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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:10:43 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:Atom.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <div class="DocNav"> | |
| 14 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AminoAcids.html" title="AminoAcids.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomicDescriptors.html" title="AtomicDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>Atom.pm</strong></td><td width="33%" align="right"><a href="././code/Atom.html" title="View source code">Code</a> | <a href="./../pdf/Atom.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/Atom.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/Atom.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/Atom.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>Atom</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>use Atom;</p> | |
| 26 <p> | |
| 27 </p> | |
| 28 <h2>DESCRIPTION</h2> | |
| 29 <p><strong>Atom</strong> class provides the following methods:</p> | |
| 30 <p> <a href="#new">new</a>, <a href="#addhydrogens">AddHydrogens</a>, <a href="#copy">Copy</a>, <a href="#deleteatom">DeleteAtom</a>, <a href="#deletehydrogens">DeleteHydrogens</a>, <a href="#doesatomneighborhoodmatch">DoesAtomNeighborhoodMatch</a> | |
| 31 , <a href="#getatomicinvariantvalue">GetAtomicInvariantValue</a>, <a href="#getatomicweight">GetAtomicWeight</a>, <a href="#getbondtoatom">GetBondToAtom</a>, <a href="#getbonds">GetBonds</a> | |
| 32 , <a href="#getbondstoheavyatoms">GetBondsToHeavyAtoms</a>, <a href="#getbondstohydrogenatoms">GetBondsToHydrogenAtoms</a>, <a href="#getbondstononhydrogenatoms">GetBondsToNonHydrogenAtoms</a> | |
| 33 , <a href="#getexactmass">GetExactMass</a>, <a href="#getexplicithydrogens">GetExplicitHydrogens</a>, <a href="#getformalcharge">GetFormalCharge</a>, <a href="#getfreeradicalelectrons">GetFreeRadicalElectrons</a> | |
| 34 , <a href="#getgroupnumber">GetGroupNumber</a>, <a href="#getheavyatomneighbors">GetHeavyAtomNeighbors</a>, <a href="#getheavyatomneighborsatominformation">GetHeavyAtomNeighborsAtomInformation</a> | |
| 35 , <a href="#getheavyatomneighborsbondformation">GetHeavyAtomNeighborsBondformation</a>, <a href="#gethighestcommonvalence">GetHighestCommonValence</a> | |
| 36 , <a href="#gethydrogenatomneighbors">GetHydrogenAtomNeighbors</a>, <a href="#gethydrogens">GetHydrogens</a>, <a href="#getimplicithydrogens">GetImplicitHydrogens</a>, <a href="#getlargestbondorder">GetLargestBondOrder</a> | |
| 37 , <a href="#getlargestbondordertoheavyatoms">GetLargestBondOrderToHeavyAtoms</a>, <a href="#getlargestbondordertononhydrogenatoms">GetLargestBondOrderToNonHydrogenAtoms</a> | |
| 38 , <a href="#getlargestring">GetLargestRing</a>, <a href="#getlowestcommonvalence">GetLowestCommonValence</a>, <a href="#getmassnumber">GetMassNumber</a>, <a href="#getmissinghydrogens">GetMissingHydrogens</a> | |
| 39 , <a href="#getneighbors">GetNeighbors</a>, <a href="#getneighborsusingatomspecification">GetNeighborsUsingAtomSpecification</a>, <a href="#getnonhydrogenatomneighbors">GetNonHydrogenAtomNeighbors</a> | |
| 40 , <a href="#getnonhydrogenatomneighborsatominformation">GetNonHydrogenAtomNeighborsAtomInformation</a> | |
| 41 , <a href="#getnonhydrogenatomneighborsbondinformation">GetNonHydrogenAtomNeighborsBondInformation</a>, <a href="#getnonhydrogenneighborofhydrogenatom">GetNonHydrogenNeighborOfHydrogenAtom</a> | |
| 42 , <a href="#getnumofaromaticbondstoheavyatoms">GetNumOfAromaticBondsToHeavyAtoms</a>, <a href="#getnumofaromaticbondstononhydrogenatoms">GetNumOfAromaticBondsToNonHydrogenAtoms</a> | |
| 43 , <a href="#getnumofbondtypestoheavyatoms">GetNumOfBondTypesToHeavyAtoms</a>, <a href="#getnumofbondtypestononhydrogenatoms">GetNumOfBondTypesToNonHydrogenAtoms</a>, <a href="#getnumofbonds">GetNumOfBonds</a> | |
| 44 , <a href="#getnumofbondstoheavyatoms">GetNumOfBondsToHeavyAtoms</a>, <a href="#getnumofbondstohydrogenatoms">GetNumOfBondsToHydrogenAtoms</a> | |
| 45 , <a href="#getnumofbondstononhydrogenatoms">GetNumOfBondsToNonHydrogenAtoms</a>, <a href="#getnumofdoublebondstoheavyatoms">GetNumOfDoubleBondsToHeavyAtoms</a> | |
| 46 , <a href="#getnumofbondsavailableforheavyatoms">GetNumOfBondsAvailableForHeavyAtoms</a>, <a href="#getnumofbondsavailablefornonhydrogenatoms">GetNumOfBondsAvailableForNonHydrogenAtoms</a> | |
| 47 , <a href="#getnumofdoublebondstononhydrogenatoms">GetNumOfDoubleBondsToNonHydrogenAtoms</a>, <a href="#getnumofexplicithydrogens">GetNumOfExplicitHydrogens</a> | |
| 48 , <a href="#getnumofheavyatomneighbors">GetNumOfHeavyAtomNeighbors</a>, <a href="#getnumofhydrogenatomneighbors">GetNumOfHydrogenAtomNeighbors</a>, <a href="#getnumofhydrogens">GetNumOfHydrogens</a> | |
| 49 , <a href="#getnumofimplicithydrogens">GetNumOfImplicitHydrogens</a>, <a href="#getnumofmissinghydrogens">GetNumOfMissingHydrogens</a>, <a href="#getnumofneighbors">GetNumOfNeighbors</a> | |
| 50 , <a href="#getnumofnonhydrogenatomneighbors">GetNumOfNonHydrogenAtomNeighbors</a>, <a href="#getnumofrings">GetNumOfRings</a>, <a href="#getnumofringswithevensize">GetNumOfRingsWithEvenSize</a> | |
| 51 , <a href="#getnumofringswithoddsize">GetNumOfRingsWithOddSize</a>, <a href="#getnumofringswithsize">GetNumOfRingsWithSize</a>, <a href="#getnumofringswithsizegreaterthan">GetNumOfRingsWithSizeGreaterThan</a> | |
| 52 , <a href="#getnumofringswithsizelessthan">GetNumOfRingsWithSizeLessThan</a>, <a href="#getnumofsigmaandpibondstoheavyatoms">GetNumOfSigmaAndPiBondsToHeavyAtoms</a> | |
| 53 , <a href="#getnumofsigmaandpibondstononhydrogenatoms">GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</a>, <a href="#getnumofsinglebondstoheavyatoms">GetNumOfSingleBondsToHeavyAtoms</a> | |
| 54 , <a href="#getnumofsinglebondstononhydrogenatoms">GetNumOfSingleBondsToNonHydrogenAtoms</a>, <a href="#getnumoftriplebondstoheavyatoms">GetNumOfTripleBondsToHeavyAtoms</a> | |
| 55 , <a href="#getnumoftriplebondstononhydrogenatoms">GetNumOfTripleBondsToNonHydrogenAtoms</a>, <a href="#getperiodnumber">GetPeriodNumber</a> | |
| 56 , <a href="#getpotentialtotalcommonvalence">GetPotentialTotalCommonValence</a>, <a href="#getrings">GetRings</a>, <a href="#getringswithevensize">GetRingsWithEvenSize</a> | |
| 57 , <a href="#getringswithoddsize">GetRingsWithOddSize</a>, <a href="#getringswithsize">GetRingsWithSize</a>, <a href="#getringswithsizegreaterthan">GetRingsWithSizeGreaterThan</a> | |
| 58 , <a href="#getringswithsizelessthan">GetRingsWithSizeLessThan</a>, <a href="#getsizeoflargestring">GetSizeOfLargestRing</a>, <a href="#getsizeofsmallestring">GetSizeOfSmallestRing</a> | |
| 59 , <a href="#getsmallestring">GetSmallestRing</a>, <a href="#getspinmultiplicity">GetSpinMultiplicity</a>, <a href="#getsumofbondorders">GetSumOfBondOrders</a> | |
| 60 , <a href="#getsumofbondorderstoheavyatoms">GetSumOfBondOrdersToHeavyAtoms</a>, <a href="#getsumofbondorderstohydrogenatoms">GetSumOfBondOrdersToHydrogenAtoms</a> | |
| 61 , <a href="#getsumofbondorderstononhydrogenatoms">GetSumOfBondOrdersToNonHydrogenAtoms</a>, <a href="#getvalence">GetValence</a>, <a href="#getvalenceelectrons">GetValenceElectrons</a> | |
| 62 , <a href="#getvalencefreeelectrons">GetValenceFreeElectrons</a>, <a href="#getx">GetX</a>, <a href="#getxyz">GetXYZ</a>, <a href="#getxyzvector">GetXYZVector</a>, <a href="#gety">GetY</a>, <a href="#getz">GetZ</a>, <a href="#isamidecarbon">IsAmideCarbon</a> | |
| 63 , <a href="#isamidenitrogen">IsAmideNitrogen</a>, <a href="#isaromatic">IsAromatic</a>, <a href="#isarsenic">IsArsenic</a>, <a href="#isbondedtoatom">IsBondedToAtom</a>, <a href="#isbromine">IsBromine</a>, <a href="#iscarbon">IsCarbon</a>, <a href="#iscarboxylcarbon">IsCarboxylCarbon</a> | |
| 64 , <a href="#iscarboxyloxygen">IsCarboxylOxygen</a>, <a href="#iscarboxylatecarbon">IsCarboxylateCarbon</a>, <a href="#iscarboxylateoxygen">IsCarboxylateOxygen</a>, <a href="#ischlorine">IsChlorine</a> | |
| 65 , <a href="#isfluorine">IsFluorine</a>, <a href="#isfunctionalclasstype">IsFunctionalClassType</a>, <a href="#isguadiniumcarbon">IsGuadiniumCarbon</a>, <a href="#isguadiniumnitrogen">IsGuadiniumNitrogen</a> | |
| 66 , <a href="#ishbondacceptor">IsHBondAcceptor</a>, <a href="#ishbonddonor">IsHBondDonor</a>, <a href="#ishalogen">IsHalogen</a>, <a href="#isheteroatom">IsHeteroAtom</a>, <a href="#ishydrogen">IsHydrogen</a> | |
| 67 , <a href="#ishydrogenbondacceptor">IsHydrogenBondAcceptor</a>, <a href="#ishydrogenbonddonor">IsHydrogenBondDonor</a>, <a href="#ishydrophobic">IsHydrophobic</a>, <a href="#isinring">IsInRing</a> | |
| 68 , <a href="#isinringofsize">IsInRingOfSize</a>, <a href="#isiodine">IsIodine</a>, <a href="#isisotope">IsIsotope</a>, <a href="#islipophilic">IsLipophilic</a>, <a href="#ismetallic">IsMetallic</a> | |
| 69 , <a href="#isnegativelyionizable">IsNegativelyIonizable</a>, <a href="#isnitrogen">IsNitrogen</a>, <a href="#isnoncarbonorhydrogen">IsNonCarbonOrHydrogen</a>, <a href="#isnotinring">IsNotInRing</a> | |
| 70 , <a href="#isonlyinonering">IsOnlyInOneRing</a>, <a href="#isoxygen">IsOxygen</a>, <a href="#isphosphateoxygen">IsPhosphateOxygen</a>, <a href="#isphosphatephosphorus">IsPhosphatePhosphorus</a>, <a href="#isphosphorus">IsPhosphorus</a> | |
| 71 , <a href="#ispolaratom">IsPolarAtom</a>, <a href="#ispolarhydrogen">IsPolarHydrogen</a>, <a href="#ispositivelyionizable">IsPositivelyIonizable</a>, <a href="#issaturated">IsSaturated</a>, <a href="#isselenium">IsSelenium</a> | |
| 72 , <a href="#issilicon">IsSilicon</a>, <a href="#isstereocenter">IsStereoCenter</a>, <a href="#issulfur">IsSulfur</a>, <a href="#issulphur">IsSulphur</a>, <a href="#istellurium">IsTellurium</a>, <a href="#isterminal">IsTerminal</a> | |
| 73 , <a href="#istopologicalpharmacophoretype">IsTopologicalPharmacophoreType</a>, <a href="#isunsaturated">IsUnsaturated</a>, <a href="#setatomsymbol">SetAtomSymbol</a>, <a href="#setatomicnumber">SetAtomicNumber</a> | |
| 74 , <a href="#setexplicithydrogens">SetExplicitHydrogens</a>, <a href="#setmassnumber">SetMassNumber</a>, <a href="#setstereocenter">SetStereoCenter</a>, <a href="#setstereochemistry">SetStereochemistry</a> | |
| 75 , <a href="#setx">SetX</a>, <a href="#setxyz">SetXYZ</a>, <a href="#sety">SetY</a>, <a href="#setz">SetZ</a>, <a href="#stringifyatom">StringifyAtom</a> | |
| 76 </p><p><strong>Atom</strong> class is derived from <strong>ObjectProperty</strong> base class which provides methods not explicitly | |
| 77 defined in <strong>Atom</strong> or <strong>ObjectProperty</strong> class using Perl's AUTOLOAD functionality. These methods | |
| 78 are generated on-the-fly for a specified object property:</p> | |
| 79 <div class="OptionsBox"> | |
| 80 Set<PropertyName>(<PropertyValue>); | |
| 81 <br/> $PropertyValue = Get<PropertyName>(); | |
| 82 <br/> Delete<PropertyName>();</div> | |
| 83 <p> | |
| 84 </p> | |
| 85 <h2>METHODS</h2> | |
| 86 <dl> | |
| 87 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> | |
| 88 <dd> | |
| 89 <div class="OptionsBox"> | |
| 90 $NewAtom = new Atom([%PropertyNameAndValues]);</div> | |
| 91 <p>Using specified <em>Atom</em> property names and values hash, <strong>new</strong> method creates a new object | |
| 92 and returns a reference to newly created <strong>Atom</strong> object. By default, following properties are | |
| 93 initialized:</p> | |
| 94 <div class="OptionsBox"> | |
| 95 ID = SequentialObjectID | |
| 96 <br/> Name = "Atom <SequentialObjectID>" | |
| 97 <br/> AtomSymbol = "" | |
| 98 <br/> AtomicNumber = 0 | |
| 99 <br/> XYZ = ZeroVector</div> | |
| 100 <p>Except for <em>ID</em> property, all other default properties and other additional properties can | |
| 101 be set during invocation of this method.</p> | |
| 102 <p>Examples:</p> | |
| 103 <div class="OptionsBox"> | |
| 104 $Atom = new Atom(); | |
| 105 <br/> $CarbonAtom = new Atom('AtomSymbol' => 'C', 'XYZ' => (0.0, 1.0, | |
| 106 0.0)); | |
| 107 <br/> $OxygenAtom = new Atom('AtomName' => 'Oxygen', AtomSymbol' => 'O', | |
| 108 'XYZ' => (1.0, 1.0, 1.0));</div> | |
| 109 </dd> | |
| 110 <dt><strong><a name="addhydrogens" class="item"><strong>AddHydrogens</strong></a></strong></dt> | |
| 111 <dd> | |
| 112 <div class="OptionsBox"> | |
| 113 $NumOfHydrogensAdded = $Atom->AddHydrogens();</div> | |
| 114 <p>Adds hydrogens to an <strong>Atom</strong> present in a <strong>Molecule</strong> object and returns | |
| 115 the number of added hydrogens. The current release of MayaChemTools doesn't | |
| 116 assign hydrogen positions.</p> | |
| 117 </dd> | |
| 118 <dt><strong><a name="copy" class="item"><strong>Copy</strong></a></strong></dt> | |
| 119 <dd> | |
| 120 <div class="OptionsBox"> | |
| 121 $AtomCopy = $Atom->Copy();</div> | |
| 122 <p>Copy <em>Atom</em> and its associated data using <strong>Storable::dclone</strong> and return a new | |
| 123 <strong>Atom</strong> object.</p> | |
| 124 </dd> | |
| 125 <dt><strong><a name="deleteatom" class="item"><strong>DeleteAtom</strong></a></strong></dt> | |
| 126 <dd> | |
| 127 <div class="OptionsBox"> | |
| 128 $Atom->DeleteAtom();</div> | |
| 129 <p>Delete <em>Atom</em> from a molecule.</p> | |
| 130 </dd> | |
| 131 <dt><strong><a name="doesatomneighborhoodmatch" class="item"><strong>DoesAtomNeighborhoodMatch</strong></a></strong></dt> | |
| 132 <dd> | |
| 133 <div class="OptionsBox"> | |
| 134 $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec); | |
| 135 <br/> $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec, | |
| 136 $NbrAtomSpecsRef); | |
| 137 <br/> $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec, | |
| 138 $NbrAtomSpecsRef, $AllowedNbrBondSpecsRef); | |
| 139 <br/> $Status = $Atom->DoesAtomNeighborhoodMatch($CentralAtomSpec, | |
| 140 $NbrAtomSpecsRef, $NbrBondSpecsRef, | |
| 141 $AllowedNbrOfNbrAtomSpecsRef);</div> | |
| 142 <p>Returns 1 or 0 based on whether atom matches central atom and its neighborhood | |
| 143 using specified atom and bonds specifications. Neighborhood atom and bond specifications | |
| 144 are specified as array references containing neighbor atom and bond specifications.</p> | |
| 145 <p>Let:</p> | |
| 146 <div class="OptionsBox"> | |
| 147 AS = Atom symbol corresponding to element symbol, atomic number (#n) | |
| 148 or any atom (A)</div> | |
| 149 <div class="OptionsBox"> | |
| 150 X<n> = Number of non-hydrogen atom neighbors or heavy atoms | |
| 151 attached to atom | |
| 152 <br/> T<n> = Total number of atom neighbors including implicit and explicit | |
| 153 hydrogens | |
| 154 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy | |
| 155 atoms attached to atom | |
| 156 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy | |
| 157 atoms attached to atom | |
| 158 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or | |
| 159 heavy atoms attached to atom | |
| 160 <br/> TSB<n> = Total number of single bonds to atom neighbors including implicit | |
| 161 and explicit hydrogens | |
| 162 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or | |
| 163 heavy atoms attached to atom | |
| 164 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or | |
| 165 heavy atoms attached to atom | |
| 166 <br/> AB<n> = Number of aromatic bonds to non-hydrogen atom neighbors or | |
| 167 heavy atoms attached to atom | |
| 168 <br/> H<n> = Number of implicit and explicit hydrogens for atom | |
| 169 <br/> Ar = Aromatic annotation indicating whether atom is aromatic | |
| 170 <br/> RA or RA<n> = Ring atom annotation indicating whether atom | |
| 171 is a ring | |
| 172 <br/> TR<n> = Total number of rings containing atom | |
| 173 <br/> FC<+n/-n> = Formal charge assigned to atom | |
| 174 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope | |
| 175 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), | |
| 176 2 (doublet) or 3 (triplet)</div> | |
| 177 <p>Then, atom specification corresponds to:</p> | |
| 178 <div class="OptionsBox"> | |
| 179 AS.X<n>.T<n>.BO<n>.LBO<n>.<SB><n>.TSB<n>.<DB><n>.<TB><n>.AB<n>.H<n>.Ar. | |
| 180 <br/> RA<n>.TR<n>FC<+n/-n>.MN<n>.SM<n></div> | |
| 181 <p>Except for AS which is a required atomic invariant in atom specification, all other atomic invariants are | |
| 182 optional. For an atom specification to match an atom, the values of all specified atomic invariants must | |
| 183 match. Exclamation in from of atomic invariant can be used to negate its effect during the match.</p> | |
| 184 <p>For <em>FC</em> value matching, the following value operators are also supported:</p> | |
| 185 <div class="OptionsBox"> | |
| 186 o +* : Any positive value | |
| 187 <br/> o -* : Any negative value | |
| 188 <br/> o > ValidNumber or >= ValidNumber | |
| 189 <br/> o < ValidNumber or <= ValidNumber</div> | |
| 190 <p>A comma delimited atom specification string is used to match any one of the specified atom specification.</p> | |
| 191 <p>Notes:</p> | |
| 192 <div class="OptionsBox"> | |
| 193 o During atom specification match to an atom, the first atomic invariant is always assumed to | |
| 194 atom symbol.</div> | |
| 195 <p>Examples:</p> | |
| 196 <div class="OptionsBox"> | |
| 197 o ('N', 'N', 'N') | |
| 198 <br/> o ('N.FC0', 'N.FC0', 'N,N.FC+1.H1') | |
| 199 <br/> o ('N.H2', 'N.H2', 'N.H1') | |
| 200 <br/> o ('C,N', '!N', '!H') | |
| 201 <br/> o ('C,N', 'N.Ar', 'N.R5')</div> | |
| 202 <p>Let:</p> | |
| 203 <div class="OptionsBox"> | |
| 204 -|1|s|Single = Single bond | |
| 205 <br/> =|2|d|Double = Double bond | |
| 206 <br/> #|3|t|Triple = Triple bond | |
| 207 <br/> :|1.5|a|Ar|Aromatic = Aromatic bond</div> | |
| 208 <div class="OptionsBox"> | |
| 209 @|RB|Ring = Ring bond | |
| 210 <br/> ~|*|Any = Any bond</div> | |
| 211 <p>Then, bond specification corresponds to:</p> | |
| 212 <div class="OptionsBox"> | |
| 213 -.: | |
| 214 <br/> =.@ | |
| 215 <br/> Double.Aromatic</div> | |
| 216 <p>For a bond specification to match bond between two atoms, the values of all specified bond symbols must | |
| 217 match. Exclamation in from of bond symbol can be used to negate its effect during the match.</p> | |
| 218 <p>A comma delimited bond specification string is used to match any one of the specified atom specification.</p> | |
| 219 <p>Notes:</p> | |
| 220 <div class="OptionsBox"> | |
| 221 o During atom neighborhood match for central atom neighborhood atom and bond specifications, | |
| 222 implicit or missing hydrogens are automatically checked for any matches to unmatched | |
| 223 specifications.</div> | |
| 224 <p>Examples:</p> | |
| 225 <div class="OptionsBox"> | |
| 226 Aromatic carbon in a 5 membered ring: | |
| 227 $Atom->DoesAtomNeighborhoodMatch('C.Ar.RA5');</div> | |
| 228 <div class="OptionsBox"> | |
| 229 AcetylenicCarbon: $Atom->DoesAtomNeighborhoodMatch('C.T2.TB1'); or | |
| 230 $Atom->DoesAtomNeighborhoodMatch('C.T2.TB1', | |
| 231 ['*', '*'], ['#', '-']);</div> | |
| 232 <div class="OptionsBox"> | |
| 233 GuadiniumCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4', | |
| 234 ['N.FC0', 'N.FC0', 'N.FC0,N.FC+1'], | |
| 235 ['-', '-', '='], | |
| 236 ['C,H', 'C,H', 'C,H']);</div> | |
| 237 <div class="OptionsBox"> | |
| 238 AmideCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3', | |
| 239 ['C,H', 'O', 'N'], | |
| 240 ['-', '=', '-'], | |
| 241 ['C,H', 'C', 'C,H,N,O,S,P,F,Cl,Br,I']);</div> | |
| 242 <div class="OptionsBox"> | |
| 243 CarboxylCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3', | |
| 244 ['C,H', 'O', 'O.X1.FC0'], | |
| 245 ['-', '=', '-'], | |
| 246 ['C,H', 'C', 'C']);</div> | |
| 247 <div class="OptionsBox"> | |
| 248 CarboxylateCarbon: $Atom->DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3', | |
| 249 ['C,H', 'O', 'O.X1.FC-1'], | |
| 250 ['-', '=', '-'], | |
| 251 ['C,H', 'C', 'C']);</div> | |
| 252 </dd> | |
| 253 <dt><strong><a name="deletehydrogens" class="item"><strong>DeleteHydrogens</strong></a></strong></dt> | |
| 254 <dd> | |
| 255 <div class="OptionsBox"> | |
| 256 $NumOfHydrogensDeleted = $Atom->AddHydrogens();</div> | |
| 257 <p>Delete hydrogens from an <strong>Atom</strong> present in a <strong>Molecule</strong> object and returns | |
| 258 the number of deleted hydrogens.</p> | |
| 259 </dd> | |
| 260 <dt><strong><a name="getatomicinvariantvalue" class="item"><strong>GetAtomicInvariantValue</strong></a></strong></dt> | |
| 261 <dd> | |
| 262 <div class="OptionsBox"> | |
| 263 $Value = $Atom->GetAtomicInvariantValue($AtomicInvariant);</div> | |
| 264 <p>Returns atomic invariant value for a specified <em>AtomicInvariant</em>. The current release | |
| 265 of MayaChemTools supports following abbreviations and descriptive names for | |
| 266 <em>AtomicInvarints</em>:</p> | |
| 267 <div class="OptionsBox"> | |
| 268 AS : Atom or element symbol | |
| 269 <br/> X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors | |
| 270 <br/> T : TotalNumOfAtomNeighbors | |
| 271 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms | |
| 272 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms | |
| 273 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms | |
| 274 <br/> TSB : TotalNumOfSingleBonds | |
| 275 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms | |
| 276 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms | |
| 277 <br/> AB : NumOfAromaticBondsToNonHydrogenAtoms or NumOfAromaticBondsToHeavyAtoms | |
| 278 <br/> H : NumOfImplicitAndExplicitHydrogens | |
| 279 <br/> Ar : Aromatic | |
| 280 <br/> Str : Stereochemistry | |
| 281 <br/> RA : RingAtom | |
| 282 <br/> FC : FormalCharge | |
| 283 <br/> AN : AtomicNumber | |
| 284 <br/> AM : AtomicMass | |
| 285 <br/> MN : MassNumber | |
| 286 <br/> SM : SpinMultiplicity</div> | |
| 287 </dd> | |
| 288 <dt><strong><a name="getatomicweight" class="item"><strong>GetAtomicWeight</strong></a></strong></dt> | |
| 289 <dd> | |
| 290 <div class="OptionsBox"> | |
| 291 $Value = $Aom->GetAtomicWeight();</div> | |
| 292 <p>Returns atomic weight of an <strong>Atom</strong> which corresponds to either explicity set <em>AtomicWeight</em> | |
| 293 atom property or atomic weight of the corresponding element in the periodic table available by | |
| 294 <strong>PeriodicTable</strong> module.</p> | |
| 295 </dd> | |
| 296 <dt><strong><a name="getbondtoatom" class="item"><strong>GetBondToAtom</strong></a></strong></dt> | |
| 297 <dd> | |
| 298 <div class="OptionsBox"> | |
| 299 $Bond = $Atom->GetBondToAtom($OtherAtom);</div> | |
| 300 <p>Returns a <strong>Bond</strong> object corresponding to bond between <em>Atom</em> and <em>OtherAtom</em> in | |
| 301 a molecule.</p> | |
| 302 </dd> | |
| 303 <dt><strong><a name="getbonds" class="item"><strong>GetBonds</strong></a></strong></dt> | |
| 304 <dd> | |
| 305 <div class="OptionsBox"> | |
| 306 @Bonds = $Aoto->GetBonds();</div> | |
| 307 <p>Returns an array of <strong>Bond</strong> objects corresponding to all bonds from <em>Atom</em> to other | |
| 308 bonded atoms in a molecule.</p> | |
| 309 </dd> | |
| 310 <dt><strong><a name="getbondstoheavyatoms" class="item"><strong>GetBondsToHeavyAtoms</strong></a></strong></dt> | |
| 311 <dd> | |
| 312 <div class="OptionsBox"> | |
| 313 @Bonds = $Atom->GetBondsToHeavyAtoms();</div> | |
| 314 <p>Returns an array of <strong>Bond</strong> objects corresponding to bonds from <em>Atom</em> to other bonded | |
| 315 non-hydrogen atoms in a molecule.</p> | |
| 316 </dd> | |
| 317 <dt><strong><a name="getbondstohydrogenatoms" class="item"><strong>GetBondsToHydrogenAtoms</strong></a></strong></dt> | |
| 318 <dd> | |
| 319 <div class="OptionsBox"> | |
| 320 @Bonds = $Atom->GetBondsToHydrogenAtoms();</div> | |
| 321 <p>Returns an array of <strong>Bond</strong> objects corresponding to bonds from <em>Atom</em> to any other | |
| 322 hydrogen atom in a molecule.</p> | |
| 323 </dd> | |
| 324 <dt><strong><a name="getbondstononhydrogenatoms" class="item"><strong>GetBondsToNonHydrogenAtoms</strong></a></strong></dt> | |
| 325 <dd> | |
| 326 <div class="OptionsBox"> | |
| 327 @Bonds = $Atom->GetBondsToNonHydrogenAtoms();</div> | |
| 328 <p>Returns an array of <strong>Bond</strong> objects corresponding to bonds from <em>Atom</em> to other bonded | |
| 329 non-hydrogen atoms in a molecule.</p> | |
| 330 </dd> | |
| 331 <dt><strong><a name="getexactmass" class="item"><strong>GetExactMass</strong></a></strong></dt> | |
| 332 <dd> | |
| 333 <div class="OptionsBox"> | |
| 334 $ExactMass = $Atom->GetExactMass();</div> | |
| 335 <p>Returns exact mass of an <em>Atom</em> which correspond to one of these three values: explicity set | |
| 336 <em>ExactMass</em> property; mass of natural isotope for an explicty set value of <em>MassNumber</em>; most | |
| 337 abundant natural isotope mass for <em>Atom</em> with valid atomic number value available by | |
| 338 <strong>PerodicTable</strong> module.</p> | |
| 339 </dd> | |
| 340 <dt><strong><a name="getexplicithydrogens" class="item"><strong>GetExplicitHydrogens</strong></a></strong></dt> | |
| 341 <dd> | |
| 342 <div class="OptionsBox"> | |
| 343 $NumOfExplicitHydrogens = $Atom->GetExplicitHydrogens();</div> | |
| 344 <p>Returns number of hydrogens explicity bonded to an <em>Atom</em> in a molecule.</p> | |
| 345 </dd> | |
| 346 <dt><strong><a name="getformalcharge" class="item"><strong>GetFormalCharge</strong></a></strong></dt> | |
| 347 <dd> | |
| 348 <div class="OptionsBox"> | |
| 349 $FormalCharge = $Atom->GetFormalCharge();</div> | |
| 350 <p>Returns formal charge of an <em>Atom</em> in a molecule.</p> | |
| 351 </dd> | |
| 352 <dt><strong><a name="getfreeradicalelectrons" class="item"><strong>GetFreeRadicalElectrons</strong></a></strong></dt> | |
| 353 <dd> | |
| 354 <div class="OptionsBox"> | |
| 355 $FreeRadicalElectrons = $Atom->GetFreeRadicalElectrons();</div> | |
| 356 <p>Returns number of free radical electrons corresponding to to one of these | |
| 357 three values: <em>FreeRadicalElectrons</em> property; <em>SpinMultiplicity</em> property; value | |
| 358 of 0.</p> | |
| 359 <p>For atoms with explicit assignment of <em>SpinMultiplicity</em> atom property values,</p> | |
| 360 <div class="OptionsBox"> | |
| 361 Singlet - two unparied electrons corresponding to one spin state | |
| 362 <br/> Doublet - free radical; an unpaired electron corresponding to two | |
| 363 spin states | |
| 364 <br/> Triplet - two unparied electrons corresponding to three spin states | |
| 365 (divalent carbon atoms: carbenes)</div> | |
| 366 <p><strong>FreeRadicalElectrons</strong> are calculated as follows:</p> | |
| 367 <div class="OptionsBox"> | |
| 368 Doublet: 1 (one valence electron not available for bonding) | |
| 369 <br/> Singlet: 2 (two valence electrons not available for bonding) | |
| 370 <br/> Triplet: 2 (two valence electrons not available for bonding)</div> | |
| 371 </dd> | |
| 372 <dt><strong><a name="getgroupnumber" class="item"><strong>GetGroupNumber</strong></a></strong></dt> | |
| 373 <dd> | |
| 374 <div class="OptionsBox"> | |
| 375 $GroupNumber = $Atom->GetGroupNumber();</div> | |
| 376 <p>Returns group number of an <em>Atom</em> in a molecule with a valid atomic number.</p> | |
| 377 </dd> | |
| 378 <dt><strong><a name="getheavyatomneighbors" class="item"><strong>GetHeavyAtomNeighbors</strong></a></strong></dt> | |
| 379 <dd> | |
| 380 <div class="OptionsBox"> | |
| 381 $NumOfHeavyAtoms = $Atom->GetHeavyAtomNeighbors(); | |
| 382 <br/> @HeavyAtoms = $Atom->GetHeavyAtomNeighbors();</div> | |
| 383 <p>Return number of heavy atoms or an array of <strong>Atom</strong> objects corresponding to heavy atoms | |
| 384 bonded to an <em>Atom</em> in a molecule.</p> | |
| 385 </dd> | |
| 386 <dt><strong><a name="getheavyatomneighborsatominformation" class="item"><strong>GetHeavyAtomNeighborsAtomInformation</strong></a></strong></dt> | |
| 387 <dd> | |
| 388 <div class="OptionsBox"> | |
| 389 ($NumOfAtomNeighbors, $AtomNeighborsRef, | |
| 390 $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom-> | |
| 391 GetHeavyAtomNeighborsAtomInformation();</div> | |
| 392 <p>Returns atoms information for all non-hydrogen atoms attached to an <em>Atom</em> | |
| 393 in a molecule.</p> | |
| 394 <p>The following values are returned:</p> | |
| 395 <div class="OptionsBox"> | |
| 396 o Number of non-hydrogen atom neighbors | |
| 397 <br/> o A reference to an array containing atom objects corresponding to | |
| 398 non-hydrogen atom neighbors | |
| 399 <br/> o Number of different types of non-hydrogen atom neighbors | |
| 400 <br/> o A reference to a hash containing atom symbol as key with value | |
| 401 corresponding to its count for non-hydrogen atom neighbors</div> | |
| 402 </dd> | |
| 403 <dt><strong><a name="getheavyatomneighborsbondformation" class="item"><strong>GetHeavyAtomNeighborsBondformation</strong></a></strong></dt> | |
| 404 <dd> | |
| 405 <div class="OptionsBox"> | |
| 406 ($NumOfBonds, $BondTypeCountMapRef, | |
| 407 <br/> $AtomsBondTypesCountMapRef, | |
| 408 <br/> $AtomsBondTypeAtomsMap) = $Atom-> | |
| 409 GetHeavyAtomNeighborsBondformation();</div> | |
| 410 <p>Returns bonds information for all non-hydrogen atoms attached to an <em>Atom</em> | |
| 411 in a molecule.</p> | |
| 412 <p>The following values are returned:</p> | |
| 413 <div class="OptionsBox"> | |
| 414 o Number of bonds to non-hydrogen atom neighbors | |
| 415 <br/> o A reference to an array containing bond objects corresponding to | |
| 416 non-hydrogen atom neighbors | |
| 417 <br/> o A reference to a hash containing bond type as key with value | |
| 418 corresponding to its count for non-hydrogen atom neighbors. Bond | |
| 419 types are: Single, Double or Triple | |
| 420 <br/> o A reference to a hash containing atom symbol as key pointing to bond | |
| 421 type as second key with values corresponding to count of bond types for atom | |
| 422 symbol for non-hydrogen atom neighbors | |
| 423 <br/> o A reference to a hash containing atom symbol as key pointing to bond | |
| 424 type as second key with values corresponding to atom objects array involved | |
| 425 in corresponding bond type for atom symbol for non-hydrogen atom neighbors</div> | |
| 426 </dd> | |
| 427 <dt><strong><a name="gethighestcommonvalence" class="item"><strong>GetHighestCommonValence</strong></a></strong></dt> | |
| 428 <dd> | |
| 429 <div class="OptionsBox"> | |
| 430 $HighestCommonValence = $Atom->GetHighestCommonValence();</div> | |
| 431 <p>Returns highest common valence of an <em>Atom</em> which corresponds to either explicity set | |
| 432 <em>HighestCommonValence</em> atom property or highest common valence of the corresponding | |
| 433 element in the periodic table available by <strong>PerodicTable</strong> module.</p> | |
| 434 </dd> | |
| 435 <dt><strong><a name="gethydrogens" class="item"><strong>GetHydrogens</strong></a></strong></dt> | |
| 436 <dd> | |
| 437 <div class="OptionsBox"> | |
| 438 $NumOfHydrogens = $Atom->GetHydrogens();</div> | |
| 439 <p>Returns total number of hydrogens for an <em>Atom</em> in a molecule including both hydrogen atom | |
| 440 neighbors and implicit hydrogens.</p> | |
| 441 </dd> | |
| 442 <dt><strong><a name="gethydrogenatomneighbors" class="item"><strong>GetHydrogenAtomNeighbors</strong></a></strong></dt> | |
| 443 <dd> | |
| 444 <div class="OptionsBox"> | |
| 445 $NumOfHydrogenAtomNeighbors = $Atom->GetHydrogenAtomNeighbors(); | |
| 446 <br/> @HydrogenAtomNeighbors = $Atom->GetHydrogenAtomNeighbors();</div> | |
| 447 <p>Return number of hydrogen atoms or an array of <em>Atom</em> objects corresponding to hydrogen | |
| 448 atoms bonded to an <em>Atom</em> in a molecule.</p> | |
| 449 </dd> | |
| 450 <dt><strong><a name="getimplicithydrogens" class="item"><strong>GetImplicitHydrogens</strong></a></strong></dt> | |
| 451 <dd> | |
| 452 <div class="OptionsBox"> | |
| 453 $NumOfImplicitHydrogens = $Atom->GetImplicitHydrogens();</div> | |
| 454 <p>Returns number of implicit hydrogens for an <em>Atom</em> in a molecule. This value either | |
| 455 corresponds to explicitly set <em>ImplicitHydrogens</em> atom property or calculated as the | |
| 456 difference between the value of potential total valence and sum of bond orders to | |
| 457 both hydrogen and non-hydrogen atom neighbors.</p> | |
| 458 </dd> | |
| 459 <dt><strong><a name="getpotentialtotalcommonvalence" class="item"><strong>GetPotentialTotalCommonValence</strong></a></strong></dt> | |
| 460 <dd> | |
| 461 <div class="OptionsBox"> | |
| 462 $PotentialTotalValence = $Atom->GetPotentialTotalCommonValence();</div> | |
| 463 <p>Returns potential total common valence of an <em>Atom</em> in a molecule corresponding | |
| 464 to a specific valence model set for the molecule using its <strong>SetValenceModel</strong> method | |
| 465 or default internal valence model. It is used during the calculation of missing or | |
| 466 implicit hydrogens.</p> | |
| 467 <p>The current release of MayaChemTools supports three valence models: <em>MDLValenceModel, | |
| 468 DaylightValenceModel, InternalValenceModel or MayaChemToolsValenceModel</em>.</p> | |
| 469 <p>For <em>MDLValenceModel</em> and <em>DaylightValenceModel</em>, the following data files, distributed | |
| 470 with the package, are used to calculate potential total valence:</p> | |
| 471 <div class="OptionsBox"> | |
| 472 lib/data/MDLValenceModelData.csv | |
| 473 <br/> lib/data/DaylightValenceModelData.csv</div> | |
| 474 <p>The calculation of potential total common valence for these two models is performed as | |
| 475 follows: Calculate current effective total valence of the <em>Atom</em> by adding up the bond | |
| 476 order of its neighbors and number of free radical electrons; Find available common valence | |
| 477 for the <em>Atom</em>, corresponding to any specified formal charge, higher than the effective | |
| 478 total valence, and return it as <em>PotentialTotalValence</em>.</p> | |
| 479 <p>The calculation of potential total common valence For <em>InternalValenceModel</em> or | |
| 480 <em>MayaChenToolsValenceModel</em> doesn't uses <strong>PeriodicTable</strong> module to retrieve values | |
| 481 for common valence, which in turn reads in PeriodicTableElements.csv file distributed with | |
| 482 the package.</p> | |
| 483 <p>For elements with one one common valence, potential total common valence corresponds | |
| 484 to:</p> | |
| 485 <div class="OptionsBox"> | |
| 486 CommonValence + FormalCharge - FreeRadicalElectrons</div> | |
| 487 <p>For elements with multiple common valences, each common valence is used to | |
| 488 calculate total potential common valence as shown above, and the first total potential | |
| 489 common valence greater than the sum of bond orders to all neighbors is selected as | |
| 490 the final total common valence.</p> | |
| 491 <p>FormalCharge sign is reversed for electropositive elements with positive formal charge | |
| 492 during common valence calculations. Electropositive elements, metals and transition elements, | |
| 493 have usually plus formal charge and it leads to decrease in common valence; the negative | |
| 494 formal charge should result in the decrease of common valence.</p> | |
| 495 <p>The sign of formal charge is adjusted as follows.</p> | |
| 496 <p>Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He):</p> | |
| 497 <p>Formal charge sign is not adjusted. Positive and negative values result in the | |
| 498 increase and decrease of valence.</p> | |
| 499 <p>Group 14 containing C, Si, Ge, Sn, Pb...:</p> | |
| 500 <p>Formal charge sign is reversed for positive values. Both positive and negative | |
| 501 values result in the decrease of valence.</p> | |
| 502 <p>Group 13 containing B, Al, Ga, In, Tl...:</p> | |
| 503 <p>Formal charge sign is always reversed. Positive and negative values result in the | |
| 504 decrease and increase of valence.</p> | |
| 505 <p>Groups 1 (H) through 12 (Zn)...:</p> | |
| 506 <p>Formal charge sign is reversed for positive values. Both positive and negative | |
| 507 values result in the decrease of valence.</p> | |
| 508 <p>Lanthanides and actinides:</p> | |
| 509 <p>Formal charge sign is reversed for positive values. Both positive and negative | |
| 510 values result in the decrease of valence.</p> | |
| 511 </dd> | |
| 512 <dt><strong><a name="getlargestbondorder" class="item"><strong>GetLargestBondOrder</strong></a></strong></dt> | |
| 513 <dd> | |
| 514 <div class="OptionsBox"> | |
| 515 $LargestBO =$Atom->GetLargestBondOrder();</div> | |
| 516 <p>Returns largest bond order for an <em>Atom</em> among the bonds to other atoms in a molecule.</p> | |
| 517 </dd> | |
| 518 <dt><strong><a name="getlargestbondordertoheavyatoms" class="item"><strong>GetLargestBondOrderToHeavyAtoms</strong></a></strong></dt> | |
| 519 <dd> | |
| 520 <div class="OptionsBox"> | |
| 521 $LargestBO =$Atom->GetLargestBondOrderToHeavyAtoms();</div> | |
| 522 <p>Returns largest bond order for an <em>Atom</em> among the bonds to other heavy atoms in a molecule.</p> | |
| 523 </dd> | |
| 524 <dt><strong><a name="getlargestbondordertononhydrogenatoms" class="item"><strong>GetLargestBondOrderToNonHydrogenAtoms</strong></a></strong></dt> | |
| 525 <dd> | |
| 526 <div class="OptionsBox"> | |
| 527 $LargestBO =$Atom->GetLargestBondOrderToNonHydrogenAtoms();</div> | |
| 528 <p>Returns largest bond order for an <em>Atom</em> among the bonds to other non-hydrogen atoms | |
| 529 in a molecule.</p> | |
| 530 </dd> | |
| 531 <dt><strong><a name="getlargestring" class="item"><strong>GetLargestRing</strong></a></strong></dt> | |
| 532 <dd> | |
| 533 <div class="OptionsBox"> | |
| 534 @RingAtoms = $Atom->GetLargestRing();</div> | |
| 535 <p>Returns an array of ring <em>Atom</em> objects corresponding to the largest ring containing <em>Atom</em> | |
| 536 in a molecule.</p> | |
| 537 </dd> | |
| 538 <dt><strong><a name="getlowestcommonvalence" class="item"><strong>GetLowestCommonValence</strong></a></strong></dt> | |
| 539 <dd> | |
| 540 <div class="OptionsBox"> | |
| 541 $LowestCommonValence = $Atom->GetLowestCommonValence();</div> | |
| 542 <p>Returns lowest common valence of an <em>Atom</em> which corresponds to either explicity set | |
| 543 <em>LowestCommonValence</em> atom property or highest common valence of the corresponding | |
| 544 element in the periodic table available by <strong>PerodicTable</strong> module.</p> | |
| 545 </dd> | |
| 546 <dt><strong><a name="getmassnumber" class="item"><strong>GetMassNumber</strong></a></strong></dt> | |
| 547 <dd> | |
| 548 <div class="OptionsBox"> | |
| 549 $MassNumber = $Aom->GetMassNumber();</div> | |
| 550 <p>Returns atomic weight of an <strong>Atom</strong> which corresponds to either explicity set <em>MassNumber</em> | |
| 551 atom property or mass number of the most abundant natural isotope of the corresponding element | |
| 552 in the periodic table available by <strong>PeriodicTable</strong> module.</p> | |
| 553 </dd> | |
| 554 <dt><strong><a name="getmissinghydrogens" class="item"><strong>GetMissingHydrogens</strong></a></strong></dt> | |
| 555 <dd> | |
| 556 <div class="OptionsBox"> | |
| 557 $NumOfMissingHydrogens = $Atom->GetMissingHydrogens();</div> | |
| 558 <p>Returns number of missing hydrogens for an <em>Atom</em> in a molecule. This value either | |
| 559 corresponds to explicitly set <em>ImplicitHydrogens</em> atom property or calculated as the | |
| 560 difference between the value of potential total valence and sum of bond orders to | |
| 561 both hydrogen and non-hydrogen atom neighbors.</p> | |
| 562 </dd> | |
| 563 <dt><strong><a name="getneighbors" class="item"><strong>GetNeighbors</strong></a></strong></dt> | |
| 564 <dd> | |
| 565 <div class="OptionsBox"> | |
| 566 $NumOfNeighbors = $Atom->GetNeighbors(); | |
| 567 <br/> @Neighbors = $Atom->GetNeighbors();</div> | |
| 568 <p>Returns number of neighbor atoms or an array of <em>Atom</em> objects corresponding to all | |
| 569 atoms bonded to an <em>Atom</em> in a molecule.</p> | |
| 570 </dd> | |
| 571 <dt><strong><a name="getneighborsusingatomspecification" class="item"><strong>GetNeighborsUsingAtomSpecification</strong></a></strong></dt> | |
| 572 <dd> | |
| 573 <div class="OptionsBox"> | |
| 574 @AtomNeighbors = $Atom->GetNeighborsUsingAtomSpecification($AtomSpec); | |
| 575 <br/> $NumOfNeighbors = $Atom->GetNeighborsUsingAtomSpecification($AtomSpec);</div> | |
| 576 <div class="OptionsBox"> | |
| 577 @AtomNeighbors = $Atom->GetNeighborsUsingAtomSpecification($AtomSpec, | |
| 578 @ExcludeNeighbors);</div> | |
| 579 <p>Returns number of neighbor atoms or an array of <em>Atom</em> objects matching atom | |
| 580 specification corresponding to atom neighbors of an <em>Atom</em> in a molecule. Optionally, | |
| 581 <em>Atom</em> neighbors can be excluded from the neighbors list using <em>ExcludeNeighbors</em>.</p> | |
| 582 <p>Notes:</p> | |
| 583 <div class="OptionsBox"> | |
| 584 o AtomSpecification correspond to any valid AtomicInvariant based atomic specifications | |
| 585 as supported by DoesAtomNeighborhoodMatch method | |
| 586 <br/> o Multiple atom specifications can be used in a string delimited by comma</div> | |
| 587 </dd> | |
| 588 <dt><strong><a name="getnonhydrogenatomneighbors" class="item"><strong>GetNonHydrogenAtomNeighbors</strong></a></strong></dt> | |
| 589 <dd> | |
| 590 <div class="OptionsBox"> | |
| 591 $NumOfNeighbors = $Atom->GetNonHydrogenAtomNeighbors(); | |
| 592 <br/> @Neighbors = $Atom->GetNonHydrogenAtomNeighbors();</div> | |
| 593 <p>Returns number of non-hydrogen atoms or an array of <strong>Atom</strong> objects corresponding to non-hydrogen | |
| 594 atoms bonded to an <em>Atom</em> in a molecule.</p> | |
| 595 </dd> | |
| 596 <dt><strong><a name="getnonhydrogenatomneighborsatominformation" class="item"><strong>GetNonHydrogenAtomNeighborsAtomInformation</strong></a></strong></dt> | |
| 597 <dd> | |
| 598 <div class="OptionsBox"> | |
| 599 ($NumOfAtomNeighbors, $AtomNeighborsRef, | |
| 600 $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom-> | |
| 601 GetNonHydrogenAtomNeighborsAtomInformation();</div> | |
| 602 <p>Returns atoms information for all non-hydrogen atoms attached to an <em>Atom</em> | |
| 603 in a molecule.</p> | |
| 604 <p>The following values are returned:</p> | |
| 605 <div class="OptionsBox"> | |
| 606 o Number of non-hydrogen atom neighbors | |
| 607 <br/> o A reference to an array containing atom objects corresponding to | |
| 608 non-hydrogen atom neighbors | |
| 609 <br/> o Number of different types of non-hydrogen atom neighbors | |
| 610 <br/> o A reference to a hash containing atom symbol as key with value | |
| 611 corresponding to its count for non-hydrogen atom neighbors</div> | |
| 612 </dd> | |
| 613 <dt><strong><a name="getnonhydrogenatomneighborsbondinformation" class="item"><strong>GetNonHydrogenAtomNeighborsBondInformation</strong></a></strong></dt> | |
| 614 <dd> | |
| 615 <div class="OptionsBox"> | |
| 616 ($NumOfBonds, $BondTypeCountMapRef, | |
| 617 <br/> $AtomsBondTypesCountMapRef, | |
| 618 <br/> $AtomsBondTypeAtomsMap) = $Atom-> | |
| 619 GetNonHydrogenAtomNeighborsBondInformation();</div> | |
| 620 <p>Returns bonds information for all non-hydrogen atoms attached to an <em>Atom</em> | |
| 621 in a molecule.</p> | |
| 622 <p>The following values are returned:</p> | |
| 623 <div class="OptionsBox"> | |
| 624 o Number of bonds to non-hydrogen atom neighbors | |
| 625 <br/> o A reference to an array containing bond objects corresponding to | |
| 626 non-hydrogen atom neighbors | |
| 627 <br/> o A reference to a hash containing bond type as key with value | |
| 628 corresponding to its count for non-hydrogen atom neighbors. Bond | |
| 629 types are: Single, Double or Triple | |
| 630 <br/> o A reference to a hash containing atom symbol as key pointing to bond | |
| 631 type as second key with values corresponding to count of bond types for atom | |
| 632 symbol for non-hydrogen atom neighbors | |
| 633 <br/> o A reference to a hash containing atom symbol as key pointing to bond | |
| 634 type as second key with values corresponding to atom objects array involved | |
| 635 in corresponding bond type for atom symbol for non-hydrogen atom neighbors</div> | |
| 636 </dd> | |
| 637 <dt><strong><a name="getnonhydrogenneighborofhydrogenatom" class="item"><strong>GetNonHydrogenNeighborOfHydrogenAtom</strong></a></strong></dt> | |
| 638 <dd> | |
| 639 <div class="OptionsBox"> | |
| 640 $Atom = $Atom->GetNonHydrogenNeighborOfHydrogenAtom();</div> | |
| 641 <p>Returns non-hydrogen or heavy atom neighbor of a hydrogen atom in a molecule..</p> | |
| 642 </dd> | |
| 643 <dt><strong><a name="getnumofaromaticbondstoheavyatoms" class="item"><strong>GetNumOfAromaticBondsToHeavyAtoms</strong></a></strong></dt> | |
| 644 <dd> | |
| 645 <div class="OptionsBox"> | |
| 646 $NumOfBonds = $Atom->GetNumOfAromaticBondsToHeavyAtoms();</div> | |
| 647 <p>Returns number of aromatic bonds from an <em>Atom</em> to other non-hydrogen or heavy atoms in | |
| 648 a molecule.</p> | |
| 649 </dd> | |
| 650 <dt><strong><a name="getnumofaromaticbondstononhydrogenatoms" class="item"><strong>GetNumOfAromaticBondsToNonHydrogenAtoms</strong></a></strong></dt> | |
| 651 <dd> | |
| 652 <div class="OptionsBox"> | |
| 653 $NumOfBonds = $Atom->GetNumOfAromaticBondsToNonHydrogenAtoms();</div> | |
| 654 <p>Returns number of aromatic bonds from an <em>Atom</em> to other non-hydrogen or heavy atoms in | |
| 655 a molecule.</p> | |
| 656 </dd> | |
| 657 <dt><strong><a name="getnumofbonds" class="item"><strong>GetNumOfBonds</strong></a></strong></dt> | |
| 658 <dd> | |
| 659 <div class="OptionsBox"> | |
| 660 $NumOfBonds = $Atom->GetNumOfBonds();</div> | |
| 661 <p>Returns number of bonds from an <em>Atom</em> to other atoms in a molecule.</p> | |
| 662 </dd> | |
| 663 <dt><strong><a name="getnumofbondsavailableforheavyatoms" class="item"><strong>GetNumOfBondsAvailableForHeavyAtoms</strong></a></strong></dt> | |
| 664 <dd> | |
| 665 <div class="OptionsBox"> | |
| 666 $NumOfBonds = $Atom->GetNumOfBondsAvailableForHeavyAtoms();</div> | |
| 667 <p>Get number of bonds available to form additional bonds with heavy atoms, excluding | |
| 668 any implicit bonds to hydrogens set using <em>ImplicitHydrogens</em> property.</p> | |
| 669 <p>It's different from number of implicit or missing hydrogens, both of which are equivalent.</p> | |
| 670 <p>For example, in a SMILES string, [nH] ring atom corresponds to an aromatic nitrogen. | |
| 671 Although the hydrogen specified for n is treated internally as implicit hydrogen and shows | |
| 672 up in missing hydrogen count, it's not available to participate in double bonds to additional | |
| 673 heavy atoms.</p> | |
| 674 </dd> | |
| 675 <dt><strong><a name="getnumofbondsavailablefornonhydrogenatoms" class="item"><strong>GetNumOfBondsAvailableForNonHydrogenAtoms</strong></a></strong></dt> | |
| 676 <dd> | |
| 677 <div class="OptionsBox"> | |
| 678 $NumOfBonds = $Atom->GetNumOfBondsAvailableForNonHydrogenAtoms();</div> | |
| 679 <p>Get number of bonds available to form additional bonds with heavy atoms, excluding | |
| 680 any implicit bonds to hydrogens set using ImplicitHydrogens property.</p> | |
| 681 </dd> | |
| 682 <dt><strong><a name="getnumofbondstoheavyatoms" class="item"><strong>GetNumOfBondsToHeavyAtoms</strong></a></strong></dt> | |
| 683 <dd> | |
| 684 <div class="OptionsBox"> | |
| 685 $NumOfBondsToHeavyAtoms = $Atom->GetNumOfBondsToHeavyAtoms();</div> | |
| 686 <p>Returns number of bonds from an <em>Atom</em> to other heavy atoms in a molecule.</p> | |
| 687 </dd> | |
| 688 <dt><strong><a name="getnumofbondstohydrogenatoms" class="item"><strong>GetNumOfBondsToHydrogenAtoms</strong></a></strong></dt> | |
| 689 <dd> | |
| 690 <div class="OptionsBox"> | |
| 691 $NumOfBonds = $Atom->GetNumOfBondsToHydrogenAtoms();</div> | |
| 692 <p>Returns number of bonds from an <em>Atom</em> to other hydrogen atoms in a molecule.</p> | |
| 693 </dd> | |
| 694 <dt><strong><a name="getnumofbondstononhydrogenatoms" class="item"><strong>GetNumOfBondsToNonHydrogenAtoms</strong></a></strong></dt> | |
| 695 <dd> | |
| 696 <div class="OptionsBox"> | |
| 697 $NumOfBonds = $Atom->GetNumOfBondsToNonHydrogenAtoms();</div> | |
| 698 <p>Returns number of bonds from an <em>Atom</em> to other non-hydrogen atoms in a molecule.</p> | |
| 699 </dd> | |
| 700 <dt><strong><a name="getnumofbondtypestoheavyatoms" class="item"><strong>GetNumOfBondTypesToHeavyAtoms</strong></a></strong></dt> | |
| 701 <dd> | |
| 702 <div class="OptionsBox"> | |
| 703 ($NumOfSingleBonds, $NumOfDoubleBonds, | |
| 704 $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom-> | |
| 705 GetNumOfBondTypesToHeavyAtoms($CountAromaticBonds);</div> | |
| 706 <p>Get number of single, double, triple, and aromatic bonds from an <em>Atom</em> to all other | |
| 707 non-hydrogen atoms in a molecule.</p> | |
| 708 <p>Value of <em>CountAtomaticBonds</em> parameter controls whether number of aromatic | |
| 709 bonds is returned; default is not to count aromatic bonds. During counting of | |
| 710 aromatic bonds, the bond marked aromatic is not included in the count | |
| 711 of other bond types.</p> | |
| 712 </dd> | |
| 713 <dt><strong><a name="getnumofbondtypestononhydrogenatoms" class="item"><strong>GetNumOfBondTypesToNonHydrogenAtoms</strong></a></strong></dt> | |
| 714 <dd> | |
| 715 <div class="OptionsBox"> | |
| 716 ($NumOfSingleBonds, $NumOfDoubleBonds, | |
| 717 $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom-> | |
| 718 GetNumOfBondTypesToNonHydrogenAtoms($CountAromaticBonds);</div> | |
| 719 <p>Get number of single, double, triple, and aromatic bonds from an <em>Atom</em> to all other | |
| 720 non-hydrogen atoms in a molecule.</p> | |
| 721 <p>Value of <em>CountAtomaticBonds</em> parameter controls whether number of aromatic | |
| 722 bonds is returned; default is not to count aromatic bonds. During counting of | |
| 723 aromatic bonds, the bond marked aromatic is not included in the count | |
| 724 of other bond types.</p> | |
| 725 </dd> | |
| 726 <dt><strong><a name="getnumofdoublebondstoheavyatoms" class="item"><strong>GetNumOfDoubleBondsToHeavyAtoms</strong></a></strong></dt> | |
| 727 <dd> | |
| 728 <div class="OptionsBox"> | |
| 729 $NumOfDoubleBonds = $Atom->GetNumOfDoubleBondsToHeavyAtoms();</div> | |
| 730 <p>Returns number of double bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen | |
| 731 atoms in a molecule.</p> | |
| 732 </dd> | |
| 733 <dt><strong><a name="getnumofdoublebondstononhydrogenatoms" class="item"><strong>GetNumOfDoubleBondsToNonHydrogenAtoms</strong></a></strong></dt> | |
| 734 <dd> | |
| 735 <div class="OptionsBox"> | |
| 736 $NumOfDoubleBonds =$Atom->GetNumOfDoubleBondsToNonHydrogenAtoms();</div> | |
| 737 <p>Returns number of double bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen | |
| 738 atoms in a molecule.</p> | |
| 739 </dd> | |
| 740 <dt><strong><a name="getnumofheavyatomneighbors" class="item"><strong>GetNumOfHeavyAtomNeighbors</strong></a></strong></dt> | |
| 741 <dd> | |
| 742 <div class="OptionsBox"> | |
| 743 $NumOfNeighbors = $Atom->GetNumOfHeavyAtomNeighbors();</div> | |
| 744 <p>Returns number heavy atom neighbors for an <em>Atom</em> in a molecule.</p> | |
| 745 </dd> | |
| 746 <dt><strong><a name="getnumofhydrogenatomneighbors" class="item"><strong>GetNumOfHydrogenAtomNeighbors</strong></a></strong></dt> | |
| 747 <dd> | |
| 748 <div class="OptionsBox"> | |
| 749 $NumOfNeighbors = $Atom->GetNumOfHydrogenAtomNeighbors();</div> | |
| 750 <p>Returns number hydrogens atom neighbors for an <em>Atom</em> in a molecule.</p> | |
| 751 </dd> | |
| 752 <dt><strong><a name="getnumofmissinghydrogens" class="item"><strong>GetNumOfMissingHydrogens</strong></a></strong></dt> | |
| 753 <dd> | |
| 754 <div class="OptionsBox"> | |
| 755 $NumOfMissingHydrogens = $Atom->GetNumOfMissingHydrogens();</div> | |
| 756 <p>Returns number of implicit hydrogens for an <em>Atom</em> in a molecule. This value either | |
| 757 corresponds to explicitly set <em>ImplicitHydrogens</em> atom property or calculated as the | |
| 758 difference between the value of potential total valence and sum of bond orders to | |
| 759 both hydrogen and non-hydrogen atom neighbors.</p> | |
| 760 </dd> | |
| 761 <dt><strong><a name="getnumofexplicithydrogens" class="item"><strong>GetNumOfExplicitHydrogens</strong></a></strong></dt> | |
| 762 <dd> | |
| 763 <div class="OptionsBox"> | |
| 764 $NumOfExplicitHydrogens = $Atom->GetNumOfExplicitHydrogens();</div> | |
| 765 <p>Returns number hydrogens atom neighbors for an <em>Atom</em> in a molecule.</p> | |
| 766 </dd> | |
| 767 <dt><strong><a name="getnumofhydrogens" class="item"><strong>GetNumOfHydrogens</strong></a></strong></dt> | |
| 768 <dd> | |
| 769 <div class="OptionsBox"> | |
| 770 $NumOfHydrogens = $Atom->GetNumOfHydrogens();</div> | |
| 771 <p>Returns total number of hydrogens for an <em>Atom</em> in a molecule including both hydrogen atom | |
| 772 neighbors and implicit hydrogens.</p> | |
| 773 </dd> | |
| 774 <dt><strong><a name="getnumofimplicithydrogens" class="item"><strong>GetNumOfImplicitHydrogens</strong></a></strong></dt> | |
| 775 <dd> | |
| 776 <div class="OptionsBox"> | |
| 777 $NumOfImplicitHydrogens = $Atom->GetNumOfImplicitHydrogens();</div> | |
| 778 <p>Returns number of implicit hydrogens for an <em>Atom</em> in a molecule. This value either | |
| 779 corresponds to explicitly set <em>ImplicitHydrogens</em> atom property or calculated as the | |
| 780 difference between the value of potential total valence and sum of bond orders to | |
| 781 both hydrogen and non-hydrogen atom neighbors.</p> | |
| 782 </dd> | |
| 783 <dt><strong><a name="getnumofneighbors" class="item"><strong>GetNumOfNeighbors</strong></a></strong></dt> | |
| 784 <dd> | |
| 785 <div class="OptionsBox"> | |
| 786 $NumOfNeighbors = $Atom->GetNumOfNeighbors();</div> | |
| 787 <p>Returns number atom neighbors for an <em>Atom</em> in a molecule.</p> | |
| 788 </dd> | |
| 789 <dt><strong><a name="getnumofnonhydrogenatomneighbors" class="item"><strong>GetNumOfNonHydrogenAtomNeighbors</strong></a></strong></dt> | |
| 790 <dd> | |
| 791 <div class="OptionsBox"> | |
| 792 $NumNeighbors = $This->GetNumOfNonHydrogenAtomNeighbors();</div> | |
| 793 <p>Returns number non-hydrogens atom neighbors for an <em>Atom</em> in a molecule.</p> | |
| 794 </dd> | |
| 795 <dt><strong><a name="getnumofrings" class="item"><strong>GetNumOfRings</strong></a></strong></dt> | |
| 796 <dd> | |
| 797 <div class="OptionsBox"> | |
| 798 $NumOfRings = $Atom->GetNumOfRings();</div> | |
| 799 <p>Returns number of rings containing <em>Atom</em> in a molecule.</p> | |
| 800 </dd> | |
| 801 <dt><strong><a name="getnumofringswithevensize" class="item"><strong>GetNumOfRingsWithEvenSize</strong></a></strong></dt> | |
| 802 <dd> | |
| 803 <div class="OptionsBox"> | |
| 804 $NumOfRings = $Atom->GetNumOfRingsWithEvenSize();</div> | |
| 805 <p>Returns number of rings with even size containing <em>Atom</em> in a molecule.</p> | |
| 806 </dd> | |
| 807 <dt><strong><a name="getnumofringswithoddsize" class="item"><strong>GetNumOfRingsWithOddSize</strong></a></strong></dt> | |
| 808 <dd> | |
| 809 <div class="OptionsBox"> | |
| 810 $NumOfRings = $Atom->GetNumOfRingsWithOddSize();</div> | |
| 811 <p>Returns number of rings with odd size containing <em>Atom</em> in a molecule.</p> | |
| 812 </dd> | |
| 813 <dt><strong><a name="getnumofringswithsize" class="item"><strong>GetNumOfRingsWithSize</strong></a></strong></dt> | |
| 814 <dd> | |
| 815 <div class="OptionsBox"> | |
| 816 $NumOfRings = $Atom->GetNumOfRingsWithSize($RingSize);</div> | |
| 817 <p>Returns number of rings with specific <em>RingSize</em> containing <em>Atom</em> in a molecule.</p> | |
| 818 </dd> | |
| 819 <dt><strong><a name="getnumofringswithsizegreaterthan" class="item"><strong>GetNumOfRingsWithSizeGreaterThan</strong></a></strong></dt> | |
| 820 <dd> | |
| 821 <div class="OptionsBox"> | |
| 822 $NumOfRings = $Atom->GetNumOfRingsWithSizeGreaterThan($RingSize);</div> | |
| 823 <p>Returns number of rings with size greater than specific <em>RingSize</em> containing <em>Atom</em> | |
| 824 in a molecule.</p> | |
| 825 </dd> | |
| 826 <dt><strong><a name="getnumofringswithsizelessthan" class="item"><strong>GetNumOfRingsWithSizeLessThan</strong></a></strong></dt> | |
| 827 <dd> | |
| 828 <div class="OptionsBox"> | |
| 829 $NumOfRings = $Atom->GetNumOfRingsWithSizeLessThan($RingSize);</div> | |
| 830 <p>Returns number of rings with size less than specific <em>RingSize</em> containing <em>Atom</em> in a molecule.</p> | |
| 831 </dd> | |
| 832 <dt><strong><a name="getnumofsigmaandpibondstoheavyatoms" class="item"><strong>GetNumOfSigmaAndPiBondsToHeavyAtoms</strong></a></strong></dt> | |
| 833 <dd> | |
| 834 <div class="OptionsBox"> | |
| 835 ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom-> | |
| 836 GetNumOfSigmaAndPiBondsToHeavyAtoms();</div> | |
| 837 <p>Get number of sigma and pi bonds from an <em>Atom</em> to all other non-hydrogen | |
| 838 atoms in a molecule.</p> | |
| 839 <p>Sigma and pi bonds are counted using the following methodology: a single bond | |
| 840 correspond to one sigma bond; a double bond contributes one to sigma bond count | |
| 841 and one to pi bond count; a triple bond contributes one to sigma bond count and | |
| 842 two to pi bond count.</p> | |
| 843 </dd> | |
| 844 <dt><strong><a name="getnumofsigmaandpibondstononhydrogenatoms" class="item"><strong>GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</strong></a></strong></dt> | |
| 845 <dd> | |
| 846 <div class="OptionsBox"> | |
| 847 ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom-> | |
| 848 GetNumOfSigmaAndPiBondsToNonHydrogenAtoms();</div> | |
| 849 <p>Get number of sigma and pi bonds from an <em>Atom</em> to all other non-hydrogen | |
| 850 atoms in a molecule.</p> | |
| 851 <p>Sigma and pi bonds are counted using the following methodology: a single bond | |
| 852 correspond to one sigma bond; a double bond contributes one to sigma bond count | |
| 853 and one to pi bond count; a triple bond contributes one to sigma bond count and | |
| 854 two to pi bond count.</p> | |
| 855 </dd> | |
| 856 <dt><strong><a name="getnumofsinglebondstononhydrogenatoms" class="item"><strong>GetNumOfSingleBondsToNonHydrogenAtoms</strong></a></strong></dt> | |
| 857 <dd> | |
| 858 <div class="OptionsBox"> | |
| 859 $NumOfSingleBonds =$Atom->GetNumOfSingleBondsToNonHydrogenAtoms();</div> | |
| 860 <p>Returns number of single bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen | |
| 861 atoms in a molecule.</p> | |
| 862 </dd> | |
| 863 <dt><strong><a name="getnumofsinglebondstoheavyatoms" class="item"><strong>GetNumOfSingleBondsToHeavyAtoms</strong></a></strong></dt> | |
| 864 <dd> | |
| 865 <div class="OptionsBox"> | |
| 866 $NumOfSingleBonds = $Atom->GetNumOfSingleBondsToHeavyAtoms();</div> | |
| 867 <p>Returns number of single bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen | |
| 868 atoms in a molecule.</p> | |
| 869 </dd> | |
| 870 <dt><strong><a name="getnumoftriplebondstononhydrogenatoms" class="item"><strong>GetNumOfTripleBondsToNonHydrogenAtoms</strong></a></strong></dt> | |
| 871 <dd> | |
| 872 <div class="OptionsBox"> | |
| 873 $NumOfTripleBonds =$Atom->GetNumOfTripleBondsToNonHydrogenAtoms();</div> | |
| 874 <p>Returns number of triple bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen | |
| 875 atoms in a molecule.</p> | |
| 876 </dd> | |
| 877 <dt><strong><a name="getnumoftriplebondstoheavyatoms" class="item"><strong>GetNumOfTripleBondsToHeavyAtoms</strong></a></strong></dt> | |
| 878 <dd> | |
| 879 <div class="OptionsBox"> | |
| 880 $NumOfTripleBonds = $Atom->GetNumOfTripleBondsToHeavyAtoms();</div> | |
| 881 <p>Returns number of triple bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen | |
| 882 atoms in a molecule.</p> | |
| 883 </dd> | |
| 884 <dt><strong><a name="getperiodnumber" class="item"><strong>GetPeriodNumber</strong></a></strong></dt> | |
| 885 <dd> | |
| 886 <div class="OptionsBox"> | |
| 887 $PeriodNumber = $Atom->GetPeriodNumber();</div> | |
| 888 <p>Returns periodic table period number for an <em>Atom</em> in a molecule with a valid atomic number .</p> | |
| 889 </dd> | |
| 890 <dt><strong><a name="getrings" class="item"><strong>GetRings</strong></a></strong></dt> | |
| 891 <dd> | |
| 892 <div class="OptionsBox"> | |
| 893 @Rings = $Aotm->GetRings();</div> | |
| 894 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings containing | |
| 895 <em>Atom</em> in a molecule.</p> | |
| 896 </dd> | |
| 897 <dt><strong><a name="getringswithevensize" class="item"><strong>GetRingsWithEvenSize</strong></a></strong></dt> | |
| 898 <dd> | |
| 899 <div class="OptionsBox"> | |
| 900 @Rings = $Aotm->GetRingsWithEvenSize();</div> | |
| 901 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with even size | |
| 902 containing <em>Atom</em> in a molecule.</p> | |
| 903 </dd> | |
| 904 <dt><strong><a name="getringswithoddsize" class="item"><strong>GetRingsWithOddSize</strong></a></strong></dt> | |
| 905 <dd> | |
| 906 <div class="OptionsBox"> | |
| 907 @Rings = $Aotm->GetRingsWithOddSize();</div> | |
| 908 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with odd size | |
| 909 containing <em>Atom</em> in a molecule.</p> | |
| 910 </dd> | |
| 911 <dt><strong><a name="getringswithsize" class="item"><strong>GetRingsWithSize</strong></a></strong></dt> | |
| 912 <dd> | |
| 913 <div class="OptionsBox"> | |
| 914 @Rings = $Aotm->GetRingsWithSize($RingSize);</div> | |
| 915 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with specific | |
| 916 <em>RingSize </em>containing <em>Atom</em> in a molecule.</p> | |
| 917 </dd> | |
| 918 <dt><strong><a name="getringswithsizegreaterthan" class="item"><strong>GetRingsWithSizeGreaterThan</strong></a></strong></dt> | |
| 919 <dd> | |
| 920 <div class="OptionsBox"> | |
| 921 @Rings = $Aotm->GetRingsWithSizeGreaterThan($RingSize);</div> | |
| 922 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with size | |
| 923 greater than specific <em>RingSize </em>containing <em>Atom</em> in a molecule.</p> | |
| 924 </dd> | |
| 925 <dt><strong><a name="getringswithsizelessthan" class="item"><strong>GetRingsWithSizeLessThan</strong></a></strong></dt> | |
| 926 <dd> | |
| 927 <div class="OptionsBox"> | |
| 928 @Rings = $Aotm->GetRingsWithSizeLessThan($RingSize);</div> | |
| 929 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with size | |
| 930 less than specific <em>RingSize </em>containing <em>Atom</em> in a molecule.</p> | |
| 931 </dd> | |
| 932 <dt><strong><a name="getsizeoflargestring" class="item"><strong>GetSizeOfLargestRing</strong></a></strong></dt> | |
| 933 <dd> | |
| 934 <div class="OptionsBox"> | |
| 935 $Size = $Atom->GetSizeOfLargestRing();</div> | |
| 936 <p>Returns size of the largest ring containing <em>Atom</em> in a molecule.</p> | |
| 937 </dd> | |
| 938 <dt><strong><a name="getsizeofsmallestring" class="item"><strong>GetSizeOfSmallestRing</strong></a></strong></dt> | |
| 939 <dd> | |
| 940 <div class="OptionsBox"> | |
| 941 $Size = $Atom->GetSizeOfSmallestRing();</div> | |
| 942 <p>Returns size of the smallest ring containing <em>Atom</em> in a molecule.</p> | |
| 943 </dd> | |
| 944 <dt><strong><a name="getsmallestring" class="item"><strong>GetSmallestRing</strong></a></strong></dt> | |
| 945 <dd> | |
| 946 <div class="OptionsBox"> | |
| 947 @RingAtoms = $Atom->GetSmallestRing();</div> | |
| 948 <p>Returns an array of ring <em>Atom</em> objects corresponding to the largest ring containing <em>Atom</em> | |
| 949 in a molecule.</p> | |
| 950 </dd> | |
| 951 <dt><strong><a name="getspinmultiplicity" class="item"><strong>GetSpinMultiplicity</strong></a></strong></dt> | |
| 952 <dd> | |
| 953 <div class="OptionsBox"> | |
| 954 $SpinMultiplicity = $Atom->GetSpinMultiplicity();</div> | |
| 955 <p>Returns spin multiplicity of an <em>Atom</em> corresponding to one of these three | |
| 956 values: explicitly set <strong>SpinMultiplicity</strong> property value; calculated from | |
| 957 <strong>FreeRadicalElectrons</strong> property; value of 0.</p> | |
| 958 <p>The <strong>SpinMultiplicity</strong> is calculate from <em>FreeRadicalElectrons</em> property as | |
| 959 follows:</p> | |
| 960 <div class="OptionsBox"> | |
| 961 FreeRadicalElectrons: 1; SpinMultiplicity: 2 | |
| 962 <br/> FreeRadicalElectrons: 2; SpinMultiplicity: 1 | |
| 963 <br/> FreeRadicalElectrons: other; SpinMultiplicity: 0</div> | |
| 964 </dd> | |
| 965 <dt><strong><a name="getsumofbondorders" class="item"><strong>GetSumOfBondOrders</strong></a></strong></dt> | |
| 966 <dd> | |
| 967 <div class="OptionsBox"> | |
| 968 $SumBondOrders = $Atom->GetSumOfBondOrders();</div> | |
| 969 <p>Returns sum of bond orders corresponding to all atoms bonded to an <em>Atom</em> in a molecule.</p> | |
| 970 </dd> | |
| 971 <dt><strong><a name="getsumofbondorderstoheavyatoms" class="item"><strong>GetSumOfBondOrdersToHeavyAtoms</strong></a></strong></dt> | |
| 972 <dd> | |
| 973 <div class="OptionsBox"> | |
| 974 $SumBondOrders = $Atom->GetSumOfBondOrdersToHeavyAtoms();</div> | |
| 975 <p>Returns sum of bond orders corresponding to all heavy atoms bonded to an <em>Atom</em> in a molecule.</p> | |
| 976 </dd> | |
| 977 <dt><strong><a name="getsumofbondorderstohydrogenatoms" class="item"><strong>GetSumOfBondOrdersToHydrogenAtoms</strong></a></strong></dt> | |
| 978 <dd> | |
| 979 <div class="OptionsBox"> | |
| 980 $SumBondOrders = $Atom->GetSumOfBondOrdersToHydrogenAtoms();</div> | |
| 981 <p>Returns sum of bond orders corresponding to all hydrogen atoms bonded to an <em>Atom</em> in a molecule.</p> | |
| 982 </dd> | |
| 983 <dt><strong><a name="getsumofbondorderstononhydrogenatoms" class="item"><strong>GetSumOfBondOrdersToNonHydrogenAtoms</strong></a></strong></dt> | |
| 984 <dd> | |
| 985 <div class="OptionsBox"> | |
| 986 $SumBondOrders = $Atom->GetSumOfBondOrdersToNonHydrogenAtoms();</div> | |
| 987 <p>Returns sum of bond orders corresponding to all non-hydrogen atoms bonded to an <em>Atom</em> | |
| 988 in a molecule.</p> | |
| 989 </dd> | |
| 990 <dt><strong><a name="getvalence" class="item"><strong>GetValence</strong></a></strong></dt> | |
| 991 <dd> | |
| 992 <div class="OptionsBox"> | |
| 993 $Valence = $Atom->GetValence();</div> | |
| 994 <p>Returns valence of an <em>Atom</em> in a molecule. Valence corresponds to number of electrons used | |
| 995 by an atom in bonding:</p> | |
| 996 <div class="OptionsBox"> | |
| 997 Valence = ValenceElectrons - ValenceFreeElectrons = BondingElectrons</div> | |
| 998 <p>Single, double and triple bonds with bond orders of 1, 2, and 3 correspond to | |
| 999 contribution of 1, 2, and 3 bonding electrons. So:</p> | |
| 1000 <div class="OptionsBox"> | |
| 1001 Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</div> | |
| 1002 <p>where positive and negative values of FormalCharge increase and decrease the number of bonding | |
| 1003 electrons, respectively.</p> | |
| 1004 <p>The current release of MayaChemTools supports the following three valence models, which | |
| 1005 are used during calculation of implicit hydrogens: MDLValenceModel, DaylightValenceModel, | |
| 1006 InternalValenceModel or MayaChemToolsValenceModel.</p> | |
| 1007 <p>Notes:</p> | |
| 1008 <div class="OptionsBox"> | |
| 1009 . Missing hydrogens are included in the valence. | |
| 1010 <br/> . For neutral molecules, valence and sum of bond orders are equal. | |
| 1011 <br/> . For molecules containing only single bonds, SumOfBondOrders and | |
| 1012 NumOfBonds are equal. | |
| 1013 <br/> . Free radical electrons lead to the decrease in valence. For atoms with | |
| 1014 explicit assignment of SpinMultiplicity property values corresponding to | |
| 1015 Singlet (two unparied electrons corresponding to one spin state), Doublet | |
| 1016 (free radical; an unpaired electron corresponding to two spin states), | |
| 1017 and Triplet (two unparied electrons corresponding to three spin states; | |
| 1018 divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</div> | |
| 1019 <div class="OptionsBox"> | |
| 1020 SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1 (one valence | |
| 1021 <br/> electron not available for bonding) | |
| 1022 <br/> SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2 (two | |
| 1023 <br/> valence electrons not available for bonding)</div> | |
| 1024 </dd> | |
| 1025 <dt><strong><a name="getvalenceelectrons" class="item"><strong>GetValenceElectrons</strong></a></strong></dt> | |
| 1026 <dd> | |
| 1027 <div class="OptionsBox"> | |
| 1028 $ValenceElectrons = $Atom->GetValenceElectrons();</div> | |
| 1029 <p>Returns valence electrons for an <strong>Atom</strong> which corresponds to either explicity set <em>ValenceElectrons</em> | |
| 1030 atom property or valence electrons for the corresponding element in the periodic table available by | |
| 1031 <strong>PeriodicTable</strong> module.</p> | |
| 1032 </dd> | |
| 1033 <dt><strong><a name="getvalencefreeelectrons" class="item"><strong>GetValenceFreeElectrons</strong></a></strong></dt> | |
| 1034 <dd> | |
| 1035 <div class="OptionsBox"> | |
| 1036 $ValenceFreeElectrons = $Atom->GetValenceFreeElectrons(); | |
| 1037 <br/> $ValenceFreeElectrons = $Atom->GetValenceFreeElectrons( | |
| 1038 $ExcludeFreeRadicalElectrons);</div> | |
| 1039 <p>Returns valence frees electrons for an <strong>Atom</strong> in a molecule. It corresponds to:</p> | |
| 1040 <div class="OptionsBox"> | |
| 1041 ValenceElectrons - Valence | |
| 1042 <br/> or | |
| 1043 <br/> ValenceElectrons - NumOfMissingHydrogens - SumOfBondOrders - FormalCharge</div> | |
| 1044 <p>Free radical electrons are included in the valence free electrons count by default.</p> | |
| 1045 <p>Examples:</p> | |
| 1046 <div class="OptionsBox"> | |
| 1047 NH3: ValenceFreeElectrons = 5 - 3 = 5 - 3 - 0 - 0 = 2 | |
| 1048 <br/> NH2: ValenceFreeElectrons = 5 - 3 = 5 - 2 - 1 - 0 = 2 | |
| 1049 <br/> NH4+; ValenceFreeElectrons = 5 - 5 = 5 - 4 - 0 - 1 = 0 | |
| 1050 <br/> NH3+; ValenceFreeElectrons = 5 - 5 = 5 - 3 - 1 - 1 = 0 | |
| 1051 <br/> C(=O)O- : ValenceFreeElectrons on O- = 6 - 0 = 6 - 1 - 0 - (-1) = 6 | |
| 1052 <br/> C(=O)O- : ValenceFreeElectrons on =O = 6 - 2 = 6 - 2 - 0 - 0 = 4</div> | |
| 1053 </dd> | |
| 1054 <dt><strong><a name="getx" class="item"><strong>GetX</strong></a></strong></dt> | |
| 1055 <dd> | |
| 1056 <div class="OptionsBox"> | |
| 1057 $X = $Atom->GetX();</div> | |
| 1058 <p>Returns value of X-coordinate for an <em>Atom</em>.</p> | |
| 1059 </dd> | |
| 1060 <dt><strong><a name="getxyz" class="item"><strong>GetXYZ</strong></a></strong></dt> | |
| 1061 <dd> | |
| 1062 <div class="OptionsBox"> | |
| 1063 @XYZ = $Atom->GetXYZ(); | |
| 1064 <br/> $XYZRef = $Atom->GetXYZ();</div> | |
| 1065 <p>Returns an array or a reference to an array containing values for <em>Atom</em> coordinates.</p> | |
| 1066 </dd> | |
| 1067 <dt><strong><a name="getxyzvector" class="item"><strong>GetXYZVector</strong></a></strong></dt> | |
| 1068 <dd> | |
| 1069 <div class="OptionsBox"> | |
| 1070 $XYZVector = $Atom->GetXYZVector();</div> | |
| 1071 <p>Returns a <em>Vector</em> object containing values for <em>Atom</em> coordinates</p> | |
| 1072 </dd> | |
| 1073 <dt><strong><a name="gety" class="item"><strong>GetY</strong></a></strong></dt> | |
| 1074 <dd> | |
| 1075 <div class="OptionsBox"> | |
| 1076 $Y = $Atom->GetY();</div> | |
| 1077 <p>Returns value of Y-coordinate for an <em>Atom</em>.</p> | |
| 1078 </dd> | |
| 1079 <dt><strong><a name="getz" class="item"><strong>GetZ</strong></a></strong></dt> | |
| 1080 <dd> | |
| 1081 <div class="OptionsBox"> | |
| 1082 $Z = $Atom->GetZ();</div> | |
| 1083 <p>Returns value of Z-coordinate for an <em>Atom</em>.</p> | |
| 1084 </dd> | |
| 1085 <dt><strong><a name="isamidecarbon" class="item"><strong>IsAmideCarbon</strong></a></strong></dt> | |
| 1086 <dd> | |
| 1087 <div class="OptionsBox"> | |
| 1088 $Status = $Atom->IsAmideCarbon();</div> | |
| 1089 <p>Returns 1 or 0 based on whether it's amide carbon <em>Atom</em>.</p> | |
| 1090 <p>An amide group is defineds as:</p> | |
| 1091 <div class="OptionsBox"> | |
| 1092 R-C(=O)-N(-R')-R''</div> | |
| 1093 <p>where:</p> | |
| 1094 <div class="OptionsBox"> | |
| 1095 o R = Hydrogen or groups of atoms attached through carbon | |
| 1096 <br/> o R' = Hydrogens or groups of atoms attached through carbon or | |
| 1097 hetro atoms | |
| 1098 <br/> o R'' = Hydrogens or groups of atoms attached through carbon or | |
| 1099 hetro atoms</div> | |
| 1100 </dd> | |
| 1101 <dt><strong><a name="isamidenitrogen" class="item"><strong>IsAmideNitrogen</strong></a></strong></dt> | |
| 1102 <dd> | |
| 1103 <div class="OptionsBox"> | |
| 1104 $Status = $Atom->IsAmideNitrogen();</div> | |
| 1105 <p>Returns 1 or 0 based on whether it's amide nitrogen <em>Atom</em>.</p> | |
| 1106 </dd> | |
| 1107 <dt><strong><a name="isaromatic" class="item"><strong>IsAromatic</strong></a></strong></dt> | |
| 1108 <dd> | |
| 1109 <div class="OptionsBox"> | |
| 1110 $Status = $Atom->IsAromatic();</div> | |
| 1111 <p>Returns 1 or 0 based on whether it's an aromatic <em>Atom</em>.</p> | |
| 1112 </dd> | |
| 1113 <dt><strong><a name="isarsenic" class="item"><strong>IsArsenic</strong></a></strong></dt> | |
| 1114 <dd> | |
| 1115 <div class="OptionsBox"> | |
| 1116 $Status = $Atom->IsArsenic();</div> | |
| 1117 <p>Returns 1 or 0 based on whether it's an arsenic <em>Atom</em>.</p> | |
| 1118 </dd> | |
| 1119 <dt><strong><a name="isbondedtoatom" class="item"><strong>IsBondedToAtom</strong></a></strong></dt> | |
| 1120 <dd> | |
| 1121 <div class="OptionsBox"> | |
| 1122 $Status = $Atom->IsBondedToAtom($OtherAtom);</div> | |
| 1123 <p>Returns 1 or 0 based on whether <em>Atom</em> is bonded to <em>OtherAtom</em>.</p> | |
| 1124 </dd> | |
| 1125 <dt><strong><a name="isbromine" class="item"><strong>IsBromine</strong></a></strong></dt> | |
| 1126 <dd> | |
| 1127 <div class="OptionsBox"> | |
| 1128 $Status = $Atom->IsBromine();</div> | |
| 1129 <p>Returns 1 or 0 based on whether it's a bromine <em>Atom</em>.</p> | |
| 1130 </dd> | |
| 1131 <dt><strong><a name="iscarbon" class="item"><strong>IsCarbon</strong></a></strong></dt> | |
| 1132 <dd> | |
| 1133 <div class="OptionsBox"> | |
| 1134 $Status = $Atom->IsCarbon();</div> | |
| 1135 <p>Returns 1 or 0 based on whether it's a carbon <em>Atom</em>.</p> | |
| 1136 </dd> | |
| 1137 <dt><strong><a name="iscarboxylcarbon" class="item"><strong>IsCarboxylCarbon</strong></a></strong></dt> | |
| 1138 <dd> | |
| 1139 <div class="OptionsBox"> | |
| 1140 $Status = $Atom->IsCarboxylCarbon();</div> | |
| 1141 <p>Returns 1 or 0 based on whether it's a carboxyl carbon atom in carboxyl group: | |
| 1142 R-C(=O)-OH.</p> | |
| 1143 </dd> | |
| 1144 <dt><strong><a name="iscarboxyloxygen" class="item"><strong>IsCarboxylOxygen</strong></a></strong></dt> | |
| 1145 <dd> | |
| 1146 <div class="OptionsBox"> | |
| 1147 $Status = $Atom->IsCarboxylOxygen();</div> | |
| 1148 <p>Returns 1 or 0 based on whether it's a carboxyl oxygen atom in carboxyl group: | |
| 1149 R-C(=O)-OH.</p> | |
| 1150 </dd> | |
| 1151 <dt><strong><a name="iscarboxylatecarbon" class="item"><strong>IsCarboxylateCarbon</strong></a></strong></dt> | |
| 1152 <dd> | |
| 1153 <div class="OptionsBox"> | |
| 1154 $Status = $Atom->IsCarboxylateCarbon();</div> | |
| 1155 <p>Returns 1 or 0 based on whether it's a carboxylate carbon atom in carboxyl group: | |
| 1156 R-C(=O)-O-.</p> | |
| 1157 </dd> | |
| 1158 <dt><strong><a name="iscarboxylateoxygen" class="item"><strong>IsCarboxylateOxygen</strong></a></strong></dt> | |
| 1159 <dd> | |
| 1160 <div class="OptionsBox"> | |
| 1161 $Status = $Atom->IsCarboxylateOxygen();</div> | |
| 1162 <p>Returns 1 or 0 based on whether it's a carboxylate oxygen atom in carboxyl group: | |
| 1163 R-C(=O)-O-.</p> | |
| 1164 </dd> | |
| 1165 <dt><strong><a name="ischlorine" class="item"><strong>IsChlorine</strong></a></strong></dt> | |
| 1166 <dd> | |
| 1167 <div class="OptionsBox"> | |
| 1168 $Status = $Atom->IsChlorine();</div> | |
| 1169 <p>Returns 1 or 0 based on whether it's a chlorine <em>Atom</em>.</p> | |
| 1170 </dd> | |
| 1171 <dt><strong><a name="isfluorine" class="item"><strong>IsFluorine</strong></a></strong></dt> | |
| 1172 <dd> | |
| 1173 <div class="OptionsBox"> | |
| 1174 $Status = $Atom->IsFluorine();</div> | |
| 1175 <p>Returns 1 or 0 based on whether it's a fluorine <em>Atom</em>.</p> | |
| 1176 </dd> | |
| 1177 <dt><strong><a name="isfunctionalclasstype" class="item"><strong>IsFunctionalClassType</strong></a></strong></dt> | |
| 1178 <dd> | |
| 1179 <div class="OptionsBox"> | |
| 1180 $Status =$Atom->IsFunctionalClassType($Type);</div> | |
| 1181 <p>Returns 1 or 0 based on whether it's a specified functional class <em>Type</em>.</p> | |
| 1182 <p>The current release of MayaChemTools supports following abbreviations and descriptive | |
| 1183 names for <em>FunctionalClassType</em>:</p> | |
| 1184 <div class="OptionsBox"> | |
| 1185 HBD: HydrogenBondDonor | |
| 1186 <br/> HBA: HydrogenBondAcceptor | |
| 1187 <br/> PI : PositivelyIonizable | |
| 1188 <br/> NI : NegativelyIonizable | |
| 1189 <br/> Ar : Aromatic | |
| 1190 <br/> Hal : Halogen | |
| 1191 <br/> H : Hydrophobic | |
| 1192 <br/> RA : RingAtom | |
| 1193 <br/> CA : ChainAtom</div> | |
| 1194 <p>The following definitions are used to determine functional class types: [ Ref 60-61, Ref 65-66 ]:</p> | |
| 1195 <div class="OptionsBox"> | |
| 1196 HydrogenBondDonor: NH, NH2, OH | |
| 1197 <br/> HydrogenBondAcceptor: N[!H], O | |
| 1198 <br/> PositivelyIonizable: +, NH2 | |
| 1199 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div> | |
| 1200 </dd> | |
| 1201 <dt><strong><a name="isguadiniumcarbon" class="item"><strong>IsGuadiniumCarbon</strong></a></strong></dt> | |
| 1202 <dd> | |
| 1203 <div class="OptionsBox"> | |
| 1204 $Status = $Atom->IsGuadiniumCarbon();</div> | |
| 1205 <p>Returns 1 or 0 based on whether it's a guadinium carbon in guadinium group by | |
| 1206 checking its neighbors for a nitrogen in guadinium group.</p> | |
| 1207 </dd> | |
| 1208 <dt><strong><a name="isguadiniumnitrogen" class="item"><strong>IsGuadiniumNitrogen</strong></a></strong></dt> | |
| 1209 <dd> | |
| 1210 <div class="OptionsBox"> | |
| 1211 $Status = $Atom->IsGuadiniumNitrogen();</div> | |
| 1212 <p>Returns 1 or 0 based on whether it's a guadinium nitrogen in guadinium group.</p> | |
| 1213 <p>A guadinium group is defined as:</p> | |
| 1214 <div class="OptionsBox"> | |
| 1215 R2N-C(=NR)-(NR2) or R2N-C(=NR2+)-(NR2)</div> | |
| 1216 <p>where:</p> | |
| 1217 <div class="OptionsBox"> | |
| 1218 o R = Hydrogens or group of atoms attached through carbon | |
| 1219 <br/> o Only one of the three nitrogens has a double bond to carbon | |
| 1220 and has optional formal charge allowing it to be neutral or charged state</div> | |
| 1221 </dd> | |
| 1222 <dt><strong><a name="ishbondacceptor" class="item"><strong>IsHBondAcceptor</strong></a></strong></dt> | |
| 1223 <dd> | |
| 1224 <div class="OptionsBox"> | |
| 1225 $Status =$Atom->IsHBondAcceptor(); | |
| 1226 <br/> $Status =$Atom->IsHBondAcceptor($HydrogenBondsType);</div> | |
| 1227 <p>Returns 1 or 0 based on whether it's a hydrogen bond acceptor <em>Atom</em>.</p> | |
| 1228 </dd> | |
| 1229 <dt><strong><a name="ishbonddonor" class="item"><strong>IsHBondDonor</strong></a></strong></dt> | |
| 1230 <dd> | |
| 1231 <div class="OptionsBox"> | |
| 1232 $Status =$Atom->IsHBondDonor(); | |
| 1233 <br/> $Status =$Atom->IsHBondDonor($HydrogenBondsType);</div> | |
| 1234 <p>Returns 1 or 0 based on whether it's a hydrogen bond donor <em>Atom</em>.</p> | |
| 1235 </dd> | |
| 1236 <dt><strong><a name="ishydrogenbondacceptor" class="item"><strong>IsHydrogenBondAcceptor</strong></a></strong></dt> | |
| 1237 <dd> | |
| 1238 <div class="OptionsBox"> | |
| 1239 $Status =$Atom->IsHydrogenBondAcceptor(); | |
| 1240 <br/> $Status =$Atom->IsHydrogenBondAcceptor($HydrogenBondsType);</div> | |
| 1241 <p>Returns 1 or 0 based on whether it's a hydrogen bond acceptor <em>Atom</em>.</p> | |
| 1242 </dd> | |
| 1243 <dt><strong><a name="ishydrogenbonddonor" class="item"><strong>IsHydrogenBondDonor</strong></a></strong></dt> | |
| 1244 <dd> | |
| 1245 <div class="OptionsBox"> | |
| 1246 $Status =$Atom->IsHydrogenBondDonor(); | |
| 1247 <br/> $Status =$Atom->IsHydrogenBondDonor($HydrogenBondsType);</div> | |
| 1248 <p>Returns 1 or 0 based on whether it's a hydrogen bond donor <em>Atom</em>.</p> | |
| 1249 <p>The current release of MayaChemTools supports identification of two types of hydrogen bond | |
| 1250 donor and acceptor atoms with these names:</p> | |
| 1251 <div class="OptionsBox"> | |
| 1252 HBondsType1 or HydrogenBondsType1 | |
| 1253 <br/> HBondsType2 or HydrogenBondsType2</div> | |
| 1254 <p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have | |
| 1255 specific meaning and are as follows:</p> | |
| 1256 <div class="OptionsBox"> | |
| 1257 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div> | |
| 1258 <div class="OptionsBox"> | |
| 1259 Donor: NH, NH2, OH - Any N and O with available H | |
| 1260 Acceptor: N[!H], O - Any N without available H and any O</div> | |
| 1261 <div class="OptionsBox"> | |
| 1262 HydrogenBondsType2 [ Ref 91 ]:</div> | |
| 1263 <div class="OptionsBox"> | |
| 1264 Donor: NH, NH2, OH - N and O with available H | |
| 1265 Acceptor: N, O - And N and O</div> | |
| 1266 <p>By default, <em>HydrogenBondsType1</em> is used to calculate number hydrogen bond donor | |
| 1267 and acceptor atoms. <em>HydrogenBondsType2</em> corresponds to <strong>RuleOf5</strong> definition | |
| 1268 of hydrogen bond donors and acceptors.</p> | |
| 1269 </dd> | |
| 1270 <dt><strong><a name="ishalogen" class="item"><strong>IsHalogen</strong></a></strong></dt> | |
| 1271 <dd> | |
| 1272 <div class="OptionsBox"> | |
| 1273 $Status =$Atom->IsHalogen();</div> | |
| 1274 <p>Returns 1 or 0 based on whether it's a halogen <em>Atom</em>.</p> | |
| 1275 </dd> | |
| 1276 <dt><strong><a name="isheteroatom" class="item"><strong>IsHeteroAtom</strong></a></strong></dt> | |
| 1277 <dd> | |
| 1278 <div class="OptionsBox"> | |
| 1279 $Status = $Atom->IsHeteroAtom();</div> | |
| 1280 <p>Returns 0 or 1 based on whether it's a hetro <em>Atom</em>. Following atoms are considered hetro atoms: | |
| 1281 <strong>N, O, F, P, S, Cl, Br, I</strong>.</p> | |
| 1282 </dd> | |
| 1283 <dt><strong><a name="ishydrogen" class="item"><strong>IsHydrogen</strong></a></strong></dt> | |
| 1284 <dd> | |
| 1285 <div class="OptionsBox"> | |
| 1286 $Status = $Atom->IsHydrogen();</div> | |
| 1287 <p>Returns 1 or 0 based on whether it's a hydrogen <em>Atom</em>.</p> | |
| 1288 </dd> | |
| 1289 <dt><strong><a name="ishydrophobic" class="item"><strong>IsHydrophobic</strong></a></strong></dt> | |
| 1290 <dd> | |
| 1291 <div class="OptionsBox"> | |
| 1292 $Status =$Atom->IsHydrophobic();</div> | |
| 1293 <p>Returns 1 or 0 based on whether it's a hydrophobic <em>Atom</em>.</p> | |
| 1294 </dd> | |
| 1295 <dt><strong><a name="isinring" class="item"><strong>IsInRing</strong></a></strong></dt> | |
| 1296 <dd> | |
| 1297 <div class="OptionsBox"> | |
| 1298 $Status = $Atom->IsInRing();</div> | |
| 1299 <p>Returns 1 or 0 based on whether <em>Atom</em> is present in a ring.</p> | |
| 1300 </dd> | |
| 1301 <dt><strong><a name="isinringofsize" class="item"><strong>IsInRingOfSize</strong></a></strong></dt> | |
| 1302 <dd> | |
| 1303 <div class="OptionsBox"> | |
| 1304 $Status = $Atom->IsInRingOfSize($Size);</div> | |
| 1305 <p>Returns 1 or 0 based on whether <em>Atom</em> is present in a ring of specific <em>Size</em>.</p> | |
| 1306 </dd> | |
| 1307 <dt><strong><a name="isiodine" class="item"><strong>IsIodine</strong></a></strong></dt> | |
| 1308 <dd> | |
| 1309 <div class="OptionsBox"> | |
| 1310 $Status = $Atom->IsIodine();</div> | |
| 1311 <p>Returns 1 or 0 based on whether it's an iodine <em>Atom</em>.</p> | |
| 1312 </dd> | |
| 1313 <dt><strong><a name="isisotope" class="item"><strong>IsIsotope</strong></a></strong></dt> | |
| 1314 <dd> | |
| 1315 <div class="OptionsBox"> | |
| 1316 $Status =$Atom->IsIsotope();</div> | |
| 1317 <p>Returns 1 or 0 based on whether it's an isotope <em>Atom</em>.</p> | |
| 1318 </dd> | |
| 1319 <dt><strong><a name="islipophilic" class="item"><strong>IsLipophilic</strong></a></strong></dt> | |
| 1320 <dd> | |
| 1321 <div class="OptionsBox"> | |
| 1322 $Status =$Atom->IsLipophilic();</div> | |
| 1323 <p>Returns 1 or 0 based on whether it's a lipophilic <em>Atom</em>.</p> | |
| 1324 </dd> | |
| 1325 <dt><strong><a name="ismetallic" class="item"><strong>IsMetallic</strong></a></strong></dt> | |
| 1326 <dd> | |
| 1327 <div class="OptionsBox"> | |
| 1328 $Status = $Atom->IsMetallic();</div> | |
| 1329 <p>Returns 1 or 0 based on whether it's a metallic <em>Atom</em>.</p> | |
| 1330 </dd> | |
| 1331 <dt><strong><a name="isnegativelyionizable" class="item"><strong>IsNegativelyIonizable</strong></a></strong></dt> | |
| 1332 <dd> | |
| 1333 <div class="OptionsBox"> | |
| 1334 $Status =$Atom->IsNegativelyIonizable();</div> | |
| 1335 <p>Returns 1 or 0 based on whether it's a negatively ionizable atom <em>Atom</em>.</p> | |
| 1336 </dd> | |
| 1337 <dt><strong><a name="isnitrogen" class="item"><strong>IsNitrogen</strong></a></strong></dt> | |
| 1338 <dd> | |
| 1339 <div class="OptionsBox"> | |
| 1340 $Status = $Atom->IsNitrogen();</div> | |
| 1341 <p>Returns 1 or 0 based on whether it's a nitrogen <em>Atom</em>.</p> | |
| 1342 </dd> | |
| 1343 <dt><strong><a name="isnoncarbonorhydrogen" class="item"><strong>IsNonCarbonOrHydrogen</strong></a></strong></dt> | |
| 1344 <dd> | |
| 1345 <div class="OptionsBox"> | |
| 1346 $Status =$Atom->IsNonCarbonOrHydrogen();</div> | |
| 1347 <p>Returns 1 or 0 based on whether it's not a carbon or hydrogen <em>Atom</em>.</p> | |
| 1348 </dd> | |
| 1349 <dt><strong><a name="isnotinring" class="item"><strong>IsNotInRing</strong></a></strong></dt> | |
| 1350 <dd> | |
| 1351 <div class="OptionsBox"> | |
| 1352 $Status = $Atom->IsNotInRing();</div> | |
| 1353 <p>Returns 1 or 0 based on whether <em>Atom</em> is not present in a ring.</p> | |
| 1354 </dd> | |
| 1355 <dt><strong><a name="isonlyinonering" class="item"><strong>IsOnlyInOneRing</strong></a></strong></dt> | |
| 1356 <dd> | |
| 1357 <div class="OptionsBox"> | |
| 1358 $Status = $Atom->IsOnlyInOneRing();</div> | |
| 1359 <p>Returns 1 or 0 based on whether <em>Atom</em> is only present in one ring.</p> | |
| 1360 </dd> | |
| 1361 <dt><strong><a name="isoxygen" class="item"><strong>IsOxygen</strong></a></strong></dt> | |
| 1362 <dd> | |
| 1363 <div class="OptionsBox"> | |
| 1364 $Status = $Atom->IsOxygen();</div> | |
| 1365 <p>Returns 0 or 1 based on whether it's an oxygen <em>Atom</em>.</p> | |
| 1366 </dd> | |
| 1367 <dt><strong><a name="isphosphorus" class="item"><strong>IsPhosphorus</strong></a></strong></dt> | |
| 1368 <dd> | |
| 1369 <div class="OptionsBox"> | |
| 1370 $Status = $Atom->IsPhosphorus();</div> | |
| 1371 <p>Returns 0 or 1 based on whether it's a phosphorus <em>Atom</em>.</p> | |
| 1372 </dd> | |
| 1373 <dt><strong><a name="isphosphateoxygen" class="item"><strong>IsPhosphateOxygen</strong></a></strong></dt> | |
| 1374 <dd> | |
| 1375 <div class="OptionsBox"> | |
| 1376 $Status = $Atom->IsPhosphateOxygen();</div> | |
| 1377 <p>Returns 1 or 0 based on whether it's a phosphate oxygen in phosphate group.</p> | |
| 1378 <p>A phosphate group is defined as:</p> | |
| 1379 <div class="OptionsBox"> | |
| 1380 AO-(O=)P(-OA)-OA</div> | |
| 1381 <p>Where:</p> | |
| 1382 <div class="OptionsBox"> | |
| 1383 A - Any group of atoms including hydrogens</div> | |
| 1384 </dd> | |
| 1385 <dt><strong><a name="isphosphatephosphorus" class="item"><strong>IsPhosphatePhosphorus</strong></a></strong></dt> | |
| 1386 <dd> | |
| 1387 <div class="OptionsBox"> | |
| 1388 $Status = $Atom->IsPhosphatePhosphorus();</div> | |
| 1389 <p>Returns 1 or 0 based on whether it's a phosphate phosphorus in phosphate group.</p> | |
| 1390 </dd> | |
| 1391 <dt><strong><a name="ispolaratom" class="item"><strong>IsPolarAtom</strong></a></strong></dt> | |
| 1392 <dd> | |
| 1393 <div class="OptionsBox"> | |
| 1394 $Status = $Atom->IsPolarAtom();</div> | |
| 1395 <p>Returns 0 or 1 based on whether it's a polar <em>Atom</em>. Following atoms are considered polar atoms: | |
| 1396 <strong>N, O, P, S</strong>.</p> | |
| 1397 </dd> | |
| 1398 <dt><strong><a name="ispolarhydrogen" class="item"><strong>IsPolarHydrogen</strong></a></strong></dt> | |
| 1399 <dd> | |
| 1400 <div class="OptionsBox"> | |
| 1401 $Status = $Atom->IsPolarHydrogen();</div> | |
| 1402 <p>Returns 0 or 1 based on whether it's a hydrogen <em>Atom</em> bonded to a polar atom.</p> | |
| 1403 </dd> | |
| 1404 <dt><strong><a name="ispositivelyionizable" class="item"><strong>IsPositivelyIonizable</strong></a></strong></dt> | |
| 1405 <dd> | |
| 1406 <div class="OptionsBox"> | |
| 1407 $Status =$Atom->IsPositivelyIonizable();</div> | |
| 1408 <p>Returns 1 or 0 based on whether it's a positively ionizable <em>Atom</em>.</p> | |
| 1409 </dd> | |
| 1410 <dt><strong><a name="issaturated" class="item"><strong>IsSaturated</strong></a></strong></dt> | |
| 1411 <dd> | |
| 1412 <div class="OptionsBox"> | |
| 1413 $Status = $Atom->IsSaturated();</div> | |
| 1414 <p>Returns 1 or 0 based on whether it's a saturated <em>Atom</em>. An atom attached | |
| 1415 to other atoms with only single bonds is considered a saturated atom.</p> | |
| 1416 </dd> | |
| 1417 <dt><strong><a name="isselenium" class="item"><strong>IsSelenium</strong></a></strong></dt> | |
| 1418 <dd> | |
| 1419 <div class="OptionsBox"> | |
| 1420 $Status = $Atom->IsSelenium();</div> | |
| 1421 <p>Returns 0 or 1 based on whether it's a selenium <em>Atom</em>.</p> | |
| 1422 </dd> | |
| 1423 <dt><strong><a name="isstereocenter" class="item"><strong>IsStereoCenter</strong></a></strong></dt> | |
| 1424 <dd> | |
| 1425 <div class="OptionsBox"> | |
| 1426 $Status = $Atom->IsStereoCenter();</div> | |
| 1427 <p>Returns 0 or 1 based on whether it's marked as a stero center <em>Atom</em> by explicit setting | |
| 1428 of <em>StereoCenter</em> atom propert to value of <em>1</em>.</p> | |
| 1429 </dd> | |
| 1430 <dt><strong><a name="issilicon" class="item"><strong>IsSilicon</strong></a></strong></dt> | |
| 1431 <dd> | |
| 1432 <div class="OptionsBox"> | |
| 1433 $Status = $Atom->IsSilicon();</div> | |
| 1434 <p>Returns 0 or 1 based on whether it's a silicon <em>Atom</em>.</p> | |
| 1435 </dd> | |
| 1436 <dt><strong><a name="issulfur" class="item"><strong>IsSulfur</strong></a></strong></dt> | |
| 1437 <dd> | |
| 1438 <div class="OptionsBox"> | |
| 1439 $Status = $Atom->IsSulfur();</div> | |
| 1440 <p>Returns 0 or 1 based on whether it's a sulfur <em>Atom</em>.</p> | |
| 1441 </dd> | |
| 1442 <dt><strong><a name="issulphur" class="item"><strong>IsSulphur</strong></a></strong></dt> | |
| 1443 <dd> | |
| 1444 <div class="OptionsBox"> | |
| 1445 $Status = $Atom->IsSulphur();</div> | |
| 1446 <p>Returns 0 or 1 based on whether it's a sulfur <em>Atom</em>.</p> | |
| 1447 </dd> | |
| 1448 <dt><strong><a name="istellurium" class="item"><strong>IsTellurium</strong></a></strong></dt> | |
| 1449 <dd> | |
| 1450 <div class="OptionsBox"> | |
| 1451 $Status = $Atom->IsTellurium();</div> | |
| 1452 <p>Returns 0 or 1 based on whether it's a tellurium <em>Atom</em>.</p> | |
| 1453 </dd> | |
| 1454 <dt><strong><a name="isterminal" class="item"><strong>IsTerminal</strong></a></strong></dt> | |
| 1455 <dd> | |
| 1456 <div class="OptionsBox"> | |
| 1457 $Status = $Atom->IsTerminal();</div> | |
| 1458 <p>Returns 0 or 1 based on whether it's a terminal <em>Atom</em> attached to no | |
| 1459 more than one non-hydrogen atom.</p> | |
| 1460 </dd> | |
| 1461 <dt><strong><a name="isunsaturated" class="item"><strong>IsUnsaturated</strong></a></strong></dt> | |
| 1462 <dd> | |
| 1463 <div class="OptionsBox"> | |
| 1464 $Status = $Atom->IsUnsaturated();</div> | |
| 1465 <p>Returns 1 or 0 based on whether it's as unsaturated <em>Atom</em>. An atom attached | |
| 1466 to other atoms with at least one non-single bond is considered an unsaturated atom.</p> | |
| 1467 </dd> | |
| 1468 <dt><strong><a name="istopologicalpharmacophoretype" class="item"><strong>IsTopologicalPharmacophoreType</strong></a></strong></dt> | |
| 1469 <dd> | |
| 1470 <div class="OptionsBox"> | |
| 1471 $Status =$Atom->IsTopologicalPharmacophoreType();</div> | |
| 1472 <p>Returns 1 or 0 based on whether it's any of the supportyed topological pharmacophore | |
| 1473 <em>Atom</em> type. See <em>IsFunctionalClassType</em> for a list of supported types.</p> | |
| 1474 </dd> | |
| 1475 <dt><strong><a name="setatomsymbol" class="item"><strong>SetAtomSymbol</strong></a></strong></dt> | |
| 1476 <dd> | |
| 1477 <div class="OptionsBox"> | |
| 1478 $Atom->SetAtomSymbol($AtomicSymbol);</div> | |
| 1479 <p>Sets atom symbol for <em>Atom</em> and returns <em>Atom</em> object. The appropriate atomic number is also | |
| 1480 set automatically.</p> | |
| 1481 </dd> | |
| 1482 <dt><strong><a name="setatomicnumber" class="item"><strong>SetAtomicNumber</strong></a></strong></dt> | |
| 1483 <dd> | |
| 1484 <div class="OptionsBox"> | |
| 1485 $Atom->SetAtomicNumber($AtomicNumber);</div> | |
| 1486 <p>Sets atomic number for <em>Atom</em> and returns <em>Atom</em> object. The appropriate atom symbol is also | |
| 1487 set automatically.</p> | |
| 1488 </dd> | |
| 1489 <dt><strong><a name="setmassnumber" class="item"><strong>SetMassNumber</strong></a></strong></dt> | |
| 1490 <dd> | |
| 1491 <div class="OptionsBox"> | |
| 1492 $Atom->SetMassNumber($MassNumber);</div> | |
| 1493 <p>Sets mass number for <em>Atom</em> and returns <em>Atom</em> object.</p> | |
| 1494 </dd> | |
| 1495 <dt><strong><a name="setstereocenter" class="item"><strong>SetStereoCenter</strong></a></strong></dt> | |
| 1496 <dd> | |
| 1497 <div class="OptionsBox"> | |
| 1498 $Atom->SetStereoCenter($StereoCenter);</div> | |
| 1499 <p>Sets stereo center for <em>Atom</em> and returns <em>Atom</em> object.</p> | |
| 1500 </dd> | |
| 1501 <dt><strong><a name="setstereochemistry" class="item"><strong>SetStereochemistry</strong></a></strong></dt> | |
| 1502 <dd> | |
| 1503 <div class="OptionsBox"> | |
| 1504 $Atom->SetStereochemistry($Stereochemistry);</div> | |
| 1505 <p>Sets stereo chemistry for <em>Atom</em> and returns <em>Atom</em> object.</p> | |
| 1506 </dd> | |
| 1507 <dt><strong><a name="setx" class="item"><strong>SetX</strong></a></strong></dt> | |
| 1508 <dd> | |
| 1509 <div class="OptionsBox"> | |
| 1510 $Atom->SetX($Value);</div> | |
| 1511 <p>Sets X-coordinate value for <em>Atom</em> and returns <em>Atom</em> object.</p> | |
| 1512 </dd> | |
| 1513 <dt><strong><a name="setxyz" class="item"><strong>SetXYZ</strong></a></strong></dt> | |
| 1514 <dd> | |
| 1515 <div class="OptionsBox"> | |
| 1516 $Atom->SetXYZ(@XYZValues); | |
| 1517 <br/> $Atom->SetXYZ($XYZValuesRef); | |
| 1518 <br/> $Atom->SetXYZ($XYZVector);</div> | |
| 1519 <p>Sets <em>Atom</em> coordinates using an array, reference to an array or a <em>Vector</em> object and | |
| 1520 returns <em>Atom</em> object.</p> | |
| 1521 </dd> | |
| 1522 <dt><strong><a name="sety" class="item"><strong>SetY</strong></a></strong></dt> | |
| 1523 <dd> | |
| 1524 <div class="OptionsBox"> | |
| 1525 $Atom->SetY($Value);</div> | |
| 1526 <p>Sets Y-coordinate value for <em>Atom</em> and returns <em>Atom</em> object.</p> | |
| 1527 </dd> | |
| 1528 <dt><strong><a name="setz" class="item"><strong>SetZ</strong></a></strong></dt> | |
| 1529 <dd> | |
| 1530 <div class="OptionsBox"> | |
| 1531 $Atom->SetZ($Value);</div> | |
| 1532 <p>Sets Z-coordinate value for <em>Atom</em> and returns <em>Atom</em> object.</p> | |
| 1533 </dd> | |
| 1534 <dt><strong><a name="stringifyatom" class="item"><strong>StringifyAtom</strong></a></strong></dt> | |
| 1535 <dd> | |
| 1536 <div class="OptionsBox"> | |
| 1537 $AtomString = $Atom->StringifyAtom();</div> | |
| 1538 <p>Returns a string containing information about <em>Atom</em> object.</p> | |
| 1539 </dd> | |
| 1540 </dl> | |
| 1541 <p> | |
| 1542 </p> | |
| 1543 <h2>AUTHOR</h2> | |
| 1544 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 1545 <p> | |
| 1546 </p> | |
| 1547 <h2>SEE ALSO</h2> | |
| 1548 <p><a href="./Bond.html">Bond.pm</a>, <a href="./Molecule.html">Molecule.pm</a>, <a href="./MoleculeFileIO.html">MoleculeFileIO.pm</a> | |
| 1549 </p> | |
| 1550 <p> | |
| 1551 </p> | |
| 1552 <h2>COPYRIGHT</h2> | |
| 1553 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 1554 <p>This file is part of MayaChemTools.</p> | |
| 1555 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 1556 the terms of the GNU Lesser General Public License as published by the Free | |
| 1557 Software Foundation; either version 3 of the License, or (at your option) | |
| 1558 any later version.</p> | |
| 1559 <p> </p><p> </p><div class="DocNav"> | |
| 1560 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 1561 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AminoAcids.html" title="AminoAcids.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomicDescriptors.html" title="AtomicDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Atom.pm</strong></td></tr> | |
| 1562 </table> | |
| 1563 </div> | |
| 1564 <br /> | |
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| 1567 </center> | |
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