proc foldCompound(sequence: cstring; mdP: ptr VrnaMdT; options: cuint): ptr VrnaFoldCompoundT {.
cdecl, importc: "vrna_fold_compound",
.}-
proc foldCompoundComparative(sequences: cstringArray; mdP: ptr VrnaMdT; options: cuint): ptr VrnaFoldCompoundT {.
cdecl, importc: "vrna_fold_compound_comparative",
.}-
proc foldCompoundTwoD(sequence: cstring; s1: cstring; s2: cstring; mdP: ptr VrnaMdT;
options: cuint): ptr VrnaFoldCompoundT {.cdecl,
importc: "vrna_fold_compound_TwoD",
.}-
proc foldCompoundPrepare(vc: ptr VrnaFoldCompoundT; options: cuint): cint {.cdecl,
importc: "vrna_fold_compound_prepare",
.}-
proc foldCompoundFree(vc: ptr VrnaFoldCompoundT) {.cdecl,
importc: "vrna_fold_compound_free",
.}-
proc foldCompoundAddAuxdata(vc: ptr VrnaFoldCompoundT; data: pointer;
f: ptr VrnaCallbackFreeAuxdata) {.cdecl,
importc: "vrna_fold_compound_add_auxdata",
.}-
proc foldCompoundAddCallback(vc: ptr VrnaFoldCompoundT;
f: ptr VrnaCallbackRecursionStatus) {.cdecl,
importc: "vrna_fold_compound_add_callback",
.}-
proc vrnaMfeTwoD(vc: ptr VrnaFoldCompoundT; distance1: cint; distance2: cint): ptr VrnaSolTwoDt {.
cdecl, importc: "vrna_mfe_TwoD",
.}-
proc vrnaBacktrack5TwoD(vc: ptr VrnaFoldCompoundT; k: cint; l: cint; j: cuint): cstring {.
cdecl, importc: "vrna_backtrack5_TwoD",
.}-
proc vrnaPfTwoD(vc: ptr VrnaFoldCompoundT; maxDistance1: cint; maxDistance2: cint): ptr VrnaSolTwoD_pfT {.
cdecl, importc: "vrna_pf_TwoD",
.}-
proc vrnaPbacktrackTwoD(vc: ptr VrnaFoldCompoundT; d1: cint; d2: cint): cstring {.cdecl,
importc: "vrna_pbacktrack_TwoD",
.}-
proc vrnaPbacktrack5TwoD(vc: ptr VrnaFoldCompoundT; d1: cint; d2: cint; length: cuint): cstring {.
cdecl, importc: "vrna_pbacktrack5_TwoD",
.}-
proc aliLduplexfold(s1: ptr cstring; s2: ptr cstring; threshold: cint;
extensionCost: cint; alignmentLength: cint; delta: cint;
fast: cint; ilA: cint; ilB: cint; bA: cint; bB: cint): ptr ptr DuplexT {.
cdecl, importc: "aliLduplexfold",
.}-
proc aliLduplexfoldXS(s1: ptr cstring; s2: ptr cstring; accessS1: ptr ptr cint;
accessS2: ptr ptr cint; threshold: cint; alignmentLength: cint;
delta: cint; fast: cint; ilA: cint; ilB: cint; bA: cint; bB: cint): ptr ptr DuplexT {.
cdecl, importc: "aliLduplexfold_XS",
.}-
proc readClustal(clust: ptr File; alignedSeqs: ptr cstring; names: ptr cstring): cint {.
cdecl, importc: "read_clustal",
.}-
proc consensus(`as`: ptr cstring): cstring {.cdecl, importc: "consensus",
.}-
proc consensMis(`as`: ptr cstring): cstring {.cdecl, importc: "consens_mis",
.}-
proc getUngappedSequence(seq: cstring): cstring {.cdecl,
importc: "get_ungapped_sequence",
.}-
proc vrnaAlnMpi(alignment: cstringArray): cint {.cdecl, importc: "vrna_aln_mpi",
.}-
proc vrnaAlnPinfo(vc: ptr VrnaFoldCompoundT; structure: cstring; threshold: cdouble): ptr VrnaPinfoT {.
cdecl, importc: "vrna_aln_pinfo",
.}-
proc vrnaAlnPscore(alignment: cstringArray; md: ptr VrnaMdT): ptr cint {.cdecl,
importc: "vrna_aln_pscore",
.}-
proc encodeAliSequence(sequence: cstring; s: ptr cshort; s5: ptr cshort; s3: ptr cshort;
ss: cstring; `as`: ptr cushort; circ: cint) {.cdecl,
importc: "encode_ali_sequence",
.}-
proc allocSequenceArrays(sequences: cstringArray; s: ptr ptr ptr cshort;
s5: ptr ptr ptr cshort; s3: ptr ptr ptr cshort;
a2s: ptr ptr ptr cushort; ss: ptr cstringArray; circ: cint) {.
cdecl, importc: "alloc_sequence_arrays",
.}-
proc freeSequenceArrays(nSeq: cuint; s: ptr ptr ptr cshort; s5: ptr ptr ptr cshort;
s3: ptr ptr ptr cshort; a2s: ptr ptr ptr cushort;
ss: ptr cstringArray) {.cdecl,
importc: "free_sequence_arrays",
.}-
proc vrnaSequenceLengthMax(options: cuint): cuint {.cdecl,
importc: "vrna_sequence_length_max",
.}-
proc vrnaNucleotideIUPAC_identity(a: char; b: char): cint {.cdecl,
importc: "vrna_nucleotide_IUPAC_identity",
.}-
proc vrnaPtypes(s: ptr cshort; md: ptr VrnaMdT): cstring {.cdecl, importc: "vrna_ptypes",
.}-
proc vrnaSeqEncode(sequence: cstring; md: ptr VrnaMdT): ptr cshort {.cdecl,
importc: "vrna_seq_encode",
.}-
proc vrnaSeqEncodeSimple(sequence: cstring; md: ptr VrnaMdT): ptr cshort {.cdecl,
importc: "vrna_seq_encode_simple",
.}-
proc vrnaNucleotideEncode(c: char; md: ptr VrnaMdT): cint {.cdecl,
importc: "vrna_nucleotide_encode",
.}-
proc vrnaNucleotideDecode(enc: cint; md: ptr VrnaMdT): char {.cdecl,
importc: "vrna_nucleotide_decode",
.}-
proc vrnaAlnEncode(sequence: cstring; s_p: ptr ptr cshort; s5P: ptr ptr cshort;
s3P: ptr ptr cshort; ssP: cstringArray; asP: ptr ptr cushort;
md: ptr VrnaMdT) {.cdecl, importc: "vrna_aln_encode",
.}-
proc vrnaPbacktrack5(vc: ptr VrnaFoldCompoundT; length: cint): cstring {.cdecl,
importc: "vrna_pbacktrack5",
.}-
proc vrnaPbacktrack(vc: ptr VrnaFoldCompoundT): cstring {.cdecl,
importc: "vrna_pbacktrack",
.}-
proc vrnaCentroid(vc: ptr VrnaFoldCompoundT; dist: ptr cdouble): cstring {.cdecl,
importc: "vrna_centroid",
.}-
proc vrnaCentroidFromPlist(length: cint; dist: ptr cdouble; pl: ptr VrnaPlistT): cstring {.
cdecl, importc: "vrna_centroid_from_plist",
.}-
proc vrnaCentroidFromProbs(length: cint; dist: ptr cdouble; probs: ptr Flt_Or_Dbl): cstring {.
cdecl, importc: "vrna_centroid_from_probs",
.}-
proc vrnaCofold(sequence: cstring; structure: cstring): cfloat {.cdecl,
importc: "vrna_cofold",
.}-
proc vrnaMessageConstraintOptions(option: cuint) {.cdecl,
importc: "vrna_message_constraint_options",
.}-
proc vrnaMessageConstraintOptionsAll() {.cdecl, importc: "vrna_message_constraint_options_all",
.}-
proc vrnaHcInit(vc: ptr VrnaFoldCompoundT) {.cdecl, importc: "vrna_hc_init",
.}-
proc vrnaHcAddUp(vc: ptr VrnaFoldCompoundT; i: cint; option: char) {.cdecl,
importc: "vrna_hc_add_up",
.}-
proc vrnaHcAddUpBatch(vc: ptr VrnaFoldCompoundT; constraints: ptr VrnaHcUpT): cint {.
cdecl, importc: "vrna_hc_add_up_batch",
.}-
proc vrnaHcAddBp(vc: ptr VrnaFoldCompoundT; i: cint; j: cint; option: char) {.cdecl,
importc: "vrna_hc_add_bp",
.}-
proc vrnaHcAddBpNonspecific(vc: ptr VrnaFoldCompoundT; i: cint; d: cint; option: char) {.
cdecl, importc: "vrna_hc_add_bp_nonspecific",
.}-
proc vrnaHcFree(hc: ptr VrnaHcT) {.cdecl, importc: "vrna_hc_free",
.}-
proc vrnaHcAddFromDb(vc: ptr VrnaFoldCompoundT; constraint: cstring; options: cuint): cint {.
cdecl, importc: "vrna_hc_add_from_db",
.}-
proc vrnaScAddHiMotif(vc: ptr VrnaFoldCompoundT; seq: cstring; structure: cstring;
energy: Flt_Or_Dbl; options: cuint): cint {.cdecl,
importc: "vrna_sc_add_hi_motif",
.}-
proc vrnaScLigandDetectMotifs(vc: ptr VrnaFoldCompoundT; structure: cstring): ptr VrnaScMotifT {.
cdecl, importc: "vrna_sc_ligand_detect_motifs",
.}-
proc vrnaScGetHiMotif(vc: ptr VrnaFoldCompoundT; i: ptr cint; j: ptr cint; k: ptr cint;
l: ptr cint): cint {.cdecl, importc: "vrna_sc_get_hi_motif",
.}-
proc vrnaConstraintsAddSHAPE(vc: ptr VrnaFoldCompoundT; shapeFile: cstring;
shapeMethod: cstring; shapeConversion: cstring;
verbose: cint; constraintType: cuint) {.cdecl,
importc: "vrna_constraints_add_SHAPE",
.}-
proc vrnaConstraintsAddSHAPE_ali(vc: ptr VrnaFoldCompoundT; shapeMethod: cstring;
shapeFiles: cstringArray;
shapeFileAssociation: ptr cint; verbose: cint;
constraintType: cuint) {.cdecl,
importc: "vrna_constraints_add_SHAPE_ali",
.}-
proc vrnaScAddSHAPE_deigan(vc: ptr VrnaFoldCompoundT; reactivities: ptr cdouble;
m: cdouble; b: cdouble; options: cuint): cint {.cdecl,
importc: "vrna_sc_add_SHAPE_deigan",
.}-
proc vrnaScAddSHAPE_deiganAli(vc: ptr VrnaFoldCompoundT; shapeFiles: cstringArray;
shapeFileAssociation: ptr cint; m: cdouble; b: cdouble;
options: cuint): cint {.cdecl,
importc: "vrna_sc_add_SHAPE_deigan_ali",
.}-
proc vrnaScAddSHAPE_zarringhalam(vc: ptr VrnaFoldCompoundT;
reactivities: ptr cdouble; b: cdouble;
defaultValue: cdouble; shapeConversion: cstring;
options: cuint): cint {.cdecl,
importc: "vrna_sc_add_SHAPE_zarringhalam",
.}-
proc vrnaScSHAPE_parseMethod(methodString: cstring; `method`: cstring;
param1: ptr cfloat; param2: ptr cfloat): cint {.cdecl,
importc: "vrna_sc_SHAPE_parse_method",
.}-
proc vrnaScSHAPE_toPr(shapeConversion: cstring; values: ptr cdouble; length: cint;
defaultValue: cdouble): cint {.cdecl,
importc: "vrna_sc_SHAPE_to_pr",
.}-
proc vrnaScInit(vc: ptr VrnaFoldCompoundT) {.cdecl, importc: "vrna_sc_init",
.}-
proc vrnaScSetBp(vc: ptr VrnaFoldCompoundT; constraints: ptr ptr Flt_Or_Dbl;
options: cuint) {.cdecl, importc: "vrna_sc_set_bp",
.}-
proc vrnaScAddBp(vc: ptr VrnaFoldCompoundT; i: cint; j: cint; energy: Flt_Or_Dbl;
options: cuint) {.cdecl, importc: "vrna_sc_add_bp",
.}-
proc vrnaScSetUp(vc: ptr VrnaFoldCompoundT; constraints: ptr Flt_Or_Dbl; options: cuint) {.
cdecl, importc: "vrna_sc_set_up",
.}-
proc vrnaScAddUp(vc: ptr VrnaFoldCompoundT; i: cint; energy: Flt_Or_Dbl; options: cuint) {.
cdecl, importc: "vrna_sc_add_up",
.}-
proc vrnaScRemove(vc: ptr VrnaFoldCompoundT) {.cdecl, importc: "vrna_sc_remove",
.}-
proc vrnaScFree(sc: ptr VrnaScT) {.cdecl, importc: "vrna_sc_free",
.}-
proc vrnaScAddData(vc: ptr VrnaFoldCompoundT; data: pointer;
freeData: ptr VrnaCallbackFreeAuxdata) {.cdecl,
importc: "vrna_sc_add_data",
.}-
proc vrnaScAddF(vc: ptr VrnaFoldCompoundT; f: ptr VrnaCallbackScEnergy) {.cdecl,
importc: "vrna_sc_add_f",
.}-
proc vrnaScAddBt(vc: ptr VrnaFoldCompoundT; f: ptr VrnaCallbackScBacktrack) {.cdecl,
importc: "vrna_sc_add_bt",
.}-
proc vrnaScAddExpF(vc: ptr VrnaFoldCompoundT; expF: ptr VrnaCallbackScExpEnergy) {.
cdecl, importc: "vrna_sc_add_exp_f",
.}-
proc convertParameterFile(iname: cstring; oname: cstring; options: cuint) {.cdecl,
importc: "convert_parameter_file",
.}-
proc mxAdd(vc: ptr VrnaFoldCompoundT; `type`: MxTypeE; options: cuint): cint {.cdecl,
importc: "vrna_mx_add",
.}-
proc mxMfeAdd(vc: ptr VrnaFoldCompoundT; mxType: MxTypeE; options: cuint): cint {.cdecl,
importc: "vrna_mx_mfe_add",
.}-
proc mxPfAdd(vc: ptr VrnaFoldCompoundT; mxType: MxTypeE; options: cuint): cint {.cdecl,
importc: "vrna_mx_pf_add",
.}-
proc mxPrepare(vc: ptr VrnaFoldCompoundT; options: cuint): cint {.cdecl,
importc: "vrna_mx_prepare",
.}-
proc mxMfeFree(vc: ptr VrnaFoldCompoundT) {.cdecl, importc: "vrna_mx_mfe_free",
.}-
proc mxPfFree(vc: ptr VrnaFoldCompoundT) {.cdecl, importc: "vrna_mx_pf_free",
.}-
proc duplexfold(s1: cstring; s2: cstring): DuplexT {.cdecl, importc: "duplexfold",
.}-
proc duplexSubopt(s1: cstring; s2: cstring; delta: cint; w: cint): ptr DuplexT {.cdecl,
importc: "duplex_subopt",
.}-
proc aliduplexfold(s1: ptr cstring; s2: ptr cstring): DuplexT {.cdecl,
importc: "aliduplexfold",
.}-
proc aliduplexSubopt(s1: ptr cstring; s2: ptr cstring; delta: cint; w: cint): ptr DuplexT {.
cdecl, importc: "aliduplex_subopt",
.}-
proc vrnaPairingProbs(vc: ptr VrnaFoldCompoundT; structure: cstring) {.cdecl,
importc: "vrna_pairing_probs",
.}-
proc vrnaMeanBpDistancePr(length: cint; pr: ptr Flt_Or_Dbl): cdouble {.cdecl,
importc: "vrna_mean_bp_distance_pr",
.}-
proc vrnaMeanBpDistance(vc: ptr VrnaFoldCompoundT): cdouble {.cdecl,
importc: "vrna_mean_bp_distance",
.}-
proc vrnaStackProb(vc: ptr VrnaFoldCompoundT; cutoff: cdouble): ptr VrnaPlistT {.cdecl,
importc: "vrna_stack_prob",
.}-
proc vrnaEvalStructure(vc: ptr VrnaFoldCompoundT; structure: cstring): cfloat {.cdecl,
importc: "vrna_eval_structure",
.}-
proc vrnaEvalCovarStructure(vc: ptr VrnaFoldCompoundT; structure: cstring): cfloat {.
cdecl, importc: "vrna_eval_covar_structure",
.}-
proc vrnaEvalStructureSimple(string: cstring; structure: cstring): cfloat {.cdecl,
importc: "vrna_eval_structure_simple",
.}-
proc vrnaEvalStructureVerbose(vc: ptr VrnaFoldCompoundT; structure: cstring;
file: ptr File): cfloat {.cdecl,
importc: "vrna_eval_structure_verbose",
.}-
proc vrnaEvalStructureV(vc: ptr VrnaFoldCompoundT; structure: cstring;
verbosityLevel: cint; file: ptr File): cfloat {.cdecl,
importc: "vrna_eval_structure_v",
.}-
proc vrnaEvalStructureSimpleVerbose(string: cstring; structure: cstring;
file: ptr File): cfloat {.cdecl,
importc: "vrna_eval_structure_simple_verbose",
.}-
proc vrnaEvalStructureSimpleV(string: cstring; structure: cstring;
verbosityLevel: cint; file: ptr File): cfloat {.cdecl,
importc: "vrna_eval_structure_simple_v",
.}-
proc vrnaEvalStructurePt(vc: ptr VrnaFoldCompoundT; pt: ptr cshort): cint {.cdecl,
importc: "vrna_eval_structure_pt",
.}-
proc vrnaEvalStructurePtSimple(string: cstring; pt: ptr cshort): cint {.cdecl,
importc: "vrna_eval_structure_pt_simple",
.}-
proc vrnaEvalStructurePtVerbose(vc: ptr VrnaFoldCompoundT; pt: ptr cshort;
file: ptr File): cint {.cdecl,
importc: "vrna_eval_structure_pt_verbose",
.}-
proc vrnaEvalStructurePtV(vc: ptr VrnaFoldCompoundT; pt: ptr cshort;
verbosityLevel: cint; file: ptr File): cint {.cdecl,
importc: "vrna_eval_structure_pt_v",
.}-
proc vrnaEvalStructurePtSimpleVerbose(string: cstring; pt: ptr cshort; file: ptr File): cint {.
cdecl, importc: "vrna_eval_structure_pt_simple_verbose",
.}-
proc vrnaEvalStructurePtSimpleV(string: cstring; pt: ptr cshort; verbosityLevel: cint;
file: ptr File): cint {.cdecl,
importc: "vrna_eval_structure_pt_simple_v",
.}-
proc vrnaEvalLoopPt(vc: ptr VrnaFoldCompoundT; i: cint; pt: ptr cshort): cint {.cdecl,
importc: "vrna_eval_loop_pt",
.}-
proc vrnaEvalMove(vc: ptr VrnaFoldCompoundT; structure: cstring; m1: cint; m2: cint): cfloat {.
cdecl, importc: "vrna_eval_move",
.}-
proc vrnaEvalMovePt(vc: ptr VrnaFoldCompoundT; pt: ptr cshort; m1: cint; m2: cint): cint {.
cdecl, importc: "vrna_eval_move_pt",
.}-
proc vrnaEvalMovePtSimple(string: cstring; pt: ptr cshort; m1: cint; m2: cint): cint {.
cdecl, importc: "vrna_eval_move_pt_simple",
.}-
proc e_ExtLoop(`type`: cint; si1: cint; sj1: cint; p: ptr VrnaParamT): cint {.cdecl,
importc: "E_ExtLoop",
.}-
proc expE_ExtLoop(`type`: cint; si1: cint; sj1: cint; p: ptr VrnaExpParamT): Flt_Or_Dbl {.
cdecl, importc: "exp_E_ExtLoop",
.}-
proc e_Stem(`type`: cint; si1: cint; sj1: cint; extLoop: cint; p: ptr VrnaParamT): cint {.
cdecl, importc: "E_Stem",
.}-
proc expE_Stem(`type`: cint; si1: cint; sj1: cint; extLoop: cint; p: ptr VrnaExpParamT): Flt_Or_Dbl {.
cdecl, importc: "exp_E_Stem",
.}-
proc e_extLoop(i: cint; j: cint; vc: ptr VrnaFoldCompoundT): cint {.cdecl,
importc: "E_ext_loop",
.}-
proc e_extLoop5(vc: ptr VrnaFoldCompoundT) {.cdecl, importc: "E_ext_loop_5",
.}-
proc vrnaBT_extLoopF5(vc: ptr VrnaFoldCompoundT; k: ptr cint; i: ptr cint; j: ptr cint;
bpStack: ptr VrnaBpStackT; stackCount: ptr cint): cint {.cdecl,
importc: "vrna_BT_ext_loop_f5",
.}-
proc vrnaFileHelixlist(seq: cstring; db: cstring; energy: cfloat; file: ptr File) {.cdecl,
importc: "vrna_file_helixlist",
.}-
proc vrnaFileConnect(seq: cstring; db: cstring; energy: cfloat; identifier: cstring;
file: ptr File) {.cdecl, importc: "vrna_file_connect",
.}-
proc vrnaFileBpseq(seq: cstring; db: cstring; file: ptr File) {.cdecl,
importc: "vrna_file_bpseq",
.}-
proc vrnaFileFastaReadRecord(header: cstringArray; sequence: cstringArray;
rest: ptr cstringArray; file: ptr File; options: cuint): cuint {.
cdecl, importc: "vrna_file_fasta_read_record",
.}-
-
proc vrnaFileSHAPE_read(fileName: cstring; length: cint; defaultValue: cdouble;
sequence: cstring; values: ptr cdouble): cint {.cdecl,
importc: "vrna_file_SHAPE_read",
.}-
proc vrnaFileMsaRead(filename: cstring; names: ptr cstringArray;
aln: ptr cstringArray; id: ptr cstring; structure: ptr cstring;
options: cuint): cint {.cdecl, importc: "vrna_file_msa_read",
.}-
proc vrnaFileMsaReadRecord(fp: ptr File; names: ptr cstringArray;
aln: ptr cstringArray; id: ptr cstring;
structure: ptr cstring; options: cuint): cint {.cdecl,
importc: "vrna_file_msa_read_record",
.}-
proc vrnaFileMsaDetectFormat(filename: cstring; options: cuint): cuint {.cdecl,
importc: "vrna_file_msa_detect_format",
.}-
proc vrnaFileCopy(`from`: ptr File; to: ptr File) {.cdecl, importc: "vrna_file_copy",
.}-
proc vrnaReadLine(fp: ptr File): cstring {.cdecl, importc: "vrna_read_line",
.}-
proc vrnaMkdirP(path: cstring): cint {.cdecl, importc: "vrna_mkdir_p",
.}-
proc vrnaBasename(path: cstring): cstring {.cdecl, importc: "vrna_basename",
.}-
proc vrnaDirname(path: cstring): cstring {.cdecl, importc: "vrna_dirname",
.}-
proc vrnaPathFindpathSaddle(vc: ptr VrnaFoldCompoundT; struc1: cstring;
struc2: cstring; max: cint): cint {.cdecl,
importc: "vrna_path_findpath_saddle",
.}-
proc vrnaPathFindpath(vc: ptr VrnaFoldCompoundT; s1: cstring; s2: cstring; maxkeep: cint): ptr VrnaPathT {.
cdecl, importc: "vrna_path_findpath",
.}-
proc vrnaFold(sequence: cstring; structure: cstring): cfloat {.cdecl,
importc: "vrna_fold",
.}-
proc vrnaCircfold(sequence: cstring; structure: cstring): cfloat {.cdecl,
importc: "vrna_circfold",
.}-
proc e_gquad(L: cint; lIdx: array[3, cint]; p: ptr VrnaParamT): cint {.cdecl,
importc: "E_gquad",
.}-
proc expE_gquad(L: cint; lIdx: array[3, cint]; pf: ptr VrnaExpParamT): Flt_Or_Dbl {.cdecl,
importc: "exp_E_gquad",
.}-
proc e_gquadAli(i: cint; L: cint; lIdx: array[3, cint]; s: ptr ptr cshort; nSeq: cint;
p: ptr VrnaParamT): cint {.cdecl, importc: "E_gquad_ali",
.}-
proc e_gquadAliEn(i: cint; L: cint; lIdx: array[3, cint]; s: ptr ptr cshort; nSeq: cint;
en: array[2, cint]; p: ptr VrnaParamT) {.cdecl,
importc: "E_gquad_ali_en",
.}-
proc getGquadMatrix(s: ptr cshort; p: ptr VrnaParamT): ptr cint {.cdecl,
importc: "get_gquad_matrix",
.}-
proc getGquadAliMatrix(s_cons: ptr cshort; s: ptr ptr cshort; nSeq: cint;
p: ptr VrnaParamT): ptr cint {.cdecl,
importc: "get_gquad_ali_matrix",
.}-
proc getGquadPfMatrix(s: ptr cshort; scale: ptr Flt_Or_Dbl; pf: ptr VrnaExpParamT): ptr Flt_Or_Dbl {.
cdecl, importc: "get_gquad_pf_matrix",
.}-
proc getGquadL_matrix(s: ptr cshort; start: cint; maxdist: cint; n: cint; g: ptr ptr cint;
p: ptr VrnaParamT): ptr ptr cint {.cdecl,
importc: "get_gquad_L_matrix",
.}-
proc vrnaGquadMxLocalUpdate(vc: ptr VrnaFoldCompoundT; start: cint) {.cdecl,
importc: "vrna_gquad_mx_local_update",
.}-
proc getGquadPatternMfe(s: ptr cshort; i: cint; j: cint; p: ptr VrnaParamT; L: ptr cint;
lIdx: array[3, cint]) {.cdecl,
importc: "get_gquad_pattern_mfe",
.}-
proc getGquadPatternExhaustive(s: ptr cshort; i: cint; j: cint; p: ptr VrnaParamT;
L: ptr cint; lIdx: ptr cint; threshold: cint) {.cdecl,
importc: "get_gquad_pattern_exhaustive",
.}-
proc getGquadPatternPf(s: ptr cshort; i: cint; j: cint; pf: ptr VrnaExpParamT; L: ptr cint;
lIdx: array[3, cint]) {.cdecl,
importc: "get_gquad_pattern_pf",
.}-
proc getPlistGquadFromPr(s: ptr cshort; gi: cint; gj: cint; g: ptr Flt_Or_Dbl;
probs: ptr Flt_Or_Dbl; scale: ptr Flt_Or_Dbl;
pf: ptr VrnaExpParamT): ptr VrnaPlistT {.cdecl,
importc: "get_plist_gquad_from_pr",
.}-
proc getPlistGquadFromPrMax(s: ptr cshort; gi: cint; gj: cint; g: ptr Flt_Or_Dbl;
probs: ptr Flt_Or_Dbl; scale: ptr Flt_Or_Dbl; L: ptr cint;
lIdx: array[3, cint]; pf: ptr VrnaExpParamT): ptr VrnaPlistT {.
cdecl, importc: "get_plist_gquad_from_pr_max",
.}-
proc getPlistGquadFromDb(structure: cstring; pr: cfloat): ptr VrnaPlistT {.cdecl,
importc: "get_plist_gquad_from_db",
.}-
proc getGquadCount(s: ptr cshort; i: cint; j: cint): cint {.cdecl,
importc: "get_gquad_count",
.}-
proc getGquadLayerCount(s: ptr cshort; i: cint; j: cint): cint {.cdecl,
importc: "get_gquad_layer_count",
.}-
proc parseGquad(struc: cstring; L: ptr cint; lIdx: array[3, cint]): cint {.cdecl,
importc: "parse_gquad",
.}-
proc vrnaE_hpLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint): cint {.cdecl,
importc: "vrna_E_hp_loop",
.}-
proc vrnaE_extHpLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint): cint {.cdecl,
importc: "vrna_E_ext_hp_loop",
.}-
proc vrnaEvalExtHpLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint): cint {.cdecl,
importc: "vrna_eval_ext_hp_loop",
.}-
proc vrnaEvalHpLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint): cint {.cdecl,
importc: "vrna_eval_hp_loop",
.}-
proc vrnaBT_hpLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint; en: cint;
bpStack: ptr VrnaBpStackT; stackCount: ptr cint): cint {.cdecl,
importc: "vrna_BT_hp_loop",
.}-
proc vrnaE_intLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint): cint {.cdecl,
importc: "vrna_E_int_loop",
.}-
proc vrnaEvalIntLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint; k: cint; l: cint): cint {.
cdecl, importc: "vrna_eval_int_loop",
.}-
proc vrnaExpE_intLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint): Flt_Or_Dbl {.cdecl,
importc: "vrna_exp_E_int_loop",
.}-
proc vrnaExpE_interiorLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint; k: cint; l: cint): Flt_Or_Dbl {.
cdecl, importc: "vrna_exp_E_interior_loop",
.}-
proc vrnaE_extIntLoop(vc: ptr VrnaFoldCompoundT; i: cint; j: cint; ip: ptr cint;
iq: ptr cint): cint {.cdecl, importc: "vrna_E_ext_int_loop",
.}-
proc vrnaE_stack(vc: ptr VrnaFoldCompoundT; i: cint; j: cint): cint {.cdecl,
importc: "vrna_E_stack",
.}-
proc vrnaBT_stack(vc: ptr VrnaFoldCompoundT; i: ptr cint; j: ptr cint; en: ptr cint;
bpStack: ptr VrnaBpStackT; stackCount: ptr cint): cint {.cdecl,
importc: "vrna_BT_stack",
.}-
proc vrnaBT_intLoop(vc: ptr VrnaFoldCompoundT; i: ptr cint; j: ptr cint; en: cint;
bpStack: ptr VrnaBpStackT; stackCount: ptr cint): cint {.cdecl,
importc: "vrna_BT_int_loop",
.}-
proc inverseFold(start: cstring; target: cstring): cfloat {.cdecl,
importc: "inverse_fold",
.}-
proc inversePfFold(start: cstring; target: cstring): cfloat {.cdecl,
importc: "inverse_pf_fold",
.}-
proc vrnaLfold(string: cstring; windowSize: cint; file: ptr File): cfloat {.cdecl,
importc: "vrna_Lfold",
.}-
proc aliLfold(strings: cstringArray; structure: cstring; maxdist: cint): cfloat {.cdecl,
importc: "aliLfold",
.}-
proc updatePfParamsLP(length: cint) {.cdecl, importc: "update_pf_paramsLP",
.}-
proc updatePfParamsLP_par(length: cint; parameters: ptr VrnaExpParamT) {.cdecl,
importc: "update_pf_paramsLP_par",
.}-
proc pflFold(sequence: cstring; winSize: cint; pairSize: cint; cutoffb: cfloat;
pU: ptr ptr cdouble; dpp2: ptr ptr VrnaPlistT; pUfp: ptr File; spup: ptr File): ptr VrnaPlistT {.
cdecl, importc: "pfl_fold",
.}-
proc pflFoldPar(sequence: cstring; winSize: cint; pairSize: cint; cutoffb: cfloat;
pU: ptr ptr cdouble; dpp2: ptr ptr VrnaPlistT; pUfp: ptr File;
spup: ptr File; parameters: ptr VrnaExpParamT): ptr VrnaPlistT {.cdecl,
importc: "pfl_fold_par",
.}-
proc putoutpU_probPar(pU: ptr ptr cdouble; length: cint; ulength: cint; fp: ptr File;
energies: cint; parameters: ptr VrnaExpParamT) {.cdecl,
importc: "putoutpU_prob_par",
.}-
proc putoutpU_prob(pU: ptr ptr cdouble; length: cint; ulength: cint; fp: ptr File;
energies: cint) {.cdecl, importc: "putoutpU_prob",
.}-
proc putoutpU_probBinPar(pU: ptr ptr cdouble; length: cint; ulength: cint; fp: ptr File;
energies: cint; parameters: ptr VrnaExpParamT) {.cdecl,
importc: "putoutpU_prob_bin_par",
.}-
proc putoutpU_probBin(pU: ptr ptr cdouble; length: cint; ulength: cint; fp: ptr File;
energies: cint) {.cdecl, importc: "putoutpU_prob_bin",
.}-
proc mea(p: ptr VrnaPlistT; structure: cstring; gamma: cdouble): cfloat {.cdecl,
importc: "MEA",
.}-
proc meaSeq(p: ptr VrnaPlistT; sequence: cstring; structure: cstring; gamma: cdouble;
pf: ptr VrnaExpParamT): cfloat {.cdecl, importc: "MEA_seq",
.}-
proc mfe(vc: ptr VrnaFoldCompoundT; structure: cstring): cfloat {.cdecl,
importc: "vrna_mfe",
.}-
proc mfeDimer(vc: ptr VrnaFoldCompoundT; structure: cstring): cfloat {.cdecl,
importc: "vrna_mfe_dimer",
.}-
proc mfeWindow(vc: ptr VrnaFoldCompoundT; file: File): cfloat {.cdecl,
importc: "vrna_mfe_window",
.}-
proc vrnaMdSetDefault(md: ptr VrnaMdT) {.cdecl, importc: "vrna_md_set_default",
.}-
proc vrnaMdUpdate(md: ptr VrnaMdT) {.cdecl, importc: "vrna_md_update",
.}-
proc vrnaMdCopy(mdTo: ptr VrnaMdT; mdFrom: ptr VrnaMdT): ptr VrnaMdT {.cdecl,
importc: "vrna_md_copy",
.}-
proc vrnaMdOptionString(md: ptr VrnaMdT): cstring {.cdecl,
importc: "vrna_md_option_string",
.}-
proc vrnaMdSetNonstandards(md: ptr VrnaMdT; nsBases: cstring) {.cdecl,
importc: "vrna_md_set_nonstandards",
.}-
proc vrnaMdDefaultsReset(mdP: ptr VrnaMdT) {.cdecl,
importc: "vrna_md_defaults_reset",
.}-
proc vrnaMdDefaultsTemperature(t: cdouble) {.cdecl,
importc: "vrna_md_defaults_temperature",
.}-
proc vrnaMdDefaultsTemperatureGet(): cdouble {.cdecl,
importc: "vrna_md_defaults_temperature_get",
.}-
proc vrnaMdDefaultsBetaScale(b: cdouble) {.cdecl,
importc: "vrna_md_defaults_betaScale",
.}-
proc vrnaMdDefaultsBetaScaleGet(): cdouble {.cdecl,
importc: "vrna_md_defaults_betaScale_get",
.}-
proc vrnaMdDefaultsDangles(d: cint) {.cdecl, importc: "vrna_md_defaults_dangles",
.}-
proc vrnaMdDefaultsDanglesGet(): cint {.cdecl,
importc: "vrna_md_defaults_dangles_get",
.}-
proc vrnaMdDefaultsSpecialHp(flag: cint) {.cdecl,
importc: "vrna_md_defaults_special_hp",
.}-
proc vrnaMdDefaultsSpecialHpGet(): cint {.cdecl, importc: "vrna_md_defaults_special_hp_get",
.}-
proc vrnaMdDefaultsNoLP(flag: cint) {.cdecl, importc: "vrna_md_defaults_noLP",
.}-
proc vrnaMdDefaultsNoLP_get(): cint {.cdecl, importc: "vrna_md_defaults_noLP_get",
.}-
proc vrnaMdDefaultsNoGU(flag: cint) {.cdecl, importc: "vrna_md_defaults_noGU",
.}-
proc vrnaMdDefaultsNoGU_get(): cint {.cdecl, importc: "vrna_md_defaults_noGU_get",
.}-
proc vrnaMdDefaultsNoGUclosure(flag: cint) {.cdecl,
importc: "vrna_md_defaults_noGUclosure",
.}-
proc vrnaMdDefaultsNoGUclosureGet(): cint {.cdecl,
importc: "vrna_md_defaults_noGUclosure_get",
.}-
proc vrnaMdDefaultsLogML(flag: cint) {.cdecl, importc: "vrna_md_defaults_logML",
.}-
proc vrnaMdDefaultsLogML_get(): cint {.cdecl, importc: "vrna_md_defaults_logML_get",
.}-
proc vrnaMdDefaultsCirc(flag: cint) {.cdecl, importc: "vrna_md_defaults_circ",
.}-
proc vrnaMdDefaultsCircGet(): cint {.cdecl, importc: "vrna_md_defaults_circ_get",
.}-
proc vrnaMdDefaultsGquad(flag: cint) {.cdecl, importc: "vrna_md_defaults_gquad",
.}-
proc vrnaMdDefaultsGquadGet(): cint {.cdecl, importc: "vrna_md_defaults_gquad_get",
.}-
proc vrnaMdDefaultsUniqML(flag: cint) {.cdecl, importc: "vrna_md_defaults_uniq_ML",
.}-
proc vrnaMdDefaultsUniqML_get(): cint {.cdecl,
importc: "vrna_md_defaults_uniq_ML_get",
.}-
proc vrnaMdDefaultsEnergySet(e: cint) {.cdecl,
importc: "vrna_md_defaults_energy_set",
.}-
proc vrnaMdDefaultsEnergySetGet(): cint {.cdecl, importc: "vrna_md_defaults_energy_set_get",
.}-
proc vrnaMdDefaultsBacktrack(flag: cint) {.cdecl,
importc: "vrna_md_defaults_backtrack",
.}-
proc vrnaMdDefaultsBacktrackGet(): cint {.cdecl, importc: "vrna_md_defaults_backtrack_get",
.}-
proc vrnaMdDefaultsBacktrackType(t: char) {.cdecl,
importc: "vrna_md_defaults_backtrack_type",
.}-
proc vrnaMdDefaultsBacktrackTypeGet(): char {.cdecl,
importc: "vrna_md_defaults_backtrack_type_get",
.}-
proc vrnaMdDefaultsComputeBpp(flag: cint) {.cdecl,
importc: "vrna_md_defaults_compute_bpp",
.}-
proc vrnaMdDefaultsComputeBppGet(): cint {.cdecl, importc: "vrna_md_defaults_compute_bpp_get",
.}-
proc vrnaMdDefaultsMaxBpSpan(span: cint) {.cdecl, importc: "vrna_md_defaults_max_bp_span",
.}-
proc vrnaMdDefaultsMaxBpSpanGet(): cint {.cdecl, importc: "vrna_md_defaults_max_bp_span_get",
.}-
proc vrnaMdDefaultsMinLoopSize(size: cint) {.cdecl,
importc: "vrna_md_defaults_min_loop_size",
.}-
proc vrnaMdDefaultsMinLoopSizeGet(): cint {.cdecl,
importc: "vrna_md_defaults_min_loop_size_get",
.}-
proc vrnaMdDefaultsWindowSize(size: cint) {.cdecl,
importc: "vrna_md_defaults_window_size",
.}-
proc vrnaMdDefaultsWindowSizeGet(): cint {.cdecl, importc: "vrna_md_defaults_window_size_get",
.}-
proc vrnaMdDefaultsOldAliEn(flag: cint) {.cdecl,
importc: "vrna_md_defaults_oldAliEn",
.}-
proc vrnaMdDefaultsOldAliEnGet(): cint {.cdecl,
importc: "vrna_md_defaults_oldAliEn_get",
.}-
proc vrnaMdDefaultsRibo(flag: cint) {.cdecl, importc: "vrna_md_defaults_ribo",
.}-
proc vrnaMdDefaultsRiboGet(): cint {.cdecl, importc: "vrna_md_defaults_ribo_get",
.}-
proc vrnaMdDefaultsCvFact(factor: cdouble) {.cdecl,
importc: "vrna_md_defaults_cv_fact",
.}-
proc vrnaMdDefaultsCvFactGet(): cdouble {.cdecl,
importc: "vrna_md_defaults_cv_fact_get",
.}-
proc vrnaMdDefaultsNcFact(factor: cdouble) {.cdecl,
importc: "vrna_md_defaults_nc_fact",
.}-
proc vrnaMdDefaultsNcFactGet(): cdouble {.cdecl,
importc: "vrna_md_defaults_nc_fact_get",
.}-
proc vrnaMdDefaultsSfact(factor: cdouble) {.cdecl,
importc: "vrna_md_defaults_sfact",
.}-
proc vrnaMdDefaultsSfactGet(): cdouble {.cdecl,
importc: "vrna_md_defaults_sfact_get",
.}-
proc printStren(`out`: ptr File; str: ptr StructEn) {.cdecl, importc: "print_stren",
.}-
proc printStr(`out`: ptr File; str: ptr cshort) {.cdecl, importc: "print_str",
.}-
proc copyArr(dest: ptr cshort; src: ptr cshort) {.cdecl, importc: "copy_arr",
.}-
proc allocopy(src: ptr cshort): ptr cshort {.cdecl, importc: "allocopy",
.}-
proc moveGradient(seq: cstring; ptable: ptr cshort; s: ptr cshort; s1: ptr cshort;
verbosityLevel: cint; shifts: cint; noLP: cint): cint {.cdecl,
importc: "move_gradient",
.}-
proc moveFirst(seq: cstring; ptable: ptr cshort; s: ptr cshort; s1: ptr cshort;
verbosityLevel: cint; shifts: cint; noLP: cint): cint {.cdecl,
importc: "move_first",
.}-
proc moveAdaptive(seq: cstring; ptable: ptr cshort; s: ptr cshort; s1: ptr cshort;
verbosityLevel: cint): cint {.cdecl, importc: "move_adaptive",
.}-
proc moveStandard(seq: cstring; struc: cstring; `type`: Move_Type;
verbosityLevel: cint; shifts: cint; noLP: cint): cint {.cdecl,
importc: "move_standard",
.}-
proc browseNeighsPt(seq: cstring; ptable: ptr cshort; s: ptr cshort; s1: ptr cshort;
verbosityLevel: cint; shifts: cint; noLP: cint; funct: proc (
a2: ptr StructEn; a3: ptr StructEn): cint {.cdecl
.}): cint {.cdecl,
importc: "browse_neighs_pt",
.}-
proc browseNeighs(seq: cstring; struc: cstring; verbosityLevel: cint; shifts: cint;
noLP: cint; funct: proc (a2: ptr StructEn; a3: ptr StructEn): cint {.cdecl
.}): cint {.
cdecl, importc: "browse_neighs",
.}-
proc e_mbLoopStack(i: cint; j: cint; vc: ptr VrnaFoldCompoundT): cint {.cdecl,
importc: "E_mb_loop_stack",
.}-
proc vrnaBT_mbLoop(vc: ptr VrnaFoldCompoundT; i: ptr cint; j: ptr cint; k: ptr cint;
en: cint; component1: ptr cint; component2: ptr cint): cint {.cdecl,
importc: "vrna_BT_mb_loop",
.}-
proc vrnaE_mbLoopFast(vc: ptr VrnaFoldCompoundT; i: cint; j: cint; dmli1: ptr cint;
dmli2: ptr cint): cint {.cdecl, importc: "vrna_E_mb_loop_fast",
.}-
proc e_mlRightmostStem(i: cint; j: cint; vc: ptr VrnaFoldCompoundT): cint {.cdecl,
importc: "E_ml_rightmost_stem",
.}-
proc vrnaE_mlStemsFast(vc: ptr VrnaFoldCompoundT; i: cint; j: cint; fmi: ptr cint;
dmli: ptr cint): cint {.cdecl, importc: "vrna_E_ml_stems_fast",
.}-
proc vrnaExpE_mbLoopFast(vc: ptr VrnaFoldCompoundT; i: cint; j: cint;
qqm1: ptr Flt_Or_Dbl): Flt_Or_Dbl {.cdecl,
importc: "vrna_exp_E_mb_loop_fast",
.}-
proc vrnaBT_mbLoopFake(vc: ptr VrnaFoldCompoundT; u: ptr cint; i: ptr cint; j: ptr cint;
bpStack: ptr VrnaBpStackT; stackCount: ptr cint): cint {.cdecl,
importc: "vrna_BT_mb_loop_fake",
.}-
proc vrnaBT_mbLoopSplit(vc: ptr VrnaFoldCompoundT; i: ptr cint; j: ptr cint; k: ptr cint;
l: ptr cint; component1: ptr cint; component2: ptr cint;
bpStack: ptr VrnaBpStackT; stackCount: ptr cint): cint {.cdecl,
importc: "vrna_BT_mb_loop_split",
.}-
proc naviewXyCoordinates(pairTable: ptr cshort; x: ptr cfloat; y: ptr cfloat): cint {.
cdecl, importc: "naview_xy_coordinates",
.}-
proc vrnaParams(md: ptr VrnaMdT): ptr VrnaParamT {.cdecl, importc: "vrna_params",
.}-
proc vrnaParamsCopy(par: ptr VrnaParamT): ptr VrnaParamT {.cdecl,
importc: "vrna_params_copy",
.}-
proc vrnaExpParams(md: ptr VrnaMdT): ptr VrnaExpParamT {.cdecl,
importc: "vrna_exp_params",
.}-
proc vrnaExpParamsComparative(nSeq: cuint; md: ptr VrnaMdT): ptr VrnaExpParamT {.cdecl,
importc: "vrna_exp_params_comparative",
.}-
proc vrnaExpParamsCopy(par: ptr VrnaExpParamT): ptr VrnaExpParamT {.cdecl,
importc: "vrna_exp_params_copy",
.}-
proc vrnaParamsSubst(vc: ptr VrnaFoldCompoundT; par: ptr VrnaParamT) {.cdecl,
importc: "vrna_params_subst",
.}-
proc vrnaExpParamsSubst(vc: ptr VrnaFoldCompoundT; params: ptr VrnaExpParamT) {.cdecl,
importc: "vrna_exp_params_subst",
.}-
proc vrnaExpParamsRescale(vc: ptr VrnaFoldCompoundT; mfe: ptr cdouble) {.cdecl,
importc: "vrna_exp_params_rescale",
.}-
proc vrnaParamsReset(vc: ptr VrnaFoldCompoundT; mdP: ptr VrnaMdT) {.cdecl,
importc: "vrna_params_reset",
.}-
proc vrnaExpParamsReset(vc: ptr VrnaFoldCompoundT; mdP: ptr VrnaMdT) {.cdecl,
importc: "vrna_exp_params_reset",
.}-
proc pf(vc: ptr VrnaFoldCompoundT; structure: ptr char): cfloat {.cdecl,
importc: "vrna_pf",
.}-
proc pfFold(sequence: cstring; structure: ptr char; pl: ptr ptr VrnaPlistT): cfloat {.
cdecl, importc: "vrna_pf_fold",
.}-
proc pfCircfold(sequence: cstring; structure: ptr char; pl: ptr ptr VrnaPlistT): cfloat {.
cdecl, importc: "vrna_pf_circfold",
.}-
proc pfFloatPrecision(): cint {.cdecl, importc: "vrna_pf_float_precision",
.}-
proc pfDimer(vc: ptr VrnaFoldCompoundT; structure: ptr char): VrnaDimerPfT {.cdecl,
importc: "vrna_pf_dimer",
.}-
proc pfDimerProbs(fab: cdouble; fa: cdouble; fb: cdouble; prAB: ptr VrnaPlistT;
prA: ptr VrnaPlistT; prB: ptr VrnaPlistT; alength: cint;
expParams: ptr VrnaExpParamT) {.cdecl,
importc: "vrna_pf_dimer_probs",
.}-
proc pfDimerConcentrations(fcAB: cdouble; fcAA: cdouble; fcBB: cdouble; fea: cdouble;
feb: cdouble; startconc: ptr cdouble;
expParams: ptr VrnaExpParamT): ptr VrnaDimerConcT {.cdecl,
importc: "vrna_pf_dimer_concentrations",
.}-
proc pfUnstru(sequence: cstring; maxW: cint): ptr PuContrib {.cdecl,
importc: "pf_unstru",
.}-
proc pfInteract(s1: cstring; s2: cstring; pC: ptr PuContrib; pC2: ptr PuContrib;
maxW: cint; cstruc: cstring; incr3: cint; incr5: cint): ptr interact {.
cdecl, importc: "pf_interact",
.}-
proc freeInteract(pin: ptr interact) {.cdecl, importc: "free_interact",
.}-
proc upPlot(pC: ptr PuContrib; pCSh: ptr PuContrib; pint: ptr interact; ofile: cstring;
unpairedValues: ptr ptr cint; selectContrib: cstring; head: cstring;
mode: cuint): cint {.cdecl, importc: "Up_plot",
.}-
proc getPuContribStruct(n: cuint; w: cuint): ptr PuContrib {.cdecl,
importc: "get_pu_contrib_struct",
.}-
proc freePuContribStruct(pu: ptr PuContrib) {.cdecl,
importc: "free_pu_contrib_struct",
.}-
proc freePuContrib(pu: ptr PuContrib) {.cdecl, importc: "free_pu_contrib",
.}-
proc vrnaScMinimizePertubation(vc: ptr VrnaFoldCompoundT;
qProbUnpaired: ptr cdouble; objectiveFunction: cint;
sigmaSquared: cdouble; tauSquared: cdouble;
algorithm: cint; sampleSize: cint;
epsilon: ptr cdouble; initialStepSize: cdouble;
minStepSize: cdouble; minImprovement: cdouble;
minimizerTolerance: cdouble;
callback: ProgressCallback) {.cdecl,
importc: "vrna_sc_minimize_pertubation",
.}-
proc pKLduplexfoldXS(s1: cstring; accessS1: ptr ptr cint; threshold: cint;
alignmentLength: cint; delta: cint): ptr ptr DupVar {.cdecl,
importc: "PKLduplexfold_XS",
.}-
proc arraySize(array: ptr ptr DuplexT): cint {.cdecl, importc: "arraySize",
.}-
proc freeDuplexT(array: ptr ptr DuplexT) {.cdecl, importc: "freeDuplexT",
.}-
proc lduplexfold(s1: cstring; s2: cstring; threshold: cint; extensionCost: cint;
alignmentLength: cint; delta: cint; fast: cint; ilA: cint; ilB: cint;
bA: cint; bB: cint): ptr ptr DuplexT {.cdecl, importc: "Lduplexfold",
.}-
proc lduplexfoldXS(s1: cstring; s2: cstring; accessS1: ptr ptr cint;
accessS2: ptr ptr cint; threshold: cint; delta: cint;
alignmentLength: cint; fast: cint; ilA: cint; ilB: cint; bA: cint;
bB: cint): ptr ptr DuplexT {.cdecl, importc: "Lduplexfold_XS",
.}-
proc lduplexfoldC(s1: cstring; s2: cstring; threshold: cint; extensionCost: cint;
alignmentLength: cint; delta: cint; fast: cint; structure: cstring;
ilA: cint; ilB: cint; bA: cint; bB: cint): ptr ptr DuplexT {.cdecl,
importc: "Lduplexfold_C",
.}-
proc lduplexfoldCXS(s1: cstring; s2: cstring; accessS1: ptr ptr cint;
accessS2: ptr ptr cint; threshold: cint; delta: cint;
alignmentLength: cint; fast: cint; structure: cstring; ilA: cint;
ilB: cint; bA: cint; bB: cint): ptr ptr DuplexT {.cdecl,
importc: "Lduplexfold_CXS",
.}-
proc psColorAln(structure: cstring; filename: cstring; seqs: ptr cstring;
names: ptr cstring): cint {.cdecl, importc: "PS_color_aln",
.}-
proc aliPsColorAln(structure: cstring; filename: cstring; seqs: ptr cstring;
names: ptr cstring): cint {.cdecl, importc: "aliPS_color_aln",
.}-
proc simpleXyCoordinates(pairTable: ptr cshort; x: ptr cfloat; y: ptr cfloat): cint {.
cdecl, importc: "simple_xy_coordinates",
.}-
proc simpleCircplotCoordinates(pairTable: ptr cshort; x: ptr cfloat; y: ptr cfloat): cint {.
cdecl, importc: "simple_circplot_coordinates",
.}-
proc psRnaPlotSnoopA(string: cstring; structure: cstring; ssfile: cstring;
relativeAccess: ptr cint; seqs: ptr cstring): cint {.cdecl,
importc: "PS_rna_plot_snoop_a",
.}-
proc vrnaFilePsRnaplot(seq: cstring; structure: cstring; file: cstring;
mdP: ptr VrnaMdT): cint {.cdecl,
importc: "vrna_file_PS_rnaplot",
.}-
proc vrnaFilePsRnaplotA(seq: cstring; structure: cstring; file: cstring; pre: cstring;
post: cstring; mdP: ptr VrnaMdT): cint {.cdecl,
importc: "vrna_file_PS_rnaplot_a",
.}-
proc gmlRNA(string: cstring; structure: cstring; ssfile: cstring; option: char): cint {.
cdecl, importc: "gmlRNA",
.}-
proc ssvRnaPlot(string: cstring; structure: cstring; ssfile: cstring): cint {.cdecl,
importc: "ssv_rna_plot",
.}-
proc svgRnaPlot(string: cstring; structure: cstring; ssfile: cstring): cint {.cdecl,
importc: "svg_rna_plot",
.}-
proc xrnaPlot(string: cstring; structure: cstring; ssfile: cstring): cint {.cdecl,
importc: "xrna_plot",
.}-
proc profileAln(t1: ptr cfloat; seq1: cstring; t2: ptr cfloat; seq2: cstring): cfloat {.
cdecl, importc: "profile_aln",
.}-
proc setPalnParams(gapOpen: cdouble; gapExt: cdouble; seqweight: cdouble;
freeEnds: cint): cint {.cdecl, importc: "set_paln_params",
.}-
proc profileEditDistance(t1: ptr cfloat; t2: ptr cfloat): cfloat {.cdecl,
importc: "profile_edit_distance",
.}-
proc makeBpProfileBppm(bppm: ptr Flt_Or_Dbl; length: cint): ptr cfloat {.cdecl,
importc: "Make_bp_profile_bppm",
.}-
proc printBppm(t: ptr cfloat) {.cdecl, importc: "print_bppm",
.}-
proc freeProfile(t: ptr cfloat) {.cdecl, importc: "free_profile",
.}-
proc vrnaPlotDpEPS(filename: cstring; sequence: cstring; upper: ptr VrnaPlistT;
lower: ptr VrnaPlistT; auxdata: ptr VrnaDotplotAuxdataT;
options: cuint): cint {.cdecl, importc: "vrna_plot_dp_EPS",
.}-
proc pS_colorDotPlot(string: cstring; pi: ptr VrnaCpairT; filename: cstring): cint {.
cdecl, importc: "PS_color_dot_plot",
.}-
proc pS_colorDotPlotTurn(seq: cstring; pi: ptr VrnaCpairT; filename: cstring;
winSize: cint): cint {.cdecl,
importc: "PS_color_dot_plot_turn",
.}-
proc pS_dotPlotList(seq: cstring; filename: cstring; pl: ptr VrnaPlistT;
mf: ptr VrnaPlistT; comment: cstring): cint {.cdecl,
importc: "PS_dot_plot_list",
.}-
proc vrnaPlotDpPS_list(seq: cstring; cp: cint; wastlfile: cstring; pl: ptr VrnaPlistT;
mf: ptr VrnaPlistT; comment: cstring): cint {.cdecl,
importc: "vrna_plot_dp_PS_list",
.}-
proc pS_dotPlotTurn(seq: cstring; pl: ptr VrnaPlistT; filename: cstring; winSize: cint): cint {.
cdecl, importc: "PS_dot_plot_turn",
.}-
proc readParameterFile(fname: cstring) {.cdecl, importc: "read_parameter_file",
.}-
proc writeParameterFile(fname: cstring) {.cdecl, importc: "write_parameter_file",
.}-
proc gettype(ident: cstring): Parset {.cdecl, importc: "gettype",
.}-
proc settype(s: Parset): cstring {.cdecl, importc: "settype",
.}-
proc getRibosum(alseq: cstringArray; nSeq: cint; length: cint): ptr ptr cfloat {.cdecl,
importc: "get_ribosum",
.}-
proc readribosum(name: cstring): ptr ptr cfloat {.cdecl, importc: "readribosum",
.}-
proc b2HIT(structure: cstring): cstring {.cdecl, importc: "b2HIT",
.}-
proc b2C(structure: cstring): cstring {.cdecl, importc: "b2C",
.}-
proc b2Shapiro(structure: cstring): cstring {.cdecl, importc: "b2Shapiro",
.}-
proc addRoot(structure: cstring): cstring {.cdecl, importc: "add_root",
.}-
proc expandShapiro(coarse: cstring): cstring {.cdecl, importc: "expand_Shapiro",
.}-
proc expandFull(structure: cstring): cstring {.cdecl, importc: "expand_Full",
.}-
proc unexpandFull(ffull: cstring): cstring {.cdecl, importc: "unexpand_Full",
.}-
proc unweight(wcoarse: cstring): cstring {.cdecl, importc: "unweight",
.}-
proc unexpandAlignedF(align: array[2, cstring]) {.cdecl,
importc: "unexpand_aligned_F",
.}-
proc parseStructure(structure: cstring) {.cdecl, importc: "parse_structure",
.}-
proc snofold(sequence: cstring; structure: cstring; maxAssym: cint; threshold: cint;
minS2: cint; maxS2: cint; halfStem: cint; maxHalfStem: cint): cint {.cdecl,
importc: "snofold",
.}-
proc snofreeArrays(length: cint) {.cdecl, importc: "snofree_arrays",
.}-
proc snoinitializeFold(length: cint) {.cdecl, importc: "snoinitialize_fold",
.}-
proc snoupdateFoldParams() {.cdecl, importc: "snoupdate_fold_params",
.}-
proc snoloopEnergy(ptable: ptr cshort; s: ptr cshort; s1: ptr cshort; i: cint): cint {.cdecl,
importc: "snoloop_energy",
.}-
proc snoexportFoldArrays(indxP: ptr ptr cint; mLoopP: ptr ptr cint; cLoop: ptr ptr cint;
foldP: ptr ptr ptr Folden; foldPXS: ptr ptr ptr Folden) {.cdecl,
importc: "snoexport_fold_arrays",
.}-
proc snobacktrackFoldFromPair(sequence: cstring; i: cint; j: cint): cstring {.cdecl,
importc: "snobacktrack_fold_from_pair",
.}-
proc alisnofold(strings: cstringArray; maxAssym: cint; threshloop: cint; minS2: cint;
maxS2: cint; halfStem: cint; maxHalfStem: cint): cfloat {.cdecl,
importc: "alisnofold",
.}-
proc alisnofreeArrays(length: cint) {.cdecl, importc: "alisnofree_arrays",
.}-
proc alisnobacktrackFoldFromPair(sequence: cstringArray; i: cint; j: cint;
cov: ptr cint): cstring {.cdecl,
importc: "alisnobacktrack_fold_from_pair",
.}-
proc snoopfold(s1: cstring; s2: cstring; penalty: cint; threshloop: cint; threshLE: cint;
threshRE: cint; threshDE: cint; threshD: cint; halfStem: cint;
maxHalfStem: cint; minS2: cint; maxS2: cint; minS1: cint; maxS1: cint;
minD1: cint; minD2: cint; fullStemEnergy: cint): SnoopT {.cdecl,
importc: "snoopfold",
.}-
proc snoopSubopt(s1: cstring; s2: cstring; delta: cint; w: cint; penalty: cint;
threshloop: cint; threshLE: cint; threshRE: cint; threshDE: cint;
threshTE: cint; threshSE: cint; threshD: cint; distance: cint;
halfStem: cint; maxHalfStem: cint; minS2: cint; maxS2: cint;
minS1: cint; maxS1: cint; minD1: cint; minD2: cint; fullStemEnergy: cint): ptr SnoopT {.
cdecl, importc: "snoop_subopt",
.}-
proc lsnoopSubopt(s1: cstring; s2: cstring; delta: cint; w: cint; penalty: cint;
threshloop: cint; threshLE: cint; threshRE: cint; threshDE: cint;
threshTE: cint; threshSE: cint; threshD: cint; distance: cint;
halfStem: cint; maxHalfStem: cint; minS2: cint; maxS2: cint;
minS1: cint; maxS1: cint; minD1: cint; minD2: cint;
alignmentLength: cint; name: cstring; fullStemEnergy: cint) {.cdecl,
importc: "Lsnoop_subopt",
.}-
proc lsnoopSuboptList(s1: cstring; s2: cstring; delta: cint; w: cint; penalty: cint;
threshloop: cint; threshLE: cint; threshRE: cint; threshDE: cint;
threshTE: cint; threshSE: cint; threshD: cint; distance: cint;
halfStem: cint; maxHalfStem: cint; minS2: cint; maxS2: cint;
minS1: cint; maxS1: cint; minD1: cint; minD2: cint;
alignmentLength: cint; name: cstring; fullStemEnergy: cint) {.
cdecl, importc: "Lsnoop_subopt_list",
.}-
proc lsnoopSuboptListXS(s1: cstring; s2: cstring; accessS1: ptr ptr cint; delta: cint;
w: cint; penalty: cint; threshloop: cint; threshLE: cint;
threshRE: cint; threshDE: cint; threshTE: cint; threshSE: cint;
threshD: cint; distance: cint; halfStem: cint;
maxHalfStem: cint; minS2: cint; maxS2: cint; minS1: cint;
maxS1: cint; minD1: cint; minD2: cint; alignmentLength: cint;
name: cstring; fullStemEnergy: cint) {.cdecl,
importc: "Lsnoop_subopt_list_XS",
.}-
proc snoopSuboptXS(s1: cstring; s2: cstring; accessS1: ptr ptr cint; delta: cint; w: cint;
penalty: cint; threshloop: cint; threshLE: cint; threshRE: cint;
threshDE: cint; threshTE: cint; threshSE: cint; threshD: cint;
distance: cint; halfStem: cint; maxHalfStem: cint; minS2: cint;
maxS2: cint; minS1: cint; maxS1: cint; minD1: cint; minD2: cint;
alignmentLength: cint; name: cstring; fullStemEnergy: cint) {.cdecl,
importc: "snoop_subopt_XS",
.}-
proc alisnoopSubopt(s1: cstringArray; s2: cstringArray; delta: cint; w: cint;
penalty: cint; threshloop: cint; threshLE: cint; threshRE: cint;
threshDE: cint; threshTE: cint; threshSE: cint; threshD: cint;
distance: cint; halfStem: cint; maxHalfStem: cint; minS2: cint;
maxS2: cint; minS1: cint; maxS1: cint; minD1: cint; minD2: cint): ptr SnoopT {.
cdecl, importc: "alisnoop_subopt",
.}-
proc aliLsnoopSuboptList(s1: cstringArray; s2: cstringArray; delta: cint; w: cint;
penalty: cint; threshloop: cint; threshLE: cint;
threshRE: cint; threshDE: cint; threshTE: cint;
threshSE: cint; threshD: cint; distance: cint; halfStem: cint;
maxHalfStem: cint; minS2: cint; maxS2: cint; minS1: cint;
maxS1: cint; minD1: cint; minD2: cint; alignmentLength: cint): ptr SnoopT {.
cdecl, importc: "aliLsnoop_subopt_list",
.}-
proc alisnoopfold(s1: cstringArray; s2: cstringArray; penalty: cint; threshloop: cint;
threshLE: cint; threshRE: cint; threshDE: cint; threshD: cint;
halfStem: cint; maxHalfStem: cint; minS2: cint; maxS2: cint;
minS1: cint; maxS1: cint; minD1: cint; minD2: cint): SnoopT {.cdecl,
importc: "alisnoopfold",
.}-
proc snoopfoldXS(s1: cstring; s2: cstring; accessS1: ptr ptr cint; pos: cint;
maxPosJ: cint; penalty: cint; threshloop: cint; threshLE: cint;
threshRE: cint; threshDE: cint; threshD: cint; halfStem: cint;
maxHalfStem: cint; minS2: cint; maxS2: cint; minS1: cint; maxS1: cint;
minD1: cint; minD2: cint; fullStemEnergy: cint): SnoopT {.cdecl,
importc: "snoopfold_XS",
.}-
proc vrnaStrdupPrintf(format: cstring): cstring {.varargs, cdecl,
importc: "vrna_strdup_printf",
.}-
proc vrnaStrcatPrintf(dest: cstringArray; format: cstring): cint {.varargs, cdecl,
importc: "vrna_strcat_printf",
.}-
proc vrnaRandomString(l: cint; symbols: ptr char): cstring {.cdecl,
importc: "vrna_random_string",
.}-
proc vrnaHammingDistance(s1: cstring; s2: cstring): cint {.cdecl,
importc: "vrna_hamming_distance",
.}-
proc vrnaHammingDistanceBound(s1: cstring; s2: cstring; n: cint): cint {.cdecl,
importc: "vrna_hamming_distance_bound",
.}-
proc vrnaSeqToRNA(sequence: cstring) {.cdecl, importc: "vrna_seq_toRNA",
.}-
proc vrnaSeqToupper(sequence: cstring) {.cdecl, importc: "vrna_seq_toupper",
.}-
proc vrnaCutPointInsert(string: cstring; cp: cint): cstring {.cdecl,
importc: "vrna_cut_point_insert",
.}-
proc vrnaCutPointRemove(string: cstring; cp: ptr cint): cstring {.cdecl,
importc: "vrna_cut_point_remove",
.}-
proc makeSwString(string: cstring): ptr SwString {.cdecl, importc: "Make_swString",
.}-
proc stringEditDistance(t1: ptr SwString; t2: ptr SwString): cfloat {.cdecl,
importc: "string_edit_distance",
.}-
proc vrnaDbPack(struc: cstring): cstring {.cdecl, importc: "vrna_db_pack",
.}-
proc vrnaDbUnpack(packed: cstring): cstring {.cdecl, importc: "vrna_db_unpack",
.}-
proc vrnaPtable(structure: cstring): ptr cshort {.cdecl, importc: "vrna_ptable",
.}-
proc vrnaPtPkGet(structure: cstring): ptr cshort {.cdecl, importc: "vrna_pt_pk_get",
.}-
proc vrnaPtableCopy(pt: ptr cshort): ptr cshort {.cdecl, importc: "vrna_ptable_copy",
.}-
proc vrnaPtAliGet(structure: cstring): ptr cshort {.cdecl, importc: "vrna_pt_ali_get",
.}-
proc vrnaPtSnoopGet(structure: cstring): ptr cshort {.cdecl,
importc: "vrna_pt_snoop_get",
.}-
proc vrnaLoopidxFromPtable(pt: ptr cshort): ptr cint {.cdecl,
importc: "vrna_loopidx_from_ptable",
.}-
proc vrnaDbFromPtable(pt: ptr cshort): cstring {.cdecl,
importc: "vrna_db_from_ptable",
.}-
proc vrnaBpDistance(str1: cstring; str2: cstring): cint {.cdecl,
importc: "vrna_bp_distance",
.}-
proc vrnaRefBPcntMatrix(referencePt: ptr cshort; turn: cuint): ptr cuint {.cdecl,
importc: "vrna_refBPcnt_matrix",
.}-
proc vrnaRefBPdistMatrix(pt1: ptr cshort; pt2: ptr cshort; turn: cuint): ptr cuint {.cdecl,
importc: "vrna_refBPdist_matrix",
.}-
proc vrnaDbFromProbs(pr: ptr Flt_Or_Dbl; length: cuint): cstring {.cdecl,
importc: "vrna_db_from_probs",
.}-
proc vrnaBppSymbol(x: ptr cfloat): char {.cdecl, importc: "vrna_bpp_symbol",
.}-
proc vrnaDbFromBpStack(bp: ptr VrnaBpStackT; length: cuint): cstring {.cdecl,
importc: "vrna_db_from_bp_stack",
.}-
proc vrnaLetterStructure(structure: cstring; bp: ptr VrnaBpStackT; length: cuint) {.
cdecl, importc: "vrna_letter_structure",
.}-
proc vrnaPlist(struc: cstring; pr: cfloat): ptr VrnaPlistT {.cdecl,
importc: "vrna_plist",
.}-
proc vrnaPlistFromProbs(vc: ptr VrnaFoldCompoundT; cutOff: cdouble): ptr VrnaPlistT {.
cdecl, importc: "vrna_plist_from_probs",
.}-
proc vrnaDbFromPlist(pairs: ptr VrnaPlistT; n: cuint): cstring {.cdecl,
importc: "vrna_db_from_plist",
.}-
proc vrnaDbToElementString(structure: cstring): cstring {.cdecl,
importc: "vrna_db_to_element_string",
.}-
proc vrnaHxFromPtable(pt: ptr cshort): ptr VrnaHxT {.cdecl,
importc: "vrna_hx_from_ptable",
.}-
proc vrnaHxMerge(list: ptr VrnaHxT; maxdist: cint): ptr VrnaHxT {.cdecl,
importc: "vrna_hx_merge",
.}-
proc vrnaSubopt(vc: ptr VrnaFoldCompoundT; delta: cint; sorted: cint; fp: File): ptr VrnaSuboptSolutionT {.
cdecl, importc: "vrna_subopt",
.}-
proc vrnaSuboptCb(vc: ptr VrnaFoldCompoundT; delta: cint; cb: ptr VrnaSuboptCallback;
data: pointer) {.cdecl, importc: "vrna_subopt_cb",
.}-
proc vrnaSuboptZuker(vc: ptr VrnaFoldCompoundT): ptr VrnaSuboptSolutionT {.cdecl,
importc: "vrna_subopt_zuker",
.}-
proc vrnaConvertEnergy(energy: cdouble; `from`: VrnaUnitEnergyE; to: VrnaUnitEnergyE): cdouble {.
cdecl, importc: "vrna_convert_energy",
.}-
proc vrnaConvertTemperature(temp: cdouble; `from`: VrnaUnitTemperatureE;
to: VrnaUnitTemperatureE): cdouble {.cdecl,
importc: "vrna_convert_temperature",
.}-
proc vrnaUdAddMotif(vc: ptr VrnaFoldCompoundT; motif: cstring; motifEn: cdouble;
loopType: cuint) {.cdecl, importc: "vrna_ud_add_motif",
.}-
proc vrnaUdGetMotifSizeAt(vc: ptr VrnaFoldCompoundT; i: cint; loopType: cuint): ptr cint {.
cdecl, importc: "vrna_ud_get_motif_size_at",
.}-
proc vrnaUdGetMotifsAt(vc: ptr VrnaFoldCompoundT; i: cint; loopType: cuint): ptr cint {.
cdecl, importc: "vrna_ud_get_motifs_at",
.}-
proc vrnaUdDetectMotifs(vc: ptr VrnaFoldCompoundT; structure: cstring): ptr VrnaUdMotifT {.
cdecl, importc: "vrna_ud_detect_motifs",
.}-
proc vrnaUdRemove(vc: ptr VrnaFoldCompoundT) {.cdecl, importc: "vrna_ud_remove",
.}-
proc vrnaUdSetData(vc: ptr VrnaFoldCompoundT; data: pointer;
freeCb: ptr VrnaCallbackFreeAuxdata) {.cdecl,
importc: "vrna_ud_set_data",
.}-
proc vrnaUdSetProdRuleCb(vc: ptr VrnaFoldCompoundT;
preCb: ptr VrnaCallbackUdProduction;
eCb: ptr VrnaCallbackUdEnergy) {.cdecl,
importc: "vrna_ud_set_prod_rule_cb",
.}-
proc vrnaUdSetExpProdRuleCb(vc: ptr VrnaFoldCompoundT;
preCb: ptr VrnaCallbackUdExpProduction;
expECb: ptr VrnaCallbackUdExpEnergy) {.cdecl,
importc: "vrna_ud_set_exp_prod_rule_cb",
.}-
proc vrnaUdSetProbCb(vc: ptr VrnaFoldCompoundT; setter: ptr VrnaCallbackUdProbsAdd;
getter: ptr VrnaCallbackUdProbsGet) {.cdecl,
importc: "vrna_ud_set_prob_cb",
.}-
proc vrnaAlloc(size: cuint): pointer {.cdecl, importc: "vrna_alloc",
.}-
proc vrnaRealloc(p: pointer; size: cuint): pointer {.cdecl, importc: "vrna_realloc",
.}-
proc vrnaMessageError(format: cstring) {.varargs, cdecl,
importc: "vrna_message_error",
.}-
proc vrnaMessageWarning(format: cstring) {.varargs, cdecl,
importc: "vrna_message_warning",
.}-
proc vrnaMessageInfo(fp: ptr File; format: cstring) {.varargs, cdecl,
importc: "vrna_message_info",
.}-
proc vrnaInitRand() {.cdecl, importc: "vrna_init_rand",
.}-
proc vrnaUrn(): cdouble {.cdecl, importc: "vrna_urn",
.}-
proc vrnaIntUrn(`from`: cint; to: cint): cint {.cdecl, importc: "vrna_int_urn",
.}-
proc vrnaTimeStamp(): cstring {.cdecl, importc: "vrna_time_stamp",
.}-
proc getInputLine(string: cstringArray; options: cuint): cuint {.cdecl,
importc: "get_input_line",
.}-
proc vrnaMessageInputSeqSimple() {.cdecl, importc: "vrna_message_input_seq_simple",
.}-
proc vrnaMessageInputSeq(s: cstring) {.cdecl, importc: "vrna_message_input_seq",
.}-
proc vrnaIdxRowWise(length: cuint): ptr cint {.cdecl, importc: "vrna_idx_row_wise",
.}-
proc vrnaIdxColWise(length: cuint): ptr cint {.cdecl, importc: "vrna_idx_col_wise",
.}-
