From d9f49d74158bb9fe89e00fb8a7b279950abe3a80 Mon Sep 17 00:00:00 2001 From: otsukay Date: Thu, 7 Jul 2022 01:25:45 +0900 Subject: 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 Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> --- .../builtin/packages/improved-rdock/package.py | 81 ++++++ .../packages/improved-rdock/rdock_const.patch | 21 ++ .../packages/improved-rdock/rdock_const2.patch | 11 + .../packages/improved-rdock/rdock_erase.patch | 21 ++ .../builtin/packages/improved-rdock/rdock_ld.patch | 11 + .../packages/improved-rdock/rdock_loop.patch | 13 + .../packages/improved-rdock/rdock_newcxx.patch | 114 +++++++++ .../packages/improved-rdock/rdock_python3.patch | 276 +++++++++++++++++++++ .../packages/improved-rdock/rdock_useint.patch | 24 ++ .../builtin/packages/improved-rdock/test/test.sh | 4 + 10 files changed, 576 insertions(+) create mode 100644 var/spack/repos/builtin/packages/improved-rdock/package.py create mode 100644 var/spack/repos/builtin/packages/improved-rdock/rdock_const.patch create mode 100644 var/spack/repos/builtin/packages/improved-rdock/rdock_const2.patch create mode 100644 var/spack/repos/builtin/packages/improved-rdock/rdock_erase.patch create mode 100644 var/spack/repos/builtin/packages/improved-rdock/rdock_ld.patch create mode 100644 var/spack/repos/builtin/packages/improved-rdock/rdock_loop.patch create mode 100644 var/spack/repos/builtin/packages/improved-rdock/rdock_newcxx.patch create mode 100644 var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch create mode 100644 var/spack/repos/builtin/packages/improved-rdock/rdock_useint.patch create mode 100644 var/spack/repos/builtin/packages/improved-rdock/test/test.sh 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 -p -i -o [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 val_; // data values (nz_ elements) +- Array1D rowptr_; // row_ptr (dim_[0]+1 elements) +- Array1D colind_; // col_ind (nz_ elements) ++ Array1D rowptr_; // row_ptr (dim_[0]+1 elements) ++ Array1D 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 +@@ -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 . 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 -- cgit v1.2.3-60-g2f50