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1 NAME
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2 Atom
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3
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4 SYNOPSIS
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5 use Atom;
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6
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7 DESCRIPTION
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8 Atom class provides the following methods:
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9
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10 new, AddHydrogens, Copy, DeleteAtom, DeleteHydrogens,
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11 DoesAtomNeighborhoodMatch, GetAtomicInvariantValue, GetAtomicWeight,
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12 GetBondToAtom, GetBonds, GetBondsToHeavyAtoms, GetBondsToHydrogenAtoms,
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13 GetBondsToNonHydrogenAtoms, GetExactMass, GetExplicitHydrogens,
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14 GetFormalCharge, GetFreeRadicalElectrons, GetGroupNumber,
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15 GetHeavyAtomNeighbors, GetHeavyAtomNeighborsAtomInformation,
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16 GetHeavyAtomNeighborsBondformation, GetHighestCommonValence,
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17 GetHydrogenAtomNeighbors, GetHydrogens, GetImplicitHydrogens,
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18 GetLargestBondOrder, GetLargestBondOrderToHeavyAtoms,
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19 GetLargestBondOrderToNonHydrogenAtoms, GetLargestRing,
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20 GetLowestCommonValence, GetMassNumber, GetMissingHydrogens,
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21 GetNeighbors, GetNeighborsUsingAtomSpecification,
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22 GetNonHydrogenAtomNeighbors, GetNonHydrogenAtomNeighborsAtomInformation,
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23 GetNonHydrogenAtomNeighborsBondInformation,
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24 GetNonHydrogenNeighborOfHydrogenAtom, GetNumOfAromaticBondsToHeavyAtoms,
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25 GetNumOfAromaticBondsToNonHydrogenAtoms, GetNumOfBondTypesToHeavyAtoms,
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26 GetNumOfBondTypesToNonHydrogenAtoms, GetNumOfBonds,
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27 GetNumOfBondsToHeavyAtoms, GetNumOfBondsToHydrogenAtoms,
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28 GetNumOfBondsToNonHydrogenAtoms, GetNumOfDoubleBondsToHeavyAtoms,
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29 GetNumOfBondsAvailableForHeavyAtoms,
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30 GetNumOfBondsAvailableForNonHydrogenAtoms,
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31 GetNumOfDoubleBondsToNonHydrogenAtoms, GetNumOfExplicitHydrogens,
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32 GetNumOfHeavyAtomNeighbors, GetNumOfHydrogenAtomNeighbors,
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33 GetNumOfHydrogens, GetNumOfImplicitHydrogens, GetNumOfMissingHydrogens,
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34 GetNumOfNeighbors, GetNumOfNonHydrogenAtomNeighbors, GetNumOfRings,
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35 GetNumOfRingsWithEvenSize, GetNumOfRingsWithOddSize,
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36 GetNumOfRingsWithSize, GetNumOfRingsWithSizeGreaterThan,
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37 GetNumOfRingsWithSizeLessThan, GetNumOfSigmaAndPiBondsToHeavyAtoms,
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38 GetNumOfSigmaAndPiBondsToNonHydrogenAtoms,
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39 GetNumOfSingleBondsToHeavyAtoms, GetNumOfSingleBondsToNonHydrogenAtoms,
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40 GetNumOfTripleBondsToHeavyAtoms, GetNumOfTripleBondsToNonHydrogenAtoms,
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41 GetPeriodNumber, GetPotentialTotalCommonValence, GetRings,
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42 GetRingsWithEvenSize, GetRingsWithOddSize, GetRingsWithSize,
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43 GetRingsWithSizeGreaterThan, GetRingsWithSizeLessThan,
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44 GetSizeOfLargestRing, GetSizeOfSmallestRing, GetSmallestRing,
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45 GetSpinMultiplicity, GetSumOfBondOrders, GetSumOfBondOrdersToHeavyAtoms,
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46 GetSumOfBondOrdersToHydrogenAtoms, GetSumOfBondOrdersToNonHydrogenAtoms,
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47 GetValence, GetValenceElectrons, GetValenceFreeElectrons, GetX, GetXYZ,
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48 GetXYZVector, GetY, GetZ, IsAmideCarbon, IsAmideNitrogen, IsAromatic,
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49 IsArsenic, IsBondedToAtom, IsBromine, IsCarbon, IsCarboxylCarbon,
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50 IsCarboxylOxygen, IsCarboxylateCarbon, IsCarboxylateOxygen, IsChlorine,
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51 IsFluorine, IsFunctionalClassType, IsGuadiniumCarbon,
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52 IsGuadiniumNitrogen, IsHBondAcceptor, IsHBondDonor, IsHalogen,
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53 IsHeteroAtom, IsHydrogen, IsHydrogenBondAcceptor, IsHydrogenBondDonor,
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54 IsHydrophobic, IsInRing, IsInRingOfSize, IsIodine, IsIsotope,
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55 IsLipophilic, IsMetallic, IsNegativelyIonizable, IsNitrogen,
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56 IsNonCarbonOrHydrogen, IsNotInRing, IsOnlyInOneRing, IsOxygen,
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57 IsPhosphateOxygen, IsPhosphatePhosphorus, IsPhosphorus, IsPolarAtom,
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58 IsPolarHydrogen, IsPositivelyIonizable, IsSaturated, IsSelenium,
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59 IsSilicon, IsStereoCenter, IsSulfur, IsSulphur, IsTellurium, IsTerminal,
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60 IsTopologicalPharmacophoreType, IsUnsaturated, SetAtomSymbol,
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61 SetAtomicNumber, SetExplicitHydrogens, SetMassNumber, SetStereoCenter,
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62 SetStereochemistry, SetX, SetXYZ, SetY, SetZ, StringifyAtom
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63
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64 Atom class is derived from ObjectProperty base class which provides
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65 methods not explicitly defined in Atom or ObjectProperty class using
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66 Perl's AUTOLOAD functionality. These methods are generated on-the-fly
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67 for a specified object property:
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68
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69 Set<PropertyName>(<PropertyValue>);
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70 $PropertyValue = Get<PropertyName>();
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71 Delete<PropertyName>();
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72
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73 METHODS
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74 new
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75 $NewAtom = new Atom([%PropertyNameAndValues]);
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76
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77 Using specified *Atom* property names and values hash, new method
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78 creates a new object and returns a reference to newly created Atom
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79 object. By default, following properties are initialized:
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80
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81 ID = SequentialObjectID
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82 Name = "Atom <SequentialObjectID>"
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83 AtomSymbol = ""
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84 AtomicNumber = 0
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85 XYZ = ZeroVector
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86
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87 Except for *ID* property, all other default properties and other
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88 additional properties can be set during invocation of this method.
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89
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90 Examples:
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91
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92 $Atom = new Atom();
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93 $CarbonAtom = new Atom('AtomSymbol' => 'C', 'XYZ' => (0.0, 1.0,
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94 0.0));
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95 $OxygenAtom = new Atom('AtomName' => 'Oxygen', AtomSymbol' => 'O',
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96 'XYZ' => (1.0, 1.0, 1.0));
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97
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98 AddHydrogens
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99 $NumOfHydrogensAdded = $Atom->AddHydrogens();
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100
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101 Adds hydrogens to an Atom present in a Molecule object and returns
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102 the number of added hydrogens. The current release of MayaChemTools
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103 doesn't assign hydrogen positions.
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104
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105 Copy
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106 $AtomCopy = $Atom->Copy();
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107
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108 Copy *Atom* and its associated data using Storable::dclone and
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109 return a new Atom object.
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110
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111 DeleteAtom
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112 $Atom->DeleteAtom();
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113
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114 Delete *Atom* from a molecule.
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115
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116 DoesAtomNeighborhoodMatch
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117 $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec);
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118 $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec,
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119 $NbrAtomSpecsRef);
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120 $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec,
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121 $NbrAtomSpecsRef, $AllowedNbrBondSpecsRef);
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122 $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec,
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123 $NbrAtomSpecsRef, $NbrBondSpecsRef,
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124 $AllowedNbrOfNbrAtomSpecsRef);
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125
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126 Returns 1 or 0 based on whether atom matches central atom and its
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127 neighborhood using specified atom and bonds specifications.
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128 Neighborhood atom and bond specifications are specified as array
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129 references containing neighbor atom and bond specifications.
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130
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131 Let:
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132
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133 AS = Atom symbol corresponding to element symbol, atomic number (#n)
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134 or any atom (A)
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135
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136 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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137 attached to atom
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138 T<n> = Total number of atom neighbors including implicit and explicit
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139 hydrogens
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140 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy
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141 atoms attached to atom
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142 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy
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143 atoms attached to atom
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144 SB<n> = Number of single bonds to non-hydrogen atom neighbors or
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145 heavy atoms attached to atom
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146 TSB<n> = Total number of single bonds to atom neighbors including implicit
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147 and explicit hydrogens
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148 DB<n> = Number of double bonds to non-hydrogen atom neighbors or
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149 heavy atoms attached to atom
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150 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or
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151 heavy atoms attached to atom
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152 AB<n> = Number of aromatic bonds to non-hydrogen atom neighbors or
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153 heavy atoms attached to atom
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154 H<n> = Number of implicit and explicit hydrogens for atom
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155 Ar = Aromatic annotation indicating whether atom is aromatic
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156 RA or RA<n> = Ring atom annotation indicating whether atom
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157 is a ring
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158 TR<n> = Total number of rings containing atom
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159 FC<+n/-n> = Formal charge assigned to atom
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160 MN<n> = Mass number indicating isotope other than most abundant isotope
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161 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet),
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162 2 (doublet) or 3 (triplet)
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163
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164 Then, atom specification corresponds to:
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165
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166 AS.X<n>.T<n>.BO<n>.LBO<n>.<SB><n>.TSB<n>.<DB><n>.<TB><n>.AB<n>.H<n>.Ar.
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167 RA<n>.TR<n>FC<+n/-n>.MN<n>.SM<n>
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168
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169 Except for AS which is a required atomic invariant in atom
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170 specification, all other atomic invariants are optional. For an atom
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171 specification to match an atom, the values of all specified atomic
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172 invariants must match. Exclamation in from of atomic invariant can
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173 be used to negate its effect during the match.
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174
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175 For *FC* value matching, the following value operators are also
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176 supported:
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177
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178 o +* : Any positive value
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179 o -* : Any negative value
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180 o > ValidNumber or >= ValidNumber
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181 o < ValidNumber or <= ValidNumber
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182
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183 A comma delimited atom specification string is used to match any one
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184 of the specified atom specification.
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185
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186 Notes:
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187
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188 o During atom specification match to an atom, the first atomic invariant is always assumed to
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189 atom symbol.
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190
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191 Examples:
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192
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193 o ('N', 'N', 'N')
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194 o ('N.FC0', 'N.FC0', 'N,N.FC+1.H1')
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195 o ('N.H2', 'N.H2', 'N.H1')
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196 o ('C,N', '!N', '!H')
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197 o ('C,N', 'N.Ar', 'N.R5')
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198
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199 Let:
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200
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201 -|1|s|Single = Single bond
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202 =|2|d|Double = Double bond
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203 #|3|t|Triple = Triple bond
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204 :|1.5|a|Ar|Aromatic = Aromatic bond
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205
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206 @|RB|Ring = Ring bond
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207 ~|*|Any = Any bond
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208
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209 Then, bond specification corresponds to:
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210
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211 -.:
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212 =.@
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213 Double.Aromatic
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214
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215 For a bond specification to match bond between two atoms, the values
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216 of all specified bond symbols must match. Exclamation in from of
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217 bond symbol can be used to negate its effect during the match.
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218
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219 A comma delimited bond specification string is used to match any one
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220 of the specified atom specification.
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221
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222 Notes:
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223
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224 o During atom neighborhood match for central atom neighborhood atom and bond specifications,
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225 implicit or missing hydrogens are automatically checked for any matches to unmatched
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226 specifications.
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227
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228 Examples:
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229
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230 Aromatic carbon in a 5 membered ring:
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231 $Atom->DoesAtomNeighborhoodMatch('C.Ar.RA5');
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232
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233 AcetylenicCarbon: $Atom->DoesAtomNeighborhoodMatch('C.T2.TB1'); or
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234 $Atom->DoesAtomNeighborhoodMatch('C.T2.TB1',
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235 ['*', '*'], ['#', '-']);
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236
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237 GuadiniumCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4',
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238 ['N.FC0', 'N.FC0', 'N.FC0,N.FC+1'],
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239 ['-', '-', '='],
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240 ['C,H', 'C,H', 'C,H']);
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241
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242 AmideCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3',
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243 ['C,H', 'O', 'N'],
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244 ['-', '=', '-'],
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245 ['C,H', 'C', 'C,H,N,O,S,P,F,Cl,Br,I']);
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246
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247 CarboxylCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3',
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248 ['C,H', 'O', 'O.X1.FC0'],
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249 ['-', '=', '-'],
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250 ['C,H', 'C', 'C']);
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251
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252 CarboxylateCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3',
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253 ['C,H', 'O', 'O.X1.FC-1'],
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254 ['-', '=', '-'],
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255 ['C,H', 'C', 'C']);
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256
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257 DeleteHydrogens
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258 $NumOfHydrogensDeleted = $Atom->AddHydrogens();
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259
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260 Delete hydrogens from an Atom present in a Molecule object and
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261 returns the number of deleted hydrogens.
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262
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263 GetAtomicInvariantValue
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264 $Value = $Atom->GetAtomicInvariantValue($AtomicInvariant);
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265
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266 Returns atomic invariant value for a specified *AtomicInvariant*.
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267 The current release of MayaChemTools supports following
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268 abbreviations and descriptive names for *AtomicInvarints*:
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269
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270 AS : Atom or element symbol
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271 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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272 T : TotalNumOfAtomNeighbors
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273 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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274 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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275 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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276 TSB : TotalNumOfSingleBonds
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277 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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278 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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279 AB : NumOfAromaticBondsToNonHydrogenAtoms or NumOfAromaticBondsToHeavyAtoms
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280 H : NumOfImplicitAndExplicitHydrogens
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281 Ar : Aromatic
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282 Str : Stereochemistry
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283 RA : RingAtom
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284 FC : FormalCharge
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285 AN : AtomicNumber
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286 AM : AtomicMass
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287 MN : MassNumber
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288 SM : SpinMultiplicity
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289
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290 GetAtomicWeight
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291 $Value = $Aom->GetAtomicWeight();
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292
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293 Returns atomic weight of an Atom which corresponds to either
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294 explicity set *AtomicWeight* atom property or atomic weight of the
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295 corresponding element in the periodic table available by
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296 PeriodicTable module.
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297
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298 GetBondToAtom
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299 $Bond = $Atom->GetBondToAtom($OtherAtom);
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300
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301 Returns a Bond object corresponding to bond between *Atom* and
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302 *OtherAtom* in a molecule.
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303
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304 GetBonds
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305 @Bonds = $Aoto->GetBonds();
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306
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307 Returns an array of Bond objects corresponding to all bonds from
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308 *Atom* to other bonded atoms in a molecule.
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309
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310 GetBondsToHeavyAtoms
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311 @Bonds = $Atom->GetBondsToHeavyAtoms();
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312
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313 Returns an array of Bond objects corresponding to bonds from *Atom*
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314 to other bonded non-hydrogen atoms in a molecule.
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315
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316 GetBondsToHydrogenAtoms
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317 @Bonds = $Atom->GetBondsToHydrogenAtoms();
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318
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319 Returns an array of Bond objects corresponding to bonds from *Atom*
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320 to any other hydrogen atom in a molecule.
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321
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322 GetBondsToNonHydrogenAtoms
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323 @Bonds = $Atom->GetBondsToNonHydrogenAtoms();
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324
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325 Returns an array of Bond objects corresponding to bonds from *Atom*
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326 to other bonded non-hydrogen atoms in a molecule.
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327
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328 GetExactMass
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329 $ExactMass = $Atom->GetExactMass();
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330
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331 Returns exact mass of an *Atom* which correspond to one of these
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332 three values: explicity set *ExactMass* property; mass of natural
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333 isotope for an explicty set value of *MassNumber*; most abundant
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334 natural isotope mass for *Atom* with valid atomic number value
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335 available by PerodicTable module.
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336
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337 GetExplicitHydrogens
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338 $NumOfExplicitHydrogens = $Atom->GetExplicitHydrogens();
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339
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340 Returns number of hydrogens explicity bonded to an *Atom* in a
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341 molecule.
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342
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343 GetFormalCharge
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344 $FormalCharge = $Atom->GetFormalCharge();
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345
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346 Returns formal charge of an *Atom* in a molecule.
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347
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348 GetFreeRadicalElectrons
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349 $FreeRadicalElectrons = $Atom->GetFreeRadicalElectrons();
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350
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351 Returns number of free radical electrons corresponding to to one of
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352 these three values: *FreeRadicalElectrons* property;
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353 *SpinMultiplicity* property; value of 0.
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354
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355 For atoms with explicit assignment of *SpinMultiplicity* atom
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356 property values,
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357
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358 Singlet - two unparied electrons corresponding to one spin state
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359 Doublet - free radical; an unpaired electron corresponding to two
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360 spin states
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361 Triplet - two unparied electrons corresponding to three spin states
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362 (divalent carbon atoms: carbenes)
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363
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364 FreeRadicalElectrons are calculated as follows:
|
|
|
365
|
|
|
366 Doublet: 1 (one valence electron not available for bonding)
|
|
|
367 Singlet: 2 (two valence electrons not available for bonding)
|
|
|
368 Triplet: 2 (two valence electrons not available for bonding)
|
|
|
369
|
|
|
370 GetGroupNumber
|
|
|
371 $GroupNumber = $Atom->GetGroupNumber();
|
|
|
372
|
|
|
373 Returns group number of an *Atom* in a molecule with a valid atomic
|
|
|
374 number.
|
|
|
375
|
|
|
376 GetHeavyAtomNeighbors
|
|
|
377 $NumOfHeavyAtoms = $Atom->GetHeavyAtomNeighbors();
|
|
|
378 @HeavyAtoms = $Atom->GetHeavyAtomNeighbors();
|
|
|
379
|
|
|
380 Return number of heavy atoms or an array of Atom objects
|
|
|
381 corresponding to heavy atoms bonded to an *Atom* in a molecule.
|
|
|
382
|
|
|
383 GetHeavyAtomNeighborsAtomInformation
|
|
|
384 ($NumOfAtomNeighbors, $AtomNeighborsRef,
|
|
|
385 $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom->
|
|
|
386 GetHeavyAtomNeighborsAtomInformation();
|
|
|
387
|
|
|
388 Returns atoms information for all non-hydrogen atoms attached to an
|
|
|
389 *Atom* in a molecule.
|
|
|
390
|
|
|
391 The following values are returned:
|
|
|
392
|
|
|
393 o Number of non-hydrogen atom neighbors
|
|
|
394 o A reference to an array containing atom objects corresponding to
|
|
|
395 non-hydrogen atom neighbors
|
|
|
396 o Number of different types of non-hydrogen atom neighbors
|
|
|
397 o A reference to a hash containing atom symbol as key with value
|
|
|
398 corresponding to its count for non-hydrogen atom neighbors
|
|
|
399
|
|
|
400 GetHeavyAtomNeighborsBondformation
|
|
|
401 ($NumOfBonds, $BondTypeCountMapRef,
|
|
|
402 $AtomsBondTypesCountMapRef,
|
|
|
403 $AtomsBondTypeAtomsMap) = $Atom->
|
|
|
404 GetHeavyAtomNeighborsBondformation();
|
|
|
405
|
|
|
406 Returns bonds information for all non-hydrogen atoms attached to an
|
|
|
407 *Atom* in a molecule.
|
|
|
408
|
|
|
409 The following values are returned:
|
|
|
410
|
|
|
411 o Number of bonds to non-hydrogen atom neighbors
|
|
|
412 o A reference to an array containing bond objects corresponding to
|
|
|
413 non-hydrogen atom neighbors
|
|
|
414 o A reference to a hash containing bond type as key with value
|
|
|
415 corresponding to its count for non-hydrogen atom neighbors. Bond
|
|
|
416 types are: Single, Double or Triple
|
|
|
417 o A reference to a hash containing atom symbol as key pointing to bond
|
|
|
418 type as second key with values corresponding to count of bond types for atom
|
|
|
419 symbol for non-hydrogen atom neighbors
|
|
|
420 o A reference to a hash containing atom symbol as key pointing to bond
|
|
|
421 type as second key with values corresponding to atom objects array involved
|
|
|
422 in corresponding bond type for atom symbol for non-hydrogen atom neighbors
|
|
|
423
|
|
|
424 GetHighestCommonValence
|
|
|
425 $HighestCommonValence = $Atom->GetHighestCommonValence();
|
|
|
426
|
|
|
427 Returns highest common valence of an *Atom* which corresponds to
|
|
|
428 either explicity set *HighestCommonValence* atom property or highest
|
|
|
429 common valence of the corresponding element in the periodic table
|
|
|
430 available by PerodicTable module.
|
|
|
431
|
|
|
432 GetHydrogens
|
|
|
433 $NumOfHydrogens = $Atom->GetHydrogens();
|
|
|
434
|
|
|
435 Returns total number of hydrogens for an *Atom* in a molecule
|
|
|
436 including both hydrogen atom neighbors and implicit hydrogens.
|
|
|
437
|
|
|
438 GetHydrogenAtomNeighbors
|
|
|
439 $NumOfHydrogenAtomNeighbors = $Atom->GetHydrogenAtomNeighbors();
|
|
|
440 @HydrogenAtomNeighbors = $Atom->GetHydrogenAtomNeighbors();
|
|
|
441
|
|
|
442 Return number of hydrogen atoms or an array of *Atom* objects
|
|
|
443 corresponding to hydrogen atoms bonded to an *Atom* in a molecule.
|
|
|
444
|
|
|
445 GetImplicitHydrogens
|
|
|
446 $NumOfImplicitHydrogens = $Atom->GetImplicitHydrogens();
|
|
|
447
|
|
|
448 Returns number of implicit hydrogens for an *Atom* in a molecule.
|
|
|
449 This value either corresponds to explicitly set *ImplicitHydrogens*
|
|
|
450 atom property or calculated as the difference between the value of
|
|
|
451 potential total valence and sum of bond orders to both hydrogen and
|
|
|
452 non-hydrogen atom neighbors.
|
|
|
453
|
|
|
454 GetPotentialTotalCommonValence
|
|
|
455 $PotentialTotalValence = $Atom->GetPotentialTotalCommonValence();
|
|
|
456
|
|
|
457 Returns potential total common valence of an *Atom* in a molecule
|
|
|
458 corresponding to a specific valence model set for the molecule using
|
|
|
459 its SetValenceModel method or default internal valence model. It is
|
|
|
460 used during the calculation of missing or implicit hydrogens.
|
|
|
461
|
|
|
462 The current release of MayaChemTools supports three valence models:
|
|
|
463 *MDLValenceModel, DaylightValenceModel, InternalValenceModel or
|
|
|
464 MayaChemToolsValenceModel*.
|
|
|
465
|
|
|
466 For *MDLValenceModel* and *DaylightValenceModel*, the following data
|
|
|
467 files, distributed with the package, are used to calculate potential
|
|
|
468 total valence:
|
|
|
469
|
|
|
470 lib/data/MDLValenceModelData.csv
|
|
|
471 lib/data/DaylightValenceModelData.csv
|
|
|
472
|
|
|
473 The calculation of potential total common valence for these two
|
|
|
474 models is performed as follows: Calculate current effective total
|
|
|
475 valence of the *Atom* by adding up the bond order of its neighbors
|
|
|
476 and number of free radical electrons; Find available common valence
|
|
|
477 for the *Atom*, corresponding to any specified formal charge, higher
|
|
|
478 than the effective total valence, and return it as
|
|
|
479 *PotentialTotalValence*.
|
|
|
480
|
|
|
481 The calculation of potential total common valence For
|
|
|
482 *InternalValenceModel* or *MayaChenToolsValenceModel* doesn't uses
|
|
|
483 PeriodicTable module to retrieve values for common valence, which in
|
|
|
484 turn reads in PeriodicTableElements.csv file distributed with the
|
|
|
485 package.
|
|
|
486
|
|
|
487 For elements with one one common valence, potential total common
|
|
|
488 valence corresponds to:
|
|
|
489
|
|
|
490 CommonValence + FormalCharge - FreeRadicalElectrons
|
|
|
491
|
|
|
492 For elements with multiple common valences, each common valence is
|
|
|
493 used to calculate total potential common valence as shown above, and
|
|
|
494 the first total potential common valence greater than the sum of
|
|
|
495 bond orders to all neighbors is selected as the final total common
|
|
|
496 valence.
|
|
|
497
|
|
|
498 FormalCharge sign is reversed for electropositive elements with
|
|
|
499 positive formal charge during common valence calculations.
|
|
|
500 Electropositive elements, metals and transition elements, have
|
|
|
501 usually plus formal charge and it leads to decrease in common
|
|
|
502 valence; the negative formal charge should result in the decrease of
|
|
|
503 common valence.
|
|
|
504
|
|
|
505 The sign of formal charge is adjusted as follows.
|
|
|
506
|
|
|
507 Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He):
|
|
|
508
|
|
|
509 Formal charge sign is not adjusted. Positive and negative values
|
|
|
510 result in the increase and decrease of valence.
|
|
|
511
|
|
|
512 Group 14 containing C, Si, Ge, Sn, Pb...:
|
|
|
513
|
|
|
514 Formal charge sign is reversed for positive values. Both positive
|
|
|
515 and negative values result in the decrease of valence.
|
|
|
516
|
|
|
517 Group 13 containing B, Al, Ga, In, Tl...:
|
|
|
518
|
|
|
519 Formal charge sign is always reversed. Positive and negative values
|
|
|
520 result in the decrease and increase of valence.
|
|
|
521
|
|
|
522 Groups 1 (H) through 12 (Zn)...:
|
|
|
523
|
|
|
524 Formal charge sign is reversed for positive values. Both positive
|
|
|
525 and negative values result in the decrease of valence.
|
|
|
526
|
|
|
527 Lanthanides and actinides:
|
|
|
528
|
|
|
529 Formal charge sign is reversed for positive values. Both positive
|
|
|
530 and negative values result in the decrease of valence.
|
|
|
531
|
|
|
532 GetLargestBondOrder
|
|
|
533 $LargestBO =$Atom->GetLargestBondOrder();
|
|
|
534
|
|
|
535 Returns largest bond order for an *Atom* among the bonds to other
|
|
|
536 atoms in a molecule.
|
|
|
537
|
|
|
538 GetLargestBondOrderToHeavyAtoms
|
|
|
539 $LargestBO =$Atom->GetLargestBondOrderToHeavyAtoms();
|
|
|
540
|
|
|
541 Returns largest bond order for an *Atom* among the bonds to other
|
|
|
542 heavy atoms in a molecule.
|
|
|
543
|
|
|
544 GetLargestBondOrderToNonHydrogenAtoms
|
|
|
545 $LargestBO =$Atom->GetLargestBondOrderToNonHydrogenAtoms();
|
|
|
546
|
|
|
547 Returns largest bond order for an *Atom* among the bonds to other
|
|
|
548 non-hydrogen atoms in a molecule.
|
|
|
549
|
|
|
550 GetLargestRing
|
|
|
551 @RingAtoms = $Atom->GetLargestRing();
|
|
|
552
|
|
|
553 Returns an array of ring *Atom* objects corresponding to the largest
|
|
|
554 ring containing *Atom* in a molecule.
|
|
|
555
|
|
|
556 GetLowestCommonValence
|
|
|
557 $LowestCommonValence = $Atom->GetLowestCommonValence();
|
|
|
558
|
|
|
559 Returns lowest common valence of an *Atom* which corresponds to
|
|
|
560 either explicity set *LowestCommonValence* atom property or highest
|
|
|
561 common valence of the corresponding element in the periodic table
|
|
|
562 available by PerodicTable module.
|
|
|
563
|
|
|
564 GetMassNumber
|
|
|
565 $MassNumber = $Aom->GetMassNumber();
|
|
|
566
|
|
|
567 Returns atomic weight of an Atom which corresponds to either
|
|
|
568 explicity set *MassNumber* atom property or mass number of the most
|
|
|
569 abundant natural isotope of the corresponding element in the
|
|
|
570 periodic table available by PeriodicTable module.
|
|
|
571
|
|
|
572 GetMissingHydrogens
|
|
|
573 $NumOfMissingHydrogens = $Atom->GetMissingHydrogens();
|
|
|
574
|
|
|
575 Returns number of missing hydrogens for an *Atom* in a molecule.
|
|
|
576 This value either corresponds to explicitly set *ImplicitHydrogens*
|
|
|
577 atom property or calculated as the difference between the value of
|
|
|
578 potential total valence and sum of bond orders to both hydrogen and
|
|
|
579 non-hydrogen atom neighbors.
|
|
|
580
|
|
|
581 GetNeighbors
|
|
|
582 $NumOfNeighbors = $Atom->GetNeighbors();
|
|
|
583 @Neighbors = $Atom->GetNeighbors();
|
|
|
584
|
|
|
585 Returns number of neighbor atoms or an array of *Atom* objects
|
|
|
586 corresponding to all atoms bonded to an *Atom* in a molecule.
|
|
|
587
|
|
|
588 GetNeighborsUsingAtomSpecification
|
|
|
589 @AtomNeighbors = $Atom->GetNeighborsUsingAtomSpecification($AtomSpec);
|
|
|
590 $NumOfNeighbors = $Atom->GetNeighborsUsingAtomSpecification($AtomSpec);
|
|
|
591
|
|
|
592 @AtomNeighbors = $Atom->GetNeighborsUsingAtomSpecification($AtomSpec,
|
|
|
593 @ExcludeNeighbors);
|
|
|
594
|
|
|
595 Returns number of neighbor atoms or an array of *Atom* objects
|
|
|
596 matching atom specification corresponding to atom neighbors of an
|
|
|
597 *Atom* in a molecule. Optionally, *Atom* neighbors can be excluded
|
|
|
598 from the neighbors list using *ExcludeNeighbors*.
|
|
|
599
|
|
|
600 Notes:
|
|
|
601
|
|
|
602 o AtomSpecification correspond to any valid AtomicInvariant based atomic specifications
|
|
|
603 as supported by DoesAtomNeighborhoodMatch method
|
|
|
604 o Multiple atom specifications can be used in a string delimited by comma
|
|
|
605
|
|
|
606 GetNonHydrogenAtomNeighbors
|
|
|
607 $NumOfNeighbors = $Atom->GetNonHydrogenAtomNeighbors();
|
|
|
608 @Neighbors = $Atom->GetNonHydrogenAtomNeighbors();
|
|
|
609
|
|
|
610 Returns number of non-hydrogen atoms or an array of Atom objects
|
|
|
611 corresponding to non-hydrogen atoms bonded to an *Atom* in a
|
|
|
612 molecule.
|
|
|
613
|
|
|
614 GetNonHydrogenAtomNeighborsAtomInformation
|
|
|
615 ($NumOfAtomNeighbors, $AtomNeighborsRef,
|
|
|
616 $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom->
|
|
|
617 GetNonHydrogenAtomNeighborsAtomInformation();
|
|
|
618
|
|
|
619 Returns atoms information for all non-hydrogen atoms attached to an
|
|
|
620 *Atom* in a molecule.
|
|
|
621
|
|
|
622 The following values are returned:
|
|
|
623
|
|
|
624 o Number of non-hydrogen atom neighbors
|
|
|
625 o A reference to an array containing atom objects corresponding to
|
|
|
626 non-hydrogen atom neighbors
|
|
|
627 o Number of different types of non-hydrogen atom neighbors
|
|
|
628 o A reference to a hash containing atom symbol as key with value
|
|
|
629 corresponding to its count for non-hydrogen atom neighbors
|
|
|
630
|
|
|
631 GetNonHydrogenAtomNeighborsBondInformation
|
|
|
632 ($NumOfBonds, $BondTypeCountMapRef,
|
|
|
633 $AtomsBondTypesCountMapRef,
|
|
|
634 $AtomsBondTypeAtomsMap) = $Atom->
|
|
|
635 GetNonHydrogenAtomNeighborsBondInformation();
|
|
|
636
|
|
|
637 Returns bonds information for all non-hydrogen atoms attached to an
|
|
|
638 *Atom* in a molecule.
|
|
|
639
|
|
|
640 The following values are returned:
|
|
|
641
|
|
|
642 o Number of bonds to non-hydrogen atom neighbors
|
|
|
643 o A reference to an array containing bond objects corresponding to
|
|
|
644 non-hydrogen atom neighbors
|
|
|
645 o A reference to a hash containing bond type as key with value
|
|
|
646 corresponding to its count for non-hydrogen atom neighbors. Bond
|
|
|
647 types are: Single, Double or Triple
|
|
|
648 o A reference to a hash containing atom symbol as key pointing to bond
|
|
|
649 type as second key with values corresponding to count of bond types for atom
|
|
|
650 symbol for non-hydrogen atom neighbors
|
|
|
651 o A reference to a hash containing atom symbol as key pointing to bond
|
|
|
652 type as second key with values corresponding to atom objects array involved
|
|
|
653 in corresponding bond type for atom symbol for non-hydrogen atom neighbors
|
|
|
654
|
|
|
655 GetNonHydrogenNeighborOfHydrogenAtom
|
|
|
656 $Atom = $Atom->GetNonHydrogenNeighborOfHydrogenAtom();
|
|
|
657
|
|
|
658 Returns non-hydrogen or heavy atom neighbor of a hydrogen atom in a
|
|
|
659 molecule..
|
|
|
660
|
|
|
661 GetNumOfAromaticBondsToHeavyAtoms
|
|
|
662 $NumOfBonds = $Atom->GetNumOfAromaticBondsToHeavyAtoms();
|
|
|
663
|
|
|
664 Returns number of aromatic bonds from an *Atom* to other
|
|
|
665 non-hydrogen or heavy atoms in a molecule.
|
|
|
666
|
|
|
667 GetNumOfAromaticBondsToNonHydrogenAtoms
|
|
|
668 $NumOfBonds = $Atom->GetNumOfAromaticBondsToNonHydrogenAtoms();
|
|
|
669
|
|
|
670 Returns number of aromatic bonds from an *Atom* to other
|
|
|
671 non-hydrogen or heavy atoms in a molecule.
|
|
|
672
|
|
|
673 GetNumOfBonds
|
|
|
674 $NumOfBonds = $Atom->GetNumOfBonds();
|
|
|
675
|
|
|
676 Returns number of bonds from an *Atom* to other atoms in a molecule.
|
|
|
677
|
|
|
678 GetNumOfBondsAvailableForHeavyAtoms
|
|
|
679 $NumOfBonds = $Atom->GetNumOfBondsAvailableForHeavyAtoms();
|
|
|
680
|
|
|
681 Get number of bonds available to form additional bonds with heavy
|
|
|
682 atoms, excluding any implicit bonds to hydrogens set using
|
|
|
683 *ImplicitHydrogens* property.
|
|
|
684
|
|
|
685 It's different from number of implicit or missing hydrogens, both of
|
|
|
686 which are equivalent.
|
|
|
687
|
|
|
688 For example, in a SMILES string, [nH] ring atom corresponds to an
|
|
|
689 aromatic nitrogen. Although the hydrogen specified for n is treated
|
|
|
690 internally as implicit hydrogen and shows up in missing hydrogen
|
|
|
691 count, it's not available to participate in double bonds to
|
|
|
692 additional heavy atoms.
|
|
|
693
|
|
|
694 GetNumOfBondsAvailableForNonHydrogenAtoms
|
|
|
695 $NumOfBonds = $Atom->GetNumOfBondsAvailableForNonHydrogenAtoms();
|
|
|
696
|
|
|
697 Get number of bonds available to form additional bonds with heavy
|
|
|
698 atoms, excluding any implicit bonds to hydrogens set using
|
|
|
699 ImplicitHydrogens property.
|
|
|
700
|
|
|
701 GetNumOfBondsToHeavyAtoms
|
|
|
702 $NumOfBondsToHeavyAtoms = $Atom->GetNumOfBondsToHeavyAtoms();
|
|
|
703
|
|
|
704 Returns number of bonds from an *Atom* to other heavy atoms in a
|
|
|
705 molecule.
|
|
|
706
|
|
|
707 GetNumOfBondsToHydrogenAtoms
|
|
|
708 $NumOfBonds = $Atom->GetNumOfBondsToHydrogenAtoms();
|
|
|
709
|
|
|
710 Returns number of bonds from an *Atom* to other hydrogen atoms in a
|
|
|
711 molecule.
|
|
|
712
|
|
|
713 GetNumOfBondsToNonHydrogenAtoms
|
|
|
714 $NumOfBonds = $Atom->GetNumOfBondsToNonHydrogenAtoms();
|
|
|
715
|
|
|
716 Returns number of bonds from an *Atom* to other non-hydrogen atoms
|
|
|
717 in a molecule.
|
|
|
718
|
|
|
719 GetNumOfBondTypesToHeavyAtoms
|
|
|
720 ($NumOfSingleBonds, $NumOfDoubleBonds,
|
|
|
721 $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom->
|
|
|
722 GetNumOfBondTypesToHeavyAtoms($CountAromaticBonds);
|
|
|
723
|
|
|
724 Get number of single, double, triple, and aromatic bonds from an
|
|
|
725 *Atom* to all other non-hydrogen atoms in a molecule.
|
|
|
726
|
|
|
727 Value of *CountAtomaticBonds* parameter controls whether number of
|
|
|
728 aromatic bonds is returned; default is not to count aromatic bonds.
|
|
|
729 During counting of aromatic bonds, the bond marked aromatic is not
|
|
|
730 included in the count of other bond types.
|
|
|
731
|
|
|
732 GetNumOfBondTypesToNonHydrogenAtoms
|
|
|
733 ($NumOfSingleBonds, $NumOfDoubleBonds,
|
|
|
734 $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom->
|
|
|
735 GetNumOfBondTypesToNonHydrogenAtoms($CountAromaticBonds);
|
|
|
736
|
|
|
737 Get number of single, double, triple, and aromatic bonds from an
|
|
|
738 *Atom* to all other non-hydrogen atoms in a molecule.
|
|
|
739
|
|
|
740 Value of *CountAtomaticBonds* parameter controls whether number of
|
|
|
741 aromatic bonds is returned; default is not to count aromatic bonds.
|
|
|
742 During counting of aromatic bonds, the bond marked aromatic is not
|
|
|
743 included in the count of other bond types.
|
|
|
744
|
|
|
745 GetNumOfDoubleBondsToHeavyAtoms
|
|
|
746 $NumOfDoubleBonds = $Atom->GetNumOfDoubleBondsToHeavyAtoms();
|
|
|
747
|
|
|
748 Returns number of double bonds from an *Atom* to other heavy atoms
|
|
|
749 or non-hydrogen atoms in a molecule.
|
|
|
750
|
|
|
751 GetNumOfDoubleBondsToNonHydrogenAtoms
|
|
|
752 $NumOfDoubleBonds =$Atom->GetNumOfDoubleBondsToNonHydrogenAtoms();
|
|
|
753
|
|
|
754 Returns number of double bonds from an *Atom* to other heavy atoms
|
|
|
755 or non-hydrogen atoms in a molecule.
|
|
|
756
|
|
|
757 GetNumOfHeavyAtomNeighbors
|
|
|
758 $NumOfNeighbors = $Atom->GetNumOfHeavyAtomNeighbors();
|
|
|
759
|
|
|
760 Returns number heavy atom neighbors for an *Atom* in a molecule.
|
|
|
761
|
|
|
762 GetNumOfHydrogenAtomNeighbors
|
|
|
763 $NumOfNeighbors = $Atom->GetNumOfHydrogenAtomNeighbors();
|
|
|
764
|
|
|
765 Returns number hydrogens atom neighbors for an *Atom* in a molecule.
|
|
|
766
|
|
|
767 GetNumOfMissingHydrogens
|
|
|
768 $NumOfMissingHydrogens = $Atom->GetNumOfMissingHydrogens();
|
|
|
769
|
|
|
770 Returns number of implicit hydrogens for an *Atom* in a molecule.
|
|
|
771 This value either corresponds to explicitly set *ImplicitHydrogens*
|
|
|
772 atom property or calculated as the difference between the value of
|
|
|
773 potential total valence and sum of bond orders to both hydrogen and
|
|
|
774 non-hydrogen atom neighbors.
|
|
|
775
|
|
|
776 GetNumOfExplicitHydrogens
|
|
|
777 $NumOfExplicitHydrogens = $Atom->GetNumOfExplicitHydrogens();
|
|
|
778
|
|
|
779 Returns number hydrogens atom neighbors for an *Atom* in a molecule.
|
|
|
780
|
|
|
781 GetNumOfHydrogens
|
|
|
782 $NumOfHydrogens = $Atom->GetNumOfHydrogens();
|
|
|
783
|
|
|
784 Returns total number of hydrogens for an *Atom* in a molecule
|
|
|
785 including both hydrogen atom neighbors and implicit hydrogens.
|
|
|
786
|
|
|
787 GetNumOfImplicitHydrogens
|
|
|
788 $NumOfImplicitHydrogens = $Atom->GetNumOfImplicitHydrogens();
|
|
|
789
|
|
|
790 Returns number of implicit hydrogens for an *Atom* in a molecule.
|
|
|
791 This value either corresponds to explicitly set *ImplicitHydrogens*
|
|
|
792 atom property or calculated as the difference between the value of
|
|
|
793 potential total valence and sum of bond orders to both hydrogen and
|
|
|
794 non-hydrogen atom neighbors.
|
|
|
795
|
|
|
796 GetNumOfNeighbors
|
|
|
797 $NumOfNeighbors = $Atom->GetNumOfNeighbors();
|
|
|
798
|
|
|
799 Returns number atom neighbors for an *Atom* in a molecule.
|
|
|
800
|
|
|
801 GetNumOfNonHydrogenAtomNeighbors
|
|
|
802 $NumNeighbors = $This->GetNumOfNonHydrogenAtomNeighbors();
|
|
|
803
|
|
|
804 Returns number non-hydrogens atom neighbors for an *Atom* in a
|
|
|
805 molecule.
|
|
|
806
|
|
|
807 GetNumOfRings
|
|
|
808 $NumOfRings = $Atom->GetNumOfRings();
|
|
|
809
|
|
|
810 Returns number of rings containing *Atom* in a molecule.
|
|
|
811
|
|
|
812 GetNumOfRingsWithEvenSize
|
|
|
813 $NumOfRings = $Atom->GetNumOfRingsWithEvenSize();
|
|
|
814
|
|
|
815 Returns number of rings with even size containing *Atom* in a
|
|
|
816 molecule.
|
|
|
817
|
|
|
818 GetNumOfRingsWithOddSize
|
|
|
819 $NumOfRings = $Atom->GetNumOfRingsWithOddSize();
|
|
|
820
|
|
|
821 Returns number of rings with odd size containing *Atom* in a
|
|
|
822 molecule.
|
|
|
823
|
|
|
824 GetNumOfRingsWithSize
|
|
|
825 $NumOfRings = $Atom->GetNumOfRingsWithSize($RingSize);
|
|
|
826
|
|
|
827 Returns number of rings with specific *RingSize* containing *Atom*
|
|
|
828 in a molecule.
|
|
|
829
|
|
|
830 GetNumOfRingsWithSizeGreaterThan
|
|
|
831 $NumOfRings = $Atom->GetNumOfRingsWithSizeGreaterThan($RingSize);
|
|
|
832
|
|
|
833 Returns number of rings with size greater than specific *RingSize*
|
|
|
834 containing *Atom* in a molecule.
|
|
|
835
|
|
|
836 GetNumOfRingsWithSizeLessThan
|
|
|
837 $NumOfRings = $Atom->GetNumOfRingsWithSizeLessThan($RingSize);
|
|
|
838
|
|
|
839 Returns number of rings with size less than specific *RingSize*
|
|
|
840 containing *Atom* in a molecule.
|
|
|
841
|
|
|
842 GetNumOfSigmaAndPiBondsToHeavyAtoms
|
|
|
843 ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom->
|
|
|
844 GetNumOfSigmaAndPiBondsToHeavyAtoms();
|
|
|
845
|
|
|
846 Get number of sigma and pi bonds from an *Atom* to all other
|
|
|
847 non-hydrogen atoms in a molecule.
|
|
|
848
|
|
|
849 Sigma and pi bonds are counted using the following methodology: a
|
|
|
850 single bond correspond to one sigma bond; a double bond contributes
|
|
|
851 one to sigma bond count and one to pi bond count; a triple bond
|
|
|
852 contributes one to sigma bond count and two to pi bond count.
|
|
|
853
|
|
|
854 GetNumOfSigmaAndPiBondsToNonHydrogenAtoms
|
|
|
855 ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom->
|
|
|
856 GetNumOfSigmaAndPiBondsToNonHydrogenAtoms();
|
|
|
857
|
|
|
858 Get number of sigma and pi bonds from an *Atom* to all other
|
|
|
859 non-hydrogen atoms in a molecule.
|
|
|
860
|
|
|
861 Sigma and pi bonds are counted using the following methodology: a
|
|
|
862 single bond correspond to one sigma bond; a double bond contributes
|
|
|
863 one to sigma bond count and one to pi bond count; a triple bond
|
|
|
864 contributes one to sigma bond count and two to pi bond count.
|
|
|
865
|
|
|
866 GetNumOfSingleBondsToNonHydrogenAtoms
|
|
|
867 $NumOfSingleBonds =$Atom->GetNumOfSingleBondsToNonHydrogenAtoms();
|
|
|
868
|
|
|
869 Returns number of single bonds from an *Atom* to other heavy atoms
|
|
|
870 or non-hydrogen atoms in a molecule.
|
|
|
871
|
|
|
872 GetNumOfSingleBondsToHeavyAtoms
|
|
|
873 $NumOfSingleBonds = $Atom->GetNumOfSingleBondsToHeavyAtoms();
|
|
|
874
|
|
|
875 Returns number of single bonds from an *Atom* to other heavy atoms
|
|
|
876 or non-hydrogen atoms in a molecule.
|
|
|
877
|
|
|
878 GetNumOfTripleBondsToNonHydrogenAtoms
|
|
|
879 $NumOfTripleBonds =$Atom->GetNumOfTripleBondsToNonHydrogenAtoms();
|
|
|
880
|
|
|
881 Returns number of triple bonds from an *Atom* to other heavy atoms
|
|
|
882 or non-hydrogen atoms in a molecule.
|
|
|
883
|
|
|
884 GetNumOfTripleBondsToHeavyAtoms
|
|
|
885 $NumOfTripleBonds = $Atom->GetNumOfTripleBondsToHeavyAtoms();
|
|
|
886
|
|
|
887 Returns number of triple bonds from an *Atom* to other heavy atoms
|
|
|
888 or non-hydrogen atoms in a molecule.
|
|
|
889
|
|
|
890 GetPeriodNumber
|
|
|
891 $PeriodNumber = $Atom->GetPeriodNumber();
|
|
|
892
|
|
|
893 Returns periodic table period number for an *Atom* in a molecule
|
|
|
894 with a valid atomic number .
|
|
|
895
|
|
|
896 GetRings
|
|
|
897 @Rings = $Aotm->GetRings();
|
|
|
898
|
|
|
899 Returns an array of references to arrays containing ring atoms
|
|
|
900 corressponding to all rings containing *Atom* in a molecule.
|
|
|
901
|
|
|
902 GetRingsWithEvenSize
|
|
|
903 @Rings = $Aotm->GetRingsWithEvenSize();
|
|
|
904
|
|
|
905 Returns an array of references to arrays containing ring atoms
|
|
|
906 corressponding to all rings with even size containing *Atom* in a
|
|
|
907 molecule.
|
|
|
908
|
|
|
909 GetRingsWithOddSize
|
|
|
910 @Rings = $Aotm->GetRingsWithOddSize();
|
|
|
911
|
|
|
912 Returns an array of references to arrays containing ring atoms
|
|
|
913 corressponding to all rings with odd size containing *Atom* in a
|
|
|
914 molecule.
|
|
|
915
|
|
|
916 GetRingsWithSize
|
|
|
917 @Rings = $Aotm->GetRingsWithSize($RingSize);
|
|
|
918
|
|
|
919 Returns an array of references to arrays containing ring atoms
|
|
|
920 corressponding to all rings with specific *RingSize *containing
|
|
|
921 *Atom* in a molecule.
|
|
|
922
|
|
|
923 GetRingsWithSizeGreaterThan
|
|
|
924 @Rings = $Aotm->GetRingsWithSizeGreaterThan($RingSize);
|
|
|
925
|
|
|
926 Returns an array of references to arrays containing ring atoms
|
|
|
927 corressponding to all rings with size greater than specific
|
|
|
928 *RingSize *containing *Atom* in a molecule.
|
|
|
929
|
|
|
930 GetRingsWithSizeLessThan
|
|
|
931 @Rings = $Aotm->GetRingsWithSizeLessThan($RingSize);
|
|
|
932
|
|
|
933 Returns an array of references to arrays containing ring atoms
|
|
|
934 corressponding to all rings with size less than specific *RingSize
|
|
|
935 *containing *Atom* in a molecule.
|
|
|
936
|
|
|
937 GetSizeOfLargestRing
|
|
|
938 $Size = $Atom->GetSizeOfLargestRing();
|
|
|
939
|
|
|
940 Returns size of the largest ring containing *Atom* in a molecule.
|
|
|
941
|
|
|
942 GetSizeOfSmallestRing
|
|
|
943 $Size = $Atom->GetSizeOfSmallestRing();
|
|
|
944
|
|
|
945 Returns size of the smallest ring containing *Atom* in a molecule.
|
|
|
946
|
|
|
947 GetSmallestRing
|
|
|
948 @RingAtoms = $Atom->GetSmallestRing();
|
|
|
949
|
|
|
950 Returns an array of ring *Atom* objects corresponding to the largest
|
|
|
951 ring containing *Atom* in a molecule.
|
|
|
952
|
|
|
953 GetSpinMultiplicity
|
|
|
954 $SpinMultiplicity = $Atom->GetSpinMultiplicity();
|
|
|
955
|
|
|
956 Returns spin multiplicity of an *Atom* corresponding to one of these
|
|
|
957 three values: explicitly set SpinMultiplicity property value;
|
|
|
958 calculated from FreeRadicalElectrons property; value of 0.
|
|
|
959
|
|
|
960 The SpinMultiplicity is calculate from *FreeRadicalElectrons*
|
|
|
961 property as follows:
|
|
|
962
|
|
|
963 FreeRadicalElectrons: 1; SpinMultiplicity: 2
|
|
|
964 FreeRadicalElectrons: 2; SpinMultiplicity: 1
|
|
|
965 FreeRadicalElectrons: other; SpinMultiplicity: 0
|
|
|
966
|
|
|
967 GetSumOfBondOrders
|
|
|
968 $SumBondOrders = $Atom->GetSumOfBondOrders();
|
|
|
969
|
|
|
970 Returns sum of bond orders corresponding to all atoms bonded to an
|
|
|
971 *Atom* in a molecule.
|
|
|
972
|
|
|
973 GetSumOfBondOrdersToHeavyAtoms
|
|
|
974 $SumBondOrders = $Atom->GetSumOfBondOrdersToHeavyAtoms();
|
|
|
975
|
|
|
976 Returns sum of bond orders corresponding to all heavy atoms bonded
|
|
|
977 to an *Atom* in a molecule.
|
|
|
978
|
|
|
979 GetSumOfBondOrdersToHydrogenAtoms
|
|
|
980 $SumBondOrders = $Atom->GetSumOfBondOrdersToHydrogenAtoms();
|
|
|
981
|
|
|
982 Returns sum of bond orders corresponding to all hydrogen atoms
|
|
|
983 bonded to an *Atom* in a molecule.
|
|
|
984
|
|
|
985 GetSumOfBondOrdersToNonHydrogenAtoms
|
|
|
986 $SumBondOrders = $Atom->GetSumOfBondOrdersToNonHydrogenAtoms();
|
|
|
987
|
|
|
988 Returns sum of bond orders corresponding to all non-hydrogen atoms
|
|
|
989 bonded to an *Atom* in a molecule.
|
|
|
990
|
|
|
991 GetValence
|
|
|
992 $Valence = $Atom->GetValence();
|
|
|
993
|
|
|
994 Returns valence of an *Atom* in a molecule. Valence corresponds to
|
|
|
995 number of electrons used by an atom in bonding:
|
|
|
996
|
|
|
997 Valence = ValenceElectrons - ValenceFreeElectrons = BondingElectrons
|
|
|
998
|
|
|
999 Single, double and triple bonds with bond orders of 1, 2, and 3
|
|
|
1000 correspond to contribution of 1, 2, and 3 bonding electrons. So:
|
|
|
1001
|
|
|
1002 Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge
|
|
|
1003
|
|
|
1004 where positive and negative values of FormalCharge increase and
|
|
|
1005 decrease the number of bonding electrons, respectively.
|
|
|
1006
|
|
|
1007 The current release of MayaChemTools supports the following three
|
|
|
1008 valence models, which are used during calculation of implicit
|
|
|
1009 hydrogens: MDLValenceModel, DaylightValenceModel,
|
|
|
1010 InternalValenceModel or MayaChemToolsValenceModel.
|
|
|
1011
|
|
|
1012 Notes:
|
|
|
1013
|
|
|
1014 . Missing hydrogens are included in the valence.
|
|
|
1015 . For neutral molecules, valence and sum of bond orders are equal.
|
|
|
1016 . For molecules containing only single bonds, SumOfBondOrders and
|
|
|
1017 NumOfBonds are equal.
|
|
|
1018 . Free radical electrons lead to the decrease in valence. For atoms with
|
|
|
1019 explicit assignment of SpinMultiplicity property values corresponding to
|
|
|
1020 Singlet (two unparied electrons corresponding to one spin state), Doublet
|
|
|
1021 (free radical; an unpaired electron corresponding to two spin states),
|
|
|
1022 and Triplet (two unparied electrons corresponding to three spin states;
|
|
|
1023 divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:
|
|
|
1024
|
|
|
1025 SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1 (one valence
|
|
|
1026 electron not available for bonding)
|
|
|
1027 SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2 (two
|
|
|
1028 valence electrons not available for bonding)
|
|
|
1029
|
|
|
1030 GetValenceElectrons
|
|
|
1031 $ValenceElectrons = $Atom->GetValenceElectrons();
|
|
|
1032
|
|
|
1033 Returns valence electrons for an Atom which corresponds to either
|
|
|
1034 explicity set *ValenceElectrons* atom property or valence electrons
|
|
|
1035 for the corresponding element in the periodic table available by
|
|
|
1036 PeriodicTable module.
|
|
|
1037
|
|
|
1038 GetValenceFreeElectrons
|
|
|
1039 $ValenceFreeElectrons = $Atom->GetValenceFreeElectrons();
|
|
|
1040 $ValenceFreeElectrons = $Atom->GetValenceFreeElectrons(
|
|
|
1041 $ExcludeFreeRadicalElectrons);
|
|
|
1042
|
|
|
1043 Returns valence frees electrons for an Atom in a molecule. It
|
|
|
1044 corresponds to:
|
|
|
1045
|
|
|
1046 ValenceElectrons - Valence
|
|
|
1047 or
|
|
|
1048 ValenceElectrons - NumOfMissingHydrogens - SumOfBondOrders - FormalCharge
|
|
|
1049
|
|
|
1050 Free radical electrons are included in the valence free electrons
|
|
|
1051 count by default.
|
|
|
1052
|
|
|
1053 Examples:
|
|
|
1054
|
|
|
1055 NH3: ValenceFreeElectrons = 5 - 3 = 5 - 3 - 0 - 0 = 2
|
|
|
1056 NH2: ValenceFreeElectrons = 5 - 3 = 5 - 2 - 1 - 0 = 2
|
|
|
1057 NH4+; ValenceFreeElectrons = 5 - 5 = 5 - 4 - 0 - 1 = 0
|
|
|
1058 NH3+; ValenceFreeElectrons = 5 - 5 = 5 - 3 - 1 - 1 = 0
|
|
|
1059 C(=O)O- : ValenceFreeElectrons on O- = 6 - 0 = 6 - 1 - 0 - (-1) = 6
|
|
|
1060 C(=O)O- : ValenceFreeElectrons on =O = 6 - 2 = 6 - 2 - 0 - 0 = 4
|
|
|
1061
|
|
|
1062 GetX
|
|
|
1063 $X = $Atom->GetX();
|
|
|
1064
|
|
|
1065 Returns value of X-coordinate for an *Atom*.
|
|
|
1066
|
|
|
1067 GetXYZ
|
|
|
1068 @XYZ = $Atom->GetXYZ();
|
|
|
1069 $XYZRef = $Atom->GetXYZ();
|
|
|
1070
|
|
|
1071 Returns an array or a reference to an array containing values for
|
|
|
1072 *Atom* coordinates.
|
|
|
1073
|
|
|
1074 GetXYZVector
|
|
|
1075 $XYZVector = $Atom->GetXYZVector();
|
|
|
1076
|
|
|
1077 Returns a *Vector* object containing values for *Atom* coordinates
|
|
|
1078
|
|
|
1079 GetY
|
|
|
1080 $Y = $Atom->GetY();
|
|
|
1081
|
|
|
1082 Returns value of Y-coordinate for an *Atom*.
|
|
|
1083
|
|
|
1084 GetZ
|
|
|
1085 $Z = $Atom->GetZ();
|
|
|
1086
|
|
|
1087 Returns value of Z-coordinate for an *Atom*.
|
|
|
1088
|
|
|
1089 IsAmideCarbon
|
|
|
1090 $Status = $Atom->IsAmideCarbon();
|
|
|
1091
|
|
|
1092 Returns 1 or 0 based on whether it's amide carbon *Atom*.
|
|
|
1093
|
|
|
1094 An amide group is defineds as:
|
|
|
1095
|
|
|
1096 R-C(=O)-N(-R')-R''
|
|
|
1097
|
|
|
1098 where:
|
|
|
1099
|
|
|
1100 o R = Hydrogen or groups of atoms attached through carbon
|
|
|
1101 o R' = Hydrogens or groups of atoms attached through carbon or
|
|
|
1102 hetro atoms
|
|
|
1103 o R'' = Hydrogens or groups of atoms attached through carbon or
|
|
|
1104 hetro atoms
|
|
|
1105
|
|
|
1106 IsAmideNitrogen
|
|
|
1107 $Status = $Atom->IsAmideNitrogen();
|
|
|
1108
|
|
|
1109 Returns 1 or 0 based on whether it's amide nitrogen *Atom*.
|
|
|
1110
|
|
|
1111 IsAromatic
|
|
|
1112 $Status = $Atom->IsAromatic();
|
|
|
1113
|
|
|
1114 Returns 1 or 0 based on whether it's an aromatic *Atom*.
|
|
|
1115
|
|
|
1116 IsArsenic
|
|
|
1117 $Status = $Atom->IsArsenic();
|
|
|
1118
|
|
|
1119 Returns 1 or 0 based on whether it's an arsenic *Atom*.
|
|
|
1120
|
|
|
1121 IsBondedToAtom
|
|
|
1122 $Status = $Atom->IsBondedToAtom($OtherAtom);
|
|
|
1123
|
|
|
1124 Returns 1 or 0 based on whether *Atom* is bonded to *OtherAtom*.
|
|
|
1125
|
|
|
1126 IsBromine
|
|
|
1127 $Status = $Atom->IsBromine();
|
|
|
1128
|
|
|
1129 Returns 1 or 0 based on whether it's a bromine *Atom*.
|
|
|
1130
|
|
|
1131 IsCarbon
|
|
|
1132 $Status = $Atom->IsCarbon();
|
|
|
1133
|
|
|
1134 Returns 1 or 0 based on whether it's a carbon *Atom*.
|
|
|
1135
|
|
|
1136 IsCarboxylCarbon
|
|
|
1137 $Status = $Atom->IsCarboxylCarbon();
|
|
|
1138
|
|
|
1139 Returns 1 or 0 based on whether it's a carboxyl carbon atom in
|
|
|
1140 carboxyl group: R-C(=O)-OH.
|
|
|
1141
|
|
|
1142 IsCarboxylOxygen
|
|
|
1143 $Status = $Atom->IsCarboxylOxygen();
|
|
|
1144
|
|
|
1145 Returns 1 or 0 based on whether it's a carboxyl oxygen atom in
|
|
|
1146 carboxyl group: R-C(=O)-OH.
|
|
|
1147
|
|
|
1148 IsCarboxylateCarbon
|
|
|
1149 $Status = $Atom->IsCarboxylateCarbon();
|
|
|
1150
|
|
|
1151 Returns 1 or 0 based on whether it's a carboxylate carbon atom in
|
|
|
1152 carboxyl group: R-C(=O)-O-.
|
|
|
1153
|
|
|
1154 IsCarboxylateOxygen
|
|
|
1155 $Status = $Atom->IsCarboxylateOxygen();
|
|
|
1156
|
|
|
1157 Returns 1 or 0 based on whether it's a carboxylate oxygen atom in
|
|
|
1158 carboxyl group: R-C(=O)-O-.
|
|
|
1159
|
|
|
1160 IsChlorine
|
|
|
1161 $Status = $Atom->IsChlorine();
|
|
|
1162
|
|
|
1163 Returns 1 or 0 based on whether it's a chlorine *Atom*.
|
|
|
1164
|
|
|
1165 IsFluorine
|
|
|
1166 $Status = $Atom->IsFluorine();
|
|
|
1167
|
|
|
1168 Returns 1 or 0 based on whether it's a fluorine *Atom*.
|
|
|
1169
|
|
|
1170 IsFunctionalClassType
|
|
|
1171 $Status =$Atom->IsFunctionalClassType($Type);
|
|
|
1172
|
|
|
1173 Returns 1 or 0 based on whether it's a specified functional class
|
|
|
1174 *Type*.
|
|
|
1175
|
|
|
1176 The current release of MayaChemTools supports following
|
|
|
1177 abbreviations and descriptive names for *FunctionalClassType*:
|
|
|
1178
|
|
|
1179 HBD: HydrogenBondDonor
|
|
|
1180 HBA: HydrogenBondAcceptor
|
|
|
1181 PI : PositivelyIonizable
|
|
|
1182 NI : NegativelyIonizable
|
|
|
1183 Ar : Aromatic
|
|
|
1184 Hal : Halogen
|
|
|
1185 H : Hydrophobic
|
|
|
1186 RA : RingAtom
|
|
|
1187 CA : ChainAtom
|
|
|
1188
|
|
|
1189 The following definitions are used to determine functional class
|
|
|
1190 types: [ Ref 60-61, Ref 65-66 ]:
|
|
|
1191
|
|
|
1192 HydrogenBondDonor: NH, NH2, OH
|
|
|
1193 HydrogenBondAcceptor: N[!H], O
|
|
|
1194 PositivelyIonizable: +, NH2
|
|
|
1195 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1196
|
|
|
1197 IsGuadiniumCarbon
|
|
|
1198 $Status = $Atom->IsGuadiniumCarbon();
|
|
|
1199
|
|
|
1200 Returns 1 or 0 based on whether it's a guadinium carbon in guadinium
|
|
|
1201 group by checking its neighbors for a nitrogen in guadinium group.
|
|
|
1202
|
|
|
1203 IsGuadiniumNitrogen
|
|
|
1204 $Status = $Atom->IsGuadiniumNitrogen();
|
|
|
1205
|
|
|
1206 Returns 1 or 0 based on whether it's a guadinium nitrogen in
|
|
|
1207 guadinium group.
|
|
|
1208
|
|
|
1209 A guadinium group is defined as:
|
|
|
1210
|
|
|
1211 R2N-C(=NR)-(NR2) or R2N-C(=NR2+)-(NR2)
|
|
|
1212
|
|
|
1213 where:
|
|
|
1214
|
|
|
1215 o R = Hydrogens or group of atoms attached through carbon
|
|
|
1216 o Only one of the three nitrogens has a double bond to carbon
|
|
|
1217 and has optional formal charge allowing it to be neutral or charged state
|
|
|
1218
|
|
|
1219 IsHBondAcceptor
|
|
|
1220 $Status =$Atom->IsHBondAcceptor();
|
|
|
1221 $Status =$Atom->IsHBondAcceptor($HydrogenBondsType);
|
|
|
1222
|
|
|
1223 Returns 1 or 0 based on whether it's a hydrogen bond acceptor
|
|
|
1224 *Atom*.
|
|
|
1225
|
|
|
1226 IsHBondDonor
|
|
|
1227 $Status =$Atom->IsHBondDonor();
|
|
|
1228 $Status =$Atom->IsHBondDonor($HydrogenBondsType);
|
|
|
1229
|
|
|
1230 Returns 1 or 0 based on whether it's a hydrogen bond donor *Atom*.
|
|
|
1231
|
|
|
1232 IsHydrogenBondAcceptor
|
|
|
1233 $Status =$Atom->IsHydrogenBondAcceptor();
|
|
|
1234 $Status =$Atom->IsHydrogenBondAcceptor($HydrogenBondsType);
|
|
|
1235
|
|
|
1236 Returns 1 or 0 based on whether it's a hydrogen bond acceptor
|
|
|
1237 *Atom*.
|
|
|
1238
|
|
|
1239 IsHydrogenBondDonor
|
|
|
1240 $Status =$Atom->IsHydrogenBondDonor();
|
|
|
1241 $Status =$Atom->IsHydrogenBondDonor($HydrogenBondsType);
|
|
|
1242
|
|
|
1243 Returns 1 or 0 based on whether it's a hydrogen bond donor *Atom*.
|
|
|
1244
|
|
|
1245 The current release of MayaChemTools supports identification of two
|
|
|
1246 types of hydrogen bond donor and acceptor atoms with these names:
|
|
|
1247
|
|
|
1248 HBondsType1 or HydrogenBondsType1
|
|
|
1249 HBondsType2 or HydrogenBondsType2
|
|
|
1250
|
|
|
1251 The names of these hydrogen bond types are rather arbitrary.
|
|
|
1252 However, their definitions have specific meaning and are as follows:
|
|
|
1253
|
|
|
1254 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:
|
|
|
1255
|
|
|
1256 Donor: NH, NH2, OH - Any N and O with available H
|
|
|
1257 Acceptor: N[!H], O - Any N without available H and any O
|
|
|
1258
|
|
|
1259 HydrogenBondsType2 [ Ref 91 ]:
|
|
|
1260
|
|
|
1261 Donor: NH, NH2, OH - N and O with available H
|
|
|
1262 Acceptor: N, O - And N and O
|
|
|
1263
|
|
|
1264 By default, *HydrogenBondsType1* is used to calculate number
|
|
|
1265 hydrogen bond donor and acceptor atoms. *HydrogenBondsType2*
|
|
|
1266 corresponds to RuleOf5 definition of hydrogen bond donors and
|
|
|
1267 acceptors.
|
|
|
1268
|
|
|
1269 IsHalogen
|
|
|
1270 $Status =$Atom->IsHalogen();
|
|
|
1271
|
|
|
1272 Returns 1 or 0 based on whether it's a halogen *Atom*.
|
|
|
1273
|
|
|
1274 IsHeteroAtom
|
|
|
1275 $Status = $Atom->IsHeteroAtom();
|
|
|
1276
|
|
|
1277 Returns 0 or 1 based on whether it's a hetro *Atom*. Following atoms
|
|
|
1278 are considered hetro atoms: N, O, F, P, S, Cl, Br, I.
|
|
|
1279
|
|
|
1280 IsHydrogen
|
|
|
1281 $Status = $Atom->IsHydrogen();
|
|
|
1282
|
|
|
1283 Returns 1 or 0 based on whether it's a hydrogen *Atom*.
|
|
|
1284
|
|
|
1285 IsHydrophobic
|
|
|
1286 $Status =$Atom->IsHydrophobic();
|
|
|
1287
|
|
|
1288 Returns 1 or 0 based on whether it's a hydrophobic *Atom*.
|
|
|
1289
|
|
|
1290 IsInRing
|
|
|
1291 $Status = $Atom->IsInRing();
|
|
|
1292
|
|
|
1293 Returns 1 or 0 based on whether *Atom* is present in a ring.
|
|
|
1294
|
|
|
1295 IsInRingOfSize
|
|
|
1296 $Status = $Atom->IsInRingOfSize($Size);
|
|
|
1297
|
|
|
1298 Returns 1 or 0 based on whether *Atom* is present in a ring of
|
|
|
1299 specific *Size*.
|
|
|
1300
|
|
|
1301 IsIodine
|
|
|
1302 $Status = $Atom->IsIodine();
|
|
|
1303
|
|
|
1304 Returns 1 or 0 based on whether it's an iodine *Atom*.
|
|
|
1305
|
|
|
1306 IsIsotope
|
|
|
1307 $Status =$Atom->IsIsotope();
|
|
|
1308
|
|
|
1309 Returns 1 or 0 based on whether it's an isotope *Atom*.
|
|
|
1310
|
|
|
1311 IsLipophilic
|
|
|
1312 $Status =$Atom->IsLipophilic();
|
|
|
1313
|
|
|
1314 Returns 1 or 0 based on whether it's a lipophilic *Atom*.
|
|
|
1315
|
|
|
1316 IsMetallic
|
|
|
1317 $Status = $Atom->IsMetallic();
|
|
|
1318
|
|
|
1319 Returns 1 or 0 based on whether it's a metallic *Atom*.
|
|
|
1320
|
|
|
1321 IsNegativelyIonizable
|
|
|
1322 $Status =$Atom->IsNegativelyIonizable();
|
|
|
1323
|
|
|
1324 Returns 1 or 0 based on whether it's a negatively ionizable atom
|
|
|
1325 *Atom*.
|
|
|
1326
|
|
|
1327 IsNitrogen
|
|
|
1328 $Status = $Atom->IsNitrogen();
|
|
|
1329
|
|
|
1330 Returns 1 or 0 based on whether it's a nitrogen *Atom*.
|
|
|
1331
|
|
|
1332 IsNonCarbonOrHydrogen
|
|
|
1333 $Status =$Atom->IsNonCarbonOrHydrogen();
|
|
|
1334
|
|
|
1335 Returns 1 or 0 based on whether it's not a carbon or hydrogen
|
|
|
1336 *Atom*.
|
|
|
1337
|
|
|
1338 IsNotInRing
|
|
|
1339 $Status = $Atom->IsNotInRing();
|
|
|
1340
|
|
|
1341 Returns 1 or 0 based on whether *Atom* is not present in a ring.
|
|
|
1342
|
|
|
1343 IsOnlyInOneRing
|
|
|
1344 $Status = $Atom->IsOnlyInOneRing();
|
|
|
1345
|
|
|
1346 Returns 1 or 0 based on whether *Atom* is only present in one ring.
|
|
|
1347
|
|
|
1348 IsOxygen
|
|
|
1349 $Status = $Atom->IsOxygen();
|
|
|
1350
|
|
|
1351 Returns 0 or 1 based on whether it's an oxygen *Atom*.
|
|
|
1352
|
|
|
1353 IsPhosphorus
|
|
|
1354 $Status = $Atom->IsPhosphorus();
|
|
|
1355
|
|
|
1356 Returns 0 or 1 based on whether it's a phosphorus *Atom*.
|
|
|
1357
|
|
|
1358 IsPhosphateOxygen
|
|
|
1359 $Status = $Atom->IsPhosphateOxygen();
|
|
|
1360
|
|
|
1361 Returns 1 or 0 based on whether it's a phosphate oxygen in phosphate
|
|
|
1362 group.
|
|
|
1363
|
|
|
1364 A phosphate group is defined as:
|
|
|
1365
|
|
|
1366 AO-(O=)P(-OA)-OA
|
|
|
1367
|
|
|
1368 Where:
|
|
|
1369
|
|
|
1370 A - Any group of atoms including hydrogens
|
|
|
1371
|
|
|
1372 IsPhosphatePhosphorus
|
|
|
1373 $Status = $Atom->IsPhosphatePhosphorus();
|
|
|
1374
|
|
|
1375 Returns 1 or 0 based on whether it's a phosphate phosphorus in
|
|
|
1376 phosphate group.
|
|
|
1377
|
|
|
1378 IsPolarAtom
|
|
|
1379 $Status = $Atom->IsPolarAtom();
|
|
|
1380
|
|
|
1381 Returns 0 or 1 based on whether it's a polar *Atom*. Following atoms
|
|
|
1382 are considered polar atoms: N, O, P, S.
|
|
|
1383
|
|
|
1384 IsPolarHydrogen
|
|
|
1385 $Status = $Atom->IsPolarHydrogen();
|
|
|
1386
|
|
|
1387 Returns 0 or 1 based on whether it's a hydrogen *Atom* bonded to a
|
|
|
1388 polar atom.
|
|
|
1389
|
|
|
1390 IsPositivelyIonizable
|
|
|
1391 $Status =$Atom->IsPositivelyIonizable();
|
|
|
1392
|
|
|
1393 Returns 1 or 0 based on whether it's a positively ionizable *Atom*.
|
|
|
1394
|
|
|
1395 IsSaturated
|
|
|
1396 $Status = $Atom->IsSaturated();
|
|
|
1397
|
|
|
1398 Returns 1 or 0 based on whether it's a saturated *Atom*. An atom
|
|
|
1399 attached to other atoms with only single bonds is considered a
|
|
|
1400 saturated atom.
|
|
|
1401
|
|
|
1402 IsSelenium
|
|
|
1403 $Status = $Atom->IsSelenium();
|
|
|
1404
|
|
|
1405 Returns 0 or 1 based on whether it's a selenium *Atom*.
|
|
|
1406
|
|
|
1407 IsStereoCenter
|
|
|
1408 $Status = $Atom->IsStereoCenter();
|
|
|
1409
|
|
|
1410 Returns 0 or 1 based on whether it's marked as a stero center *Atom*
|
|
|
1411 by explicit setting of *StereoCenter* atom propert to value of *1*.
|
|
|
1412
|
|
|
1413 IsSilicon
|
|
|
1414 $Status = $Atom->IsSilicon();
|
|
|
1415
|
|
|
1416 Returns 0 or 1 based on whether it's a silicon *Atom*.
|
|
|
1417
|
|
|
1418 IsSulfur
|
|
|
1419 $Status = $Atom->IsSulfur();
|
|
|
1420
|
|
|
1421 Returns 0 or 1 based on whether it's a sulfur *Atom*.
|
|
|
1422
|
|
|
1423 IsSulphur
|
|
|
1424 $Status = $Atom->IsSulphur();
|
|
|
1425
|
|
|
1426 Returns 0 or 1 based on whether it's a sulfur *Atom*.
|
|
|
1427
|
|
|
1428 IsTellurium
|
|
|
1429 $Status = $Atom->IsTellurium();
|
|
|
1430
|
|
|
1431 Returns 0 or 1 based on whether it's a tellurium *Atom*.
|
|
|
1432
|
|
|
1433 IsTerminal
|
|
|
1434 $Status = $Atom->IsTerminal();
|
|
|
1435
|
|
|
1436 Returns 0 or 1 based on whether it's a terminal *Atom* attached to
|
|
|
1437 no more than one non-hydrogen atom.
|
|
|
1438
|
|
|
1439 IsUnsaturated
|
|
|
1440 $Status = $Atom->IsUnsaturated();
|
|
|
1441
|
|
|
1442 Returns 1 or 0 based on whether it's as unsaturated *Atom*. An atom
|
|
|
1443 attached to other atoms with at least one non-single bond is
|
|
|
1444 considered an unsaturated atom.
|
|
|
1445
|
|
|
1446 IsTopologicalPharmacophoreType
|
|
|
1447 $Status =$Atom->IsTopologicalPharmacophoreType();
|
|
|
1448
|
|
|
1449 Returns 1 or 0 based on whether it's any of the supportyed
|
|
|
1450 topological pharmacophore *Atom* type. See *IsFunctionalClassType*
|
|
|
1451 for a list of supported types.
|
|
|
1452
|
|
|
1453 SetAtomSymbol
|
|
|
1454 $Atom->SetAtomSymbol($AtomicSymbol);
|
|
|
1455
|
|
|
1456 Sets atom symbol for *Atom* and returns *Atom* object. The
|
|
|
1457 appropriate atomic number is also set automatically.
|
|
|
1458
|
|
|
1459 SetAtomicNumber
|
|
|
1460 $Atom->SetAtomicNumber($AtomicNumber);
|
|
|
1461
|
|
|
1462 Sets atomic number for *Atom* and returns *Atom* object. The
|
|
|
1463 appropriate atom symbol is also set automatically.
|
|
|
1464
|
|
|
1465 SetMassNumber
|
|
|
1466 $Atom->SetMassNumber($MassNumber);
|
|
|
1467
|
|
|
1468 Sets mass number for *Atom* and returns *Atom* object.
|
|
|
1469
|
|
|
1470 SetStereoCenter
|
|
|
1471 $Atom->SetStereoCenter($StereoCenter);
|
|
|
1472
|
|
|
1473 Sets stereo center for *Atom* and returns *Atom* object.
|
|
|
1474
|
|
|
1475 SetStereochemistry
|
|
|
1476 $Atom->SetStereochemistry($Stereochemistry);
|
|
|
1477
|
|
|
1478 Sets stereo chemistry for *Atom* and returns *Atom* object.
|
|
|
1479
|
|
|
1480 SetX
|
|
|
1481 $Atom->SetX($Value);
|
|
|
1482
|
|
|
1483 Sets X-coordinate value for *Atom* and returns *Atom* object.
|
|
|
1484
|
|
|
1485 SetXYZ
|
|
|
1486 $Atom->SetXYZ(@XYZValues);
|
|
|
1487 $Atom->SetXYZ($XYZValuesRef);
|
|
|
1488 $Atom->SetXYZ($XYZVector);
|
|
|
1489
|
|
|
1490 Sets *Atom* coordinates using an array, reference to an array or a
|
|
|
1491 *Vector* object and returns *Atom* object.
|
|
|
1492
|
|
|
1493 SetY
|
|
|
1494 $Atom->SetY($Value);
|
|
|
1495
|
|
|
1496 Sets Y-coordinate value for *Atom* and returns *Atom* object.
|
|
|
1497
|
|
|
1498 SetZ
|
|
|
1499 $Atom->SetZ($Value);
|
|
|
1500
|
|
|
1501 Sets Z-coordinate value for *Atom* and returns *Atom* object.
|
|
|
1502
|
|
|
1503 StringifyAtom
|
|
|
1504 $AtomString = $Atom->StringifyAtom();
|
|
|
1505
|
|
|
1506 Returns a string containing information about *Atom* object.
|
|
|
1507
|
|
|
1508 AUTHOR
|
|
|
1509 Manish Sud <msud@san.rr.com>
|
|
|
1510
|
|
|
1511 SEE ALSO
|
|
|
1512 Bond.pm, Molecule.pm, MoleculeFileIO.pm
|
|
|
1513
|
|
|
1514 COPYRIGHT
|
|
|
1515 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
1516
|
|
|
1517 This file is part of MayaChemTools.
|
|
|
1518
|
|
|
1519 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
1520 under the terms of the GNU Lesser General Public License as published by
|
|
|
1521 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
1522 your option) any later version.
|
|
|
1523
|
