scripting_documentation/RosettaScripts/xsd/sfxn_loader_ScoreFunction

Autogenerated Tag Syntax Documentation:

XRW TO DO

<ScoreFunction name="(&string;)" weights="(&string;)" patch="(&string;)"
        symmetric="(&bool;)" hs_hash="(&real;)" >
    <Reweight scoretype="(&string;)" weight="(&real;)" />
    <Set exclude_DNA_DNA_hbond="(&bool;)" use_hb_env_dep_DNA="(&bool;)"
            use_hb_env_dep="(&bool;)" smooth_hb_env_dep="(&bool;)"
            decompose_bb_hb_into_pair_energies="(&bool;)"
            hbonds__hb_max_energy="(&real;)"
            hbonds__exclude_DNA_DNA_hbond="(&bool;)"
            hbonds__use_hb_env_dep_DNA="(&bool;)"
            hbonds__put_intra_into_total="(&bool;)"
            hbonds__exclude_self_hbonds="(&bool;)" hbonds__use_hb_env_dep="(&bool;)"
            hbonds__smooth_hb_env_dep="(&bool;)"
            hbonds__decompose_bb_hb_into_pair_energies="(&bool;)"
            hbonds__exclude_intra_res_protein="(&bool;)"
            hbonds__exclude_intra_res_RNA="(&bool;)"
            hbonds__bb_donor_acceptor_check="(&bool;)"
            hbonds__params_database_tag="(&string;)"
            hbonds__use_sp2_chi_penalty="(&bool;)"
            hbonds__sp2_BAH180_rise="(&real;)" hbonds__sp2_outer_width="(&real;)"
            hbonds__measure_sp3acc_BAH_from_hvy="(&bool;)"
            hbonds__fade_energy="(&bool;)" hbonds__exclude_ether_oxygens="(&bool;)"
            hbonds__Mbhbond="(&bool;)" hbonds__mphbond="(&bool;)"
            lj_hbond_OH_donor_dis="(&real;)" lj_hbond_hdis="(&real;)"
            fa_max_dis="(&real;)" aa_composition_setup_file="(&string;)"
            mhc_epitope_setup_file="(&string;)" netcharge_setup_file="(&string;)"
            softrep_etable="(&bool;)" fa_elec_min_dis="(&real;)"
            fa_elec_max_dis="(&real;)" fa_elec_dielectric="(&real;)"
            fa_elec_no_dis_dep_die="(&bool;)"
            exclude_protein_protein_fa_elec="(&bool;)" exclude_DNA_DNA="(&bool;)"
            pb_bound_tag="(&string;)" pb_unbound_tag="(&string;)"
            scale_sc_dens="(&real;)" scale_sc_dens_byres="(&string;)"
            nmer_ref_seq_length="(&non_negative_integer;)"
            nmer_svm_term_length="(&non_negative_integer;)"
            nmer_svm_pssm_feat="(&bool;)" nmer_svm_scorecut="(&real;)"
            nmer_svm_avg_rank_as_energy="(&bool;)" nmer_svm_aa_matrix="(&string;)"
            nmer_svm_list="(&string;)" nmer_svm="(&string;)"
            nmer_svm_rank_list="(&string;)" nmer_svm_rank="(&string;)"
            approximate_buried_unsat_penalty_hbond_energy_threshold="(&real;)"
            approximate_buried_unsat_penalty_burial_atomic_depth="(&real;)"
            approximate_buried_unsat_penalty_burial_probe_radius="(&real;)"
            approximate_buried_unsat_penalty_burial_resolution="(&real;)"
            approximate_buried_unsat_penalty_oversat_penalty="(&real;)"
            approximate_buried_unsat_penalty_assume_const_backbone="(&bool;)"
            approximate_buried_unsat_penalty_natural_corrections1="(&bool;)"
            approximate_buried_unsat_penalty_hbond_bonus_cross_chain="(&real;)"
            approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb="(&real;)"
            approximate_buried_unsat_penalty_lys_ok_with_1="(&bool;)"
            buried_unsatisfied_penalty_cone_angle_exponent="(&real;)"
            buried_unsatisfied_penalty_cone_angle_shift_factor="(&real;)"
            buried_unsatisfied_penalty_cone_dist_exponent="(&real;)"
            buried_unsatisfied_penalty_cone_dist_midpoint="(&real;)"
            buried_unsatisfied_penalty_burial_threshold="(&real;)"
            buried_unsatisfied_penalty_hbond_energy_threshold="(&real;)"
            target_clash_pdb="(&string;)" dump_trajectory_prefix="(&string;)"
            dump_trajectory_gz="(&bool;)"
            dump_trajectory_stride="(&positive_integer;)"
            voids_penalty_energy_containing_cones_cutoff="(&non_negative_integer;)"
            voids_penalty_energy_voxel_size="(&real;)"
            voids_penalty_energy_voxel_grid_padding="(&real;)"
            voids_penalty_energy_cone_dotproduct_cutoff="(&real;)"
            voids_penalty_energy_cone_distance_cutoff="(&real;)"
            voids_penalty_energy_disabled_except_during_packing="(&bool;)"
            hbnet_bonus_function_ramping="(&hbnet_bonus_function_allowed_types;)"
            hbnet_max_network_size="(&non_negative_integer;)" />
</ScoreFunction>

weights: A .wts file specifying the relative weights of score terms.
patch: A patch file specifying how the relative weights of score terms given in a weights file should be modified.
symmetric: If true, this scorefunction can be used to score symmetric poses. If false, it can only be used on asymmetric poses.
hs_hash: XRW TO DO

Subtag Reweight:

scoretype: (REQUIRED) The name of a score term to be reweighted.
weight: The score term weight to be assigned.

Subtag Set:

exclude_DNA_DNA_hbond: Do not score hydrogen bonds between DNA residues
use_hb_env_dep_DNA: Enable environmental dependent weighting of hydrogen bonds involving DNA
use_hb_env_dep: Enable environmental dependent weighting of hydrogen bond terms
smooth_hb_env_dep: Smooth environmental dependence of hbond term
decompose_bb_hb_into_pair_energies: Should backbone-backbone hydrogen bonds be split between the two participating residues?
hbonds__hb_max_energy: Max possible hbond energy. Under nearly all circumstances this should be set to 0.0.
hbonds__exclude_DNA_DNA_hbond: Same as exclude_DNA_DNA_hbond
hbonds__use_hb_env_dep_DNA: Same as use_hb_env_dep_DNA
hbonds__put_intra_into_total: Include intra-res hbond score in total
hbonds__exclude_self_hbonds: Do not include intra-residue hydrogen bonds
hbonds__use_hb_env_dep: Same as use_hb_env_dep
hbonds__smooth_hb_env_dep: Same as smooth_hb_env_dep
hbonds__decompose_bb_hb_into_pair_energies: Same as decompose_bb_hb_into_pair_energies
hbonds__exclude_intra_res_protein: Do not include intra-residue protein hydrogen bonds
hbonds__exclude_intra_res_RNA: exclude intra-residue RNA hydrogen bonds
hbonds__bb_donor_acceptor_check: XRW TO DO
hbonds__params_database_tag: XRW TO DO
hbonds__use_sp2_chi_penalty: XRW TO DO
hbonds__sp2_BAH180_rise: XRW TO DO
hbonds__sp2_outer_width: XRW TO DO
hbonds__measure_sp3acc_BAH_from_hvy: XRW TO DO
hbonds__fade_energy: XRW TO DO
hbonds__exclude_ether_oxygens: XRW TO DO
hbonds__Mbhbond: XRW TO DO: pba
hbonds__mphbond: Membrane framework hbonding correction
lj_hbond_OH_donor_dis: Lennard Jones sigma value for O in OH donor groups
lj_hbond_hdis: Lennard Jones sigma value for hatms, classically it's been at 1.95 but the average A-H distance for hydrogen bonding is 1.75 from crystal structures
fa_max_dis: Max distance for energy function calculations, in angstroms
aa_composition_setup_file: A list of one or more .comp files specifying desired amino acid compositions, used to set up the aa_composition score term.
mhc_epitope_setup_file: A list of one or more .mhc files specifying epitope prediction details for the mhc_epitope score term.
netcharge_setup_file: A list of one or more .charge files specifying desired net charges, used to set up the netcharge score term.
softrep_etable: Should this scorefunction use a softened energy table for the fa_rep score term?
fa_elec_min_dis: The minimum distance for the fa_elec (Coulombic) score term.
fa_elec_max_dis: The maximum distance for the fa_elec (Coulombic) score term.
fa_elec_dielectric: The dielectric constant for the fa_elec (Coulombic) score term.
fa_elec_no_dis_dep_die: If true, the distance dependence of the dielectric constant used for the fa_elec (Coulombic) term is disabled.
exclude_protein_protein_fa_elec: If true, then the electrostatic interactions between protein residues are not calculated. Used with exclude_DNA_DNA, this can be useful to speed up the calculation of DNA-protein interactions.
exclude_DNA_DNA: If true, then the electrostatic interactions between DNA residues are not calculated. Used with exclude_protein_protein, this can be useful to speed up the calculation of DNA-protein interactions.
pb_bound_tag: XRW TO DO
pb_unbound_tag: XRW TO DO
scale_sc_dens: XRW TO DO
scale_sc_dens_byres: XRW TO DO
nmer_ref_seq_length: Length of N-mers in nmer_ref score.
nmer_svm_term_length: How many up/downstream residues to average and include in SVM sequence encodingin nmer_ref score.
nmer_svm_pssm_feat: Add pssm features to svm encoding in nmer_ref score?
nmer_svm_scorecut: N-mer SVM scorecut gate for ignoring low-scoring N-mers in nmer_ref score.
nmer_svm_avg_rank_as_energy: Use average of SVM score ranks as residue energy for NmerSVM scoring method (nmer_ref score term). This option is good for normalizing across mhc/hla alleles.
nmer_svm_aa_matrix: N-mer SVM sequence-encoding matrix filename for nmer_ref score.
nmer_svm_list: File with list of N-mer SVM filenames (libsvm) for nmer_ref score.
nmer_svm: N-mer SVM filename (libsvm) for nmer_ref score.
nmer_svm_rank_list: File with list of N-mer svm rank scores filenames (libsvm) for nmer_ref score.
nmer_svm_rank: N-mer SVM rank scores filename (libsvm) for nmer_ref score.
approximate_buried_unsat_penalty_hbond_energy_threshold: Energy threshold for a h-bond to be considered satisfying a buried polar. Should be a negative number. (Setting to -0.001 will be much faster than 0 at runtime)
approximate_buried_unsat_penalty_burial_atomic_depth: The atomic depth cutoff to determine whether or not a polar atom is buried. Measured from the Sasa surface.
approximate_buried_unsat_penalty_burial_probe_radius: The probe radius for the atomic depth calculation.
approximate_buried_unsat_penalty_burial_resolution: The resolution for the atomic depth calculation.
approximate_buried_unsat_penalty_oversat_penalty: The penalty between atoms that both satisfy the same atom. If we let X = weight_of_approximate_buried_unsat_penalty. Then in general, a buried unsat is worth X, a satisfied unsat is worth 0, a doubly satisfied unsat is worth X * ( setting-1.0 ), a triply satisfied unsat is worth X * ( -2 + 3 * setting ), a N-ly satisfied unsat is worth X * ( 1 - N + 0.5 * N * (N - 1) ).
approximate_buried_unsat_penalty_assume_const_backbone: Should we assume that the backbone atoms will not change during a packing trajectory? (i.e. no positions that include normal aa and proline or n-methyl) If set to false, this energy method takes longer to compute. (~ 2X as long)
approximate_buried_unsat_penalty_natural_corrections1: Apply the following corrections to buried unsat penalty: nh2_wants_2, nh1_wants_1, hydroxyl_wants_h, carboxyl_wants_2
approximate_buried_unsat_penalty_hbond_bonus_cross_chain: Apply a bonus factor to hydrogen bonds accross chains.
approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb: Apply a bonus factor to the classic SER/THR i - i-4 h-bond. OG/OG1 - O. Set this positive to penalize.
approximate_buried_unsat_penalty_lys_ok_with_1: Make LYS N work like carbonyl O where it prefers 1 or 2 h-bonds.
buried_unsatisfied_penalty_cone_angle_exponent: The angle exponent for calculating burial by the method of sidechain neighbor cones, used by the BuriedUnsatPenalty energy.
buried_unsatisfied_penalty_cone_angle_shift_factor: The angle shift factor for calculating burial by the method of sidechain neighbor cones, used by the BuriedUnsatPenalty energy.
buried_unsatisfied_penalty_cone_dist_exponent: The distance exponent for calculating burial by the method of sidechain neighbor cones, used by the BuriedUnsatPenalty energy.
buried_unsatisfied_penalty_cone_dist_midpoint: The distance midpoint for calculating burial by the method of sidechain neighbor cones, used by the BuriedUnsatPenalty energy.
buried_unsatisfied_penalty_burial_threshold: The number of cones in which a point must lie to be considered buried by the method of sidechain neighbor cones, used by the BuriedUnsatPenalty energy.
buried_unsatisfied_penalty_hbond_energy_threshold: The energy threshold above which a hydrogen bond is not counted, used by the BuriedUnsatPenalty energy.
target_clash_pdb: The target pdb file for clash checking.
dump_trajectory_prefix: If the dump_trajectory scoreterm is used, this is the prefix for the filename to which we're dumping.
dump_trajectory_gz: If the dump_trajectory scoreterm is used, this determines whether we write to gzipped files. False by defualt.
dump_trajectory_stride: If the dump_trajectory scoreterm is used, this is the frequency with which we write. Every Nth evaluation of the score term, a pose will be written. Default 1.
voids_penalty_energy_containing_cones_cutoff: The minimum number of sidechain cones in which a voxel must lie in order for that voxel to be considered to be buried. Defaults to 6 cones.
voids_penalty_energy_voxel_size: The voxel size (in Angstroms) used in the voids_penalty score term's calculation. Default 0.5 Angstroms.
voids_penalty_energy_voxel_grid_padding: The voxel grid padding (in Angstroms) used in the voids_penalty score term's calculation. The bounding box for the pose is enlarged on every side by this amount. Default 1.0 Angstroms.
voids_penalty_energy_cone_dotproduct_cutoff: The dot product cutoff used in the voids_penalty score term's calculation. This effectively sets the width of the cone projected along each side-chain when determining the number of neighbors to a test point in space. The value can range from -1.0 to 1.0, though negative values are not recommended (since they yield cone angles greater than 180 degrees). Default 0.1.
voids_penalty_energy_cone_distance_cutoff: The cutoff distance used in the voids_penalty score term's calculation when determining whether a point lies near to a residue. Default 8.0 Angstroms.
voids_penalty_energy_disabled_except_during_packing: If true, then the voids_penalty score term is disabled outside of the context of the packer. If false, then the voids_penalty score term is evaluated for packing and scoring (but not for minimizing). True by default.
hbnet_bonus_function_ramping: The hbnet score term's bonus function can scale in different ways as the size of a network grows. The default is quadratic growth, though linear, logarithmic, and square root growth are all allowed.
hbnet_max_network_size: The maximum size of a hydrogen bond network, beyond which the hbnet score term no longer gives a bonus. Defaults to 0 (unlimited).

scripting_documentation/RosettaScripts/xsd/sfxn_loader_ScoreFunction_type