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1 NAME
2 InfoAminoAcids.pl - List properties of amino acids
3
4 SYNOPSIS
5 InfoAminoAcids.pl AminoAcidIDs...
6
7 InfoAminoAcids.pl [-h, --help] [--outdelim comma | tab | semicolon]
8 [--output STDOUT | File] [--outputstyle AminoAcidBlock | AminoAcidRows]
9 [-o, --overwrite] [--precision number] [--propertiesmode Categories |
10 Names | All] [-p, --properties CategoryName,[CategoryName,...] |
11 PropertyName,[PropertyName,...]] [--propertieslinting ByGroup |
12 Alphabetical] [-q, --quote yes | no] [-r, --root rootname] [-w,
13 --workingdir dirname] AminoAcidIDs...
14
15 DESCRIPTION
16 List amino acid properties. Amino acids identification supports these
17 three types of IDs: one letter code, three letter code or name. Amino
18 acid properties data, in addition to basic information about amino acids
19 - one and three letter codes, name, DNA and RNA codons, molecular weight
20 - include variety of other properties: polarity, acidity,
21 hydrophobicity, and so on.
22
23 PARAMETERS
24 AminoAcidIDs *ThreeLetterCode [OneLetterCode AminoAcidName...]*
25 *AminoAcidIDs* is a space delimited list of values to identify amino
26 acids.
27
28 Input value format is: *ThreeLetterCode [OneLetterCode
29 AminoAcidName...]*. Default: *Ala*. Examples:
30
31 Ala
32 Glu A
33 Alanine Glu Y "Aspartic acid"
34
35 OPTIONS
36 -h, --help
37 Print this help message.
38
39 --outdelim *comma | tab | semicolon*
40 Output text file delimiter. Possible values: *comma, tab, or
41 semicolon* Default value: *comma*.
42
43 --output *STDOUT | File*
44 List information at STDOUT or write it to a file. Possible values:
45 *STDOUT or File*. Default: *STDOUT*. -r, --root option is used to
46 generate output file name.
47
48 --outputstyle *AminoAcidBlock | AminoAcidRows*
49 Specify how to list amino acid information: add a new line for each
50 property and present it as a block for each amino acid; or include
51 all properties in one line and show it as a single line.
52
53 Possible values: *AminoAcidBlock | AminoAcidRows*. Default:
54 *AminoAcidBlock*
55
56 An example for *AminoAcidBlock* output style:
57
58 ThreeLetterCode: Ala
59 OneLetterCode: A
60 AminoAcid: Alanine
61 MolecularWeight: 89.0941
62 ... ...
63 ... ...
64 ... ...
65
66 ThreeLetterCode: Glu
67 OneLetterCode: E
68 AminoAcid: Glutamic acid
69 MolecularWeight: 147.1308
70 ... ...
71 ... ...
72 ... ...
73
74 An example for *AminoAcidRows* output style:
75
76 ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight
77 Ala,A,Alanine,89.0941..
78 Glu,E,Glutamic acid,147.1308..
79
80 -o, --overwrite
81 Overwrite existing files.
82
83 --precision *number*
84 Precision for listing numerical values. Default: up to *4* decimal
85 places. Valid values: positive integers.
86
87 --propertiesmode *Categories | Names | All*
88 Specify how property names are specified: use category names;
89 explicit list of property names; or use all available properties.
90 Possible values: *Categories, Names, or All*. Default: *Categories*.
91
92 This option is used in conjunction with -p, --properties option to
93 specify properties of interest.
94
95 -p, --properties *CategoryName,[CategoryName,...] |
96 PropertyName,[PropertyName,...]*
97 This option is --propertiesmode specific. In general, it's a list of
98 comma separated category or property names.
99
100 Specify which amino acid properties information to list for the
101 amino acid IDs specified using command: line parameters: list basic
102 and/or hydrophobicity information; list all available information;
103 or specify a comma separated list of amino acid property names.
104
105 Possible values: *Basic | BasicPlus | BasicAndHydrophobicity |
106 BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]*.
107 Default: *Basic*.
108
109 *Basic* includes: *ThreeLetterCode, OneLetterCode, AminoAcid,
110 DNACodons, RNACodons, ChemicalFormula, MolecularWeight,
111 LinearStructure, LinearStructureAtpH7.4*
112
113 *BasicPlus* includes: *ThreeLetterCode, OneLetterCode, AminoAcid,
114 DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic,
115 HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+,
116 ChemicalFormula, MolecularWeight, ExactMass,
117 ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524),
118 ExactMassMinusH2O(18.01056), LinearStructure,
119 LinearStructureAtpH7.4*
120
121 *BasicAndHydrophobicity* includes: *ThreeLetterCode, OneLetterCode,
122 AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight,
123 LinearStructure, LinearStructureAtpH7.4,
124 HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods,
125 HydrophobicityJanin, HydrophobicityKyteAndDoolittle,
126 HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers*
127
128 *BasicAndHydrophobicityPlus* includes: *(ThreeLetterCode,
129 OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula,
130 MolecularWeight, LinearStructure, LinearStructureAtpH7.4,
131 HydrophobicityAbrahamAndLeo, HydrophobicityBlack,
132 HydrophobicityBullAndBreese, HydrophobicityChothia,
133 HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers,
134 HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan,
135 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers,
136 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods,
137 HydrophobicityJanin, HydrophobicityKyteAndDoolittle,
138 HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers,
139 HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos,
140 HydrophobicityRfMobility, HydrophobicityRoseAndOthers,
141 HydrophobicityRoseman, HydrophobicityWellingAndOthers,
142 HydrophobicityWolfendenAndOthers*
143
144 Here is a complete list of available properties: ThreeLetterCode,
145 OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic,
146 PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic,
147 IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight,
148 ExactMass, ChemicalFormulaMinusH2O,
149 MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056),
150 vanderWaalsVolume, %AccessibleResidues, %BuriedResidues,
151 AlphaHelixChouAndFasman, AlphaHelixDeleageAndRoux, AlphaHelixLevitt,
152 AminoAcidsComposition, AminoAcidsCompositionInSwissProt,
153 AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility,
154 BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt,
155 BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt,
156 Bulkiness, CoilDeleageAndRoux, HPLCHFBARetention,
157 HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4, HPLCTFARetention,
158 HydrophobicityAbrahamAndLeo, HydrophobicityBlack,
159 HydrophobicityBullAndBreese, HydrophobicityChothia,
160 HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers,
161 HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan,
162 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers,
163 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods,
164 HydrophobicityJanin, HydrophobicityKyteAndDoolittle,
165 HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers,
166 HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos,
167 HydrophobicityRfMobility, HydrophobicityRoseAndOthers,
168 HydrophobicityRoseman, HydrophobicityWellingAndOthers,
169 HydrophobicityWolfendenAndOthers, ParallelBetaStrand,
170 PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide,
171 RecognitionFactors, Refractivity, RelativeMutability,
172 TotalBetaStrand, LinearStructure, LinearStructureAtpH7.4
173
174 --propertieslisting *ByGroup | Alphabetical*
175 Specify how to list properties for amino acids: group by category or
176 an alphabetical by property names. Possible values: *ByGroup or
177 Alphabetical*. Default: *ByGroup*.
178
179 -q, --quote *yes | no*
180 Put quotes around column values in output text file. Possible
181 values: *yes or no*. Default value: *yes*.
182
183 -r, --root *rootname*
184 New text file name is generated using the root: <Root>.<Ext>. File
185 name is only used during *File* value of -o, --output option.
186
187 Default file name: AminoAcidInfo<mode>.<Ext>. The csv, and tsv <Ext>
188 values are used for comma/semicolon, and tab delimited text files
189 respectively.
190
191 -w, --workingdir *dirname*
192 Location of working directory. Default: current directory.
193
194 EXAMPLES
195 To list basic properties information for amino acid Ala, type:
196
197 % InfoAminoAcids.pl
198
199 To list all available properties information for amino acid Ala, type:
200
201 % InfoAminoAcids.pl --propertiesmode all
202
203 To list basic properties information for amino acids Ala, Arg, and Asp
204 type:
205
206 % InfoAminoAcids.pl Ala Arg Asp
207 % InfoAminoAcids.pl A Arg "Aspartic acid"
208
209 To list all available properties information for amino acids Ala, Arg,
210 and Asp type:
211
212 % InfoAminoAcids.pl --propertiesmode all Ala Arg Asp
213
214 To list basic and hydrophobicty properties information for amino acids
215 Ala, Arg, and Asp type:
216
217 % InfoAminoAcids.pl --propertiesmode Categories
218 --properties BasicAndHydrophobicity Ala Arg Asp
219
220 To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight
221 for amino acids Ala, Arg, and Asp type:
222
223 % InfoAminoAcids.pl --propertiesmode Names
224 --properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight
225 Ala Arg Asp
226
227 To alphabetically list basic and hydrophobicty properties information
228 for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks
229 with quotes around the values, type:
230
231 % InfoAminoAcids.pl --propertiesmode Categories
232 --properties BasicAndHydrophobicity --propertieslisting alphabetical
233 --outdelim comma --outputstyle AminoAcidRows --quote yes Ala Arg Asp
234
235 To alphabetically list basic and hydrophobicty properties information
236 for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks
237 with quotes around the values and write them into a file
238 AminoAcidProperties.csv, type:
239
240 % InfoAminoAcids.pl --propertiesmode Categories
241 --properties BasicAndHydrophobicity --propertieslisting alphabetical
242 --outdelim comma --outputstyle AminoAcidRows --quote yes
243 --output File -r AminoAcidProperties -o Ala Arg Asp
244
245 AUTHOR
246 Manish Sud <msud@san.rr.com>
247
248 SEE ALSO
249 InfoNucleicAcids.pl InfoPeriodicTableElements.pl
250
251 COPYRIGHT
252 Copyright (C) 2015 Manish Sud. All rights reserved.
253
254 This file is part of MayaChemTools.
255
256 MayaChemTools is free software; you can redistribute it and/or modify it
257 under the terms of the GNU Lesser General Public License as published by
258 the Free Software Foundation; either version 3 of the License, or (at
259 your option) any later version.
260