Difference between revisions of "Parameter List"
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{| class="wikitable" | {| class="wikitable" | ||
| Line 186: | Line 6: | ||
! Default | ! Default | ||
|- | |- | ||
| − | | | + | | conformer_search_type |
| − | | Choose between flex, rigid or | + | | Choose between flex, rigid, denovo, or genetic |
| Flex | | Flex | ||
|- | |- | ||
| − | | | + | | dn_fraglib_scaffold_file |
| The path to the fragment library for just scaffolds | | The path to the fragment library for just scaffolds | ||
| | | | ||
|- | |- | ||
| − | | | + | |dn_fraglib_linker_file |
|The path to the fragment library for just linkers | |The path to the fragment library for just linkers | ||
| | | | ||
|- | |- | ||
| − | | | + | |dn_fraglib_sidechain_file |
|The path to the fragment library for just side chains | |The path to the fragment library for just side chains | ||
| | | | ||
|- | |- | ||
| − | | | + | |dn_user_specified_anchor |
|Does the user have a specific anchor to use? | |Does the user have a specific anchor to use? | ||
|Yes | |Yes | ||
|- | |- | ||
| − | | | + | |dn_fraglib_anchor_file |
|The path to the anchor .mol2 file | |The path to the anchor .mol2 file | ||
| | | | ||
|- | |- | ||
| − | | | + | |dn_use_torenv_table |
|Will torsion environment be used? | |Will torsion environment be used? | ||
|Yes | |Yes | ||
|- | |- | ||
| − | | | + | |dn_torenv_table |
|The path to the torsion environment (.dat) | |The path to the torsion environment (.dat) | ||
| | | | ||
|- | |- | ||
| − | | | + | |dn_sampling_method |
|Choose which method to use when choosing fragments for each layer (ex, random, graph) | |Choose which method to use when choosing fragments for each layer (ex, random, graph) | ||
|Graph | |Graph | ||
|- | |- | ||
| − | | | + | | dn_graph_max_picks |
|The number of fragment picks per layer per Dummy atom | |The number of fragment picks per layer per Dummy atom | ||
|30 | |30 | ||
|- | |- | ||
| − | | | + | | dn_graph_breadth |
|The number of fragments chosen that are similar to successful fragment through Tanimoto | |The number of fragments chosen that are similar to successful fragment through Tanimoto | ||
|3 | |3 | ||
|- | |- | ||
| − | | | + | | dn_graph_depth |
|The number of fragments choosen that are similar to successful fragments through Tanimoto | |The number of fragments choosen that are similar to successful fragments through Tanimoto | ||
|2 | |2 | ||
|- | |- | ||
| − | | | + | | dn_graph_temp |
|The beginning annealing temperature | |The beginning annealing temperature | ||
|100.0 | |100.0 | ||
|- | |- | ||
| − | | | + | | dn_num_random_picks |
|Number of fragments randomly chosen to add to anchor | |Number of fragments randomly chosen to add to anchor | ||
|20 | |20 | ||
|- | |- | ||
| − | | | + | |dn_pruning_conformer_score_cutoff |
|The max score allowed for fragment conformer addition to be accepted (kcal/mol) | |The max score allowed for fragment conformer addition to be accepted (kcal/mol) | ||
|100.0 | |100.0 | ||
|- | |- | ||
| − | | | + | |dn_pruning_conformer_score_scaling_factor |
|The weight put on the score cutoff | |The weight put on the score cutoff | ||
|1.0 | |1.0 | ||
|- | |- | ||
| − | | | + | |dn_pruning_clustering_cutoff |
|The max score allowed post clustering | |The max score allowed post clustering | ||
|100.0 | |100.0 | ||
|- | |- | ||
| − | | | + | |dn_constraint_mol_wt |
|The max molecular weight allowed | |The max molecular weight allowed | ||
| − | | | + | |550 |
|- | |- | ||
| − | | | + | |dn_constraint_rot_bon |
|The max rotatable bonds allowed | |The max rotatable bonds allowed | ||
|15 | |15 | ||
|- | |- | ||
| − | | | + | |dn_constraint_formal_charge |
|Largest absolute charge of molecule | |Largest absolute charge of molecule | ||
|2.0 | |2.0 | ||
|- | |- | ||
| − | | | + | |dn_heur_unmatched_num |
|# of unmatched heavy atoms for hRMSD to be considered a different molecule when pruning between root and layer | |# of unmatched heavy atoms for hRMSD to be considered a different molecule when pruning between root and layer | ||
|1 | |1 | ||
|- | |- | ||
| − | | | + | |dn_heur_matched_rmsd |
| − | | | + | |Max rmsd of matching heavy atoms of molecules to be considered similar molecule when pruning root to layer |
|2.0 | |2.0 | ||
|- | |- | ||
| − | | | + | |dn_unique_anchors |
|The number of unique anchors post clustering | |The number of unique anchors post clustering | ||
| − | | | + | |1 |
|- | |- | ||
| − | | | + | |dn_max_grow_layers |
|Max numbers of layers that will be added to the anchor | |Max numbers of layers that will be added to the anchor | ||
|9 | |9 | ||
|- | |- | ||
| − | | | + | |dn_max_root_size |
|The number of new anchors that seed the next layer of growth | |The number of new anchors that seed the next layer of growth | ||
| − | | | + | |25 |
|- | |- | ||
| − | | | + | |dn_max_layer_size |
|The number of partially grown molecules that advance through the search to subsequent attachment points | |The number of partially grown molecules that advance through the search to subsequent attachment points | ||
| − | | | + | |25 |
|- | |- | ||
| − | | | + | |dn_max_current_aps |
|Maximum attachment points the molecule can have at any one time (stop adding new scaffolds when the current fragment has this many open attachment points) | |Maximum attachment points the molecule can have at any one time (stop adding new scaffolds when the current fragment has this many open attachment points) | ||
|5 | |5 | ||
|- | |- | ||
| − | | | + | |dn_max_scaffolds_per_layer |
|The max number of scaffolds added per layer per molecule | |The max number of scaffolds added per layer per molecule | ||
|1 | |1 | ||
|- | |- | ||
| − | | | + | |dn_write_checkpoints |
|Write molecules for each layer | |Write molecules for each layer | ||
|Yes | |Yes | ||
|- | |- | ||
| − | | | + | |dn_write_prune_dump |
|Write all molecules pruned out at every step | |Write all molecules pruned out at every step | ||
|No (lots of molecules) | |No (lots of molecules) | ||
|- | |- | ||
| − | | | + | |dn_write_orients |
|Write out the orients | |Write out the orients | ||
|No | |No | ||
|- | |- | ||
| − | | | + | |dn_write_growth_trees |
|Shows growth for every accepted molecule | |Shows growth for every accepted molecule | ||
|No | |No | ||
|- | |- | ||
| − | | | + | |dn_output_prefix |
|The name of the output file with final molecules | |The name of the output file with final molecules | ||
|output | |output | ||
|- | |- | ||
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|} | |} | ||
Latest revision as of 10:43, 25 January 2019
| Parameter | Description | Default |
|---|---|---|
| conformer_search_type | Choose between flex, rigid, denovo, or genetic | Flex |
| dn_fraglib_scaffold_file | The path to the fragment library for just scaffolds | |
| dn_fraglib_linker_file | The path to the fragment library for just linkers | |
| dn_fraglib_sidechain_file | The path to the fragment library for just side chains | |
| dn_user_specified_anchor | Does the user have a specific anchor to use? | Yes |
| dn_fraglib_anchor_file | The path to the anchor .mol2 file | |
| dn_use_torenv_table | Will torsion environment be used? | Yes |
| dn_torenv_table | The path to the torsion environment (.dat) | |
| dn_sampling_method | Choose which method to use when choosing fragments for each layer (ex, random, graph) | Graph |
| dn_graph_max_picks | The number of fragment picks per layer per Dummy atom | 30 |
| dn_graph_breadth | The number of fragments chosen that are similar to successful fragment through Tanimoto | 3 |
| dn_graph_depth | The number of fragments choosen that are similar to successful fragments through Tanimoto | 2 |
| dn_graph_temp | The beginning annealing temperature | 100.0 |
| dn_num_random_picks | Number of fragments randomly chosen to add to anchor | 20 |
| dn_pruning_conformer_score_cutoff | The max score allowed for fragment conformer addition to be accepted (kcal/mol) | 100.0 |
| dn_pruning_conformer_score_scaling_factor | The weight put on 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 | 550 |
| dn_constraint_rot_bon | The max rotatable bonds allowed | 15 |
| dn_constraint_formal_charge | Largest absolute charge of molecule | 2.0 |
| dn_heur_unmatched_num | # of unmatched heavy atoms for hRMSD to be considered a different molecule when pruning between root and layer | 1 |
| dn_heur_matched_rmsd | Max rmsd of matching heavy atoms of molecules to be considered similar molecule when pruning root to layer | 2.0 |
| dn_unique_anchors | The number of unique anchors post clustering | 1 |
| dn_max_grow_layers | Max numbers of layers that will be added to the anchor | 9 |
| dn_max_root_size | The number of new anchors that seed the next layer of growth | 25 |
| dn_max_layer_size | The number of partially grown molecules that advance through the search to subsequent attachment points | 25 |
| dn_max_current_aps | Maximum attachment points the molecule can have at any one time (stop adding new scaffolds when the current fragment has this many open attachment points) | 5 |
| dn_max_scaffolds_per_layer | The max number of scaffolds added per layer per molecule | 1 |
| dn_write_checkpoints | Write molecules for each layer | Yes |
| dn_write_prune_dump | Write all molecules pruned out at every step | No (lots of molecules) |
| dn_write_orients | Write out the orients | No |
| dn_write_growth_trees | Shows growth for every accepted molecule | No |
| dn_output_prefix | The name of the output file with final molecules | output |
