score::rna Namespace Reference

Functions
BooleanOptionKey const	rna ("score:rna")
StringOptionKey const	rna_base_pair_xy_filename ("score:rna:rna_base_pair_xy_filename")
BooleanOptionKey const	disable_orientation_dependent_rna_ch_o_bonds ("score:rna:disable_orientation_dependent_rna_ch_o_bonds")
StringOptionKey const	rna_suite_potential ("score:rna:rna_suite_potential")
StringOptionKey const	suiteness_bonus ("score:rna:suiteness_bonus")
BooleanOptionKey const	rna_torsion_skip_chainbreak ("score:rna:rna_torsion_skip_chainbreak")
BooleanOptionKey const	rna_chemical_shift_verbose ("score:rna:rna_chemical_shift_verbose")
BooleanOptionKey const	rna_chemical_shift_larmord ("score:rna:rna_chemical_shift_larmord")
StringOptionKey const	rna_chemical_shift_exp_data ("score:rna:rna_chemical_shift_exp_data")
StringOptionKey const	rna_chemical_shift_larmord_par ("score:rna:rna_chemical_shift_larmord_par")
StringOptionKey const	rna_chemical_shift_larmord_wt ("score:rna:rna_chemical_shift_larmord_wt")
StringOptionKey const	rna_chemical_shift_larmord_ref ("score:rna:rna_chemical_shift_larmord_ref")
StringOptionKey const	rna_chemical_shift_larmord_nei ("score:rna:rna_chemical_shift_larmord_nei")
RealOptionKey const	rna_chemical_shift_larmord_cut ("score:rna:rna_chemical_shift_larmord_cut")
RealOptionKey const	rna_chemical_shift_larmord_beta ("score:rna:rna_chemical_shift_larmord_beta")
StringOptionKey const	rna_chemical_shift_H5_prime_mode ("score:rna:rna_chemical_shift_H5_prime_mode")
IntegerVectorOptionKey const	rna_chemical_shift_include_res ("score:rna:rna_chemical_shift_include_res")
BooleanOptionKey const	DMS_separate_features ("score:rna:DMS_separate_features")
BooleanOptionKey const	DMS_careful_base_pair_classifier ("score:rna:DMS_careful_base_pair_classifier")
RealOptionKey const	rna_chem_map_lores_weight ("score:rna:rna_chem_map_lores_weight")
BooleanOptionKey const	use_2prime_OH_potential ("score:rna:use_2prime_OH_potential")
BooleanOptionKey const	use_rna_chi_potential ("score:rna:use_rna_chi_potential")
BooleanOptionKey const	include_neighbor_base_stacks ("score:rna:include_neighbor_base_stacks")
BooleanOptionKey const	FA_low_res_rnp_scoring ("score:rna:FA_low_res_rnp_scoring")
RealOptionKey const	free_suite_bonus ("score:rna:free_suite_bonus")
RealOptionKey const	free_sugar_bonus ("score:rna:free_sugar_bonus")
RealOptionKey const	free_2HOprime_bonus ("score:rna:free_2HOprime_bonus")
RealOptionKey const	syn_G_potential_bonus ("score:rna:syn_G_potential_bonus")
BooleanOptionKey const	rna_bulge_bonus_once_per_loop ("score:rna:rna_bulge_bonus_once_per_loop")
RealOptionKey const	pack_phosphate_penalty ("score:rna:pack_phosphate_penalty")

Function Documentation

disable_orientation_dependent_rna_ch_o_bonds()

BooleanOptionKey const score::rna::disable_orientation_dependent_rna_ch_o_bonds

(

"score:rna:disable_orientation_dependent_rna_ch_o_bonds"

)

DMS_careful_base_pair_classifier()

BooleanOptionKey const score::rna::DMS_careful_base_pair_classifier

(

"score:rna:DMS_careful_base_pair_classifier"

)

DMS_separate_features()

BooleanOptionKey const score::rna::DMS_separate_features

(

"score:rna:DMS_separate_features"

)

FA_low_res_rnp_scoring()

BooleanOptionKey const score::rna::FA_low_res_rnp_scoring

(

"score:rna:FA_low_res_rnp_scoring"

)

free_2HOprime_bonus()

RealOptionKey const score::rna::free_2HOprime_bonus

(

"score:rna:free_2HOprime_bonus"

)

free_sugar_bonus()

RealOptionKey const score::rna::free_sugar_bonus

(

"score:rna:free_sugar_bonus"

)

free_suite_bonus()

RealOptionKey const score::rna::free_suite_bonus

(

"score:rna:free_suite_bonus"

)

include_neighbor_base_stacks()

BooleanOptionKey const score::rna::include_neighbor_base_stacks

(

"score:rna:include_neighbor_base_stacks"

)

pack_phosphate_penalty()

RealOptionKey const score::rna::pack_phosphate_penalty

(

"score:rna:pack_phosphate_penalty"

)

rna()

BooleanOptionKey const score::rna::rna

(

"score:rna"

)

rna_base_pair_xy_filename()

StringOptionKey const score::rna::rna_base_pair_xy_filename

(

"score:rna:rna_base_pair_xy_filename"

)

rna_bulge_bonus_once_per_loop()

BooleanOptionKey const score::rna::rna_bulge_bonus_once_per_loop

(

"score:rna:rna_bulge_bonus_once_per_loop"

)

rna_chem_map_lores_weight()

RealOptionKey const score::rna::rna_chem_map_lores_weight

(

"score:rna:rna_chem_map_lores_weight"

)

rna_chemical_shift_exp_data()

StringOptionKey const score::rna::rna_chemical_shift_exp_data

(

"score:rna:rna_chemical_shift_exp_data"

)

rna_chemical_shift_H5_prime_mode()

StringOptionKey const score::rna::rna_chemical_shift_H5_prime_mode

(

"score:rna:rna_chemical_shift_H5_prime_mode"

)

rna_chemical_shift_include_res()

IntegerVectorOptionKey const score::rna::rna_chemical_shift_include_res

(

"score:rna:rna_chemical_shift_include_res"

)

rna_chemical_shift_larmord()

BooleanOptionKey const score::rna::rna_chemical_shift_larmord

(

"score:rna:rna_chemical_shift_larmord"

)

rna_chemical_shift_larmord_beta()

RealOptionKey const score::rna::rna_chemical_shift_larmord_beta

(

"score:rna:rna_chemical_shift_larmord_beta"

)

rna_chemical_shift_larmord_cut()

RealOptionKey const score::rna::rna_chemical_shift_larmord_cut

(

"score:rna:rna_chemical_shift_larmord_cut"

)

rna_chemical_shift_larmord_nei()

StringOptionKey const score::rna::rna_chemical_shift_larmord_nei

(

"score:rna:rna_chemical_shift_larmord_nei"

)

rna_chemical_shift_larmord_par()

StringOptionKey const score::rna::rna_chemical_shift_larmord_par

(

"score:rna:rna_chemical_shift_larmord_par"

)

rna_chemical_shift_larmord_ref()

StringOptionKey const score::rna::rna_chemical_shift_larmord_ref

(

"score:rna:rna_chemical_shift_larmord_ref"

)

rna_chemical_shift_larmord_wt()

StringOptionKey const score::rna::rna_chemical_shift_larmord_wt

(

"score:rna:rna_chemical_shift_larmord_wt"

)

rna_chemical_shift_verbose()

BooleanOptionKey const score::rna::rna_chemical_shift_verbose

(

"score:rna:rna_chemical_shift_verbose"

)

rna_suite_potential()

StringOptionKey const score::rna::rna_suite_potential

(

"score:rna:rna_suite_potential"

)

rna_torsion_skip_chainbreak()

BooleanOptionKey const score::rna::rna_torsion_skip_chainbreak

(

"score:rna:rna_torsion_skip_chainbreak"

)

suiteness_bonus()

StringOptionKey const score::rna::suiteness_bonus

(

"score:rna:suiteness_bonus"

)

syn_G_potential_bonus()

RealOptionKey const score::rna::syn_G_potential_bonus

(

"score:rna:syn_G_potential_bonus"

)

use_2prime_OH_potential()

BooleanOptionKey const score::rna::use_2prime_OH_potential

(

"score:rna:use_2prime_OH_potential"

)

use_rna_chi_potential()

BooleanOptionKey const score::rna::use_rna_chi_potential

(

"score:rna:use_rna_chi_potential"

)