Difference between revisions of "Parameter List"

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−
<table style="width:100%">
 
−
  <tr>
 
−
    <th>Input_Parameter</th>
 
−
    <th>Description</th>
 
−
    <th>Default_value</th>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>conformer_search_type</td>
 
−
    <td>Choose between flex, rigid, or denovo docking</td>
 
−
    <td>Flex</td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>dn_fraglib_scaffold_file</td>
 
−
    <td>The path to the fragment library for just scaffold fragments</td>
 
−
    <td> </td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>dn_fraglib_linker_file</td>
 
−
    <td>The path to the fragment library for just linker fragments</td>
 
−
    <td> </td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>dn_fraglib_sidechain_file</td>
 
−
    <td>The path to the fragment library for just sidechain fragments</td>
 
−
    <td> </td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>dn_user_specified_anchor</td>
 
−
    <td>Does the user have a specific anchor to use with Dummy atom notated in the .mol2?</td>
 
−
    <td>yes</td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>dn_fraglib_anchor_file</td>
 
−
    <td>The path to the anchor .mol2 file with attachment point notated as "Du"</td>
 
−
    <td> </td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>dn_use_torenv_table</td>
 
−
    <td>Will torsion environment table be used for checking bond connectivity?</td>
 
−
    <td>yes</td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>dn_torenv_table</td>
 
−
    <td>The path to the torsion environment .dat file</td>
 
−
    <td> </td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>dn_sampling_method</td>
 
−
    <td>which method will be used to choose fragments for each layer: exhaustive (ex), random, or graph</td>
 
−
    <td>graph</td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td><span style="font-weight:bold">GRAPH:</span> dn_graph_max_picks</td>
 
−
    <td>The number of fragments chosen to add to the anchor per layer per attachment point(Du)
 
−
  </td>
 
−
    <td> </td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td><span style="font-weight:bold">GRAPH:</span> dn_graph_breadth</td>
 
−
    <td>The number of fragments chosen that are similar to successful fragment in the row through Tanimoto similarity</td>
 
−
    <td> </td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td><span style="font-weight:bold">GRAPH:</span> dn_graph_depth</td>
 
−
    <td>The number of fragments chosen that are similar to successful fragment in the column through Tanimoto similarity</td>
 
−
    <td> </td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td><span style="font-weight:bold">GRAPH:</span> dn_graph_temp</td>
 
−
    <td>The beginning annealing temperature (usually 100 and scales down to one for each layer)</td>
 
−
    <td>100</td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td><span style="font-weight:bold">RANDOM:</span> dn_num_random_picks</td>
 
−
    <td>The number of fragments randomly chosen to add to each attachment point (Du)</td>
 
−
    <td>20</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_pruning_conformer_score_cutoffr</td>
 
−
    <td>the max score allowed for each fragment conformer addition to be accepted (kcal/mol)</td>
 
−
    <td>100.0</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_pruning_conformer_score_sclaing_factor</td>
 
−
    <td>The coefficient of the score cutoff</td>
 
−
    <td>1.0</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_pruning_clustering_cutoff</td>
 
−
    <td>The max score allowed post clustering</td>
 
−
    <td>100.0</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_constraint_mol_wt</td>
 
−
    <td>The max molecular weight allowed</td>
 
−
    <td>1000.0</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_constraint_rot_bon</td>
 
−
    <td>the max rotatable bonds allowed</td>
 
−
    <td>15</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_constraint_formal_charge</td>
 
−
    <td>largest absolute charge of the molecule</td>
 
−
    <td>2.0</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_heur_unmatched_num</td>
 
−
    <td>Tanimoto similarity*</td>
 
−
    <td>1</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_heur_matched_rmsd</td>
 
−
    <td>The pruning cutoff for RMSD similarity</td>
 
−
    <td>2.0</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_unique_anchors</td>
 
−
    <td>The number of unique anchors post clustering</td>
 
−
    <td>3.0</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_max_grow_layers</td>
 
−
    <td>The max number of layers that will be added to the anchor</td>
 
−
    <td>9.0</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_max_root_size</td>
 
−
    <td>The number of new anchors that seed the next layer of growth</td>
 
−
    <td>100</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_max_layer_size</td>
 
−
    <td>The number of partially grown molecules that advance through the search to subsequent attachment points</td>
 
−
    <td>100</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_max_current_aps</td>
 
−
    <td>Currently unknown*</td>
 
−
    <td>5</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_max_scaffolds_per_layer</td>
 
−
    <td>The max number of scaffolds added per layer per anchor</td>
 
−
    <td>1</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_write_checkpoints</td>
 
−
    <td>Write molecules for each layer for each anchor</td>
 
−
    <td>yes</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_write_prune_dump</td>
 
−
    <td>Write all molecules pruned out at every layer (lots of molecules)</td>
 
−
    <td>no</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_write_orients</td>
 
−
    <td>Write out the orients into an orient file</td>
 
−
    <td>no</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_write_growth_trees</td>
 
−
    <td>Shows growth at every layer for every accepted molecule</td>
 
−
    <td>no</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_output_prefix</td>
 
−
    <td>The name of the output file with the final ensemble of molecules</td>
 
−
    <td>output</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td><span style="font-weight:bold">ORIENT:</span> orient_ligand</td>
 
−
    <td>Do you want to orient the ligand (no if it's in the correct orientation prior to denovo)</td>
 
−
    <td>yes</td>
 
−
  </tr>
 
−
</table>
 
−
 
−
 
  
 
{| class="wikitable"
 
{| class="wikitable"
Line 186: Line 6:
 
! Default
 
! Default
 
|-
 
|-
−
| Conformer Search Type
+
| conformer_search_type
−
| Choose between flex, rigid or denovo docking
+
| Choose between flex, rigid, denovo, or genetic
 
| Flex
 
| Flex
 
|-
 
|-
−
| DN fraglib scaffold file
+
| 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
+
|dn_fraglib_linker_file
 
|The path to the fragment library for just linkers
 
|The path to the fragment library for just linkers
 
|
 
|
 
|-
 
|-
−
|DN fraglib side chain file
+
|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
+
|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
+
|dn_fraglib_anchor_file
 
|The path to the anchor .mol2 file
 
|The path to the anchor .mol2 file
 
|
 
|
 
|-
 
|-
−
|DN use torenv table
+
|dn_use_torenv_table
 
|Will torsion environment be used?
 
|Will torsion environment be used?
 
|Yes
 
|Yes
 
|-
 
|-
−
|DN torenv table
+
|dn_torenv_table
 
|The path to the torsion environment (.dat)
 
|The path to the torsion environment (.dat)
 
|
 
|
 
|-
 
|-
−
|DN Sampling method
+
|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
 
|-
 
|-
−
|Graph DN graph max picks
+
| 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
 
|-
 
|-
−
|Graph DN graph breadth
+
| 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
 
|-
 
|-
−
|Graph DN graph depth
+
| 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
 
|-
 
|-
−
|Graph DN graph temp
+
| dn_graph_temp
 
|The beginning annealing temperature  
 
|The beginning annealing temperature  
 
|100.0
 
|100.0
 
|-
 
|-
−
|Random DN num random picks
+
| 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
+
|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
+
|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
+
|dn_pruning_clustering_cutoff
 
|The max score allowed post clustering
 
|The max score allowed post clustering
 
|100.0
 
|100.0
 
|-
 
|-
−
|DN constraint mol wt
+
|dn_constraint_mol_wt
 
|The max molecular weight allowed  
 
|The max molecular weight allowed  
−
|1000.0
+
|550
 
|-
 
|-
−
|DN constraint rot bon
+
|dn_constraint_rot_bon
 
|The max rotatable bonds allowed
 
|The max rotatable bonds allowed
 
|15
 
|15
 
|-
 
|-
−
|DN constraint formal charge
+
|dn_constraint_formal_charge
 
|Largest absolute charge of molecule
 
|Largest absolute charge of molecule
 
|2.0
 
|2.0
 
|-
 
|-
−
|DN heur unmatched num
+
|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
+
|dn_heur_matched_rmsd
 
|Max rmsd of matching heavy atoms of molecules to be considered similar molecule when pruning root to layer
 
|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
+
|dn_unique_anchors
 
|The number of unique anchors post clustering
 
|The number of unique anchors post clustering
−
|3
+
|1
 
|-
 
|-
−
|DN max grow layers
+
|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
+
|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
−
|100
+
|25
 
|-
 
|-
−
|Dn max layer size
+
|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
−
|100
+
|25
 
|-
 
|-
−
|DN max current aps
+
|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
+
|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
+
|dn_write_checkpoints
 
|Write molecules for each layer
 
|Write molecules for each layer
 
|Yes
 
|Yes
 
|-
 
|-
−
|DN write prune dump
+
|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
+
|dn_write_orients
 
|Write out the orients
 
|Write out the orients
 
|No
 
|No
 
|-
 
|-
−
|DN write growth trees
+
|dn_write_growth_trees
 
|Shows growth for every accepted molecule
 
|Shows growth for every accepted molecule
 
|No
 
|No
 
|-
 
|-
−
|DN output prefix
+
|dn_output_prefix
 
|The name of the output file with final molecules
 
|The name of the output file with final molecules
 
|output
 
|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
 
−
|Tolerance (like sd/se?) ***needs to be edited
 
−
|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
 
 
|}
 
|}

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
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