| /dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/graph/ |
| H A D | CyclesTest.java | 185 IAtomContainer biphenyl = makeBiphenyl(); in toRingSet() local
191 assertThat(r1.getAtom(0), is(biphenyl.getAtom(0))); in toRingSet()
192 assertThat(r1.getAtom(1), is(biphenyl.getAtom(1))); in toRingSet()
193 assertThat(r1.getAtom(2), is(biphenyl.getAtom(2))); in toRingSet()
194 assertThat(r1.getAtom(3), is(biphenyl.getAtom(3))); in toRingSet()
195 assertThat(r1.getAtom(4), is(biphenyl.getAtom(4))); in toRingSet()
196 assertThat(r1.getAtom(5), is(biphenyl.getAtom(5))); in toRingSet()
225 IAtomContainer biphenyl = makeBiphenyl(); in markAtomsAndBonds() local
226 Cycles.markRingAtomsAndBonds(biphenyl); in markAtomsAndBonds()
229 for (IAtom atom : biphenyl.atoms()) { in markAtomsAndBonds()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/ringsearch/ |
| H A D | RingSearchTest_Biphenyl.java | 43 private final IAtomContainer biphenyl = TestMoleculeFactory.makeBiphenyl(); field in RingSearchTest_Biphenyl
47 assertThat(new RingSearch(biphenyl).cyclic().length, is(biphenyl.getAtomCount())); in testCyclic()
52 int n = biphenyl.getAtomCount(); in testCyclic_Int()
53 RingSearch ringSearch = new RingSearch(biphenyl); in testCyclic_Int()
61 RingSearch search = new RingSearch(biphenyl); in testIsolated()
70 assertThat(new RingSearch(biphenyl).fused().length, is(0)); in testFused()
75 IAtomContainer fragment = new RingSearch(biphenyl).ringFragments(); in testRingFragments()
76 assertThat(fragment.getAtomCount(), is(biphenyl.getAtomCount())); in testRingFragments()
77 assertThat(fragment.getBondCount(), is(biphenyl.getBondCount() - 1)); in testRingFragments()
82 RingSearch search = new RingSearch(biphenyl); in testIsolatedRingFragments()
[all …]
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| H A D | RingPartitionerTest.java | 66 IAtomContainer biphenyl = TestMoleculeFactory.makeBiphenyl(); in testPartitionIntoRings() local
67 ringSet = Cycles.sssr(biphenyl).toRingSet(); in testPartitionIntoRings()
|
| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/contrib/t3d@nersc/ |
| H A D | nqs_script | 1 #QSUB -o biphenyl.032
8 setenv RUNDIR /u/nwchem/wong/atw/biphenyl
14 $NWCHEM_EXE -npes 32 biphenyl.nw
|
| H A D | biphenyl.nw | 1 start biphenyl
5 title "biphenyl, Dupont, r=bohrs"
|
| /dports/science/nwchem-data/nwchem-7.0.2-release/contrib/t3d@nersc/ |
| H A D | nqs_script | 1 #QSUB -o biphenyl.032
8 setenv RUNDIR /u/nwchem/wong/atw/biphenyl
14 $NWCHEM_EXE -npes 32 biphenyl.nw
|
| H A D | biphenyl.nw | 1 start biphenyl
5 title "biphenyl, Dupont, r=bohrs"
|
| /dports/science/nwchem-data/nwchem-7.0.2-release/QA/tests/hess_biph/ |
| H A D | hess_biph.nw | 2 start biphenyl
3 title "biphenyl"
|
| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/QA/tests/hess_biph/ |
| H A D | hess_biph.nw | 2 start biphenyl
3 title "biphenyl"
|
| /dports/science/openbabel/openbabel-3.1.1/test/pdb_ligands_sdf/ |
| H A D | 4oc7_2qo.sdf | 122 (2E)-3-[6-hydroxy-3'-(prop-2-en-1-yl)biphenyl-3-yl]prop-2-enoic acid
128 (E)-3-(3'-allyl-6-hydroxy-[1,1'-biphenyl]-3-yl)acrylic acid
|
| H A D | 3ehx_bdl.sdf | 134 N-(biphenyl-4-ylsulfonyl)-D-leucine
140 (R)-2-(biphenyl-4-ylsulfonamido)-4-methylpentanoic acid
|
| H A D | 4h76_10b.sdf | 138 N-2-(biphenyl-4-ylsulfonyl)-N-2-(isopropyloxy)-acetohydroxamic acid
144 N~2~-(biphenyl-4-ylsulfonyl)-N-hydroxy-N~2~-(propan-2-yloxy)glycinamide
|
| H A D | 4jl4_axy.sdf | 160 (2S)-3-(biphenyl-4-yl)-2-(biphenyl-4-yloxy)propanoic acid
|
| H A D | 5uwn_8o7.sdf | 164 …(4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)thio)methyl)-[1,1'-biphenyl]-4-sulfonamide
170 …oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)sulfanyl]methyl}[1,1'-biphenyl]-4-sulfonamide
|
| H A D | 3gzx_bnl.sdf | 89 1,1'-biphenyl
|
| H A D | 3ccb_b2y.sdf | 94 1-biphenyl-2-ylmethanamine
|
| H A D | 5jao_6hx.sdf | 98 2'-chloro-6-methyl[1,1'-biphenyl]-3-amine
|
| H A D | 3g93_pb2.sdf | 111 1-(biphenyl-4-ylmethyl)-1H-imidazole
|
| H A D | 4xuc_43g.sdf | 119 1-(biphenyl-3-yl)-3-hydroxypyridin-4(1H)-one
|
| /dports/science/cdk/cdk-cdk-2.3/tool/fragment/src/test/java/org/openscience/cdk/fragment/ |
| H A D | MurckoFragmenterTest.java | 302 IAtomContainer biphenyl = TestMoleculeFactory.makeBiphenyl(); in testGetFragmentsAsContainers() local
303 AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(biphenyl); in testGetFragmentsAsContainers()
304 Aromaticity.cdkLegacy().apply(biphenyl); in testGetFragmentsAsContainers()
307 fragmenter.generateFragments(biphenyl); in testGetFragmentsAsContainers()
|
| /dports/science/cdk/cdk-cdk-2.3/base/testdata/src/test/resources/data/mdl/ |
| H A D | bug-1788686-adamantane-biphenyl.mol | 1 adamantane-biphenyl.mol
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/External/RingFamilies/RingDecomposerLib/test/ |
| H A D | molecule_03_0.dimacs | 1 c biphenyl
|
| /dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Ring-0.19/ |
| H A D | MANIFEST | 27 t/rings2/biphenyl.ring
|
| /dports/science/p5-Chemistry-Ring/Chemistry-Ring-0.20/ |
| H A D | MANIFEST | 27 t/rings2/biphenyl.ring
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Depictor/Wrap/ |
| H A D | testDepictor.py | 350 biphenyl = Chem.MolFromSmiles("c1ccccc1-c1ccccc1")
356 for mol in (ortho, meta, biphenyl, phenyl):
392 for mol in (ortho, meta, biphenyl, phenyl):
|