Parameter List

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