add recipe for improved-rdock (#31158)

* add recipe for improved-rdock

* style: fix format

* style: fix format again

* Fix location of the directory

* Fix copyright

* Fix according to the reviewer's comments.

* Revert "Fix according to the reviewer's comments."

This reverts commit 4877877dafda4566a18a33c6ffef6e681b4da896.

* Fix according to the reviewer's comments.

* style: fix format

* Update var/spack/repos/builtin/packages/improved-rdock/package.py

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

Co-authored-by: Yuichi Otsuka <otsukay@riken.jp>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

10 files changed, 576 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/improved-rdock/package.py b/var/spack/repos/builtin/packages/improved-rdock/package.py
new file mode 100644
index 0000000000..a32cd3ed2e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/package.py
@@ -0,0 +1,81 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class ImprovedRdock(MakefilePackage):
+    """Improved version of rDock.
+    rDock is a fast and versatile Open Source docking program
+    that can be used to dock small molecules against proteins and
+    nucleic acids.
+    The original version is found at the following URL:
+    https://sourceforge.net/projects/rdock/files/rDock_2013.1_src.tar.gz
+    """
+
+    homepage = "https://github.com/clinfo/improved_rDock"
+    git = "https://github.com/clinfo/improved_rDock.git"
+
+    version('main', branch='main')
+
+    depends_on('popt')
+    depends_on('cppunit')
+    depends_on('openbabel @3.0.0: +python', type='run')
+    depends_on('py-numpy', type='run')
+    depends_on('mpi')
+
+    patch('rdock_ld.patch')
+    patch('rdock_python3.patch', when='^python@3:')
+    patch('rdock_newcxx.patch')
+    patch('rdock_useint.patch')
+    patch('rdock_erase.patch')
+    patch('rdock_loop.patch', when='target=aarch64:')
+    patch('rdock_const.patch', when='%fj')
+    patch('rdock_const2.patch', when='%fj')
+
+    def edit(self, spec, prefix):
+        # compiler path
+        tm = FileFilter(join_path('build', 'tmakelib', 'linux-g++-64',
+                        'tmake.conf'))
+        tm.filter('/usr/bin/gcc', spack_cc)
+        tm.filter('mpicxx', self.spec['mpi'].mpicxx)
+        # compiler option
+        if self.spec.target.family == 'aarch64':
+            tm.filter('-m64', '')
+        if not self.spec.satisfies('%gcc'):
+            tm.filter('-pipe', '')
+
+    def build(self, spec, prefix):
+        with working_dir("build"):
+            make('linux-g++-64')
+
+    def install(self, spec, prefix):
+        for shfile in find('bin', '*'):
+            set_executable(shfile)
+        install_tree('.', prefix)
+
+    def setup_run_environment(self, env):
+        env.set('RBT_ROOT', self.prefix)
+
+    def test(self):
+        copy(join_path(self.prefix.example, '1sj0', '*'), '.')
+        opts = ['-r', '1sj0_rdock.prm', '-was']
+        self.run_test('rbcavity', options=opts)
+
+        mpiexe = self.spec['mpi'].prefix.bin.mpirun
+        opts = [self.prefix.bin.rbdock, '-r', '1sj0_rdock.prm',
+                '-p', 'dock.prm', '-n', '100', '-i', '1sj0_ligand.sd',
+                '-o', '1sj0_docking_out', '-s', '1']
+        self.run_test(str(mpiexe), options=opts)
+
+        opts = [join_path(self.test_suite.current_test_data_dir, 'test.sh')]
+        self.run_test('bash', options=opts)
+
+        pythonexe = self.spec['python'].command.path
+        opts = [self.spec.prefix.bin.sdrmsd,
+                '1sj0_ligand.sd', '1sj0_docking_out_sorted.sd']
+        expected = ['1\t0.55', '100\t7.91']
+        self.run_test(pythonexe, options=opts, expected=expected)
diff --git a/var/spack/repos/builtin/packages/improved-rdock/rdock_const.patch b/var/spack/repos/builtin/packages/improved-rdock/rdock_const.patch
new file mode 100644
index 0000000000..4efadae308
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/rdock_const.patch
@@ -0,0 +1,21 @@
+diff -u -r -N e/src/lib/RbtToken.cxx f/src/lib/RbtToken.cxx
+--- e/src/lib/RbtToken.cxx	2020-10-14 13:45:40.000000000 +0900
++++ f/src/lib/RbtToken.cxx	2020-10-14 13:46:34.000000000 +0900
+@@ -15,7 +15,7 @@
+ #include "RbtDebug.h"
+ 
+ RbtString RbtToken::_CT("RbtToken");
+-
++const RbtVble& _ff = RbtVble();
+     ///////////////////
+     // Constructors
+     ///////////////////
+@@ -24,7 +24,7 @@
+     _RBTOBJECTCOUNTER_CONSTR_(_CT);
+ }
+ 
+-RbtToken::RbtToken(RbtCommands c) : isvble(false), comm(c), vble(RbtVble()) 
++RbtToken::RbtToken(RbtCommands c) : isvble(false), comm(c), vble(_ff) 
+ {
+     _RBTOBJECTCOUNTER_CONSTR_(_CT);
+ }
diff --git a/var/spack/repos/builtin/packages/improved-rdock/rdock_const2.patch b/var/spack/repos/builtin/packages/improved-rdock/rdock_const2.patch
new file mode 100644
index 0000000000..1866e1e1eb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/rdock_const2.patch
@@ -0,0 +1,11 @@
+--- a/src/exe/rbdock.cxx	2021-02-04 13:32:41.561458052 +0900
++++ b/src/exe/rbdock.cxx	2021-02-04 13:33:07.033202240 +0900
+@@ -465,7 +465,7 @@
+ 

+ #ifdef _VISUAL_STUDIO 

+ #else

+-	optCon = poptGetContext(NULL, argc, argv, optionsTable, 0);

++	optCon = poptGetContext(NULL, argc, (const char **) argv, optionsTable, 0);

+ 	poptSetOtherOptionHelp(optCon, "-r<receptor.prm> -p<protocol.prm> -i<infile> -o<outfile> [options]");

+ #endif

+ 	

diff --git a/var/spack/repos/builtin/packages/improved-rdock/rdock_erase.patch b/var/spack/repos/builtin/packages/improved-rdock/rdock_erase.patch
new file mode 100644
index 0000000000..ce87a0bc32
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/rdock_erase.patch
@@ -0,0 +1,21 @@
+diff -u -r -N a/src/lib/RbtBaseMolecularFileSource.cxx b/src/lib/RbtBaseMolecularFileSource.cxx
+--- a/src/lib/RbtBaseMolecularFileSource.cxx	2018-03-28 16:38:36.000000000 +0900
++++ b/src/lib/RbtBaseMolecularFileSource.cxx	2021-02-01 20:20:04.688973560 +0900
+@@ -420,7 +420,7 @@
+ #ifdef _VISUAL_STUDIO
+ 	but_iterator = std::remove(atList.begin(), atList.end(), _MANDATORY);
+ #else
+-	std::remove(atList.begin(), atList.end(), _MANDATORY);
++	atList.erase(std::remove(atList.begin(), atList.end(), _MANDATORY), atList.end());
+ #endif
+ 
+   }
+@@ -440,7 +440,7 @@
+ #ifdef _VISUAL_STUDIO
+ 	but_iterator = std::remove(atList.begin(), atList.end(), _FORBIDDEN);
+ #else
+-	std::remove(atList.begin(), atList.end(), _FORBIDDEN);
++	atList.erase(std::remove(atList.begin(), atList.end(), _FORBIDDEN), atList.end());
+ #endif
+ 
+   }
diff --git a/var/spack/repos/builtin/packages/improved-rdock/rdock_ld.patch b/var/spack/repos/builtin/packages/improved-rdock/rdock_ld.patch
new file mode 100644
index 0000000000..4085034f3e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/rdock_ld.patch
@@ -0,0 +1,11 @@
+--- a/build/makefile	2021-02-04 15:24:38.488425167 +0900
++++ b/build/makefile	2021-02-04 15:25:26.053775490 +0900
+@@ -61,7 +61,7 @@
+ # Environment for running rDock unit tests
+ export RBT_ROOT	= ../
+ export RBT_HOME	= ./test/RBT_HOME
+-export LD_LIBRARY_PATH = ../lib
++export LD_LIBRARY_PATH = $(shell echo $$LD_LIBRARY_PATH):../lib
+ 
+ ##################################################
+ # Main rDock build targets
diff --git a/var/spack/repos/builtin/packages/improved-rdock/rdock_loop.patch b/var/spack/repos/builtin/packages/improved-rdock/rdock_loop.patch
new file mode 100644
index 0000000000..c9c5d73600
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/rdock_loop.patch
@@ -0,0 +1,13 @@
+diff -u -r -N d/src/lib/RbtBaseMolecularFileSource.cxx y/src/lib/RbtBaseMolecularFileSource.cxx
+--- d/src/lib/RbtBaseMolecularFileSource.cxx	2020-10-19 09:50:06.000000000 +0900
++++ y/src/lib/RbtBaseMolecularFileSource.cxx	2020-10-19 09:35:16.000000000 +0900
+@@ -260,7 +260,8 @@
+   const RbtBondMap& bondMap = spAtom->GetBondMap();
+ 
+   //First remove all bonds from the atom
+-  for (RbtBondMapConstIter mapIter = bondMap.begin(); mapIter != bondMap.end(); mapIter++) {
++  RbtBondMapConstIter mapIter = bondMap.begin();
++  for (int i = 0; i < spAtom->GetNumBonds(); i++, mapIter++) {
+     RbtBondListIter bIter = Rbt::FindBond(m_bondList,Rbt::isBond_eq((*mapIter).first));
+     if (bIter != m_bondList.end()) {
+ #ifdef _DEBUG
diff --git a/var/spack/repos/builtin/packages/improved-rdock/rdock_newcxx.patch b/var/spack/repos/builtin/packages/improved-rdock/rdock_newcxx.patch
new file mode 100644
index 0000000000..5168d57835
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/rdock_newcxx.patch
@@ -0,0 +1,114 @@
+diff -u -r -N a/build/test/OccupancyTest.h b/build/test/OccupancyTest.h
+--- a/build/test/OccupancyTest.h	2017-02-17 17:29:25.000000000 +0900
++++ b/build/test/OccupancyTest.h	2021-02-01 19:23:53.921991677 +0900
+@@ -32,7 +32,11 @@
+ CPPUNIT_TEST_SUITE_END();
+ 
+ public:
++#if __cplusplus < 201103L
+   static const RbtDouble TINY = 1E-4;
++#else
++  static constexpr RbtDouble TINY = 1E-4;
++#endif
+   //TextFixture methods
+   void setUp();
+   void tearDown();
+diff -u -r -N a/build/test/RbtChromTest.h b/build/test/RbtChromTest.h
+--- a/build/test/RbtChromTest.h	2017-02-17 17:29:25.000000000 +0900
++++ b/build/test/RbtChromTest.h	2021-02-01 19:23:53.921991677 +0900
+@@ -68,7 +68,11 @@
+ CPPUNIT_TEST_SUITE_END();
+ 
+ public:
++#if __cplusplus < 201103L
+   static const RbtDouble TINY = 1E-4;
++#else
++  static constexpr RbtDouble TINY = 1E-4;
++#endif
+   //TextFixture methods
+   void setUp();
+   void tearDown();
+diff -u -r -N a/build/test/SearchTest.h b/build/test/SearchTest.h
+--- a/build/test/SearchTest.h	2017-02-17 17:29:25.000000000 +0900
++++ b/build/test/SearchTest.h	2021-02-01 19:23:53.921991677 +0900
+@@ -33,7 +33,11 @@
+ CPPUNIT_TEST_SUITE_END();
+ 
+ public:
++#if __cplusplus < 201103L
+   static const RbtDouble TINY = 1E-4;
++#else
++  static constexpr RbtDouble TINY = 1E-4;
++#endif
+   //TextFixture methods
+   void setUp();
+   void tearDown();
+diff -u -r -N a/import/simplex/src/NMSearch.cxx b/import/simplex/src/NMSearch.cxx
+--- a/import/simplex/src/NMSearch.cxx	2018-03-28 16:26:43.000000000 +0900
++++ b/import/simplex/src/NMSearch.cxx	2021-02-01 19:24:36.587991448 +0900
+@@ -391,7 +391,7 @@
+ 
+ #ifdef _VISUAL_STUDIO 
+ #else
+-	if (fp == NULL) {
++	if (!fp) {
+ 		cerr << "No Input Stream in ReadSimplexFile()!\n";
+ 		return; // There's no file handle!!
+ 	}
+diff -u -r -N a/import/tnt/include/tnt_sparse_matrix_csr.h b/import/tnt/include/tnt_sparse_matrix_csr.h
+--- a/import/tnt/include/tnt_sparse_matrix_csr.h	2014-05-05 19:18:06.000000000 +0900
++++ b/import/tnt/include/tnt_sparse_matrix_csr.h	2021-02-01 19:23:53.950991677 +0900
+@@ -49,8 +49,8 @@
+ 
+ private:
+ 	Array1D<T>    val_;       // data values (nz_ elements)
+-    Array1D<int>  rowptr_;    // row_ptr (dim_[0]+1 elements)
+-    Array1D<int>  colind_;    // col_ind  (nz_ elements)
++    Array1D<T>  rowptr_;    // row_ptr (dim_[0]+1 elements)
++    Array1D<T>  colind_;    // col_ind  (nz_ elements)
+ 
+     int dim1_;        // number of rows
+     int dim2_;        // number of cols
+diff -u -r -N a/include/RbtAromIdxSF.h b/include/RbtAromIdxSF.h
+--- a/include/RbtAromIdxSF.h	2016-12-28 17:16:27.000000000 +0900
++++ b/include/RbtAromIdxSF.h	2021-02-01 19:23:53.951991677 +0900
+@@ -68,7 +68,7 @@
+   //Generic scoring function params
+   struct f1prms {
+     RbtDouble R0,DRMin,DRMax,slope;
+-    f1prms::f1prms(RbtDouble R, RbtDouble DMin, RbtDouble DMax)
++    f1prms(RbtDouble R, RbtDouble DMin, RbtDouble DMax)
+       : R0(R),DRMin(DMin),DRMax(DMax),slope(1.0/(DMax-DMin)) {};
+   };
+ 
+diff -u -r -N a/include/RbtContainers.h b/include/RbtContainers.h
+--- a/include/RbtContainers.h	2018-03-28 18:25:19.000000000 +0900
++++ b/include/RbtContainers.h	2021-02-01 19:26:10.667990942 +0900
+@@ -37,6 +37,7 @@
+ 
+ #ifdef _VISUAL_STUDIO 
+ #else
++#if __cplusplus < 201103L
+ namespace std
+ {
+ 	template <class InputIterator, class OutputIterator, class Predicate>
+@@ -51,6 +52,7 @@
+ 	}
+ }
+ #endif
++#endif
+ 
+ // Container Typedefs
+ 	
+diff -u -r -N a/include/RbtPolarSF.h b/include/RbtPolarSF.h
+--- a/include/RbtPolarSF.h	2016-12-28 17:16:27.000000000 +0900
++++ b/include/RbtPolarSF.h	2021-02-01 19:23:53.951991677 +0900
+@@ -78,7 +78,7 @@
+   //Generic scoring function params
+   struct f1prms {
+     RbtDouble R0,DRMin,DRMax,slope;
+-    f1prms::f1prms(RbtDouble R, RbtDouble DMin, RbtDouble DMax)
++    f1prms(RbtDouble R, RbtDouble DMin, RbtDouble DMax)
+       : R0(R),DRMin(DMin),DRMax(DMax),slope(1.0/(DMax-DMin)) {};
+   };
+ 
diff --git a/var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch b/var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch
new file mode 100644
index 0000000000..bedcadc5b4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch
@@ -0,0 +1,276 @@
+diff -u -r -N a/bin/sdrmsd b/bin/sdrmsd
+--- a/bin/sdrmsd	2020-10-15 13:34:27.000000000 +0900
++++ b/bin/sdrmsd	2020-10-19 09:21:43.000000000 +0900
+@@ -11,7 +11,7 @@
+ # Date: 08-11-2013
+ 
+ import math
+-import pybel
++from openbabel import pybel
+ import numpy as npy
+ import optparse
+ 
+@@ -103,24 +103,24 @@
+     return mappingpose[0]
+ 
+ def parseArguments():
+-	optparse.OptionParser.format_epilog = lambda self, formatter: self.epilog
+-	epilog = """Args:
+-	reference.sdf		SDF file with the reference molecule.
+-	input.sdf		SDF file with the molecules to be compared to reference.\n"""
+-	parser = optparse.OptionParser("usage: %prog [options] reference.sdf input.sdf", epilog=epilog)
+-	parser.add_option("-f", "--fit",dest="fit", action="store_true", default=False,
++        optparse.OptionParser.format_epilog = lambda self, formatter: self.epilog
++        epilog = """Args:
++        reference.sdf                SDF file with the reference molecule.
++        input.sdf                SDF file with the molecules to be compared to reference.\n"""
++        parser = optparse.OptionParser("usage: %prog [options] reference.sdf input.sdf", epilog=epilog)
++        parser.add_option("-f", "--fit",dest="fit", action="store_true", default=False,
+                   help="Superpose molecules before RMSD calculation")
+-	parser.add_option("--threshold","-t",dest="threshold", action="store", nargs=1, 
++        parser.add_option("--threshold","-t",dest="threshold", action="store", nargs=1, 
+                   help="Discard poses with RMSD < THRESHOLD with respect previous poses which where not rejected based on same principle. A Population SDField will be added to output SD with the population number.", type=float)
+-	parser.add_option("-o","--out", dest="outfilename", metavar="FILE", default=False,
++        parser.add_option("-o","--out", dest="outfilename", metavar="FILE", default=False,
+                   help="If declared, write an output SDF file with the input molecules with a new sdfield <RMSD>. If molecule was fitted, the fitted molecule coordinates will be saved.")
+-	(options, args) =  parser.parse_args()
+-	
+-	#Check we have two arguments
+-	if len(args) < 2:
+-		parser.error("Incorrect number of arguments. Use -h or --help options to print help.")
++        (options, args) =  parser.parse_args()
++        
++        #Check we have two arguments
++        if len(args) < 2:
++                parser.error("Incorrect number of arguments. Use -h or --help options to print help.")
+ 
+-	return options, args
++        return options, args
+ 
+ def updateCoords(obmol, newcoords):
+     "Update OBMol coordinates. newcoords is a numpy array"
+@@ -133,8 +133,8 @@
+     for correct RMSD comparison. Only the lowest RMSD will be returned.
+     
+     Returns:
+-      If fit=False: 	bestRMSD	(float)					RMSD of the best matching mapping.
+-      If fit=True:	(bestRMSD, molecCoordinates)	(float, npy.array)	RMSD of best match and its molecule fitted coordinates.	
++      If fit=False:         bestRMSD        (float)                                        RMSD of the best matching mapping.
++      If fit=True:        (bestRMSD, molecCoordinates)        (float, npy.array)        RMSD of best match and its molecule fitted coordinates.        
+     """
+     mappings = pybel.ob.vvpairUIntUInt()
+     bitvec = pybel.ob.OBBitVec()
+@@ -148,18 +148,18 @@
+     posecoords = npy.array([atom.coords for atom in molec])[mappose]
+     resultrmsd = 999999999999
+     for mapping in mappings:
+-	automorph_coords = [None] * len(targetcoords)
+-	for x, y in mapping:
+-	    automorph_coords[lookup.index(x)] = targetcoords[lookup.index(y)]
+-	mapping_rmsd = rmsd(posecoords, automorph_coords)
+-	if mapping_rmsd < resultrmsd:
+-	    resultrmsd = mapping_rmsd
+-	    fitted_result = False
+-	if fit: 
+-	    fitted_pose, fitted_rmsd = superpose3D(npy.array(automorph_coords), npy.array(posecoords))
+-	    if fitted_rmsd < resultrmsd:
+-		resultrmsd = fitted_rmsd
+-		fitted_result = fitted_pose
++        automorph_coords = [None] * len(targetcoords)
++        for x, y in mapping:
++            automorph_coords[lookup.index(x)] = targetcoords[lookup.index(y)]
++        mapping_rmsd = rmsd(posecoords, automorph_coords)
++        if mapping_rmsd < resultrmsd:
++            resultrmsd = mapping_rmsd
++            fitted_result = False
++        if fit: 
++            fitted_pose, fitted_rmsd = superpose3D(npy.array(automorph_coords), npy.array(posecoords))
++            if fitted_rmsd < resultrmsd:
++                resultrmsd = fitted_rmsd
++                fitted_result = fitted_pose
+     
+     if fit:
+       return (resultrmsd, fitted_pose)
+@@ -167,16 +167,16 @@
+       return resultrmsd
+ 
+ def saveMolecWithRMSD(outsdf, molec, rmsd, population=False):
+-    newData = pybel.ob.OBPairData()	
++    newData = pybel.ob.OBPairData()        
+     newData.SetAttribute("RMSD")
+     newData.SetValue('%.3f'%rmsd)
+     
+     if population:
+-	popData = pybel.ob.OBPairData()
+-	popData.SetAttribute("Population")
+-	popData.SetValue('%i'%population)
+-	molec.OBMol.CloneData(popData)
+-	
++        popData = pybel.ob.OBPairData()
++        popData.SetAttribute("Population")
++        popData.SetValue('%i'%population)
++        molec.OBMol.CloneData(popData)
++        
+     molec.OBMol.CloneData(newData)           # Add new data
+     outsdf.write(molec)
+     
+@@ -184,13 +184,13 @@
+     import sys, os
+    
+     (opts, args) = parseArguments() 
+-	
++        
+     xtal = args[0]
+     poses = args[1]
+ 
+     if not os.path.exists(xtal) or not os.path.exists(poses):
+-	sys.exit("Input files not found. Please check the path given is correct.")
+-	
++        sys.exit("Input files not found. Please check the path given is correct.")
++        
+     fit = opts.fit
+     outfname = opts.outfilename
+     threshold = opts.threshold
+@@ -202,71 +202,71 @@
+ 
+     #If outfname is defined, prepare an output SDF sink to write molecules
+     if outfname:
+-	outsdf = pybel.Outputfile('sdf', outfname, overwrite=True)
++        outsdf = pybel.Outputfile('sdf', outfname, overwrite=True)
+ 
+     # Find the RMSD between the crystal pose and each docked pose
+     dockedposes = pybel.readfile("sdf", poses)
+-    if fit: print "POSE\tRMSD_FIT"
+-    else: print "POSE\tRMSD_NOFIT"
++    if fit: print ("POSE\tRMSD_FIT")
++    else: print ("POSE\tRMSD_NOFIT")
+     skipped = []
+-    moleclist = {}	# Save all poses with their dockid
+-    population = {}	# Poses to be written
++    moleclist = {}        # Save all poses with their dockid
++    population = {}        # Poses to be written
+     outlist = {}
+     for docki, dockedpose in enumerate(dockedposes):
+         dockedpose.removeh()
+-	natoms = len(dockedpose.atoms)
+-	if natoms != crystalnumatoms: 
+-		skipped.append(docki+1)
+-		continue
+-	if fit: 
+-	    resultrmsd, fitted_result = getAutomorphRMSD(crystal, dockedpose, fit=True)
+-	    updateCoords(dockedpose, fitted_result)
+-	else:
+-	    resultrmsd = getAutomorphRMSD(crystal, dockedpose, fit=False)
+-	
+-	if threshold:
+-	    # Calculate RMSD between all previous poses
+-	    # Discard if rmsd < FILTER threshold
+-	    if moleclist:
+-		match = None
+-		bestmatchrmsd = 999999
+-		for did,prevmol in moleclist.iteritems():
+-		    tmprmsd = getAutomorphRMSD(prevmol, dockedpose)
+-		    if tmprmsd < threshold:
+-			if tmprmsd < bestmatchrmsd:
+-			    bestmatchrmsd = tmprmsd
+-			    match = did
+-			
+-		if match != None:
+-		    # Do not write this one
+-		    # sum one up to the matching previous molecule id
+-		    print >> sys.stderr, "Pose %i matches pose %i with %.3f RMSD"%(docki+1, match+1, bestmatchrmsd)
+-		    population[match] += 1
+-		else:
+-		    # There's no match. Print info for this one and write to outsdf if needed
+-		    # Save this one!
+-		    if outfname: outlist[docki] = (dockedpose, resultrmsd)
+-		    print "%d\t%.2f"%((docki+1),resultrmsd)
+-		    moleclist[docki] = dockedpose
+-		    population[docki] = 1
+-	    else:
+-		# First molecule in list. Append for sure
+-		moleclist[docki] = dockedpose
+-		population[docki] = 1
+-		if outfname: outlist[docki] = (dockedpose, resultrmsd)
+-	else:
+-	    # Just write best rmsd found and the molecule to outsdf if demanded
+-	    if outfname: saveMolecWithRMSD(outsdf, dockedpose, resultrmsd)
+-	    print "%d\t%.2f"%((docki+1),resultrmsd)
++        natoms = len(dockedpose.atoms)
++        if natoms != crystalnumatoms: 
++                skipped.append(docki+1)
++                continue
++        if fit: 
++            resultrmsd, fitted_result = getAutomorphRMSD(crystal, dockedpose, fit=True)
++            updateCoords(dockedpose, fitted_result)
++        else:
++            resultrmsd = getAutomorphRMSD(crystal, dockedpose, fit=False)
++        
++        if threshold:
++            # Calculate RMSD between all previous poses
++            # Discard if rmsd < FILTER threshold
++            if moleclist:
++                match = None
++                bestmatchrmsd = 999999
++                for did,prevmol in moleclist.iteritems():
++                    tmprmsd = getAutomorphRMSD(prevmol, dockedpose)
++                    if tmprmsd < threshold:
++                        if tmprmsd < bestmatchrmsd:
++                            bestmatchrmsd = tmprmsd
++                            match = did
++                        
++                if match != None:
++                    # Do not write this one
++                    # sum one up to the matching previous molecule id
++                    print >> sys.stderr, "Pose %i matches pose %i with %.3f RMSD"%(docki+1, match+1, bestmatchrmsd)
++                    population[match] += 1
++                else:
++                    # There's no match. Print info for this one and write to outsdf if needed
++                    # Save this one!
++                    if outfname: outlist[docki] = (dockedpose, resultrmsd)
++                    print ("%d\t%.2f"%((docki+1),resultrmsd))
++                    moleclist[docki] = dockedpose
++                    population[docki] = 1
++            else:
++                # First molecule in list. Append for sure
++                moleclist[docki] = dockedpose
++                population[docki] = 1
++                if outfname: outlist[docki] = (dockedpose, resultrmsd)
++        else:
++            # Just write best rmsd found and the molecule to outsdf if demanded
++            if outfname: saveMolecWithRMSD(outsdf, dockedpose, resultrmsd)
++            print ("%d\t%.2f"%((docki+1),resultrmsd))
+ 
+     if outlist:
+-	# Threshold applied and outlist need to be written
+-	for docki in sorted(outlist.iterkeys()):
+-	    molrmsd = outlist[docki]
+-	    # Get number of matchs in thresholding operation
+-	    pop = population.get(docki)
+-	    if not pop: pop = 1
+-	    # Save molecule
+-	    saveMolecWithRMSD(outsdf, molrmsd[0], molrmsd[1], pop)
+-	    
+-    if skipped: print >> sys.stderr, "SKIPPED input molecules due to number of atom missmatch: %s"%skipped
++        # Threshold applied and outlist need to be written
++        for docki in sorted(outlist.iterkeys()):
++            molrmsd = outlist[docki]
++            # Get number of matchs in thresholding operation
++            pop = population.get(docki)
++            if not pop: pop = 1
++            # Save molecule
++            saveMolecWithRMSD(outsdf, molrmsd[0], molrmsd[1], pop)
++            
++    if skipped: print("SKIPPED input molecules due to number of atom missmatch: %s"%skipped, file=sys.stderr)
+diff -u -r -N a/build/test/RBT_HOME/check_test.py b/build/test/RBT_HOME/check_test.py
+--- a/build/test/RBT_HOME/check_test.py	2020-10-14 11:48:36.000000000 +0900
++++ b/build/test/RBT_HOME/check_test.py	2020-10-19 09:23:31.000000000 +0900
+@@ -21,6 +21,6 @@
+ 	error = 1
+ 
+ if error == 1:
+-	print "The test failed, please check the compilation is OK and no errors were raised."
++	print ("The test failed, please check the compilation is OK and no errors were raised.")
+ else:
+-	print "The test succeeded! The results agree with the reference ones.\nHave fun using rDock!!"
++	print ("The test succeeded! The results agree with the reference ones.\nHave fun using rDock!!")
diff --git a/var/spack/repos/builtin/packages/improved-rdock/rdock_useint.patch b/var/spack/repos/builtin/packages/improved-rdock/rdock_useint.patch
new file mode 100644
index 0000000000..f0be2fa2cc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/rdock_useint.patch
@@ -0,0 +1,24 @@
+diff -u -r -N a/src/exe/rbcavity.cxx b/src/exe/rbcavity.cxx
+--- a/src/exe/rbcavity.cxx	2016-12-28 17:16:27.000000000 +0900
++++ b/src/exe/rbcavity.cxx	2021-02-01 20:14:47.508975264 +0900
+@@ -50,7 +50,7 @@
+ 
+ int main(int argc,const char* argv[])
+ {
+-	char 			c;					// for argument parsing
++	int 			c;					// for argument parsing
+ 	poptContext		optCon;				// ditto
+ 	char 			*prmFile=NULL;		// will be strReceptorPrmFile
+ 	char 			*listDist=NULL;		// will be 'dist' 
+diff -u -r -N a/src/exe/rbdock.cxx b/src/exe/rbdock.cxx
+--- a/src/exe/rbdock.cxx	2018-04-06 20:14:32.000000000 +0900
++++ b/src/exe/rbdock.cxx	2021-02-01 20:17:20.359974443 +0900
+@@ -401,7 +401,7 @@
+ 	RbtInt		iTrace(0);//Trace level, for debugging

+ 

+ 	// variables for popt command-line parsing

+-	char 			c;						// for argument parsing

++	int 			c;						// for argument parsing

+ 	

+ #ifdef _VISUAL_STUDIO

+ #else

diff --git a/var/spack/repos/builtin/packages/improved-rdock/test/test.sh b/var/spack/repos/builtin/packages/improved-rdock/test/test.sh
new file mode 100644
index 0000000000..f59cb334bb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/improved-rdock/test/test.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+#sdsort for sorting the results according to their score
+sdsort -n -f'SCORE' 1sj0_docking_out.sd > 1sj0_docking_out_sorted.sd
+cat 1sj0_docking_out_sorted.sd