Difference between revisions of "Parameter List"

From Rizzo_Lab
Jump to: navigation, search
 
(21 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
<table style="width:100%">
+
 
−
  <tr>
+
{| class="wikitable"
−
    <th>Input_Parameter</th>
+
|-
−
    <th>Description</th>
+
! Parameter
−
    <th>Default_value</th>
+
! Description
−
  </tr>
+
! Default
−
  <tr>
+
|-
−
    <td>Conformer Search Type</td>
+
| conformer_search_type
−
    <td>Choose between flex, rigid, or denovo docking</td>
+
| Choose between flex, rigid, denovo, or genetic
−
    <td>Flex</td>
+
| Flex
−
  </tr>
+
|-
−
  <tr>
+
| dn_fraglib_scaffold_file
−
    <td>Dn fraglib scaffold file</td>
+
| The path to the fragment library for just scaffolds
−
    <td>The path to the fragment library for just scaffold fragments</td>
+
|
−
    <td> </td>
+
|-
−
  </tr>
+
|dn_fraglib_linker_file
−
  <tr>
+
|The path to the fragment library for just linkers
−
    <td>Dn fraglib linker file</td>
+
|
−
    <td>The path to the fragment library for just linker fragments</td>
+
|-
−
    <td> </td>
+
|dn_fraglib_sidechain_file
−
  </tr>
+
|The path to the fragment library for just side chains
−
  <tr>
+
|
−
    <td>Dn fraglib sidechain file</td>
+
|-
−
    <td>The path to the fragment library for just sidechain fragments</td>
+
|dn_user_specified_anchor
−
    <td> </td>
+
|Does the user have a specific anchor to use?
−
  </tr>
+
|Yes
−
  <tr>
+
|-
−
    <td>Dn user specified anchor</td>
+
|dn_fraglib_anchor_file
−
    <td>Does the user have a specific anchor to use with Dummy atom notated in the .mol2?</td>
+
|The path to the anchor .mol2 file
−
    <td>yes</td>
+
|
−
  </tr>
+
|-
−
  <tr>
+
|dn_use_torenv_table
−
    <td>Dn fraglib anchor file</td>
+
|Will torsion environment be used?
−
    <td>The path to the anchor .mol2 file with attachment point notated as "Du"</td>
+
|Yes
−
    <td> </td>
+
|-
−
  </tr>
+
|dn_torenv_table  
−
  <tr>
+
|The path to the torsion environment (.dat)
−
    <td>dn_use_torenv_table</td>
+
|
−
    <td>Will torsion environment table be used for checking bond connectivity?</td>
+
|-
−
    <td>yes</td>
+
|dn_sampling_method
−
  </tr>
+
|Choose which method to use when choosing fragments for each layer (ex, random, graph)
−
  <tr>
+
|Graph
−
    <td>dn_torenv_table</td>
+
|-
−
    <td>The path to the torsion environment .dat file</td>
+
| dn_graph_max_picks
−
    <td> </td>
+
|The number of fragment picks per layer per Dummy atom
−
  </tr>
+
|30
−
  <tr>
+
|-
−
    <td>dn_sampling_method</td>
+
| dn_graph_breadth
−
    <td>which method will be used to choose fragments for each layer: exhaustive (ex), random, or graph</td>
+
|The number of fragments chosen that are similar to successful fragment through Tanimoto
−
    <td>graph</td>
+
|3
−
  </tr>
+
|-
−
  <tr>
+
| dn_graph_depth
−
    <td><span style="font-weight:bold">GRAPH</span> dn_graph_max_picks</td>
+
|The number of fragments choosen that are similar to successful fragments through Tanimoto
−
    <td>The number of fragments chosen to add to the anchor per layer per attachment point(Du)</td>
+
|2
−
    <td> </td>
+
|-
−
  </tr>
+
| dn_graph_temp
−
  <tr>
+
|The beginning annealing temperature
−
    <td><span style="font-weight:bold">GRAPH</span> dn_graph_breadth</td>
+
|100.0
−
    <td>The number of fragments chosen that are simnilar to successful fragment through Tanimoto similarity</td>
+
|-
−
    <td> </td>
+
| dn_num_random_picks
−
  </tr>
+
|Number of fragments randomly chosen to add to anchor
−
</table>
+
|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
 +
|-
 +
 
 +
|}

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
Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=Parameter_List&oldid=11157"