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3 <title>MayaChemTools:Documentation:MolecularDescriptors::MolecularComplexityDescriptors.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./HydrogenBondsDescriptors.html" title="HydrogenBondsDescriptors.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./MolecularDescriptors.html" title="MolecularDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::MolecularComplexityDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/MolecularComplexityDescriptors.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/MolecularComplexityDescriptors.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/MolecularComplexityDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/MolecularComplexityDescriptors.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/MolecularComplexityDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>MolecularComplexityDescriptors</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use MolecularDescriptors::MolecularComplexityDescriptors;</p>
26 <p>use MolecularDescriptors::MolecularComplexityDescriptors qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>MolecularComplexityDescriptors</strong> class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>
32 , <a href="#getmolecularcomplexitytypeabbreviation">GetMolecularComplexityTypeAbbreviation</a>, <a href="#maccskeyssize">MACCSKeysSize</a>, <a href="#setatomidentifiertype">SetAtomIdentifierType</a>
33 , <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setdistancebinsize">SetDistanceBinSize</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>
34 , <a href="#setmaxdistance">SetMaxDistance</a>, <a href="#setmaxpathlength">SetMaxPathLength</a>, <a href="#setmindistance">SetMinDistance</a>, <a href="#setminpathlength">SetMinPathLength</a>
35 , <a href="#setmolecularcomplexitytype">SetMolecularComplexityType</a>, <a href="#setneighborhoodradius">SetNeighborhoodRadius</a>, <a href="#setnormalizationmethodology">SetNormalizationMethodology</a>
36 , <a href="#stringifymolecularcomplexitydescriptors">StringifyMolecularComplexityDescriptors</a>
37 </p><p><strong>MolecularComplexityDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn
38 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
39 in <strong>MolecularComplexityDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's
40 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
41 <div class="OptionsBox">
42 Set&lt;PropertyName&gt;(&lt;PropertyValue&gt;);
43 <br/> $PropertyValue = Get&lt;PropertyName&gt;();
44 <br/> Delete&lt;PropertyName&gt;();</div>
45 <p>The current release of MayaChemTools supports calculation of molecular complexity using
46 <em>MolecularComplexityType</em> parameter corresponding to number of bits-set or unique
47 keys [ Ref 117-119 ] in molecular fingerprints. The valid values for <em>MolecularComplexityType</em>
48 are:</p>
49 <div class="OptionsBox">
50 AtomTypesFingerprints
51 <br/> ExtendedConnectivityFingerprints
52 <br/> MACCSKeys
53 <br/> PathLengthFingerprints
54 <br/> TopologicalAtomPairsFingerprints
55 <br/> TopologicalAtomTripletsFingerprints
56 <br/> TopologicalAtomTorsionsFingerprints
57 <br/> TopologicalPharmacophoreAtomPairsFingerprints
58 <br/> TopologicalPharmacophoreAtomTripletsFingerprints</div>
59 <p>Default value for <em>MolecularComplexityType</em>: <em>MACCSKeys</em>.</p>
60 <p><em>AtomIdentifierType</em> parameter name corresponds to atom types used during generation of
61 fingerprints. The valid values for <em>AtomIdentifierType</em> are: <em>AtomicInvariantsAtomTypes,
62 DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
63 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</em>. <em>AtomicInvariantsAtomTypes</em>
64 is not supported for following values of <em>MolecularComplexityType</em>: <em>MACCSKeys,
65 TopologicalPharmacophoreAtomPairsFingerprints, TopologicalPharmacophoreAtomTripletsFingerprints</em>.
66 <em>FunctionalClassAtomTypes</em> is the only valid value of <em>AtomIdentifierType</em> for topological
67 pharmacophore fingerprints.</p>
68 <p>Default value for <em>AtomIdentifierType</em>: <em>AtomicInvariantsAtomTypes</em> for all fingerprints;
69 <em>FunctionalClassAtomTypes</em> for topological pharmacophore fingerprints.</p>
70 <p><em>AtomicInvariantsToUse</em> parameter name and values are used during <em>AtomicInvariantsAtomTypes</em>
71 value of parameter <em>AtomIdentifierType</em>. It's a list of space separated valid atomic invariant atom types.</p>
72 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB, H, Ar, RA, FC, MN, SM</em>.
73 Default value for <em>AtomicInvariantsToUse</em> parameter are set differently for different fingerprints
74 using <em>MolecularComplexityType</em> parameter as shown below:</p>
75 <div class="OptionsBox">
76 MolecularComplexityType AtomicInvariantsToUse</div>
77 <div class="OptionsBox">
78 AtomTypesFingerprints AS X BO H FC
79 <br/> TopologicalAtomPairsFingerprints AS X BO H FC
80 <br/> TopologicalAtomTripletsFingerprints AS X BO H FC
81 <br/> TopologicalAtomTorsionsFingerprints AS X BO H FC</div>
82 <div class="OptionsBox">
83 ExtendedConnectivityFingerprints AS X BO H FC MN
84 <br/> PathLengthFingerprints AS</div>
85 <p><em>FunctionalClassesToUse</em> parameter name and values are used during <em>FunctionalClassAtomTypes</em>
86 value of parameter <em>AtomIdentifierType</em>. It's a list of space separated valid atomic invariant atom types.</p>
87 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.</p>
88 <p>Default value for <em>FunctionalClassesToUse</em> parameter is set to:</p>
89 <div class="OptionsBox">
90 HBD HBA PI NI Ar Hal</div>
91 <p>for all fingerprints except for the following two <em>MolecularComplexityType</em> fingerints:</p>
92 <div class="OptionsBox">
93 MolecularComplexityType FunctionalClassesToUse</div>
94 <div class="OptionsBox">
95 TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H
96 <br/> TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar</div>
97 <p><em>MACCSKeysSize</em> parameter name is only used during <em>MACCSKeys</em> value of
98 <em>MolecularComplexityType</em> and corresponds to size of MACCS key set. Possible
99 values: <em>166 or 322</em>. Default value: <em>166</em>.</p>
100 <p><em>NeighborhoodRadius</em> parameter name is only used during <em>ExtendedConnectivityFingerprints</em>
101 value of <em>MolecularComplexityType</em> and corresponds to atomic neighborhoods radius for
102 generating extended connectivity fingerprints. Possible values: positive integer. Default value:
103 <em>2</em>.</p>
104 <p><em>MinPathLength</em> and <em>MaxPathLength</em> parameters are only used during <em>PathLengthFingerprints</em>
105 value of <em>MolecularComplexityType</em> and correspond to minimum and maximum path lengths to use
106 for generating path length fingerprints. Possible values: positive integers. Default value: <em>MinPathLength - 1</em>;
107 <em>MaxPathLength - 8</em>.</p>
108 <p><em>UseBondSymbols</em> parameter is only used during <em>PathLengthFingerprints</em> value of
109 <em>MolecularComplexityType</em> and indicates whether bond symbols are included in atom path
110 strings used to generate path length fingerprints. Possible value: <em>Yes or No</em>. Default value:
111 <em>Yes</em>.</p>
112 <p><em>MinDistance</em> and <em>MaxDistance</em> parameters are only used during <em>TopologicalAtomPairsFingerprints</em>
113 and <em>TopologicalAtomTripletsFingerprints</em> values of <em>MolecularComplexityType</em> and correspond to
114 minimum and maximum bond distance between atom pairs during topological pharmacophore fingerprints.
115 Possible values: positive integers. Default value: <em>MinDistance - 1</em>; <em>MaxDistance - 10</em>.</p>
116 <p><em>UseTriangleInequality</em> parameter is used during these values for <em>MolecularComplexityType</em>:
117 <em>TopologicalAtomTripletsFingerprints</em> and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.
118 Possible values: <em>Yes or No</em>. It determines wheter to apply triangle inequality to distance triplets.
119 Default value: <em>TopologicalAtomTripletsFingerprints - No</em>;
120 <em>TopologicalPharmacophoreAtomTripletsFingerprints - Yes</em>.</p>
121 <p><em>DistanceBinSize</em> parameter is used during <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>
122 value of <em>MolecularComplexityType</em> and corresponds to distance bin size used for binning
123 distances during generation of topological pharmacophore atom triplets fingerprints. Possible
124 value: positive integer. Default value: <em>2</em>.</p>
125 <p><em>NormalizationMethodology</em> is only used for these values for <em>MolecularComplexityType</em>:
126 <em>ExtendedConnectivityFingerprints</em>, <em>TopologicalPharmacophoreAtomPairsFingerprints</em>
127 and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>. It corresponds to normalization
128 methodology to use for scaling the number of bits-set or unique keys during generation of
129 fingerprints. Possible values during <em>ExtendedConnectivityFingerprints</em>: <em>None or
130 ByHeavyAtomsCount</em>; Default value: <em>None</em>. Possible values during topological
131 pharmacophore atom pairs and triplets fingerprints: <em>None or ByPossibleKeysCount</em>;
132 Default value: <em>None</em>. <em>ByPossibleKeysCount</em> corresponds to total number of
133 possible topological pharmacophore atom pairs or triplets in a molecule.</p>
134 <p>
135 </p>
136 <h2>METHODS</h2>
137 <dl>
138 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
139 <dd>
140 <div class="OptionsBox">
141 $NewMolecularComplexityDescriptors = new MolecularDescriptors::
142 MolecularComplexityDescriptors(
143 <br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; %NamesAndValues);</div>
144 <p>Using specified <em>MolecularComplexityDescriptors</em> property names and values hash, <strong>new</strong>
145 method creates a new object and returns a reference to newly created <strong>MolecularComplexityDescriptors</strong>
146 object. By default, the following properties are initialized:</p>
147 <div class="OptionsBox">
148 Molecule = ''
149 <br/> Type = 'MolecularComplexity'
150 <br/> MolecularComplexityType = 'MACCSKeys'
151 <br/> AtomIdentifierType = ''
152 <br/> MACCSKeysSize = 166
153 <br/> NeighborhoodRadius = 2
154 <br/> MinPathLength = 1
155 <br/> MaxPathLength = 8
156 <br/> UseBondSymbols = 1
157 <br/> MinDistance = 1
158 <br/> MaxDistance = 10
159 <br/> UseTriangleInequality = ''
160 <br/> DistanceBinSize = 2
161 <br/> NormalizationMethodology = 'None'
162 <br/> @DescriptorNames = ('MolecularComplexity')
163 <br/> @DescriptorValues = ('None')</div>
164 <p>Examples:</p>
165 <div class="OptionsBox">
166 $MolecularComplexityDescriptors = new MolecularDescriptors::
167 MolecularComplexityDescriptors(
168 'Molecule' =&gt; $Molecule);</div>
169 <div class="OptionsBox">
170 $MolecularComplexityDescriptors = new MolecularDescriptors::
171 MolecularComplexityDescriptors();</div>
172 <div class="OptionsBox">
173 $MolecularComplexityDescriptors-&gt;SetMolecule($Molecule);
174 <br/> $MolecularComplexityDescriptors-&gt;GenerateDescriptors();
175 <br/> print &quot;MolecularComplexityDescriptors: $MolecularComplexityDescriptors\n&quot;;</div>
176 </dd>
177 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
178 <dd>
179 <div class="OptionsBox">
180 $MolecularComplexityDescriptors-&gt;GenerateDescriptors();</div>
181 <p>Calculates MolecularComplexity value for a molecule and returns <em>MolecularComplexityDescriptors</em>.</p>
182 </dd>
183 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
184 <dd>
185 <div class="OptionsBox">
186 @DescriptorNames = $MolecularComplexityDescriptors-&gt;GetDescriptorNames();
187 <br/> @DescriptorNames = MolecularDescriptors::MolecularComplexityDescriptors::
188 GetDescriptorNames();</div>
189 <p>Returns all available descriptor names as an array.</p>
190 </dd>
191 <dt><strong><a name="getmolecularcomplexitytypeabbreviation" class="item"><strong>GetMolecularComplexityTypeAbbreviation</strong></a></strong></dt>
192 <dd>
193 <div class="OptionsBox">
194 $Abbrev = $MolecularComplexityDescriptors-&gt;
195 GetMolecularComplexityTypeAbbreviation();
196 <br/> $Abbrev = MolecularDescriptors::MolecularComplexityDescriptors::
197 GetMolecularComplexityTypeAbbreviation($ComplexityType);</div>
198 <p>Returns abbreviation for a specified molecular complexity type or corresponding to
199 <em>MolecularComplexityDescriptors</em> object.</p>
200 </dd>
201 <dt><strong><a name="setmaccskeyssize" class="item"><strong>SetMACCSKeysSize</strong></a></strong></dt>
202 <dd>
203 <div class="OptionsBox">
204 $MolecularComplexityDescriptors-&gt;MACCSKeysSize($Size);</div>
205 <p>Sets MACCS keys size and returns <em>MolecularComplexityDescriptors</em>.</p>
206 </dd>
207 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
208 <dd>
209 <div class="OptionsBox">
210 $MolecularComplexityDescriptors-&gt;SetAtomIdentifierType($IdentifierType);</div>
211 <p>Sets atom <em>IdentifierType</em> to use during fingerprints generation corresponding to
212 <em>MolecularComplexityType</em> and returns <em>MolecularComplexityDescriptors</em>.</p>
213 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
214 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
215 TPSAAtomTypes, UFFAtomTypes</em>.</p>
216 </dd>
217 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
218 <dd>
219 <div class="OptionsBox">
220 $MolecularComplexityDescriptors-&gt;SetAtomicInvariantsToUse($ValuesRef);
221 <br/> $MolecularComplexityDescriptors-&gt;SetAtomicInvariantsToUse(@Values);</div>
222 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
223 for fingerprints generation and returns <em>MolecularComplexityDescriptors</em>.</p>
224 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
225 H, Ar, RA, FC, MN, SM</em>. Default value [ Ref 24 ]: <em>AS,X,BO,H,FC,MN</em>.</p>
226 <p>The atomic invariants abbreviations correspond to:</p>
227 <div class="OptionsBox">
228 AS = Atom symbol corresponding to element symbol</div>
229 <div class="OptionsBox">
230 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
231 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
232 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
233 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
234 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
235 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
236 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
237 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
238 <br/> RA = Ring atom annotation indicating whether atom is a ring
239 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
240 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
241 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
242 3 (triplet)</div>
243 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
244 <div class="OptionsBox">
245 AS.X&lt;n&gt;.BO&lt;n&gt;.LBO&lt;n&gt;.&lt;SB&gt;&lt;n&gt;.&lt;DB&gt;&lt;n&gt;.&lt;TB&gt;&lt;n&gt;.H&lt;n&gt;.Ar.RA.FC&lt;+n/-n&gt;.MN&lt;n&gt;.SM&lt;n&gt;</div>
246 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
247 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
248 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
249 are also allowed:</p>
250 <div class="OptionsBox">
251 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
252 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
253 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
254 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
255 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
256 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
257 <br/> H : NumOfImplicitAndExplicitHydrogens
258 <br/> Ar : Aromatic
259 <br/> RA : RingAtom
260 <br/> FC : FormalCharge
261 <br/> MN : MassNumber
262 <br/> SM : SpinMultiplicity</div>
263 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
264 atom types.</p>
265 </dd>
266 <dt><strong><a name="setdistancebinsize" class="item"><strong>SetDistanceBinSize</strong></a></strong></dt>
267 <dd>
268 <div class="OptionsBox">
269 $MolecularComplexityDescriptors-&gt;SetDistanceBinSize($BinSize);</div>
270 <p>Sets distance bin size used to bin distances between atom pairs in atom triplets for
271 topological pharmacophore atom triplets fingerprints generation and returns
272 <em>MolecularComplexityDescriptors</em>.</p>
273 </dd>
274 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
275 <dd>
276 <div class="OptionsBox">
277 $MolecularComplexityDescriptors-&gt;SetFunctionalClassesToUse($ValuesRef);
278 <br/> $MolecularComplexityDescriptors-&gt;SetFunctionalClassesToUse(@Values);</div>
279 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
280 for fingerprints generation and returns <em>MolecularComplexityDescriptors</em>.</p>
281 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
282 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
283 <p>The functional class abbreviations correspond to:</p>
284 <div class="OptionsBox">
285 HBD: HydrogenBondDonor
286 <br/> HBA: HydrogenBondAcceptor
287 <br/> PI : PositivelyIonizable
288 <br/> NI : NegativelyIonizable
289 <br/> Ar : Aromatic
290 <br/> Hal : Halogen
291 <br/> H : Hydrophobic
292 <br/> RA : RingAtom
293 <br/> CA : ChainAtom</div>
294 <div class="OptionsBox">
295 Functional class atom type specification for an atom corresponds to:</div>
296 <div class="OptionsBox">
297 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
298 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
299 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
300 <div class="OptionsBox">
301 HydrogenBondDonor: NH, NH2, OH
302 <br/> HydrogenBondAcceptor: N[!H], O
303 <br/> PositivelyIonizable: +, NH2
304 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
305 </dd>
306 <dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt>
307 <dd>
308 <div class="OptionsBox">
309 $MolecularComplexityDescriptors-&gt;SetMaxDistance($MaxDistance);</div>
310 <p>Sets maximum distance to use during topological atom pairs and triplets fingerprints
311 generation and returns <em>MolecularComplexityDescriptors</em>.</p>
312 </dd>
313 <dt><strong><a name="setmaxpathlength" class="item"><strong>SetMaxPathLength</strong></a></strong></dt>
314 <dd>
315 <div class="OptionsBox">
316 $MolecularComplexityDescriptors-&gt;SetMaxPathLength($Length);</div>
317 <p>Sets maximum path length to use during path length fingerprints generation and returns
318 <em>MolecularComplexityDescriptors</em>.</p>
319 </dd>
320 <dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt>
321 <dd>
322 <div class="OptionsBox">
323 $MolecularComplexityDescriptors-&gt;SetMinDistance($MinDistance);</div>
324 <p>Sets minimum distance to use during topological atom pairs and triplets fingerprints
325 generation and returns <em>MolecularComplexityDescriptors</em>.</p>
326 </dd>
327 <dt><strong><a name="setminpathlength" class="item"><strong>SetMinPathLength</strong></a></strong></dt>
328 <dd>
329 <div class="OptionsBox">
330 $MolecularComplexityDescriptors-&gt;SetMinPathLength($MinPathLength);</div>
331 <p>Sets minimum path length to use during path length fingerprints generation and returns
332 <em>MolecularComplexityDescriptors</em>.</p>
333 </dd>
334 <dt><strong><a name="setmolecularcomplexitytype" class="item"><strong>SetMolecularComplexityType</strong></a></strong></dt>
335 <dd>
336 <div class="OptionsBox">
337 $MolecularComplexityDescriptors-&gt;SetMolecularComplexityType($ComplexityType);</div>
338 <p>Sets molecular complexity type to use for calculating its value and returns
339 <em>MolecularComplexityDescriptors</em>.</p>
340 </dd>
341 <dt><strong><a name="setneighborhoodradius" class="item"><strong>SetNeighborhoodRadius</strong></a></strong></dt>
342 <dd>
343 <div class="OptionsBox">
344 $MolecularComplexityDescriptors-&gt;SetNeighborhoodRadius($Radius);</div>
345 <p>Sets neighborhood radius to use during extended connectivity fingerprints generation and
346 returns <em>MolecularComplexityDescriptors</em>.</p>
347 </dd>
348 <dt><strong><a name="setnormalizationmethodology" class="item"><strong>SetNormalizationMethodology</strong></a></strong></dt>
349 <dd>
350 <div class="OptionsBox">
351 $MolecularComplexityDescriptors-&gt;SetNormalizationMethodology($Methodology);</div>
352 <p>Sets normalization methodology to use during calculation of molecular complexity
353 corresponding to extended connectivity, topological pharmacophore atom pairs and
354 tripletes fingerprints returns <em>MolecularComplexityDescriptors</em>.</p>
355 </dd>
356 <dt><strong><a name="stringifymolecularcomplexitydescriptors" class="item"><strong>StringifyMolecularComplexityDescriptors</strong></a></strong></dt>
357 <dd>
358 <div class="OptionsBox">
359 $String = $MolecularComplexityDescriptors-&gt;
360 StringifyMolecularComplexityDescriptors();</div>
361 <p>Returns a string containing information about <em>MolecularComplexityDescriptors</em> object.</p>
362 </dd>
363 </dl>
364 <p>
365 </p>
366 <h2>AUTHOR</h2>
367 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
368 <p>
369 </p>
370 <h2>SEE ALSO</h2>
371 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>,&nbsp<a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
372 </p>
373 <p>
374 </p>
375 <h2>COPYRIGHT</h2>
376 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
377 <p>This file is part of MayaChemTools.</p>
378 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
379 the terms of the GNU Lesser General Public License as published by the Free
380 Software Foundation; either version 3 of the License, or (at your option)
381 any later version.</p>
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