| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/ |
| H A D | testMol2ToMol.cpp | 47 void testGeneral(std::string rdbase) { in testGeneral() argument
135 rdbase + in testGeneral()
225 rdbase + in testGeneral()
234 rdbase + in testGeneral()
321 void testIssue114(std::string rdbase) { in testIssue114() argument
414 testGeneral(rdbase); in main()
415 testAromaticChargedFail(rdbase); in main()
416 testIssue3399798(rdbase); in main()
417 testIssue114(rdbase); in main()
418 testGithub438(rdbase); in main()
[all …]
|
| H A D | test1.cpp | 115 fName = rdbase + in test1()
3069 rdbase + in testThreeCoordinateChirality()
3082 rdbase + in testThreeCoordinateChirality()
3095 rdbase + in testThreeCoordinateChirality()
3105 rdbase + in testThreeCoordinateChirality()
3115 rdbase + in testThreeCoordinateChirality()
3127 rdbase + in testThreeCoordinateChirality()
3209 rdbase + in testChiralPhosphorous()
3222 rdbase + in testChiralPhosphorous()
3235 rdbase + in testChiralPhosphorous()
[all …]
|
| H A D | testMolSupplier.cpp | 38 std::string rdbase = getenv("RDBASE"); in testMolSup() local
317 std::string rdbase = getenv("RDBASE"); in testRandMolSup() local
377 std::string rdbase = getenv("RDBASE"); in testSmilesSup() local
807 std::string rdbase = getenv("RDBASE"); in testSmilesWriter() local
868 std::string rdbase = getenv("RDBASE"); in testSDWriter() local
874 rdbase + in testSDWriter()
930 std::string rdbase = getenv("RDBASE"); in testSDSupplierEnding() local
951 std::string rdbase = getenv("RDBASE"); in testSuppliersEmptyFile() local
1053 std::string rdbase = getenv("RDBASE"); in testStereoRound() local
1065 rdbase + in testStereoRound()
[all …]
|
| H A D | testMolWriter.cpp | 29 std::string rdbase = getenv("RDBASE"); in testSmilesWriter() local
125 std::string rdbase = getenv("RDBASE"); in testSmilesWriterNoNames() local
180 std::string rdbase = getenv("RDBASE"); in testSmilesWriterClose() local
235 std::string rdbase = getenv("RDBASE"); in testSDWriter() local
241 rdbase + in testSDWriter()
293 std::string rdbase = getenv("RDBASE"); in testTDTWriter() local
397 rdbase + in testSDWriterStrm()
498 std::string ofile = rdbase + in testSDMemoryCorruption()
781 fName = rdbase + "rxn1.mol"; in testMolFileWithRxn()
973 fName = rdbase + "FeCO5.mol"; in testZBO()
[all …]
|
| H A D | testMultithreadedMolSupplier.cpp | 79 std::string rdbase = getenv("RDBASE"); in testSmiConcurrent() local
80 std::string fname = rdbase + path; in testSmiConcurrent()
108 std::string rdbase = getenv("RDBASE"); in testSmiProperties() local
143 std::string rdbase = getenv("RDBASE"); in testSmiCorrectness() local
158 path = rdbase + "/Regress/Data/znp.50k.smi.gz"; in testSmiCorrectness()
208 std::string rdbase = getenv("RDBASE"); in testSDConcurrent() local
209 std::string fname = rdbase + path; in testSDConcurrent()
217 std::string rdbase = getenv("RDBASE"); in testSDProperties() local
270 std::string rdbase = getenv("RDBASE"); in testSDCorrectness() local
295 path = rdbase + "/Regress/Data/mols.1000.sdf.gz"; in testSDCorrectness()
[all …]
|
| H A D | testGeneralFileReader.cpp | 72 std::string rdbase = getenv("RDBASE"); in testSdf() local
74 rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf"; in testSdf()
108 fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf.gz"; in testSdf()
127 std::string rdbase = getenv("RDBASE"); in testSmi() local
129 rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.2.csv"; in testSmi()
168 std::string rdbase = getenv("RDBASE"); in testMae() local
170 rdbase + "/Code/GraphMol/FileParsers/test_data/props_test.mae"; in testMae()
221 fname = rdbase + "/Code/GraphMol/FileParsers/test_data/1kv1.maegz"; in testMae()
236 std::string rdbase = getenv("RDBASE"); in testTdt() local
238 rdbase + "/Code/GraphMol/FileParsers/test_data/acd_few.tdt"; in testTdt()
|
| H A D | testTpls.cpp | 25 std::string rdbase = getenv("RDBASE"); in test1() local
26 std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/cmpd2.tpl"; in test1()
71 std::string rdbase = getenv("RDBASE"); in test2() local
72 std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/cmpd1.tpl"; in test2()
|
| H A D | file_parsers_catch.cpp | 2037 std::string rdbase = getenv("RDBASE"); variable
2111 rdbase +
2308 rdbase +
2354 rdbase +
2403 rdbase +
2413 rdbase +
2428 rdbase +
2444 rdbase +
2480 rdbase +
2502 rdbase +
[all …]
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolAlign/ |
| H A D | testMolAlign.cpp | 30 std::string rdbase = getenv("RDBASE"); in test1MolAlign() local
34 rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol"; in test1MolAlign()
41 rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_trans.mol"; in test1MolAlign()
68 std::string rdbase = getenv("RDBASE"); in test1GetBestRMS() local
70 rdbase + "/Code/GraphMol/MolAlign/test_data/probe_mol.sdf"; in test1GetBestRMS()
88 std::string rdbase = getenv("RDBASE"); in test1MolWithQueryAlign() local
93 rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol"; in test1MolWithQueryAlign()
141 std::string rdbase = getenv("RDBASE"); in test2AtomMap() local
161 std::string rdbase = getenv("RDBASE"); in test3Weights() local
189 std::string rdbase = getenv("RDBASE"); in testIssue241() local
[all …]
|
| H A D | testO3AAlign.cpp | 32 std::string rdbase = getenv("RDBASE"); in testMMFFO3A() local
33 std::string sdf = rdbase + "/Code/GraphMol/MolAlign/test_data/ref_e2"; in testMMFFO3A()
63 std::string rdbase = getenv("RDBASE"); in testCrippenO3A() local
108 std::string rdbase = getenv("RDBASE"); in testMMFFO3AMolHist() local
146 std::string rdbase = getenv("RDBASE"); in testCrippenO3AMolHist() local
301 std::string rdbase = getenv("RDBASE"); in testMMFFO3AConstraintsAndLocalOnly() local
366 std::string rdbase = getenv("RDBASE"); in testCrippenO3AConstraintsAndLocalOnly() local
487 std::string rdbase = getenv("RDBASE"); in testMMFFO3AMultiThread() local
540 std::string rdbase = getenv("RDBASE"); in testCrippenO3AMultiThread() local
608 std::string rdbase = getenv("RDBASE"); in testGetO3AForProbeConfs() local
[all …]
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolTransforms/ |
| H A D | test1.cpp | 118 std::string rdbase = getenv("RDBASE"); in test1Canonicalization() local
120 rdbase + "/Code/GraphMol/MolTransforms/test_data/1oir.mol"; in test1Canonicalization()
146 std::string rdbase = getenv("RDBASE"); in testGetSetBondLength() local
148 rdbase + in testGetSetBondLength()
165 std::string rdbase = getenv("RDBASE"); in testGetSetAngle() local
167 rdbase + in testGetSetAngle()
186 std::string rdbase = getenv("RDBASE"); in testGetSetDihedral() local
188 rdbase + in testGetSetDihedral()
210 std::string rdbase = getenv("RDBASE"); in testGetSetDihedralThroughTripleBond() local
259 std::string rdbase = getenv("RDBASE"); in testGithub1262() local
[all …]
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Scripts/ |
| H A D | PythonFormat.py | 19 rdbase = os.environ.get('RDBASE', '') variable
20 styleConfig = os.path.join(rdbase, 'setup.cfg')
22 excludeDirs = [os.path.join(rdbase, 'build'),
23 os.path.join(rdbase, 'External'), ]
26 def pythonFiles(dirname=rdbase):
65 for s in sorted(set(s.replace(rdbase, '').split(os.sep)[1] for s in changedFiles)):
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ShapeHelpers/ |
| H A D | testShapeHelpers.cpp | 27 std::string rdbase = getenv("RDBASE"); in test1Encode() local
29 rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol"; in test1Encode()
41 std::string rdbase = getenv("RDBASE"); in test2Compare() local
43 rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol"; in test2Compare()
60 rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir_conf.mol"; in test2Compare()
88 std::string rdbase = getenv("RDBASE"); in testGithub4364() local
90 rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol"; in testGithub4364()
95 rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir_conf.mol"; in testGithub4364()
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolStandardize/ |
| H A D | testPCS.cpp | 153 std::string rdbase = std::getenv("RDBASE"); in readCSV() local
158 rdbase + "/rdkit/Chem/MolStandardize/test_data/1kPCS_metals.csv.gz"; in readCSV()
162 rdbase + "/rdkit/Chem/MolStandardize/test_data/100kPCS_metals.csv.gz"; in readCSV()
166 rdbase + in readCSV()
171 rdbase + in readCSV()
176 rdbase + "/rdkit/Chem/MolStandardize/test_data/1kPCS_validate.csv.gz"; in readCSV()
180 filename = rdbase + in readCSV()
189 filename = rdbase + in readCSV()
197 filename = rdbase + in readCSV()
201 filename = rdbase + in readCSV()
[all …]
|
| H A D | MolStandardize.h | 46 std::string rdbase = rdbase_cstr != nullptr ? rdbase_cstr : "";
78 normalizations(rdbase + "/Data/MolStandardize/normalizations.txt"), in CleanupParameters()
79 acidbaseFile(rdbase + "/Data/MolStandardize/acid_base_pairs.txt"), in CleanupParameters()
80 fragmentFile(rdbase + "/Data/MolStandardize/fragmentPatterns.txt"), in CleanupParameters()
82 tautomerTransforms(rdbase + in CleanupParameters()
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Wrap/ |
| H A D | testTrajectory.py | 142 rdbase = os.environ['RDBASE']
166 fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords.trx')
170 fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trx')
179 rdbase = os.environ['RDBASE']
180 fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trx')
224 rdbase = os.environ['RDBASE']
248 fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords.trc')
414 rdbase = os.environ['RDBASE']
415 fName = os.path.join(rdbase, 'Code', 'GraphMol', 'Wrap', 'test_data',
444 rdbase = os.environ['RDBASE']
[all …]
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Trajectory/ |
| H A D | trajectoryTest.cpp | 203 std::string rdbase = getenv("RDBASE"); in testReadAmber() local
238 fName = rdbase + "/Code/GraphMol/test_data/water_coords.trx"; in testReadAmber()
244 fName = rdbase + "/Code/GraphMol/test_data/water_coords2.trx"; in testReadAmber()
258 std::string rdbase = getenv("RDBASE"); in testReadGromos() local
293 fName = rdbase + "/Code/GraphMol/test_data/water_coords.trc"; in testReadGromos()
299 fName = rdbase + "/Code/GraphMol/test_data/water_coords2.trc"; in testReadGromos()
469 std::string rdbase = getenv("RDBASE"); in testAddConformersFromTrajectory() local
512 std::string rdbase = getenv("RDBASE"); in testAddConformersFromAmberTrajectory() local
535 fName = rdbase + "/Code/GraphMol/test_data/water_coords2.trx"; in testAddConformersFromAmberTrajectory()
557 std::string rdbase = getenv("RDBASE"); in testAddConformersFromGromosTrajectory() local
[all …]
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/ConformerParser/ |
| H A D | test.cpp | 63 std::string rdbase = getenv("RDBASE"); in test1() local
64 std::string fName = rdbase + "/Code/GraphMol/test_data/water_coords_bad.trx"; in test1()
73 fName = rdbase + "/Code/GraphMol/test_data/water_coords_bad2.trx"; in test1()
83 fName = rdbase + "/Code/GraphMol/test_data/water_coords.trx"; in test1()
102 fName = rdbase + "/Code/GraphMol/test_data/water_coords2.trx"; in test1()
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
| H A D | testSGroup.cpp | 304 void testParseSubstanceGroups(const std::string &rdbase) { in testParseSubstanceGroups() argument
418 rdbase + in testSubstanceGroupsRoundTrip()
568 void testSubstanceGroupChanges(const std::string &rdbase) { in testSubstanceGroupChanges() argument
573 rdbase + in testSubstanceGroupChanges()
1033 std::string rdbase = std::string(getenv("RDBASE")); in main() local
1034 if (rdbase.empty()) { in main()
1042 testParseSubstanceGroups(rdbase); in main()
1043 testSubstanceGroupsRoundTrip(rdbase, false); // test V2000 in main()
1047 testSubstanceGroupChanges(rdbase); in main()
1049 testSubstanceGroupsAndRemoveAtoms(rdbase); in main()
[all …]
|
| H A D | testChirality.cpp | 35 std::string rdbase = getenv("RDBASE"); in testMol1() local
124 std::string rdbase = getenv("RDBASE"); in testRoundTrip() local
280 std::string rdbase = getenv("RDBASE"); in testMol2() local
1068 std::string rdbase = getenv("RDBASE"); in testChiralityFrom3D() local
1150 std::string rdbase = getenv("RDBASE"); in testIterativeChirality() local
1649 std::string rdbase = getenv("RDBASE"); in testBondDirRemoval() local
1709 std::string rdbase = getenv("RDBASE"); in testIssue2705543() local
1873 std::string rdbase = getenv("RDBASE"); in testIssue2762917() local
2295 std::string rdbase = getenv("RDBASE"); in testGithub87() local
2777 std::string rdbase = getenv("RDBASE"); in testStereoGroupUpdating() local
[all …]
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/StructChecker/ |
| H A D | testStructChecker.cpp | 93 const std::string rdbase = getenv("RDBASE") ? getenv("RDBASE") : "."; in doLoadOptionsFromFiles() local
96 testDataDir = rdbase + "/Code/GraphMol/StructChecker/test/"; in doLoadOptionsFromFiles()
320 const std::string rdbase = getenv("RDBASE") ? getenv("RDBASE") : "."; in testStereo() local
321 const std::string testDataDir = rdbase + "/Code/GraphMol/StructChecker/test/"; in testStereo()
483 const std::string rdbase = getenv("RDBASE") ? getenv("RDBASE") : "."; in testCheckAtomFiles() local
485 rdbase + "/Code/GraphMol/StructChecker/test/atom_check_failed/"; in testCheckAtomFiles()
565 const std::string rdbase = getenv("RDBASE") ? getenv("RDBASE") : "."; in testNitro() local
566 const std::string testDataDir = rdbase + "/Code/GraphMol/StructChecker/test/"; in testNitro()
586 const std::string rdbase = getenv("RDBASE"); in testSpecificExamples() local
587 const std::string testDataDir = rdbase + "/Data/struchk/"; in testSpecificExamples()
[all …]
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FragCatalog/ |
| H A D | test1.cpp | 92 std::string rdbase = getenv("RDBASE"); in test1() local
93 std::string fname = rdbase + "/Code/GraphMol/FragCatalog/test_data/mols.smi"; in test1()
95 rdbase + "/Code/GraphMol/FragCatalog/test_data/funcGroups.txt"; in test1()
216 std::string rdbase = getenv("RDBASE"); in testIssue294() local
217 std::string fname = rdbase + "/Code/GraphMol/FragCatalog/test_data/mols.smi"; in testIssue294()
219 rdbase + "/Code/GraphMol/FragCatalog/test_data/funcGroups.txt"; in testIssue294()
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolInterchange/ |
| H A D | test1.cpp | 33 std::string rdbase = getenv("RDBASE"); in test1() local
36 rdbase + "/Code/GraphMol/MolInterchange/test_data/test1.json"; in test1()
75 rdbase + "/Code/GraphMol/MolInterchange/test_data/test2.json"; in test1()
205 std::string rdbase = getenv("RDBASE"); in test3() local
208 rdbase + "/Code/GraphMol/MolInterchange/test_data/test2.json"; in test3()
283 std::string rdbase = getenv("RDBASE"); in benchmarking() local
286 rdbase + "/Code/GraphMol/MolInterchange/test_data/znp.50k.smi"; in benchmarking()
347 std::string rdbase = getenv("RDBASE"); in test6() local
349 rdbase + "/Code/GraphMol/MolInterchange/test_data/test3.json"; in test6()
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/Basement/BinaryIO/ |
| H A D | iotest.cpp | 41 std::string rdbase = getenv("RDBASE"); in test1() local
43 rdbase + "/Code/Demos/RDKit/BinaryIO/test_data/triazine.mol.gz"; in test1()
105 std::string rdbase = getenv("RDBASE"); in test3() local
106 std::string fname2 = rdbase + "/Code/Demos/RDKit/BinaryIO/test_data/mols.rdb"; in test3()
209 std::string rdbase = getenv("RDBASE"); in test4() local
210 std::string fname2 = rdbase + "/Code/Demos/RDKit/BinaryIO/test_data/mols.rdz"; in test4()
311 std::string rdbase = getenv("RDBASE"); in test5() local
312 std::string fname2 = rdbase + "/Code/Demos/RDKit/BinaryIO/test_data/tmp.rdz"; in test5()
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/DistGeomHelpers/ |
| H A D | testDgeomHelpers.cpp | 1744 rdbase + in testEmbedParameters()
1765 rdbase + in testEmbedParameters()
1787 rdbase + in testEmbedParameters()
1810 rdbase + in testEmbedParameters()
1834 rdbase + in testEmbedParameters()
1858 rdbase + in testEmbedParameters()
1879 rdbase + in testEmbedParameters()
1900 rdbase + in testEmbedParameters()
1921 std::string fname = rdbase + in testEmbedParameters()
1943 std::string fname = rdbase + in testEmbedParameters()
[all …]
|