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/dports/science/cdk/cdk-cdk-2.3/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/
H A DMmffTest.java69 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
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/templates/
H A DMoleculeFactory.java54 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
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/dports/science/py-pyscf/pyscf-2.0.1/examples/gto/
H A D04-input_basis.py28 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
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H A D03-ghost_atom.py16 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
H A D05-input_ecp.py10 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
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A Dcatch_chirality.cpp26 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
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/
H A DRWMol.i68 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
/dports/science/cdk/cdk-cdk-2.3/storage/smiles/src/test/java/org/openscience/cdk/smiles/
H A DSmilesParserTest.java150 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
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H A DCxSmilesTest.java102 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
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/dports/science/cdk/cdk-cdk-2.3/tool/smarts/src/test/java/org/openscience/cdk/smarts/
H A DSmartsExprWriteTest.java255 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
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/dports/science/cdk/cdk-cdk-2.3/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/
H A DATASaturationCheckerTest.java69 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
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/dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/test/java/org/openscience/cdk/io/
H A DMDLV3000WriterTest.java61 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
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/
H A Dtest.cpp66 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
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/dports/science/cdk/cdk-cdk-2.3/descriptor/signature/src/test/java/org/openscience/cdk/signature/
H A DAbstractSignatureTest.java41 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
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/Draw/
H A Ddemo.cpp27 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
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/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/
H A DXLogPDescriptorTest.java56 … 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
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H A DTPSADescriptorTest.java53 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
H A DLargestChainDescriptorTest.java33 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
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SLNParse/
H A Dtest.cpp47 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
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/dports/science/cdk/cdk-cdk-2.3/app/depict/src/test/java/org/openscience/cdk/depict/
H A DAbbreviationsTest.java82 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
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/
H A DSmilesDetailsTests.java42 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
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/scf/
H A D__init__.py123 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
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/
H A DGraphDescriptors.py134 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
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/dports/science/xtb/xtb-6.4.1/TESTSUITE/
H A Dmolstock.f9061 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
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/
H A DIPAtomicLearningDescriptorTest.java180 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
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