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3 <title>MayaChemTools:Documentation:InfoAminoAcids.pl</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FilterSDFiles.html" title="FilterSDFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./InfoFingerprintsFiles.html" title="InfoFingerprintsFiles.html">Next</a></td><td width="34%" align="middle"><strong>InfoAminoAcids.pl</strong></td><td width="33%" align="right"><a href="././code/InfoAminoAcids.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/InfoAminoAcids.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/InfoAminoAcids.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/InfoAminoAcids.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/InfoAminoAcids.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>InfoAminoAcids.pl - List properties of amino acids</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>InfoAminoAcids.pl AminoAcidIDs...</p>
26 <p>InfoAminoAcids.pl [<strong>-h, --help</strong>] [<strong>--outdelim</strong> comma | tab | semicolon]
27 [<strong>--output</strong> STDOUT | File] [<strong>--outputstyle</strong> AminoAcidBlock | AminoAcidRows]
28 [<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>--propertiesmode</strong> Categories | Names | All]
29 [<strong>-p, --properties</strong> CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]]
30 [<strong>--propertieslinting</strong> ByGroup | Alphabetical] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname]
31 [<strong>-w, --workingdir</strong> dirname] AminoAcidIDs...</p>
32 <p>
33 </p>
34 <h2>DESCRIPTION</h2>
35 <p>List amino acid properties. Amino acids identification supports these three types of IDs: one letter
36 code, three letter code or name. Amino acid properties data, in addition to basic information about
37 amino acids - one and three letter codes, name, DNA and RNA codons, molecular weight - include
38 variety of other properties: polarity, acidity, hydrophobicity, and so on.</p>
39 <p>
40 </p>
41 <h2>PARAMETERS</h2>
42 <dl>
43 <dt><strong><strong>AminoAcidIDs</strong> <em>ThreeLetterCode [OneLetterCode AminoAcidName...]</em></strong></dt>
44 <dd>
45 <p><em>AminoAcidIDs</em> is a space delimited list of values to identify amino acids.</p>
46 <p>Input value format is: <em>ThreeLetterCode [OneLetterCode AminoAcidName...]</em>. Default: <em>Ala</em>.
47 Examples:</p>
48 <div class="OptionsBox">
49 Ala
50 <br/> Glu A
51 <br/> Alanine Glu Y &quot;Aspartic acid&quot;</div>
52 </dd>
53 </dl>
54 <p>
55 </p>
56 <h2>OPTIONS</h2>
57 <dl>
58 <dt><strong><strong>-h, --help</strong></strong></dt>
59 <dd>
60 <p>Print this help message.</p>
61 </dd>
62 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt>
63 <dd>
64 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>
65 Default value: <em>comma</em>.</p>
66 </dd>
67 <dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt>
68 <dd>
69 <p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default:
70 <em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p>
71 </dd>
72 <dt><strong><strong>--outputstyle</strong> <em>AminoAcidBlock | AminoAcidRows</em></strong></dt>
73 <dd>
74 <p>Specify how to list amino acid information: add a new line for each property and present it as a block
75 for each amino acid; or include all properties in one line and show it as a single line.</p>
76 <p>Possible values: <em>AminoAcidBlock | AminoAcidRows</em>. Default: <em>AminoAcidBlock</em></p>
77 <p>An example for <em>AminoAcidBlock</em> output style:</p>
78 <div class="OptionsBox">
79 ThreeLetterCode: Ala
80 <br/> OneLetterCode: A
81 <br/> AminoAcid: Alanine
82 <br/> MolecularWeight: 89.0941
83 <br/> ... ...
84 <br/> ... ...
85 <br/> ... ...</div>
86 <div class="OptionsBox">
87 ThreeLetterCode: Glu
88 <br/> OneLetterCode: E
89 <br/> AminoAcid: Glutamic acid
90 <br/> MolecularWeight: 147.1308
91 <br/> ... ...
92 <br/> ... ...
93 <br/> ... ...</div>
94 <p>An example for <em>AminoAcidRows</em> output style:</p>
95 <div class="OptionsBox">
96 ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight
97 <br/> Ala,A,Alanine,89.0941..
98 <br/> Glu,E,Glutamic acid,147.1308..</div>
99 </dd>
100 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
101 <dd>
102 <p>Overwrite existing files.</p>
103 </dd>
104 <dt><strong><strong>--precision</strong> <em>number</em></strong></dt>
105 <dd>
106 <p>Precision for listing numerical values. Default: up to <em>4</em> decimal places.
107 Valid values: positive integers.</p>
108 </dd>
109 <dt><strong><strong>--propertiesmode</strong> <em>Categories | Names | All</em></strong></dt>
110 <dd>
111 <p>Specify how property names are specified: use category names; explicit list of property names; or
112 use all available properties. Possible values: <em>Categories, Names, or All</em>. Default: <em>Categories</em>.</p>
113 <p>This option is used in conjunction with <strong>-p, --properties</strong> option to specify properties of
114 interest.</p>
115 </dd>
116 <dt><strong><strong>-p, --properties</strong> <em>CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]</em></strong></dt>
117 <dd>
118 <p>This option is <strong>--propertiesmode</strong> specific. In general, it's a list of comma separated category or
119 property names.</p>
120 <p>Specify which amino acid properties information to list for the amino acid IDs specified using command:
121 line parameters: list basic and/or hydrophobicity information; list all available information; or specify a comma
122 separated list of amino acid property names.</p>
123 <p>Possible values: <em>Basic | BasicPlus | BasicAndHydrophobicity | BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]</em>.
124 Default: <em>Basic</em>.</p>
125 <p><em>Basic</em> includes: <em>ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4</em></p>
126 <p><em>BasicPlus</em> includes: <em>ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), LinearStructure, LinearStructureAtpH7.4</em></p>
127 <p><em>BasicAndHydrophobicity</em> includes: <em>ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers</em></p>
128 <p><em>BasicAndHydrophobicityPlus</em> includes: <em>(ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers</em></p>
129 <p>Here is a complete list of available properties: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume, %AccessibleResidues, %BuriedResidues, AlphaHelixChouAndFasman, AlphaHelixDeleageAndRoux, AlphaHelixLevitt, AminoAcidsComposition, AminoAcidsCompositionInSwissProt, AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility, BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt, BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, Bulkiness, CoilDeleageAndRoux, HPLCHFBARetention, HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4, HPLCTFARetention, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers, ParallelBetaStrand, PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide, RecognitionFactors, Refractivity, RelativeMutability, TotalBetaStrand, LinearStructure, LinearStructureAtpH7.4</p>
130 </dd>
131 <dt><strong><strong>--propertieslisting</strong> <em>ByGroup | Alphabetical</em></strong></dt>
132 <dd>
133 <p>Specify how to list properties for amino acids: group by category or an alphabetical by
134 property names. Possible values: <em>ByGroup or Alphabetical</em>. Default: <em>ByGroup</em>.</p>
135 </dd>
136 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt>
137 <dd>
138 <p>Put quotes around column values in output text file. Possible values: <em>yes or
139 no</em>. Default value: <em>yes</em>.</p>
140 </dd>
141 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
142 <dd>
143 <p>New text file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. File name is only
144 used during <em>File</em> value of <strong>-o, --output</strong> option.</p>
145 <p>Default file name: AminoAcidInfo&lt;mode&gt;.&lt;Ext&gt;. The csv, and tsv
146 &lt;Ext&gt; values are used for comma/semicolon, and tab delimited text files respectively.</p>
147 </dd>
148 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
149 <dd>
150 <p>Location of working directory. Default: current directory.</p>
151 </dd>
152 </dl>
153 <p>
154 </p>
155 <h2>EXAMPLES</h2>
156 <p>To list basic properties information for amino acid Ala, type:</p>
157 <div class="ExampleBox">
158 % InfoAminoAcids.pl</div>
159 <p>To list all available properties information for amino acid Ala, type:</p>
160 <div class="ExampleBox">
161 % InfoAminoAcids.pl --propertiesmode all</div>
162 <p>To list basic properties information for amino acids Ala, Arg, and Asp type:</p>
163 <div class="ExampleBox">
164 % InfoAminoAcids.pl Ala Arg Asp
165 <br/>% InfoAminoAcids.pl A Arg &quot;Aspartic acid&quot;</div>
166 <p>To list all available properties information for amino acids Ala, Arg, and Asp type:</p>
167 <div class="ExampleBox">
168 % InfoAminoAcids.pl --propertiesmode all Ala Arg Asp</div>
169 <p>To list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp type:</p>
170 <div class="ExampleBox">
171 % InfoAminoAcids.pl --propertiesmode Categories
172 --properties BasicAndHydrophobicity Ala Arg Asp</div>
173 <p>To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight for amino
174 acids Ala, Arg, and Asp type:</p>
175 <div class="ExampleBox">
176 % InfoAminoAcids.pl --propertiesmode Names
177 --properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight
178 Ala Arg Asp</div>
179 <p>To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
180 in rows insetad of amino acid blocks with quotes around the values, type:</p>
181 <div class="ExampleBox">
182 % InfoAminoAcids.pl --propertiesmode Categories
183 --properties BasicAndHydrophobicity --propertieslisting alphabetical
184 --outdelim comma --outputstyle AminoAcidRows --quote yes Ala Arg Asp</div>
185 <p>To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
186 in rows insetad of amino acid blocks with quotes around the values and write them into a file
187 AminoAcidProperties.csv, type:</p>
188 <div class="ExampleBox">
189 % InfoAminoAcids.pl --propertiesmode Categories
190 --properties BasicAndHydrophobicity --propertieslisting alphabetical
191 --outdelim comma --outputstyle AminoAcidRows --quote yes
192 --output File -r AminoAcidProperties -o Ala Arg Asp</div>
193 <p>
194 </p>
195 <h2>AUTHOR</h2>
196 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
197 <p>
198 </p>
199 <h2>SEE ALSO</h2>
200 <p><a href="./InfoNucleicAcids.plInfoPeriodicTableElements.html">InfoNucleicAcids.plInfoPeriodicTableElements.pl</a>
201 </p>
202 <p>
203 </p>
204 <h2>COPYRIGHT</h2>
205 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
206 <p>This file is part of MayaChemTools.</p>
207 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
208 the terms of the GNU Lesser General Public License as published by the Free
209 Software Foundation; either version 3 of the License, or (at your option)
210 any later version.</p>
211 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
212 <table width="100%" border=0 cellpadding=0 cellspacing=2>
213 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FilterSDFiles.html" title="FilterSDFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./InfoFingerprintsFiles.html" title="InfoFingerprintsFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoAminoAcids.pl</strong></td></tr>
214 </table>
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