Difference between revisions of "Parameter List"
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<tr> | <tr> | ||
<td>dn_max_layer_size</td> | <td>dn_max_layer_size</td> | ||
| − | <td>The number of partially grown molecules that advance through the | + | <td>The number of partially grown molecules that advance through the search to subsequent attachment points</td> |
<td>100</td> | <td>100</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_max_current_aps</td> | ||
| + | <td>Currently unknown*</td> | ||
| + | <td>5</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_max_scaffolds_per_layer</td> | ||
| + | <td>The max number of scaffolds added per layer per anchor</td> | ||
| + | <td>1</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_write_checkpoints</td> | ||
| + | <td>Write molecules for each layer for each anchor</td> | ||
| + | <td>yes</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_write_prune_dump</td> | ||
| + | <td>Write all molecules pruned out at every layer (lots of molecules)</td> | ||
| + | <td>no</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_write_orients</td> | ||
| + | <td>Write out the orients into an orient file</td> | ||
| + | <td>no</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_write_growth_trees</td> | ||
| + | <td>Shows growth at every layer for every accepted molecule</td> | ||
| + | <td>no</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_output_prefix</td> | ||
| + | <td>The name of the output file with the final ensemble of molecules</td> | ||
| + | <td>output</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td><span style="font-weight:bold">ORIENT</span> orient_ligand</td> | ||
| + | <td>Do you want to orient the ligand (no if it's in the correct orientation prior to denovo)</td> | ||
| + | <td>yes</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
Revision as of 16:52, 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 |
| dn_pruning_conformer_score_cutoffr | the max score allowed for each fragment conformer addition to be accepted (kcal/mol) | 100.0 |
| dn_pruning_conformer_score_sclaing_factor | The coefficient of the score cutoff | 1.0 |
| dn_pruning_clustering_cutoff | The max score allowed post clustering | 100.0 |
| dn_constraint_mol_wt | The max molecular weight allowed | 1000.0 |
| dn_constraint_rot_bon | the max rotatable bonds allowed | 15 |
| dn_constraint_formal_charge | largest absolute charge of the molecule | 2.0 |
| dn_heur_unmatched_num | Tanimoto similarity* | 1 |
| dn_heur_matched_num | The pruning cutoff for RMSD similarity | 2.0 |
| dn_unique_anchors | The number of unique anchors post clustering | 3.0 |
| dn_max_grow_layers | The max number of layers that will be added to the anchor | 9.0 |
| dn_max_root_size | The number of new anchors that seed the next layer of growth | 100 |
| dn_max_layer_size | The number of partially grown molecules that advance through the search to subsequent attachment points | 100 |
| dn_max_current_aps | Currently unknown* | 5 |
| dn_max_scaffolds_per_layer | The max number of scaffolds added per layer per anchor | 1 |
| dn_write_checkpoints | Write molecules for each layer for each anchor | yes |
| dn_write_prune_dump | Write all molecules pruned out at every layer (lots of molecules) | no |
| dn_write_orients | Write out the orients into an orient file | no |
| dn_write_growth_trees | Shows growth at every layer for every accepted molecule | no |
| dn_output_prefix | The name of the output file with the final ensemble of molecules | output |
| ORIENT orient_ligand | Do you want to orient the ligand (no if it's in the correct orientation prior to denovo) | yes |
