View source for DOCK DN Parameters

{| class="wikitable"
|-
! 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, rand, 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
|-

|}