Difference between revisions of "Parameter List"
From Rizzo_Lab
Stonybrook (talk | contribs) |
Stonybrook (talk | contribs) |
||
| Line 75: | Line 75: | ||
<td>The number of fragments randomly chosen to add to each attachment point (Du)</td> | <td>The number of fragments randomly chosen to add to each attachment point (Du)</td> | ||
<td>20</td> | <td>20</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_pruning_conformer_score_cutoffr</td> | ||
| + | <td>the max score allowed for each fragment conformer addition to be accepted (kcal/mol)</td> | ||
| + | <td>100.0</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_pruning_conformer_score_sclaing_factor</td> | ||
| + | <td>The coefficient of the score cutoff</td> | ||
| + | <td>1.0</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_pruning_clustering_cutoff</td> | ||
| + | <td>The max score allowed post clustering</td> | ||
| + | <td>100.0</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_constraint_mol_wt</td> | ||
| + | <td>The max molecular weight allowed</td> | ||
| + | <td>1000.0</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_constraint_rot_bon</td> | ||
| + | <td>the max rotatable bonds allowed</td> | ||
| + | <td>15</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_constraint_formal_charge</td> | ||
| + | <td>largest absolute charge of the molecule</td> | ||
| + | <td>2.0</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_heur_unmatched_num</td> | ||
| + | <td>Tanimoto similarity*</td> | ||
| + | <td>1</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_heur_matched_num</td> | ||
| + | <td>The pruning cutoff for RMSD similarity</td> | ||
| + | <td>2.0</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_unique_anchors</td> | ||
| + | <td>The number of unique anchors post clustering</td> | ||
| + | <td>3.0</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_max_grow_layers</td> | ||
| + | <td>The max number of layers that will be added to the anchor</td> | ||
| + | <td>9.0</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_max_root_size</td> | ||
| + | <td>The number of new anchors that seed the next layer of growth</td> | ||
| + | <td>100</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>dn_max_layer_size</td> | ||
| + | <td>The number of partially grown molecules that advance through the seaarch to subsequent attachment points</td> | ||
| + | <td>100</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
Revision as of 16:26, 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 seaarch to subsequent attachment points | 100 |
