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/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/
H A DSMILESWriterTest.java28 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Subgraphs/
H A Dtest2.cpp22 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()
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/aromaticity/
H A DDaylightModelTest.java32 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()
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H A DPiBondModelTest.java32 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()
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H A DAtomTypeModelTest.java32 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()
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H A DExocyclicAtomTypeModelTest.java32 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()
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H A DAromaticityTest.java34 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/
H A DUnitTestEnumerateHeterocycles.py28 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']
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H A DUnitTestMol3D.py195 smiles = set(
197 print(smiles)
203 smiles = set(
261 smiles,
278 smiles = [
308 smiles,
319 smiles = [
335 smiles = [
349 smiles = [
362 smiles,
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/
H A Dtest2.cpp25 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
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H A Dtest.cpp2510 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
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H A Dcxsmiles_test.cpp22 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolDraw2D/
H A Drxn_test1.cpp70 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
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SMILES-0.44/t/
H A Dnames.t8 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)");
H A Dwrite.t8 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");
/dports/science/p5-Chemistry-File-SMILES/Chemistry-File-SMILES-0.47/t/
H A Dnames.t8 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)");
H A Dwrite.t8 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");
/dports/chinese/phpbb-tw/phpBB2/templates/subSilver/admin/
H A Dsmile_list_body.tpl13 <!-- 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 -->
/dports/www/phpbb/phpBB2/templates/subSilver/admin/
H A Dsmile_list_body.tpl13 <!-- 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 -->
/dports/science/p5-PerlMol/PerlMol-0.3500/examples/polar_surface_area/
H A Dpsa.pl58 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;
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/dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book/data/
H A Dsolubility.train.sdf27 > <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)
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/dports/science/openbabel/openbabel-3.1.1/test/
H A Dtestsym.py59 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']
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/dports/biology/babel/babel-1.6/
H A Dsmilesto.c27 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()
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/dports/science/cdk/cdk-cdk-2.3/storage/smiles/src/test/java/org/openscience/cdk/smiles/
H A DSmilesParserTest.java19 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
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/dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/
H A DSMILESFragmentBuilder.java129 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()
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