Joe and Brian de novo stuff

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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


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.

Experiments Run with Current Binary

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 above.

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

5-15 rotatable bonds? I think that's 703 systems

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