/dports/science/cdk/cdk-cdk-2.3/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/ |
H A D | MmffTest.java | 69 IAtomContainer mol = loadSmi("N1N=CN=N1"); in tetrazole() local 87 IAtomContainer mol = loadSmi("o1cccc1"); in clearProps() local 115 IAtomContainer mol = loadSmi("CO"); in methanol() local 125 IAtomContainer mol = loadSmi("CN"); in methylamine() local 135 IAtomContainer mol = loadSmi("CC#N"); in acetonitrile() local 145 IAtomContainer mol = loadSmi("COC"); in dimethylether() local 155 IAtomContainer mol = loadSmi("CS"); in methanethiol() local 165 IAtomContainer mol = loadSmi("CCl"); in chloromethane() local 175 IAtomContainer mol = loadSmi("CC"); in ethane() local 265 IAtomContainer mol = loadSmi("O"); in water() local [all …]
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/templates/ |
H A D | MoleculeFactory.java | 54 IAtomContainer mol = new AtomContainer(); in makeAlphaPinene() local 107 IAtomContainer mol = new AtomContainer(); in makeEthylCyclohexane() local 134 IAtomContainer mol = new AtomContainer(); in makeCyclohexene() local 157 IAtomContainer mol = new AtomContainer(); in makeCyclohexane() local 180 IAtomContainer mol = new AtomContainer(); in makeCyclopentane() local 201 IAtomContainer mol = new AtomContainer(); in makeCyclobutane() local 220 IAtomContainer mol = new AtomContainer(); in makeCyclobutadiene() local 234 IAtomContainer mol = new AtomContainer(); in makePropylCycloPropane() local 257 IAtomContainer mol = new AtomContainer(); in makeBiphenyl() local 289 IAtomContainer mol = new AtomContainer(); in makePhenylEthylBenzene() local [all …]
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/dports/science/py-pyscf/pyscf-2.0.1/examples/gto/ |
H A D | 04-input_basis.py | 28 mol = gto.M(atom = '''O 0 0 0; H 0 1 0; H 0 0 1''', variable 39 mol = gto.M(atom = '''O 0 0 0; 1 0 1 0; H 0 0 1''', variable 57 mol = gto.M( variable 65 mol = gto.M( variable 88 mol = gto.M( variable 100 mol = gto.M( variable 112 mol = gto.M( variable 203 mol = gto.M( variable 221 mol = gto.M( variable 232 mol = gto.M( variable [all …]
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H A D | 03-ghost_atom.py | 16 mol = gto.M( variable 24 mol = gto.M(atom=''' variable 44 mol = gto.M(atom=''' variable 56 mol = gto.M(atom=''' variable 69 mol = gto.M(atom=''' variable
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H A D | 05-input_ecp.py | 10 mol = gto.M(atom=''' variable 17 mol = gto.M(atom=''' variable 43 mol = gto.M(atom=''' variable 70 mol = gto.M(atom='Na 0. 0. 0.; H 0 0 2.', variable 84 mol = gto.M(atom='Cu 0. 0. 0.; H 0 0 2.', variable
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | catch_chirality.cpp | 26 auto mol = "CC=C(C#C)C=C"_smiles; variable 40 auto mol = "CC=NC=N"_smiles; variable 145 auto mol = "CC=NC=N"_smiles; variable 423 auto mol = "FC(O)C"_smiles; variable 433 auto mol = "CC(O)C"_smiles; variable 457 auto mol = "CC=CC"_smiles; variable 474 auto mol = "CC=C"_smiles; variable 726 auto mol = "CC=CC"_smiles; variable 750 auto mol = "CC=CC"_smiles; variable 761 auto mol = "CC=CC"_smiles; variable [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/ |
H A D | RWMol.i | 68 RDKit::RWMol *mol=0; variable 74 RDKit::RWMol *mol=0; variable 80 RDKit::RWMol *mol=0; variable 86 RDKit::RWMol *mol=0; variable 92 RDKit::RWMol *mol=0; variable 100 RDKit::RWMol *mol=0; variable 108 RDKit::RWMol *mol=0; variable 114 RDKit::RWMol *mol=0; variable 120 RDKit::RWMol *mol=0; variable 126 RDKit::RWMol *mol=0; variable
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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 | 150 IAtomContainer mol = load(smiles); in testBug1363882() local 161 IAtomContainer mol = load(smiles); in testBug1535587() local 174 IAtomContainer mol = load(smiles); in testBug1579235() local 206 IAtomContainer mol = load(smiles); in testBug1579230() local 612 IAtomContainer mol = load("Cocc"); in testOrganicSubsetUnderstanding2() local 778 IAtomContainer mol = load("H"); in testSingleH() local 788 IAtomContainer mol = load("D"); in testSingleD() local 799 IAtomContainer mol = load("T"); in testSingleT() local 1357 IAtomContainer mol = sp in testBug1719287() local 1523 IAtomContainer mol = load(smiles); in testSP2HybridizedSulphur() local [all …]
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H A D | CxSmilesTest.java | 102 IAtomContainer mol = smipar.parseSmiles("c1ccccc1 |<benzene>|"); in nonCXSMILESLayer() local 109 IAtomContainer mol = smipar.parseSmiles("c1ccccc1 |"); in truncatedCXSMILES() local 123 IAtomContainer mol = smipar.parseSmiles("**.c1ccccc1CC |$R'$|"); in atomLabels() local 174 IAtomContainer mol = smipar.parseSmiles("CCC |(0,1,;0,2,;0,3,)|"); in atomCoordinates2D() local 196 IAtomContainer mol = smipar.parseSmiles("[N]1C=CC=C1 |c:1,3,^1:0|"); in monovalentRadical() local 224 IAtomContainer mol = new AtomContainer(); in generateLabelledSmiles() local 239 IAtomContainer mol = new AtomContainer(); in generateCanonLabelledSmiles() local 298 IAtomContainer mol = smipar.parseSmiles("CCO |(,,;1,1,;2,2,)|"); in coordsEtOH() local 307 IAtomContainer mol = smipar.parseSmiles("CCO |(,,;1,1,;2,2,)|"); in canonCoordsEtOH() local 317 IAtomContainer mol = smipar.parseSmiles("CCO |(,,;1,1,;2,2,)|"); in noCoordsOptEtOH() local [all …]
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/dports/science/cdk/cdk-cdk-2.3/tool/smarts/src/test/java/org/openscience/cdk/smarts/ |
H A D | SmartsExprWriteTest.java | 255 QueryAtomContainer mol = new QueryAtomContainer(null); in indoleRoundTrip() local 263 QueryAtomContainer mol = new QueryAtomContainer(null); in indoleWithExprRoundTrip() local 271 QueryAtomContainer mol = new QueryAtomContainer(null); in bondTrue() local 277 QueryAtomContainer mol = new QueryAtomContainer(null); in bondFalse() local 283 QueryAtomContainer mol = new QueryAtomContainer(null); in bondInChain() local 289 QueryAtomContainer mol = new QueryAtomContainer(null); in bondInRing() local 295 QueryAtomContainer mol = new QueryAtomContainer(null); in tripleBond() local 301 QueryAtomContainer mol = new QueryAtomContainer(null); in notTripleBond() local 307 QueryAtomContainer mol = new QueryAtomContainer(null); in aromaticBond() local 313 QueryAtomContainer mol = new QueryAtomContainer(null); in ringClosureExprs() local [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/ |
H A D | ATASaturationCheckerTest.java | 69 IAtomContainer mol = new AtomContainer(); in testASimpleCarbonRing() local 220 IAtomContainer mol = sp.parseSmiles(smiles); in testALargeRingSystem() local 240 IAtomContainer mol = sp.parseSmiles(smiles); in testLargeRingSystem1() local 254 IAtomContainer mol = sp.parseSmiles(smiles); in testLargeRingSystem2() local 271 IAtomContainer mol = sp.parseSmiles(smiles); in testADoubleRingWithANitrogenAtom() local 291 IAtomContainer mol = sp.parseSmiles(smiles); in testLargeRingSystem3() local 305 IAtomContainer mol = sp.parseSmiles(smiles); in testLargeRingSystem4() local 552 IAtomContainer mol = sp in testIndoles2() local 597 IAtomContainer mol = new AtomContainer(); in testButadiene() local 661 IAtomContainer mol = sp.parseSmiles("C"); in testOnlyOneAtom() local [all …]
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/dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/test/java/org/openscience/cdk/io/ |
H A D | MDLV3000WriterTest.java | 61 IAtomContainer mol = new AtomContainer(); in outputValencyWhenNeeded() local 73 IAtomContainer mol = new AtomContainer(); in outputFormalCharge() local 87 IAtomContainer mol = new AtomContainer(); in outputMassNumber() local 102 IAtomContainer mol = new AtomContainer(); in outputRadical() local 112 IAtomContainer mol = new AtomContainer(); in nullBondOrder() local 124 IAtomContainer mol = new AtomContainer(); in unsetBondOrder() local 136 IAtomContainer mol = new AtomContainer(); in solidWedgeBonds() local 148 IAtomContainer mol = new AtomContainer(); in hashedWedgeBonds() local 160 IAtomContainer mol = new AtomContainer(); in solidWedgeInvBonds() local 172 IAtomContainer mol = new AtomContainer(); in hashedWedgeInvBonds() local [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/ |
H A D | test.cpp | 66 ROMol *mol; in test2() local 287 ROMol *mol; in testLabute() local 489 ROMol *mol; in testVSADescriptors() local 545 ROMol *mol; in testVSADescriptors() local 587 ROMol *mol; in testVSADescriptors() local 813 ROMol *mol; in testIssue3433771() local 911 ROMol *mol; in testCrippenContribs() local 944 ROMol *mol; in testIssue252() local 958 ROMol *mol; in testIssue252() local 969 ROMol *mol; in testIssue252() local [all …]
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/dports/science/cdk/cdk-cdk-2.3/descriptor/signature/src/test/java/org/openscience/cdk/signature/ |
H A D | AbstractSignatureTest.java | 41 public static void print(IAtomContainer mol) { in print() 69 public static void addCarbons(IAtomContainer mol, int count) { in addCarbons() 105 IAtomContainer mol = builder.newInstance(IAtomContainer.class); in makeCycleWheel() local 114 IAtomContainer mol = builder.newInstance(IAtomContainer.class); in makeSandwich() local 143 IAtomContainer mol = builder.newInstance(IAtomContainer.class); in makeC7H16A() local 162 IAtomContainer mol = builder.newInstance(IAtomContainer.class); in makeC7H16B() local 181 IAtomContainer mol = builder.newInstance(IAtomContainer.class); in makeC7H16C() local 281 IAtomContainer mol = builder.newInstance(IAtomContainer.class); in makeCubane() local 299 IAtomContainer mol = builder.newInstance(IAtomContainer.class); in makeCuneane() local 317 IAtomContainer mol = builder.newInstance(IAtomContainer.class); in makeCyclobutane() local [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/Draw/ |
H A D | demo.cpp | 27 std::string MolToSVG(const ROMol &mol) { in MolToSVG() 45 RWMol *mol = SmilesToMol("c1c(C#N)cccc1C~C2CC2"); in DrawDemo() local 52 RWMol *mol = in DrawDemo() local 60 RWMol *mol = SmilesToMol( in DrawDemo() local 69 RWMol *mol = SmilesToMol("BrO"); in DrawDemo() local 76 RWMol *mol = SmilesToMol("BrC(O)(Cl)N"); in DrawDemo() local 83 RWMol *mol = SmilesToMol("[14NH2+]=[14NH2+]"); in DrawDemo() local 93 RWMol *mol = in DrawDemo() local 106 RWMol *mol = SmilesToMol("c1c[12cH]ccn1"); in DrawDemo() local 156 RWMol *mol = SmilesToMol("BrO", 0, false); in DrawDemo() local [all …]
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/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ |
H A D | XLogPDescriptorTest.java | 56 … IAtomContainer mol = sp.parseSmiles("O=C(O)c1[nH0]cccc1"); // xlogp training set molecule no688 in testno688() local 81 IAtomContainer mol = sp.parseSmiles("O=C(O)C(N)CCCN"); // xlogp training set molecule no367 in testno367() local 93 …IAtomContainer mol = sp.parseSmiles("O=P(N1CC1)(N2CC2)N3CC3"); // xlogp training set molecule no18… in testno1837() local 129 … IAtomContainer mol = sp.parseSmiles("C(#Cc1ccccc1)c1ccccc1"); // xlogp training set molecule no30 in testno30() local 154 …IAtomContainer mol = sp.parseSmiles("FC(F)(F)c1ccc(cc1)C(=O)N"); // xlogp training set molecule no… in testno990() local 178 IAtomContainer mol = sp.parseSmiles("CC(=O)OC1=CC=CC=C1C(=O)O"); // aspirin in testApirinBug1296383() local 190 …IAtomContainer mol = sp.parseSmiles("O=C(OC)CNC(=O)c1ccc(N)cc1"); // xlogp training set molecule n… in testno1429() local 230 … IAtomContainer mol = sp.parseSmiles("O=C1N(C)C=CC(=O)N1C"); // xlogp training set molecule no498 in testno498() local 295 IAtomContainer mol = sp.parseSmiles("C1=CC=CC=C1"); // benzene in testAromaticBenzene() local 308 IAtomContainer mol = sp.parseSmiles("C1=CC=CC=C1"); // benzene in testNonAromaticBenzene() local [all …]
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H A D | TPSADescriptorTest.java | 53 IAtomContainer mol = sp.parseSmiles("O=C(O)CC"); in testTPSA1() local 60 IAtomContainer mol = sp.parseSmiles("C=NC(CC#N)N(C)C"); in testTPSA2() local 67 IAtomContainer mol = sp.parseSmiles("CCCN(=O)=O"); in testTPSA3() local 74 IAtomContainer mol = sp.parseSmiles("C#N=CC(CNC)N1CC1"); in testTPSA4() local 81 IAtomContainer mol = sp.parseSmiles("c1ccncc1"); in testTPSA5() local 88 IAtomContainer mol = sp.parseSmiles("[H][N+]([H])(C)C");//at: 16 in testTPSA6() local 95 IAtomContainer mol = sp.parseSmiles("C(I)I");//at: 16 in testTPSA7() local 102 IAtomContainer mol = sp.parseSmiles("C(O)O");//at: 16 in testTPSA8() local 110 IAtomContainer mol = sp.parseSmiles("C1CCCC1CCC2CCCNC2"); in testRing() local
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H A D | LargestChainDescriptorTest.java | 33 IAtomContainer mol = sp.parseSmiles("c1ccccc1"); // benzol in test1LargestChainDescriptor() local 43 IAtomContainer mol = sp.parseSmiles("C=CC=Cc1ccccc1"); in test2LargestChainDescriptor() local 53 IAtomContainer mol = sp.parseSmiles("C=CC=CCc2ccc(Cc1ccncc1C=C)cc2"); in test3LargestChainDescriptor() local 63 IAtomContainer mol = sp.parseSmiles("CC=CNCC"); in test4LargestChainDescriptor() local 73 IAtomContainer mol = sp.parseSmiles("C=C[NH2+]CC"); in test5LargestChainDescriptor() local 83 IAtomContainer mol = sp.parseSmiles("CCNOC"); in test6LargestChainDescriptor() local 93 IAtomContainer mol = sp.parseSmiles("CC=CC(C)=O"); in test7LargestChainDescriptor() local 103 IAtomContainer mol = sp.parseSmiles("C"); in testSingleCAtom() local 113 IAtomContainer mol = sp.parseSmiles("O"); in testSingleOAtom() local 132 IAtomContainer mol = sp.parseSmiles("Nc1c(cn[nH]1)C#N"); in test9LargestChainDescriptor() local [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SLNParse/ |
H A D | test.cpp | 47 RDKit::RWMol *mol; in test1() local 150 RDKit::RWMol *mol; in test2() local 231 RDKit::RWMol *mol; in test3() local 343 RDKit::RWMol *mol; in test4() local 372 RDKit::RWMol *patt, *mol; in test5() local 1267 RDKit::RWMol *mol; in test11() local 1475 RDKit::RWMol *mol; in test13() local 1622 RDKit::RWMol *mol; in test14() local 1642 RDKit::RWMol *mol; in test15() local 1728 RDKit::RWMol *mol; in test16() local [all …]
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/dports/science/cdk/cdk-cdk-2.3/app/depict/src/test/java/org/openscience/cdk/depict/ |
H A D | AbbreviationsTest.java | 82 IAtomContainer mol = smi("c1ccccc1"); in phenylShouldNotMatchBenzene() local 91 IAtomContainer mol = smi("Clc1ccccc1"); in avoidOverZealousAbbreviations() local 99 IAtomContainer mol = smi("Oc1ccc(O)cc1"); in phenylShouldNotMatchC4H6() local 121 IAtomContainer mol = smi("CCCCC1=CC=CC=C1"); in phenylShouldMatchKekuleForm() local 150 IAtomContainer mol = smi("c1ccccc1CCC"); in abbreviationsHavePriority() local 162 IAtomContainer mol = smi("c1ccccc1CCC"); in dontOverwriteExistingSgroups() local 261 IAtomContainer mol = smi("Cl[Sn]Cl"); in SnCl2() local 269 IAtomContainer mol = smi("OO"); in HOOH() local 280 IAtomContainer mol = smi(smi); in multipleDisconnectedAbbreviations() local 291 IAtomContainer mol = smi(smi); in multipleDisconnectedAbbreviations2() local [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/ |
H A D | SmilesDetailsTests.java | 42 ROMol mol; in testDetails() local 71 ROMol mol; in testProblems() local 111 ROMol mol; in testBasicCanon() local 188 ROMol mol; in testStereochem() local 622 ROMol mol; in testIssue143() local 833 ROMol mol; in testIssue159() local 856 ROMol mol; in testIssue175() local 872 ROMol mol; in testIssue176() local 898 ROMol mol; in testIssue184() local 926 ROMol mol; in testIssue185() local [all …]
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/scf/ |
H A D | __init__.py | 123 def HF(mol, *args): argument 132 def RHF(mol, *args): argument 157 def UHF(mol, *args): argument 169 def GHF(mol, *args): argument 176 def DHF(mol, *args): argument 186 def X2C(mol, *args): argument 204 def KS(mol, *args): argument 208 def RKS(mol, *args): argument 216 def UKS(mol, *args): argument 220 def GKS(mol, *args): argument [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/ |
H A D | GraphDescriptors.py | 134 def _pyKappa1(mol): argument 152 def _pyKappa2(mol): argument 170 def _pyKappa3(mol): argument 200 def Chi0(mol): argument 215 def Chi1(mol): argument 259 def _pyChi0v(mol): argument 271 def _pyChi1v(mol): argument 302 def _pyChi2v(mol): argument 309 def _pyChi3v(mol): argument 316 def _pyChi4v(mol): argument [all …]
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/dports/science/xtb/xtb-6.4.1/TESTSUITE/ |
H A D | molstock.f90 | 61 subroutine mindless01(mol) argument 88 subroutine mindless02(mol) argument 116 subroutine mindless03(mol) argument 143 subroutine mindless04(mol) argument 170 subroutine mindless05(mol) argument 337 subroutine caffeine(mol) argument 433 subroutine grubbs(mol) argument 617 subroutine taxol(mol) argument 974 subroutine vcpco4(mol) argument 1005 subroutine feco5(mol) argument [all …]
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/ |
H A D | IPAtomicLearningDescriptorTest.java | 180 IAtomContainer mol = sp.parseSmiles("C-Cl"); in testIPDescriptor_1() local 199 IAtomContainer mol = sp.parseSmiles("C-C-Br"); in testIPDescriptor_2() local 217 IAtomContainer mol = sp.parseSmiles("C-C-C-I"); in testIPDescriptor_3() local 237 IAtomContainer mol = sp.parseSmiles("C-C-O"); in testIPDescriptor_4() local 278 IAtomContainer mol = sp.parseSmiles("C-N-C"); in testIPDescriptor_6() local 300 IAtomContainer mol = sp.parseSmiles("C-C-N"); in testIPDescriptor_7() local 322 IAtomContainer mol = sp.parseSmiles("C-C-P-C-C"); in testIPDescriptor_8() local 384 IAtomContainer mol = sp.parseSmiles("CCOCCCO"); in testIPDescriptor_14() local 464 IAtomContainer mol = sp.parseSmiles("O(C=CC=C)C"); in testIPPySystemWithHeteroatomDescriptor3() local 489 IAtomContainer mol = sp.parseSmiles("OC=CC"); in testIPPySystemWithHeteroatomDescriptor2() local [all …]
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