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3 <title>MayaChemTools:Documentation:CalculatePhysicochemicalProperties.pl</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./DBSchemaTablesToTextFiles.html" title="DBSchemaTablesToTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>CalculatePhysicochemicalProperties.pl</strong></td><td width="33%" align="right"><a href="././code/CalculatePhysicochemicalProperties.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/CalculatePhysicochemicalProperties.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/CalculatePhysicochemicalProperties.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/CalculatePhysicochemicalProperties.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/CalculatePhysicochemicalProperties.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>CalculatePhysicochemicalProperties.pl - Calculate physicochemical properties for SD files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>CalculatePhysicochemicalProperties.pl SDFile(s)...</p>
26 <p>PhysicochemicalProperties.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
27 [<strong>--CompoundID</strong> DataFieldName or LabelPrefixString]
28 [<strong>--CompoundIDLabel</strong> text] [<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> &quot;FieldLabel1, FieldLabel2,...&quot;]
29 [<strong>-d, --DataFieldsMode</strong> All | Common | Specify | CompoundID] [<strong>-f, --Filter</strong> Yes | No] [<strong>-h, --help</strong>]
30 [<strong>--HydrogenBonds</strong> HBondsType1 | HBondsType2] [<strong>-k, --KeepLargestComponent</strong> Yes | No]
31 [<strong>-m, --mode</strong> All | RuleOf5 | RuleOf3 | &quot;name1, [name2,...]&quot;]
32 [<strong>--MolecularComplexity</strong> <em>Name,Value, [Name,Value,...]</em>]
33 [<strong>--OutDelim</strong> comma | tab | semicolon] [<strong>--output</strong> SD | text | both] [<strong>-o, --overwrite</strong>]
34 [<strong>--Precision</strong> Name,Number,[Name,Number,..]] [<strong>--RotatableBonds</strong> Name,Value, [Name,Value,...]]
35 [<strong>--RuleOf3Violations</strong> Yes | No] [<strong>--RuleOf5Violations</strong> Yes | No]
36 [<strong>-q, --quote</strong> Yes | No] [<strong>-r, --root</strong> RootName]
37 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
38 <p>
39 </p>
40 <h2>DESCRIPTION</h2>
41 <p>Calculate physicochemical properties for <em>SDFile(s)</em> and create appropriate SD or CSV/TSV
42 text file(s) containing calculated properties.</p>
43 <p>The current release of MayaChemTools supports the calculation of these physicochemical
44 properties:</p>
45 <div class="OptionsBox">
46 MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings,
47 <br/> van der Waals MolecularVolume [ Ref 93 ], RotatableBonds,
48 <br/> HydrogenBondDonors, HydrogenBondAcceptors, LogP and
49 <br/> Molar Refractivity (SLogP and SMR) [ Ref 89 ], Topological Polar
50 <br/> Surface Area (TPSA) [ Ref 90 ], Fraction of SP3 carbons (Fsp3Carbons)
51 <br/> and SP3 carbons (Sp3Carbons) [ Ref 115-116, Ref 119 ],
52 <br/> MolecularComplexity [ Ref 117-119 ]</div>
53 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
54 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
55 can be specified either by <em>*.sdf</em> or the current directory name.</p>
56 <p>The calculation of molecular complexity using <em>MolecularComplexityType</em> parameter
57 corresponds to the number of bits-set or unique keys [ Ref 117-119 ] in molecular fingerprints.
58 Default value for <em>MolecularComplexityType</em>: <em>MACCSKeys</em> of size 166. The calculation
59 of MACCSKeys is relatively expensive and can take rather substantial amount of time.</p>
60 <p>
61 </p>
62 <h2>OPTIONS</h2>
63 <dl>
64 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
65 <dd>
66 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
67 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
68 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
69 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
70 <p>The supported aromaticity model names along with model specific control parameters
71 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
72 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
73 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
74 for detecting aromaticity corresponding to a specific model.</p>
75 </dd>
76 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
77 <dd>
78 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
79 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
80 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
81 IDs like LabelPrefixString&lt;Number&gt;. Default value, <em>Cmpd</em>, generates compound IDs which
82 look like Cmpd&lt;Number&gt;.</p>
83 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
84 <div class="OptionsBox">
85 MolID
86 <br/> ExtReg</div>
87 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
88 <div class="OptionsBox">
89 Compound</div>
90 <p>The value specified above generates compound IDs which correspond to Compound&lt;Number&gt;
91 instead of default value of Cmpd&lt;Number&gt;.</p>
92 </dd>
93 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
94 <dd>
95 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
96 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
97 </dd>
98 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
99 <dd>
100 <p>Specify how to generate compound IDs and write to CSV/TSV text file(s) along with calculated
101 physicochemical properties for <em>text | both</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em>
102 datafield value; use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix;
103 use combination of both MolName and LabelPrefix with usage of LabelPrefix values for empty
104 molname lines.</p>
105 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
106 Default value: <em>LabelPrefix</em>.</p>
107 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
108 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
109 values are replaced with sequential compound IDs.</p>
110 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
111 </dd>
112 <dt><strong><strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em></strong></dt>
113 <dd>
114 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
115 with calculated physicochemical properties for <em>text | both</em> values of <strong>--output</strong> option.</p>
116 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
117 <p>Examples:</p>
118 <div class="OptionsBox">
119 Extreg
120 <br/> MolID,CompoundName</div>
121 </dd>
122 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
123 <dd>
124 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
125 with calculated physicochemical properties for <em>text | both</em> values of <strong>--output</strong> option:
126 transfer all SD data field; transfer SD data files common to all compounds; extract specified
127 data fields; generate a compound ID using molname line, a compound prefix, or a combination
128 of both. Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
129 </dd>
130 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
131 <dd>
132 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
133 Default value: <em>Yes</em>.</p>
134 <p>By default, compound data is checked before calculating physiochemical properties and compounds
135 containing atom data corresponding to non-element symbols or no atom data are ignored.</p>
136 </dd>
137 <dt><strong><strong>-h, --help</strong></strong></dt>
138 <dd>
139 <p>Print this help message.</p>
140 </dd>
141 <dt><strong><strong>--HydrogenBonds</strong> <em>HBondsType1 | HBondsType2</em></strong></dt>
142 <dd>
143 <p>Parameters to control calculation of hydrogen bond donors and acceptors. Possible values:
144 <em>HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2</em>. Default value:
145 <em>HBondsType2</em> which corresponds to <strong>RuleOf5</strong> definition for number of hydrogen bond
146 donors and acceptors.</p>
147 <p>The current release of MayaChemTools supports identification of two types of hydrogen bond
148 donor and acceptor atoms with these names:</p>
149 <div class="OptionsBox">
150 HBondsType1 or HydrogenBondsType1
151 <br/> HBondsType2 or HydrogenBondsType2</div>
152 <p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have
153 specific meaning and are as follows:</p>
154 <div class="OptionsBox">
155 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div>
156 <div class="OptionsBox">
157 &nbsp;&nbsp;&nbsp;&nbsp; Donor: NH, NH2, OH - Any N and O with available H
158 Acceptor: N[!H], O - Any N without available H and any O</div>
159 <div class="OptionsBox">
160 HydrogenBondsType2 [ Ref 91 ]:</div>
161 <div class="OptionsBox">
162 &nbsp;&nbsp;&nbsp;&nbsp; Donor: NH, NH2, OH - N and O with available H
163 Acceptor: N, O - And N and O</div>
164 </dd>
165 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
166 <dd>
167 <p>Calculate physicochemical properties for only the largest component in molecule. Possible values:
168 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
169 <p>For molecules containing multiple connected components, physicochemical properties can be
170 calculated in two different ways: use all connected components or just the largest connected
171 component. By default, all atoms except for the largest connected component are
172 deleted before calculation of physicochemical properties.</p>
173 </dd>
174 <dt><strong><strong>-m, --mode</strong> <em>All | RuleOf5 | RuleOf3 | &quot;name1, [name2,...]&quot;</em></strong></dt>
175 <dd>
176 <p>Specify physicochemical properties to calculate for SDFile(s): calculate all available physical
177 chemical properties; calculate properties corresponding to Rule of 5; or use a comma delimited
178 list of supported physicochemical properties. Possible values: <em>All | RuleOf5 | RuleOf3 |
179 &quot;name1, [name2,...]&quot;</em>.</p>
180 <p>Default value: <em>MolecularWeight, HeavyAtoms, MolecularVolume, RotatableBonds, HydrogenBondDonors,
181 HydrogenBondAcceptors, SLogP, TPSA</em>. These properties are calculated by default.</p>
182 <p><em>RuleOf5</em> [ Ref 91 ] includes these properties: <em>MolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors,
183 SLogP</em>. <em>RuleOf5</em> states: MolecularWeight &lt;= 500, HydrogenBondDonors &lt;= 5, HydrogenBondAcceptors &lt;= 10, and
184 logP &lt;= 5.</p>
185 <p><em>RuleOf3</em> [ Ref 92 ] includes these properties: <em>MolecularWeight, RotatableBonds, HydrogenBondDonors,
186 HydrogenBondAcceptors, SLogP, TPSA</em>. <em>RuleOf3</em> states: MolecularWeight &lt;= 300, RotatableBonds &lt;= 3,
187 HydrogenBondDonors &lt;= 3, HydrogenBondAcceptors &lt;= 3, logP &lt;= 3, and TPSA &lt;= 60.</p>
188 <p><em>All</em> calculates all supported physicochemical properties: <em>MolecularWeight, ExactMass,
189 HeavyAtoms, Rings, AromaticRings, MolecularVolume, RotatableBonds, HydrogenBondDonors,
190 HydrogenBondAcceptors, SLogP, SMR, TPSA, Fsp3Carbons, Sp3Carbons, MolecularComplexity</em>.</p>
191 </dd>
192 <dt><strong><strong>--MolecularComplexity</strong> <em>Name,Value, [Name,Value,...]</em></strong></dt>
193 <dd>
194 <p>Parameters to control calculation of molecular complexity: it's a comma delimited list of parameter
195 name and value pairs.</p>
196 <p>Possible parameter names: <em>MolecularComplexityType, AtomIdentifierType,
197 AtomicInvariantsToUse, FunctionalClassesToUse, MACCSKeysSize, NeighborhoodRadius,
198 MinPathLength, MaxPathLength, UseBondSymbols, MinDistance, MaxDistance,
199 UseTriangleInequality, DistanceBinSize, NormalizationMethodology</em>.</p>
200 <p>The valid paramater valuse for each parameter name are described in the following sections.</p>
201 <p>The current release of MayaChemTools supports calculation of molecular complexity using
202 <em>MolecularComplexityType</em> parameter corresponding to the number of bits-set or unique
203 keys [ Ref 117-119 ] in molecular fingerprints. The valid values for <em>MolecularComplexityType</em>
204 are:</p>
205 <div class="OptionsBox">
206 AtomTypesFingerprints
207 <br/> ExtendedConnectivityFingerprints
208 <br/> MACCSKeys
209 <br/> PathLengthFingerprints
210 <br/> TopologicalAtomPairsFingerprints
211 <br/> TopologicalAtomTripletsFingerprints
212 <br/> TopologicalAtomTorsionsFingerprints
213 <br/> TopologicalPharmacophoreAtomPairsFingerprints
214 <br/> TopologicalPharmacophoreAtomTripletsFingerprints</div>
215 <p>Default value for <em>MolecularComplexityType</em>: <em>MACCSKeys</em>.</p>
216 <p><em>AtomIdentifierType</em> parameter name correspods to atom types used during generation of
217 fingerprints. The valid values for <em>AtomIdentifierType</em> are: <em>AtomicInvariantsAtomTypes,
218 DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
219 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</em>. <em>AtomicInvariantsAtomTypes</em>
220 is not supported for during the following values of <em>MolecularComplexityType</em>: <em>MACCSKeys,
221 TopologicalPharmacophoreAtomPairsFingerprints, TopologicalPharmacophoreAtomTripletsFingerprints</em>.
222 <em>FunctionalClassAtomTypes</em> is the only valid value for <em>AtomIdentifierType</em> for topological
223 pharmacophore fingerprints.</p>
224 <p>Default value for <em>AtomIdentifierType</em>: <em>AtomicInvariantsAtomTypes</em>
225 for all except topological pharmacophore fingerprints where it is <em>FunctionalClassAtomTypes</em>.</p>
226 <p><em>AtomicInvariantsToUse</em> parameter name and values are used during <em>AtomicInvariantsAtomTypes</em>
227 value of parameter <em>AtomIdentifierType</em>. It's a list of space separated valid atomic invariant atom types.</p>
228 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB, H, Ar, RA, FC, MN, SM</em>.
229 Default value for <em>AtomicInvariantsToUse</em> parameter are set differently for different fingerprints
230 using <em>MolecularComplexityType</em> parameter as shown below:</p>
231 <div class="OptionsBox">
232 MolecularComplexityType AtomicInvariantsToUse</div>
233 <div class="OptionsBox">
234 AtomTypesFingerprints AS X BO H FC
235 <br/> TopologicalAtomPairsFingerprints AS X BO H FC
236 <br/> TopologicalAtomTripletsFingerprints AS X BO H FC
237 <br/> TopologicalAtomTorsionsFingerprints AS X BO H FC</div>
238 <div class="OptionsBox">
239 ExtendedConnectivityFingerprints AS X BO H FC MN
240 <br/> PathLengthFingerprints AS</div>
241 <p>The atomic invariants abbreviations correspond to:</p>
242 <div class="OptionsBox">
243 AS = Atom symbol corresponding to element symbol</div>
244 <div class="OptionsBox">
245 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
246 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
247 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
248 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
249 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
250 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
251 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
252 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
253 <br/> RA = Ring atom annotation indicating whether atom is a ring
254 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
255 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
256 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
257 3 (triplet)</div>
258 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
259 <div class="OptionsBox">
260 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>
261 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
262 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
263 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
264 are also allowed:</p>
265 <div class="OptionsBox">
266 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
267 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
268 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
269 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
270 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
271 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
272 <br/> H : NumOfImplicitAndExplicitHydrogens
273 <br/> Ar : Aromatic
274 <br/> RA : RingAtom
275 <br/> FC : FormalCharge
276 <br/> MN : MassNumber
277 <br/> SM : SpinMultiplicity</div>
278 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
279 atom types.</p>
280 <p><em>FunctionalClassesToUse</em> parameter name and values are used during <em>FunctionalClassAtomTypes</em>
281 value of parameter <em>AtomIdentifierType</em>. It's a list of space separated valid atomic invariant atom types.</p>
282 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.</p>
283 <p>Default value for <em>FunctionalClassesToUse</em> parameter is set to:</p>
284 <div class="OptionsBox">
285 HBD HBA PI NI Ar Hal</div>
286 <p>for all fingerprints except for the following two <em>MolecularComplexityType</em> fingerints:</p>
287 <div class="OptionsBox">
288 MolecularComplexityType FunctionalClassesToUse</div>
289 <div class="OptionsBox">
290 TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H
291 <br/> TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar</div>
292 <p>The functional class abbreviations correspond to:</p>
293 <div class="OptionsBox">
294 HBD: HydrogenBondDonor
295 <br/> HBA: HydrogenBondAcceptor
296 <br/> PI : PositivelyIonizable
297 <br/> NI : NegativelyIonizable
298 <br/> Ar : Aromatic
299 <br/> Hal : Halogen
300 <br/> H : Hydrophobic
301 <br/> RA : RingAtom
302 <br/> CA : ChainAtom</div>
303 <div class="OptionsBox">
304 Functional class atom type specification for an atom corresponds to:</div>
305 <div class="OptionsBox">
306 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div>
307 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
308 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
309 <div class="OptionsBox">
310 HydrogenBondDonor: NH, NH2, OH
311 <br/> HydrogenBondAcceptor: N[!H], O
312 <br/> PositivelyIonizable: +, NH2
313 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
314 <p><em>MACCSKeysSize</em> parameter name is only used during <em>MACCSKeys</em> value of
315 <em>MolecularComplexityType</em> and corresponds to the size of MACCS key set. Possible
316 values: <em>166 or 322</em>. Default value: <em>166</em>.</p>
317 <p><em>NeighborhoodRadius</em> parameter name is only used during <em>ExtendedConnectivityFingerprints</em>
318 value of <em>MolecularComplexityType</em> and corresponds to atomic neighborhoods radius for
319 generating extended connectivity fingerprints. Possible values: positive integer. Default value:
320 <em>2</em>.</p>
321 <p><em>MinPathLength</em> and <em>MaxPathLength</em> parameters are only used during <em>PathLengthFingerprints</em>
322 value of <em>MolecularComplexityType</em> and correspond to minimum and maximum path lengths to use
323 for generating path length fingerprints. Possible values: positive integers. Default value: <em>MinPathLength - 1</em>;
324 <em>MaxPathLength - 8</em>.</p>
325 <p><em>UseBondSymbols</em> parameter is only used during <em>PathLengthFingerprints</em> value of
326 <em>MolecularComplexityType</em> and indicates whether bond symbols are included in atom path
327 strings used to generate path length fingerprints. Possible value: <em>Yes or No</em>. Default value:
328 <em>Yes</em>.</p>
329 <p><em>MinDistance</em> and <em>MaxDistance</em> parameters are only used during <em>TopologicalAtomPairsFingerprints</em>
330 and <em>TopologicalAtomTripletsFingerprints</em> values of <em>MolecularComplexityType</em> and correspond to
331 minimum and maximum bond distance between atom pairs during topological pharmacophore fingerprints.
332 Possible values: positive integers. Default value: <em>MinDistance - 1</em>; <em>MaxDistance - 10</em>.</p>
333 <p><em>UseTriangleInequality</em> parameter is used during these values for <em>MolecularComplexityType</em>:
334 <em>TopologicalAtomTripletsFingerprints</em> and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.
335 Possible values: <em>Yes or No</em>. It determines wheter to apply triangle inequality to distance triplets.
336 Default value: <em>TopologicalAtomTripletsFingerprints - No</em>;
337 <em>TopologicalPharmacophoreAtomTripletsFingerprints - Yes</em>.</p>
338 <p><em>DistanceBinSize</em> parameter is used during <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>
339 value of <em>MolecularComplexityType</em> and correspons to distance bin size used for binning
340 distances during generation of topological pharmacophore atom triplets fingerprints. Possible
341 value: positive integer. Default value: <em>2</em>.</p>
342 <p><em>NormalizationMethodology</em> is only used for these values for <em>MolecularComplexityType</em>:
343 <em>ExtendedConnectivityFingerprints</em>, <em>TopologicalPharmacophoreAtomPairsFingerprints</em>
344 and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>. It corresponds to normalization
345 methodology to use for scaling the number of bits-set or unique keys during generation of
346 fingerprints. Possible values during <em>ExtendedConnectivityFingerprints</em>: <em>None or
347 ByHeavyAtomsCount</em>; Default value: <em>None</em>. Possible values during topological
348 pharmacophore atom pairs and tripletes fingerprints: <em>None or ByPossibleKeysCount</em>;
349 Default value: <em>None</em>. <em>ByPossibleKeysCount</em> corresponds to total number of
350 possible topological pharmacophore atom pairs or triplets in a molecule.</p>
351 <p>Examples of <em>MolecularComplexity</em> name and value parameters:</p>
352 <div class="OptionsBox">
353 MolecularComplexityType,AtomTypesFingerprints,AtomIdentifierType,
354 <br/> AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS X BO H FC</div>
355 <div class="OptionsBox">
356 MolecularComplexityType,ExtendedConnectivityFingerprints,
357 <br/> AtomIdentifierType,AtomicInvariantsAtomTypes,
358 <br/> AtomicInvariantsToUse,AS X BO H FC MN,NeighborhoodRadius,2,
359 <br/> NormalizationMethodology,None</div>
360 <div class="OptionsBox">
361 MolecularComplexityType,MACCSKeys,MACCSKeysSize,166</div>
362 <div class="OptionsBox">
363 MolecularComplexityType,PathLengthFingerprints,AtomIdentifierType,
364 <br/> AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS,MinPathLength,
365 <br/> 1,MaxPathLength,8,UseBondSymbols,Yes</div>
366 <div class="OptionsBox">
367 MolecularComplexityType,TopologicalAtomPairsFingerprints,
368 <br/> AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
369 <br/> AS X BO H FC,MinDistance,1,MaxDistance,10</div>
370 <div class="OptionsBox">
371 MolecularComplexityType,TopologicalAtomTripletsFingerprints,
372 <br/> AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
373 <br/> AS X BO H FC,MinDistance,1,MaxDistance,10,UseTriangleInequality,No</div>
374 <div class="OptionsBox">
375 MolecularComplexityType,TopologicalAtomTorsionsFingerprints,
376 <br/> AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
377 <br/> AS X BO H FC</div>
378 <div class="OptionsBox">
379 MolecularComplexityType,TopologicalPharmacophoreAtomPairsFingerprints,
380 <br/> AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
381 <br/> HBD HBA PI NI H,MinDistance,1,MaxDistance,10,NormalizationMethodology,
382 <br/> None</div>
383 <div class="OptionsBox">
384 MolecularComplexityType,TopologicalPharmacophoreAtomTripletsFingerprints,
385 <br/> AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
386 <br/> HBD HBA PI NI H Ar,MinDistance,1,MaxDistance,10,NormalizationMethodology,
387 <br/> None,UseTriangleInequality,Yes,NormalizationMethodology,None,
388 <br/> DistanceBinSize,2</div>
389 </dd>
390 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
391 <dd>
392 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
393 Default value: <em>comma</em>.</p>
394 </dd>
395 <dt><strong><strong>--output</strong> <em>SD | text | both</em></strong></dt>
396 <dd>
397 <p>Type of output files to generate. Possible values: <em>SD, text, or both</em>. Default value: <em>text</em>.</p>
398 </dd>
399 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
400 <dd>
401 <p>Overwrite existing files.</p>
402 </dd>
403 <dt><strong><strong>--Precision</strong> <em>Name,Number,[Name,Number,..]</em></strong></dt>
404 <dd>
405 <p>Precision of calculated property values in the output file: it's a comma delimited list of
406 property name and precision value pairs. Possible property names: <em>MolecularWeight,
407 ExactMass</em>. Possible values: positive intergers. Default value: <em>MolecularWeight,2,
408 ExactMass,4</em>.</p>
409 <p>Examples:</p>
410 <div class="OptionsBox">
411 ExactMass,3
412 <br/> MolecularWeight,1,ExactMass,2</div>
413 </dd>
414 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
415 <dd>
416 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
417 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
418 </dd>
419 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
420 <dd>
421 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file names:
422 &lt;SDFileName&gt;&lt;PhysicochemicalProperties&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt; value.
423 The sdf, csv, and tsv &lt;Ext&gt; values are used for SD, comma/semicolon, and tab
424 delimited text files, respectively.This option is ignored for multiple input files.</p>
425 </dd>
426 <dt><strong><strong>--RotatableBonds</strong> <em>Name,Value, [Name,Value,...]</em></strong></dt>
427 <dd>
428 <p>Parameters to control calculation of rotatable bonds [ Ref 92 ]: it's a comma delimited list of parameter
429 name and value pairs. Possible parameter names: <em>IgnoreTerminalBonds, IgnoreBondsToTripleBonds,
430 IgnoreAmideBonds, IgnoreThioamideBonds, IgnoreSulfonamideBonds</em>. Possible parameter values:
431 <em>Yes or No</em>. By default, value of all parameters is set to <em>Yes</em>.</p>
432 </dd>
433 <dt><strong><strong>--RuleOf3Violations</strong> <em>Yes | No</em></strong></dt>
434 <dd>
435 <p>Specify whether to calculate <strong>RuleOf3Violations</strong> for SDFile(s). Possible values: <em>Yes or No</em>.
436 Default value: <em>No</em>.</p>
437 <p>For <em>Yes</em> value of <strong>RuleOf3Violations</strong>, in addition to calculating total number of <strong>RuleOf3</strong> violations,
438 individual violations for compounds are also written to output files.</p>
439 <p><strong>RuleOf3</strong> [ Ref 92 ] states: MolecularWeight &lt;= 300, RotatableBonds &lt;= 3, HydrogenBondDonors &lt;= 3,
440 HydrogenBondAcceptors &lt;= 3, logP &lt;= 3, and TPSA &lt;= 60.</p>
441 </dd>
442 <dt><strong><strong>--RuleOf5Violations</strong> <em>Yes | No</em></strong></dt>
443 <dd>
444 <p>Specify whether to calculate <strong>RuleOf5Violations</strong> for SDFile(s). Possible values: <em>Yes or No</em>.
445 Default value: <em>No</em>.</p>
446 <p>For <em>Yes</em> value of <strong>RuleOf5Violations</strong>, in addition to calculating total number of <strong>RuleOf5</strong> violations,
447 individual violations for compounds are also written to output files.</p>
448 <p><strong>RuleOf5</strong> [ Ref 91 ] states: MolecularWeight &lt;= 500, HydrogenBondDonors &lt;= 5, HydrogenBondAcceptors &lt;= 10,
449 and logP &lt;= 5.</p>
450 </dd>
451 <dt><strong><strong>--TPSA</strong> <em>Name,Value, [Name,Value,...]</em></strong></dt>
452 <dd>
453 <p>Parameters to control calculation of TPSA: it's a comma delimited list of parameter name and value
454 pairs. Possible parameter names: <em>IgnorePhosphorus, IgnoreSulfur</em>. Possible parameter values:
455 <em>Yes or No</em>. By default, value of all parameters is set to <em>Yes</em>.</p>
456 <p>By default, TPSA atom contributions from Phosphorus and Sulfur atoms are not included during
457 TPSA calculations. [ Ref 91 ]</p>
458 </dd>
459 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
460 <dd>
461 <p>Location of working directory. Default value: current directory.</p>
462 </dd>
463 </dl>
464 <p>
465 </p>
466 <h2>EXAMPLES</h2>
467 <p>To calculate default set of physicochemical properties - MolecularWeight, HeavyAtoms,
468 MolecularVolume, RotatableBonds, HydrogenBondDonor, HydrogenBondAcceptors, SLogP,
469 TPSA - and generate a SamplePhysicochemicalProperties.csv file containing sequential
470 compound IDs along with properties data, type:</p>
471 <div class="ExampleBox">
472 % CalculatePhysicochemicalProperties.pl -o Sample.sdf</div>
473 <p>To calculate all available physicochemical properties and generate both SampleAllProperties.csv
474 and SampleAllProperties.sdf files containing sequential compound IDs in CSV file along with
475 properties data, type:</p>
476 <div class="ExampleBox">
477 % CalculatePhysicochemicalProperties.pl -m All --output both
478 -r SampleAllProperties -o Sample.sdf</div>
479 <p>To calculate RuleOf5 physicochemical properties and generate a SampleRuleOf5Properties.csv file
480 containing sequential compound IDs along with properties data, type:</p>
481 <div class="ExampleBox">
482 % CalculatePhysicochemicalProperties.pl -m RuleOf5
483 -r SampleRuleOf5Properties -o Sample.sdf</div>
484 <p>To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate
485 a SampleRuleOf5Properties.csv file containing sequential compound IDs along with properties data, type:</p>
486 <div class="ExampleBox">
487 % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
488 -r SampleRuleOf5Properties -o Sample.sdf</div>
489 <p>To calculate RuleOf3 physicochemical properties and generate a SampleRuleOf3Properties.csv file
490 containing sequential compound IDs along with properties data, type:</p>
491 <div class="ExampleBox">
492 % CalculatePhysicochemicalProperties.pl -m RuleOf3
493 -r SampleRuleOf3Properties -o Sample.sdf</div>
494 <p>To calculate RuleOf3 physicochemical properties along with counting RuleOf3 violations and generate
495 a SampleRuleOf3Properties.csv file containing sequential compound IDs along with properties data, type:</p>
496 <div class="ExampleBox">
497 % CalculatePhysicochemicalProperties.pl -m RuleOf3 --RuleOf3Violations Yes
498 -r SampleRuleOf3Properties -o Sample.sdf</div>
499 <p>To calculate a specific set of physicochemical properties and generate a SampleProperties.csv file
500 containing sequential compound IDs along with properties data, type:</p>
501 <div class="ExampleBox">
502 % CalculatePhysicochemicalProperties.pl -m &quot;Rings,AromaticRings&quot;
503 -r SampleProperties -o Sample.sdf</div>
504 <p>To calculate HydrogenBondDonors and HydrogenBondAcceptors using HydrogenBondsType1 definition
505 and generate a SampleProperties.csv file containing sequential compound IDs along with properties
506 data, type:</p>
507 <div class="ExampleBox">
508 % CalculatePhysicochemicalProperties.pl -m &quot;HydrogenBondDonors,HydrogenBondAcceptors&quot;
509 --HydrogenBonds HBondsType1 -r SampleProperties -o Sample.sdf</div>
510 <p>To calculate TPSA using sulfur and phosphorus atoms along with nitrogen and oxygen atoms and
511 generate a SampleProperties.csv file containing sequential compound IDs along with properties
512 data, type:</p>
513 <div class="ExampleBox">
514 % CalculatePhysicochemicalProperties.pl -m &quot;TPSA&quot; --TPSA &quot;IgnorePhosphorus,No,
515 IgnoreSulfur,No&quot; -r SampleProperties -o Sample.sdf</div>
516 <p>To calculate MolecularComplexity using extendend connectivity fingerprints corresponding
517 to atom neighborhood radius of 2 with atomic invariant atom types without any scaling and
518 generate a SampleProperties.csv file containing sequential compound IDs along with properties
519 data, type:</p>
520 <div class="ExampleBox">
521 % CalculatePhysicochemicalProperties.pl -m MolecularComplexity --MolecularComplexity
522 &quot;MolecularComplexityType,ExtendedConnectivityFingerprints,NeighborhoodRadius,2,
523 AtomIdentifierType, AtomicInvariantsAtomTypes,
524 AtomicInvariantsToUse,AS X BO H FC MN,NormalizationMethodology,None&quot;
525 -r SampleProperties -o Sample.sdf</div>
526 <p>To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate
527 a SampleRuleOf5Properties.csv file containing compound IDs from molecule name line along with
528 properties data, type:</p>
529 <div class="ExampleBox">
530 % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
531 --DataFieldsMode CompoundID --CompoundIDMode MolName
532 -r SampleRuleOf5Properties -o Sample.sdf</div>
533 <p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv
534 file containing compound ID using specified data field along with along with properties data,
535 type:</p>
536 <div class="ExampleBox">
537 % CalculatePhysicochemicalProperties.pl -m All
538 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID Mol_ID
539 -r SampleAllProperties -o Sample.sdf</div>
540 <p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv
541 file containing compound ID using combination of molecule name line and an explicit compound
542 prefix along with properties data, type:</p>
543 <div class="ExampleBox">
544 % CalculatePhysicochemicalProperties.pl -m All
545 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
546 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleAllProperties
547 -o Sample.sdf</div>
548 <p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv
549 file containing specific data fields columns along with with properties data, type:</p>
550 <div class="ExampleBox">
551 % CalculatePhysicochemicalProperties.pl -m All
552 --DataFieldsMode Specify --DataFields Mol_ID -r SampleAllProperties
553 -o Sample.sdf</div>
554 <p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv
555 file containing common data fields columns along with with properties data, type:</p>
556 <div class="ExampleBox">
557 % CalculatePhysicochemicalProperties.pl -m All
558 --DataFieldsMode Common -r SampleAllProperties -o Sample.sdf</div>
559 <p>To calculate all available physicochemical properties and generate both SampleAllProperties.csv
560 and CSV files containing all data fields columns in CSV files along with with properties data, type:</p>
561 <div class="ExampleBox">
562 % CalculatePhysicochemicalProperties.pl -m All
563 --DataFieldsMode All --output both -r SampleAllProperties
564 -o Sample.sdf</div>
565 <p>
566 </p>
567 <h2>AUTHOR</h2>
568 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
569 <p>
570 </p>
571 <h2>SEE ALSO</h2>
572 <p><a href="./ExtractFromSDtFiles.html">ExtractFromSDtFiles.pl</a>,&nbsp<a href="./ExtractFromTextFiles.html">ExtractFromTextFiles.pl</a>,&nbsp<a href="./InfoSDFiles.html">InfoSDFiles.pl</a>,&nbsp<a href="./InfoTextFiles.html">InfoTextFiles.pl</a>
573 </p>
574 <p>
575 </p>
576 <h2>COPYRIGHT</h2>
577 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
578 <p>This file is part of MayaChemTools.</p>
579 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
580 the terms of the GNU Lesser General Public License as published by the Free
581 Software Foundation; either version 3 of the License, or (at your option)
582 any later version.</p>
583 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
584 <table width="100%" border=0 cellpadding=0 cellspacing=2>
585 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./DBSchemaTablesToTextFiles.html" title="DBSchemaTablesToTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>CalculatePhysicochemicalProperties.pl</strong></td></tr>
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