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add recipe for improved-rdock

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Yuichi Otsuka 2022-06-15 17:08:18 +09:00
parent 38a8d4d2fe
commit 29133cfbe3
10 changed files with 578 additions and 0 deletions
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83
var/spack/repos/builtin/improved-rdock/package.py Normal file
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# Copyright 2013-2021 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 import *
import os
class ImprovedRdock(MakefilePackage):
"""rDock is a fast and versatile Open Source docking program
that can be used to dock small molecules against proteins and
nucleic acids. """
homepage = "https://github.com/clinfo/improved_rDock"
# url = "https://sourceforge.net/projects/rdock/files/rDock_2013.1_src.tar.gz"
# url = "file://{0}/rDock_2013.1_src_AdvanceSoft_2018.tar.gz".format(os.getcwd())
git = "https://github.com/clinfo/improved_rDock.git"
#version('2013.1', sha256='33eb3aa0c4ede3efe275eb7b7f98c8cb54b0f54d774f400e00cb172e7921b99c')
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):
test_dir = self.test_suite.current_test_data_dir
copy(join_path(self.prefix.example, '1sj0', '*'), test_dir)
opts = ['-r', '1sj0_rdock.prm', '-was']
self.run_test('rbcavity', options=opts, work_dir=test_dir)
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(mpiexe, options=opts, work_dir=test_dir)
opts = [join_path(test_dir, 'test.sh')]
self.run_test('bash', options=opts, work_dir=test_dir)
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,
work_dir=test_dir)

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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);
}

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--- 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

21
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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
}

11
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@ -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

13
var/spack/repos/builtin/improved-rdock/rdock_loop.patch Normal file
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@ -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

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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)) {};
};

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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!!")

24
var/spack/repos/builtin/improved-rdock/rdock_useint.patch Normal file
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@ -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

4
var/spack/repos/builtin/improved-rdock/test/test.sh Normal file
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@ -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