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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Documentation:Molecule.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="./MolecularFormula.html" title="MolecularFormula.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MoleculeFileIO.html" title="MoleculeFileIO.html">Next</a></td><td width="34%" align="middle"><strong>Molecule.pm</strong></td><td width="33%" align="right"><a href="././code/Molecule.html" title="View source code">Code</a> | <a href="./../pdf/Molecule.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/Molecule.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/Molecule.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/Molecule.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>Molecule - Molecule class</p> | |
22 <p> | |
23 </p> | |
24 <h2>SYNOPSIS</h2> | |
25 <p>use Molecule;</p> | |
26 <p>use Molecule qw(:all);</p> | |
27 <p> | |
28 </p> | |
29 <h2>DESCRIPTION</h2> | |
30 <p><strong>Molecule</strong> class provides the following methods:</p> | |
31 <p> <a href="#new">new</a>, <a href="#addatom">AddAtom</a>, <a href="#addatoms">AddAtoms</a>, <a href="#addbond">AddBond</a>, <a href="#addbonds">AddBonds</a>, <a href="#addhydrogens">AddHydrogens</a>, <a href="#addpolarhydrogens">AddPolarHydrogens</a> | |
32 , <a href="#clearrings">ClearRings</a>, <a href="#copy">Copy</a>, <a href="#deletearomaticity">DeleteAromaticity</a>, <a href="#deleteatom">DeleteAtom</a>, <a href="#deleteatoms">DeleteAtoms</a>, <a href="#deletebond">DeleteBond</a> | |
33 , <a href="#deletebonds">DeleteBonds</a>, <a href="#deletehydrogens">DeleteHydrogens</a>, <a href="#deletepolarhydrogens">DeletePolarHydrogens</a>, <a href="#detectaromaticity">DetectAromaticity</a> | |
34 , <a href="#detectrings">DetectRings</a>, <a href="#formatelementalcompositioninformation">FormatElementalCompositionInformation</a>, <a href="#getallatompaths">GetAllAtomPaths</a> | |
35 , <a href="#getallatompathsstartingat">GetAllAtomPathsStartingAt</a>, <a href="#getallatompathsstartingatwithlength">GetAllAtomPathsStartingAtWithLength</a> | |
36 , <a href="#getallatompathsstartingatwithlengthupto">GetAllAtomPathsStartingAtWithLengthUpto</a>, <a href="#getallatompathswithlength">GetAllAtomPathsWithLength</a> | |
37 , <a href="#getallatompathswithlengthupto">GetAllAtomPathsWithLengthUpto</a>, <a href="#getaromaticrings">GetAromaticRings</a>, <a href="#getaromaticitymodel">GetAromaticityModel</a> | |
38 , <a href="#getatomneighborhoods">GetAtomNeighborhoods</a>, <a href="#getatomneighborhoodswithradiusupto">GetAtomNeighborhoodsWithRadiusUpto</a> | |
39 , <a href="#getatomneighborhoodswithsuccessoratoms">GetAtomNeighborhoodsWithSuccessorAtoms</a> | |
40 , <a href="#getatomneighborhoodswithsuccessoratomsandradiusupto">GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</a>, <a href="#getatompathbonds">GetAtomPathBonds</a> | |
41 , <a href="#getatompaths">GetAtomPaths</a>, <a href="#getatompathsbetween">GetAtomPathsBetween</a>, <a href="#getatompathsstartingat">GetAtomPathsStartingAt</a> | |
42 , <a href="#getatompathsstartingatwithlength">GetAtomPathsStartingAtWithLength</a>, <a href="#getatompathsstartingatwithlengthupto">GetAtomPathsStartingAtWithLengthUpto</a> | |
43 , <a href="#getatompathswithlength">GetAtomPathsWithLength</a>, <a href="#getatompathswithlengthupto">GetAtomPathsWithLengthUpto</a>, <a href="#getatoms">GetAtoms</a>, <a href="#getbonds">GetBonds</a>, <a href="#getcharge">GetCharge</a> | |
44 , <a href="#getconnectedcomponents">GetConnectedComponents</a>, <a href="#getconnectedcomponentsatoms">GetConnectedComponentsAtoms</a>, <a href="#getdimensionality">GetDimensionality</a> | |
45 , <a href="#getelementalcomposition">GetElementalComposition</a>, <a href="#getelementsandnonelements">GetElementsAndNonElements</a>, <a href="#getexactmass">GetExactMass</a>, <a href="#getformalcharge">GetFormalCharge</a> | |
46 , <a href="#getfreeradicalelectrons">GetFreeRadicalElectrons</a>, <a href="#getfusedandnonfusedrings">GetFusedAndNonFusedRings</a>, <a href="#getlargestconnectedcomponent">GetLargestConnectedComponent</a> | |
47 , <a href="#getlargestconnectedcomponentatoms">GetLargestConnectedComponentAtoms</a>, <a href="#getlargestring">GetLargestRing</a>, <a href="#getmolecularformula">GetMolecularFormula</a> | |
48 , <a href="#getmolecularweight">GetMolecularWeight</a>, <a href="#getnumofaromaticrings">GetNumOfAromaticRings</a>, <a href="#getnumofatoms">GetNumOfAtoms</a>, <a href="#getnumofbonds">GetNumOfBonds</a> | |
49 , <a href="#getnumofconnectedcomponents">GetNumOfConnectedComponents</a>, <a href="#getnumofelementsandnonelements">GetNumOfElementsAndNonElements</a>, <a href="#getnumofheavyatoms">GetNumOfHeavyAtoms</a> | |
50 , <a href="#getnumofhydrogenatoms">GetNumOfHydrogenAtoms</a>, <a href="#getnumofmissinghydrogenatoms">GetNumOfMissingHydrogenAtoms</a>, <a href="#getnumofnonhydrogenatoms">GetNumOfNonHydrogenAtoms</a> | |
51 , <a href="#getnumofrings">GetNumOfRings</a>, <a href="#getnumofringswithevensize">GetNumOfRingsWithEvenSize</a>, <a href="#getnumofringswithoddsize">GetNumOfRingsWithOddSize</a> | |
52 , <a href="#getnumofringswithsize">GetNumOfRingsWithSize</a>, <a href="#getnumofringswithsizegreaterthan">GetNumOfRingsWithSizeGreaterThan</a> | |
53 , <a href="#getnumofringswithsizelessthan">GetNumOfRingsWithSizeLessThan</a>, <a href="#getringbonds">GetRingBonds</a>, <a href="#getringbondsfromrings">GetRingBondsFromRings</a>, <a href="#getrings">GetRings</a> | |
54 , <a href="#getringswithevensize">GetRingsWithEvenSize</a>, <a href="#getringswithoddsize">GetRingsWithOddSize</a>, <a href="#getringswithsize">GetRingsWithSize</a> | |
55 , <a href="#getringswithsizegreaterthan">GetRingsWithSizeGreaterThan</a>, <a href="#getringswithsizelessthan">GetRingsWithSizeLessThan</a>, <a href="#getsizeoflargestring">GetSizeOfLargestRing</a> | |
56 , <a href="#getsizeofsmallestring">GetSizeOfSmallestRing</a>, <a href="#getsmallestring">GetSmallestRing</a>, <a href="#getspinmultiplicity">GetSpinMultiplicity</a> | |
57 , <a href="#getsupportedaromaticitymodels">GetSupportedAromaticityModels</a>, <a href="#gettopologicallysortedatoms">GetTopologicallySortedAtoms</a>, <a href="#getvalencemodel">GetValenceModel</a> | |
58 , <a href="#hasaromaticatomsinrings">HasAromaticAtomsInRings</a>, <a href="#hasaromaticatomsnotinrings">HasAromaticAtomsNotInRings</a>, <a href="#hasaromaticrings">HasAromaticRings</a>, <a href="#hasatom">HasAtom</a> | |
59 , <a href="#hasbond">HasBond</a>, <a href="#hasfusedrings">HasFusedRings</a>, <a href="#hasnorings">HasNoRings</a>, <a href="#hasonlyonering">HasOnlyOneRing</a>, <a href="#hasrings">HasRings</a>, <a href="#isaromatic">IsAromatic</a> | |
60 , <a href="#ismolecule">IsMolecule</a>, <a href="#isringaromatic">IsRingAromatic</a>, <a href="#issupportedaromaticitymodel">IsSupportedAromaticityModel</a>, <a href="#isthreedimensional">IsThreeDimensional</a> | |
61 , <a href="#istwodimensional">IsTwoDimensional</a>, <a href="#keeplargestcomponent">KeepLargestComponent</a>, <a href="#kekulizearomaticatoms">KekulizeAromaticAtoms</a>, <a href="#newatom">NewAtom</a>, <a href="#newbond">NewBond</a> | |
62 , <a href="#setactiverings">SetActiveRings</a>, <a href="#setaromaticitymodel">SetAromaticityModel</a>, <a href="#setid">SetID</a>, <a href="#setvalencemodel">SetValenceModel</a>, <a href="#stringifymolecule">StringifyMolecule</a> | |
63 </p><p>The following methods can also be used as functions:</p> | |
64 <p>FormatElementalCompositionInformation, IsMolecule</p> | |
65 <p><strong>Molecule</strong> class is derived from <strong>ObjectProperty</strong> base class which provides methods not explicitly | |
66 defined in <strong>Molecule</strong> or <strong>ObjectProperty</strong> class using Perl's AUTOLOAD functionality. These methods | |
67 are generated on-the-fly for a specified object property:</p> | |
68 <div class="OptionsBox"> | |
69 Set<PropertyName>(<PropertyValue>); | |
70 <br/> $PropertyValue = Get<PropertyName>(); | |
71 <br/> Delete<PropertyName>();</div> | |
72 <p> | |
73 </p> | |
74 <h2>METHODS</h2> | |
75 <dl> | |
76 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> | |
77 <dd> | |
78 <div class="OptionsBox"> | |
79 $NewMolecule = new Molecule([%PropertyNameAndValues]);</div> | |
80 <p>Using specified <em>Atom</em> property names and values hash, <strong>new</strong> method creates a new object | |
81 and returns a reference to newly created <strong>Atom</strong> object. By default, the following properties are | |
82 initialized:</p> | |
83 <div class="OptionsBox"> | |
84 ID = SequentialObjectID | |
85 <br/> Name = "Molecule <SequentialObjectID>"</div> | |
86 <p>Examples:</p> | |
87 <div class="OptionsBox"> | |
88 $Molecule = new Molecule();</div> | |
89 <div class="OptionsBox"> | |
90 $WaterMolecule = new Molecule('Name' => 'Water');</div> | |
91 <div class="OptionsBox"> | |
92 $Oxygen = new Atom('AtomSymbol' => 'O', 'XYZ' => [0, 0, 0]); | |
93 <br/> $Hydrogen1 = new Atom('AtomSymbol' => 'H', | |
94 'XYZ' => [0.7144, 0.4125, 0]); | |
95 <br/> $Hydrogen2 = new Atom('AtomSymbol' => 'H', | |
96 'XYZ' => [1.1208, -0.2959, 0]); | |
97 <br/> $WaterMolecule->AddAtoms($Oxygen, $Hydrogen1, $Hydrogen2);</div> | |
98 <div class="OptionsBox"> | |
99 $Bond1 = new Bond('Atoms' => [$Oxygen, $Hydrogen1], | |
100 'BondOrder' => 1); | |
101 <br/> $Bond2 = new Bond('Atoms' => [$Oxygen, $Hydrogen2], | |
102 'BondOrder' => 1); | |
103 <br/> $WaterMolecule->AddBonds($Bond1, $Bond2);</div> | |
104 </dd> | |
105 <dt><strong><a name="addatom" class="item"><strong>AddAtom</strong></a></strong></dt> | |
106 <dd> | |
107 <div class="OptionsBox"> | |
108 $Molecule->AddAtom($Atom);</div> | |
109 <p>Adds an <em>Atom</em> to a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
110 </dd> | |
111 <dt><strong><a name="addatoms" class="item"><strong>AddAtoms</strong></a></strong></dt> | |
112 <dd> | |
113 <div class="OptionsBox"> | |
114 $Molecule->AddAtoms(@Atoms);</div> | |
115 <p>Adds <em>Atoms</em> to a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
116 </dd> | |
117 <dt><strong><a name="addbond" class="item"><strong>AddBond</strong></a></strong></dt> | |
118 <dd> | |
119 <div class="OptionsBox"> | |
120 $Molecule->AddBond($Bond);</div> | |
121 <p>Adds a <em>Bond</em> to a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
122 </dd> | |
123 <dt><strong><a name="addbonds" class="item"><strong>AddBonds</strong></a></strong></dt> | |
124 <dd> | |
125 <div class="OptionsBox"> | |
126 $Molecule->AddBonds(@Bonds);</div> | |
127 <p>Adds <em>Bonds</em> to a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
128 </dd> | |
129 <dt><strong><a name="addhydrogens" class="item"><strong>AddHydrogens</strong></a></strong></dt> | |
130 <dd> | |
131 <div class="OptionsBox"> | |
132 $NumOfHydrogensAdded = $Molecule->AddHydrogens();</div> | |
133 <p>Adds hydrogens to each atom in a <em>Molecule</em> and returns total number of hydrogens | |
134 added. The current release of MayaChemTools doesn't assign hydrogen positions.</p> | |
135 </dd> | |
136 <dt><strong><a name="addpolarhydrogens" class="item"><strong>AddPolarHydrogens</strong></a></strong></dt> | |
137 <dd> | |
138 <div class="OptionsBox"> | |
139 $NumOfHydrogensAdded = $Molecule->AddPolarHydrogens();</div> | |
140 <p>Adds hydrogens to each polar atom - N, O, P or S - in a <em>Molecule</em> and returns total | |
141 number of polar hydrogens added. The current release of MayaChemTools doesn't | |
142 assign hydrogen positions.</p> | |
143 </dd> | |
144 <dt><strong><a name="clearrings" class="item"><strong>ClearRings</strong></a></strong></dt> | |
145 <dd> | |
146 <div class="OptionsBox"> | |
147 $Molecule->ClearRings();</div> | |
148 <p>Deletes all rings associated with <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
149 </dd> | |
150 <dt><strong><a name="copy" class="item"><strong>Copy</strong></a></strong></dt> | |
151 <dd> | |
152 <div class="OptionsBox"> | |
153 $MoleculeCopy = $Molecule->Copy();</div> | |
154 <p>Copies <em>Molecule</em> and its associated data using <strong>Storable::dclone</strong> and returns a new | |
155 <strong>Molecule</strong> object.</p> | |
156 </dd> | |
157 <dt><strong><a name="deletearomaticity" class="item"><strong>DeleteAromaticity</strong></a></strong></dt> | |
158 <dd> | |
159 <div class="OptionsBox"> | |
160 $Molecule->DeleteAromaticity();</div> | |
161 <p>Deletes aromatic property associated with all atoms and bonds in a <em>Molecule</em> and returns | |
162 <em>Molecule</em>.</p> | |
163 </dd> | |
164 <dt><strong><a name="deleteatom" class="item"><strong>DeleteAtom</strong></a></strong></dt> | |
165 <dd> | |
166 <div class="OptionsBox"> | |
167 $Molecule->DeleteAtom($Atom);</div> | |
168 <p>Deletes <em>Atom</em> from a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
169 </dd> | |
170 <dt><strong><a name="deleteatoms" class="item"><strong>DeleteAtoms</strong></a></strong></dt> | |
171 <dd> | |
172 <div class="OptionsBox"> | |
173 $Molecule->DeleteAtoms(@Atoms);</div> | |
174 <p>Deletes <em>Atoms</em> from a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
175 </dd> | |
176 <dt><strong><a name="deletebond" class="item"><strong>DeleteBond</strong></a></strong></dt> | |
177 <dd> | |
178 <div class="OptionsBox"> | |
179 $Molecule->DeleteBond($Bond);</div> | |
180 <p>Deletes <em>Bond</em> from a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
181 </dd> | |
182 <dt><strong><a name="deletebonds" class="item"><strong>DeleteBonds</strong></a></strong></dt> | |
183 <dd> | |
184 <div class="OptionsBox"> | |
185 $Molecule->DeleteBonds(@Bonds);</div> | |
186 <p>Deletes <em>Bonds</em> from a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
187 </dd> | |
188 <dt><strong><a name="deletehydrogens" class="item"><strong>DeleteHydrogens</strong></a></strong></dt> | |
189 <dd> | |
190 <div class="OptionsBox"> | |
191 $NumOfHydrogensDeleted = $Molecule->DeleteHydrogens();</div> | |
192 <p>Removes hydrogens from each atom in a <em>Molecule</em> and returns total number of hydrogens | |
193 deleted.</p> | |
194 </dd> | |
195 <dt><strong><a name="deletepolarhydrogens" class="item"><strong>DeletePolarHydrogens</strong></a></strong></dt> | |
196 <dd> | |
197 <div class="OptionsBox"> | |
198 $NumOfHydrogensDeleted = $Molecule->DeletePolarHydrogens();</div> | |
199 <p>Removes hydrogens to each polar atom - N, O, P or S - in a <em>Molecule</em> and returns total | |
200 number of polar hydrogens deleted.</p> | |
201 </dd> | |
202 <dt><strong><a name="detectaromaticity" class="item"><strong>DetectAromaticity</strong></a></strong></dt> | |
203 <dd> | |
204 <div class="OptionsBox"> | |
205 $Molecule->DetectAromaticity();</div> | |
206 <p>Associates <em>Aromatic</em> property to atoms and bonds involved in aromatic rings or ring | |
207 systems in a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
208 <p>This method assumes the ring detection has already been perfomed using <strong>DetectRings</strong>. | |
209 And any existing <em>Aromatic</em> property associated with atoms and bonds is deleted before | |
210 performing aromaticity detection.</p> | |
211 <p>What is aromaticity? [ Ref 124 ] It's in the code of the implementer, did you | |
212 say? Agree. The implementation of aromaticity varies widely across different | |
213 packages [ Ref 125 ]; additionally, the implementation details are not always | |
214 completely available, and it's not possible to figure out the exact implementation | |
215 of aromaticity across various packages. Using the publicly available information, | |
216 however, one can try to reproduce the available results to the extent possible, | |
217 along with parameterizing all the control parameters used to implement different | |
218 aromaticity models, and that's exactly what the current release of MayaChemTools | |
219 does.</p> | |
220 <p>The implementation of aromaticity corresponding to various aromaticity models in | |
221 MayaChemTools package is driven by an external CSV file AromaticityModelsData.csv, | |
222 which is distributed with the package and is available in lib/data directory. The CSV | |
223 files contains names of supported aromaticity models, along with various control | |
224 parameters and their values. This file is loaded and processed during instantiation | |
225 of Molecule class and data corresponding to specific aromaticity model are used | |
226 to detect aromaticity for that model. Any new aromaticity model added to the | |
227 aromaticity data file, using different combinations of values for existing control | |
228 parameters, would work without any changes to the code; the addition of any new | |
229 control parameters, however, requires its implementation in the code used to | |
230 calculate number of pi electrons available towards delocalization in a ring or ring | |
231 systems.</p> | |
232 <p>The current release of MayaChemTools package supports these aromaticity | |
233 models: MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, | |
234 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, | |
235 DaylightAromaticityModel, MayaChemToolsAromaticityModel.</p> | |
236 <p>The current list of control parameters available to detect aromaticity corresponding | |
237 to different aromaticity models are: AllowHeteroRingAtoms, HeteroRingAtomsList, | |
238 AllowExocyclicDoubleBonds, AllowHomoNuclearExocyclicDoubleBonds, | |
239 AllowElectronegativeRingAtomExocyclicDoubleBonds, AllowRingAtomFormalCharge, | |
240 AllowHeteroRingAtomFormalCharge, MinimumRingSize. The values for these control | |
241 parameters are specified in AromaticityModelsData.csv file.</p> | |
242 <p>Although definition of aromaticity differs across various aromaticity models, a ring | |
243 or a ring system containing 4n + 2 pi electrons (Huckel's rule) corresponding to | |
244 alternate single and double bonds, in general, is considered aromatic.</p> | |
245 <p>The available valence free electrons on heterocyclic ring atoms, involved in two single | |
246 ring bonds, are also allowed to participate in pi electron delocalizaiton for most of | |
247 the supported aromaticity models.</p> | |
248 <p>The presence of exocyclic terminal double bond on ring atoms involved in pi electron | |
249 delocalization is only allowed for some of the aromaticity models. Additionally, the type | |
250 atoms involved in exocyclic terminal double bonds may result in making a ring or ring | |
251 system non-aromatic.</p> | |
252 <p>For molecules containing fused rings, each fused ring set is considered as one aromatic | |
253 system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in | |
254 fused set are treated individually for aromaticity detection. Additionally, non-fused | |
255 rings are handled on their own during aromaticity detection.</p> | |
256 </dd> | |
257 <dt><strong><a name="detectrings" class="item"><strong>DetectRings</strong></a></strong></dt> | |
258 <dd> | |
259 <div class="OptionsBox"> | |
260 $Molecule->DetectRings();</div> | |
261 <p>Detects rings in a <em>Molecule</em> and returns <em>Molecule</em>. Ring detection is performed using | |
262 <strong>DetectCycles</strong> method avaible in <strong>Graph</strong> class which in turn uses methods available | |
263 <strong>Graph::CyclesDetection</strong> class. <strong>Graph::CyclesDetection</strong> class implements collapsing path graph | |
264 [Ref 31] methodology to detect all cycles in a graph.</p> | |
265 </dd> | |
266 <dt><strong><a name="formatelementalcompositioninformation" class="item"><strong>FormatElementalCompositionInformation</strong></a></strong></dt> | |
267 <dd> | |
268 <div class="OptionsBox"> | |
269 $FormattedInfo = $Molecule->FormatElementalCompositionInformation( | |
270 $ElementsRef, $ElementCompositionRef, | |
271 [$Precision]); | |
272 <br/> $FormattedInfo = Molecule::FormatElementalCompositionInformation( | |
273 $ElementsRef, $ElementCompositionRef, | |
274 [$Precision]);</div> | |
275 <p>Using <em>ElementsRef</em> and <em>ElementCompositionRef</em> arrays referneces containg informatio | |
276 about elements and their composition, formats elemental composition information and returns | |
277 a <em>FormattedInfo</em> string. Defaule <em>Precision</em> value: <em>2</em>.</p> | |
278 </dd> | |
279 <dt><strong><a name="getaromaticitymodel" class="item"><strong>GetAromaticityModel</strong></a></strong></dt> | |
280 <dd> | |
281 <div class="OptionsBox"> | |
282 $AromaticityModel = $Molecule->GetAromaticityModel();</div> | |
283 <p>Returns name of <strong>AromaticityModel</strong> set for <em>Molecule</em> corresponding to <strong>AromaticityModel</strong> | |
284 property or default model name of <strong>MayaChemToolsAromaticityModel</strong>.</p> | |
285 </dd> | |
286 <dt><strong><a name="getallatompaths" class="item"><strong>GetAllAtomPaths</strong></a></strong></dt> | |
287 <dd> | |
288 <div class="OptionsBox"> | |
289 $AtomPathsRef = $Molecule->GetAllAtomPaths([$AllowCycles]);</div> | |
290 <p>Returns all paths as a reference to an array containing reference to arrays with path | |
291 <strong>Atom</strong> objects.</p> | |
292 <p>Path atoms correspond to to all possible paths for each atom in molecule with all | |
293 possible lengths and sharing of bonds in paths traversed. By default, rings are | |
294 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
295 <p>For molecule without any rings, this method returns the same set of atom paths as | |
296 <strong>GetAtomPaths</strong> method.</p> | |
297 </dd> | |
298 <dt><strong><a name="getallatompathsstartingat" class="item"><strong>GetAllAtomPathsStartingAt</strong></a></strong></dt> | |
299 <dd> | |
300 <div class="OptionsBox"> | |
301 $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAt($StartAtom, | |
302 [$AllowCycles]);</div> | |
303 <p>Returns all atom paths starting from <em>StartAtom</em> as a reference to an array containing | |
304 reference to arrays with path <strong>Atom</strong> objects.</p> | |
305 <p>Path atoms atoms correspond to to all possible paths for specified atom in molecule with all | |
306 possible lengths and sharing of bonds in paths traversed. By default, rings are | |
307 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
308 <p>For molecule without any rings, this method returns the same set of atom paths as | |
309 <strong>GetAtomPathsStartingAt</strong> method.</p> | |
310 </dd> | |
311 <dt><strong><a name="getallatompathsstartingatwithlength" class="item"><strong>GetAllAtomPathsStartingAtWithLength</strong></a></strong></dt> | |
312 <dd> | |
313 <div class="OptionsBox"> | |
314 $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAtWithLength( | |
315 $StartAtom, $Length, [$AllowCycles]);</div> | |
316 <p>Returns all atom paths starting from <em>StartAtom</em> with specified <em>Length</em>as a reference | |
317 to an array containing reference to arrays with path <strong>Atom</strong> objects.</p> | |
318 <p>Path atoms atoms correspond to to all possible paths for specified atom in molecule with all | |
319 possible lengths and sharing of bonds in paths traversed. By default, rings are | |
320 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
321 <p>For molecule without any rings, this method returns the same set of atom paths as | |
322 <strong>GetAtomPathsStartingAtWithLength</strong> method.</p> | |
323 </dd> | |
324 <dt><strong><a name="getallatompathsstartingatwithlengthupto" class="item"><strong>GetAllAtomPathsStartingAtWithLengthUpto</strong></a></strong></dt> | |
325 <dd> | |
326 <div class="OptionsBox"> | |
327 $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAtWithLengthUpto( | |
328 $StartAtom, $Length, [$AllowCycles]);</div> | |
329 <p>Returns atom paths starting from <em>StartAtom</em> with length up to <em>Length</em> as a reference | |
330 to an array containing reference to arrays with path <strong>Atom</strong> objects.</p> | |
331 <p>Path atoms atoms correspond to all possible paths for specified atom in molecule with length | |
332 up to a specified length and sharing of bonds in paths traversed. By default, rings are | |
333 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
334 <p>For molecule without any rings, this method returns the same set of atom paths as | |
335 <em>GetAtomPathsStartingAtWithLengthUpto</em> method.</p> | |
336 </dd> | |
337 <dt><strong><a name="getallatompathswithlength" class="item"><strong>GetAllAtomPathsWithLength</strong></a></strong></dt> | |
338 <dd> | |
339 <div class="OptionsBox"> | |
340 $AtomPathsRef = $Molecule->GetAllAtomPathsWithLength($Length, | |
341 [$AllowCycles]);</div> | |
342 <p>Returns all atom paths with specified <em>Length</em> as a reference to an array containing | |
343 reference to arrays with path <strong>Atom</strong> objects.</p> | |
344 <p>Path atoms correspond to to all possible paths for each atom in molecule with length | |
345 up to a specified length and sharing of bonds in paths traversed. By default, rings are | |
346 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
347 <p>For molecule without any rings, this method returns the same set of atom paths as | |
348 as <em>GetAtomPathsWithLength</em> method.</p> | |
349 </dd> | |
350 <dt><strong><a name="getallatompathswithlengthupto" class="item"><strong>GetAllAtomPathsWithLengthUpto</strong></a></strong></dt> | |
351 <dd> | |
352 <div class="OptionsBox"> | |
353 $AtomPathsRef = $Molecule->GetAllAtomPathsWithLengthUpto($Length, | |
354 [$AllowCycles]);</div> | |
355 <p>Returns all atom paths with length up to <em>Length</em> as a reference to an array containing | |
356 reference to arrays with path <strong>Atom</strong> objects.</p> | |
357 <p>Path atoms correspond to to all possible paths for each atom in molecule with length | |
358 up to a specified length and sharing of bonds in paths traversed. By default, rings are | |
359 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
360 <p>For molecule without any rings, this method returns the same set of atom paths as | |
361 as <em>GetAtomPathsWithLengthUpto</em> method.</p> | |
362 </dd> | |
363 <dt><strong><a name="getaromaticrings" class="item"><strong>GetAromaticRings</strong></a></strong></dt> | |
364 <dd> | |
365 <div class="OptionsBox"> | |
366 @AtomaticRings = $Molecule->GetAromaticRings();</div> | |
367 <p>Returns aromatic rings as an array containing references to arrays of ring <em>Atom</em> objects | |
368 in a <em>Molecule</em>.</p> | |
369 </dd> | |
370 <dt><strong><a name="getatomneighborhoods" class="item"><strong>GetAtomNeighborhoods</strong></a></strong></dt> | |
371 <dd> | |
372 <div class="OptionsBox"> | |
373 @Neighborhoods = $Molecule->GetAtomNeighborhoods($StartAtom);</div> | |
374 <p>Returns atom neighborhoods around a <em>StartAtom</em> as an array containing references | |
375 to arrays with neighborhood <em>Atom</em> objects at possible radii.</p> | |
376 </dd> | |
377 <dt><strong><a name="getatomneighborhoodswithradiusupto" class="item"><strong>GetAtomNeighborhoodsWithRadiusUpto</strong></a></strong></dt> | |
378 <dd> | |
379 <div class="OptionsBox"> | |
380 @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithRadiusUpto($StartAtom, | |
381 $Radius);</div> | |
382 <p>Returns atom neighborhoods around a <em>StartAtom</em> as an array containing references | |
383 to arrays with neighborhood <em>Atom</em> objects up to <em>Radius</em>.</p> | |
384 </dd> | |
385 <dt><strong><a name="getatomneighborhoodswithsuccessoratoms" class="item"><strong>GetAtomNeighborhoodsWithSuccessorAtoms</strong></a></strong></dt> | |
386 <dd> | |
387 <div class="OptionsBox"> | |
388 @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithSuccessorAtoms( | |
389 $StartAtom);</div> | |
390 <p>Returns atom neighborhood around a specified <em>StartAtom</em>, along with their successor | |
391 connected atoms, collected at all radii as an array containing references to arrays with first | |
392 value corresponding to neighborhood atom at a specific radius and second value as reference | |
393 to an array containing its successor connected atoms.</p> | |
394 <p>For a neighborhood atom at each radius level, the successor connected atoms correspond to the | |
395 neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last | |
396 radius level don't contain any successor atoms which fall outside the range of specified radius.</p> | |
397 </dd> | |
398 <dt><strong><a name="getatomneighborhoodswithsuccessoratomsandradiusupto" class="item"><strong>GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</strong></a></strong></dt> | |
399 <dd> | |
400 <div class="OptionsBox"> | |
401 @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto( | |
402 $StartAtom, $Radius);</div> | |
403 <p>Returns atom neighborhood around a specified <em>StartAtom</em>, along with their successor | |
404 connected atoms, collected upto specified <em>Radiud</em> as an array containing references to arrays | |
405 with first value corresponding to neighborhood atom at a specific radius and second value as | |
406 reference to an array containing its successor connected atoms.</p> | |
407 <p>For a neighborhood atom at each radius level, the successor connected atoms correspond to the | |
408 neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last | |
409 radius level don't contain any successor atoms which fall outside the range of specified radius.</p> | |
410 </dd> | |
411 <dt><strong><a name="getatompathbonds" class="item"><strong>GetAtomPathBonds</strong></a></strong></dt> | |
412 <dd> | |
413 <div class="OptionsBox"> | |
414 $Return = $Molecule->GetAtomPathBonds(@PathAtoms);</div> | |
415 <p>Returns an array containing <strong>Bond</strong> objects corresponding to successive pair of | |
416 atoms in <em>PathAtoms</em></p> | |
417 </dd> | |
418 <dt><strong><a name="getatompaths" class="item"><strong>GetAtomPaths</strong></a></strong></dt> | |
419 <dd> | |
420 <div class="OptionsBox"> | |
421 $AtomPathsRef = $Molecule->GetAtomPaths([$AllowCycles]);</div> | |
422 <p>Returns all paths as a reference to an array containing reference to arrays with path | |
423 <strong>Atom</strong> objects.</p> | |
424 <p>Path atoms correspond to to all possible paths for each atom in molecule with all | |
425 possible lengths and no sharing of bonds in paths traversed. By default, rings are | |
426 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
427 </dd> | |
428 <dt><strong><a name="getatompathsbetween" class="item"><strong>GetAtomPathsBetween</strong></a></strong></dt> | |
429 <dd> | |
430 <div class="OptionsBox"> | |
431 $AtomPathsRef = $Molecule->GetAtomPathsBetween($StartAtom, $EndAtom);</div> | |
432 <p>Returns all paths as between <em>StartAtom</em> and <em>EndAtom</em> as a reference to an array | |
433 containing reference to arrays with path <strong>Atom</strong> objects.</p> | |
434 <p>For molecules with rings, atom paths array contains may contain two paths.</p> | |
435 </dd> | |
436 <dt><strong><a name="getatompathsstartingat" class="item"><strong>GetAtomPathsStartingAt</strong></a></strong></dt> | |
437 <dd> | |
438 <div class="OptionsBox"> | |
439 $AtomPathsRef = $Molecule->GetAtomPathsStartingAt($StartAtom, [$AllowCycles]);</div> | |
440 <p>Returns paths starting at <em>StartAtom</em> as a reference to an array containing reference to | |
441 arrays with path <strong>Atom</strong> objects.</p> | |
442 <p>Path atoms correspond to all possible paths for specified atom in molecule with all | |
443 possible lengths and no sharing of bonds in paths traversed. By default, rings are | |
444 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
445 </dd> | |
446 <dt><strong><a name="getatompathsstartingatwithlength" class="item"><strong>GetAtomPathsStartingAtWithLength</strong></a></strong></dt> | |
447 <dd> | |
448 <div class="OptionsBox"> | |
449 $AtomPathsRef = $Molecule->GetAtomPathsStartingAtWithLength($StartAtom, | |
450 $Length, [$AllowCycles]);</div> | |
451 <p>Returns paths starting at <em>StartAtom</em> with length <em>Length</em> as a reference to an array | |
452 containing reference to arrays with path <strong>Atom</strong> objects.</p> | |
453 <p>Path atoms correspond to all possible paths for specified atom in molecule with length | |
454 upto a specified length and no sharing of bonds in paths traversed. By default, rings are | |
455 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
456 </dd> | |
457 <dt><strong><a name="getatompathsstartingatwithlengthupto" class="item"><strong>GetAtomPathsStartingAtWithLengthUpto</strong></a></strong></dt> | |
458 <dd> | |
459 <div class="OptionsBox"> | |
460 $AtomPathsRef = $Molecule->GetAtomPathsStartingAtWithLengthUpto($StartAtom, | |
461 $Length, [$AllowCycles]);</div> | |
462 <p>Returns paths starting at <em>StartAtom</em> with length up to <em>Length</em> as a reference to an array | |
463 containing reference to arrays with path <strong>Atom</strong> objects.</p> | |
464 <p>Path atoms correspond to all possible paths for specified atom in molecule with length | |
465 upto a specified length and no sharing of bonds in paths traversed. By default, rings are | |
466 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
467 </dd> | |
468 <dt><strong><a name="getatompathswithlength" class="item"><strong>GetAtomPathsWithLength</strong></a></strong></dt> | |
469 <dd> | |
470 <div class="OptionsBox"> | |
471 $AtomPathsRef = $Molecule->GetAtomPathsWithLength($Length, [$AllowCycles]);</div> | |
472 <p>Returns all paths with specified <em>Length</em> as a reference to an array containing reference | |
473 to arrays with path <strong>Atom</strong> objects.</p> | |
474 <p>Path atoms correspond to all possible paths for each atom in molecule with length | |
475 upto a specified length and no sharing of bonds in paths traversed. By default, rings are | |
476 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
477 </dd> | |
478 <dt><strong><a name="getatompathswithlengthupto" class="item"><strong>GetAtomPathsWithLengthUpto</strong></a></strong></dt> | |
479 <dd> | |
480 <div class="OptionsBox"> | |
481 $AtomPathsRef = $Molecule->GetAtomPathsWithLengthUpto($Length, [$AllowCycles]);</div> | |
482 <p>Returns all paths with length up to <em>Length</em> as a reference to an array containing reference | |
483 to arrays with path <strong>Atom</strong> objects.</p> | |
484 <p>Path atoms correspond to all possible paths for each atom in molecule with length | |
485 upto a specified length and no sharing of bonds in paths traversed. By default, rings are | |
486 included in paths. A path containing a ring is terminated at an atom completing the ring.</p> | |
487 </dd> | |
488 <dt><strong><a name="getatoms" class="item"><strong>GetAtoms</strong></a></strong></dt> | |
489 <dd> | |
490 <div class="OptionsBox"> | |
491 @AllAtoms = $Molecule->GetAtoms(); | |
492 <br/> @PolarAtoms = $Molecule->GetAtoms('IsPolarAtom');</div> | |
493 <div class="OptionsBox"> | |
494 $NegateMethodResult = 1; | |
495 <br/> @NonHydrogenAtoms = $Molecule->GetAtoms('IsHydrogenAtom', | |
496 $NegateMethodResult);</div> | |
497 <div class="OptionsBox"> | |
498 $AtomsCount = $Molecule->GetAtoms();</div> | |
499 <p>Returns an array of <em>Atoms</em> in a <em>Molecule</em>. In scalar context, it returns number of atoms. | |
500 Additionally, <strong>Atoms</strong> array can be filtered by any user specifiable valid <strong>Atom</strong> class method | |
501 and the result of the <strong>Atom</strong> class method used to filter the atoms can also be negated by | |
502 an optional negate results flag as third parameter.</p> | |
503 </dd> | |
504 <dt><strong><a name="getbonds" class="item"><strong>GetBonds</strong></a></strong></dt> | |
505 <dd> | |
506 <div class="OptionsBox"> | |
507 @Bonds = $Molecule->GetBonds(); | |
508 <br/> $BondsCount = $Molecule->GetBonds();</div> | |
509 <p>Returns an array of <em>Bonds</em> in a <em>Molecule</em>. In scalar context, it returns number of bonds.</p> | |
510 </dd> | |
511 <dt><strong><a name="getcharge" class="item"><strong>GetCharge</strong></a></strong></dt> | |
512 <dd> | |
513 <div class="OptionsBox"> | |
514 $Charge = $Molecule->GetCharge();</div> | |
515 <p>Returns net charge on a <em>Molecule</em> using one of the following two methods: explicitly | |
516 set <strong>Charge</strong> property or sum of partial atomic charges on each atom.</p> | |
517 </dd> | |
518 <dt><strong><a name="getconnectedcomponents" class="item"><strong>GetConnectedComponents</strong></a></strong></dt> | |
519 <dd> | |
520 <div class="OptionsBox"> | |
521 @ConnectedComponents = $Molecule->GetConnectedComponents();</div> | |
522 <p>Returns a reference to an array containing <em>Molecule</em> objects corresponding | |
523 to connected components sorted in decreasing order of component size in a <em>Molecule</em>.</p> | |
524 </dd> | |
525 <dt><strong><a name="getconnectedcomponentsatoms" class="item"><strong>GetConnectedComponentsAtoms</strong></a></strong></dt> | |
526 <dd> | |
527 <div class="OptionsBox"> | |
528 @ConnectedComponentsAtoms = | |
529 $Molecule->GetConnectedComponentsAtoms();</div> | |
530 <p>Returns an array containing references to arrays with <em>Atom</em> objects corresponding to | |
531 atoms of connected components sorted in order of component decreasing size in a | |
532 <em>Molecule</em>.</p> | |
533 </dd> | |
534 <dt><strong><a name="getdimensionality" class="item"><strong>GetDimensionality</strong></a></strong></dt> | |
535 <dd> | |
536 <div class="OptionsBox"> | |
537 $Dimensionality = $Molecule->GetDimensionality();</div> | |
538 <p>Returns <em>Dimensionality</em> of a <em>Molecule</em> corresponding to explicitly set | |
539 <em>Dimensionality</em> property value or by processing atomic.</p> | |
540 <p>The <em>Dimensionality</em> value from atomic coordinates is calculated as follows:</p> | |
541 <div class="OptionsBox"> | |
542 3D - Three dimensional: One of X, Y or Z coordinate is non-zero | |
543 <br/> 2D - Two dimensional: One of X or Y coordinate is non-zero; All Z | |
544 coordinates are zero | |
545 <br/> 0D - Zero dimensional: All atomic coordinates are zero</div> | |
546 </dd> | |
547 <dt><strong><a name="getelementalcomposition" class="item"><strong>GetElementalComposition</strong></a></strong></dt> | |
548 <dd> | |
549 <div class="OptionsBox"> | |
550 ($ElementsRef, $CompositionRef) = | |
551 $Molecule->GetElementalComposition([$IncludeMissingHydrogens]);</div> | |
552 <p>Calculates elemental composition and returns references to arrays containing elements | |
553 and their percent composition in a <em>Molecule</em>. By default, missing hydrogens are included | |
554 during the calculation.</p> | |
555 </dd> | |
556 <dt><strong><a name="getelementsandnonelements" class="item"><strong>GetElementsAndNonElements</strong></a></strong></dt> | |
557 <dd> | |
558 <div class="OptionsBox"> | |
559 ($ElementsRef, $NonElementsRef) = | |
560 $Molecule->GetElementsAndNonElements([$IncludeMissingHydrogens]);</div> | |
561 <p>Counts elements and non-elements in a <em>Molecule</em> and returns references to hashes | |
562 containing element and non-element as hash keys with values corresponding to their | |
563 count. By default, missing hydrogens are not added to the element hash.</p> | |
564 </dd> | |
565 <dt><strong><a name="getexactmass" class="item"><strong>GetExactMass</strong></a></strong></dt> | |
566 <dd> | |
567 <div class="OptionsBox"> | |
568 $ExactMass = $Molecule->GetExactMass();</div> | |
569 <p>Returns exact mass of a <em>Molecule</em> corresponding to sum of exact masses of all | |
570 the atoms.</p> | |
571 </dd> | |
572 <dt><strong><a name="getformalcharge" class="item"><strong>GetFormalCharge</strong></a></strong></dt> | |
573 <dd> | |
574 <div class="OptionsBox"> | |
575 $FormalCharge = $Molecule->GetFormalCharge();</div> | |
576 <p>Returns net formal charge on a <em>Molecule</em> using one of the following two methods: explicitly | |
577 set <strong>FormalCharge</strong> property or sum of formal charges on each atom.</p> | |
578 <p><strong>FormalCharge</strong> is different from <strong>Charge</strong> property of the molecule which corresponds to | |
579 sum of partial atomic charges explicitly set for each atom using a specific methodology.</p> | |
580 </dd> | |
581 <dt><strong><a name="getfreeradicalelectrons" class="item"><strong>GetFreeRadicalElectrons</strong></a></strong></dt> | |
582 <dd> | |
583 <div class="OptionsBox"> | |
584 $FreeRadicalElectrons = $Molecule->GetFreeRadicalElectrons();</div> | |
585 <p>Returns total number of free radical electrons available in a <em>Molecule</em> using one of the | |
586 following two methods: explicitly set <strong>FreeRadicalElectrons</strong> property or sum of available | |
587 free radical electrons on each atom.</p> | |
588 </dd> | |
589 <dt><strong><a name="getfusedandnonfusedrings" class="item"><strong>GetFusedAndNonFusedRings</strong></a></strong></dt> | |
590 <dd> | |
591 <div class="OptionsBox"> | |
592 ($FusedRingSetRef, $NonFusedRingsRef) = | |
593 $Molecule->GetFusedAndNonFusedRings();</div> | |
594 <p>Returns references to array of fused ring sets and non-fused rings in a <em>Molecule</em>. Fused ring sets | |
595 array reference contains refernces to arrays of rings corresponding to ring <em>Atom</em> objects; | |
596 Non-fused rings array reference contains references to arrays of ring <em>Atom</em> objects.</p> | |
597 </dd> | |
598 <dt><strong><a name="getlargestconnectedcomponent" class="item"><strong>GetLargestConnectedComponent</strong></a></strong></dt> | |
599 <dd> | |
600 <div class="OptionsBox"> | |
601 $ComponentMolecule = $Molecule->GetLargestConnectedComponent();</div> | |
602 <p>Returns a reference to <strong>Molecule</strong> object corresponding to a largest connected component | |
603 in a <em>Molecule</em>.</p> | |
604 </dd> | |
605 <dt><strong><a name="getlargestconnectedcomponentatoms" class="item"><strong>GetLargestConnectedComponentAtoms</strong></a></strong></dt> | |
606 <dd> | |
607 <div class="OptionsBox"> | |
608 @ComponentAtoms = $Molecule->GetLargestConnectedComponentAtoms();</div> | |
609 <p>Returns a reference to an array of <strong>Atom</strong> objects corresponding to a largest connected | |
610 component in a <em>Molecule</em>.</p> | |
611 </dd> | |
612 <dt><strong><a name="getlargestring" class="item"><strong>GetLargestRing</strong></a></strong></dt> | |
613 <dd> | |
614 <div class="OptionsBox"> | |
615 @RingAtoms = $Molecule->GetLargestRing();</div> | |
616 <p>Returns an array of <em>Atoms</em> objects corresponding to a largest ring in a <em>Molecule</em>.</p> | |
617 </dd> | |
618 <dt><strong><a name="getmolecularformula" class="item"><strong>GetMolecularFormula</strong></a></strong></dt> | |
619 <dd> | |
620 <div class="OptionsBox"> | |
621 $FormulaString = $Molecule->GetMolecularFormula( | |
622 [$IncludeMissingHydrogens, | |
623 $IncludeNonElements]);</div> | |
624 <p>Returns molecular formula of a <em>Molecule</em> by collecting information about all atoms in | |
625 the molecule and composing the formula using Hills ordering system:</p> | |
626 <div class="OptionsBox"> | |
627 o C shows up first and H follows assuming C is present. | |
628 <br/> o All other standard elements are sorted alphanumerically. | |
629 <br/> o All other non-stanard atom symbols are also sorted | |
630 alphanumerically and follow standard elements.</div> | |
631 <p>Notes:</p> | |
632 <div class="OptionsBox"> | |
633 o By default, missing hydrogens and nonelements are also included. | |
634 <br/> o Elements for disconnected fragments are combined into the same | |
635 formula. | |
636 <br/> o Formal charge is also used during compoisiton of molecular formula.</div> | |
637 </dd> | |
638 <dt><strong><a name="getmolecularweight" class="item"><strong>GetMolecularWeight</strong></a></strong></dt> | |
639 <dd> | |
640 <div class="OptionsBox"> | |
641 $MolWeight = $Molecule->GetMolecularWeight();</div> | |
642 <p>Returns molecular weight of a <em>Molecule</em> corresponding to sum of atomic weights of all | |
643 the atoms.</p> | |
644 </dd> | |
645 <dt><strong><a name="getnumofaromaticrings" class="item"><strong>GetNumOfAromaticRings</strong></a></strong></dt> | |
646 <dd> | |
647 <div class="OptionsBox"> | |
648 $NumOfAromaticRings = $Molecule->GetNumOfAromaticRings();</div> | |
649 <p>Returns number of aromatic rings in a <em>Molecule</em>.</p> | |
650 </dd> | |
651 <dt><strong><a name="getnumofatoms" class="item"><strong>GetNumOfAtoms</strong></a></strong></dt> | |
652 <dd> | |
653 <div class="OptionsBox"> | |
654 $NumOfAtoms = $Molecule->GetNumOfAtoms();</div> | |
655 <p>Returns number of atoms in a <em>Molecule</em>.</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 = $Molecule->GetNumOfBonds();</div> | |
661 <p>Returns number of bonds in a <em>Molecule</em>.</p> | |
662 </dd> | |
663 <dt><strong><a name="getnumofconnectedcomponents" class="item"><strong>GetNumOfConnectedComponents</strong></a></strong></dt> | |
664 <dd> | |
665 <div class="OptionsBox"> | |
666 $NumOfComponents = $Molecule->GetNumOfConnectedComponents();</div> | |
667 <p>Returns number of connected components in a <em>Molecule</em>.</p> | |
668 </dd> | |
669 <dt><strong><a name="getnumofelementsandnonelements" class="item"><strong>GetNumOfElementsAndNonElements</strong></a></strong></dt> | |
670 <dd> | |
671 <div class="OptionsBox"> | |
672 ($NumOfElements, $NumOfNonElements) = $Molecule-> | |
673 GetNumOfElementsAndNonElements(); | |
674 <br/> ($NumOfElements, $NumOfNonElements) = $Molecule-> | |
675 GetNumOfElementsAndNonElements($IncludeMissingHydrogens);</div> | |
676 <p>Returns number of elements and non-elements in a <em>Molecule</em>. By default, missing | |
677 hydrogens are not added to element count.</p> | |
678 </dd> | |
679 <dt><strong><a name="getnumofheavyatoms" class="item"><strong>GetNumOfHeavyAtoms</strong></a></strong></dt> | |
680 <dd> | |
681 <div class="OptionsBox"> | |
682 $NumOfHeavyAtoms = $Molecule->GetNumOfHeavyAtoms();</div> | |
683 <p>Returns number of heavy atoms, non-hydrogen atoms, in a <em>Molecule</em>.</p> | |
684 </dd> | |
685 <dt><strong><a name="getnumofhydrogenatoms" class="item"><strong>GetNumOfHydrogenAtoms</strong></a></strong></dt> | |
686 <dd> | |
687 <div class="OptionsBox"> | |
688 $NumOfHydrogenAtoms = $Molecule->GetNumOfHydrogenAtoms();</div> | |
689 <p>Returns number of hydrogen atoms in a <em>Molecule</em>.</p> | |
690 </dd> | |
691 <dt><strong><a name="getnumofmissinghydrogenatoms" class="item"><strong>GetNumOfMissingHydrogenAtoms</strong></a></strong></dt> | |
692 <dd> | |
693 <div class="OptionsBox"> | |
694 $NumOfMissingHydrogenAtoms = $Molecule->GetNumOfMissingHydrogenAtoms();</div> | |
695 <p>Returns number of hydrogen atoms in a <em>Molecule</em>.</p> | |
696 </dd> | |
697 <dt><strong><a name="getnumofnonhydrogenatoms" class="item"><strong>GetNumOfNonHydrogenAtoms</strong></a></strong></dt> | |
698 <dd> | |
699 <div class="OptionsBox"> | |
700 $NumOfNonHydrogenAtoms = $Molecule->GetNumOfNonHydrogenAtoms();</div> | |
701 <p>Returns number of non-hydrogen atoms in a <em>Molecule</em>.</p> | |
702 </dd> | |
703 <dt><strong><a name="getnumofrings" class="item"><strong>GetNumOfRings</strong></a></strong></dt> | |
704 <dd> | |
705 <div class="OptionsBox"> | |
706 $RingCount = $Molecule->GetNumOfRings();</div> | |
707 <p>Returns number of rings in a <em>Molecule</em>.</p> | |
708 </dd> | |
709 <dt><strong><a name="getnumofringswithevensize" class="item"><strong>GetNumOfRingsWithEvenSize</strong></a></strong></dt> | |
710 <dd> | |
711 <div class="OptionsBox"> | |
712 $RingCount = $Molecule->GetNumOfRingsWithEvenSize();</div> | |
713 <p>Returns number of rings with even size in a <em>Molecule</em>.</p> | |
714 </dd> | |
715 <dt><strong><a name="getnumofringswithoddsize" class="item"><strong>GetNumOfRingsWithOddSize</strong></a></strong></dt> | |
716 <dd> | |
717 <div class="OptionsBox"> | |
718 $RingCount = $Molecule->GetNumOfRingsWithOddSize();</div> | |
719 <p>Returns number of rings with odd size in a <em>Molecule</em>.</p> | |
720 </dd> | |
721 <dt><strong><a name="getnumofringswithsize" class="item"><strong>GetNumOfRingsWithSize</strong></a></strong></dt> | |
722 <dd> | |
723 <div class="OptionsBox"> | |
724 $RingCount = $Molecule->GetNumOfRingsWithSize($Size);</div> | |
725 <p>Returns number of rings with <em>Size</em> in a <em>Molecule</em>.</p> | |
726 </dd> | |
727 <dt><strong><a name="getnumofringswithsizegreaterthan" class="item"><strong>GetNumOfRingsWithSizeGreaterThan</strong></a></strong></dt> | |
728 <dd> | |
729 <div class="OptionsBox"> | |
730 $RingCount = $Molecule->GetNumOfRingsWithSizeGreaterThan($Size);</div> | |
731 <p>Returns number of rings with size greater than <em>Size</em> in a <em>Molecule</em>.</p> | |
732 </dd> | |
733 <dt><strong><a name="getnumofringswithsizelessthan" class="item"><strong>GetNumOfRingsWithSizeLessThan</strong></a></strong></dt> | |
734 <dd> | |
735 <div class="OptionsBox"> | |
736 $RingCount = $Molecule->GetNumOfRingsWithSizeLessThan($Size);</div> | |
737 <p>Returns number of rings with size less than <em>Size</em> in a <em>Molecule</em>.</p> | |
738 </dd> | |
739 <dt><strong><a name="getringbonds" class="item"><strong>GetRingBonds</strong></a></strong></dt> | |
740 <dd> | |
741 <div class="OptionsBox"> | |
742 @RingBonds = $Molecule->GetRingBonds(@RingAtoms);</div> | |
743 <p>Returns an array of ring <strong>Bond</strong> objects correponding to an array of ring <em>Atoms</em> in a | |
744 <em>Molecule</em>.</p> | |
745 </dd> | |
746 <dt><strong><a name="getringbondsfromrings" class="item"><strong>GetRingBondsFromRings</strong></a></strong></dt> | |
747 <dd> | |
748 <div class="OptionsBox"> | |
749 @RingBondsSets = $Molecule->GetRingBondsFromRings(@RingAtomsSets);</div> | |
750 <p>Returns an array containing references to arrays of ring <strong>Bond</strong> objects for rings specified | |
751 in an array of references to ring <em>Atom</em> objects.</p> | |
752 </dd> | |
753 <dt><strong><a name="getrings" class="item"><strong>GetRings</strong></a></strong></dt> | |
754 <dd> | |
755 <div class="OptionsBox"> | |
756 @Rings = $Molecule->GetRings();</div> | |
757 <p>Returns rings as an array containing references to arrays of ring <em>Atom</em> objects in a <em>Molecule</em>.</p> | |
758 </dd> | |
759 <dt><strong><a name="getringswithevensize" class="item"><strong>GetRingsWithEvenSize</strong></a></strong></dt> | |
760 <dd> | |
761 <div class="OptionsBox"> | |
762 @Rings = $Molecule->GetRingsWithEvenSize();</div> | |
763 <p>Returns even size rings as an array containing references to arrays of ring <em>Atom</em> objects in | |
764 a <em>Molecule</em>.</p> | |
765 </dd> | |
766 <dt><strong><a name="getringswithoddsize" class="item"><strong>GetRingsWithOddSize</strong></a></strong></dt> | |
767 <dd> | |
768 <div class="OptionsBox"> | |
769 @Rings = $Molecule->GetRingsWithOddSize();</div> | |
770 <p>Returns odd size rings as an array containing references to arrays of ring <em>Atom</em> objects in | |
771 a <em>Molecule</em>.</p> | |
772 </dd> | |
773 <dt><strong><a name="getringswithsize" class="item"><strong>GetRingsWithSize</strong></a></strong></dt> | |
774 <dd> | |
775 <div class="OptionsBox"> | |
776 @Rings = $Molecule->GetRingsWithSize($Size);</div> | |
777 <p>Returns rings with <em>Size</em> as an array containing references to arrays of ring <em>Atom</em> objects in | |
778 a <em>Molecule</em>.</p> | |
779 </dd> | |
780 <dt><strong><a name="getringswithsizegreaterthan" class="item"><strong>GetRingsWithSizeGreaterThan</strong></a></strong></dt> | |
781 <dd> | |
782 <div class="OptionsBox"> | |
783 @Rings = $Molecule->GetRingsWithSizeGreaterThan($Size);</div> | |
784 <p>Returns rings with size greater than <em>Size</em> as an array containing references to arrays of | |
785 ring <em>Atom</em> objects in a <em>Molecule</em>.</p> | |
786 </dd> | |
787 <dt><strong><a name="getringswithsizelessthan" class="item"><strong>GetRingsWithSizeLessThan</strong></a></strong></dt> | |
788 <dd> | |
789 <div class="OptionsBox"> | |
790 @Rings = $Molecule->GetRingsWithSizeLessThan($Size);</div> | |
791 <p>Returns rings with size less than <em>Size</em> as an array containing references to arrays of | |
792 ring <em>Atom</em> objects in a <em>Molecule</em>.</p> | |
793 </dd> | |
794 <dt><strong><a name="getsizeoflargestring" class="item"><strong>GetSizeOfLargestRing</strong></a></strong></dt> | |
795 <dd> | |
796 <div class="OptionsBox"> | |
797 $Size = $Molecule->GetSizeOfLargestRing();</div> | |
798 <p>Returns size of the largest ring in a <em>Molecule</em>.</p> | |
799 </dd> | |
800 <dt><strong><a name="getsizeofsmallestring" class="item"><strong>GetSizeOfSmallestRing</strong></a></strong></dt> | |
801 <dd> | |
802 <div class="OptionsBox"> | |
803 $Size = $Molecule->GetSizeOfSmallestRing();</div> | |
804 <p>Returns size of the smalles ring in a <em>Molecule</em>.</p> | |
805 </dd> | |
806 <dt><strong><a name="getsmallestring" class="item"><strong>GetSmallestRing</strong></a></strong></dt> | |
807 <dd> | |
808 <div class="OptionsBox"> | |
809 @RingAtoms = $Molecule->GetSmallestRing();</div> | |
810 <p>Returns an array containing <em>Atom</em> objects corresponding to the smallest ring in | |
811 a <em>Molecule</em>.</p> | |
812 </dd> | |
813 <dt><strong><a name="getspinmultiplicity" class="item"><strong>GetSpinMultiplicity</strong></a></strong></dt> | |
814 <dd> | |
815 <div class="OptionsBox"> | |
816 $SpinMultiplicity = $Molecule->GetSpinMultiplicity();</div> | |
817 <p>Returns net spin multiplicity of a <em>Molecule</em> using one of the following two methods: explicitly | |
818 set <strong>SpinMultiplicity</strong> property or sum of spin multiplicity on each atom.</p> | |
819 </dd> | |
820 <dt><strong><a name="getsupportedaromaticitymodels" class="item"><strong>GetSupportedAromaticityModels</strong></a></strong></dt> | |
821 <dd> | |
822 <div class="OptionsBox"> | |
823 @SupportedModels = $Molecule->GetSupportedAromaticityModels();</div> | |
824 <p>Returns an array containing a list of supported aromaticity models.</p> | |
825 </dd> | |
826 <dt><strong><a name="getvalencemodel" class="item"><strong>GetValenceModel</strong></a></strong></dt> | |
827 <dd> | |
828 <div class="OptionsBox"> | |
829 $ValenceModel = $Molecule->GetValenceModel();</div> | |
830 <p>Returns valence model for <em>Molecule</em> using one of the following two methods: explicitly | |
831 set <strong>ValenceModel</strong> property or defaul value of <em>InternalValenceModel</em>.</p> | |
832 </dd> | |
833 <dt><strong><a name="gettopologicallysortedatoms" class="item"><strong>GetTopologicallySortedAtoms</strong></a></strong></dt> | |
834 <dd> | |
835 <div class="OptionsBox"> | |
836 @SortedAtoms = $Molecule->GetTopologicallySortedAtoms([$StartAtom]);</div> | |
837 <p>Returns an array of topologically sorted <em>Atom</em> objects starting from <em>StartAtom</em> or | |
838 an arbitrary atom in a <em>Molecule</em>.</p> | |
839 </dd> | |
840 <dt><strong><a name="hasaromaticrings" class="item"><strong>HasAromaticRings</strong></a></strong></dt> | |
841 <dd> | |
842 <div class="OptionsBox"> | |
843 $Status = $Molecule->HasAromaticRings();</div> | |
844 <p>Returns 1 or 0 based on whether any aromatic ring is present in a <em>Molecule</em>.</p> | |
845 </dd> | |
846 <dt><strong><a name="hasaromaticatomsinrings" class="item"><strong>HasAromaticAtomsInRings</strong></a></strong></dt> | |
847 <dd> | |
848 <div class="OptionsBox"> | |
849 $Status = $Molecule->HasAromaticAtomsInRings();</div> | |
850 <p>Returns 1 or 0 based on whether any aromatic ring atom is present in a <em>Molecule</em>.</p> | |
851 </dd> | |
852 <dt><strong><a name="hasaromaticatomsnotinrings" class="item"><strong>HasAromaticAtomsNotInRings</strong></a></strong></dt> | |
853 <dd> | |
854 <div class="OptionsBox"> | |
855 $Status = $Molecule->HasAromaticAtomsNotInRings();</div> | |
856 <p>Returns 1 or 0 based on whether any non-ring atom is marked aromatic in a <em>Molecule</em>.</p> | |
857 </dd> | |
858 <dt><strong><a name="hasatom" class="item"><strong>HasAtom</strong></a></strong></dt> | |
859 <dd> | |
860 <div class="OptionsBox"> | |
861 $Status = $Molecule->HasAtom($Atom);</div> | |
862 <p>Returns 1 or 0 based on whether <em>Atom</em> is present in a <em>Molecule</em>.</p> | |
863 </dd> | |
864 <dt><strong><a name="hasbond" class="item"><strong>HasBond</strong></a></strong></dt> | |
865 <dd> | |
866 <div class="OptionsBox"> | |
867 $Status = $Molecule->HasBond($Bond);</div> | |
868 <p>Returns 1 or 0 based on whether <em>Bond</em> is present in a <em>Molecule</em>.</p> | |
869 </dd> | |
870 <dt><strong><a name="hasfusedrings" class="item"><strong>HasFusedRings</strong></a></strong></dt> | |
871 <dd> | |
872 <div class="OptionsBox"> | |
873 $Status = $Molecule->HasFusedRings();</div> | |
874 <p>Returns 1 or 0 based on whether any fused rings set is present in a <em>Molecule</em>.</p> | |
875 </dd> | |
876 <dt><strong><a name="hasnorings" class="item"><strong>HasNoRings</strong></a></strong></dt> | |
877 <dd> | |
878 <div class="OptionsBox"> | |
879 $Status = $Molecule->HasNoRings();</div> | |
880 <p>Returns 0 or 1 based on whether any ring is present in a <em>Molecule</em>.</p> | |
881 </dd> | |
882 <dt><strong><a name="hasonlyonering" class="item"><strong>HasOnlyOneRing</strong></a></strong></dt> | |
883 <dd> | |
884 <div class="OptionsBox"> | |
885 $Status = $Molecule->HasOnlyOneRing();</div> | |
886 <p>Returns 1 or 0 based on whether only one ring is present in a <em>Molecule</em>.</p> | |
887 </dd> | |
888 <dt><strong><a name="hasrings" class="item"><strong>HasRings</strong></a></strong></dt> | |
889 <dd> | |
890 <div class="OptionsBox"> | |
891 $Status = $Molecule->HasRings();</div> | |
892 <p>Returns 1 or 0 based on whether rings are present in a <em>Molecule</em>.</p> | |
893 </dd> | |
894 <dt><strong><a name="isaromatic" class="item"><strong>IsAromatic</strong></a></strong></dt> | |
895 <dd> | |
896 <div class="OptionsBox"> | |
897 $Status = $Molecule->IsAromatic();</div> | |
898 <p>Returns 1 or 0 based on whether <em>Molecule</em> is aromatic.</p> | |
899 </dd> | |
900 <dt><strong><a name="ismolecule" class="item"><strong>IsMolecule</strong></a></strong></dt> | |
901 <dd> | |
902 <div class="OptionsBox"> | |
903 $Status = Molecule::IsMolecule();</div> | |
904 <p>Returns 1 or 0 based on whether <em>Object</em> is a <strong>Molecule</strong> object.</p> | |
905 </dd> | |
906 <dt><strong><a name="isringaromatic" class="item"><strong>IsRingAromatic</strong></a></strong></dt> | |
907 <dd> | |
908 <div class="OptionsBox"> | |
909 $Status = $Molecule->IsRingAromatic(@RingAtoms);</div> | |
910 <p>Returns 1 or 0 based on whether all <em>RingAtoms</em> are aromatic.</p> | |
911 </dd> | |
912 <dt><strong><a name="issupportedaromaticitymodel" class="item"><strong>IsSupportedAromaticityModel</strong></a></strong></dt> | |
913 <dd> | |
914 <div class="OptionsBox"> | |
915 $Status = $Molecule->IsSupportedAromaticityModel($AromaticityModel); | |
916 <br/> $Status = Molecule::IsSupportedAromaticityModel($AromaticityModel);</div> | |
917 <p>Returns 1 or 0 based on whether specified <em>AromaticityModel</em> is supported.</p> | |
918 </dd> | |
919 <dt><strong><a name="istwodimensional" class="item"><strong>IsTwoDimensional</strong></a></strong></dt> | |
920 <dd> | |
921 <div class="OptionsBox"> | |
922 $Status = $Molecule->IsTwoDimensional();</div> | |
923 <p>Returns 1 or 0 based on whether any atom in <em>Molecule</em> has a non-zero value | |
924 for X or Y coordinate and all atoms have zero value for Z coordinates.</p> | |
925 </dd> | |
926 <dt><strong><a name="isthreedimensional" class="item"><strong>IsThreeDimensional</strong></a></strong></dt> | |
927 <dd> | |
928 <div class="OptionsBox"> | |
929 $Status = $Molecule->IsThreeDimensional();</div> | |
930 <p>Returns 1 or 0 based on whether any atom in <em>Molecule</em> has a non-zero value | |
931 for Z coordinate.</p> | |
932 </dd> | |
933 <dt><strong><a name="keeplargestcomponent" class="item"><strong>KeepLargestComponent</strong></a></strong></dt> | |
934 <dd> | |
935 <div class="OptionsBox"> | |
936 $Molecule->KeepLargestComponent();</div> | |
937 <p>Deletes atoms corresponding to all other connected components Except for the largest | |
938 connected component in a <em>Molecule</em> and returns <em>Molecule</em>.</p> | |
939 </dd> | |
940 <dt><strong><a name="kekulizearomaticatoms" class="item"><strong>KekulizeAromaticAtoms</strong></a></strong></dt> | |
941 <dd> | |
942 <div class="OptionsBox"> | |
943 $Status = $Molecule->KekulizeAromaticAtoms();</div> | |
944 <p>Kekulize marked ring and non-ring aromatic atoms in a molecule and return 1 or 1 based | |
945 on whether the kekulization succeeded.</p> | |
946 </dd> | |
947 <dt><strong><a name="newatom" class="item"><strong>NewAtom</strong></a></strong></dt> | |
948 <dd> | |
949 <div class="OptionsBox"> | |
950 $NewAtom = $Molecule->NewAtom(%AtomPropertyNamesAndValues);</div> | |
951 <p>Creates a new atom using <em>AtomPropertyNamesAndValues</em>, add its to <em>Molecule</em>, and returns | |
952 new <strong>Atom</strong> object.</p> | |
953 </dd> | |
954 <dt><strong><a name="newbond" class="item"><strong>NewBond</strong></a></strong></dt> | |
955 <dd> | |
956 <div class="OptionsBox"> | |
957 $NewBond = $Molecule->NewBond(%BondPropertyNamesAndValues);</div> | |
958 <p>Creates a new bond using <em>AtomPropertyNamesAndValues</em>, add its to <em>Molecule</em>, and returns | |
959 new <strong>Bond</strong> object.</p> | |
960 </dd> | |
961 <dt><strong><a name="setactiverings" class="item"><strong>SetActiveRings</strong></a></strong></dt> | |
962 <dd> | |
963 <div class="OptionsBox"> | |
964 $Molecule->SetActiveRings($RingsType);</div> | |
965 <p>Sets up type of detected ring sets to use during all ring related methods and returns <em>Molecule</em>. | |
966 Possible <em>RingType</em> values: <em>Independent or All</em>. By default, <em>Independent</em> ring set is used | |
967 during all ring methods.</p> | |
968 </dd> | |
969 <dt><strong><a name="setaromaticitymodel" class="item"><strong>SetAromaticityModel</strong></a></strong></dt> | |
970 <dd> | |
971 <div class="OptionsBox"> | |
972 $Molecule = $Molecule->SetAromaticityModel($AromaticityModel);</div> | |
973 <p>Sets up <em>AromaticityModel</em> property value for <em>Molecule</em> and retrurns <em>Molecule</em>.</p> | |
974 </dd> | |
975 <dt><strong><a name="setvalencemodel" class="item"><strong>SetValenceModel</strong></a></strong></dt> | |
976 <dd> | |
977 <div class="OptionsBox"> | |
978 $Molecule = $Molecule->SetValenceModel(ValenceModel);</div> | |
979 <p>Sets up <em>ValenceModel</em> property value for <em>Molecule</em> and retrurns <em>Molecule</em>.</p> | |
980 </dd> | |
981 <dt><strong><a name="stringifymolecule" class="item"><strong>StringifyMolecule</strong></a></strong></dt> | |
982 <dd> | |
983 <div class="OptionsBox"> | |
984 $MoleculeString = $Molecule->StringifyMolecule();</div> | |
985 <p>Returns a string containing information about <em>Molecule</em> object</p> | |
986 </dd> | |
987 </dl> | |
988 <p> | |
989 </p> | |
990 <h2>AUTHOR</h2> | |
991 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
992 <p> | |
993 </p> | |
994 <h2>SEE ALSO</h2> | |
995 <p><a href="./Atom.html">Atom.pm</a>, <a href="./Bond.html">Bond.pm</a>, <a href="./MoleculeFileIO.html">MoleculeFileIO.pm</a>, <a href="./MolecularFormula.html">MolecularFormula.pm</a> | |
996 </p> | |
997 <p> | |
998 </p> | |
999 <h2>COPYRIGHT</h2> | |
1000 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
1001 <p>This file is part of MayaChemTools.</p> | |
1002 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
1003 the terms of the GNU Lesser General Public License as published by the Free | |
1004 Software Foundation; either version 3 of the License, or (at your option) | |
1005 any later version.</p> | |
1006 <p> </p><p> </p><div class="DocNav"> | |
1007 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
1008 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularFormula.html" title="MolecularFormula.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MoleculeFileIO.html" title="MoleculeFileIO.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Molecule.pm</strong></td></tr> | |
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