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/dports/science/p5-PerlMol/PerlMol-0.3500/examples/polar_surface_area/
H A Dpsa.pl185 my $formalCharge;
267 $formalCharge = $oneAtom->formal_charge;
268 if ($formalCharge == "") { $formalCharge = 0; }
351 if(($hydrogenCount == 0) && ($tripleBondCount == 1) && ($formalCharge == 0))
356 elsif(($hydrogenCount == 1) && ($doubleBondCount == 1) && ($formalCharge == 0))
361 elsif(($hydrogenCount == 2) && ($singleBondCount == 1) && ($formalCharge == 0))
366 elsif(($hydrogenCount == 2) && ($doubleBondCount == 1) && ($formalCharge == 1))
371 elsif(($hydrogenCount == 3) && ($singleBondCount == 1) && ($formalCharge == 1))
403 elsif(($hydrogenCount == 2) && ($singleBondCount == 2) && ($formalCharge == 1))
461 if(($hydrogenCount == 0) && ($singleBondCount == 4) && ($formalCharge == 1))
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/dports/science/cdk/cdk-cdk-2.3/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/
H A DAtomSymbolElement.java33 public final int formalCharge; field in AtomSymbolElement
41 …public AtomSymbolElement(double x, double y, String symbol, Integer formalCharge, Integer hydrogen… in AtomSymbolElement() argument
44 this.formalCharge = formalCharge != null ? formalCharge : -1; in AtomSymbolElement()
/dports/science/cdk/cdk-cdk-2.3/base/testdata/src/test/resources/data/cml/
H A DmolAndspect.cml6 formalCharge="0" hydrogenCount="0" />
8 formalCharge="0" hydrogenCount="0" />
10 formalCharge="0" hydrogenCount="0" />
12 formalCharge="0" hydrogenCount="0" />
14 formalCharge="0" hydrogenCount="0" />
16 formalCharge="0" hydrogenCount="0" />
18 formalCharge="0" hydrogenCount="0" />
20 formalCharge="0" hydrogenCount="0" />
22 formalCharge="0" hydrogenCount="0" />
24 formalCharge="0" hydrogenCount="0" />
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H A Dphosphate.cml5 <atom id="a2" elementType="O" formalCharge="-1" x3="2.0667" y3="-0.625" z3="0">
9 <atom id="a4" elementType="O" formalCharge="-1" x3="0.4125" y3="-0.6209" z3="0">
11 <atom id="a5" elementType="O" formalCharge="-1" x3="1.2375" y3="-1.45" z3="0">
H A Ddictref.cml3 <atom id="a1" elementType="R" formalCharge="1" x2="0.3114" y2="-3.223"
6 <atom id="a3" elementType="O" formalCharge="-1" x2="0.0865" y2="-4.4458"/>
H A Dnitrate.cml7 <atom id="a3" elementType="N" formalCharge="1" x3="1.3667" y3="0.1292" z3="0">
9 <atom id="a4" elementType="O" formalCharge="-1" x3="2.0808" y3="-0.2869" z3="0">
H A DCOONa.cml3 <atom id="a1" elementType="Na" formalCharge="1" x3="0.3114" y3="-3.223" z3="0">
7 <atom id="a3" elementType="O" formalCharge="-1" x3="0.0865" y3="-4.4458" z3="0">
/dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/forcefield/
H A DAtomType.java34 float formalCharge; field in AtomType
74 …AtomType(int elemNo, int mmType, int hType, float formalCharge, int val, String descr, String smar… in AtomType() argument
78 this.formalCharge = formalCharge; in AtomType()
/dports/science/py-pymol/pymol-open-source-2.4.0/layer2/
H A DMmodTyping.cpp18 switch (ai->formalCharge) { in getMacroModelAtomType()
100 switch (ai->formalCharge) { in getMacroModelAtomType()
106 switch (ai->formalCharge) { in getMacroModelAtomType()
145 switch (ai->formalCharge) { in getMacroModelAtomType()
H A DMol2Typing.cpp28 charge += neighbor->formalCharge; in isGuanidiniumCarbon()
150 if (ai->valence == 2 && ai->formalCharge == 0) in getMOL2Type()
154 return (ai->formalCharge == 1) ? "N.4" : "N.3"; in getMOL2Type()
H A DObjectMolecule2.cpp863 ai1->formalCharge = -1; in assign_pdb_known_residue()
866 ai2->formalCharge = -1; in assign_pdb_known_residue()
921 ai1->formalCharge = -1; in assign_pdb_known_residue()
924 ai2->formalCharge = -1; in assign_pdb_known_residue()
952 ai1->formalCharge = -1; in assign_pdb_known_residue()
955 ai2->formalCharge = -1; in assign_pdb_known_residue()
1149 ai1->formalCharge = -1; in assign_pdb_known_residue()
1152 ai2->formalCharge = -1; in assign_pdb_known_residue()
1258 ai1->formalCharge = -1; in assign_pdb_known_residue()
1261 ai2->formalCharge = -1; in assign_pdb_known_residue()
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H A DAtomInfoHistory.h47 signed char formalCharge; // values typically in range -2..+2 member
143 signed char formalCharge; // values typically in range -2..+2 member
221 signed char formalCharge; // values typically in range -2..+2 member
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/xml/
H A DXmlOdysseyReader.java50 private int formalCharge = Integer.MIN_VALUE; field in XmlOdysseyReader
97 formalCharge = PT.parseInt(charge); in processStartElement()
101 if ("member".equals(localName) && formalCharge != Integer.MIN_VALUE) { in processStartElement()
104 atom.formalCharge = formalCharge; in processStartElement()
170 formalCharge = Integer.MIN_VALUE; in processEndElement()
/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/
H A DFormalChargeAtom.java45 this.formalCharge = charge; in FormalChargeAtom()
56 return Objects.equals(atom.getFormalCharge(), this.formalCharge); in matches()
68 s.append("C:").append(this.formalCharge); in toString()
/dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/
H A DAtomType.java78 protected Integer formalCharge = (Integer) CDKConstants.UNSET; field in AtomType
113 this.formalCharge = 0; in AtomType()
145 this.formalCharge = ((IAtomType) element).getFormalCharge(); in AtomType()
234 this.formalCharge = charge; in setFormalCharge()
246 return this.formalCharge; in getFormalCharge()
/dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/
H A DAtomType.java81 protected Integer formalCharge = (Integer) CDKConstants.UNSET; field in AtomType
116 this.formalCharge = 0; in AtomType()
148 this.formalCharge = ((IAtomType) element).getFormalCharge(); in AtomType()
240 this.formalCharge = charge; in setFormalCharge()
253 return this.formalCharge; in getFormalCharge()
/dports/science/cdk/cdk-cdk-2.3/tool/hash/src/main/java/org/openscience/cdk/hash/
H A DBasicAtomEncoder.java94 Integer formalCharge = atom.getFormalCharge(); in encode() local
95 return formalCharge != null ? formalCharge : 32451193; in encode()
/dports/science/cdk/cdk-cdk-2.3/display/renderextra/src/main/java/org/openscience/cdk/renderer/elements/
H A DAtomMassSymbolElement.java48 public AtomMassSymbolElement(double xCoord, double yCoord, String symbol, Integer formalCharge, in AtomMassSymbolElement() argument
50 super(xCoord, yCoord, symbol, formalCharge, hydrogenCount, alignment, color); in AtomMassSymbolElement()
/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/
H A DHOSECodeGenerator.java299 Integer formalCharge = atom.getFormalCharge(); in createChargeCode() local
300 if (formalCharge == CDKConstants.UNSET) formalCharge = 0; in createChargeCode()
302 if (formalCharge != 0) { in createChargeCode()
304 if (Math.abs(formalCharge) == 1) { in createChargeCode()
305 if (formalCharge < 0) in createChargeCode()
311 if (formalCharge > 0) tempCode.append('+'); in createChargeCode()
312 tempCode.append(formalCharge).append('\''); in createChargeCode()
/dports/science/cdk/cdk-cdk-2.3/storage/pdb/src/main/java/org/openscience/cdk/io/
H A DPDBWriter.java228 Integer formalCharge = atom.getFormalCharge(); in writeMolecule() local
229 if (formalCharge == CDKConstants.UNSET) { in writeMolecule()
232 if (formalCharge < 0) { in writeMolecule()
233 buffer.append(formalCharge); in writeMolecule()
235 buffer.append('+').append(formalCharge); in writeMolecule()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/simple/
H A DJmeReader.java90 atom.formalCharge = 1; in readAtoms()
93 atom.formalCharge = -1; in readAtoms()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/core/
H A Datom.h155 signed char formalCharge() const;
317 signed char AtomTemplate<Molecule_T>::formalCharge() const in formalCharge() function
319 return m_molecule->formalCharge(m_index); in formalCharge()
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/core/
H A Datom.h155 signed char formalCharge() const;
317 signed char AtomTemplate<Molecule_T>::formalCharge() const in formalCharge() function
319 return m_molecule->formalCharge(m_index); in formalCharge()
/dports/science/cdk/cdk-cdk-2.3/storage/io/src/main/java/org/openscience/cdk/io/program/
H A DMopac7Writer.java107 int formalCharge = AtomContainerManipulator.getTotalFormalCharge(container); in write() local
108 if (formalCharge != 0) writer.write(" CHARGE=" + formalCharge); in write()
/dports/science/cdk/cdk-cdk-2.3/storage/io/src/test/resources/org/openscience/cdk/io/
H A DUS06358966-20020319-C00001-enr.cml3 <atom id="a1" elementType="C" x2="5.2527" y2="-0.9769" formalCharge="0" hydrogenCount="0"/>
4 <atom id="a2" elementType="C" x2="-0.8973" y2="-1.5269" formalCharge="0" hydrogenCount="0"/>
5 <atom id="a3" elementType="C" x2="-0.9073" y2="-3.5769" formalCharge="0" hydrogenCount="1"/>
6 <atom id="a4" elementType="C" x2="0.2027" y2="-2.9469" formalCharge="0" hydrogenCount="1"/>
7 <atom id="a5" elementType="C" x2="-0.3473" y2="-2.6169" formalCharge="0" hydrogenCount="0"/>
8 <atom id="a6" elementType="C" x2="4.4727" y2="-1.7769" formalCharge="0" hydrogenCount="1"/>
9 <atom id="a7" elementType="C" x2="5.7027" y2="-1.4469" formalCharge="0" hydrogenCount="1"/>
10 <atom id="a8" elementType="C" x2="-0.0273" y2="-0.9369" formalCharge="0" hydrogenCount="0"/>
11 <atom id="a9" elementType="C" x2="-1.7573" y2="-0.5669" formalCharge="0" hydrogenCount="1"/>
13 <atom id="a11" elementType="C" x2="4.2027" y2="-0.5869" formalCharge="0" hydrogenCount="0"/>
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