/dports/science/p5-PerlMol/PerlMol-0.3500/examples/polar_surface_area/ |
H A D | psa.pl | 185 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)) [all …]
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/dports/science/cdk/cdk-cdk-2.3/display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/ |
H A D | AtomSymbolElement.java | 33 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()
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/dports/science/cdk/cdk-cdk-2.3/base/testdata/src/test/resources/data/cml/ |
H A D | molAndspect.cml | 6 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" /> [all …]
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H A D | phosphate.cml | 5 <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">
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H A D | dictref.cml | 3 <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"/>
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H A D | nitrate.cml | 7 <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">
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H A D | COONa.cml | 3 <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">
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/forcefield/ |
H A D | AtomType.java | 34 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()
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/dports/science/py-pymol/pymol-open-source-2.4.0/layer2/ |
H A D | MmodTyping.cpp | 18 switch (ai->formalCharge) { in getMacroModelAtomType() 100 switch (ai->formalCharge) { in getMacroModelAtomType() 106 switch (ai->formalCharge) { in getMacroModelAtomType() 145 switch (ai->formalCharge) { in getMacroModelAtomType()
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H A D | Mol2Typing.cpp | 28 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()
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H A D | ObjectMolecule2.cpp | 863 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() [all …]
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H A D | AtomInfoHistory.h | 47 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
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/xml/ |
H A D | XmlOdysseyReader.java | 50 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()
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ |
H A D | FormalChargeAtom.java | 45 this.formalCharge = charge; in FormalChargeAtom() 56 return Objects.equals(atom.getFormalCharge(), this.formalCharge); in matches() 68 s.append("C:").append(this.formalCharge); in toString()
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/dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/ |
H A D | AtomType.java | 78 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()
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/dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/ |
H A D | AtomType.java | 81 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()
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/dports/science/cdk/cdk-cdk-2.3/tool/hash/src/main/java/org/openscience/cdk/hash/ |
H A D | BasicAtomEncoder.java | 94 Integer formalCharge = atom.getFormalCharge(); in encode() local 95 return formalCharge != null ? formalCharge : 32451193; in encode()
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/dports/science/cdk/cdk-cdk-2.3/display/renderextra/src/main/java/org/openscience/cdk/renderer/elements/ |
H A D | AtomMassSymbolElement.java | 48 public AtomMassSymbolElement(double xCoord, double yCoord, String symbol, Integer formalCharge, in AtomMassSymbolElement() argument 50 super(xCoord, yCoord, symbol, formalCharge, hydrogenCount, alignment, color); in AtomMassSymbolElement()
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/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/ |
H A D | HOSECodeGenerator.java | 299 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()
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/dports/science/cdk/cdk-cdk-2.3/storage/pdb/src/main/java/org/openscience/cdk/io/ |
H A D | PDBWriter.java | 228 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/simple/ |
H A D | JmeReader.java | 90 atom.formalCharge = 1; in readAtoms() 93 atom.formalCharge = -1; in readAtoms()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
H A D | atom.h | 155 signed char formalCharge() const; 317 signed char AtomTemplate<Molecule_T>::formalCharge() const in formalCharge() function 319 return m_molecule->formalCharge(m_index); in formalCharge()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
H A D | atom.h | 155 signed char formalCharge() const; 317 signed char AtomTemplate<Molecule_T>::formalCharge() const in formalCharge() function 319 return m_molecule->formalCharge(m_index); in formalCharge()
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/dports/science/cdk/cdk-cdk-2.3/storage/io/src/main/java/org/openscience/cdk/io/program/ |
H A D | Mopac7Writer.java | 107 int formalCharge = AtomContainerManipulator.getTotalFormalCharge(container); in write() local 108 if (formalCharge != 0) writer.write(" CHARGE=" + formalCharge); in write()
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/dports/science/cdk/cdk-cdk-2.3/storage/io/src/test/resources/org/openscience/cdk/io/ |
H A D | US06358966-20020319-C00001-enr.cml | 3 <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"/> [all …]
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