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1 NAME
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2 Molecule - Molecule class
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3
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4 SYNOPSIS
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5 use Molecule;
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6
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7 use Molecule qw(:all);
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8
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9 DESCRIPTION
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10 Molecule class provides the following methods:
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11
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12 new, AddAtom, AddAtoms, AddBond, AddBonds, AddHydrogens,
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13 AddPolarHydrogens, ClearRings, Copy, DeleteAromaticity, DeleteAtom,
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14 DeleteAtoms, DeleteBond, DeleteBonds, DeleteHydrogens,
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15 DeletePolarHydrogens, DetectAromaticity, DetectRings,
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16 FormatElementalCompositionInformation, GetAllAtomPaths,
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17 GetAllAtomPathsStartingAt, GetAllAtomPathsStartingAtWithLength,
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18 GetAllAtomPathsStartingAtWithLengthUpto, GetAllAtomPathsWithLength,
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19 GetAllAtomPathsWithLengthUpto, GetAromaticRings, GetAromaticityModel,
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20 GetAtomNeighborhoods, GetAtomNeighborhoodsWithRadiusUpto,
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21 GetAtomNeighborhoodsWithSuccessorAtoms,
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22 GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto, GetAtomPathBonds,
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23 GetAtomPaths, GetAtomPathsBetween, GetAtomPathsStartingAt,
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24 GetAtomPathsStartingAtWithLength, GetAtomPathsStartingAtWithLengthUpto,
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25 GetAtomPathsWithLength, GetAtomPathsWithLengthUpto, GetAtoms, GetBonds,
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26 GetCharge, GetConnectedComponents, GetConnectedComponentsAtoms,
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27 GetDimensionality, GetElementalComposition, GetElementsAndNonElements,
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28 GetExactMass, GetFormalCharge, GetFreeRadicalElectrons,
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29 GetFusedAndNonFusedRings, GetLargestConnectedComponent,
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30 GetLargestConnectedComponentAtoms, GetLargestRing, GetMolecularFormula,
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31 GetMolecularWeight, GetNumOfAromaticRings, GetNumOfAtoms, GetNumOfBonds,
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32 GetNumOfConnectedComponents, GetNumOfElementsAndNonElements,
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33 GetNumOfHeavyAtoms, GetNumOfHydrogenAtoms, GetNumOfMissingHydrogenAtoms,
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34 GetNumOfNonHydrogenAtoms, GetNumOfRings, GetNumOfRingsWithEvenSize,
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35 GetNumOfRingsWithOddSize, GetNumOfRingsWithSize,
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36 GetNumOfRingsWithSizeGreaterThan, GetNumOfRingsWithSizeLessThan,
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37 GetRingBonds, GetRingBondsFromRings, GetRings, GetRingsWithEvenSize,
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38 GetRingsWithOddSize, GetRingsWithSize, GetRingsWithSizeGreaterThan,
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39 GetRingsWithSizeLessThan, GetSizeOfLargestRing, GetSizeOfSmallestRing,
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40 GetSmallestRing, GetSpinMultiplicity, GetSupportedAromaticityModels,
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41 GetTopologicallySortedAtoms, GetValenceModel, HasAromaticAtomsInRings,
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42 HasAromaticAtomsNotInRings, HasAromaticRings, HasAtom, HasBond,
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43 HasFusedRings, HasNoRings, HasOnlyOneRing, HasRings, IsAromatic,
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44 IsMolecule, IsRingAromatic, IsSupportedAromaticityModel,
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45 IsThreeDimensional, IsTwoDimensional, KeepLargestComponent,
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46 KekulizeAromaticAtoms, NewAtom, NewBond, SetActiveRings,
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47 SetAromaticityModel, SetID, SetValenceModel, StringifyMolecule
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48
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49 The following methods can also be used as functions:
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50
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51 FormatElementalCompositionInformation, IsMolecule
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52
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53 Molecule class is derived from ObjectProperty base class which provides
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54 methods not explicitly defined in Molecule or ObjectProperty class using
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55 Perl's AUTOLOAD functionality. These methods are generated on-the-fly
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56 for a specified object property:
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57
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58 Set<PropertyName>(<PropertyValue>);
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59 $PropertyValue = Get<PropertyName>();
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60 Delete<PropertyName>();
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61
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62 METHODS
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63 new
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64 $NewMolecule = new Molecule([%PropertyNameAndValues]);
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65
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66 Using specified *Atom* property names and values hash, new method
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67 creates a new object and returns a reference to newly created Atom
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68 object. By default, the following properties are initialized:
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69
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70 ID = SequentialObjectID
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71 Name = "Molecule <SequentialObjectID>"
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72
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73 Examples:
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74
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75 $Molecule = new Molecule();
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76
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77 $WaterMolecule = new Molecule('Name' => 'Water');
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78
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79 $Oxygen = new Atom('AtomSymbol' => 'O', 'XYZ' => [0, 0, 0]);
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80 $Hydrogen1 = new Atom('AtomSymbol' => 'H',
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81 'XYZ' => [0.7144, 0.4125, 0]);
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82 $Hydrogen2 = new Atom('AtomSymbol' => 'H',
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83 'XYZ' => [1.1208, -0.2959, 0]);
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84 $WaterMolecule->AddAtoms($Oxygen, $Hydrogen1, $Hydrogen2);
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85
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86 $Bond1 = new Bond('Atoms' => [$Oxygen, $Hydrogen1],
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87 'BondOrder' => 1);
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88 $Bond2 = new Bond('Atoms' => [$Oxygen, $Hydrogen2],
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89 'BondOrder' => 1);
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90 $WaterMolecule->AddBonds($Bond1, $Bond2);
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91
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92 AddAtom
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93 $Molecule->AddAtom($Atom);
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94
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95 Adds an *Atom* to a *Molecule* and returns *Molecule*.
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96
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97 AddAtoms
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98 $Molecule->AddAtoms(@Atoms);
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99
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100 Adds *Atoms* to a *Molecule* and returns *Molecule*.
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101
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102 AddBond
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103 $Molecule->AddBond($Bond);
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104
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105 Adds a *Bond* to a *Molecule* and returns *Molecule*.
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106
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107 AddBonds
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108 $Molecule->AddBonds(@Bonds);
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109
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110 Adds *Bonds* to a *Molecule* and returns *Molecule*.
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111
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112 AddHydrogens
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113 $NumOfHydrogensAdded = $Molecule->AddHydrogens();
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114
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115 Adds hydrogens to each atom in a *Molecule* and returns total number
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116 of hydrogens added. The current release of MayaChemTools doesn't
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117 assign hydrogen positions.
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118
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119 AddPolarHydrogens
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120 $NumOfHydrogensAdded = $Molecule->AddPolarHydrogens();
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121
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122 Adds hydrogens to each polar atom - N, O, P or S - in a *Molecule*
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123 and returns total number of polar hydrogens added. The current
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124 release of MayaChemTools doesn't assign hydrogen positions.
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125
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126 ClearRings
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127 $Molecule->ClearRings();
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128
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129 Deletes all rings associated with *Molecule* and returns *Molecule*.
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130
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131 Copy
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132 $MoleculeCopy = $Molecule->Copy();
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133
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134 Copies *Molecule* and its associated data using Storable::dclone and
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135 returns a new Molecule object.
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136
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137 DeleteAromaticity
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138 $Molecule->DeleteAromaticity();
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139
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140 Deletes aromatic property associated with all atoms and bonds in a
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141 *Molecule* and returns *Molecule*.
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142
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143 DeleteAtom
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144 $Molecule->DeleteAtom($Atom);
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145
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146 Deletes *Atom* from a *Molecule* and returns *Molecule*.
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147
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148 DeleteAtoms
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149 $Molecule->DeleteAtoms(@Atoms);
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150
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151 Deletes *Atoms* from a *Molecule* and returns *Molecule*.
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152
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153 DeleteBond
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154 $Molecule->DeleteBond($Bond);
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155
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156 Deletes *Bond* from a *Molecule* and returns *Molecule*.
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157
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158 DeleteBonds
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159 $Molecule->DeleteBonds(@Bonds);
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160
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161 Deletes *Bonds* from a *Molecule* and returns *Molecule*.
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162
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163 DeleteHydrogens
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164 $NumOfHydrogensDeleted = $Molecule->DeleteHydrogens();
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165
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166 Removes hydrogens from each atom in a *Molecule* and returns total
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167 number of hydrogens deleted.
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168
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169 DeletePolarHydrogens
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170 $NumOfHydrogensDeleted = $Molecule->DeletePolarHydrogens();
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171
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172 Removes hydrogens to each polar atom - N, O, P or S - in a
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173 *Molecule* and returns total number of polar hydrogens deleted.
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174
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175 DetectAromaticity
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176 $Molecule->DetectAromaticity();
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177
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178 Associates *Aromatic* property to atoms and bonds involved in
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179 aromatic rings or ring systems in a *Molecule* and returns
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180 *Molecule*.
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181
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182 This method assumes the ring detection has already been perfomed
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183 using DetectRings. And any existing *Aromatic* property associated
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184 with atoms and bonds is deleted before performing aromaticity
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185 detection.
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186
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187 What is aromaticity? [ Ref 124 ] It's in the code of the
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188 implementer, did you say? Agree. The implementation of aromaticity
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189 varies widely across different packages [ Ref 125 ]; additionally,
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190 the implementation details are not always completely available, and
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191 it's not possible to figure out the exact implementation of
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192 aromaticity across various packages. Using the publicly available
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193 information, however, one can try to reproduce the available results
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194 to the extent possible, along with parameterizing all the control
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195 parameters used to implement different aromaticity models, and
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196 that's exactly what the current release of MayaChemTools does.
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197
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198 The implementation of aromaticity corresponding to various
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199 aromaticity models in MayaChemTools package is driven by an external
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200 CSV file AromaticityModelsData.csv, which is distributed with the
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201 package and is available in lib/data directory. The CSV files
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202 contains names of supported aromaticity models, along with various
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203 control parameters and their values. This file is loaded and
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204 processed during instantiation of Molecule class and data
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205 corresponding to specific aromaticity model are used to detect
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206 aromaticity for that model. Any new aromaticity model added to the
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207 aromaticity data file, using different combinations of values for
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208 existing control parameters, would work without any changes to the
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209 code; the addition of any new control parameters, however, requires
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210 its implementation in the code used to calculate number of pi
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211 electrons available towards delocalization in a ring or ring
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212 systems.
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213
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214 The current release of MayaChemTools package supports these
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215 aromaticity models: MDLAromaticityModel, TriposAromaticityModel,
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216 MMFFAromaticityModel, ChemAxonBasicAromaticityModel,
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217 ChemAxonGeneralAromaticityModel, DaylightAromaticityModel,
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218 MayaChemToolsAromaticityModel.
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219
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220 The current list of control parameters available to detect
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221 aromaticity corresponding to different aromaticity models are:
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222 AllowHeteroRingAtoms, HeteroRingAtomsList,
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223 AllowExocyclicDoubleBonds, AllowHomoNuclearExocyclicDoubleBonds,
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224 AllowElectronegativeRingAtomExocyclicDoubleBonds,
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225 AllowRingAtomFormalCharge, AllowHeteroRingAtomFormalCharge,
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226 MinimumRingSize. The values for these control parameters are
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227 specified in AromaticityModelsData.csv file.
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228
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229 Although definition of aromaticity differs across various
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230 aromaticity models, a ring or a ring system containing 4n + 2 pi
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231 electrons (Huckel's rule) corresponding to alternate single and
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232 double bonds, in general, is considered aromatic.
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233
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234 The available valence free electrons on heterocyclic ring atoms,
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235 involved in two single ring bonds, are also allowed to participate
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236 in pi electron delocalizaiton for most of the supported aromaticity
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237 models.
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238
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239 The presence of exocyclic terminal double bond on ring atoms
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240 involved in pi electron delocalization is only allowed for some of
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241 the aromaticity models. Additionally, the type atoms involved in
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242 exocyclic terminal double bonds may result in making a ring or ring
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243 system non-aromatic.
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244
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245 For molecules containing fused rings, each fused ring set is
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246 considered as one aromatic system for counting pi electrons to
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247 satisfy Huckel's rule; In case of a failure, rings in fused set are
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248 treated individually for aromaticity detection. Additionally,
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249 non-fused rings are handled on their own during aromaticity
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250 detection.
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251
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252 DetectRings
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253 $Molecule->DetectRings();
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254
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255 Detects rings in a *Molecule* and returns *Molecule*. Ring detection
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256 is performed using DetectCycles method avaible in Graph class which
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257 in turn uses methods available Graph::CyclesDetection class.
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258 Graph::CyclesDetection class implements collapsing path graph [Ref
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259 31] methodology to detect all cycles in a graph.
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260
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261 FormatElementalCompositionInformation
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262 $FormattedInfo = $Molecule->FormatElementalCompositionInformation(
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263 $ElementsRef, $ElementCompositionRef,
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264 [$Precision]);
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265 $FormattedInfo = Molecule::FormatElementalCompositionInformation(
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266 $ElementsRef, $ElementCompositionRef,
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267 [$Precision]);
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268
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269 Using *ElementsRef* and *ElementCompositionRef* arrays referneces
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270 containg informatio about elements and their composition, formats
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271 elemental composition information and returns a *FormattedInfo*
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272 string. Defaule *Precision* value: *2*.
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273
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274 GetAromaticityModel
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275 $AromaticityModel = $Molecule->GetAromaticityModel();
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276
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277 Returns name of AromaticityModel set for *Molecule* corresponding to
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278 AromaticityModel property or default model name of
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279 MayaChemToolsAromaticityModel.
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280
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281 GetAllAtomPaths
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282 $AtomPathsRef = $Molecule->GetAllAtomPaths([$AllowCycles]);
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283
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284 Returns all paths as a reference to an array containing reference to
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285 arrays with path Atom objects.
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286
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287 Path atoms correspond to to all possible paths for each atom in
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288 molecule with all possible lengths and sharing of bonds in paths
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289 traversed. By default, rings are included in paths. A path
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290 containing a ring is terminated at an atom completing the ring.
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291
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292 For molecule without any rings, this method returns the same set of
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293 atom paths as GetAtomPaths method.
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294
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295 GetAllAtomPathsStartingAt
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296 $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAt($StartAtom,
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297 [$AllowCycles]);
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298
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299 Returns all atom paths starting from *StartAtom* as a reference to
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300 an array containing reference to arrays with path Atom objects.
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301
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302 Path atoms atoms correspond to to all possible paths for specified
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303 atom in molecule with all possible lengths and sharing of bonds in
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304 paths traversed. By default, rings are included in paths. A path
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305 containing a ring is terminated at an atom completing the ring.
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306
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307 For molecule without any rings, this method returns the same set of
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308 atom paths as GetAtomPathsStartingAt method.
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309
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310 GetAllAtomPathsStartingAtWithLength
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311 $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAtWithLength(
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312 $StartAtom, $Length, [$AllowCycles]);
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313
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314 Returns all atom paths starting from *StartAtom* with specified
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315 *Length*as a reference to an array containing reference to arrays
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316 with path Atom objects.
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317
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318 Path atoms atoms correspond to to all possible paths for specified
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319 atom in molecule with all possible lengths and sharing of bonds in
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320 paths traversed. By default, rings are included in paths. A path
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321 containing a ring is terminated at an atom completing the ring.
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322
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323 For molecule without any rings, this method returns the same set of
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324 atom paths as GetAtomPathsStartingAtWithLength method.
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325
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326 GetAllAtomPathsStartingAtWithLengthUpto
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327 $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAtWithLengthUpto(
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328 $StartAtom, $Length, [$AllowCycles]);
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329
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330 Returns atom paths starting from *StartAtom* with length up to
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331 *Length* as a reference to an array containing reference to arrays
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332 with path Atom objects.
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333
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334 Path atoms atoms correspond to all possible paths for specified atom
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335 in molecule with length up to a specified length and sharing of
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336 bonds in paths traversed. By default, rings are included in paths. A
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337 path containing a ring is terminated at an atom completing the ring.
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338
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339 For molecule without any rings, this method returns the same set of
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340 atom paths as *GetAtomPathsStartingAtWithLengthUpto* method.
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341
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342 GetAllAtomPathsWithLength
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343 $AtomPathsRef = $Molecule->GetAllAtomPathsWithLength($Length,
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344 [$AllowCycles]);
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345
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346 Returns all atom paths with specified *Length* as a reference to an
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347 array containing reference to arrays with path Atom objects.
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348
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349 Path atoms correspond to to all possible paths for each atom in
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350 molecule with length up to a specified length and sharing of bonds
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351 in paths traversed. By default, rings are included in paths. A path
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352 containing a ring is terminated at an atom completing the ring.
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353
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354 For molecule without any rings, this method returns the same set of
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355 atom paths as as *GetAtomPathsWithLength* method.
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356
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357 GetAllAtomPathsWithLengthUpto
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358 $AtomPathsRef = $Molecule->GetAllAtomPathsWithLengthUpto($Length,
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359 [$AllowCycles]);
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360
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361 Returns all atom paths with length up to *Length* as a reference to
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362 an array containing reference to arrays with path Atom objects.
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363
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364 Path atoms correspond to to all possible paths for each atom in
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365 molecule with length up to a specified length and sharing of bonds
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366 in paths traversed. By default, rings are included in paths. A path
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367 containing a ring is terminated at an atom completing the ring.
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368
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369 For molecule without any rings, this method returns the same set of
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370 atom paths as as *GetAtomPathsWithLengthUpto* method.
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371
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372 GetAromaticRings
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373 @AtomaticRings = $Molecule->GetAromaticRings();
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374
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375 Returns aromatic rings as an array containing references to arrays
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376 of ring *Atom* objects in a *Molecule*.
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377
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378 GetAtomNeighborhoods
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379 @Neighborhoods = $Molecule->GetAtomNeighborhoods($StartAtom);
|
|
|
380
|
|
|
381 Returns atom neighborhoods around a *StartAtom* as an array
|
|
|
382 containing references to arrays with neighborhood *Atom* objects at
|
|
|
383 possible radii.
|
|
|
384
|
|
|
385 GetAtomNeighborhoodsWithRadiusUpto
|
|
|
386 @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithRadiusUpto($StartAtom,
|
|
|
387 $Radius);
|
|
|
388
|
|
|
389 Returns atom neighborhoods around a *StartAtom* as an array
|
|
|
390 containing references to arrays with neighborhood *Atom* objects up
|
|
|
391 to *Radius*.
|
|
|
392
|
|
|
393 GetAtomNeighborhoodsWithSuccessorAtoms
|
|
|
394 @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithSuccessorAtoms(
|
|
|
395 $StartAtom);
|
|
|
396
|
|
|
397 Returns atom neighborhood around a specified *StartAtom*, along with
|
|
|
398 their successor connected atoms, collected at all radii as an array
|
|
|
399 containing references to arrays with first value corresponding to
|
|
|
400 neighborhood atom at a specific radius and second value as reference
|
|
|
401 to an array containing its successor connected atoms.
|
|
|
402
|
|
|
403 For a neighborhood atom at each radius level, the successor
|
|
|
404 connected atoms correspond to the neighborhood atoms at the next
|
|
|
405 radius level. Consequently, the neighborhood atoms at the last
|
|
|
406 radius level don't contain any successor atoms which fall outside
|
|
|
407 the range of specified radius.
|
|
|
408
|
|
|
409 GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto
|
|
|
410 @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto(
|
|
|
411 $StartAtom, $Radius);
|
|
|
412
|
|
|
413 Returns atom neighborhood around a specified *StartAtom*, along with
|
|
|
414 their successor connected atoms, collected upto specified *Radiud*
|
|
|
415 as an array containing references to arrays with first value
|
|
|
416 corresponding to neighborhood atom at a specific radius and second
|
|
|
417 value as reference to an array containing its successor connected
|
|
|
418 atoms.
|
|
|
419
|
|
|
420 For a neighborhood atom at each radius level, the successor
|
|
|
421 connected atoms correspond to the neighborhood atoms at the next
|
|
|
422 radius level. Consequently, the neighborhood atoms at the last
|
|
|
423 radius level don't contain any successor atoms which fall outside
|
|
|
424 the range of specified radius.
|
|
|
425
|
|
|
426 GetAtomPathBonds
|
|
|
427 $Return = $Molecule->GetAtomPathBonds(@PathAtoms);
|
|
|
428
|
|
|
429 Returns an array containing Bond objects corresponding to successive
|
|
|
430 pair of atoms in *PathAtoms*
|
|
|
431
|
|
|
432 GetAtomPaths
|
|
|
433 $AtomPathsRef = $Molecule->GetAtomPaths([$AllowCycles]);
|
|
|
434
|
|
|
435 Returns all paths as a reference to an array containing reference to
|
|
|
436 arrays with path Atom objects.
|
|
|
437
|
|
|
438 Path atoms correspond to to all possible paths for each atom in
|
|
|
439 molecule with all possible lengths and no sharing of bonds in paths
|
|
|
440 traversed. By default, rings are included in paths. A path
|
|
|
441 containing a ring is terminated at an atom completing the ring.
|
|
|
442
|
|
|
443 GetAtomPathsBetween
|
|
|
444 $AtomPathsRef = $Molecule->GetAtomPathsBetween($StartAtom, $EndAtom);
|
|
|
445
|
|
|
446 Returns all paths as between *StartAtom* and *EndAtom* as a
|
|
|
447 reference to an array containing reference to arrays with path Atom
|
|
|
448 objects.
|
|
|
449
|
|
|
450 For molecules with rings, atom paths array contains may contain two
|
|
|
451 paths.
|
|
|
452
|
|
|
453 GetAtomPathsStartingAt
|
|
|
454 $AtomPathsRef = $Molecule->GetAtomPathsStartingAt($StartAtom, [$AllowCycles]);
|
|
|
455
|
|
|
456 Returns paths starting at *StartAtom* as a reference to an array
|
|
|
457 containing reference to arrays with path Atom objects.
|
|
|
458
|
|
|
459 Path atoms correspond to all possible paths for specified atom in
|
|
|
460 molecule with all possible lengths and no sharing of bonds in paths
|
|
|
461 traversed. By default, rings are included in paths. A path
|
|
|
462 containing a ring is terminated at an atom completing the ring.
|
|
|
463
|
|
|
464 GetAtomPathsStartingAtWithLength
|
|
|
465 $AtomPathsRef = $Molecule->GetAtomPathsStartingAtWithLength($StartAtom,
|
|
|
466 $Length, [$AllowCycles]);
|
|
|
467
|
|
|
468 Returns paths starting at *StartAtom* with length *Length* as a
|
|
|
469 reference to an array containing reference to arrays with path Atom
|
|
|
470 objects.
|
|
|
471
|
|
|
472 Path atoms correspond to all possible paths for specified atom in
|
|
|
473 molecule with length upto a specified length and no sharing of bonds
|
|
|
474 in paths traversed. By default, rings are included in paths. A path
|
|
|
475 containing a ring is terminated at an atom completing the ring.
|
|
|
476
|
|
|
477 GetAtomPathsStartingAtWithLengthUpto
|
|
|
478 $AtomPathsRef = $Molecule->GetAtomPathsStartingAtWithLengthUpto($StartAtom,
|
|
|
479 $Length, [$AllowCycles]);
|
|
|
480
|
|
|
481 Returns paths starting at *StartAtom* with length up to *Length* as
|
|
|
482 a reference to an array containing reference to arrays with path
|
|
|
483 Atom objects.
|
|
|
484
|
|
|
485 Path atoms correspond to all possible paths for specified atom in
|
|
|
486 molecule with length upto a specified length and no sharing of bonds
|
|
|
487 in paths traversed. By default, rings are included in paths. A path
|
|
|
488 containing a ring is terminated at an atom completing the ring.
|
|
|
489
|
|
|
490 GetAtomPathsWithLength
|
|
|
491 $AtomPathsRef = $Molecule->GetAtomPathsWithLength($Length, [$AllowCycles]);
|
|
|
492
|
|
|
493 Returns all paths with specified *Length* as a reference to an array
|
|
|
494 containing reference to arrays with path Atom objects.
|
|
|
495
|
|
|
496 Path atoms correspond to all possible paths for each atom in
|
|
|
497 molecule with length upto a specified length and no sharing of bonds
|
|
|
498 in paths traversed. By default, rings are included in paths. A path
|
|
|
499 containing a ring is terminated at an atom completing the ring.
|
|
|
500
|
|
|
501 GetAtomPathsWithLengthUpto
|
|
|
502 $AtomPathsRef = $Molecule->GetAtomPathsWithLengthUpto($Length, [$AllowCycles]);
|
|
|
503
|
|
|
504 Returns all paths with length up to *Length* as a reference to an
|
|
|
505 array containing reference to arrays with path Atom objects.
|
|
|
506
|
|
|
507 Path atoms correspond to all possible paths for each atom in
|
|
|
508 molecule with length upto a specified length and no sharing of bonds
|
|
|
509 in paths traversed. By default, rings are included in paths. A path
|
|
|
510 containing a ring is terminated at an atom completing the ring.
|
|
|
511
|
|
|
512 GetAtoms
|
|
|
513 @AllAtoms = $Molecule->GetAtoms();
|
|
|
514 @PolarAtoms = $Molecule->GetAtoms('IsPolarAtom');
|
|
|
515
|
|
|
516 $NegateMethodResult = 1;
|
|
|
517 @NonHydrogenAtoms = $Molecule->GetAtoms('IsHydrogenAtom',
|
|
|
518 $NegateMethodResult);
|
|
|
519
|
|
|
520 $AtomsCount = $Molecule->GetAtoms();
|
|
|
521
|
|
|
522 Returns an array of *Atoms* in a *Molecule*. In scalar context, it
|
|
|
523 returns number of atoms. Additionally, Atoms array can be filtered
|
|
|
524 by any user specifiable valid Atom class method and the result of
|
|
|
525 the Atom class method used to filter the atoms can also be negated
|
|
|
526 by an optional negate results flag as third parameter.
|
|
|
527
|
|
|
528 GetBonds
|
|
|
529 @Bonds = $Molecule->GetBonds();
|
|
|
530 $BondsCount = $Molecule->GetBonds();
|
|
|
531
|
|
|
532 Returns an array of *Bonds* in a *Molecule*. In scalar context, it
|
|
|
533 returns number of bonds.
|
|
|
534
|
|
|
535 GetCharge
|
|
|
536 $Charge = $Molecule->GetCharge();
|
|
|
537
|
|
|
538 Returns net charge on a *Molecule* using one of the following two
|
|
|
539 methods: explicitly set Charge property or sum of partial atomic
|
|
|
540 charges on each atom.
|
|
|
541
|
|
|
542 GetConnectedComponents
|
|
|
543 @ConnectedComponents = $Molecule->GetConnectedComponents();
|
|
|
544
|
|
|
545 Returns a reference to an array containing *Molecule* objects
|
|
|
546 corresponding to connected components sorted in decreasing order of
|
|
|
547 component size in a *Molecule*.
|
|
|
548
|
|
|
549 GetConnectedComponentsAtoms
|
|
|
550 @ConnectedComponentsAtoms =
|
|
|
551 $Molecule->GetConnectedComponentsAtoms();
|
|
|
552
|
|
|
553 Returns an array containing references to arrays with *Atom* objects
|
|
|
554 corresponding to atoms of connected components sorted in order of
|
|
|
555 component decreasing size in a *Molecule*.
|
|
|
556
|
|
|
557 GetDimensionality
|
|
|
558 $Dimensionality = $Molecule->GetDimensionality();
|
|
|
559
|
|
|
560 Returns *Dimensionality* of a *Molecule* corresponding to explicitly
|
|
|
561 set *Dimensionality* property value or by processing atomic.
|
|
|
562
|
|
|
563 The *Dimensionality* value from atomic coordinates is calculated as
|
|
|
564 follows:
|
|
|
565
|
|
|
566 3D - Three dimensional: One of X, Y or Z coordinate is non-zero
|
|
|
567 2D - Two dimensional: One of X or Y coordinate is non-zero; All Z
|
|
|
568 coordinates are zero
|
|
|
569 0D - Zero dimensional: All atomic coordinates are zero
|
|
|
570
|
|
|
571 GetElementalComposition
|
|
|
572 ($ElementsRef, $CompositionRef) =
|
|
|
573 $Molecule->GetElementalComposition([$IncludeMissingHydrogens]);
|
|
|
574
|
|
|
575 Calculates elemental composition and returns references to arrays
|
|
|
576 containing elements and their percent composition in a *Molecule*.
|
|
|
577 By default, missing hydrogens are included during the calculation.
|
|
|
578
|
|
|
579 GetElementsAndNonElements
|
|
|
580 ($ElementsRef, $NonElementsRef) =
|
|
|
581 $Molecule->GetElementsAndNonElements([$IncludeMissingHydrogens]);
|
|
|
582
|
|
|
583 Counts elements and non-elements in a *Molecule* and returns
|
|
|
584 references to hashes containing element and non-element as hash keys
|
|
|
585 with values corresponding to their count. By default, missing
|
|
|
586 hydrogens are not added to the element hash.
|
|
|
587
|
|
|
588 GetExactMass
|
|
|
589 $ExactMass = $Molecule->GetExactMass();
|
|
|
590
|
|
|
591 Returns exact mass of a *Molecule* corresponding to sum of exact
|
|
|
592 masses of all the atoms.
|
|
|
593
|
|
|
594 GetFormalCharge
|
|
|
595 $FormalCharge = $Molecule->GetFormalCharge();
|
|
|
596
|
|
|
597 Returns net formal charge on a *Molecule* using one of the following
|
|
|
598 two methods: explicitly set FormalCharge property or sum of formal
|
|
|
599 charges on each atom.
|
|
|
600
|
|
|
601 FormalCharge is different from Charge property of the molecule which
|
|
|
602 corresponds to sum of partial atomic charges explicitly set for each
|
|
|
603 atom using a specific methodology.
|
|
|
604
|
|
|
605 GetFreeRadicalElectrons
|
|
|
606 $FreeRadicalElectrons = $Molecule->GetFreeRadicalElectrons();
|
|
|
607
|
|
|
608 Returns total number of free radical electrons available in a
|
|
|
609 *Molecule* using one of the following two methods: explicitly set
|
|
|
610 FreeRadicalElectrons property or sum of available free radical
|
|
|
611 electrons on each atom.
|
|
|
612
|
|
|
613 GetFusedAndNonFusedRings
|
|
|
614 ($FusedRingSetRef, $NonFusedRingsRef) =
|
|
|
615 $Molecule->GetFusedAndNonFusedRings();
|
|
|
616
|
|
|
617 Returns references to array of fused ring sets and non-fused rings
|
|
|
618 in a *Molecule*. Fused ring sets array reference contains refernces
|
|
|
619 to arrays of rings corresponding to ring *Atom* objects; Non-fused
|
|
|
620 rings array reference contains references to arrays of ring *Atom*
|
|
|
621 objects.
|
|
|
622
|
|
|
623 GetLargestConnectedComponent
|
|
|
624 $ComponentMolecule = $Molecule->GetLargestConnectedComponent();
|
|
|
625
|
|
|
626 Returns a reference to Molecule object corresponding to a largest
|
|
|
627 connected component in a *Molecule*.
|
|
|
628
|
|
|
629 GetLargestConnectedComponentAtoms
|
|
|
630 @ComponentAtoms = $Molecule->GetLargestConnectedComponentAtoms();
|
|
|
631
|
|
|
632 Returns a reference to an array of Atom objects corresponding to a
|
|
|
633 largest connected component in a *Molecule*.
|
|
|
634
|
|
|
635 GetLargestRing
|
|
|
636 @RingAtoms = $Molecule->GetLargestRing();
|
|
|
637
|
|
|
638 Returns an array of *Atoms* objects corresponding to a largest ring
|
|
|
639 in a *Molecule*.
|
|
|
640
|
|
|
641 GetMolecularFormula
|
|
|
642 $FormulaString = $Molecule->GetMolecularFormula(
|
|
|
643 [$IncludeMissingHydrogens,
|
|
|
644 $IncludeNonElements]);
|
|
|
645
|
|
|
646 Returns molecular formula of a *Molecule* by collecting information
|
|
|
647 about all atoms in the molecule and composing the formula using
|
|
|
648 Hills ordering system:
|
|
|
649
|
|
|
650 o C shows up first and H follows assuming C is present.
|
|
|
651 o All other standard elements are sorted alphanumerically.
|
|
|
652 o All other non-stanard atom symbols are also sorted
|
|
|
653 alphanumerically and follow standard elements.
|
|
|
654
|
|
|
655 Notes:
|
|
|
656
|
|
|
657 o By default, missing hydrogens and nonelements are also included.
|
|
|
658 o Elements for disconnected fragments are combined into the same
|
|
|
659 formula.
|
|
|
660 o Formal charge is also used during compoisiton of molecular formula.
|
|
|
661
|
|
|
662 GetMolecularWeight
|
|
|
663 $MolWeight = $Molecule->GetMolecularWeight();
|
|
|
664
|
|
|
665 Returns molecular weight of a *Molecule* corresponding to sum of
|
|
|
666 atomic weights of all the atoms.
|
|
|
667
|
|
|
668 GetNumOfAromaticRings
|
|
|
669 $NumOfAromaticRings = $Molecule->GetNumOfAromaticRings();
|
|
|
670
|
|
|
671 Returns number of aromatic rings in a *Molecule*.
|
|
|
672
|
|
|
673 GetNumOfAtoms
|
|
|
674 $NumOfAtoms = $Molecule->GetNumOfAtoms();
|
|
|
675
|
|
|
676 Returns number of atoms in a *Molecule*.
|
|
|
677
|
|
|
678 GetNumOfBonds
|
|
|
679 $NumOfBonds = $Molecule->GetNumOfBonds();
|
|
|
680
|
|
|
681 Returns number of bonds in a *Molecule*.
|
|
|
682
|
|
|
683 GetNumOfConnectedComponents
|
|
|
684 $NumOfComponents = $Molecule->GetNumOfConnectedComponents();
|
|
|
685
|
|
|
686 Returns number of connected components in a *Molecule*.
|
|
|
687
|
|
|
688 GetNumOfElementsAndNonElements
|
|
|
689 ($NumOfElements, $NumOfNonElements) = $Molecule->
|
|
|
690 GetNumOfElementsAndNonElements();
|
|
|
691 ($NumOfElements, $NumOfNonElements) = $Molecule->
|
|
|
692 GetNumOfElementsAndNonElements($IncludeMissingHydrogens);
|
|
|
693
|
|
|
694 Returns number of elements and non-elements in a *Molecule*. By
|
|
|
695 default, missing hydrogens are not added to element count.
|
|
|
696
|
|
|
697 GetNumOfHeavyAtoms
|
|
|
698 $NumOfHeavyAtoms = $Molecule->GetNumOfHeavyAtoms();
|
|
|
699
|
|
|
700 Returns number of heavy atoms, non-hydrogen atoms, in a *Molecule*.
|
|
|
701
|
|
|
702 GetNumOfHydrogenAtoms
|
|
|
703 $NumOfHydrogenAtoms = $Molecule->GetNumOfHydrogenAtoms();
|
|
|
704
|
|
|
705 Returns number of hydrogen atoms in a *Molecule*.
|
|
|
706
|
|
|
707 GetNumOfMissingHydrogenAtoms
|
|
|
708 $NumOfMissingHydrogenAtoms = $Molecule->GetNumOfMissingHydrogenAtoms();
|
|
|
709
|
|
|
710 Returns number of hydrogen atoms in a *Molecule*.
|
|
|
711
|
|
|
712 GetNumOfNonHydrogenAtoms
|
|
|
713 $NumOfNonHydrogenAtoms = $Molecule->GetNumOfNonHydrogenAtoms();
|
|
|
714
|
|
|
715 Returns number of non-hydrogen atoms in a *Molecule*.
|
|
|
716
|
|
|
717 GetNumOfRings
|
|
|
718 $RingCount = $Molecule->GetNumOfRings();
|
|
|
719
|
|
|
720 Returns number of rings in a *Molecule*.
|
|
|
721
|
|
|
722 GetNumOfRingsWithEvenSize
|
|
|
723 $RingCount = $Molecule->GetNumOfRingsWithEvenSize();
|
|
|
724
|
|
|
725 Returns number of rings with even size in a *Molecule*.
|
|
|
726
|
|
|
727 GetNumOfRingsWithOddSize
|
|
|
728 $RingCount = $Molecule->GetNumOfRingsWithOddSize();
|
|
|
729
|
|
|
730 Returns number of rings with odd size in a *Molecule*.
|
|
|
731
|
|
|
732 GetNumOfRingsWithSize
|
|
|
733 $RingCount = $Molecule->GetNumOfRingsWithSize($Size);
|
|
|
734
|
|
|
735 Returns number of rings with *Size* in a *Molecule*.
|
|
|
736
|
|
|
737 GetNumOfRingsWithSizeGreaterThan
|
|
|
738 $RingCount = $Molecule->GetNumOfRingsWithSizeGreaterThan($Size);
|
|
|
739
|
|
|
740 Returns number of rings with size greater than *Size* in a
|
|
|
741 *Molecule*.
|
|
|
742
|
|
|
743 GetNumOfRingsWithSizeLessThan
|
|
|
744 $RingCount = $Molecule->GetNumOfRingsWithSizeLessThan($Size);
|
|
|
745
|
|
|
746 Returns number of rings with size less than *Size* in a *Molecule*.
|
|
|
747
|
|
|
748 GetRingBonds
|
|
|
749 @RingBonds = $Molecule->GetRingBonds(@RingAtoms);
|
|
|
750
|
|
|
751 Returns an array of ring Bond objects correponding to an array of
|
|
|
752 ring *Atoms* in a *Molecule*.
|
|
|
753
|
|
|
754 GetRingBondsFromRings
|
|
|
755 @RingBondsSets = $Molecule->GetRingBondsFromRings(@RingAtomsSets);
|
|
|
756
|
|
|
757 Returns an array containing references to arrays of ring Bond
|
|
|
758 objects for rings specified in an array of references to ring *Atom*
|
|
|
759 objects.
|
|
|
760
|
|
|
761 GetRings
|
|
|
762 @Rings = $Molecule->GetRings();
|
|
|
763
|
|
|
764 Returns rings as an array containing references to arrays of ring
|
|
|
765 *Atom* objects in a *Molecule*.
|
|
|
766
|
|
|
767 GetRingsWithEvenSize
|
|
|
768 @Rings = $Molecule->GetRingsWithEvenSize();
|
|
|
769
|
|
|
770 Returns even size rings as an array containing references to arrays
|
|
|
771 of ring *Atom* objects in a *Molecule*.
|
|
|
772
|
|
|
773 GetRingsWithOddSize
|
|
|
774 @Rings = $Molecule->GetRingsWithOddSize();
|
|
|
775
|
|
|
776 Returns odd size rings as an array containing references to arrays
|
|
|
777 of ring *Atom* objects in a *Molecule*.
|
|
|
778
|
|
|
779 GetRingsWithSize
|
|
|
780 @Rings = $Molecule->GetRingsWithSize($Size);
|
|
|
781
|
|
|
782 Returns rings with *Size* as an array containing references to
|
|
|
783 arrays of ring *Atom* objects in a *Molecule*.
|
|
|
784
|
|
|
785 GetRingsWithSizeGreaterThan
|
|
|
786 @Rings = $Molecule->GetRingsWithSizeGreaterThan($Size);
|
|
|
787
|
|
|
788 Returns rings with size greater than *Size* as an array containing
|
|
|
789 references to arrays of ring *Atom* objects in a *Molecule*.
|
|
|
790
|
|
|
791 GetRingsWithSizeLessThan
|
|
|
792 @Rings = $Molecule->GetRingsWithSizeLessThan($Size);
|
|
|
793
|
|
|
794 Returns rings with size less than *Size* as an array containing
|
|
|
795 references to arrays of ring *Atom* objects in a *Molecule*.
|
|
|
796
|
|
|
797 GetSizeOfLargestRing
|
|
|
798 $Size = $Molecule->GetSizeOfLargestRing();
|
|
|
799
|
|
|
800 Returns size of the largest ring in a *Molecule*.
|
|
|
801
|
|
|
802 GetSizeOfSmallestRing
|
|
|
803 $Size = $Molecule->GetSizeOfSmallestRing();
|
|
|
804
|
|
|
805 Returns size of the smalles ring in a *Molecule*.
|
|
|
806
|
|
|
807 GetSmallestRing
|
|
|
808 @RingAtoms = $Molecule->GetSmallestRing();
|
|
|
809
|
|
|
810 Returns an array containing *Atom* objects corresponding to the
|
|
|
811 smallest ring in a *Molecule*.
|
|
|
812
|
|
|
813 GetSpinMultiplicity
|
|
|
814 $SpinMultiplicity = $Molecule->GetSpinMultiplicity();
|
|
|
815
|
|
|
816 Returns net spin multiplicity of a *Molecule* using one of the
|
|
|
817 following two methods: explicitly set SpinMultiplicity property or
|
|
|
818 sum of spin multiplicity on each atom.
|
|
|
819
|
|
|
820 GetSupportedAromaticityModels
|
|
|
821 @SupportedModels = $Molecule->GetSupportedAromaticityModels();
|
|
|
822
|
|
|
823 Returns an array containing a list of supported aromaticity models.
|
|
|
824
|
|
|
825 GetValenceModel
|
|
|
826 $ValenceModel = $Molecule->GetValenceModel();
|
|
|
827
|
|
|
828 Returns valence model for *Molecule* using one of the following two
|
|
|
829 methods: explicitly set ValenceModel property or defaul value of
|
|
|
830 *InternalValenceModel*.
|
|
|
831
|
|
|
832 GetTopologicallySortedAtoms
|
|
|
833 @SortedAtoms = $Molecule->GetTopologicallySortedAtoms([$StartAtom]);
|
|
|
834
|
|
|
835 Returns an array of topologically sorted *Atom* objects starting
|
|
|
836 from *StartAtom* or an arbitrary atom in a *Molecule*.
|
|
|
837
|
|
|
838 HasAromaticRings
|
|
|
839 $Status = $Molecule->HasAromaticRings();
|
|
|
840
|
|
|
841 Returns 1 or 0 based on whether any aromatic ring is present in a
|
|
|
842 *Molecule*.
|
|
|
843
|
|
|
844 HasAromaticAtomsInRings
|
|
|
845 $Status = $Molecule->HasAromaticAtomsInRings();
|
|
|
846
|
|
|
847 Returns 1 or 0 based on whether any aromatic ring atom is present in
|
|
|
848 a *Molecule*.
|
|
|
849
|
|
|
850 HasAromaticAtomsNotInRings
|
|
|
851 $Status = $Molecule->HasAromaticAtomsNotInRings();
|
|
|
852
|
|
|
853 Returns 1 or 0 based on whether any non-ring atom is marked aromatic
|
|
|
854 in a *Molecule*.
|
|
|
855
|
|
|
856 HasAtom
|
|
|
857 $Status = $Molecule->HasAtom($Atom);
|
|
|
858
|
|
|
859 Returns 1 or 0 based on whether *Atom* is present in a *Molecule*.
|
|
|
860
|
|
|
861 HasBond
|
|
|
862 $Status = $Molecule->HasBond($Bond);
|
|
|
863
|
|
|
864 Returns 1 or 0 based on whether *Bond* is present in a *Molecule*.
|
|
|
865
|
|
|
866 HasFusedRings
|
|
|
867 $Status = $Molecule->HasFusedRings();
|
|
|
868
|
|
|
869 Returns 1 or 0 based on whether any fused rings set is present in a
|
|
|
870 *Molecule*.
|
|
|
871
|
|
|
872 HasNoRings
|
|
|
873 $Status = $Molecule->HasNoRings();
|
|
|
874
|
|
|
875 Returns 0 or 1 based on whether any ring is present in a *Molecule*.
|
|
|
876
|
|
|
877 HasOnlyOneRing
|
|
|
878 $Status = $Molecule->HasOnlyOneRing();
|
|
|
879
|
|
|
880 Returns 1 or 0 based on whether only one ring is present in a
|
|
|
881 *Molecule*.
|
|
|
882
|
|
|
883 HasRings
|
|
|
884 $Status = $Molecule->HasRings();
|
|
|
885
|
|
|
886 Returns 1 or 0 based on whether rings are present in a *Molecule*.
|
|
|
887
|
|
|
888 IsAromatic
|
|
|
889 $Status = $Molecule->IsAromatic();
|
|
|
890
|
|
|
891 Returns 1 or 0 based on whether *Molecule* is aromatic.
|
|
|
892
|
|
|
893 IsMolecule
|
|
|
894 $Status = Molecule::IsMolecule();
|
|
|
895
|
|
|
896 Returns 1 or 0 based on whether *Object* is a Molecule object.
|
|
|
897
|
|
|
898 IsRingAromatic
|
|
|
899 $Status = $Molecule->IsRingAromatic(@RingAtoms);
|
|
|
900
|
|
|
901 Returns 1 or 0 based on whether all *RingAtoms* are aromatic.
|
|
|
902
|
|
|
903 IsSupportedAromaticityModel
|
|
|
904 $Status = $Molecule->IsSupportedAromaticityModel($AromaticityModel);
|
|
|
905 $Status = Molecule::IsSupportedAromaticityModel($AromaticityModel);
|
|
|
906
|
|
|
907 Returns 1 or 0 based on whether specified *AromaticityModel* is
|
|
|
908 supported.
|
|
|
909
|
|
|
910 IsTwoDimensional
|
|
|
911 $Status = $Molecule->IsTwoDimensional();
|
|
|
912
|
|
|
913 Returns 1 or 0 based on whether any atom in *Molecule* has a
|
|
|
914 non-zero value for X or Y coordinate and all atoms have zero value
|
|
|
915 for Z coordinates.
|
|
|
916
|
|
|
917 IsThreeDimensional
|
|
|
918 $Status = $Molecule->IsThreeDimensional();
|
|
|
919
|
|
|
920 Returns 1 or 0 based on whether any atom in *Molecule* has a
|
|
|
921 non-zero value for Z coordinate.
|
|
|
922
|
|
|
923 KeepLargestComponent
|
|
|
924 $Molecule->KeepLargestComponent();
|
|
|
925
|
|
|
926 Deletes atoms corresponding to all other connected components Except
|
|
|
927 for the largest connected component in a *Molecule* and returns
|
|
|
928 *Molecule*.
|
|
|
929
|
|
|
930 KekulizeAromaticAtoms
|
|
|
931 $Status = $Molecule->KekulizeAromaticAtoms();
|
|
|
932
|
|
|
933 Kekulize marked ring and non-ring aromatic atoms in a molecule and
|
|
|
934 return 1 or 1 based on whether the kekulization succeeded.
|
|
|
935
|
|
|
936 NewAtom
|
|
|
937 $NewAtom = $Molecule->NewAtom(%AtomPropertyNamesAndValues);
|
|
|
938
|
|
|
939 Creates a new atom using *AtomPropertyNamesAndValues*, add its to
|
|
|
940 *Molecule*, and returns new Atom object.
|
|
|
941
|
|
|
942 NewBond
|
|
|
943 $NewBond = $Molecule->NewBond(%BondPropertyNamesAndValues);
|
|
|
944
|
|
|
945 Creates a new bond using *AtomPropertyNamesAndValues*, add its to
|
|
|
946 *Molecule*, and returns new Bond object.
|
|
|
947
|
|
|
948 SetActiveRings
|
|
|
949 $Molecule->SetActiveRings($RingsType);
|
|
|
950
|
|
|
951 Sets up type of detected ring sets to use during all ring related
|
|
|
952 methods and returns *Molecule*. Possible *RingType* values:
|
|
|
953 *Independent or All*. By default, *Independent* ring set is used
|
|
|
954 during all ring methods.
|
|
|
955
|
|
|
956 SetAromaticityModel
|
|
|
957 $Molecule = $Molecule->SetAromaticityModel($AromaticityModel);
|
|
|
958
|
|
|
959 Sets up *AromaticityModel* property value for *Molecule* and
|
|
|
960 retrurns *Molecule*.
|
|
|
961
|
|
|
962 SetValenceModel
|
|
|
963 $Molecule = $Molecule->SetValenceModel(ValenceModel);
|
|
|
964
|
|
|
965 Sets up *ValenceModel* property value for *Molecule* and retrurns
|
|
|
966 *Molecule*.
|
|
|
967
|
|
|
968 StringifyMolecule
|
|
|
969 $MoleculeString = $Molecule->StringifyMolecule();
|
|
|
970
|
|
|
971 Returns a string containing information about *Molecule* object
|
|
|
972
|
|
|
973 AUTHOR
|
|
|
974 Manish Sud <msud@san.rr.com>
|
|
|
975
|
|
|
976 SEE ALSO
|
|
|
977 Atom.pm, Bond.pm, MoleculeFileIO.pm, MolecularFormula.pm
|
|
|
978
|
|
|
979 COPYRIGHT
|
|
|
980 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
981
|
|
|
982 This file is part of MayaChemTools.
|
|
|
983
|
|
|
984 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
985 under the terms of the GNU Lesser General Public License as published by
|
|
|
986 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
987 your option) any later version.
|
|
|
988
|
