Report the total score for each structure using whatever score function you like. The difference between this reporter and the many others that deal with scores is simplicity. This reporter only reports total scores and has a very simple schema. In most cases, this is exactly what you want. But if you need to break down your scores by type or by residue, then you will need to use one or more of the other reporters described in this section.
Example:
<TotalScoreFeatures scorefxn="talaris2013"/>Options:
Schema:
CREATE TABLE `total_scores` (
`struct_id` bigint(20) NOT NULL,
`score` double NOT NULL,
PRIMARY KEY (`struct_id`)
)The ScoreTypeFeatures store the score types for as for all EnergyMethods.
<ScoreTypeFeatures scorefxn="(default_scorefxn &string)"/>
CREATE TABLE IF NOT EXISTS score_types (
batch_id INTEGER,
score_type_id INTEGER,
score_type_name TEXT,
FOREIGN KEY (batch_id) REFERENCES batches (batch_id) DEFERRABLE INITIALLY DEFERRED),
PRIMARY KEY (batch_id, score_type_id);
The ScoreFunctionFeatures store the weights and energy method options for the score function.
<ScoreFunctionFeatures scorefxn="(default_scorefxn &string)"/>
CREATE TABLE IF NOT EXISTS score_function_weights (
batch_id INTEGER,
score_function_name INTEGER,
score_type_id INTEGER,
weight REAL,
FOREIGN KEY (batch_id, score_type_id) REFERENCES score_types (batch_id, score_type_id) DEFERRABLE INITIALLY DEFERRED,
PRIMARY KEY (batch_id, score_type_id));
CREATE TABLE IF NOT EXISTS score_function_method_options (
batch_id INTEGER,
score_function_name INTEGER,
option_key TEXT,
option_value TEXT,
FOREIGN KEY (batch_id) REFERENCES batches (batch_id) DEFERRABLE INITIALLY DEFERRED,
PRIMARY KEY (batch_id, score_function_name, option_key);
<StructureScoresFeatures scorefxn="(&scorefxn)"/>
The StructureScoresFeatures stores the overall score information for all enabled EnergyMethods.
Depends on ScoreTypesFeatures
structure_scores :
CREATE TABLE IF NOT EXISTS structure_scores (
batch_id INTEGER
struct_id INTEGER AUTOINCREMENT,
score_type_id INTEGER,
score_value INTEGER,
FOREIGN KEY (struct_id) REFERENCES structures (struct_id) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY (batch_id, score_type_id) REFERENCES score_types (batch_id, score_type_id) DEFERRABLE INITIALLY DEFERRED,
PRIMARY KEY (batch_id, struct_id, score_type_id));
<ResidueScoresFeatures scorefxn="(&scorefxn)"/>
The ResidueScoresFeatures stores the score of a structure at the residue level. Terms that evaluate a single residue are stored in residue_scores_1b . Terms that evaluate pairs of residues are stored in residue_scores_2b . Terms that depend on the whole structure are stored via the StructureScoresFeatures.
CREATE TABLE IF NOT EXISTS residue_scores_1b (
batch_id INTEGER,
struct_id INTEGER AUTOINCREMENT,
resNum INTEGER,
score_type_id INTEGER,
score_value REAL,
context_dependent INTEGER,
FOREIGN KEY (struct_id, resNum) REFERENCES residues (struct_id, resNum) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY (batch_id, score_type_id) REFERENCES score_types (batch_id, score_type_id) DEFERRABLE INITIALLY DEFERRED,
PRIMARY KEY(batch_id, struct_id, resNum, score_type));
CREATE TABLE IF NOT EXISTS residue_scores_2b (
batch_id INTEGER,
struct_id INTEGER AUTOINCREMENT,
resNum1 INTEGER,
resNum2 INTEGER,
score_type_id INTEGER,
score_value REAL,
context_dependent INTEGER,
FOREIGN KEY (struct_id, resNum1) REFERENCES residues (struct_id, resNum) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY (struct_id, resNum2) REFERENCES residues (struct_id, resNum) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY (batch_id, score_type_id) REFERENCES score_types (batch_id, score_type_id) DEFERRABLE INITIALLY DEFERRED,
PRIMARY KEY(batch_id, struct_id, resNum1, resNum2, score_type));
<ResidueTotalScoresFeatures scorefxn="(&scorefxn)"/>
The ResidueTotalScoresFeatures stores for each residue the total score for the one body terms for that residue and half the total score for the two body terms involving that residue. Note that terms that depend on the whole structure are stored via the StructureScoresFeatures. In order to include hydrogen bonding in the totals, the score function must specify the decompose_bb_hb_into_pair_energies flag.
CREATE TABLE IF NOT EXISTS residue_total_scores (
struct_id INTEGER AUTOINCREMENT,
resNum INTEGER,
score_value REAL,
FOREIGN KEY (struct_id, resNum) REFERENCES residues (struct_id, resNum) DEFERRABLE INITIALLY DEFERRED,
PRIMARY KEY(struct_id, resNum));
The parameters for the hydrogen bond potential are specified in the Rosetta database as parameter sets. Each parameter set specifies polynomials, fade functions, and which are applied to which hydrogen bond chemical types. To indicate parameter set, either use -hbond_params <database_tag> set on the command line, or set score_function.energy_method_options().hbond_options()->params_database_tag(<database_tag>) .
CREATE TABLE IF NOT EXISTS hbond_fade_interval(
database_tag TEXT,
name TEXT,
junction_type TEXT,
min0 REAL,
fmin REAL,
fmax REAL,
max0 REAL,
PRIMARY KEY(database_tag, name));
CREATE TABLE IF NOT EXISTS hbond_polynomial_1d (
database_tag TEXT,
name TEXT,
dimension TEXT,
xmin REAL,
xmax REAL,
root1 REAL,
root2 REAL,
degree INTEGER,
c_a REAL,
c_b REAL,
c_c REAL,
c_d REAL,
c_e REAL,
c_f REAL,
c_g REAL,
c_h REAL,
c_i REAL,
c_j REAL,
c_k REAL,
PRIMARY KEY(database_tag, name));
CREATE TABLE IF NOT EXISTS hbond_evaluation_types (
database_tag TEXT,
don_chem_type TEXT,
acc_chem_type TEXT,
separation TEXT,
AHdist_short_fade TEXT,
AHdist_long_fade TEXT,
cosBAH_fade TEXT,
cosAHD_fade TEXT,
AHdist TEXT,
cosBAH_short TEXT,
cosBAH_long TEXT,
cosAHD_short TEXT,
cosAHD_long TEXT,
weight_type TEXT,
FOREIGN KEY(database_tag, AHdist_short_fade) REFERENCES hbond_fade_interval(database_tag, name) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY(database_tag, AHdist_long_fade) REFERENCES hbond_fade_interval(database_tag, name) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY(database_tag, cosBAH_fade) REFERENCES hbond_fade_interval(database_tag, name) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY(database_tag, cosAHD_fade) REFERENCES hbond_fade_interval(database_tag, name) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY(database_tag, AHdist) REFERENCES hbond_polynomial_1d(database_tag, name) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY(database_tag, cosBAH_short) REFERENCES hbond_polynomial_1d(database_tag, name) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY(database_tag, cosBAH_long) REFERENCES hbond_polynomial_1d(database_tag, name) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY(database_tag, cosAHD_short) REFERENCES hbond_polynomial_1d(database_tag, name) DEFERRABLE INITIALLY DEFERRED,
FOREIGN KEY(database_tag, cosAHD_long) REFERENCES hbond_polynomial_1d(database_tag, name) DEFERRABLE INITIALLY DEFERRED,
PRIMARY KEY (database_tag, don_chem_type, acc_chem_type, separation));
ScreeningFeatures is used to consolidate scoring information related to a ligand into a table for later processing. It is most useful when you would otherwise need to join multiple very large tables, and was originally intended for use in a High Throughput Screening Pipeline. This mover must be used in conjunction with the screening_job_inputter.
<ScreeningFeatures chain="(chain &string)">
<descriptor type="(descriptor_name &string)"/>
<descriptor type="(descriptor_name &string)"/>
</ScreeningFeatures>
In the XML definition above, chain is a ligand chain and the descriptor type is the string key in a string_real or string_string pair added to the job. This mover currently assumes that ligands consist of one residue.
CREATE TABLE `screening_features` (
`struct_id` bigint(20) NOT NULL,
`residue_number` int(11) NOT NULL,
`chain_id` varchar(1) NOT NULL,
`name3` text NOT NULL,
`group_name` text NOT NULL,
`descriptor_data` text NOT NULL,
PRIMARY KEY (`struct_id`,`residue_number`),
CONSTRAINT `screening_features_ibfk_1` FOREIGN KEY (`struct_id`) REFERENCES `structures` (`struct_id`)
)