| /dports/science/p5-Chemistry-Ring/Chemistry-Ring-0.20/t/rings/ |
| H A D | cycloheptatriene.ring | 4 Ring: atoms(a1 a2 a3 a4 a5 a6 a7); bonds(b1 b2 b3 b4 b5 b6 b7); aromatic(0)
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| /dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SMILES-0.44/t/ |
| H A D | multiline.t | 12 aromatic => 1);
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| H A D | write.t | 14 my $out = $mol->print(format => 'smiles', aromatic => 1);
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| /dports/science/p5-Chemistry-File-SMILES/Chemistry-File-SMILES-0.47/t/ |
| H A D | multiline.t | 12 aromatic => 1);
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| H A D | write.t | 14 my $out = $mol->print(format => 'smiles', aromatic => 1);
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| /dports/science/nwchem-data/nwchem-7.0.2-release/src/data/amber_s/ |
| H A D | amber.par | 759 # 3 = aromatic;
771 # 5 i5 aromatic ring : -1 = not in aromatic ring
773 # 1 = in at least one aromatic ring
774 # 5 = in 5-membered aromatic ring
775 # 6 = in 6-membered aromatic ring
776 # 56 = junction 5 & 6 membered aromatic rings
777 # 66 = junction two 6 membered aromatic rings
778 # 666 = junction three 6 membered aromatic rings
927 # aromatic carbon in 6-membered ring
983 # aromatic amine
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| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/data/amber_s/ |
| H A D | amber.par | 759 # 3 = aromatic;
771 # 5 i5 aromatic ring : -1 = not in aromatic ring
773 # 1 = in at least one aromatic ring
774 # 5 = in 5-membered aromatic ring
775 # 6 = in 6-membered aromatic ring
776 # 56 = junction 5 & 6 membered aromatic rings
777 # 66 = junction two 6 membered aromatic rings
778 # 666 = junction three 6 membered aromatic rings
927 # aromatic carbon in 6-membered ring
983 # aromatic amine
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| /dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/SimpleEnum/test_data/ |
| H A D | boronic1.rxn | 14 V 1 halogen.bromine.aromatic
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| H A D | bad_value1.rxn | 14 V 1 halogen.bromine.aromatic
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| /dports/biology/emboss/EMBOSS-6.6.0/emboss/data/ |
| H A D | Eaa_properties.dat | 10 # aromatic polar positive
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
| H A D | QueryOps.h | 131 static inline int makeAtomType(int atomic_num, bool aromatic) { in makeAtomType() argument
132 return atomic_num + 1000 * static_cast<int>(aromatic); in makeAtomType()
134 static inline void parseAtomType(int val, int &atomic_num, bool &aromatic) { in parseAtomType() argument
136 aromatic = true; in parseAtomType()
139 aromatic = false; in parseAtomType()
371 T *makeAtomTypeQuery(int num, int aromatic, const std::string &descr) { in makeAtomTypeQuery() argument
372 return makeAtomSimpleQuery<T>(makeAtomType(num, aromatic), queryAtomType, in makeAtomTypeQuery()
377 int aromatic);
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| H A D | Aromaticity.cpp | 314 bool aromatic = false; in applyHuckel() local
327 aromatic = true; in applyHuckel()
332 aromatic = true; in applyHuckel()
337 std::cerr <<" rlw: "<<rlw<<" rup: "<<rup<<" aromatic? "<<aromatic<<std::endl; in applyHuckel()
339 return aromatic; in applyHuckel()
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| /dports/science/cdk/cdk-cdk-2.3/base/testdata/src/test/resources/data/ctx/ |
| H A D | methanol_with_descriptors.ctx | 52 Number of aromatic atoms
136 Number of aromatic atoms
220 Atom belongs to an aromatic ring [0 = false, 1 = true]
532 Bond belongs to an aromatic ring [0 = false, 1 = true]
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| /dports/science/p5-Chemistry-File-SLN/Chemistry-File-SLN-0.11/lib/Chemistry/File/ |
| H A D | SLN.pm | 254 $_->aromatic(1) for ($atom1, $atom2, $bond);
349 if ($opts{aromatic}) {
485 my $s = $bond->aromatic ? ':' : $ORDER_TO_TYPE{$bond->order};
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| /dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SLN-0.11/lib/Chemistry/File/ |
| H A D | SLN.pm | 254 $_->aromatic(1) for ($atom1, $atom2, $bond);
349 if ($opts{aromatic}) {
485 my $s = $bond->aromatic ? ':' : $ORDER_TO_TYPE{$bond->order};
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| /dports/science/lammps/lammps-stable_29Sep2021/tools/drude/ |
| H A D | drude.dff | 23 # aromatic (CHARMM)
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| /dports/science/openbabel/openbabel-3.1.1/test/ |
| H A D | README | 14 // aromatic perception
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| /dports/science/xdrawchem/xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5/xdrawchem/ |
| H A D | molecule_tools_1.cpp | 132 if ((tmp_pt->aromatic == true) && (tmp_pt2->aromatic == true)) { in Calc13CNMR()
466 if (tmp_pt->aromatic == true) { in CalcIR()
565 if (tmp_pt->aromatic) { in CalcKOW()
617 if (tmp_pt->aromatic) { in CalcKOW()
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book/ |
| H A D | RDKit_Book.rst | 21 An aromatic bond must be between aromatic atoms, but a bond between aromatic atoms does not need to…
71 **Notation** a: any aromatic atom; A: any atom, include H; \*: a dummy atom
153 - fused rings (i.e. azulene) can be aromatic
154 - five-membered rings are not aromatic (though they can be part of fused aromatic systems)
155 - only C and N can be aromatic
157 - atoms with exocyclic double bonds are not aromatic
363 a "aromatic atom"
396 "" "single or aromatic" "unspecified bonds"
400 : aromatic
1159 to aromatic.
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/storage/smiles/src/main/java/org/openscience/cdk/smiles/ |
| H A D | CDKToBeam.java | 210 …final boolean aromatic = SmiFlavor.isSet(flavour, SmiFlavor.UseAromaticSymbols) && a.getFlag(CDKCo… in toBeamAtom()
217 AtomBuilder ab = aromatic ? AtomBuilder.aromatic(element) : AtomBuilder.aliphatic(element); in toBeamAtom()
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| /dports/science/cdk/cdk-cdk-2.3/tool/fragment/src/test/java/org/openscience/cdk/fragment/ |
| H A D | MurckoFragmenterTest.java | 232 SmilesGenerator sg = SmilesGenerator.unique().aromatic(); in testCarbinoxamine_Bug3088164()
245 SmilesGenerator sg = SmilesGenerator.unique().aromatic(); in testPirenperone_Bug3088164()
278 SmilesGenerator sg = SmilesGenerator.unique().aromatic(); in testIsomoltane_Bug3088164()
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| /dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/ |
| H A D | Changes | 54 - New methods: Mol::printf, sprintf, charge; Atom::aromatic,
55 formal_charge; Bond::aromatic
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| /dports/science/plumed/plumed2-2.7.2/regtest/basic/rt-hrex-2/ |
| H A D | processed.top | 2785 … CA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
2788 … CR X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
2789 … CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
2790 … CU X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
2791 … CW X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
2792 … NC X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
2795 … CB X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
2797 … CS X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
2798 … NA X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
2799 … NB X 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; aromatic ring
[all …]
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| /dports/science/lammps/lammps-stable_29Sep2021/tools/ch2lmp/example/ |
| H A D | top_all27_na.rtf | 35 MASS 4 HN3 1.008000 H ! Nucleic acid aromatic carbon proton
36 MASS 5 HN3B 1.008000 H ! NAD+ aromatic hydrogen
38 MASS 7 HNP 1.008000 H ! pure aromatic H
51 MASS 24 CN3 12.011000 C ! Nucleic acid aromatic carbon
52 MASS 25 CN3A 12.011000 C ! NAD+ aromatic carbon
53 MASS 26 CN3B 12.011000 C ! NAD+ aromatic carbon
54 MASS 27 CN3C 12.011000 C ! NADH aromatic carbon
55 MASS 28 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC
56 MASS 29 CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5
69 MASS 42 CNA 12.011000 C ! pure aromatic carbon
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/ |
| H A D | MmffAtomTypeValidationSuiteTest.java | 65 mesg = SmilesGenerator.generic().aromatic().withAtomClasses().create(container); in assertMatchingTypes()
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