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comparison rdkit_descriptors.xml @ 8:a1c53f0533b0 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
author bgruening
date Wed, 17 Feb 2021 12:59:43 +0000
parents cf725c82c865
children
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7:cf725c82c865 8:a1c53f0533b0
1 <tool id="ctb_rdkit_descriptors" name="Descriptors" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="ctb_rdkit_descriptors" name="Descriptors" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>calculated with RDKit</description>
2 <macros> 3 <macros>
3 <token name="@TOOL_VERSION@">2020.03.4</token> 4 <token name="@TOOL_VERSION@">2020.03.4</token>
4 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@GALAXY_VERSION@">1</token>
5 </macros> 6 </macros>
6 <description>calculated with RDKit</description>
7 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> 7 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"> 11 <command detect_errors="exit_code">
12 <![CDATA[ 12 <![CDATA[
13 python '$__tool_directory__/rdkit_descriptors.py' 13 python '$__tool_directory__/rdkit_descriptors.py'
14 -i '${infile}' 14 -i '${infile}'
15 --iformat '${infile.ext}' 15 --iformat '${infile.ext}'
16 -o '${outfile}' 16 -o '${outfile}'
17 #if $select_multiple:
18 -s '${select_multiple}'
19 #end if
17 $header 20 $header
18 ]]> 21 ]]>
19 </command> 22 </command>
20 <inputs> 23 <inputs>
21 <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data" 24 <param name="infile" format="smi,sdf,mol2,pdb,inchi" type="data" label="Molecule data"
22 help="In SDF or SMILES format"/> 25 help="In SDF, SMILES, MOL2, PDB or InChI format"/>
23 <param name="header" type="boolean" label="Include the descriptor name as header" 26 <param name="header" type="boolean" label="Include the descriptor name as header"
24 truevalue="--header" falsevalue="" checked="false" /> 27 truevalue="--header" falsevalue="" checked="false" />
28 <param name="select_multiple" type="select" label="Calculate only a subset of the descriptors"
29 multiple="true" help="If left blank, all descriptors will be calculated">
30 <option value="BalabanJ">BalabanJ</option>
31 <option value="BertzCT">BertzCT</option>
32 <option value="Chi0">Chi0</option>
33 <option value="Chi0n">Chi0n</option>
34 <option value="Chi0v">Chi0v</option>
35 <option value="Chi1">Chi1</option>
36 <option value="Chi1n">Chi1n</option>
37 <option value="Chi1v">Chi1v</option>
38 <option value="Chi2n">Chi2n</option>
39 <option value="Chi2v">Chi2v</option>
40 <option value="Chi3n">Chi3n</option>
41 <option value="Chi3v">Chi3v</option>
42 <option value="Chi4n">Chi4n</option>
43 <option value="Chi4v">Chi4v</option>
44 <option value="EState_VSA1">EState_VSA1</option>
45 <option value="EState_VSA10">EState_VSA10</option>
46 <option value="EState_VSA11">EState_VSA11</option>
47 <option value="EState_VSA2">EState_VSA2</option>
48 <option value="EState_VSA3">EState_VSA3</option>
49 <option value="EState_VSA4">EState_VSA4</option>
50 <option value="EState_VSA5">EState_VSA5</option>
51 <option value="EState_VSA6">EState_VSA6</option>
52 <option value="EState_VSA7">EState_VSA7</option>
53 <option value="EState_VSA8">EState_VSA8</option>
54 <option value="EState_VSA9">EState_VSA9</option>
55 <option value="ExactMolWt">ExactMolWt</option>
56 <option value="FormalCharge">FormalCharge</option>
57 <option value="FpDensityMorgan1">FpDensityMorgan1</option>
58 <option value="FpDensityMorgan2">FpDensityMorgan2</option>
59 <option value="FpDensityMorgan3">FpDensityMorgan3</option>
60 <option value="FractionCSP3">FractionCSP3</option>
61 <option value="HallKierAlpha">HallKierAlpha</option>
62 <option value="HeavyAtomCount">HeavyAtomCount</option>
63 <option value="HeavyAtomMolWt">HeavyAtomMolWt</option>
64 <option value="Ipc">Ipc</option>
65 <option value="Kappa1">Kappa1</option>
66 <option value="Kappa2">Kappa2</option>
67 <option value="Kappa3">Kappa3</option>
68 <option value="LabuteASA">LabuteASA</option>
69 <option value="MaxAbsEStateIndex">MaxAbsEStateIndex</option>
70 <option value="MaxAbsPartialCharge">MaxAbsPartialCharge</option>
71 <option value="MaxEStateIndex">MaxEStateIndex</option>
72 <option value="MaxPartialCharge">MaxPartialCharge</option>
73 <option value="MinAbsEStateIndex">MinAbsEStateIndex</option>
74 <option value="MinAbsPartialCharge">MinAbsPartialCharge</option>
75 <option value="MinEStateIndex">MinEStateIndex</option>
76 <option value="MinPartialCharge">MinPartialCharge</option>
77 <option value="MolLogP">MolLogP</option>
78 <option value="MolMR">MolMR</option>
79 <option value="MolWt">MolWt</option>
80 <option value="NHOHCount">NHOHCount</option>
81 <option value="NOCount">NOCount</option>
82 <option value="NumAliphaticCarbocycles">NumAliphaticCarbocycles</option>
83 <option value="NumAliphaticHeterocycles">NumAliphaticHeterocycles</option>
84 <option value="NumAliphaticRings">NumAliphaticRings</option>
85 <option value="NumAromaticCarbocycles">NumAromaticCarbocycles</option>
86 <option value="NumAromaticHeterocycles">NumAromaticHeterocycles</option>
87 <option value="NumAromaticRings">NumAromaticRings</option>
88 <option value="NumHAcceptors">NumHAcceptors</option>
89 <option value="NumHDonors">NumHDonors</option>
90 <option value="NumHeteroatoms">NumHeteroatoms</option>
91 <option value="NumRadicalElectrons">NumRadicalElectrons</option>
92 <option value="NumRotatableBonds">NumRotatableBonds</option>
93 <option value="NumSaturatedCarbocycles">NumSaturatedCarbocycles</option>
94 <option value="NumSaturatedHeterocycles">NumSaturatedHeterocycles</option>
95 <option value="NumSaturatedRings">NumSaturatedRings</option>
96 <option value="NumValenceElectrons">NumValenceElectrons</option>
97 <option value="PEOE_VSA1">PEOE_VSA1</option>
98 <option value="PEOE_VSA10">PEOE_VSA10</option>
99 <option value="PEOE_VSA11">PEOE_VSA11</option>
100 <option value="PEOE_VSA12">PEOE_VSA12</option>
101 <option value="PEOE_VSA13">PEOE_VSA13</option>
102 <option value="PEOE_VSA14">PEOE_VSA14</option>
103 <option value="PEOE_VSA2">PEOE_VSA2</option>
104 <option value="PEOE_VSA3">PEOE_VSA3</option>
105 <option value="PEOE_VSA4">PEOE_VSA4</option>
106 <option value="PEOE_VSA5">PEOE_VSA5</option>
107 <option value="PEOE_VSA6">PEOE_VSA6</option>
108 <option value="PEOE_VSA7">PEOE_VSA7</option>
109 <option value="PEOE_VSA8">PEOE_VSA8</option>
110 <option value="PEOE_VSA9">PEOE_VSA9</option>
111 <option value="RingCount">RingCount</option>
112 <option value="SMR_VSA1">SMR_VSA1</option>
113 <option value="SMR_VSA10">SMR_VSA10</option>
114 <option value="SMR_VSA2">SMR_VSA2</option>
115 <option value="SMR_VSA3">SMR_VSA3</option>
116 <option value="SMR_VSA4">SMR_VSA4</option>
117 <option value="SMR_VSA5">SMR_VSA5</option>
118 <option value="SMR_VSA6">SMR_VSA6</option>
119 <option value="SMR_VSA7">SMR_VSA7</option>
120 <option value="SMR_VSA8">SMR_VSA8</option>
121 <option value="SMR_VSA9">SMR_VSA9</option>
122 <option value="SSSR">SSSR</option>
123 <option value="SlogP_VSA1">SlogP_VSA1</option>
124 <option value="SlogP_VSA10">SlogP_VSA10</option>
125 <option value="SlogP_VSA11">SlogP_VSA11</option>
126 <option value="SlogP_VSA12">SlogP_VSA12</option>
127 <option value="SlogP_VSA2">SlogP_VSA2</option>
128 <option value="SlogP_VSA3">SlogP_VSA3</option>
129 <option value="SlogP_VSA4">SlogP_VSA4</option>
130 <option value="SlogP_VSA5">SlogP_VSA5</option>
131 <option value="SlogP_VSA6">SlogP_VSA6</option>
132 <option value="SlogP_VSA7">SlogP_VSA7</option>
133 <option value="SlogP_VSA8">SlogP_VSA8</option>
134 <option value="SlogP_VSA9">SlogP_VSA9</option>
135 <option value="TPSA">TPSA</option>
136 <option value="VSA_EState1">VSA_EState1</option>
137 <option value="VSA_EState10">VSA_EState10</option>
138 <option value="VSA_EState2">VSA_EState2</option>
139 <option value="VSA_EState3">VSA_EState3</option>
140 <option value="VSA_EState4">VSA_EState4</option>
141 <option value="VSA_EState5">VSA_EState5</option>
142 <option value="VSA_EState6">VSA_EState6</option>
143 <option value="VSA_EState7">VSA_EState7</option>
144 <option value="VSA_EState8">VSA_EState8</option>
145 <option value="VSA_EState9">VSA_EState9</option>
146 <option value="fr_Al_COO">fr_Al_COO</option>
147 <option value="fr_Al_OH">fr_Al_OH</option>
148 <option value="fr_Al_OH_noTert">fr_Al_OH_noTert</option>
149 <option value="fr_ArN">fr_ArN</option>
150 <option value="fr_Ar_COO">fr_Ar_COO</option>
151 <option value="fr_Ar_N">fr_Ar_N</option>
152 <option value="fr_Ar_NH">fr_Ar_NH</option>
153 <option value="fr_Ar_OH">fr_Ar_OH</option>
154 <option value="fr_COO">fr_COO</option>
155 <option value="fr_COO2">fr_COO2</option>
156 <option value="fr_C_O">fr_C_O</option>
157 <option value="fr_C_O_noCOO">fr_C_O_noCOO</option>
158 <option value="fr_C_S">fr_C_S</option>
159 <option value="fr_HOCCN">fr_HOCCN</option>
160 <option value="fr_Imine">fr_Imine</option>
161 <option value="fr_NH0">fr_NH0</option>
162 <option value="fr_NH1">fr_NH1</option>
163 <option value="fr_NH2">fr_NH2</option>
164 <option value="fr_N_O">fr_N_O</option>
165 <option value="fr_Ndealkylation1">fr_Ndealkylation1</option>
166 <option value="fr_Ndealkylation2">fr_Ndealkylation2</option>
167 <option value="fr_Nhpyrrole">fr_Nhpyrrole</option>
168 <option value="fr_SH">fr_SH</option>
169 <option value="fr_aldehyde">fr_aldehyde</option>
170 <option value="fr_alkyl_carbamate">fr_alkyl_carbamate</option>
171 <option value="fr_alkyl_halide">fr_alkyl_halide</option>
172 <option value="fr_allylic_oxid">fr_allylic_oxid</option>
173 <option value="fr_amide">fr_amide</option>
174 <option value="fr_amidine">fr_amidine</option>
175 <option value="fr_aniline">fr_aniline</option>
176 <option value="fr_aryl_methyl">fr_aryl_methyl</option>
177 <option value="fr_azide">fr_azide</option>
178 <option value="fr_azo">fr_azo</option>
179 <option value="fr_barbitur">fr_barbitur</option>
180 <option value="fr_benzene">fr_benzene</option>
181 <option value="fr_benzodiazepine">fr_benzodiazepine</option>
182 <option value="fr_bicyclic">fr_bicyclic</option>
183 <option value="fr_diazo">fr_diazo</option>
184 <option value="fr_dihydropyridine">fr_dihydropyridine</option>
185 <option value="fr_epoxide">fr_epoxide</option>
186 <option value="fr_ester">fr_ester</option>
187 <option value="fr_ether">fr_ether</option>
188 <option value="fr_furan">fr_furan</option>
189 <option value="fr_guanido">fr_guanido</option>
190 <option value="fr_halogen">fr_halogen</option>
191 <option value="fr_hdrzine">fr_hdrzine</option>
192 <option value="fr_hdrzone">fr_hdrzone</option>
193 <option value="fr_imidazole">fr_imidazole</option>
194 <option value="fr_imide">fr_imide</option>
195 <option value="fr_isocyan">fr_isocyan</option>
196 <option value="fr_isothiocyan">fr_isothiocyan</option>
197 <option value="fr_ketone">fr_ketone</option>
198 <option value="fr_ketone_Topliss">fr_ketone_Topliss</option>
199 <option value="fr_lactam">fr_lactam</option>
200 <option value="fr_lactone">fr_lactone</option>
201 <option value="fr_methoxy">fr_methoxy</option>
202 <option value="fr_morpholine">fr_morpholine</option>
203 <option value="fr_nitrile">fr_nitrile</option>
204 <option value="fr_nitro">fr_nitro</option>
205 <option value="fr_nitro_arom">fr_nitro_arom</option>
206 <option value="fr_nitro_arom_nonortho">fr_nitro_arom_nonortho</option>
207 <option value="fr_nitroso">fr_nitroso</option>
208 <option value="fr_oxazole">fr_oxazole</option>
209 <option value="fr_oxime">fr_oxime</option>
210 <option value="fr_para_hydroxylation">fr_para_hydroxylation</option>
211 <option value="fr_phenol">fr_phenol</option>
212 <option value="fr_phenol_noOrthoHbond">fr_phenol_noOrthoHbond</option>
213 <option value="fr_phos_acid">fr_phos_acid</option>
214 <option value="fr_phos_ester">fr_phos_ester</option>
215 <option value="fr_piperdine">fr_piperdine</option>
216 <option value="fr_piperzine">fr_piperzine</option>
217 <option value="fr_priamide">fr_priamide</option>
218 <option value="fr_prisulfonamd">fr_prisulfonamd</option>
219 <option value="fr_pyridine">fr_pyridine</option>
220 <option value="fr_quatN">fr_quatN</option>
221 <option value="fr_sulfide">fr_sulfide</option>
222 <option value="fr_sulfonamd">fr_sulfonamd</option>
223 <option value="fr_sulfone">fr_sulfone</option>
224 <option value="fr_term_acetylene">fr_term_acetylene</option>
225 <option value="fr_tetrazole">fr_tetrazole</option>
226 <option value="fr_thiazole">fr_thiazole</option>
227 <option value="fr_thiocyan">fr_thiocyan</option>
228 <option value="fr_thiophene">fr_thiophene</option>
229 <option value="fr_unbrch_alkane">fr_unbrch_alkane</option>
230 <option value="fr_urea">fr_urea</option>
231 <option value="qed">qed</option>
232 </param>
25 </inputs> 233 </inputs>
26 <outputs> 234 <outputs>
27 <data format="tabular" name="outfile" /> 235 <data format="tabular" name="outfile" />
28 </outputs> 236 </outputs>
29 <tests> 237 <tests>
30 <test> 238 <test>
31 <param name="infile" ftype='sdf' value="CID_3037.sdf" /> 239 <param name="infile" ftype='sdf' value="CID_3037.sdf" />
32 <param name="header" value="True" /> 240 <param name="header" value="True" />
33 <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" /> 241 <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" />
34 </test> 242 </test>
243 <test>
244 <param name="infile" ftype='sdf' value="CID_3037.sdf" />
245 <param name="header" value="True" />
246 <param name="select_multiple" value="qed,FormalCharge,MolWt" />
247 <output name="outfile" ftype='tabular' file="rdkit_descriptors_subset.tab" />
248 </test>
249 <test>
250 <param name="infile" ftype='pdb' value="mol.pdb" />
251 <param name="header" value="False" />
252 <param name="select_multiple" value="FormalCharge" />
253 <output name="outfile" ftype='tabular' file="mol_pdb_charges.tab" />
254 </test>
35 </tests> 255 </tests>
36 <help> 256 <help>
37 <![CDATA[ 257 <![CDATA[
38 258
39 .. class:: infomark 259 .. class:: infomark
40 260
41 **What this tool does** 261 **What this tool does**
42 262
43 | RDKit is an open source toolkit for cheminformatics and machine learning. 263 | RDKit is an open source toolkit for cheminformatics and machine learning.
44 | This tool calculates various molecular descriptors for the input data. The table below shows a brief overview of the descriptors. 264 | This tool calculates various molecular descriptors for the input data. The table below shows a brief overview of the descriptors (or families of related descriptors) which are calculated.
45 | 265 |
46 266 | - Gasteiger/Marsili Partial Charges
47 +-----------------------------------+------------+ 267 | - BalabanJ
48 | Descriptor/Descriptor Family | Language | 268 | - BertzCT
49 +===================================+============+ 269 | - Ipc
50 | Gasteiger/Marsili Partial Charges | C++ | 270 | - HallKierAlpha
51 +-----------------------------------+------------+ 271 | - Kappa1 - Kappa3
52 | BalabanJ | Python | 272 | - Chi0, Chi1
53 +-----------------------------------+------------+ 273 | - Chi0n - Chi4n
54 | BertzCT | Python | 274 | - Chi0v - Chi4v
55 +-----------------------------------+------------+ 275 | - FormalCharge
56 | Ipc | Python | 276 | - MolLogP
57 +-----------------------------------+------------+ 277 | - MolMR
58 | HallKierAlpha | Python | 278 | - MolWt
59 +-----------------------------------+------------+ 279 | - HeavyAtomCount
60 | Kappa1 - Kappa3 | Python | 280 | - HeavyAtomMolWt
61 +-----------------------------------+------------+ 281 | - NHOHCount
62 | Chi0, Chi1 | Python | 282 | - NOCount
63 +-----------------------------------+------------+ 283 | - NumHAcceptors
64 | Chi0n - Chi4n | Python | 284 | - NumHDonors
65 +-----------------------------------+------------+ 285 | - NumHeteroatoms
66 | Chi0v - Chi4v | Python | 286 | - NumRotatableBonds
67 +-----------------------------------+------------+ 287 | - NumValenceElectrons
68 | MolLogP | C++ | 288 | - RingCount
69 +-----------------------------------+------------+ 289 | - SSSR
70 | MolMR | C++ | 290 | - TPSA
71 +-----------------------------------+------------+ 291 | - LabuteASA
72 | MolWt | C++ | 292 | - PEOE_VSA1 - PEOE_VSA14
73 +-----------------------------------+------------+ 293 | - SMR_VSA1 - SMR_VSA10
74 | HeavyAtomCount | Python | 294 | - SlogP_VSA1 - SlogP_VSA12
75 +-----------------------------------+------------+ 295 | - EState_VSA1 - EState_VSA11
76 | HeavyAtomMolWt | Python | 296 | - VSA_EState1 - VSA_EState10
77 +-----------------------------------+------------+ 297 | - Topliss fragments
78 | NHOHCount | C++ |
79 +-----------------------------------+------------+
80 | NOCount | C++ |
81 +-----------------------------------+------------+
82 | NumHAcceptors | C++ |
83 +-----------------------------------+------------+
84 | NumHDonors | C++ |
85 +-----------------------------------+------------+
86 | NumHeteroatoms | C++ |
87 +-----------------------------------+------------+
88 | NumRotatableBonds | C++ |
89 +-----------------------------------+------------+
90 | NumValenceElectrons | Python |
91 +-----------------------------------+------------+
92 | RingCount | C++ |
93 +-----------------------------------+------------+
94 | TPSA | C++ |
95 +-----------------------------------+------------+
96 | LabuteASA | C++ |
97 +-----------------------------------+------------+
98 | PEOE_VSA1 - PEOE_VSA14 | Python/C++ |
99 +-----------------------------------+------------+
100 | SMR_VSA1 - SMR_VSA10 | Python/C++ |
101 +-----------------------------------+------------+
102 | SlogP_VSA1 - SlogP_VSA12 | Python/C++ |
103 +-----------------------------------+------------+
104 | EState_VSA1 - EState_VSA11 | Python |
105 +-----------------------------------+------------+
106 | VSA_EState1 - VSA_EState10 | Python |
107 +-----------------------------------+------------+
108 | Topliss fragments | Python |
109 +-----------------------------------+------------+
110
111 | 298 |
112 | A full list of the descriptors can be obtained here_. 299 | A full list of the descriptors can be obtained here_.
113 300
114 .. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors 301 .. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors
115 302
117 304
118 .. class:: warningmark 305 .. class:: warningmark
119 306
120 **Hint** 307 **Hint**
121 308
122 Use the **cut columns from a table** tool to select just the desired descriptors. 309 Use the **cut columns from a table** tool to select just the desired descriptors. Alternatively, if you just want to calculate a subset of the descriptors, there is an option available to do so.
123 310
124 ----- 311 -----
125 312
126 .. class:: infomark 313 .. class:: infomark
127 314
128 **Input** 315 **Input**
129 316
130 | - `SDF Format`_ 317 | - `SDF Format`_
131 | - `SMILES Format`_ 318 | - `SMILES Format`_
132 | - `Corina MOL2`_ 319 | - `Corina MOL2`_
320 | - PDB
321 | - InChi
133 322
134 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file 323 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
135 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification 324 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
136 .. _Corina MOL2: http://www.molecular-networks.com/products/corina 325 .. _Corina MOL2: http://www.molecular-networks.com/products/corina
137 326