Mercurial > repos > bgruening > openbabel_filter
comparison ob_filter.xml @ 7:0e382252d23d draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author | bgruening |
---|---|
date | Tue, 07 May 2019 13:35:05 -0400 |
parents | 0d6e836460be |
children | da03b00048b1 |
comparison
equal
deleted
inserted
replaced
6:69e02cf88856 | 7:0e382252d23d |
---|---|
43 }' | 43 }' |
44 ]]> | 44 ]]> |
45 </command> | 45 </command> |
46 <inputs> | 46 <inputs> |
47 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" | 47 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" |
48 label="Select input file previously annotated with the 'Compute physico-chemical properties' tool"/> | 48 label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/> |
49 <conditional name="filter_methods"> | 49 <conditional name="filter_methods"> |
50 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set"> | 50 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set"> |
51 <option value="user">User-defined properties</option> | 51 <option value="user">User-defined properties</option> |
52 <option value="ruleof5">Lipinski's Rule-of-Five</option> | 52 <option value="ruleof5">Lipinski's Rule-of-Five</option> |
53 <option value="LeadLike">Lead-like properties</option> | 53 <option value="LeadLike">Lead-like properties</option> |
57 <when value="ruleof5" /> | 57 <when value="ruleof5" /> |
58 <when value="LeadLike" /> | 58 <when value="LeadLike" /> |
59 <when value="DrugLike" /> | 59 <when value="DrugLike" /> |
60 <when value="FragmentLike" /> | 60 <when value="FragmentLike" /> |
61 <when value="user"> | 61 <when value="user"> |
62 <repeat name="filter_set" title="Filters selection"> | 62 <repeat name="filter_set" title="Select custom filters"> |
63 <conditional name="filter_sel"> | 63 <conditional name="filter_sel"> |
64 <param name="filter_sel_opts" type="select" label="Select properties to filter"> | 64 <param name="filter_sel_opts" type="select" label="Select properties to filter"> |
65 <option value="hbd">Number of Hydrogen-bond donor groups</option> | 65 <option value="hbd">Number of hydrogen-bond donor groups</option> |
66 <option value="hba">Number of Hydrogen-bond acceptor groups</option> | 66 <option value="hba">Number of hydrogen-bond acceptor groups</option> |
67 <option value="psa">Total polar Surface Area</option> | 67 <option value="psa">Total polar surface area</option> |
68 <option value="rotbonds">Number of rotatable bonds</option> | 68 <option value="rotbonds">Number of rotatable bonds</option> |
69 <option value="molwt">Molecular weight</option> | 69 <option value="molwt">Molecular weight</option> |
70 <option value="logp">Predicted value of LogP</option> | 70 <option value="logp">Predicted value of logP</option> |
71 <option value="mr">Predicted value for the Molecular Refractivity</option> | 71 <option value="mr">Predicted value for the molecular refractivity</option> |
72 <option value="atoms">Number of atoms</option> | 72 <option value="atoms">Number of atoms</option> |
73 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt | 73 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt |
74 <option value="hatoms">Number of heavy atoms</option>--> | 74 <option value="hatoms">Number of heavy atoms</option>--> |
75 <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html --> | 75 <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html --> |
76 <!--<option value="rings">Number of rings</option>--> | 76 <!--<option value="rings">Number of rings</option>--> |
77 </param> | 77 </param> |
78 <when value="hbd"> | 78 <when value="hbd"> |
79 <param name="hbd_min" type="integer" value="" label="Minimum number of HB donors"/> | 79 <param name="hbd_min" type="integer" value="" label="Minimum number of hydrogen bond donors"/> |
80 <param name="hbd_max" type="integer" value="" label="Maximum number of HB donors"/> | 80 <param name="hbd_max" type="integer" value="" label="Maximum number of hydrogen bond donors"/> |
81 </when> | 81 </when> |
82 <when value="hba"> | 82 <when value="hba"> |
83 <param name="hba_min" type="integer" value="" label="Minimum number of HB acceptors"/> | 83 <param name="hba_min" type="integer" value="" label="Minimum number of hydrogen bond acceptors"/> |
84 <param name="hba_max" type="integer" value="" label="Maximum number of HB acceptors"/> | 84 <param name="hba_max" type="integer" value="" label="Maximum number of hydrogen bond acceptors"/> |
85 </when> | 85 </when> |
86 <when value="psa"> | 86 <when value="psa"> |
87 <param name="psa_min" type="integer" value="" label="Minimum threshold for the Total Polar Surface Area"/> | 87 <param name="psa_min" type="integer" value="" label="Minimum threshold for the total polar surface area"/> |
88 <param name="psa_max" type="integer" value="" label="Maximum threshold for the Total Polar Surface Area"/> | 88 <param name="psa_max" type="integer" value="" label="Maximum threshold for the total polar surface area"/> |
89 </when> | 89 </when> |
90 <when value="rotbonds"> | 90 <when value="rotbonds"> |
91 <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/> | 91 <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/> |
92 <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/> | 92 <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/> |
93 </when> | 93 </when> |
94 <when value="molwt"> | 94 <when value="molwt"> |
95 <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the Molecular Weight"/> | 95 <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the molecular weight"/> |
96 <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the Molecular Weight"/> | 96 <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the molecular weight"/> |
97 </when> | 97 </when> |
98 <when value="logp"> | 98 <when value="logp"> |
99 <param name="logp_min" type="float" value="" label="Minimum threshold value for the log-P"/> | 99 <param name="logp_min" type="float" value="" label="Minimum threshold value for log P"/> |
100 <param name="logp_max" type="float" value="" label="Maximum threshold value for the log-P"/> | 100 <param name="logp_max" type="float" value="" label="Maximum threshold value for log P"/> |
101 </when> | 101 </when> |
102 <when value="mr"> | 102 <when value="mr"> |
103 <param name="mr_min" type="float" value="" label="Minimum threshold value for the Molecular Refractivity"/> | 103 <param name="mr_min" type="float" value="" label="Minimum threshold value for the molecular refractivity"/> |
104 <param name="mr_max" type="float" value="" label="Maximum threshold value for the Molecular Refractivity"/> | 104 <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/> |
105 </when> | 105 </when> |
106 <when value="atoms"> | 106 <when value="atoms"> |
107 <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/> | 107 <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/> |
108 <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/> | 108 <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/> |
109 </when> | 109 </when> |
152 | 152 |
153 .. class:: warningmark | 153 .. class:: warningmark |
154 | 154 |
155 **Hint** | 155 **Hint** |
156 | 156 |
157 | If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file. | 157 | If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. This should be faster and the file can be reused, although it is larger than a SMILES file. |
158 | | 158 | |
159 | For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value). | 159 | For exact matches use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value). |
160 | | 160 | |
161 | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds). | 161 | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds). |
162 | 162 |
163 ----- | 163 ----- |
164 | 164 |