Joe and Brian de novo stuff
From Rizzo_Lab
Revision as of 15:17, 19 September 2015 by Stonybrook (talk | contribs) (→Here is our list of things that we definitely want to do for the release)
This is Joe and Brian's secret wiki page. If you are not Joe and Brian, why are you here?
Contents
- 1 This is the version of the code on cluster that we should be using
- 2 This is the list of systems that we will use for tests
- 3 Experiments Run with Current Binary
- 4 Here is our list of things that we definitely want to do for the release
- 5 Here is our list of things that would be nice to have, but not necessary for release
- 6 This is the input file we should be using
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.
This is the list of systems that we will use for tests
For now, let's use 5-15 rotatable bonds inclusive; total = 709 systems. [Joe]: I like this set because it represents "drug-like" size molecules, and they should not be too easy / too hard.
{5RB = 107; 6RB = 96; 7RB = 103; 8RB = 75; 9RB = 66; 10RB = 75; 11RB = 57; 12RB = 41; 13RB = 38; 14RB = 26; 15RB = 25}
Experiments Run with Current Binary
| TAN_CUT | UNMAT_NUM | MAT_RMSD | MAX_LAY | MAX_APS | MAX_ROOT_SZ | MAX_LAY_SZ | RES_MIN | SYS | LIB | SCR_FN_GR | NOTES |
| 1.0 | 0 | 2.0 | 9 | 7 | 50 | 50 | no | 5-15 | focused | des_grid | 005hhh |
| 1.0 | 6 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpUM6 |
| 1.0 | 4 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpUM4 |
| 1.0 | 2 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpUM2 |
| 1.0 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005hh |
| 1.0 | 0 | 2.0 | 9 | 3 | 50 | 50 | no | 5-15 | focused | des_grid | 005h |
| 1.0 | 0 | 2.0 | 7 | 7 | 50 | 50 | no | 5-15 | focused | des_grid | 005ggg |
| 1.0 | 0 | 2.0 | 7 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005gg |
| 1.0 | 0 | 2.0 | 7 | 3 | 50 | 50 | no | 5-15 | focused | des_grid | 005g |
| 1.0 | 0 | 2.0 | 7 | 3 | 50 | 50 | yes | 5-15 | focused | des_grid | 005i |
| 0.95 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpTan095 |
| 0.90 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpTan090 |
| 0.85 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpTan085 |
| 0.80 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpTan080 |
Here is our list of things that we definitely want to do for the release
| Task | Owner |
|---|---|
| Molecular Properties in mol2 header | |
| check formal charge prune | BCF |
| combination of horizontal pruning metrics | |
| growth trees | |
Here is our list of things that would be nice to have, but not necessary for release
- Stereo Centers
- Volume Overlap
- Capping Groups (H, CH3, Halogen)
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
