Parameter List
From Rizzo_Lab
Revision as of 11:58, 5 May 2017 by Stonybrook (talk | contribs)
| Input_Parameter | Description | Default_value |
|---|---|---|
| Conformer Search Type | Choose between flex, rigid, or denovo docking | Flex |
| Dn fraglib scaffold file | The path to the fragment library for just scaffold fragments | |
| Dn fraglib linker file | The path to the fragment library for just linker fragments | |
| Dn fraglib sidechain file | The path to the fragment library for just sidechain fragments | |
| Dn user specified anchor | Does the user have a specific anchor to use with Dummy atom notated in the .mol2? | yes |
| Dn fraglib anchor file | The path to the anchor .mol2 file with attachment point notated as "Du" | |
| dn_use_torenv_table | Will torsion environment table be used for checking bond connectivity? | yes |
| dn_torenv_table | The path to the torsion environment .dat file | |
| dn_sampling_method | which method will be used to choose fragments for each layer: exhaustive (ex), random, or graph | graph |
| GRAPH dn_graph_max_picks | The number of fragments chosen to add to the anchor per layer per attachment point(Du) | |
| GRAPH dn_graph_breadth | The number of fragments chosen that are simnilar to successful fragment through Tanimoto similarity |
