov 2021 19:40:55 +0000
Subject: [PATCH 11/15] Badges and review usage

---
 README.md | 44 +++++++++++++++++++++++++++++++++-----------
 1 file changed, 33 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 86c22d7d..54026a1d 100644
--- a/README.md
+++ b/README.md
@@ -1,12 +1,17 @@
 # ACPYPE
 
-![GitHub](https://img.shields.io/github/license/alanwilter/acpype?style=social)
-![GitHub All Releases](https://img.shields.io/github/downloads/alanwilter/acpype/total?style=social)
-![Docker Pulls](https://img.shields.io/docker/pulls/acpype/acpype?style=social&logo=docker)
-![Docker Image Size (tag)](https://img.shields.io/docker/image-size/lpkagami/acpype/latest?style=social&logo=docker)
-![GitHub Relase](https://img.shields.io/github/release-date/alanwilter/acpype?style=social)
-![Conda Version](https://img.shields.io/conda/vn/conda-forge/acpype.svg)
-![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/acpype.svg)
+![GitHub](https://img.shields.io/github/license/alanwilter/acpype?style=plastic)
+![GitHub release (latest by date)](https://img.shields.io/github/v/release/alanwilter/acpype?display_name=tag&logo=github&style=plastic)
+![GitHub Relase](https://img.shields.io/github/release-date/alanwilter/acpype?style=plastic&logo=github)<!-- ![GitHub All Releases](https://img.shields.io/github/downloads/alanwilter/acpype/total?style=plastic) -->
+![Docker Pulls](https://img.shields.io/docker/pulls/acpype/acpype?style=plastic&logo=docker)
+![Docker Image Size (tag)](https://img.shields.io/docker/image-size/acpype/acpype/latest?style=plastic&logo=docker)
+![Conda Version](https://img.shields.io/conda/vn/conda-forge/acpype.svg?style=plastic&logo=conda-forge)
+![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/acpype.svg?style=plastic&logo=conda-forge)<!-- ![Conda](https://img.shields.io/conda/pn/conda-forge/acpype?logo=conda-forge&style=plastic) -->
+![PyPI](https://img.shields.io/pypi/v/acpype?style=plastic&logo=pypi)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/acpype?style=plastic&logo=pypi)
+![GitHub Workflow Status](https://img.shields.io/github/workflow/status/alanwilter/acpype/check_acpype)
+<!-- ![Scrutinizer code quality (GitHub/Bitbucket)](https://img.shields.io/scrutinizer/quality/g/alanwilter/acpype) -->
+<!-- ![Scrutinizer coverage (GitHub/BitBucket)](https://img.shields.io/scrutinizer/coverage/g/alanwilter/acpype) -->
 
 ## AnteChamber PYthon Parser interfacE
 
@@ -87,21 +92,33 @@ There are several ways of obtaining `acpype`:
 
 1. Via **[CONDA](https://anaconda.org/search?q=acpype)**:
 
+   *(It should be wholesome, fully funcional, all batteries included)*
+
    ```bash
    conda install -c conda-forge acpype
    ```
 
 2. Via **[PyPI](https://pypi.org/project/acpype/)**:
 
+   *(Make sure you  have `AmberTools` and, optionally but highly recommended, `OpenBabel` )*
+
    ```bash
+   # You can use conda to get the needed 3rd parties for example
+   conda create -n acpype --channel conda-forge ambertools openbabel
+
+   pip install acpype
+   
+   # or if you daring
+   
    pip install git+https://github.com/alanwilter/acpype.git
    ```
 
-   note that `pip install acpype`, unfortunately, is not *yet* picking the original one.
-
 3. By downloading it via `git`:
 
+   *(Make sure you  have `AmberTools` and, optionally but highly recommended, `OpenBabel` )*
+
    ```bash
+   # You can use conda to get the needed 3rd parties for example
    conda create -n acpype --channel conda-forge ambertools openbabel
    git clone https://github.com/alanwilter/acpype.git
    ```
@@ -110,6 +127,8 @@ There are several ways of obtaining `acpype`:
 
 4. Via **[Docker](https://hub.docker.com/repository/docker/acpype/acpype/)**:
 
+   *(It should be wholesome, fully funcional, all batteries included)*
+
    If you have Docker installed, you can run `acpype_docker.sh` by:
 
    NOTE: first time may take some time as it pulls the `acpype` docker image.
@@ -137,7 +156,10 @@ There are several ways of obtaining `acpype`:
    docker run -i -t --rm -v ${PWD}:/wdir -w /wdir acpype bash
    ```
 
-**NB:** Installing via `conda` or via `pip/git` you get `AmberTools v.21.11` and `OpenBabel v3.11`. Our `AmberTools v.21.11` comes with binary `charmmgen` from `AmberTools17` in order to generate CHARMM topologies.
+**NB:**
+
+- By installing via `conda` or using via `docker` you get `AmberTools v.21.11` and `OpenBabel v3.1.1`. Our `AmberTools v.21.11` comes with binary `charmmgen` from `AmberTools17` in order to generate CHARMM topologies.
+- By installing via `pip` you get `AmberTools` (as described above) embeded. However, the included binaries may not work in your system (library dependecies issues) and with only provide binaries for Linux (Ubuntu20) and Mac OSX.
 
 ##### To Test, if doing via `git`
 
@@ -236,4 +258,4 @@ cns < FFF_CNS.inp
 
 #### To Verify with NAMD
 
-- see [TutorialNAMD]
+- see [TutorialNAMD](../../Tutorial-NAMD)

From ceef3f57c9c43a5e2038b0cbad9e39ba85d479ae Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Mon, 29 Nov 2021 19:59:26 +0000
Subject: [PATCH 12/15] Fixed typos

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 54026a1d..62aae06c 100644
--- a/README.md
+++ b/README.md
@@ -108,7 +108,7 @@ There are several ways of obtaining `acpype`:
 
    pip install acpype
    
-   # or if you daring
+   # or if you feel daring
    
    pip install git+https://github.com/alanwilter/acpype.git
    ```
@@ -258,4 +258,4 @@ cns < FFF_CNS.inp
 
 #### To Verify with NAMD
 
-- see [TutorialNAMD](../../Tutorial-NAMD)
+- see [TutorialNAMD](../../wiki/Tutorial-NAMD)

From e4cd7b0a9d580497e3eb5610588289903b4b8fff Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Mon, 29 Nov 2021 20:23:44 +0000
Subject: [PATCH 13/15] Better documented tests, total coverage 92%

---
 tests/conftest.py     | 10 ++++++++++
 tests/test_acpype.py  | 12 ------------
 tests/test_acs_api.py | 12 ------------
 3 files changed, 10 insertions(+), 24 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index aae41e23..3f681d1c 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,3 +1,13 @@
+"""
+Requirements:
+* pytest
+* pytest-html
+
+To run:
+pytest -s --html=report.html
+pytest --cov=acpype_lib --cov-report=term-missing:skip-covered
+"""
+
 from acpype_lib import __version__ as version
 
 
diff --git a/tests/test_acpype.py b/tests/test_acpype.py
index 9dc4b6da..788d6aa3 100644
--- a/tests/test_acpype.py
+++ b/tests/test_acpype.py
@@ -1,15 +1,3 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-"""
-Requirements:
-* pytest
-* pytest-html
-
-To run:
-pytest -s --html=report.html
-
-"""
 import os
 import shutil
 import pytest
diff --git a/tests/test_acs_api.py b/tests/test_acs_api.py
index 560ba0ed..ab0db65c 100644
--- a/tests/test_acs_api.py
+++ b/tests/test_acs_api.py
@@ -1,15 +1,3 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-"""
-Requirements:
-* pytest
-* pytest-html
-
-To run:
-pytest -s --html=report.html
-
-"""
 import os
 import ujson as json
 from acpype_lib.acs_api import acpype_api

From ac289b17a7a92ae8d975e23d88fe390f7f00d713 Mon Sep 17 00:00:00 2001
From: lkagami <luciano.kagami@ufrgs.br>
Date: Mon, 29 Nov 2021 18:45:32 -0300
Subject: [PATCH 14/15] add acpype_docker.bat file

---
 README.md         | 20 +++++++++-----------
 acpype_docker.bat |  2 ++
 2 files changed, 11 insertions(+), 11 deletions(-)
 create mode 100755 acpype_docker.bat

diff --git a/README.md b/README.md
index 62aae06c..58095da6 100644
--- a/README.md
+++ b/README.md
@@ -107,9 +107,9 @@ There are several ways of obtaining `acpype`:
    conda create -n acpype --channel conda-forge ambertools openbabel
 
    pip install acpype
-   
+
    # or if you feel daring
-   
+
    pip install git+https://github.com/alanwilter/acpype.git
    ```
 
@@ -138,24 +138,22 @@ There are several ways of obtaining `acpype`:
    ```bash
    ln -fsv "$PWD/acpype_docker.sh" /usr/local/bin/acpype_docker
 
-   acpype_docker -i CCCC
-   
-   acpype_docker -i tests/DDD.pdb -c gas
    ```
 
    On Windows:
    Using Command Prompt:
 
-   ```bash
-   docker run -i -t --rm -v%cd%:/wdir -w /wdir acpype bash
-   ```
-
-   Using PowerShell:
+    In the directory where the `acpype_docker.bat` file is found:
 
    ```bash
-   docker run -i -t --rm -v ${PWD}:/wdir -w /wdir acpype bash
+   setx /M path "%path%;%cd%"
    ```
+   Commands:
+   ```bash
+   acpype_docker -i CCCC
 
+   acpype_docker -i tests/DDD.pdb -c gas
+   ```
 **NB:**
 
 - By installing via `conda` or using via `docker` you get `AmberTools v.21.11` and `OpenBabel v3.1.1`. Our `AmberTools v.21.11` comes with binary `charmmgen` from `AmberTools17` in order to generate CHARMM topologies.
diff --git a/acpype_docker.bat b/acpype_docker.bat
new file mode 100755
index 00000000..ff9d0232
--- /dev/null
+++ b/acpype_docker.bat
@@ -0,0 +1,2 @@
+@echo on
+docker run -i -t -v %cd%:/wdir -w /wdir acpype/acpype acpype %*
\ No newline at end of file

From 69302b0af7bc4be0bc3affa51fbcd4d39ad34dc7 Mon Sep 17 00:00:00 2001
From: Alan Silva <3899850+alanwilter@users.noreply.github.com>
Date: Mon, 29 Nov 2021 21:57:14 +0000
Subject: [PATCH 15/15] Bump version

---
 acpype_lib/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/acpype_lib/__init__.py b/acpype_lib/__init__.py
index 99f6808d..42bb8fdb 100644
--- a/acpype_lib/__init__.py
+++ b/acpype_lib/__init__.py
@@ -1,3 +1,4 @@
 # from https://packaging.python.org/guides/single-sourcing-package-version/
 # using option 2
-__version__ = "2021.11.28"
+# updated automatically via pre-commit git-hook
+__version__ = "2021.11.29"