- This topic has 2 replies, 2 voices, and was last updated 10 years, 9 months ago by Anonymous.
February 20, 2013 at 11:31 am #1520Anonymous
score_fxn5=create_score_function( ‘score5’ )
score_fxn2=create_score_function( ‘score2’ )
and printing them I obtain the same output, I thought they were meant to be different.
weights: (vdw 1) (cenpack 0.5) (pair 1) (env 1) (cbeta 0.25) (hs_pair 1) (ss_pair 1) (sheet 1)
energy_method_options: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT
EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12
EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid
EnergyMethodOptions::show: exclude_protein_protein_hack_elec: false
EnergyMethodOptions::show: exclude_monomer_hack_elec: false
EnergyMethodOptions::show: hackelec_max_dis: 5.5
EnergyMethodOptions::show: hackelec_min_dis: 1.5
EnergyMethodOptions::show: hackelec_die: 10
EnergyMethodOptions::show: hackelec_no_dis_dep_die: false
EnergyMethodOptions::show: exclude_DNA_DNA: true
EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615
EnergyMethodOptions::show: bond_angle_residue_type_param_set: none
HBondOptions::show: exclude_DNA_DNA: true
HBondOptions::show: include_intra_res_RNA_: false
HBondOptions::show: exclude_self_hbonds: true
HBondOptions::show: use_hb_env_dep: true
HBondOptions::show: use_hb_env_dep_DNA: true
HBondOptions::show: smooth_hb_env_dep: true
HBondOptions::show: bb_donor_acceptor_check: true
HBondOptions::show: decompose_bb_hb_into_pair_energies: false
HBondOptions::show: params_database_tag_: standard_params
HBondOptions::show: use_incorrect_deriv_: false
HBondOptions::show: use_sp2_chi_penalty_: false
HBondOptions::show: Mbhbond: false
I thought they were meant to be different.
February 20, 2013 at 3:11 pm #8435Anonymous
Here are the weights files from the scoring database:
rosetta_database/scoring/weights> cat score2.wts
# score2 from rosetta++, used in stage 3 of ClassicAbinitio protocol.
STRAND_STRAND_WEIGHTS 1 6
rosetta_database/scoring/weights> cat score5.wts
# score5.wts, used in stage 3 of ClassicAbinitio protocol
STRAND_STRAND_WEIGHTS 1 11
STRAND_STRAND_WEIGHTS is different, whatever that is. I’ll see if I can dig out what that does.
February 20, 2013 at 3:28 pm #8436Anonymous
Apparently scores 2 and 5 are both for stage 3 of ClassicAbinitio (as it says). Here’s the code comment:
– Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions
is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch,
running tunable numbers of 2000-cycle iterations between the two scoring functions.
The STRAND_STRAND_WEIGHTS line ultimately weasels its way to the class SecondaryStructurePotential, which controls hs_pair, ss_pair, rsigma, and sheet. I *think* those two numbers are the distance, in angstroms, bounding how far apart two strands can be and still be considered in a “sheet”, but I’m not at all confident of that. This chunk of code was originally written in FORTRAN more than a decade ago, so it’s gotten a little obscure over the years. Look at SecondaryStructurePotential::sspair to see them in action (as lowstrand and cutoff).
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