| /dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/ |
| H A D | AtomMatcherTest.java | 49 when(atom1.getAtomicNumber()).thenReturn(6); in anyMatch()
50 when(atom2.getAtomicNumber()).thenReturn(7); in anyMatch()
51 when(atom3.getAtomicNumber()).thenReturn(8); in anyMatch()
66 when(atom1.getAtomicNumber()).thenReturn(6); in elementMatch()
67 when(atom2.getAtomicNumber()).thenReturn(6); in elementMatch()
77 when(atom1.getAtomicNumber()).thenReturn(6); in elementMismatch()
78 when(atom2.getAtomicNumber()).thenReturn(8); in elementMismatch()
97 when(atom1.getAtomicNumber()).thenReturn(null); in elementError()
98 when(atom2.getAtomicNumber()).thenReturn(null); in elementError()
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| H A D | ExprTest.java | 237 when(atom.getAtomicNumber()).thenReturn(1); in testIsHetero()
239 when(atom.getAtomicNumber()).thenReturn(6); in testIsHetero()
442 when(h.getAtomicNumber()).thenReturn(1); in testTotalHCountT()
456 when(h.getAtomicNumber()).thenReturn(1); in testTotalHCountF()
470 when(h.getAtomicNumber()).thenReturn(1); in testTotalHCountNullImplT()
484 when(h.getAtomicNumber()).thenReturn(1); in testTotalHCountImplF()
533 when(h.getAtomicNumber()).thenReturn(1); in testHeavyDegreeT()
548 when(h.getAtomicNumber()).thenReturn(1); in testHeavyDegreeF()
563 when(o.getAtomicNumber()).thenReturn(8); in testHeteroSubT()
578 when(o.getAtomicNumber()).thenReturn(8); in testHeteroSubFailFastF()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/ |
| H A D | AtomicNumberRule.java | 39 return getAtomicNumber(ligand1).compareTo(getAtomicNumber(ligand2)); in compare()
42 private Integer getAtomicNumber(ILigand ligand) { in getAtomicNumber() method in AtomicNumberRule
43 Integer atomNumber = ligand.getLigandAtom().getAtomicNumber(); in getAtomicNumber()
45 return PeriodicTable.getAtomicNumber(ligand.getLigandAtom().getSymbol()); in getAtomicNumber()
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| /dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/ |
| H A D | Element.java | 83 this.atomicNumber = element.getAtomicNumber(); in Element()
126 public Integer getAtomicNumber() { in getAtomicNumber() method in Element
189 if (getAtomicNumber() != null) { in toString()
190 resultString.append(", AN:").append(getAtomicNumber()); in toString()
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| /dports/science/cdk/cdk-cdk-2.3/base/data/src/test/java/org/openscience/cdk/ |
| H A D | AtomTest.java | 84 Assert.assertEquals((Integer) 7, a.getAtomicNumber()); in testAtom_NH4plus_direct()
96 Assert.assertEquals((Integer) 6, a.getAtomicNumber()); in testAtom_CH3_direct()
108 Assert.assertEquals((Integer) 17, a.getAtomicNumber()); in testAtom_Cl_direct()
120 Assert.assertEquals((Integer) 7, a.getAtomicNumber()); in testAtom_NH4plus()
132 Assert.assertEquals((Integer) 8, a.getAtomicNumber()); in testAtom_Ominus()
144 Assert.assertEquals((Integer) 20, a.getAtomicNumber()); in testAtom_Ca2plus()
157 Assert.assertEquals((Integer) 6, a.getAtomicNumber()); in testAtom_13CH3()
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| H A D | ElementTest.java | 77 Assert.assertNotNull(e.getAtomicNumber()); in testElement_X()
78 Assert.assertThat(e.getAtomicNumber(), is(0)); in testElement_X()
85 Assert.assertEquals(1, e.getAtomicNumber().intValue()); in testElement_String_Integer()
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| /dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/ |
| H A D | Element.java | 79 this.atomicNumber = element.getAtomicNumber(); in Element()
122 public Integer getAtomicNumber() { in getAtomicNumber() method in Element
183 if (getAtomicNumber() != null) { in toString()
184 resultString.append(", AN:").append(getAtomicNumber()); in toString()
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| /dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ |
| H A D | AtomTypeManipulator.java | 91 …if (atomType.getAtomicNumber() != CDKConstants.UNSET) atom.setAtomicNumber(atomType.getAtomicNumbe… in configure()
132 …if (atom.getAtomicNumber() == CDKConstants.UNSET && atomType.getAtomicNumber() != CDKConstants.UNS… in configureUnsetProperties()
133 atom.setAtomicNumber(atomType.getAtomicNumber()); in configureUnsetProperties()
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| /dports/science/cdk/cdk-cdk-2.3/base/silent/src/test/java/org/openscience/cdk/silent/ |
| H A D | AtomTest.java | 78 Assert.assertEquals((Integer) 7, a.getAtomicNumber()); in testAtom_NH4plus_direct()
90 Assert.assertEquals((Integer) 6, a.getAtomicNumber()); in testAtom_CH3_direct()
102 Assert.assertEquals((Integer) 17, a.getAtomicNumber()); in testAtom_Cl_direct()
114 Assert.assertEquals((Integer) 7, a.getAtomicNumber()); in testAtom_NH4plus()
126 Assert.assertEquals((Integer) 8, a.getAtomicNumber()); in testAtom_Ominus()
138 Assert.assertEquals((Integer) 20, a.getAtomicNumber()); in testAtom_Ca2plus()
151 Assert.assertEquals((Integer) 6, a.getAtomicNumber()); in testAtom_13CH3()
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| H A D | ElementTest.java | 74 Assert.assertNotNull(e.getAtomicNumber()); in testElement_X()
75 Assert.assertThat(e.getAtomicNumber(), is(0)); in testElement_X()
82 Assert.assertEquals(1, e.getAtomicNumber().intValue()); in testElement_String_Integer()
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| /dports/science/coordgenlibs/coordgenlibs-3.0.0/test/ |
| H A D | test_smilesparser.cpp | 27 BOOST_TEST(c->getAtomicNumber() == 6); in BOOST_AUTO_TEST_CASE()
28 BOOST_TEST(n->getAtomicNumber() == 7); in BOOST_AUTO_TEST_CASE()
29 BOOST_TEST(o->getAtomicNumber() == 8); in BOOST_AUTO_TEST_CASE()
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/tools/ |
| H A D | DeAromatizationTool.java | 274 if ((atom.getAtomicNumber()==7 && atom.getImplicitHydrogenCount()>=1) || // nH in Dearomatize566Rings()
275 atom.getAtomicNumber()==8 || // o in Dearomatize566Rings()
276 atom.getAtomicNumber()==16) // s in Dearomatize566Rings()
368 if ((atom.getAtomicNumber()==7 && atom.getImplicitHydrogenCount()>=1) || // nH in Dearomatize56Rings()
369 atom.getAtomicNumber()==8 || // o in Dearomatize56Rings()
370 atom.getAtomicNumber()==16) // s in Dearomatize56Rings()
446 if ((atom.getAtomicNumber()==7 && atom.getImplicitHydrogenCount()>=1) || // nH in Dearomatize5Ring()
447 atom.getAtomicNumber()==8 || // o in Dearomatize5Ring()
448 atom.getAtomicNumber()==16) // s in Dearomatize5Ring()
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| /dports/science/cdk/cdk-cdk-2.3/base/datadebug/src/test/java/org/openscience/cdk/debug/ |
| H A D | DebugElementTest.java | 73 Assert.assertNotNull(e.getAtomicNumber()); in testElement_X()
74 Assert.assertThat(e.getAtomicNumber(), is(0)); in testElement_X()
81 Assert.assertEquals(1, e.getAtomicNumber().intValue()); in testDebugElement_String_int()
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| /dports/science/cdk/cdk-cdk-2.3/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/ |
| H A D | AbstractElementTest.java | 54 Assert.assertEquals(1, e.getAtomicNumber().intValue()); in testSetAtomicNumber_Integer()
61 Assert.assertEquals(1, e.getAtomicNumber().intValue()); in testGetAtomicNumber()
103 Assert.assertEquals(6, clone.getAtomicNumber().intValue()); in testClone_IAtomicNumber()
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| /dports/science/cdk/cdk-cdk-2.3/app/depict/src/main/java/org/openscience/cdk/depict/ |
| H A D | Abbreviations.java | 188 int elem = atom.getAtomicNumber(); in findCutBonds()
459 || attach.getAtomicNumber() == 6 in generate()
460 || attach.getAtomicNumber() < 2) in generate()
496 } else if (nbr.getAtomicNumber() == 1) { in generate()
499 } else if (nbr.getAtomicNumber() > 0){ in generate()
519 sb.append(newSymbol(attach.getAtomicNumber(), hcount, newbonds.size() == 0)); in generate()
696 int elem = atom.getAtomicNumber(); in matchExact()
709 if (bond.getOther(atom).getAtomicNumber() == 1) in matchExact()
819 if (atom.getAtomicNumber() == 0) in add()
847 if (atom.getAtomicNumber() == null || atom.getAtomicNumber() < 1) in getBasicElementSymbol()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ |
| H A D | AtomicNumberAtom.java | 58 … return Preconditions.checkNotNull(atom.getAtomicNumber(), "Atomic number is not set.").equals( in matches()
59 this.getAtomicNumber()); in matches()
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ |
| H A D | ALOGPDescriptor.java | 452 switch (atom.getAtomicNumber()) { in isHetero()
622 if (nbr.getAtomicNumber() == 1) in calcGroup015()
775 if (nbor.getAtomicNumber() == 1) in calcGroup021_to_023_040()
1040 switch (atom.getAtomicNumber()) { in isPyrroleLikeHetero()
1213 if (nbor.getAtomicNumber() == 6) in calcGroup056_57()
1233 (nbor2.getAtomicNumber() == 6 || nbor2.getAtomicNumber() == 8)) { in calcGroup056_57()
1333 if (nbor.getAtomicNumber() == 1) { in calcGroup066_to_079()
1553 if (ca0.getAtomicNumber() == 6) { in calcGroup081_to_085()
1629 if (ca0.getAtomicNumber() == 6) { in calcGroup086_to_090()
1706 if (ca0.getAtomicNumber() == 6) { in calcGroup091_to_095()
[all …]
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| H A D | BPolDescriptor.java | 152 atomicNumber0 = element0.getAtomicNumber(); in calculate()
153 atomicNumber1 = element1.getAtomicNumber(); in calculate()
164 int atnum = elem.getAtomicNumber(); in calculate()
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| /dports/science/cdk/cdk-cdk-2.3/tool/sdg/src/main/java/org/openscience/cdk/layout/ |
| H A D | NonplanarBonds.java | 288 if (a.getAtomicNumber() > b.getAtomicNumber()) in doMirror()
771 Integer elem = atom.getAtomicNumber(); in isSp3Carbon()
782 if (Objects.equals(terminal.getAtomicNumber(), in isSp3Carbon()
783 nbr.getAtomicNumber()) && in isSp3Carbon()
838 if (iAtom.getAtomicNumber() > 0 && jAtom.getAtomicNumber() == 0) in hasPriority()
840 if (iAtom.getAtomicNumber() == 0 && jAtom.getAtomicNumber() > 0) in hasPriority()
844 int iElem = iAtom.getAtomicNumber(); in hasPriority()
846 int jElem = jAtom.getAtomicNumber(); in hasPriority()
1003 if (atom.getAtomicNumber() == null || in isCisTransEndPoint()
1009 switch (atom.getAtomicNumber()) { in isCisTransEndPoint()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/standard/ |
| H A D | HydrogenPositionTest.java | 91 when(atom.getAtomicNumber()).thenReturn(8); in hydrogensAppearBeforeOxygen()
98 when(atom.getAtomicNumber()).thenReturn(16); in hydrogensAppearBeforeSulfur()
105 when(atom.getAtomicNumber()).thenReturn(7); in hydrogensAppearAfterNitrogen()
112 when(atom.getAtomicNumber()).thenReturn(6); in hydrogensAppearAfterCarbon()
148 when(atom.getAtomicNumber()).thenReturn(8); in useDefaultPlacementWithNoBonds()
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| /dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/graph/invariant/ |
| H A D | CanonTest.java | 72 return Integer.compare(o1.getAtomicNumber(), o2.getAtomicNumber()); in atomComparatorLabelling()
83 return -Integer.compare(o1.getAtomicNumber(), o2.getAtomicNumber()); in atomComparatorLabelling()
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| /dports/science/cdk/cdk-cdk-2.3/tool/hash/src/test/java/org/openscience/cdk/hash/ |
| H A D | BasicAtomEncoderTest.java | 54 when(atom.getAtomicNumber()).thenReturn(6); in testAtomicNumber()
57 verify(atom, times(1)).getAtomicNumber(); in testAtomicNumber()
67 when(atom.getAtomicNumber()).thenReturn(null); in testAtomicNumber_Null()
69 verify(atom, times(1)).getAtomicNumber(); in testAtomicNumber_Null()
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| /dports/science/cdk/cdk-cdk-2.3/display/render/src/main/java/org/openscience/cdk/renderer/color/ |
| H A D | CDKAtomColors.java | 68 if (atom.getAtomicNumber() == null) return defaultColor; in getAtomColor()
69 int atomnumber = atom.getAtomicNumber(); in getAtomColor()
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| /dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/config/ |
| H A D | BODRIsotopeTest.java | 34 Assert.assertEquals(6, isotope.getAtomicNumber().intValue()); in testConstructor()
57 Assert.assertEquals(6, isotope.getAtomicNumber().intValue()); in testImmutable()
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| /dports/science/cdk/cdk-cdk-2.3/base/datadebug/src/main/java/org/openscience/cdk/debug/ |
| H A D | DebugElement.java | 66 public Integer getAtomicNumber() { in getAtomicNumber() method in DebugElement
67 logger.debug("Getting atomic number: ", super.getAtomicNumber()); in getAtomicNumber()
68 return super.getAtomicNumber(); in getAtomicNumber()
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