Difference between revisions of "Parameter List"
From Rizzo_Lab
Stonybrook (talk | contribs) |
Stonybrook (talk | contribs) |
||
| Line 327: | Line 327: | ||
|- | |- | ||
|Orient Distance tolerance | |Orient Distance tolerance | ||
| − | | | + | |The tolerance in angstroms within which a pair of spheres is considered equivalent to |
| + | a pair of centers (Parameter used with automated matching for sphere selection) | ||
|0.25 | |0.25 | ||
|- | |- | ||
Revision as of 08:48, 12 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_rmsd | 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 |
| Parameter | Description | Default |
|---|---|---|
| Conformer Search Type | Choose between flex, rigid or denovo docking | 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 side chain 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 |
| Graph DN graph max picks | The number of fragment picks per layer per Dummy atom | 30 |
| Graph DN graph breadth | The number of fragments chosen that are similar to successful fragment through Tanimoto | 3 |
| Graph DN graph depth | The number of fragments choosen that are similar to successful fragments through Tanimoto | 2 |
| Graph DN graph temp | The beginning annealing temperature | 100.0 |
| Random 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 | 1000.0 |
| 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 | 3 |
| 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 | 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 | 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 |
| Orient orient ligand | If the anchor/ligand is in the binding pose orienting isn't necessary | Yes |
| Orient Automated Matching | The dock program will input the orient matching parameters (all default values) | Yes |
| Orient Distance tolerance | The tolerance in angstroms within which a pair of spheres is considered equivalent to
a pair of centers (Parameter used with automated matching for sphere selection) |
0.25 |
| Orient Distance minimum | The minimum distance to be considered separate orients (avoid clustering) | 2.0 |
| Orient Nodes minimum | The minimum number of heavy atoms to match for clustering | 3 |
| Orient Nodes Max | The max number of heavy atoms to match to for clustering | 10 |
| Orient Receptor site file | The selected spheres file | |
| Orient Max orientations | Max number of orients sampled | 1000 |
| Orient Critical points | Used to focus initial anchor orientation into a subsite of the receptors active site. Spheres generated using sphgen deemed critical must be identified manually. (See Dock manual section 2.7.2 and 3.4.2 on Critical Points.) | No |
| Orient Chemical Matching | Aids anchor orientation based on chemical complementarity as defined in the chem_match.tbl file. Also must be done manually. (See Dock Manual section 2.7.3 and section 3.3.3 on Chemical Matching) | No |
| Orient Use ligand spheres | Use spheres generated from a ligand | No |
