| /dports/science/cdk/cdk-cdk-2.3/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/ |
| H A D | AbstractPDBMonomerTest.java | 34 IPDBMonomer monomer = (IPDBMonomer) newChemObject(); in testSetICode_String() local
41 IPDBMonomer monomer = (IPDBMonomer) newChemObject(); in testGetICode() local
50 IPDBMonomer monomer = (IPDBMonomer) newChemObject(); in testSetChainID_String() local
57 IPDBMonomer monomer = (IPDBMonomer) newChemObject(); in testGetChainID() local
66 IPDBMonomer monomer = (IPDBMonomer) newChemObject(); in testSetResSeq_String() local
73 IPDBMonomer monomer = (IPDBMonomer) newChemObject(); in testGetResSeq() local
83 IPDBMonomer monomer = (IPDBMonomer) newChemObject(); in testToString() local
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| /dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/gui/ |
| H A D | monomerModificationDlg.cpp | 177 const Monomer *monomer = polymer->at(iter); in populateModifAndModifiedMonomerLists() local
228 const Monomer *monomer = polymer->at(iter); in populateModifiedMonomerList() local
264 const Monomer *monomer = polymer->at(iter); in populateModifList() local
342 Monomer *monomer = reinterpret_cast<Monomer *>(pointerCastToInt); in populateModifList() local
410 Monomer *monomer = polChemDef->monomerList().at(iter); in populateMonomerList() local
493 const Monomer *monomer = in updateSelectionData() local
561 const Monomer *monomer = polymer->monomerList().at(iter); in prepareIndicesList() local
589 const Monomer *monomer = polymer->monomerList().at(jter); in prepareIndicesList() local
723 const Monomer *monomer = polymer->monomerList().at(index); in modify() local
832 Monomer *monomer = reinterpret_cast<Monomer *>(pointerCastToInt); in unmodify() local
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| H A D | monomerDefDlg.cpp | 108 Monomer *monomer = mp_list->at(iter); in initialize() local
242 Monomer *monomer = mp_list->takeAt(index); in removeMonomerPushButtonClicked() local
347 Monomer *monomer = mp_list->at(index); in applyMonomerPushButtonClicked() local
442 Monomer *monomer = mp_list->at(iter); in validatePushButtonClicked() local
491 Monomer *monomer = mp_list->at(index); in monomerListWidgetItemSelectionChanged() local
526 MonomerDefDlg::updateMonomerDetails(Monomer *monomer) in updateMonomerDetails()
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| H A D | monomerCrossLinkDlg.cpp | 198 const Monomer *monomer = crossLink->monomerList()->at(jter); in populateCrossLinkedMonomerList() local
306 const Monomer *monomer = polymer->at(index); in populateCrossLinkList() local
454 Monomer *monomer =reinterpret_cast<Monomer *>(monomerCastToInt); in crossLinkedMonomerListWidgetItemActivated() local
567 const Monomer *monomer = crossLink->monomerList()->at(iter); in crossLinkListWidgetItemSelectionChanged() local
609 const Monomer *monomer = crossLink->monomerList()->at(iter); in crossLinkListWidgetItemActivated() local
690 const Monomer *monomer = polymer->at(index); in parseTargetMonomerString() local
821 const Monomer *monomer = targetMonomerList.at(iter); in crossLink() local
852 const Monomer *monomer = targetMonomerList.at(iter); in crossLink() local
956 const Monomer *monomer = crossLink->monomerList()->at(iter); in uncrossLink() local
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| H A D | monomerCodeEvaluator.cpp | 88 Monomer *monomer = new Monomer(polChemDef, "NOT_SET"); in evaluateCode() local
193 Monomer *monomer = refList.at(index); in upperCaseChar() local
266 Monomer *monomer = refList.at(index); in lowerCaseChar() local
315 Monomer *monomer = refList.at(iter); in autoComplete() local
342 Monomer *monomer = refList.at(index); in debugCompletionsPutStdErr() local
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| H A D | compositionTreeViewItem.cpp | 152 CompositionTreeViewItem::setMonomer(Monomer *monomer) in setMonomer()
160 CompositionTreeViewItem::monomer() in monomer() function in massXpert::CompositionTreeViewItem
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| H A D | sequenceEditorGraphicsView.cpp | 779 SequenceEditorGraphicsView::renderVignette(const Monomer &monomer) in renderVignette()
1102 const Monomer *monomer = mp_polymer->monomerList().at(iter); in renderVignettes() local
1133 const Monomer *monomer = crossLink->monomerList()->at(jter); in renderVignettes() local
1438 SequenceEditorGraphicsView::insertMonomerAtPoint(const Monomer *monomer, in insertMonomerAtPoint()
1452 SequenceEditorGraphicsView::insertMonomerAt(const Monomer *monomer, in insertMonomerAt()
1510 const Monomer *monomer = in insertSequenceAtPoint() local
1564 const Monomer *monomer = mp_polymer->at(index); in prepareMonomerRemovalAt() local
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| H A D | calculatorWnd.cpp | 400 Monomer *monomer = m_polChemDef.monomerList().at(iter); in populatePolChemDefComboBoxes() local
1309 Monomer monomer(&m_polChemDef, "NOT_SET"); in accountMonomer() local
1421 const Monomer *monomer = sequence.at(iter); in accountSequence() local
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| /dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/lib/ |
| H A D | crossLink.cpp | 83 CrossLink::setMonomerAt(Monomer *monomer, int index) in setMonomerAt()
95 CrossLink::appendMonomer(const Monomer *monomer) in appendMonomer()
240 const Monomer *monomer = m_monomerList.at(iter); in monomerIndexList() local
277 const Monomer *monomer = m_monomerList.at(iter); in monomerIndexText() local
294 const Monomer *monomer = m_monomerList.at(iter); in monomerPosText() local
344 const Monomer *monomer = m_monomerList.at(iter); in encompassedBy() local
388 const Monomer *monomer = m_monomerList.at(iter); in encompassedBy() local
494 const Monomer *monomer = m_monomerList.at(iter); in validate() local
551 const Monomer *monomer = m_monomerList.at(iter); in prepareResultsTxtString() local
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| H A D | sequence.cpp | 211 const Monomer *monomer = m_monomerList.at(iter); in monomerText() local
338 Monomer *monomer = new Monomer(polChemDef, "NOT_SET"); in makeMonomerList() local
577 const Monomer *monomer = at(iter); in findForwardMotif() local
719 Sequence::monomerIndex(const Monomer *monomer) in monomerIndex()
746 Sequence::insertMonomerAt(const Monomer *monomer, int index) in insertMonomerAt()
758 Sequence::prepareMonomerRemoval(const Monomer *monomer) in prepareMonomerRemoval()
781 const Monomer *monomer = at(index); in removeMonomerAt() local
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| H A D | cleaver.cpp | 367 const Monomer *monomer = monomerList.at(iterIndex); in findCleaveMotif() local
461 const Monomer &monomer = oligomer->atLeftEnd(); in accountCleaveRule() local
493 const Monomer &monomer = oligomer->atRightEnd(); in accountCleaveRule() local
894 const Monomer *monomer = mp_polymer->at(iter); in analyzeCrossLinkedOligomer() local
1012 const Monomer *monomer = mp_polymer->at(iter); in analyzeCrossLinkedOligomer() local
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| H A D | fragmenter.cpp | 456 const Monomer *monomer = mp_polymer->at(iter); in fragmentEndNone() local
772 const Monomer *monomer = mp_polymer->at(iter); in fragmentEndLeft() local
883 const Monomer *monomer = mp_polymer->at(iter); in fragmentEndLeft() local
1193 const Monomer *monomer = mp_polymer->at(iter); in fragmentEndRight() local
1304 const Monomer *monomer = mp_polymer->at(iter); in fragmentEndRight() local
1590 const Monomer *monomer = mp_polymer->at(index); in accountFragRule() local
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| H A D | polymer.cpp | 443 Polymer::prepareMonomerRemoval(Monomer *monomer) in prepareMonomerRemoval()
484 Monomer *monomer = const_cast<Monomer *>(at(index)); in removeMonomerAt() local
592 Monomer *monomer = const_cast<Monomer *>(polymer->at(jter)); in calculateMasses() local
1548 Monomer *monomer = 0; in renderXmlPolymerFile() local
1986 const Monomer *monomer = 0; in formatXmlPolSeqElement() local
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| H A D | pkaPhPiDataParser.cpp | 183 Monomer *monomer = new Monomer(mp_polChemDef, "NOT_SET", in renderXmlFile() local
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| H A D | pkaPhPi.cpp | 212 const Monomer *monomer = mpa_monomerList->at(index); in calculateCharges() local
774 PkaPhPi::accountMonomerModif(const Monomer &monomer, in accountMonomerModif()
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| /dports/science/clipper/clipper-2.1/clipper/minimol/ |
| H A D | minimol_utils.h | 63 …MAtomIndex( const int& polymer, const int& monomer, const int& atom ) : p(polymer), m(monomer), a(… in MAtomIndex()
67 const int& monomer() const { return m; } //!< return monomer index in monomer() function
83 …MAtomIndexSymmetry( const int& polymer, const int& monomer, const int& atom , const int& symm ) : … in MAtomIndexSymmetry()
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| /dports/science/cdk/cdk-cdk-2.3/base/data/src/test/java/org/openscience/cdk/ |
| H A D | PolymerTest.java | 76 Monomer monomer = new Monomer(); in testPolymerClone() local
105 Monomer monomer = new Monomer(); in testPolymerClone2() local
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/lammps/ |
| H A D | utils.py | 45 monomer, argument
103 def _create(self, monomer, mon_vector): argument
130 def _align_monomer(self, monomer, mon_vector, move_direction): argument
147 def _add_monomer(self, monomer, mon_vector, move_direction): argument
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| /dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/ |
| H A D | Polymer.java | 137 Monomer monomer = (Monomer) monomers.get(name); in removeMonomer() local
163 IMonomer monomer = e.getValue().clone(); in clone() local
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| /dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/ |
| H A D | Polymer.java | 137 Monomer monomer = (Monomer) monomers.get(name); in removeMonomer() local
244 IMonomer monomer = getMonomer(monomerName); in atomIsInMonomer() local
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| /dports/science/cdk/cdk-cdk-2.3/base/datadebug/src/test/java/org/openscience/cdk/debug/ |
| H A D | DebugPDBMonomerTest.java | 50 IPDBMonomer monomer = new DebugPDBMonomer(); in testDebugPDBMonomer() local
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| /dports/science/cdk/cdk-cdk-2.3/base/data/src/test/java/org/openscience/cdk/protein/data/ |
| H A D | PDBMonomerTest.java | 52 IPDBMonomer monomer = new PDBMonomer(); in testPDBMonomer() local
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| /dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/xtp-2a31d70/src/libxtp/ |
| H A D | couplingbase.cc | 44 const QMAtom* monomer = nullptr; in CheckAtomCoordinates() local
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| /dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/src/libxtp/ |
| H A D | couplingbase.cc | 44 const QMAtom* monomer = nullptr; in CheckAtomCoordinates() local
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| /dports/science/cdk/cdk-cdk-2.3/base/silent/src/test/java/org/openscience/cdk/silent/ |
| H A D | PDBMonomerTest.java | 50 IPDBMonomer monomer = new PDBMonomer(); in testPDBMonomer() local
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