ViennaRNA
Contents:
ViennaRNA Python API
Python Examples
News
License
ViennaRNA
Index
Index
A
|
B
|
C
|
D
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E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
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N
|
O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
|
Y
|
Z
A
a2s (RNA.fold_compound attribute)
abstract_shapes() (in module RNA)
add_auxdata() (RNA.fold_compound method)
add_callback() (RNA.fold_compound method)
add_root() (in module RNA)
advance() (RNA.SwigPyIterator method)
alias (RNA.md attribute)
(RNA.md property)
aliduplex_subopt() (in module RNA)
aliduplexfold() (in module RNA)
alifold() (in module RNA)
alignment (RNA.fold_compound attribute)
aliLfold() (in module RNA)
aliLfold_cb() (in module RNA)
allowFlipping (RNA.plot_options_puzzler attribute)
,
[1]
(RNA.plot_options_puzzler property)
aln_consensus_mis() (in module RNA)
aln_consensus_sequence() (in module RNA)
aln_conservation_col() (in module RNA)
aln_conservation_struct() (in module RNA)
aln_mpi() (in module RNA)
aln_pscore() (in module RNA)
alpha (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
append() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
assign() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
aux_grammar (RNA.fold_compound attribute)
auxdata (RNA.fold_compound attribute)
available (RNA.sc_mod_param attribute)
,
[1]
B
b2C() (in module RNA)
b2HIT() (in module RNA)
b2Shapiro() (in module RNA)
back() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
backbone_length (RNA.md attribute)
(RNA.md property)
backtrack (RNA.md attribute)
(RNA.md property)
backtrack() (RNA.fold_compound method)
backtrack_GQuad_IntLoop_L() (in module RNA)
backtrack_GQuad_IntLoop_L_comparative() (in module RNA)
backtrack_type (RNA.md attribute)
(RNA.md property)
basepair (class in RNA)
begin() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
benchmark() (RNA.fold_compound method)
betaScale (RNA.md attribute)
(RNA.md property)
boustrophedon() (in module RNA)
bp_distance() (in module RNA)
bpdist (RNA.fold_compound attribute)
bpp() (RNA.fold_compound method)
bulge (RNA.param attribute)
,
[1]
(RNA.param property)
C
c (RNA.mx_mfe property)
capacity() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
cast() (RNA.doubleArray method)
(RNA.floatArray method)
(RNA.intArray method)
cdata() (in module RNA)
centroid() (in module RNA)
(RNA.fold_compound method)
checkAncestorIntersections (RNA.plot_options_puzzler attribute)
,
[1]
(RNA.plot_options_puzzler property)
checkExteriorIntersections (RNA.plot_options_puzzler attribute)
,
[1]
(RNA.plot_options_puzzler property)
checkSiblingIntersections (RNA.plot_options_puzzler attribute)
,
[1]
(RNA.plot_options_puzzler property)
circ (RNA.md attribute)
(RNA.md property)
circ_alpha0 (RNA.md attribute)
(RNA.md property)
circ_penalty (RNA.md attribute)
(RNA.md property)
circalifold() (in module RNA)
circfold() (in module RNA)
clear() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
cmd (class in RNA)
co_pf_fold() (in module RNA)
cofold() (in module RNA)
commands_apply() (RNA.fold_compound method)
compare() (RNA.move method)
compare_structure() (in module RNA)
compute_bpp (RNA.md attribute)
(RNA.md property)
config (RNA.plot_options_puzzler attribute)
,
[1]
cons_seq (RNA.fold_compound attribute)
consens_mis() (in module RNA)
ConstCharVector (class in RNA)
constraints_add() (RNA.fold_compound method)
COORDINATE (class in RNA)
CoordinateVector (class in RNA)
copy() (RNA.SwigPyIterator method)
cutpoint (RNA.fold_compound attribute)
cv_fact (RNA.md attribute)
(RNA.md property)
D
dangle3 (RNA.param attribute)
,
[1]
(RNA.param property)
dangle3_dG (RNA.sc_mod_param attribute)
,
[1]
dangle3_dH (RNA.sc_mod_param attribute)
,
[1]
dangle5 (RNA.param attribute)
,
[1]
(RNA.param property)
dangle5_dG (RNA.sc_mod_param attribute)
,
[1]
dangle5_dH (RNA.sc_mod_param attribute)
,
[1]
dangles (RNA.md attribute)
(RNA.md property)
data (RNA.hc attribute)
,
[1]
db_flatten() (in module RNA)
db_from_plist() (in module RNA)
db_from_probs() (RNA.fold_compound method)
db_from_ptable() (in module RNA)
db_from_WUSS() (in module RNA)
db_pack() (in module RNA)
db_pk_remove() (in module RNA)
db_to_element_string() (in module RNA)
db_to_tree_string() (in module RNA)
db_unpack() (in module RNA)
ddG (RNA.duplexT attribute)
(RNA.duplexT property)
decr() (RNA.SwigPyIterator method)
delete_doubleP() (in module RNA)
delete_floatP() (in module RNA)
delete_intP() (in module RNA)
delete_shortP() (in module RNA)
delete_ushortP() (in module RNA)
depot (RNA.hc attribute)
,
[1]
deref_any() (in module RNA)
dG1 (RNA.duplexT attribute)
(RNA.duplexT property)
dG2 (RNA.duplexT attribute)
(RNA.duplexT property)
dist_mountain() (in module RNA)
distance() (RNA.SwigPyIterator method)
domains_struc (RNA.fold_compound attribute)
domains_up (RNA.fold_compound attribute)
doubleArray (class in RNA)
DoubleDoubleVector (class in RNA)
doubleP_getitem() (in module RNA)
doubleP_setitem() (in module RNA)
DoublePair (class in RNA)
DoubleVector (class in RNA)
drawArcs (RNA.plot_options_puzzler attribute)
,
[1]
duplex_list_t (class in RNA)
duplex_subopt() (in module RNA)
duplexfold() (in module RNA)
DuplexInit (RNA.param attribute)
,
[1]
(RNA.param property)
duplexT (class in RNA)
DuplexVector (class in RNA)
E
E_ext_hp_loop() (RNA.fold_compound method)
E_ext_int_loop() (RNA.fold_compound method)
E_ExtLoop() (in module RNA)
E_gquad() (in module RNA)
E_gquad_ali_en() (in module RNA)
E_GQuad_IntLoop_L() (in module RNA)
E_GQuad_IntLoop_L_comparative() (in module RNA)
E_Hairpin() (in module RNA)
E_hp_loop() (RNA.fold_compound method)
E_int_loop() (RNA.fold_compound method)
E_IntLoop() (in module RNA)
E_IntLoop_Co() (in module RNA)
E_ml_rightmost_stem() (in module RNA)
E_MLstem() (in module RNA)
E_stack() (RNA.fold_compound method)
E_Stem() (in module RNA)
ElemProbVector (class in RNA)
empty() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
en (RNA.path property)
encode_seq() (in module RNA)
encoding3 (RNA.fold_compound attribute)
encoding5 (RNA.fold_compound attribute)
end (RNA.duplexT attribute)
(RNA.duplexT property)
(RNA.hx property)
end() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
energy (RNA.duplex_list_t property)
(RNA.duplexT attribute)
(RNA.duplexT property)
(RNA.SOLUTION property)
(RNA.struct_en attribute)
,
[1]
(RNA.struct_en property)
(RNA.subopt_solution property)
energy_backtrack (RNA.duplexT attribute)
(RNA.duplexT property)
energy_of_circ_struct() (in module RNA)
energy_of_circ_structure() (in module RNA)
energy_of_gquad_structure() (in module RNA)
energy_of_move() (in module RNA)
energy_of_move_pt() (in module RNA)
energy_of_struct() (in module RNA)
energy_of_struct_pt() (in module RNA)
energy_of_structure() (in module RNA)
energy_of_structure_pt() (in module RNA)
energy_set (RNA.md attribute)
(RNA.md property)
ensemble_defect() (RNA.fold_compound method)
enumerate_necklaces() (in module RNA)
ep (class in RNA)
equal() (RNA.SwigPyIterator method)
equilibrium_conc() (in module RNA)
equilibrium_constants() (in module RNA)
erase() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
eval_circ_gquad_structure() (in module RNA)
eval_circ_structure() (in module RNA)
eval_covar_structure() (RNA.fold_compound method)
eval_ext (RNA.hc attribute)
,
[1]
eval_ext_hp_loop() (RNA.fold_compound method)
eval_ext_stem() (RNA.fold_compound method)
eval_gquad_structure() (in module RNA)
eval_hp (RNA.hc attribute)
,
[1]
eval_hp_loop() (RNA.fold_compound method)
eval_int (RNA.hc attribute)
,
[1]
eval_int_loop() (RNA.fold_compound method)
eval_loop_pt() (RNA.fold_compound method)
eval_mb (RNA.hc attribute)
,
[1]
eval_move() (RNA.fold_compound method)
eval_move_pt() (RNA.fold_compound method)
eval_structure() (RNA.fold_compound method)
eval_structure_pt() (RNA.fold_compound method)
eval_structure_pt_simple() (in module RNA)
eval_structure_pt_verbose() (RNA.fold_compound method)
eval_structure_simple() (in module RNA)
eval_structure_verbose() (RNA.fold_compound method)
exp_E_ext_stem() (RNA.fold_compound method)
exp_E_ExtLoop() (in module RNA)
exp_E_gquad() (in module RNA)
exp_E_gquad_ali() (in module RNA)
exp_E_Hairpin() (in module RNA)
exp_E_hp_loop() (RNA.fold_compound method)
exp_E_int_loop() (RNA.fold_compound method)
exp_E_interior_loop() (RNA.fold_compound method)
exp_E_IntLoop() (in module RNA)
exp_E_MLstem() (in module RNA)
exp_E_Stem() (in module RNA)
exp_matrices (RNA.fold_compound attribute)
(RNA.fold_compound property)
exp_param (class in RNA)
exp_params (RNA.fold_compound attribute)
(RNA.fold_compound property)
exp_params_rescale() (RNA.fold_compound method)
exp_params_reset() (RNA.fold_compound method)
exp_params_subst() (RNA.fold_compound method)
expand_Full() (in module RNA)
expand_Shapiro() (in module RNA)
expbulge (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expdangle3 (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expdangle5 (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expDuplexInit (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expgquad (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expgquadLayerMismatch (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
exphairpin (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
exphex (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expint11 (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expint21 (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expint22 (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expinternal (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expmismatch1nI (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expmismatch23I (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expmismatchExt (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expmismatchH (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expmismatchI (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expmismatchM (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expMLbase (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.mx_pf property)
expMLclosing (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expMLintern (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expMultipleCA (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expMultipleCB (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expninio (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expSaltLoop (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expSaltStack (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expstack (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expTermAU (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
exptetra (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
exptri (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expTriloop (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
expTripleC (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
extract_record_rest_structure() (in module RNA)
F
f (RNA.hc attribute)
,
[1]
F1 (RNA.score property)
f3 (RNA.mx_mfe property)
f5 (RNA.mx_mfe property)
fallback (RNA.sc_mod_param attribute)
,
[1]
fallback_encoding (RNA.sc_mod_param attribute)
,
[1]
Fc (RNA.mx_mfe property)
fc_add_pycallback() (in module RNA)
fc_add_pydata() (in module RNA)
FcH (RNA.mx_mfe property)
FcI (RNA.mx_mfe property)
FcM (RNA.mx_mfe property)
FDR (RNA.score property)
file_commands_apply() (RNA.fold_compound method)
file_commands_read() (in module RNA)
file_connect_read_record() (in module RNA)
file_fasta_read() (in module RNA)
file_msa_detect_format() (in module RNA)
file_msa_read() (in module RNA)
file_msa_read_record() (in module RNA)
file_msa_write() (in module RNA)
file_PS_aln() (in module RNA)
file_PS_rnaplot() (in module RNA)
file_PS_rnaplot_a() (in module RNA)
file_RNAstrand_db_read_record() (in module RNA)
file_SHAPE_read() (in module RNA)
filename (RNA.plot_options_puzzler attribute)
,
[1]
filename_sanitize() (in module RNA)
find_saddle() (in module RNA)
first (RNA.DoublePair property)
floatArray (class in RNA)
floatP_getitem() (in module RNA)
floatP_setitem() (in module RNA)
fM1 (RNA.mx_mfe property)
fM2 (RNA.mx_mfe property)
fML (RNA.mx_mfe property)
FN (RNA.score property)
FNR (RNA.score property)
fold() (in module RNA)
fold_compound (class in RNA)
FOR (RNA.score property)
FP (RNA.score property)
FPR (RNA.score property)
free_alifold_arrays() (in module RNA)
free_arrays() (in module RNA)
free_auxdata (RNA.fold_compound attribute)
free_co_arrays() (in module RNA)
free_co_pf_arrays() (in module RNA)
free_data (RNA.hc attribute)
,
[1]
free_path() (in module RNA)
free_pf_arrays() (in module RNA)
free_profile() (in module RNA)
free_tree() (in module RNA)
frompointer() (RNA.doubleArray static method)
(RNA.floatArray static method)
(RNA.intArray static method)
front() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
G
get() (RNA.COORDINATE method)
(RNA.SOLUTION method)
(RNA.varArrayChar method)
(RNA.varArrayFLTorDBL method)
(RNA.varArrayInt method)
(RNA.varArrayMove method)
(RNA.varArrayShort method)
(RNA.varArrayUChar method)
(RNA.varArrayUInt method)
get_aligned_line() (in module RNA)
get_allocator() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
get_centroid_struct_pl() (in module RNA)
get_centroid_struct_pr() (in module RNA)
get_concentrations() (in module RNA)
get_gquad_ali_matrix() (in module RNA)
get_gquad_L_matrix() (in module RNA)
get_gquad_matrix() (in module RNA)
get_gquad_pattern_pf() (in module RNA)
get_gquad_pf_matrix() (in module RNA)
get_gquad_pf_matrix_comparative() (in module RNA)
get_multi_input_line() (in module RNA)
get_path() (in module RNA)
get_plist_gquad_from_db() (in module RNA)
get_plist_gquad_from_pr() (in module RNA)
get_plist_gquad_from_pr_max() (in module RNA)
get_pr() (in module RNA)
get_xy_coordinates() (in module RNA)
gettype() (in module RNA)
gmlRNA() (in module RNA)
gq_parse() (in module RNA)
gquad (RNA.md attribute)
(RNA.md property)
(RNA.param attribute)
,
[1]
(RNA.param property)
gquadLayerMismatch (RNA.param attribute)
,
[1]
(RNA.param property)
gquadLayerMismatchMax (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
H
hairpin (RNA.param attribute)
,
[1]
(RNA.param property)
hamming() (in module RNA)
hamming_bound() (in module RNA)
hamming_distance() (in module RNA)
hamming_distance_bound() (in module RNA)
hc (class in RNA)
(RNA.fold_compound attribute)
(RNA.fold_compound property)
hc_add_bp() (RNA.fold_compound method)
hc_add_bp_nonspecific() (RNA.fold_compound method)
hc_add_bp_strand() (RNA.fold_compound method)
hc_add_from_db() (RNA.fold_compound method)
hc_add_up() (RNA.fold_compound method)
hc_add_up_strand() (RNA.fold_compound method)
hc_init() (RNA.fold_compound method)
heat_capacity (RNA.heat_capacity_result property)
heat_capacity() (in module RNA)
(RNA.fold_compound method)
heat_capacity_cb() (RNA.fold_compound method)
heat_capacity_result (class in RNA)
HeatCapacityVector (class in RNA)
helical_rise (RNA.md attribute)
(RNA.md property)
HelixVector (class in RNA)
Hexaloop_E (RNA.param attribute)
,
[1]
(RNA.param property)
Hexaloops (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
hx (class in RNA)
hx_from_ptable() (in module RNA)
hx_merge() (in module RNA)
I
i (RNA.basepair attribute)
,
[1]
(RNA.basepair property)
(RNA.duplex_list_t property)
(RNA.duplexT attribute)
(RNA.duplexT property)
(RNA.ep attribute)
,
[1]
(RNA.ep property)
id (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
iindx (RNA.fold_compound attribute)
(RNA.fold_compound property)
incr() (RNA.SwigPyIterator method)
init_pf_circ_fold() (in module RNA)
init_pf_fold() (in module RNA)
init_rand() (in module RNA)
initialize_cofold() (in module RNA)
insert() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
int11 (RNA.param attribute)
,
[1]
(RNA.param property)
int21 (RNA.param attribute)
,
[1]
(RNA.param property)
int22 (RNA.param attribute)
,
[1]
(RNA.param property)
int_urn() (in module RNA)
intArray (class in RNA)
internal_loop (RNA.param attribute)
,
[1]
(RNA.param property)
IntIntVector (class in RNA)
intP_getitem() (in module RNA)
intP_setitem() (in module RNA)
IntVector (class in RNA)
inverse_fold() (in module RNA)
inverse_pf_fold() (in module RNA)
is_insertion() (RNA.move method)
is_removal() (RNA.move method)
is_shift() (RNA.move method)
iterator() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
J
j (RNA.basepair attribute)
,
[1]
(RNA.basepair property)
(RNA.duplex_list_t property)
(RNA.duplexT attribute)
(RNA.duplexT property)
(RNA.ep attribute)
,
[1]
(RNA.ep property)
jindx (RNA.fold_compound attribute)
(RNA.fold_compound property)
K
kT (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
L
last_parameter_file() (in module RNA)
length (RNA.fold_compound attribute)
(RNA.fold_compound property)
(RNA.hx property)
(RNA.mx_mfe property)
(RNA.mx_pf property)
Lfold() (in module RNA)
Lfold_cb() (in module RNA)
Lfoldz() (in module RNA)
Lfoldz_cb() (in module RNA)
log_cb_add() (in module RNA)
log_cb_add_pycallback() (in module RNA)
log_cb_num() (in module RNA)
log_fp() (in module RNA)
log_fp_set() (in module RNA)
log_level() (in module RNA)
log_level_set() (in module RNA)
log_options() (in module RNA)
log_options_set() (in module RNA)
log_reset() (in module RNA)
logML (RNA.md attribute)
(RNA.md property)
loop_energy() (in module RNA)
loopidx_from_ptable() (in module RNA)
lxc (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
M
Make_bp_profile() (in module RNA)
Make_bp_profile_bppm() (in module RNA)
make_loop_index() (in module RNA)
Make_swString() (in module RNA)
make_tree() (in module RNA)
matrices (RNA.fold_compound attribute)
(RNA.fold_compound property)
matrix_local (RNA.hc attribute)
,
[1]
max_bp_span (RNA.md attribute)
(RNA.md property)
maxD1 (RNA.fold_compound attribute)
maxD2 (RNA.fold_compound attribute)
maximum_matching() (in module RNA)
maximumNumberOfConfigChangesAllowed (RNA.plot_options_puzzler attribute)
,
[1]
maxmimum_matching() (RNA.fold_compound method)
MCC (RNA.score property)
md (class in RNA)
(RNA.plot_data property)
MEA() (RNA.fold_compound method)
MEA_from_plist() (in module RNA)
mean_bp_distance() (in module RNA)
(RNA.fold_compound method)
memmove() (in module RNA)
mfe() (RNA.fold_compound method)
mfe_dimer() (RNA.fold_compound method)
mfe_window() (RNA.fold_compound method)
mfe_window_cb() (RNA.fold_compound method)
mfe_window_zscore() (RNA.fold_compound method)
mfe_window_zscore_cb() (RNA.fold_compound method)
min_loop_size (RNA.md attribute)
(RNA.md property)
mismatch1nI (RNA.param attribute)
,
[1]
(RNA.param property)
mismatch23I (RNA.param attribute)
,
[1]
(RNA.param property)
mismatch_dG (RNA.sc_mod_param attribute)
,
[1]
mismatch_dH (RNA.sc_mod_param attribute)
,
[1]
mismatchExt (RNA.param attribute)
,
[1]
(RNA.param property)
mismatchH (RNA.param attribute)
,
[1]
(RNA.param property)
mismatchI (RNA.param attribute)
,
[1]
(RNA.param property)
mismatchM (RNA.param attribute)
,
[1]
(RNA.param property)
MLbase (RNA.param attribute)
,
[1]
(RNA.param property)
MLclosing (RNA.param attribute)
,
[1]
(RNA.param property)
MLintern (RNA.param attribute)
,
[1]
(RNA.param property)
mm1 (RNA.fold_compound attribute)
mm2 (RNA.fold_compound attribute)
model_details (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
module
RNA
move (class in RNA)
(RNA.path property)
move_neighbor_diff() (RNA.fold_compound method)
move_standard() (in module RNA)
MoveVector (class in RNA)
MultipleCA (RNA.param attribute)
,
[1]
(RNA.param property)
MultipleCB (RNA.param attribute)
,
[1]
(RNA.param property)
mx (RNA.hc attribute)
,
[1]
(RNA.hc property)
mx_mfe (class in RNA)
mx_pf (class in RNA)
my_aln_consensus_sequence2() (in module RNA)
my_PS_rna_plot_snoop_a() (in module RNA)
N
n (RNA.hc attribute)
,
[1]
(RNA.hc property)
n_multichoose_k() (in module RNA)
n_seq (RNA.fold_compound attribute)
name (RNA.sc_mod_param attribute)
,
[1]
naview_xy_coordinates() (in module RNA)
nc_fact (RNA.md attribute)
(RNA.md property)
neighbors() (RNA.fold_compound method)
new_doubleP() (in module RNA)
new_floatP() (in module RNA)
new_intP() (in module RNA)
new_shortP() (in module RNA)
new_ushortP() (in module RNA)
next (RNA.move attribute)
,
[1]
next() (RNA.SwigPyIterator method)
(RNA.var_array_Iterator method)
ninio (RNA.param attribute)
,
[1]
(RNA.param property)
noGU (RNA.md attribute)
(RNA.md property)
noGUclosure (RNA.md attribute)
(RNA.md property)
noLP (RNA.md attribute)
(RNA.md property)
nonstandards (RNA.md attribute)
(RNA.md property)
NPV (RNA.score property)
nucleotides (RNA.fold_compound attribute)
num_ptypes (RNA.sc_mod_param attribute)
,
[1]
numberOfChangesAppliedToConfig (RNA.plot_options_puzzler attribute)
,
[1]
O
offset (RNA.duplexT attribute)
(RNA.duplexT property)
oldAliEn (RNA.fold_compound attribute)
(RNA.md attribute)
(RNA.md property)
one_letter_code (RNA.sc_mod_param attribute)
,
[1]
opening_backtrack_x (RNA.duplexT attribute)
(RNA.duplexT property)
opening_backtrack_y (RNA.duplexT attribute)
(RNA.duplexT property)
optimize (RNA.plot_options_puzzler attribute)
,
[1]
(RNA.plot_options_puzzler property)
option_string() (RNA.md method)
options (RNA.plot_data property)
P
p (RNA.ep attribute)
,
[1]
(RNA.ep property)
pack_structure() (in module RNA)
pair (RNA.md attribute)
(RNA.md property)
pair_dist (RNA.md attribute)
paired (RNA.plot_options_puzzler attribute)
,
[1]
pairing_partners (RNA.sc_mod_param attribute)
,
[1]
pairing_partners_encoding (RNA.sc_mod_param attribute)
,
[1]
param (class in RNA)
param_file (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
params (RNA.fold_compound attribute)
(RNA.fold_compound property)
params_load() (in module RNA)
params_load_DNA_Mathews1999() (in module RNA)
params_load_DNA_Mathews2004() (in module RNA)
params_load_from_string() (in module RNA)
params_load_RNA_Andronescu2007() (in module RNA)
params_load_RNA_Langdon2018() (in module RNA)
params_load_RNA_misc_special_hairpins() (in module RNA)
params_load_RNA_Turner1999() (in module RNA)
params_load_RNA_Turner2004() (in module RNA)
params_reset() (RNA.fold_compound method)
params_save() (in module RNA)
params_subst() (RNA.fold_compound method)
parse_gquad() (in module RNA)
parse_structure() (in module RNA)
path (class in RNA)
path() (RNA.fold_compound method)
path_direct() (RNA.fold_compound method)
path_findpath() (RNA.fold_compound method)
path_findpath_saddle() (RNA.fold_compound method)
path_gradient() (RNA.fold_compound method)
path_options (class in RNA)
path_options_findpath() (in module RNA)
path_random() (RNA.fold_compound method)
PathVector (class in RNA)
pbacktrack() (in module RNA)
(RNA.fold_compound method)
pbacktrack5() (in module RNA)
(RNA.fold_compound method)
pbacktrack_circ() (in module RNA)
pbacktrack_mem (class in RNA)
pbacktrack_sub() (RNA.fold_compound method)
pf() (RNA.fold_compound method)
pf_add() (in module RNA)
pf_circ_fold() (in module RNA)
pf_dimer() (RNA.fold_compound method)
pf_float_precision() (in module RNA)
pf_fold() (in module RNA)
pf_scale (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
pf_smooth (RNA.md attribute)
(RNA.md property)
pfl_fold() (in module RNA)
pfl_fold_cb() (in module RNA)
pfl_fold_up() (in module RNA)
pfl_fold_up_cb() (in module RNA)
plist() (in module RNA)
plist_from_probs() (RNA.fold_compound method)
plot_data (class in RNA)
plot_dp_EPS() (in module RNA)
plot_layout (class in RNA)
plot_layout_circular() (in module RNA)
plot_layout_naview() (in module RNA)
plot_layout_puzzler() (in module RNA)
plot_layout_simple() (in module RNA)
plot_layout_turtle() (in module RNA)
plot_options_puzzler (class in RNA)
plot_options_puzzler() (RNA.plot_options_puzzler method)
plot_structure() (in module RNA)
plot_structure_eps() (in module RNA)
plot_structure_gml() (in module RNA)
plot_structure_ssv() (in module RNA)
plot_structure_svg() (in module RNA)
plot_structure_xrna() (in module RNA)
pop() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
pop_back() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
pos_3 (RNA.move attribute)
,
[1]
(RNA.move property)
pos_5 (RNA.move attribute)
,
[1]
(RNA.move property)
positional_entropy() (RNA.fold_compound method)
post (RNA.plot_data property)
PPV (RNA.score property)
pr_energy() (RNA.fold_compound method)
pr_structure() (RNA.fold_compound method)
pre (RNA.plot_data property)
previous() (RNA.SwigPyIterator method)
print_bppm() (in module RNA)
print_tree() (in module RNA)
probing_data (class in RNA)
probing_data_deigan() (in module RNA)
probing_data_deigan_comparative() (in module RNA)
probing_data_eddy() (in module RNA)
probing_data_eddy_comparative() (in module RNA)
probing_data_free() (in module RNA)
probing_data_linear() (in module RNA)
probing_data_linear_energies() (RNA.probing_data method)
probing_data_linear_num() (RNA.probing_data method)
probing_data_linear_raw() (RNA.probing_data method)
probing_data_linear_weight() (RNA.probing_data method)
probing_data_zarringhalam() (in module RNA)
probing_data_zarringhalam_comparative() (in module RNA)
probs (RNA.mx_pf property)
probs_window() (RNA.fold_compound method)
profile_edit_distance() (in module RNA)
PS_color_dot_plot() (in module RNA)
PS_color_dot_plot_turn() (in module RNA)
PS_dot_plot() (in module RNA)
PS_dot_plot_list() (in module RNA)
PS_dot_plot_turn() (in module RNA)
PS_rna_plot() (in module RNA)
PS_rna_plot_a() (in module RNA)
PS_rna_plot_a_gquad() (in module RNA)
pscore (RNA.fold_compound attribute)
pscore_local (RNA.fold_compound attribute)
pscore_pf_compat (RNA.fold_compound attribute)
psNumber (RNA.plot_options_puzzler attribute)
,
[1]
pt_pk_remove() (in module RNA)
ptable() (in module RNA)
ptable_pk() (in module RNA)
ptype (RNA.fold_compound attribute)
ptype_local (RNA.fold_compound attribute)
ptype_pf_compat (RNA.fold_compound attribute)
ptypes (RNA.sc_mod_param attribute)
,
[1]
push_back() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
Q
q (RNA.mx_pf property)
q1k (RNA.mx_pf property)
qb (RNA.duplexT attribute)
(RNA.duplexT property)
(RNA.mx_pf property)
qe (RNA.duplexT attribute)
(RNA.duplexT property)
qho (RNA.mx_pf property)
qio (RNA.mx_pf property)
qln (RNA.mx_pf property)
qm (RNA.mx_pf property)
qm1 (RNA.mx_pf property)
qm2 (RNA.mx_pf property)
qmo (RNA.mx_pf property)
qo (RNA.mx_pf property)
R
random_string() (in module RNA)
rbegin() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
read_parameter_file() (in module RNA)
read_record() (in module RNA)
reference_pt1 (RNA.fold_compound attribute)
reference_pt2 (RNA.fold_compound attribute)
referenceBPs1 (RNA.fold_compound attribute)
referenceBPs2 (RNA.fold_compound attribute)
rend() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
reserve() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
reset() (RNA.md method)
resize() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
ribo (RNA.md attribute)
(RNA.md property)
RNA
module
rotational_symmetry() (in module RNA)
rotational_symmetry_db() (RNA.fold_compound method)
rtype (RNA.md attribute)
(RNA.md property)
S
S (RNA.fold_compound attribute)
s (RNA.path property)
S3 (RNA.fold_compound attribute)
S5 (RNA.fold_compound attribute)
S_cons (RNA.fold_compound attribute)
salt (RNA.md attribute)
(RNA.md property)
salt_duplex_init() (in module RNA)
salt_loop() (in module RNA)
salt_loop_int() (in module RNA)
salt_ml() (in module RNA)
salt_stack() (in module RNA)
SaltDPXInit (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
saltDPXInit (RNA.md attribute)
(RNA.md property)
SaltDPXInit (RNA.param attribute)
,
[1]
(RNA.param property)
saltDPXInitFact (RNA.md attribute)
(RNA.md property)
SaltLoop (RNA.param attribute)
,
[1]
(RNA.param property)
SaltLoopDbl (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
SaltMLbase (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
SaltMLclosing (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
SaltMLintern (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
saltMLLower (RNA.md attribute)
(RNA.md property)
saltMLUpper (RNA.md attribute)
(RNA.md property)
SaltStack (RNA.param attribute)
,
[1]
(RNA.param property)
sc (RNA.fold_compound attribute)
sc_add_bp() (RNA.fold_compound method)
sc_add_bt() (RNA.fold_compound method)
sc_add_bt_pycallback() (in module RNA)
sc_add_data() (RNA.fold_compound method)
sc_add_exp_f() (RNA.fold_compound method)
sc_add_exp_f_pycallback() (in module RNA)
sc_add_f() (RNA.fold_compound method)
sc_add_f_pycallback() (in module RNA)
sc_add_hi_motif() (RNA.fold_compound method)
sc_add_pydata() (in module RNA)
sc_add_SHAPE_deigan() (RNA.fold_compound method)
sc_add_SHAPE_deigan_ali() (RNA.fold_compound method)
sc_add_SHAPE_eddy_2() (RNA.fold_compound method)
sc_add_SHAPE_zarringhalam() (RNA.fold_compound method)
sc_add_stack() (RNA.fold_compound method)
sc_add_up() (RNA.fold_compound method)
sc_init() (RNA.fold_compound method)
sc_mod() (RNA.fold_compound method)
sc_mod_7DA() (RNA.fold_compound method)
sc_mod_dihydrouridine() (RNA.fold_compound method)
sc_mod_inosine() (RNA.fold_compound method)
sc_mod_json() (RNA.fold_compound method)
sc_mod_jsonfile() (RNA.fold_compound method)
sc_mod_m6A() (RNA.fold_compound method)
sc_mod_param (class in RNA)
sc_mod_parameters_free() (in module RNA)
sc_mod_pseudouridine() (RNA.fold_compound method)
sc_mod_purine() (RNA.fold_compound method)
sc_mod_read_from_json() (in module RNA)
sc_mod_read_from_jsonfile() (in module RNA)
sc_multi_cb_add() (RNA.fold_compound method)
sc_multi_cb_add_pycallback() (in module RNA)
sc_probing() (RNA.fold_compound method)
sc_remove() (RNA.fold_compound method)
sc_set_bp() (RNA.fold_compound method)
sc_set_stack() (RNA.fold_compound method)
sc_set_up() (RNA.fold_compound method)
scale (RNA.mx_pf property)
score (class in RNA)
scs (RNA.fold_compound attribute)
second (RNA.DoublePair property)
seq_encode() (in module RNA)
sequence (RNA.fold_compound attribute)
(RNA.fold_compound property)
sequence_add() (RNA.fold_compound method)
sequence_encoding (RNA.fold_compound attribute)
(RNA.fold_compound property)
sequence_encoding2 (RNA.fold_compound attribute)
(RNA.fold_compound property)
sequence_prepare() (RNA.fold_compound method)
sequence_remove() (RNA.fold_compound method)
sequence_remove_all() (RNA.fold_compound method)
sequences (RNA.fold_compound attribute)
set_from_globals() (RNA.md method)
settype() (in module RNA)
sfact (RNA.md attribute)
(RNA.md property)
shortP_getitem() (in module RNA)
shortP_setitem() (in module RNA)
simple_circplot_coordinates() (in module RNA)
simple_xy_coordinates() (in module RNA)
size() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTION method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
(RNA.varArrayChar method)
(RNA.varArrayFLTorDBL method)
(RNA.varArrayInt method)
(RNA.varArrayMove method)
(RNA.varArrayShort method)
(RNA.varArrayUChar method)
(RNA.varArrayUInt method)
sn (RNA.hc attribute)
,
[1]
SOLUTION (class in RNA)
SOLUTIONVector (class in RNA)
special_hp (RNA.md attribute)
(RNA.md property)
Ss (RNA.fold_compound attribute)
ssv_rna_plot() (in module RNA)
stack (RNA.param attribute)
,
[1]
(RNA.param property)
stack_dG (RNA.sc_mod_param attribute)
,
[1]
stack_dH (RNA.sc_mod_param attribute)
,
[1]
stack_prob() (RNA.fold_compound method)
start (RNA.hx property)
stat_cb (RNA.fold_compound attribute)
state (RNA.hc attribute)
,
[1]
str_to_dbl_array() (in module RNA)
strand_end (RNA.fold_compound attribute)
(RNA.fold_compound property)
strand_number (RNA.fold_compound attribute)
(RNA.fold_compound property)
strand_order (RNA.fold_compound attribute)
(RNA.fold_compound property)
strand_order_uniq (RNA.fold_compound attribute)
strand_start (RNA.fold_compound attribute)
(RNA.fold_compound property)
strands (RNA.fold_compound attribute)
(RNA.fold_compound property)
(RNA.hc attribute)
,
[1]
(RNA.mx_mfe property)
string_edit_distance() (in module RNA)
StringVector (class in RNA)
strtrim() (in module RNA)
struct_en (class in RNA)
structure (RNA.duplex_list_t property)
(RNA.duplexT attribute)
(RNA.duplexT property)
(RNA.SOLUTION property)
(RNA.struct_en attribute)
,
[1]
(RNA.struct_en property)
(RNA.subopt_solution property)
subopt() (in module RNA)
(RNA.fold_compound method)
subopt_cb() (RNA.fold_compound method)
subopt_solution (class in RNA)
subopt_zuker() (RNA.fold_compound method)
SuboptVector (class in RNA)
svg_rna_plot() (in module RNA)
swap() (RNA.ConstCharVector method)
(RNA.CoordinateVector method)
(RNA.DoubleDoubleVector method)
(RNA.DoubleVector method)
(RNA.DuplexVector method)
(RNA.ElemProbVector method)
(RNA.HeatCapacityVector method)
(RNA.HelixVector method)
(RNA.IntIntVector method)
(RNA.IntVector method)
(RNA.MoveVector method)
(RNA.PathVector method)
(RNA.SOLUTIONVector method)
(RNA.StringVector method)
(RNA.SuboptVector method)
(RNA.UIntUIntVector method)
(RNA.UIntVector method)
SwigPyIterator (class in RNA)
T
tb (RNA.duplexT attribute)
(RNA.duplexT property)
te (RNA.duplexT attribute)
(RNA.duplexT property)
temperature (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.heat_capacity_result property)
(RNA.md attribute)
(RNA.md property)
(RNA.param attribute)
,
[1]
(RNA.param property)
terminal_dG (RNA.sc_mod_param attribute)
,
[1]
terminal_dH (RNA.sc_mod_param attribute)
,
[1]
TerminalAU (RNA.param attribute)
,
[1]
(RNA.param property)
Tetraloop_E (RNA.param attribute)
,
[1]
(RNA.param property)
Tetraloops (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
thisown (RNA.basepair property)
(RNA.cmd property)
(RNA.ConstCharVector property)
(RNA.COORDINATE property)
(RNA.CoordinateVector property)
(RNA.doubleArray property)
(RNA.DoubleDoubleVector property)
(RNA.DoublePair property)
(RNA.DoubleVector property)
(RNA.duplex_list_t property)
(RNA.duplexT property)
(RNA.DuplexVector property)
(RNA.ElemProbVector property)
(RNA.ep property)
(RNA.exp_param property)
(RNA.floatArray property)
(RNA.fold_compound property)
(RNA.hc property)
(RNA.heat_capacity_result property)
(RNA.HeatCapacityVector property)
(RNA.HelixVector property)
(RNA.hx property)
(RNA.intArray property)
(RNA.IntIntVector property)
(RNA.IntVector property)
(RNA.md property)
(RNA.move property)
(RNA.MoveVector property)
(RNA.mx_mfe property)
(RNA.mx_pf property)
(RNA.param property)
(RNA.path property)
(RNA.path_options property)
(RNA.PathVector property)
(RNA.pbacktrack_mem property)
(RNA.plot_data property)
(RNA.plot_layout property)
(RNA.plot_options_puzzler property)
(RNA.probing_data property)
(RNA.sc_mod_param property)
(RNA.score property)
(RNA.SOLUTION property)
(RNA.SOLUTIONVector property)
(RNA.StringVector property)
(RNA.struct_en property)
(RNA.subopt_solution property)
(RNA.SuboptVector property)
(RNA.SwigPyIterator property)
(RNA.UIntUIntVector property)
(RNA.UIntVector property)
(RNA.varArrayChar property)
(RNA.varArrayFLTorDBL property)
(RNA.varArrayInt property)
(RNA.varArrayMove property)
(RNA.varArrayShort property)
(RNA.varArrayUChar property)
(RNA.varArrayUInt property)
TN (RNA.score property)
TNR (RNA.score property)
TP (RNA.score property)
TPR (RNA.score property)
tree_edit_distance() (in module RNA)
tree_string_to_db() (in module RNA)
tree_string_unweight() (in module RNA)
Triloop_E (RNA.param attribute)
,
[1]
(RNA.param property)
Triloops (RNA.exp_param attribute)
,
[1]
(RNA.exp_param property)
(RNA.param attribute)
,
[1]
(RNA.param property)
TripleC (RNA.param attribute)
,
[1]
(RNA.param property)
type (RNA.ep attribute)
,
[1]
(RNA.ep property)
(RNA.fold_compound attribute)
(RNA.fold_compound property)
(RNA.hc attribute)
,
[1]
(RNA.hc property)
(RNA.mx_mfe property)
(RNA.mx_pf property)
(RNA.path property)
type() (RNA.varArrayChar method)
(RNA.varArrayFLTorDBL method)
(RNA.varArrayInt method)
(RNA.varArrayMove method)
(RNA.varArrayShort method)
(RNA.varArrayUChar method)
(RNA.varArrayUInt method)
U
ubf_eval_ext_int_loop() (in module RNA)
ubf_eval_int_loop() (in module RNA)
ubf_eval_int_loop2() (in module RNA)
ud_add_motif() (RNA.fold_compound method)
ud_remove() (RNA.fold_compound method)
ud_set_data() (RNA.fold_compound method)
ud_set_exp_prod_cb() (in module RNA)
ud_set_exp_prod_rule_cb() (RNA.fold_compound method)
ud_set_prob_cb() (in module RNA)
(RNA.fold_compound method)
ud_set_prod_cb() (in module RNA)
ud_set_prod_rule_cb() (RNA.fold_compound method)
ud_set_pydata() (in module RNA)
UIntUIntVector (class in RNA)
UIntVector (class in RNA)
unexpand_aligned_F() (in module RNA)
unexpand_Full() (in module RNA)
uniq_ML (RNA.md attribute)
(RNA.md property)
unmodified (RNA.sc_mod_param attribute)
,
[1]
unmodified_encoding (RNA.sc_mod_param attribute)
,
[1]
unpack_structure() (in module RNA)
unpaired (RNA.plot_options_puzzler attribute)
,
[1]
unweight() (in module RNA)
up3 (RNA.hx property)
up5 (RNA.hx property)
up_ext (RNA.hc attribute)
,
[1]
(RNA.hc property)
up_hp (RNA.hc attribute)
,
[1]
(RNA.hc property)
up_int (RNA.hc attribute)
,
[1]
(RNA.hc property)
up_ml (RNA.hc attribute)
,
[1]
(RNA.hc property)
update_co_pf_params() (in module RNA)
update_cofold_params() (in module RNA)
update_fold_params() (in module RNA)
update_pf_params() (in module RNA)
urn() (in module RNA)
ushortP_getitem() (in module RNA)
ushortP_setitem() (in module RNA)
V
value() (RNA.SwigPyIterator method)
var_array_Iterator (class in RNA)
varArrayChar (class in RNA)
varArrayFLTorDBL (class in RNA)
varArrayInt (class in RNA)
varArrayMove (class in RNA)
varArrayShort (class in RNA)
varArrayUChar (class in RNA)
varArrayUInt (class in RNA)
W
window_size (RNA.fold_compound attribute)
(RNA.md attribute)
(RNA.md property)
write_parameter_file() (in module RNA)
X
X (RNA.COORDINATE attribute)
,
[1]
(RNA.COORDINATE property)
xrna_plot() (in module RNA)
Y
Y (RNA.COORDINATE attribute)
,
[1]
(RNA.COORDINATE property)
Z
zsc_compute() (RNA.fold_compound method)
zsc_compute_raw() (RNA.fold_compound method)
zsc_filter_free() (RNA.fold_compound method)
zsc_filter_init() (RNA.fold_compound method)
zsc_filter_on() (RNA.fold_compound method)
zsc_filter_threshold() (RNA.fold_compound method)
zsc_filter_update() (RNA.fold_compound method)
zscore_data (RNA.fold_compound attribute)
zukersubopt() (in module RNA)