Difference between revisions of "Parameter List"

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<table style="width:100%">
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  <tr>
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{| class="wikitable"
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    <th>Input_Parameter</th>
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|-
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    <th>Description</th>
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! Parameter
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    <th>Default_value</th>
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! Description
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  </tr>
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! Default
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  <tr>
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|-
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    <td>conformer_search_type</td>
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| conformer_search_type
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    <td>Choose between flex, rigid, or denovo docking</td>
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| Choose between flex, rigid, denovo, or genetic
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    <td>Flex</td>
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| Flex
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  </tr>
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|-
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  <tr>
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| dn_fraglib_scaffold_file
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    <td>dn_fraglib_scaffold_file</td>
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| The path to the fragment library for just scaffolds
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    <td>The path to the fragment library for just scaffold fragments</td>
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|
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    <td> </td>
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|-
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  </tr>
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|dn_fraglib_linker_file
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  <tr>
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|The path to the fragment library for just linkers
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    <td>dn_fraglib_linker_file</td>
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|
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    <td>The path to the fragment library for just linker fragments</td>
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|-
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    <td> </td>
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|dn_fraglib_sidechain_file
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  </tr>
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|The path to the fragment library for just side chains
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  <tr>
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|
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    <td>dn_fraglib_sidechain_file</td>
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|-
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    <td>The path to the fragment library for just sidechain fragments</td>
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|dn_user_specified_anchor
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    <td> </td>
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|Does the user have a specific anchor to use?
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  </tr>
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|Yes
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  <tr>
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|-
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    <td>dn_user_specified_anchor</td>
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|dn_fraglib_anchor_file
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    <td>Does the user have a specific anchor to use with Dummy atom notated in the .mol2?</td>
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|The path to the anchor .mol2 file
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    <td>yes</td>
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|
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  </tr>
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|-
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  <tr>
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|dn_use_torenv_table
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    <td>dn_fraglib_anchor_file</td>
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|Will torsion environment be used?
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    <td>The path to the anchor .mol2 file with attachment point notated as "Du"</td>
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|Yes
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    <td> </td>
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|-
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  </tr>
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|dn_torenv_table  
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  <tr>
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|The path to the torsion environment (.dat)
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    <td>dn_use_torenv_table</td>
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|
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    <td>Will torsion environment table be used for checking bond connectivity?</td>
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|-
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    <td>yes</td>
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|dn_sampling_method
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  </tr>
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|Choose which method to use when choosing fragments for each layer (ex, random, graph)
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  <tr>
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|Graph
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    <td>dn_torenv_table</td>
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|-
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    <td>The path to the torsion environment .dat file</td>
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| dn_graph_max_picks  
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    <td> </td>
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|The number of fragment picks per layer per Dummy atom
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  </tr>
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|30
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  <tr>
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|-
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    <td>dn_sampling_method</td>
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| dn_graph_breadth
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    <td>which method will be used to choose fragments for each layer: exhaustive (ex), random, or graph</td>
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|The number of fragments chosen that are similar to successful fragment through Tanimoto
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    <td>graph</td>
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|3
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  </tr>
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|-
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  <tr>
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| dn_graph_depth
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    <td><span style="font-weight:bold">GRAPH:</span> dn_graph_max_picks</td>
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|The number of fragments choosen that are similar to successful fragments through Tanimoto
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    <td>The number of fragments chosen to add to the anchor per layer per attachment point(Du)
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|2
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  </td>
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|-
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    <td> </td>
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| dn_graph_temp
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  </tr>
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|The beginning annealing temperature  
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  <tr>
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|100.0
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    <td><span style="font-weight:bold">GRAPH:</span> dn_graph_breadth</td>
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|-
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    <td>The number of fragments chosen that are similar to successful fragment in the row through Tanimoto similarity</td>
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| dn_num_random_picks
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    <td> </td>
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|Number of fragments randomly chosen to add to anchor
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  </tr>
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|20
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  <tr>
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|-
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    <td><span style="font-weight:bold">GRAPH:</span> dn_graph_depth</td>
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|dn_pruning_conformer_score_cutoff
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    <td>The number of fragments chosen that are similar to successful fragment in the column through Tanimoto similarity</td>
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|The max score allowed for fragment conformer addition to be accepted (kcal/mol)
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    <td> </td>
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|100.0
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  </tr>
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|-
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  <tr>
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|dn_pruning_conformer_score_scaling_factor
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    <td><span style="font-weight:bold">GRAPH:</span> dn_graph_temp</td>
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|The weight put on the score cutoff
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    <td>The beginning annealing temperature (usually 100 and scales down to one for each layer)</td>
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|1.0
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    <td>100</td>
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|-
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  </tr>
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|dn_pruning_clustering_cutoff
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  <tr>
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|The max score allowed post clustering
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    <td><span style="font-weight:bold">RANDOM:</span> dn_num_random_picks</td>
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|100.0
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    <td>The number of fragments randomly chosen to add to each attachment point (Du)</td>
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|-
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    <td>20</td>
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|dn_constraint_mol_wt
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  </tr>
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|The max molecular weight allowed  
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<tr>
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|550
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    <td>dn_pruning_conformer_score_cutoffr</td>
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|-
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    <td>the max score allowed for each fragment conformer addition to be accepted (kcal/mol)</td>
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|dn_constraint_rot_bon
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    <td>100.0</td>
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|The max rotatable bonds allowed
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  </tr>
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|15
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<tr>
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|-
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    <td>dn_pruning_conformer_score_sclaing_factor</td>
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|dn_constraint_formal_charge
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    <td>The coefficient of the score cutoff</td>
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|Largest absolute charge of molecule
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    <td>1.0</td>
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|2.0
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  </tr>
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|-
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<tr>
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|dn_heur_unmatched_num
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    <td>dn_pruning_clustering_cutoff</td>
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|# of unmatched heavy atoms for hRMSD to be considered a different molecule when pruning between root and layer
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    <td>The max score allowed post clustering</td>
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|1
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    <td>100.0</td>
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|-
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  </tr>
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|dn_heur_matched_rmsd
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<tr>
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|Max rmsd of matching heavy atoms of molecules to be considered similar molecule when pruning root to layer
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    <td>dn_constraint_mol_wt</td>
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|2.0
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    <td>The max molecular weight allowed</td>
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|-
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    <td>1000.0</td>
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|dn_unique_anchors
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  </tr>
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|The number of unique anchors post clustering
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<tr>
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|1
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    <td>dn_constraint_rot_bon</td>
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|-
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    <td>the max rotatable bonds allowed</td>
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|dn_max_grow_layers
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    <td>15</td>
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|Max numbers of layers that will be added to the anchor
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  </tr>
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|9
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<tr>
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|-
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    <td>dn_constraint_formal_charge</td>
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|dn_max_root_size
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    <td>largest absolute charge of the molecule</td>
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|The number of new anchors that seed the next layer of growth
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    <td>2.0</td>
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|25
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  </tr>
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|-
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<tr>
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|dn_max_layer_size  
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    <td>dn_heur_unmatched_num</td>
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|The number of partially grown molecules that advance through the search to subsequent attachment points
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    <td>Tanimoto similarity*</td>
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|25
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    <td>1</td>
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|-
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  </tr>
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|dn_max_current_aps
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<tr>
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|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)
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    <td>dn_heur_matched_rmsd</td>
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|5
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    <td>The pruning cutoff for RMSD similarity</td>
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|-
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    <td>2.0</td>
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|dn_max_scaffolds_per_layer
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  </tr>
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|The max number of scaffolds added per layer per molecule
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<tr>
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|1
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    <td>dn_unique_anchors</td>
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|-
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    <td>The number of unique anchors post clustering</td>
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|dn_write_checkpoints
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    <td>3.0</td>
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|Write molecules for each layer
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  </tr>
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|Yes
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<tr>
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|-
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    <td>dn_max_grow_layers</td>
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|dn_write_prune_dump
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    <td>The max number of layers that will be added to the anchor</td>
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|Write all molecules pruned out at every step
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    <td>9.0</td>
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|No (lots of molecules)
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  </tr>
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|-
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<tr>
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|dn_write_orients
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    <td>dn_max_root_size</td>
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|Write out the orients
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    <td>The number of new anchors that seed the next layer of growth</td>
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|No
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    <td>100</td>
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|-
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  </tr>
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|dn_write_growth_trees
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<tr>
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|Shows growth for every accepted molecule
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    <td>dn_max_layer_size</td>
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|No
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    <td>The number of partially grown molecules that advance through the search to subsequent attachment points</td>
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|-
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    <td>100</td>
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|dn_output_prefix
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  </tr>
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|The name of the output file with final molecules
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<tr>
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|output
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    <td>dn_max_current_aps</td>
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|-
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    <td>Currently unknown*</td>
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    <td>5</td>
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|}
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  </tr>
 
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<tr>
 
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    <td>dn_max_scaffolds_per_layer</td>
 
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    <td>The max number of scaffolds added per layer per anchor</td>
 
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    <td>1</td>
 
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  </tr>
 
−
<tr>
 
−
    <td>dn_write_checkpoints</td>
 
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    <td>Write molecules for each layer for each anchor</td>
 
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    <td>yes</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_write_prune_dump</td>
 
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    <td>Write all molecules pruned out at every layer (lots of molecules)</td>
 
−
    <td>no</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_write_orients</td>
 
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    <td>Write out the orients into an orient file</td>
 
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    <td>no</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_write_growth_trees</td>
 
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    <td>Shows growth at every layer for every accepted molecule</td>
 
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    <td>no</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td>dn_output_prefix</td>
 
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    <td>The name of the output file with the final ensemble of molecules</td>
 
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    <td>output</td>
 
−
  </tr>
 
−
<tr>
 
−
    <td><span style="font-weight:bold">ORIENT:</span> orient_ligand</td>
 
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    <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>
 

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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