Difference between revisions of "Parameter List"
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</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>conformer_search_type</td> |
<td>Choose between flex, rigid, or denovo docking</td> | <td>Choose between flex, rigid, or denovo docking</td> | ||
<td>Flex</td> | <td>Flex</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>dn_fraglib_scaffold_file</td> |
<td>The path to the fragment library for just scaffold fragments</td> | <td>The path to the fragment library for just scaffold fragments</td> | ||
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>dn_fraglib_linker_file</td> |
<td>The path to the fragment library for just linker fragments</td> | <td>The path to the fragment library for just linker fragments</td> | ||
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>dn_fraglib_sidechain_file</td> |
<td>The path to the fragment library for just sidechain fragments</td> | <td>The path to the fragment library for just sidechain fragments</td> | ||
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>dn_user_specified_anchor</td> |
<td>Does the user have a specific anchor to use with Dummy atom notated in the .mol2?</td> | <td>Does the user have a specific anchor to use with Dummy atom notated in the .mol2?</td> | ||
<td>yes</td> | <td>yes</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>dn_fraglib_anchor_file</td> |
<td>The path to the anchor .mol2 file with attachment point notated as "Du"</td> | <td>The path to the anchor .mol2 file with attachment point notated as "Du"</td> | ||
<td> </td> | <td> </td> | ||
| Line 52: | Line 52: | ||
<tr> | <tr> | ||
<td><span style="font-weight:bold">GRAPH</span> dn_graph_max_picks</td> | <td><span style="font-weight:bold">GRAPH</span> dn_graph_max_picks</td> | ||
| − | <td>The number of fragments chosen to add to the anchor per layer per attachment point(Du)</td> | + | <td>The number of fragments chosen to add to the anchor per layer per attachment point(Du) |
| + | </td> | ||
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><span style="font-weight:bold">GRAPH</span> dn_graph_breadth</td> | <td><span style="font-weight:bold">GRAPH</span> dn_graph_breadth</td> | ||
| − | <td>The number of fragments chosen that are | + | <td>The number of fragments chosen that are similar to successful fragment in the row through Tanimoto similarity</td> |
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
| − | <tr> | + | <tr> |
| − | <td><span style="font-weight:bold">GRAPH</span> | + | <td><span style="font-weight:bold">GRAPH</span> dn_graph_depth</td> |
| − | <td>The number of fragments chosen that are | + | <td>The number of fragments chosen that are similar to successful fragment in the column through Tanimoto similarity</td> |
<td> </td> | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td><span style="font-weight:bold">GRAPH</span> dn_graph_temp</td> | ||
| + | <td>The beginning annealing temperature (usually 100 and scales down to one for each layer)</td> | ||
| + | <td>100</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
Revision as of 16:11, 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 |
