pyrosetta_help.weights package

Submodules

pyrosetta_help.weights.terms module

Module contents

class pyrosetta_help.weights.WeightWatcher

Bases: object

A class to easily look at the weights for the terms of different scorefunctions. It has various functionalities.

List available scorefunctions:

Find a scorefunction that mentions a word:

Get the comment block of a scorefunction:

Get a scorefunction by name by calling the appropriate options first.

Get weights (including ref) for a scorefunction or a name of one

Get a pandas table of the weights

compare(scorefxn_names: List[str], different_only: bool = False) → DataFrame

find_metion(word: str) → List[str]

Find all the scorefxn names whose files contain the string word (case insensitive).

>>> find_metion('spades')

returns ['hydrate_score12']

folder = '/home/docs/checkouts/readthedocs.org/user_builds/pyrosetta-help/envs/latest/lib/python3.8/site-packages/pyrosetta/database/scoring/weights'

get_ref_values_badly(scorefxn: ScoreFunction, prefix: bool | None = True) → Dict[str, float]

I could not find a direct way to get_method_weights. Here this horrid way.

get_scorefxn(scorefxn_name: str) → ScoreFunction

Gets the scorefxn with appropriate corrections.

get_scorefxn_block(scorefxn_name: str) → str

Read the file given a scorefxn name

get_scorefxn_comments(scorefxn_name: str) → str

Get only the comments

get_weight(scorefxn: ScoreFunction, score_type: ScoreType) → float

get_weights(scorefxn: str | ScoreFunction) → Dict[str, float]

Gets weights for scorefxn

property possible_scorefxn_names: List[str]

Returns the scorefxn names

pyrosetta_folder = '/home/docs/checkouts/readthedocs.org/user_builds/pyrosetta-help/envs/latest/lib/python3.8/site-packages/pyrosetta'

term_meanings = {'METHOD_WEIGHTS': 'Not an energy term itself, but the parameters for each amino acid used by the ref energy term.', 'dslf_fa13': 'Disulfide geometry potential.', 'fa_atr': 'Lennard-Jones attractive between atoms in different residues (r^6 term, London dispersion forces).', 'fa_dun': "Internal energy of sidechain rotamers as derived from Dunbrack's statistics (2010 Rotamer Library used in Talaris2013).", 'fa_dun_semi': "Internal energy of sidechain semi-rotamers as derived from Dunbrack's statistics (2010 Rotamer Library used in Talaris2013).", 'fa_elec': 'Coulombic electrostatic potential with a distance-dependent dielectric.', 'fa_intra_atr_xover4': 'Intra-residue LJ attraction, counted for the atom-pairs beyond torsion-relationship.', 'fa_intra_elec': 'Intra-residue Coulombic interaction, counted for the atom-pairs beyond torsion-relationship.', 'fa_intra_rep': 'Lennard-Jones repulsive between atoms in the same residue.', 'fa_intra_rep_xover4': 'Intra-residue LJ repulsion, counted for the atom-pairs beyond torsion-relationship.', 'fa_intra_sol_xover4': 'Intra-residue LK solvation, counted for the atom-pairs beyond torsion-relationship.', 'fa_rep': 'Lennard-Jones repulsive between atoms in different residues (r^12 term, Pauli repulsion forces).', 'fa_sol': 'Lazaridis-Karplus solvation energy.', 'hbond_bb_sc': 'Sidechain-backbone hydrogen bond energy.', 'hbond_lr_bb': 'Backbone-backbone hbonds distant in primary sequence.', 'hbond_sc': 'Sidechain-sidechain hydrogen bond energy.', 'hbond_sr_bb': 'Backbone-backbone hbonds close in primary sequence.', 'hxl_tors': 'Sidechain hydroxyl group torsion preference for Ser/Thr/Tyr, supersedes yhh_planarity (that covers L- and D-Tyr only).', 'lk_ball': 'Anisotropic contribution to the solvation.', 'lk_ball_bridge': "Bonus to solvation coming from bridging waters, measured by overlap of the 'balls' from two interacting polar atoms.", 'lk_ball_bridge_uncpl': 'Same as lk_ball_bridge, but the value is uncoupled with dGfree (i.e. constant bonus, whereas lk_ball_bridge is proportional to dGfree values).', 'lk_ball_iso': 'Same as fa_sol; see below.', 'lk_ball_wtd': 'weighted sum of lk_ball & lk_ball_iso (w1*lk_ball + w2*lk_ball_iso); w2 is negative so that anisotropic contribution(lk_ball) replaces some portion of isotropic contribution (fa_sol=lk_ball_iso).', 'omega': 'Omega dihedral in the backbone. A Harmonic constraint on planarity with standard deviation of ~6 deg.', 'p_aa_pp': 'Probability of amino acid at Φ/Ψ.', 'pro_close': 'Proline ring closure energy and energy of psi angle of preceding residue.', 'rama': 'Ramachandran preferences.', 'rama_prepro': 'Backbone torsion preference term that takes into account of whether preceding amono acid is Proline or not.', 'ref': 'Reference energy for each amino acid. Balances internal energy of amino acid terms.  Plays role in design.', 'yhh_planarity': 'Sidechain hydroxyl group torsion preference for Tyr, superseded by hxl_tors'}