/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/ |
H A D | SMILESWriterTest.java | 28 assertEquals("C", smiles); in testRoundTrip1() 36 assertEquals("C#N", smiles); in testRoundTrip2() 52 assertEquals("O=C=O", smiles); in testRoundTrip4() 126 assertEquals("[S]", smiles); in testOrganic1() 133 assertEquals("[SH]", smiles); in testOrganic2() 140 assertEquals("S", smiles); in testOrganic3() 345 if (!smiles.equals("C/C=C/C") && !smiles.equals("C\\C=C\\C")){ in testDoubleBondSupport1() 356 if (!smiles.equals("C/C=C\\C") && !smiles.equals("C\\C=C/C")){ in testDoubleBondSupport2() 367 if (!smiles.equals("C/C=C\\C=C/C") && !smiles.equals("C\\C=C/C=C\\C")){ in testDoubleBondSupport3() 389 if (!smiles.equals("C/C=N\\O") && !smiles.equals("C\\C=N/O")){ in testDoubleBondSupport5() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Subgraphs/ |
H A D | test2.cpp | 22 std::string canon(std::string smiles) { in canon() argument 31 std::string smiles = "CC1CC1"; in test1() local 32 RWMol *mol = SmilesToMol(smiles); in test1() 73 std::string smiles = "CC1CC1"; in test2() local 74 RWMol *mol = SmilesToMol(smiles); in test2() 105 std::string smiles = "CC1CC1"; in test2() local 106 RWMol *mol = SmilesToMol(smiles); in test2() 123 RWMol *mol = SmilesToMol(smiles); in test2() 125 smiles = MolToSmiles(*mol); in test2() 164 smiles = MolToSmarts(*frag); in testGithubIssue103() [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/aromaticity/ |
H A D | DaylightModelTest.java | 32 import org.openscience.cdk.smiles.SmilesParser; 62 test(smiles("O1C=CC=C1"), 2, 1, 1, 1, 1); in furan() 67 test(smiles("N1C=CC=C1"), 2, 1, 1, 1, 1); in pyrrole() 72 test(smiles("CN1C=CC=C1"), -1, 2, 1, 1, 1, 1); in methylpyrrole() 77 test(smiles("C1=CC=NC=C1"), 1, 1, 1, 1, 1, 1); in pyridine() 87 test(smiles("[CH-]1C=CC=C1"), 2, 1, 1, 1, 1); in cyclopentadienyl() 122 test(smiles("[CH+]1C=CC=CC=C1"), 0, 1, 1, 1, 1, 1, 1); in tropyliumcation() 143 test(smiles("C1=CC=C1"), 1, 1, 1, 1); in cyclobutadiene() 164 test(smiles("O=N1=CC=CC=C1"), -1, 1, 1, 1, 1, 1, 1); in oxidepyridine() 170 test(smiles("O=C1NC=CC=C1"), -1, 0, 2, 1, 1, 1, 1); in pyridinone() [all …]
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H A D | PiBondModelTest.java | 32 import org.openscience.cdk.smiles.SmilesParser; 61 test(smiles("O1C=CC=C1"), -1, 1, 1, 1, 1); in furan() 66 test(smiles("N1C=CC=C1"), -1, 1, 1, 1, 1); in pyrrole() 71 test(smiles("CN1C=CC=C1"), -1, -1, 1, 1, 1, 1); in methylpyrrole() 76 test(smiles("C1=CC=NC=C1"), 1, 1, 1, 1, 1, 1); in pyridine() 86 test(smiles("[CH-]1C=CC=C1"), -1, 1, 1, 1, 1); in cyclopentadienyl() 121 test(smiles("[CH+]1C=CC=CC=C1"), -1, 1, 1, 1, 1, 1, 1); in tropyliumcation() 142 test(smiles("C1=CC=C1"), 1, 1, 1, 1); in cyclobutadiene() 163 test(smiles("O=N1=CC=CC=C1"), -1, 1, 1, 1, 1, 1, 1); in oxidepyridine() 169 test(smiles("O=C1NC=CC=C1"), -1, -1, -1, 1, 1, 1, 1); in pyridinone() [all …]
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H A D | AtomTypeModelTest.java | 32 import org.openscience.cdk.smiles.SmilesParser; 62 test(smiles("O1C=CC=C1"), 2, 1, 1, 1, 1); in furan() 67 test(smiles("N1C=CC=C1"), 2, 1, 1, 1, 1); in pyrrole() 72 test(smiles("CN1C=CC=C1"), -1, 2, 1, 1, 1, 1); in methylpyrrole() 77 test(smiles("C1=CC=NC=C1"), 1, 1, 1, 1, 1, 1); in pyridine() 87 test(smiles("[CH-]1C=CC=C1"), 2, 1, 1, 1, 1); in cyclopentadienyl() 122 test(smiles("[CH+]1C=CC=CC=C1"), 0, 1, 1, 1, 1, 1, 1); in tropyliumcation() 143 test(smiles("C1=CC=C1"), 1, 1, 1, 1); in cyclobutadiene() 164 test(smiles("O=N1=CC=CC=C1"), -1, 1, 1, 1, 1, 1, 1); in oxidepyridine() 170 test(smiles("O=C1NC=CC=C1"), -1, -1, 2, 1, 1, 1, 1); in pyridinone() [all …]
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H A D | ExocyclicAtomTypeModelTest.java | 32 import org.openscience.cdk.smiles.SmilesParser; 62 test(smiles("O1C=CC=C1"), 2, 1, 1, 1, 1); in furan() 67 test(smiles("N1C=CC=C1"), 2, 1, 1, 1, 1); in pyrrole() 72 test(smiles("CN1C=CC=C1"), -1, 2, 1, 1, 1, 1); in methylpyrrole() 77 test(smiles("C1=CC=NC=C1"), 1, 1, 1, 1, 1, 1); in pyridine() 87 test(smiles("[CH-]1C=CC=C1"), 2, 1, 1, 1, 1); in cyclopentadienyl() 122 test(smiles("[CH+]1C=CC=CC=C1"), 0, 1, 1, 1, 1, 1, 1); in tropyliumcation() 143 test(smiles("C1=CC=C1"), 1, 1, 1, 1); in cyclobutadiene() 164 test(smiles("O=N1=CC=CC=C1"), -1, 1, 1, 1, 1, 1, 1); in oxidepyridine() 170 test(smiles("O=C1NC=CC=C1"), -1, 1, 2, 1, 1, 1, 1); in pyridinone() [all …]
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H A D | AromaticityTest.java | 34 import org.openscience.cdk.smiles.SmilesParser; 55 assertThat(cdk.findBonds(type(smiles("C1=CC=CC=C1"))).size(), is(6)); in benzene() 56 assertThat(daylight.findBonds(smiles("C1=CC=CC=C1")).size(), is(6)); in benzene() 61 assertThat(cdk.findBonds(type(smiles("C1=CC=CO1"))).size(), is(5)); in furan() 62 assertThat(daylight.findBonds(smiles("C1=CC=CO1")).size(), is(5)); in furan() 91 assertThat(daylight.findBonds(smiles("O=C1NC=CC=C1")).size(), is(6)); in pyridinone() 102 IAtomContainer cyclobutadiene = smiles("c1ccc1"); in clearFlags_cyclobutadiene() 112 IAtomContainer quinone = smiles("O=c1ccc(=O)cc1"); in clearFlags_quinone() 159 IAtomContainer a = smiles("C1=CC2=CC3=CC4=C(C=CC=C4)C=C3C=C2C=C1"); in ensureConsistentRepresentation() 160 IAtomContainer b = smiles("c1cc2cc3cc4c(cccc4)cc3cc2cc1"); in ensureConsistentRepresentation() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/ |
H A D | UnitTestEnumerateHeterocycles.py | 28 def check_smiles(smiles): argument 29 mol = Chem.MolFromSmiles(smiles) 30 assert mol is not None, smiles 37 assert orig_can_smi != smiles, "%s != %s" % (orig_can_smi, smiles) 40 mol = check_smiles(smiles) 75 assert smiles 80 if not smiles: 91 if not smiles: 125 assert smiles 143 smiles = row['SMILES'] [all …]
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H A D | UnitTestMol3D.py | 195 smiles = set( 197 print(smiles) 203 smiles = set( 261 smiles, 278 smiles = [ 308 smiles, 319 smiles = [ 335 smiles = [ 349 smiles = [ 362 smiles, [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/ |
H A D | test2.cpp | 25 std::vector<std::string> smiles = {"C", "[NH4+]", "[13C@H]"}; in testParseAtomSmiles() local 26 for (const auto &pr : smiles) { in testParseAtomSmiles() 35 for (const auto &pr : smiles) { in testParseAtomSmiles() 47 for (const auto &pr : smiles) { in testParseBondSmiles() 54 std::vector<std::string> smiles = {"C", "", "C-O", "*"}; in testParseBondSmiles() local 55 for (const auto &pr : smiles) { in testParseBondSmiles() 68 for (const auto &pr : smiles) { in testParseAtomSmarts() 76 for (const auto &pr : smiles) { in testParseAtomSmarts() 89 for (const auto &pr : smiles) { in testParseBondSmarts() 96 std::vector<std::string> smiles = {"C", "", "-O", "*"}; in testParseBondSmarts() local [all …]
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H A D | test.cpp | 2510 std::string smiles = in testBug3139534() local 2542 std::string smiles = in testBug3139534() local 2572 std::string smiles = in testBug3139534() local 2602 std::string smiles = in testBug3139534() local 2670 smiles = "C1.C11.C"; in testBug3145697() 2684 smiles = "C1.C1=1.O1"; in testBug3145697() 2691 smiles = "C1.C=11.O1"; in testBug3145697() 2706 smiles = "C1C.CC11CCC"; in testBug3145697() 2971 std::string smiles = in testBug3526815() local 3840 std::string smiles = in testGithub786() local [all …]
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H A D | cxsmiles_test.cpp | 22 std::string smiles = "CC"; in testBase() local 25 ROMol *m = SmilesToMol(smiles, params); in testBase() 38 ROMol *m = SmilesToMol(smiles, params); in testCoords2D() 55 ROMol *m = SmilesToMol(smiles, params); in testCoords2D() 127 std::string smiles = "** |$;AH_p;$|"; in testAtomLabels() local 147 std::string smiles = "** |$;XH_p;$|"; in testAtomLabels() local 309 std::string smiles = in testAtomValues() local 338 std::string smiles = in testAtomProps() local 360 std::string smiles = in testAtomProps() local 512 m = SmilesToMol(smiles, params); in testErrorsInCXSmiles() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolDraw2D/ |
H A D | rxn_test1.cpp | 70 std::string smiles = in test1() local 83 std::string smiles = in test1() local 96 std::string smiles = in test1() local 108 std::string smiles = in test1() local 120 std::string smiles = in test1() local 132 std::string smiles = in test1() local 145 std::string smiles = in test1() local 164 std::string smiles = in test2() local 213 std::string smiles = in test3() local 239 std::string smiles = in test4() local [all …]
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SMILES-0.44/t/ |
H A D | names.t | 8 my @smiles = <F>; 9 plan tests => @smiles * 2; 11 for my $smiles (@smiles) { 12 chomp $smiles; 13 my $mol = Chemistry::Mol->parse($smiles, format => 'smiles'); 15 is($out, $smiles, "$smiles (name => 0)"); 17 is($out, $smiles, "$smiles (name => 1)");
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H A D | write.t | 8 my @smiles = <F>; 9 plan tests => scalar @smiles; 11 for my $smiles (@smiles) { 12 chomp $smiles; 13 my $mol = Chemistry::Mol->parse($smiles, format => 'smiles'); 15 is($out, $smiles, "$smiles");
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/dports/science/p5-Chemistry-File-SMILES/Chemistry-File-SMILES-0.47/t/ |
H A D | names.t | 8 my @smiles = <F>; 9 plan tests => @smiles * 2; 11 for my $smiles (@smiles) { 12 chomp $smiles; 13 my $mol = Chemistry::Mol->parse($smiles, format => 'smiles'); 15 is($out, $smiles, "$smiles (name => 0)"); 17 is($out, $smiles, "$smiles (name => 1)");
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H A D | write.t | 8 my @smiles = <F>; 9 plan tests => scalar @smiles; 11 for my $smiles (@smiles) { 12 chomp $smiles; 13 my $mol = Chemistry::Mol->parse($smiles, format => 'smiles'); 15 is($out, $smiles, "$smiles");
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/dports/chinese/phpbb-tw/phpBB2/templates/subSilver/admin/ |
H A D | smile_list_body.tpl | 13 <!-- BEGIN smiles --> 15 <td class="{smiles.ROW_CLASS}">{smiles.CODE}</td> 16 <td class="{smiles.ROW_CLASS}"><img src="{smiles.SMILEY_IMG}" alt="{smiles.CODE}" /></td> 17 <td class="{smiles.ROW_CLASS}">{smiles.EMOT}</td> 18 <td class="{smiles.ROW_CLASS}"><a href="{smiles.U_SMILEY_EDIT}">{L_EDIT}</a></td> 19 <td class="{smiles.ROW_CLASS}"><a href="{smiles.U_SMILEY_DELETE}">{L_DELETE}</a></td> 21 <!-- END smiles -->
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/dports/www/phpbb/phpBB2/templates/subSilver/admin/ |
H A D | smile_list_body.tpl | 13 <!-- BEGIN smiles --> 15 <td class="{smiles.ROW_CLASS}">{smiles.CODE}</td> 16 <td class="{smiles.ROW_CLASS}"><img src="{smiles.SMILEY_IMG}" alt="{smiles.CODE}" /></td> 17 <td class="{smiles.ROW_CLASS}">{smiles.EMOT}</td> 18 <td class="{smiles.ROW_CLASS}"><a href="{smiles.U_SMILEY_EDIT}">{L_EDIT}</a></td> 19 <td class="{smiles.ROW_CLASS}"><a href="{smiles.U_SMILEY_DELETE}">{L_DELETE}</a></td> 21 <!-- END smiles -->
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/dports/science/p5-PerlMol/PerlMol-0.3500/examples/polar_surface_area/ |
H A D | psa.pl | 58 my $smiles; 86 while($smiles = <INFILE>) 88 chomp $smiles; 124 $smiles = $ARGV[0]; 125 chomp $smiles; 133 print "$smiles\t$psa\n"; 138 $smiles = <STDIN>; 139 chomp $smiles; 152 $smiles = <STDIN>; 153 chomp $smiles; [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book/data/ |
H A D | solubility.train.sdf | 27 > <smiles> (1) 58 > <smiles> (2) 90 > <smiles> (3) 122 > <smiles> (4) 154 > <smiles> (5) 187 > <smiles> (6) 220 > <smiles> (7) 254 > <smiles> (8) 289 > <smiles> (9) 325 > <smiles> (10) [all …]
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/dports/science/openbabel/openbabel-3.1.1/test/ |
H A D | testsym.py | 59 self.smiles = [ 96 self.smiles = [ 114 self.smiles = [ 130 self.smiles = [ 162 for smiles, can, inchi in self.data: 209 smiles, can = self.data[i][0:2] 248 smiles, can = self.data[i][0:2] 317 smiles, can = self.data[6][0:2] 320 smiles, can = self.data[i + 4][0:2] 352 smiles = [can, '[S@](Cl)(=O)C', 'O=[S@](Cl)C'] [all …]
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/dports/biology/babel/babel-1.6/ |
H A D | smilesto.c | 27 smilestocontab(char *smiles) in smilestocontab() argument 95 if(strncmp(&smiles[i], "Cl", 2) == 0 || strncmp(&smiles[i], "Br", 2) == 0) in smilestocontab() 97 atname[0] = smiles[i]; in smilestocontab() 98 atname[1] = smiles[i+1]; in smilestocontab() 103 atname[0] = smiles[i]; in smilestocontab() 113 if(smiles[i+1] == ']') in smilestocontab() 115 atname[0] = smiles[i]; in smilestocontab() 121 atname[0] = smiles[i]; in smilestocontab() 131 if(smiles[i] == '%') in smilestocontab() 133 rno = (10 * (smiles[i+1] - '0')) + (smiles[i+2] - '0'); in smilestocontab() [all …]
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/dports/science/cdk/cdk-cdk-2.3/storage/smiles/src/test/java/org/openscience/cdk/smiles/ |
H A D | SmilesParserTest.java | 19 package org.openscience.cdk.smiles; 602 smiles = "Co"; in testOrganicSubsetUnderstanding() 658 String smiles = "C-C"; in testExplicitSingleBond() local 681 String smiles = "*C"; in testUnkownAtomType() local 688 smiles = "[*]C"; in testUnkownAtomType() 717 String smiles = "CC"; in testBondCreation() local 722 smiles = "cc"; in testBondCreation() 765 String smiles = "[H]"; in testSingleBracketH() local 1092 String smiles = "C"; in testImplicitHydrogenCount() local 1103 String smiles = "[W]"; in testTungsten() local [all …]
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/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/ |
H A D | SMILESFragmentBuilder.java | 129 private final String smiles; field in SMILESFragmentBuilder.ParserInstance 136 this.smiles = smiles; in ParserInstance() 144 char ch = smiles.charAt(i); in parseSmiles() 322 isotope += smiles.charAt(i); in processBracketedAtom() 328 ch = smiles.charAt(i); in processBracketedAtom() 392 ch = smiles.charAt(i); in processBracketedAtom() 441 ch = smiles.charAt(i + 1); in processBracketedAtom() 516 if (i + 2 < endOfSmiles && is_0_to_9(smiles.charAt(i + 1)) && is_0_to_9(smiles.charAt(i + 2))) { in processRingOpeningOrClosure() 671 if (smiles == null){ in build() 677 if (smiles.length() == 0){ in build() [all …]
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