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part_func.h
Go to the documentation of this file.
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#ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_H__
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#define __VIENNA_RNA_PACKAGE_PART_FUNC_H__
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#include "
data_structures.h
"
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#ifdef __GNUC__
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#define DEPRECATED(func) func __attribute__ ((deprecated))
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#else
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#define DEPRECATED(func) func
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#endif
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extern
int
st_back
;
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/*
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#################################################
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# PARTITION FUNCTION COMPUTATION #
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#################################################
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*/
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float
pf_fold_par
(
const
char
*sequence,
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char
*structure,
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pf_paramT
*parameters,
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int
calculate_bppm,
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int
is_constrained,
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int
is_circular);
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float
pf_fold
(
const
char
*sequence,
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char
*structure);
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float
pf_circ_fold
(
const
char
*sequence,
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char
*structure);
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char
*
pbacktrack
(
char
*sequence);
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char
*
pbacktrack_circ
(
char
*sequence);
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void
free_pf_arrays
(
void
);
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void
update_pf_params
(
int
length);
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void
update_pf_params_par
(
int
length,
pf_paramT
*parameters);
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FLT_OR_DBL *
export_bppm
(
void
);
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/*
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#################################################
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# OTHER PARTITION FUNCTION RELATED DECLARATIONS #
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#################################################
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*/
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void
assign_plist_from_pr
(
plist
**pl,
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FLT_OR_DBL *probs,
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int
length,
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double
cutoff);
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/* this doesn't work if free_pf_arrays() is called before */
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void
assign_plist_gquad_from_pr(
plist
**pl,
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int
length,
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double
cut_off);
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char
*get_centroid_struct_gquad_pr(
int
length,
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double
*dist);
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int
get_pf_arrays
(
short
**S_p,
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short
**S1_p,
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char
**ptype_p,
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FLT_OR_DBL **qb_p,
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FLT_OR_DBL **qm_p,
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FLT_OR_DBL **q1k_p,
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FLT_OR_DBL **qln_p);
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double
get_subseq_F
(
int
i,
int
j);
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char
*
get_centroid_struct_pl
(
int
length,
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double
*dist,
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plist
*pl);
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char
*
get_centroid_struct_pr
(
int
length,
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double
*dist,
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FLT_OR_DBL *pr);
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double
mean_bp_distance
(
int
length);
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double
mean_bp_distance_pr
(
int
length,
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FLT_OR_DBL *pr);
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void
bppm_to_structure
(
char
*structure,
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FLT_OR_DBL *pr,
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unsigned
int
length);
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plist
*stackProb(
double
cutoff);
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char
bppm_symbol
(
const
float
*x);
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/*
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#################################################
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# DEPRECATED FUNCTIONS #
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#################################################
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*/
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DEPRECATED(
void
init_pf_fold
(
int
length));
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DEPRECATED(
char
*
centroid
(
int
length,
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double
*dist));
/* mean pair distance of ensemble */
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DEPRECATED(
double
mean_bp_dist
(
int
length));
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DEPRECATED(
double
expLoopEnergy
(
int
u1,
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int
u2,
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int
type,
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int
type2,
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short
si1,
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short
sj1,
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short
sp1,
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short
sq1));
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DEPRECATED(
double
expHairpinEnergy
(
int
u,
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int
type,
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short
si1,
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short
sj1,
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const
char
*
string
));
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#endif
H
part_func.h
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1.8.1.1