View source for Joe and Brian de novo stuff

This is Joe and Brian's secret wiki page. If you are not Joe and Brian, why are you here?

=== This is the version of the code on cluster that we should be using ===

 /sbhome1/wjallen/work/build/dock.6.7_2015-02-17.denovo_paper
 /sbhome1/wjallen/work/build/dock.6.7_2015-02-17.denovo_paper/src/dock/dock6

We will probably do a merge after 6.8 is released. Brian: If you have any edits to the code, do a diff and e-mail me the results. I will merge it into my branch and confirm with you that I made that change.


=== Here is our list of things that we definitely want to do for the release ===

put a table here, leave a column for joe and brian to add initials to claim an item

=== Here is our list of things that would be nice to have, but not necessary for release ===

put a bulleted list here, important things we can move into the table below.

=== This is the list of systems that we will use for tests ===

=== This is the input file we should be using ===

Note: these are not all the current default parameter. I am going to update the version of the code above so that everything below is the current default.

 conformer_search_type                                        denovo
 dn_fraglib_scaffold_file                                     fraglib_scaffold.mol2
 dn_fraglib_linker_file                                       fraglib_linker.mol2
 dn_fraglib_sidechain_file                                    fraglib_sidechain.mol2
 dn_user_specified_anchor                                     yes
 dn_fraglib_anchor_file                                       fraglib_anchor.mol2
 dn_use_torenv_table                                          yes
 dn_torenv_table                                              torenv_table.dat
 dn_sampling_method                                           graph
 dn_graph_starting_points                                     10
 dn_graph_breadth                                             5
 dn_graph_depth                                               2
 dn_graph_temperature                                         100
 dn_pruning_conformer_score_cutoff                            100.0
 dn_torsion_rmsd_cutoff                                       0.5
 dn_constraint_mol_wt                                         1000.0
 dn_constraint_rot_bon                                        15
 dn_constraint_formal_charge                                  2.0
 dn_constraint_charge_groups                                  4
 dn_tanimoto_cutoff                                           0.7
 dn_heur_unmatched_num                                        5
 dn_heur_matched_rmsd                                         2.0
 dn_max_grow_layers                                           7
 dn_max_current_aps                                           5
 dn_max_root_size                                             50
 dn_max_layer_size                                            50
 dn_write_checkpoints                                         yes
 dn_write_orients                                             no
 dn_write_growth_trees                                        no
 dn_output_prefix                                             output
 use_internal_energy                                          yes
 internal_energy_rep_exp                                      12
 use_database_filter                                          no
 orient_ligand                                                yes
 automated_matching                                           yes
 receptor_site_file                                           receptor.sph
 max_orientations                                             1000
 critical_points                                              no
 chemical_matching                                            no
 use_ligand_spheres                                           no
 bump_filter                                                  no
 score_molecules                                              yes
 contact_score_primary                                        no
 contact_score_secondary                                      no
 grid_score_primary                                           yes
 grid_score_secondary                                         no
 grid_score_rep_rad_scale                                     1
 grid_score_vdw_scale                                         1
 grid_score_es_scale                                          1
 grid_score_grid_prefix                                       grid
 multigrid_score_secondary                                    no
 dock3.5_score_secondary                                      no
 continuous_score_secondary                                   no
 footprint_similarity_score_secondary                         no
 ph4_score_secondary                                          no
 descriptor_score_secondary                                   no
 gbsa_zou_score_secondary                                     no
 gbsa_hawkins_score_secondary                                 no
 SASA_descriptor_score_secondary                              no
 amber_score_secondary                                        no
 minimize_ligand                                              yes
 minimize_anchor                                              yes
 minimize_flexible_growth                                     yes
 use_advanced_simplex_parameters                              no
 simplex_max_cycles                                           1
 simplex_score_converge                                       0.1
 simplex_cycle_converge                                       1.0
 simplex_trans_step                                           1.0
 simplex_rot_step                                             0.1
 simplex_tors_step                                            10.0
 simplex_anchor_max_iterations                                500
 simplex_grow_max_iterations                                  500
 simplex_grow_tors_premin_iterations                          0
 simplex_random_seed                                          0
 simplex_restraint_min                                        no
 atom_model                                                   all
 vdw_defn_file                                                vdw.defn
 flex_defn_file                                               flex.defn
 flex_drive_file                                              flex_drive.tbl