Difference between revisions of "Parameter List"
From Rizzo_Lab
Stonybrook (talk | contribs) |
Stonybrook (talk | contribs) |
||
| Line 70: | Line 70: | ||
<td>The beginning annealing temperature (usually 100 and scales down to one for each layer)</td> | <td>The beginning annealing temperature (usually 100 and scales down to one for each layer)</td> | ||
<td>100</td> | <td>100</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td><span style="font-weight:bold">RANDOM</span> dn_num_random_picks</td> | ||
| + | <td>The number of fragments randomly chosen to add to each attachment point (Du)</td> | ||
| + | <td>20</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
Revision as of 16:13, 5 May 2017
| 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 similar to successful fragment in the row through Tanimoto similarity | |
| GRAPH dn_graph_depth | The number of fragments chosen that are similar to successful fragment in the column through Tanimoto similarity | |
| GRAPH dn_graph_temp | The beginning annealing temperature (usually 100 and scales down to one for each layer) | 100 |
| RANDOM dn_num_random_picks | The number of fragments randomly chosen to add to each attachment point (Du) | 20 |
