Author: Andreas Tille
Description: Use 2to3 to port from Python2 to Python3
Bug-Debian: https://bugs.debian.org/942909
Last-Update: Fri, 10 Jan 2020 15:23:50 +0100

--- a/README
+++ b/README
@@ -100,7 +100,7 @@ The general process is:
     On Microsoft Windows when building for MINGW within Cygwin, 
     you need to type here:   rm .deps/*; ../configure
     to run "configure" a second time for reasons we do not understand.
- make check  (optional but recommended, requires "python")
+ make check  (optional but recommended, requires "python3")
  make install (optional, this will install autodock4 executable)
 
  Second, in the src/autogrid directory, do the same steps 
--- a/autodock/Makefile.am
+++ b/autodock/Makefile.am
@@ -608,7 +608,7 @@ test : autodock4 $(srcdir)/Tests/test_au
 endif
 #if HAVE_PYTHON
 	@echo " "
-	@echo "Running the Python test_autodock4.py unit-tests on autodock4"
+	@echo "Running the Python3 test_autodock4.py unit-tests on autodock4"
 	@echo " "
 # for technical reasons, autodock must be run in the directory where the
 # test files reside because it writes its logs into its current directory
@@ -627,13 +627,13 @@ endif
 	cp $(srcdir)/Tests/*.map*  $$outputdir/Testruns;\
 	chmod -fR a+w $$outputdir/Testruns;
 	-cd Testruns; rm -f test_*.dlg ; \
-	python ./test_autodock4.py -d . -e ../autodock4$(EXEEXT) -o . ;
+	python3 ./test_autodock4.py -d . -e ../autodock4$(EXEEXT) -o . ;
 if WANT_OMP
 	@echo " "
-	@echo "Running the Python test_autodock4.py unit-tests on autodock4.omp"
+	@echo "Running the Python3 test_autodock4.py unit-tests on autodock4.omp"
 	@echo " "
 	-cd Testruns; rm -f test_*.dlg ; \
-	python ./test_autodock4.py -d . -e ../autodock4.omp$(EXEEXT) -o . ;
+	python3 ./test_autodock4.py -d . -e ../autodock4.omp$(EXEEXT) -o . ;
 endif
 
 #else
--- a/autodock/Makefile.in
+++ b/autodock/Makefile.in
@@ -3982,7 +3982,7 @@ check : test
 @WANT_OMP_FALSE@test : autodock4 $(srcdir)/Tests/test_autodock4.py
 #if HAVE_PYTHON
 	@echo " "
-	@echo "Running the Python test_autodock4.py unit-tests on autodock4"
+	@echo "Running the Python3 test_autodock4.py unit-tests on autodock4"
 	@echo " "
 # for technical reasons, autodock must be run in the directory where the
 # test files reside because it writes its logs into its current directory
@@ -4001,12 +4001,12 @@ check : test
 	cp $(srcdir)/Tests/*.map*  $$outputdir/Testruns;\
 	chmod -fR a+w $$outputdir/Testruns;
 	-cd Testruns; rm -f test_*.dlg ; \
-	python ./test_autodock4.py -d . -e ../autodock4$(EXEEXT) -o . ;
+	python3 ./test_autodock4.py -d . -e ../autodock4$(EXEEXT) -o . ;
 @WANT_OMP_TRUE@	@echo " "
-@WANT_OMP_TRUE@	@echo "Running the Python test_autodock4.py unit-tests on autodock4.omp"
+@WANT_OMP_TRUE@	@echo "Running the Python3 test_autodock4.py unit-tests on autodock4.omp"
 @WANT_OMP_TRUE@	@echo " "
 @WANT_OMP_TRUE@	-cd Testruns; rm -f test_*.dlg ; \
-@WANT_OMP_TRUE@	python ./test_autodock4.py -d . -e ../autodock4.omp$(EXEEXT) -o . ;
+@WANT_OMP_TRUE@	python3 ./test_autodock4.py -d . -e ../autodock4.omp$(EXEEXT) -o . ;
 
 #else
 #	@echo " "
--- a/autodock/README
+++ b/autodock/README
@@ -100,7 +100,7 @@ The general process is:
     On Microsoft Windows when building for MINGW within Cygwin, 
     you need to type here:   rm .deps/*; ../configure
     to run "configure" a second time for reasons we do not understand.
- make check  (optional but recommended, requires "python")
+ make check  (optional but recommended, requires "python3")
  make install (optional, this will install autodock4 executable)
 
  Second, in the src/autogrid directory, do the same steps 
--- a/autodock/Tests/DlgParser.py
+++ b/autodock/Tests/DlgParser.py
@@ -23,7 +23,6 @@ This Object parses the result of an Auto
 
 """
 import os
-from string import find, join, replace, split, rfind, strip
 import re
 #import Numeric
 
@@ -125,7 +124,7 @@ class DlgParser:
 
     def getReDict(self):
         if hasattr(self, 'reDict'):
-            for k, d in self.reDict.items():
+            for k, d in list(self.reDict.items()):
                 d['lines'] = []
             return
         self.reDict = {}
@@ -195,19 +194,19 @@ class DlgParser:
                 input_key = 'INPUT-LIGAND-PDBQT: '
                 if k==input_key:
                     if verbose and self.version[:3]!="4.0":
-                        print "!!no lines found for key=", k, "!!"
+                        print("!!no lines found for key=", k, "!!")
                 else:
                     if verbose:
-                        print "!!no lines found for key=", k, "!!"
+                        print("!!no lines found for key=", k, "!!")
             else:
-                apply(d['func'], (lines,), {})
+                d['func'](*(lines,), **{})
 
 
     def setADVersion(self,lines):
         if len(lines):
             for l in lines:
-                if find(l, 'AutoDock')>-1:
-                    ll = split(l)
+                if l.find('AutoDock')>-1:
+                    ll = l.split()
                     self.version = ll[2]
                     break
         else:
@@ -216,7 +215,7 @@ class DlgParser:
 
     def setOutlev(self,lines):
         if len(lines):
-            ll = split(lines[0])
+            ll = lines[0].split()
             self.outlev = int(ll[2])
         else:
             self.outlev = None
@@ -228,7 +227,7 @@ class DlgParser:
 
 
     def getLigandAtomCount(self, lines):
-        self.ligand_atom_count = int(split(lines[0])[-2])
+        self.ligand_atom_count = int(lines[0].split()[-2])
         #print "parsed ligand_atom_count =", self.ligand_atom_count
 
     def getNonBondTable(self, lines, echo=False):
@@ -244,7 +243,7 @@ class DlgParser:
                 
         if echo:
             for l in nb_lines:
-                print l,
+                print(l, end=' ')
         for i in range(ct):
             l = nb_lines[i][10:-1]
             for j in range(ct):
@@ -252,15 +251,15 @@ class DlgParser:
                 if l[jind]=='X':
                     self.nb_array[i][j]=1
             if echo:
-                print
-                print l
-                print self.nb_array[i]
+                print()
+                print(l)
+                print(self.nb_array[i])
 
 
     def getSeedInfo(self, lines):
         seeds = []
         for l in lines:
-            ilist = split(l)
+            ilist = l.split()
             slist = []
             for item in ilist[1:]:
                 slist.append(int(item))
@@ -269,7 +268,7 @@ class DlgParser:
         if len(seeds)==len(self.clist):
             for i in range(len(seeds)):
                 conf = self.clist[i]
-                if not conf.has_key('run'):
+                if 'run' not in conf:
                     continue
                     #outlev -1 prints States in order
                     #s = seeds[i]
@@ -295,9 +294,9 @@ class DlgParser:
         cl = self.clusterlines
         hl = self.histogramlines
         for l in lines:
-            if find(l, 'RANKING')>-1:
+            if l.find('RANKING')>-1:
                 cl.append(l[:-1])
-            elif find(l, '#')>-1:
+            elif l.find('#')>-1:
                 hl.append(l[:-1])
         if len(cl):
             self.getClusterRecord(cl)
@@ -310,19 +309,19 @@ class DlgParser:
         clRecList = []
         curList = []
         #curList gets list of conf info
-        curInd = int(split(cl[0])[0])
+        curInd = int(cl[0].split()[0])
         ctr = 1
         for l in cl:
-            ll = split(l)
+            ll = l.split()
             #when built, newList is
             #[Rank,SubRank,Run,DockedEnergy,ClusterRMSD,RefREMSD]
-            newList = map(lambda x:int(x),ll[:3])
+            newList = [int(x) for x in ll[:3]]
             #3/29/05
             if self.wroteAll and self.version[:3]!="4.0":
                 #print "setting run number to ", ctr
                 newList[2] = ctr
                 ctr = ctr + 1
-            newList2 = map(lambda x:float(x),ll[3:-1])
+            newList2 = [float(x) for x in ll[3:-1]]
             newList.extend(newList2)
             if newList[0]==curInd:
                 curList.append(newList)
@@ -340,7 +339,7 @@ class DlgParser:
             if len(l[:-1])>5:
                 self.dpfLines.append(l[5:-1])
                 if l.find('ga_run')>-1:
-                    ll = split(l)
+                    ll = l.split()
                     self.runs = int(ll[2])
                     #print "self.runs=", self.runs
 
@@ -351,7 +350,7 @@ class DlgParser:
         dpfLines = []
         keys = []
         for l in lines:
-            ll = split(l)
+            ll = l.split()
             ind = ll.index('NEWDPF')
             k = ll[ind+1]
             #only add each key once
@@ -371,9 +370,9 @@ class DlgParser:
         foundRun = 0
         for l in lines:
             #in clustering dlg, multiple copies of input-pdbq are present
-            if find(l, 'Run')>-1 and foundRun:
+            if l.find('Run')>-1 and foundRun:
                 break
-            elif find(l, 'Run')>-1:
+            elif l.find('Run')>-1:
                 foundRun = 1
             else:
                 ligLINES.append(l[12:-1])
@@ -389,18 +388,18 @@ class DlgParser:
     def processFlexResLinesV4(self, lines):
         #print "in processFlexResLinesV4: len(self.ligLines=)", len(self.ligLines)
         if self.version[:3]!="4.0":
-            print "not version 4.0! RETURNING!!"
+            print("not version 4.0! RETURNING!!")
             return
         ligLINES = []
         foundRun = 0
         ind = 21
         for l in lines:
             #in clustering dlg, multiple copies of input-pdbq are present
-            if find(l, 'Run')>-1 and foundRun:
+            if l.find('Run')>-1 and foundRun:
                 break
-            elif find(l, 'Run')>-1:
+            elif l.find('Run')>-1:
                 foundRun = 1
-            elif find(l, '^_____________________')>-1:
+            elif l.find('^_____________________')>-1:
                 #last line is ________________-
                 break
             else:
@@ -431,18 +430,18 @@ class DlgParser:
             return
         ligLINES = []
         foundRun = 0
-        if find(lines[0], 'INPUT-LIGAND-PDBQT')==0:
+        if lines[0].find('INPUT-LIGAND-PDBQT')==0:
             ind = 20
-        elif find(lines[0], 'INPUT-PDBQ')==0:
+        elif lines[0].find('INPUT-PDBQ')==0:
             ind = 13
 
         for l in lines:
             #in clustering dlg, multiple copies of input-pdbq are present
-            if find(l, 'Run')>-1 and foundRun:
+            if l.find('Run')>-1 and foundRun:
                 break
-            elif find(l, 'Run')>-1:
+            elif l.find('Run')>-1:
                 foundRun = 1
-            elif find(l, 'TORSDOF')>-1:
+            elif l.find('TORSDOF')>-1:
                 #eg run-on TORSDOF line: 
                 #TORSDOF 3___
                 lastChar = l.find('_')
@@ -454,8 +453,8 @@ class DlgParser:
                     #print "found TORSDOF on last line!"
                     break
                 next_line = lines[l_index+1]
-                if find(next_line, 'BEGIN_RES')<0:
-                    print len(lines[l_index:]), ' lines left unparsed!!!'
+                if next_line.find('BEGIN_RES')<0:
+                    print(len(lines[l_index:]), ' lines left unparsed!!!')
                     break
             else:
                 #ligLINES.append(l[13:-1])
@@ -474,11 +473,11 @@ class DlgParser:
         if not len(lines):
             return
         modelList = []
-        if find(lines[0], 'DOCKED')==0:
+        if lines[0].find('DOCKED')==0:
             ind = 8
-        elif find(lines[0], 'INPUT-LIGAND-PDBQT')==0:
+        elif lines[0].find('INPUT-LIGAND-PDBQT')==0:
             ind = 20
-        elif find(lines[0], 'INPUT-PDBQ')==0:
+        elif lines[0].find('INPUT-PDBQ')==0:
             ind = 12
         #preprocess lines to remove DOCKED or INPUT-PDBQ
         nlines = []
@@ -489,7 +488,7 @@ class DlgParser:
             #if self.version[:3]!=4.0:
             #    nlines.append(l[ind:-1])
             #else:
-            #    if find(l, 'ATOM')>-1:
+            #    if l.find('ATOM')>-1:
             #        newLine = l[ind:64] + l[66:-1]
             #        nlines.append(newLine)
             #    else:
@@ -512,7 +511,7 @@ class DlgParser:
                         try:
                             nlines.append(l[ind:-1])
                         except:
-                            print 'cutting out 64+65 of ', l
+                            print('cutting out 64+65 of ', l)
                             nlines.append(l[ind:64]+ l[66:-1])
                     else:
                         nlines.append(l[ind:-1])
@@ -522,7 +521,7 @@ class DlgParser:
         if self.version[:3]!=4.0:
             curMod = [nlines[0]]
             for l in nlines[1:]:
-                if find(l, 'MODEL')>-1:
+                if l.find('MODEL')>-1:
                     modelList.append(curMod)
                     curMod = [l]
                 else:
@@ -548,7 +547,7 @@ class DlgParser:
             #use endmdl because cluster dlg format
             # has MODEL then lines w/o MODEL then MODEL
             #again in desc of 1 model...
-            if find(l, 'ENDMDL')>-1:
+            if l.find('ENDMDL')>-1:
                 curMod.append(l)
                 modelList.append(curMod)
                 endmdl = 1
@@ -576,7 +575,7 @@ class DlgParser:
             self.clist = []
         for l in lines:
             # in test-1 State= + 17 items: 3 trans, 4quat + ndihe(10) torsions
-            xx = split(l)
+            xx = l.split()
             # remove possible punctuation
             for ind in range(len(xx)):
                 if xx[ind][-1]==',': 
@@ -643,74 +642,74 @@ class DlgParser:
         binding_energy2 = None
         version = self.version[:3]
         for l in lines:
-            ll = split(l)
-            #if find(l, 'MODEL')>-1:
+            ll = l.split()
+            #if l.find('MODEL')>-1:
             #    d['num'] = int((ll)[1])
-            if find(l, 'Run')>-1 and find(l, 'Rank')==-1:
+            if l.find('Run')>-1 and l.find('Rank')==-1:
                 d['run'] = int((ll)[3])
-            elif find(l, 'Estimated Free Energy of Binding')>-1:
+            elif l.find('Estimated Free Energy of Binding')>-1:
                 d['binding_energy'] = float((ll)[7])
                 if version==4.0: d['energy'] = float((ll)[7])
-            elif find(l, 'vdW + Hbond + desolv Energy')>-1:
+            elif l.find('vdW + Hbond + desolv Energy')>-1:
                 d['vdw_hb_desolv_energy'] = float((ll)[8])
-            elif find(l, 'Electrostatic Energy')>-1:
+            elif l.find('Electrostatic Energy')>-1:
                 d['electrostatic_energy'] = float((ll)[4])
-            elif find(l, 'Moving Ligand-Fixed Receptor')>-1:
+            elif l.find('Moving Ligand-Fixed Receptor')>-1:
                 d['moving_ligand_fixed_receptor'] = float((ll)[5])
-            elif find(l, 'Moving Ligand-Moving Receptor')>-1:
+            elif l.find('Moving Ligand-Moving Receptor')>-1:
                 d['moving_ligand_moving_receptor'] = float((ll)[5])
-            elif find(l, 'Total Internal Energy')>-1:
+            elif l.find('Total Internal Energy')>-1:
                 d['total_internal'] = float((ll)[7])
-            elif find(l, 'Internal Energy Ligand')>-1:
+            elif l.find('Internal Energy Ligand')>-1:
                 d['ligand_internal'] = float((ll)[5])
-            elif find(l, 'Internal Energy Receptor')>-1:
+            elif l.find('Internal Energy Receptor')>-1:
                 d['receptor_internal'] = float((ll)[5])
-            elif find(l, 'Torsional Free Energy')>-1:
+            elif l.find('Torsional Free Energy')>-1:
                 d['torsional_energy'] = float((ll)[6])
-            elif find(l, 'Estimated Inhibition Constant')>-1:
-                if find(l, 'N/A') < 0:
+            elif l.find('Estimated Inhibition Constant')>-1:
+                if l.find('N/A') < 0:
                     d['inhib_constant'] = float((ll)[6])
                     if version==4.0:
                         d['inhib_constant_units'] = ll[7]
-            elif find(l, 'Final Docked Energy')>-1:
+            elif l.find('Final Docked Energy')>-1:
                 d['docking_energy'] = float((ll)[5])
-            elif find(l, 'Final Intermolecular Energy')>-1:
+            elif l.find('Final Intermolecular Energy')>-1:
                 d['intermol_energy'] = float((ll)[6])
-            elif find(l, 'Final Internal Energy of Ligand')>-1:
+            elif l.find('Final Internal Energy of Ligand')>-1:
                 d['internal_energy'] = float((ll)[8])
-            elif find(l, 'Final Internal Energy')>-1:
+            elif l.find('Final Internal Energy')>-1:
                 d['internal_energy'] = float((ll)[6])
-            elif find(l, 'Torsional Free Energy')>-1:
+            elif l.find('Torsional Free Energy')>-1:
                 d['torsional_energy'] = float((ll)[6])
-            elif find(l, 'NEWDPF tran0')>-1:
+            elif l.find('NEWDPF tran0')>-1:
                 d['trn_x'] = float(ll[3])
                 d['trn_y'] = float(ll[4])
                 d['trn_z'] = float(ll[5])
-            elif find(l, 'NEWDPF quat0')>-1:
+            elif l.find('NEWDPF quat0')>-1:
                 d['qtn_nx'] = float(ll[3])
                 d['qtn_ny'] = float(ll[4])
                 d['qtn_nz'] = float(ll[5])
                 d['qtn_ang_deg'] = float(ll[6])
-            elif find(l, 'NEWDPF dihe0')>-1:
+            elif l.find('NEWDPF dihe0')>-1:
                 angList = []
                 for n in ll[3:]:
                     angList.append(float(n))
                 d['torsion_values'] = angList
                 d['num_torsions'] = len(angList)
-            elif find(l, 'Intermol. vdW + Hbond Energy ')>-1:
+            elif l.find('Intermol. vdW + Hbond Energy ')>-1:
                 #AD4 specific model information:
                 # USER         Intermol. vdW + Hbond Energy   =  -14.63 kcal/mol
                 d['vdw_energy'] = float((ll)[7])
-            elif find(l, 'Intermol. Electrostatic Energy')>-1:
+            elif l.find('Intermol. Electrostatic Energy')>-1:
                 #USER         Intermol. Electrostatic Energy =   -0.62 kcal/mol
                 d['estat_energy'] = float((ll)[5])
-            elif find(l, '(3) Torsional Free Energy')>-1:
+            elif l.find('(3) Torsional Free Energy')>-1:
                 #USER    (3) Torsional Free Energy           =   +3.84 kcal/mol
                 d['torsional_energy'] = float((ll)[6])
-            elif find(l, "(4) Unbound System's Energy")>-1:
+            elif l.find("(4) Unbound System's Energy")>-1:
                 #USER    (4) Unbound System's Energy         =   -0.85 kcal/mol
                 d['unbound_energy'] = float((ll)[-2])
-            elif find(l, 'ATOM')>-1:
+            elif l.find('ATOM')>-1:
                 coords.append([float(l[30:38]),float(l[38:46]),float(l[46:54])])
                 try:
                     vdW.append(float(l[54:60]))
@@ -727,7 +726,7 @@ class DlgParser:
                         binding_energy2 = float(l[70:76])
                     except:
                         pass
-            elif find(l, 'HETA')>-1:
+            elif l.find('HETA')>-1:
                 coords.append([float(l[30:38]),float(l[38:46]),float(l[46:54])])
                 try:
                     vdW.append(float(l[54:60]))
@@ -744,7 +743,7 @@ class DlgParser:
             for i in range(len(vdW)):
                 d['total_energies'].append(vdW[i]+Elec[i])
             #d['total_energies'] = Numeric.array(Numeric.array(vdW)+Numeric.array(Elec)).tolist()
-            if binding_energy2 and not d.has_key('binding_energy'):
+            if binding_energy2 and 'binding_energy' not in d:
                 d['binding_energy'] = binding_energy2
                 d['docking_energy'] = binding_energy2
         return d
--- a/autodock/Tests/test_autodock4.py
+++ b/autodock/Tests/test_autodock4.py
@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#!/usr/bin/python3
 #
 # $Id: test_autodock4.py,v 1.74 2014/07/16 23:27:27 mp Exp $
 #
@@ -28,7 +28,7 @@ fnull = open(os.devnull, "w")
 try:
     opts, argv = getopt.getopt(sys.argv[1:], "d:e:o:",
     ["dpf-directory=","executable=","test-output-directory="]) 
-except getopt.GetoptError, v:
+except getopt.GetoptError as v:
     usage() 
     sys.exit(2)
 
@@ -45,7 +45,7 @@ for o,a in opts:
 
 def usage():
     """Print out the usage of this command."""
-    print """Usage:  python test_autodock4.py [-d <string>] [-e <string>] [-o <string>]
+    print("""Usage: python3 test_autodock4.py [-d <string>] [-e <string>] [-o <string>]
 
 where:
     -d, --dpf-directory
@@ -59,7 +59,7 @@ where:
         this flag is optional; default is '.'
 
 NOTE:  these may be relative to the directory where this script was invoked.
-"""
+""")
 
 #______________________________________________________________________________
 
@@ -72,13 +72,13 @@ def run_AutoDock( dpf_filename, dlg_file
     dlg = test_output_directory + os.sep + dlg_filename
     rm( dlg )
     command =   [autodock_executable, '-p', dpf, '-l', dlg ] 
-    print '\nRunning ' + autodock_executable + ' using DPF "'+dpf+'", saving results in "'+dlg+'":'
+    print('\nRunning ' + autodock_executable + ' using DPF "'+dpf+'", saving results in "'+dlg+'":')
     try:
         rc = subprocess.call( command, stdout = fnull, stderr = fnull )
 	#print 'autodock returned ', rc  # DEBUG
         return find_success_in_DLG( dlg_filename )
-    except OSError,e:
-        print "\nUnable to run " + autodock_executable + " :", e
+    except OSError as e:
+        print("\nUnable to run " + autodock_executable + " :", e)
         return False
 
 #______________________________________________________________________________
@@ -93,7 +93,7 @@ def parse_energy_from_DLG( dlg_filename,
     result = []
     for energy_type in energy_list:
         newVal = docked.get(energy_type, 'ERROR')
-        print energy_type, ' is now ', newVal
+        print(energy_type, ' is now ', newVal)
         result.append(docked.get(energy_type, 'ERROR'))
     #intermol_energy = docked['intermol_energy']  #-6.17
     #internal_energy = docked['total_internal']  # -1.58
@@ -132,8 +132,8 @@ def rm( filename ):
     if os.access(filename, os.F_OK) :
        try:
           os.remove( filename )
-       except OSError,e:
-         print 'unable to remove '+filename
+       except OSError as e:
+         print('unable to remove '+filename)
 
 
 #______________________________________________________________________________
@@ -173,9 +173,9 @@ class AutoDock_simple_test( unittest.Tes
         """Check that run finished and a new DLG has been computed."""
         # Check that run finished and a new DLG has been computed.
         if (self.expected_outcome == True ):
-            print "Testing that DLG exists and AutoDock successfully completed."
+            print("Testing that DLG exists and AutoDock successfully completed.")
         else:
-            print "Testing that DLG exists and AutoDock did not complete."
+            print("Testing that DLG exists and AutoDock did not complete.")
         self.assertEqual( self.computed, self.expected_outcome )
 #______________________________________________________________________________
 
@@ -183,7 +183,7 @@ class AutoDock4_1pgp_no_extension( AutoD
     """Test that autodock4 stops early if .dpf extension is missing
     keywords are specified."""
     dpf_stem = "1pgp_no_extension"
-    print "in 1pgp_no_extension"
+    print("in 1pgp_no_extension")
     expected_outcome = False # True means Successful Completion!
     def setUp( self ):
         """Set up for autodock4 tests. Locate the autodock binary now during setUp."""
@@ -196,7 +196,7 @@ class AutoDock4_1pgp_wrong_extension( Au
     """Test that autodock4 stops early if extension is not '.dpf'
     keywords are specified."""
     dpf_stem = "1pgp.fpd"
-    print "in 1pgp_wrong_extension"
+    print("in 1pgp_wrong_extension")
     expected_outcome = False # True means Successful Completion!
     def setUp( self ):
         """Set up for autodock4 tests. Locate the autodock binary now during setUp."""
@@ -210,7 +210,7 @@ class AutoDock4_1pgp_two_extensions( Aut
     """Test that autodock4 stops early if dpf name includes two .dpf
     keywords are specified."""
     dpf_stem = "1pgp.dpf"
-    print "in 1pgp_two_extensions"
+    print("in 1pgp_two_extensions")
     expected_outcome = False # True means Successful Completion!
     def setUp( self ):
         """Set up for autodock4 tests. Locate the autodock binary now during setUp."""
@@ -557,18 +557,18 @@ class AutoDock_test( AutoDock_base_test
         Also check the final energy is the expected value."""
         # Check that run finished and a new DLG has been computed.
         if (self.expected_outcome == True ):
-            print "Testing that DLG exists and AutoDock successfully completed."
+            print("Testing that DLG exists and AutoDock successfully completed.")
         else:
-            print "Testing that DLG exists and AutoDock did not complete."
+            print("Testing that DLG exists and AutoDock did not complete.")
         self.assertEqual( self.computed, self.expected_outcome )
         # Check the final energy is expected value.
         # These values are for the quick GALS search in 1pgp.dpf and relatives
         expected_intermol_energy = -6.17  # -6.44 for Real==float, -6.17 for Real==double
         expected_internal_energy = -3.23  # -3.28 for Real==float, -3.23 for Real==double
         (intermol_energy, internal_energy) = parse_energy_from_DLG( self.dlg_filename, ['intermol_energy','total_internal'] )
-        print "Testing that intermolecular energy = %.2f kcal/mol." % (expected_intermol_energy,)
+        print("Testing that intermolecular energy = %.2f kcal/mol." % (expected_intermol_energy,))
         self.assertEqual( round(intermol_energy,6), round(expected_intermol_energy,6))
-        print "Testing that internal energy = %.2f kcal/mol." % (expected_internal_energy,)
+        print("Testing that internal energy = %.2f kcal/mol." % (expected_internal_energy,))
         self.assertEqual( round(internal_energy,6), round(expected_internal_energy,6))
 #______________________________________________________________________________
 
@@ -741,16 +741,16 @@ class AutoDock4_energy_test( AutoDock_ba
         Also check the final energy is the expected value."""
         # Check that run finished and a new DLG has been computed.
         if (self.expected_outcome == True ):
-            print "Testing that DLG exists and AutoDock successfully completed."
+            print("Testing that DLG exists and AutoDock successfully completed.")
         else:
-            print "Testing that DLG exists and AutoDock did not complete."
+            print("Testing that DLG exists and AutoDock did not complete.")
         self.assertEqual( self.computed, self.expected_outcome )
         # Check the final energy is expected value.
         #expected_unbound_energy = -3.23
         #expected_binding_energy = +843.59     -5.87
         (binding_energy) = parse_energy_from_DLG( self.dlg_filename, ['binding_energy'])[0]
-        print "Testing that binding energy = %.2f kcal/mol." % (self.expected_binding_energy,)
-        print "binding_energy=", binding_energy
+        print("Testing that binding energy = %.2f kcal/mol." % (self.expected_binding_energy,))
+        print("binding_energy=", binding_energy)
         self.assertEqual( round(binding_energy,6), round(self.expected_binding_energy,6))
 #______________________________________________________________________________
 
@@ -764,15 +764,15 @@ class AutoDock4_unbound_test( AutoDock_b
         Also check the final energy is the expected value."""
         # Check that run finished and a new DLG has been computed.
         if (self.expected_outcome == True ):
-            print "Testing that DLG exists and AutoDock successfully completed."
+            print("Testing that DLG exists and AutoDock successfully completed.")
         else:
-            print "Testing that DLG exists and AutoDock did not complete."
+            print("Testing that DLG exists and AutoDock did not complete.")
         self.assertEqual( self.computed, self.expected_outcome )
         # Check the final energy is expected value.
         #expected_unbound_energy = -3.23
         (unbound_energy) = parse_energy_from_DLG( self.dlg_filename, ['unbound_energy'])[0]
-        print "Testing that unbound energy = %.2f kcal/mol." % (self.expected_unbound_energy,)
-        print "unbound_energy=", unbound_energy
+        print("Testing that unbound energy = %.2f kcal/mol." % (self.expected_unbound_energy,))
+        print("unbound_energy=", unbound_energy)
         self.assertEqual( round(unbound_energy,6), round(self.expected_unbound_energy,6))
 #______________________________________________________________________________
 
--- a/autodock/makecheck
+++ b/autodock/makecheck
@@ -4,7 +4,7 @@
 #
 # $Id: makecheck,v 1.2 2012/10/25 16:55:21 mp Exp $
 #
-echo "Running the Python test_autodock4.py unit-tests on ../autodock4"
+echo "Running the Python3 test_autodock4.py unit-tests on ../autodock4"
 outputdir=`pwd` ;\
 	umask 0 ;\
 	test -d $outputdir/Tests || mkdir $outputdir/Tests ;\
@@ -15,4 +15,4 @@ outputdir=`pwd` ;\
     cp ../Tests/*.dpf  $outputdir/Tests;\
     cp ../Tests/*.pdbqt  $outputdir/Tests;\
     cp ../Tests/*.map*  $outputdir/Tests;\
-	cd Tests ;  python ./test_autodock4.py -d . -e ../autodock4 -o .
+	cd Tests ;  python3 ./test_autodock4.py -d . -e ../autodock4 -o .
--- a/autogrid/Makefile.am
+++ b/autogrid/Makefile.am
@@ -129,7 +129,7 @@ check : test
 test : autogrid4 $(srcdir)/Tests/test_autogrid4.py
 #if HAVE_PYTHON
 	@echo " "
-	@echo "Running the Python test_autogrid4.py unit-tests on autogrid4"
+	@echo "Running the Python3 test_autogrid4.py unit-tests on autogrid4"
 	@echo " "
 # for technical reasons, autogrid must be run in the directory where the
 # test files reside because it writes its maps into its current directory
@@ -147,7 +147,7 @@ test : autogrid4 $(srcdir)/Tests/test_au
 	cp $(srcdir)/Tests/*.map*  $$outputdir/Testruns;\
 	chmod -fR a+w $$outputdir/Testruns;\
 	cd $$outputdir/Testruns;\
-	python ./test_autogrid4.py -d . -e ../autogrid4$(EXEEXT) -o .
+	python3 ./test_autogrid4.py -d . -e ../autogrid4$(EXEEXT) -o .
 #else
 #	@echo " "
 #	@echo "Python version 2.1 or higher needed for 'make test', but not found."
--- a/autogrid/Makefile.in
+++ b/autogrid/Makefile.in
@@ -1097,7 +1097,7 @@ check : test
 test : autogrid4 $(srcdir)/Tests/test_autogrid4.py
 #if HAVE_PYTHON
 	@echo " "
-	@echo "Running the Python test_autogrid4.py unit-tests on autogrid4"
+	@echo "Running the Python3 test_autogrid4.py unit-tests on autogrid4"
 	@echo " "
 # for technical reasons, autogrid must be run in the directory where the
 # test files reside because it writes its maps into its current directory
@@ -1115,7 +1115,7 @@ test : autogrid4 $(srcdir)/Tests/test_au
 	cp $(srcdir)/Tests/*.map*  $$outputdir/Testruns;\
 	chmod -fR a+w $$outputdir/Testruns;\
 	cd $$outputdir/Testruns;\
-	python ./test_autogrid4.py -d . -e ../autogrid4$(EXEEXT) -o .
+	python3 ./test_autogrid4.py -d . -e ../autogrid4$(EXEEXT) -o .
 #else
 #	@echo " "
 #	@echo "Python version 2.1 or higher needed for 'make test', but not found."
--- a/autogrid/Tests/test_autogrid4.py
+++ b/autogrid/Tests/test_autogrid4.py
@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#!/usr/bin/python3
 # 
 #
 # $Id: test_autogrid4.py,v 1.18 2013/11/14 22:16:02 mp Exp $
@@ -15,7 +15,6 @@ import types
 import unittest
 import getopt
 import subprocess
-from string import split, strip
 
 #______________________________________________________________________________
 #
@@ -28,7 +27,7 @@ test_output_directory = '.' # where the
 try:
     opts, argv = getopt.getopt(sys.argv[1:], "d:g:e:o:",
     ["gpf-directory=","gpf-directory=","executable=","test-output-directory="]) 
-except getopt.GetoptError, v:
+except getopt.GetoptError as v:
     usage() 
     sys.exit(2)
 
@@ -59,7 +58,7 @@ built_missing_map = False
 
 def usage():
     """Print out the usage of this command."""
-    print """Usage:  python test_autogrid4.py [-d <string>] [-e <string>] [-o <string>]
+    print("""Usage: python3 test_autogrid4.py [-d <string>] [-e <string>] [-o <string>]
 
 where:
     -d, --gpf-directory
@@ -73,7 +72,7 @@ where:
         this flag is optional; default is '.'
 
 NOTE:  these may be relative to the directory where this script was invoked.
-"""
+""")
 
 #______________________________________________________________________________
 
@@ -85,13 +84,13 @@ def run_AutoGrid( gpf_filename, glg_file
     glg = test_output_directory + os.sep + glg_filename
     rm(glg)
     command = [ autogrid_executable, '-p', gpf, '-l', glg ]
-    print '\nRunning ' + autogrid_executable + ' using GPF "'+gpf+'", saving results in "'+glg+'":'
+    print('\nRunning ' + autogrid_executable + ' using GPF "'+gpf+'", saving results in "'+glg+'":')
     try:
-	rc = subprocess.call( command )
-	#print 'autogrid returned ', rc  # DEBUG
+        rc = subprocess.call( command )
+        #print 'autogrid returned ', rc  # DEBUG
         return find_success_in_GLG(glg_filename)
-    except OSError, e:
-        print "\nUnable to run " + autogrid_executable + " :", e
+    except OSError as e:
+        print("\nUnable to run " + autogrid_executable + " :", e)
         return False
 
 #______________________________________________________________________________
@@ -121,8 +120,8 @@ def rm( filename ):
     if os.access(filename, os.F_OK) :
        try:
           os.remove( filename )
-       except OSError,e:
-         print 'unable to remove '+filename
+       except OSError as e:
+         print('unable to remove '+filename)
 
 #______________________________________________________________________________
 
@@ -169,14 +168,14 @@ class AutoGrid_hsg1_sm_test(unittest.Tes
         # skip starting lines
         self.assertEqual(len(c_autogrid4_lines), len(py_autogrid4_lines))
         for atomL, py_atomL in zip(c_autogrid4_lines[6:], py_autogrid4_lines[6:]):
-            c_num = float(strip(atomL))
-            py_num = float(strip(py_atomL))
+            c_num = float(atomL.strip())
+            py_num = float(py_atomL.strip())
             if abs(c_num)>.30:
                 # use percentage difference for large(r) values:
                 #  allowing up to 0.5% error 
                 #if ((abs(c_num-py_num)/(c_num))*100.<.5)==False:
                 #    print  "c_num=", c_num," py_num=", py_num, "test=", (abs(c_num-py_num)/(c_num))*100.
-                self.assertEquals(((abs(c_num-py_num)/(c_num))*100.)<.5, True)
+                self.assertEqual(((abs(c_num-py_num)/(c_num))*100.)<.5, True)
             else:
                 #but use precision only for smaller values
                 cutoff = 10**(-precision)
@@ -285,14 +284,14 @@ class AutoGrid_simple_test(unittest.Test
         """ Set up for autogrid4 tests. Locate the autogrid binary now during setUp."""
         self.glg_filename = "test_" + self.gpf_stem + ".glg"
         self.computed = run_AutoGrid(self.gpf_stem + ".gpf", self.glg_filename)
-        print "after call to run_AutoGrid"
+        print("after call to run_AutoGrid")
 
     def test_glg_exists(self):
         #Check that autogrid calculation finished and a new GLG has been computed
         if (self.expected_outcome == True):
-            print "Testing that GLG exists and AutoGrid successfully completed."
+            print("Testing that GLG exists and AutoGrid successfully completed.")
         else:
-            print "Testing that GLG exists and AutoGrid did not complete."
+            print("Testing that GLG exists and AutoGrid did not complete.")
         self.assertEqual(self.computed, self.expected_outcome)
 
 #------------------------------------------------------------------
@@ -350,10 +349,10 @@ if __name__ == '__main__':
         'AutoGrid_control_test',
         #'AutoGrid_ligand_types_before_receptor_test', 
         #3/18/09 not sure of status of ligand_types_before_receptor test, rh
-	'AutoGrid_nbpreps_test',
-	'AutoGrid_nbpreps_illegal_atom_test',
-	'AutoGrid_nbpreps_toofew_test',
-	'AutoGrid_nbpcoeffs_test',
+        'AutoGrid_nbpreps_test',
+        'AutoGrid_nbpreps_illegal_atom_test',
+        'AutoGrid_nbpreps_toofew_test',
+        'AutoGrid_nbpcoeffs_test',
     ]
     unittest.main( argv=([__name__,] + test_cases))  # non-verbose output
     # optional:  for verbose output, use this:
--- a/autogrid/makecheck
+++ b/autogrid/makecheck
@@ -4,7 +4,7 @@
 #
 # $Id: makecheck,v 1.2 2012/10/24 23:40:27 mp Exp $
 #
-echo "Running the Python test_autogrid4.py unit-tests on ../autogrid4"
+echo "Running the Python3 test_autogrid4.py unit-tests on ../autogrid4"
 outputdir=`pwd` ;\
 	umask 0 ;\
 	test -d $outputdir/Tests || mkdir $outputdir/Tests ;\
@@ -16,4 +16,4 @@ outputdir=`pwd` ;\
 	cp ../Tests/*.map*  $outputdir/Tests;\
 	chmod a+w $outputdir/Tests/*;\
 	cd $outputdir/Tests;\
-	python ./test_autogrid4.py -d . -e ../autogrid4 -o .
+	python3 ./test_autogrid4.py -d . -e ../autogrid4 -o .