| BOOLEAN ChInStr(char *String, char Char); |
| BOOLEAN ExistsSecStr(CHAIN **Chain, int NChain); |
| BOOLEAN ExistSSBond(CHAIN **Chain,int NChain,int Cn1,int Cn2,char *Res1,char *Res2); |
| BOOLEAN IsHydrogen(char *AtomName) ; |
| BOOLEAN Specified(char **List, int ListLength, char Option); |
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| FILE *efopen(char *file, char *mode, char *progname); |
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| char **AllocAsn(CHAIN **Chain, int NChain); |
| char **CharMatrix(int M, int N); |
| char *OneToThree(char One); |
| char SpaceToDash(char Id); |
| char *Tim(void); |
| char ThreeToOne(char *Three); |
| char *tolostr(char *InputString); |
| char *Translate(char Code); |
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| double GetAtomRadius(char *AtomType); |
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| float Ang(float *Coord1, float *Coord2, float *Coord3); |
| float **DefaultHelixMap(COMMAND *Cmd); |
| float **DefaultSheetMap(COMMAND *Cmd); |
| float Dist(float *Coord1, float *Coord2); |
| float ***FloatCube(int M, int N, int K); |
| float **FloatMatrix(int M, int N); |
| float PercentCorrect(char *TestAsn, char *KnownAsn, int Length); |
| float SecStrContent(CHAIN *Chain, int *HelAlp, int *HelPI, int *Hel310, int *Sheet, int *Turn); |
| float Torsion(float *Coord1, float *Coord2, float *Coord3, float *Coord4); |
| float VectorProduct(float *Vector1, float *Vector2, float *Product); |
| float factrl(int n); |
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| int AssessCorr(QUALITY *Qual); |
| int AssessPerc(QUALITY *Qual); |
| int Boundaries(char *Asn, int L, char SecondStr, int (*Bound)[2]); |
| int CheckAtom(char *At); |
| int CheckChain(CHAIN *Chain, COMMAND *Cmd); |
| int CheckRes(char *Res); |
| int CompareElements(char *Asn1, char *Asn2, char *Asn3, int Length, |
| char SecStrType, int *Better, int *Worse); |
| int CompPdbDssp(CHAIN *Chain, DSSP *Dssp); |
| int CollectOptions(char **List, int ListLength, int Stream, int *Options); |
| int DefineAcceptor(CHAIN *Chain, ACCEPTOR **Acc, int *ac, int Res, enum HYBRID Hybrid, |
| enum GROUP Group, float HB_Radius, int N); |
| int DefineDnr(CHAIN *Chain, DONOR **Dnr, int *dc, int Res, enum HYBRID Hybrid, |
| enum GROUP Group, float HB_Radius, int N); |
| int Delete(char *String, char From); |
| int Difference(char *TestAsn, char *KnownAsn, int Length, char SecStrType, QUALITY *Qual); |
| int escape(int RetVal, char *format, ... ); |
| int FindAcc(CHAIN *Chain, ACCEPTOR **Acc, int *NAcc, COMMAND *Cmd); |
| int FindAtom(CHAIN *Chain, int ResNumb, char *Atom, int *AtNumb); |
| int FindBnd(HBOND **HBond, RESIDUE *Res1, RESIDUE *Res2); |
| int FindChain(CHAIN **Chain, int NChain, char ChainId); |
| int FindDnr(CHAIN *Chain, DONOR **Dnr, int *NDnr, COMMAND *Cmd); |
| int FindHydrogenBonds(CHAIN **Chain, int NChain, HBOND **HBond, COMMAND *Cmd); |
| int FindPolInt(HBOND **HBond, RESIDUE *Res1, RESIDUE *Res2); |
| int FullElement(char *Asn1, char *Asn2, char *Asn3, int Length, char SecStrType, |
| int ElemLength, char EditChar, int *YYN, int *NYY, int *YNN, int *NNY); |
| int GetPdbChain(CHAIN **Chain, FILE *Db, long int Start); |
| int ***IntCube(int M, int N, int K); |
| int **IntMatrix(int M, int N); |
| int Link(HBOND **HBond, CHAIN **Chain, int Cn1, int Cn2, RESIDUE *Res1_1, |
| RESIDUE *Res1_2, RESIDUE *Res2_2, RESIDUE *Res2_1, RESIDUE *CRes1, RESIDUE *CRes2, |
| float **PhiPsiMap, PATTERN **Pattern, int *NumPat, char *Text, float Treshold, |
| COMMAND *Cmd, int Test); |
| int MakeEnds(int *Beg1, int ResBeg1, int NeiBeg1, char *Beg1Cn, char ResBeg1Cn, |
| int *End1, int ResEnd1, int NeiEnd1, char ResEnd1Cn, int *Beg2, |
| int ResBeg2, int NeiBeg2, char *Beg2Cn, char ResBeg2Cn, int *End2, |
| int ResEnd2, int NeiEnd2, char ResEnd2Cn, PATTERN **Pat, int NPat); |
| int MolScript(CHAIN **Chain, int NChain, COMMAND *Cmd); |
| int Near(int Res1, int Res2, int Res3, int Res4, int Res5, int Res6, int Res7, int Res8, |
| char Cn1, char Cn2, char Cn3, char Cn4, int *DistBest, int *DistWorst); |
| int NearPar(int Res1, int Res2, int Res3, int Res4, int Res5, int Res6, int Res7, int Res8, |
| char Cn1, char Cn2, char Cn3, char Cn4, int *DistBest, int *DistWorst); |
| int NoDoubleHBond(HBOND **HBond, int NHBond); |
| int OutSeq(CHAIN **Chain, int NChain, COMMAND *Cmd); |
| int Parse(char **List, int ListLength, char *Option); |
| int PdbN2SeqN(CHAIN *Chain, char *PdbN, int *SeqN); |
| int PlaceHydrogens(CHAIN *Chain); |
| int Presnell(char *Asn1, int L1, char *Asn2, int L2, char SecStr, float Threshold, |
| float *Q2, float *O); |
| int Process_ATOM(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, |
| BOOLEAN *First_ATOM, COMMAND *Cmd); |
| int Process_COMPND(BUFFER Buffer, enum METHOD *Method); |
| int Process_ENDMDL(BUFFER Buffer, CHAIN **Chain, int *ChainNumber); |
| int Process_EXPDTA(BUFFER Buffer, enum METHOD *Method); |
| int Process_HELIX(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd); |
| int Process_JRNL(BUFFER Buffer, BOOLEAN *Published); |
| int Process_MODEL(enum METHOD *Method); |
| int Process_REMARK(BUFFER Buffer, enum METHOD *Method, float *Resolution, BOOLEAN *DsspAssigned); |
| int Process_SHEET(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd); |
| int Process_SSBOND(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd); |
| int Process_TER(BUFFER Buffer, CHAIN **Chain, int *ChainNumber); |
| int Process_TURN(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd); |
| int ReadDSSP(CHAIN **Chain, DSSP **Dssp, COMMAND *Cmd); |
| int ReadPDBFile(CHAIN **Chain, int *NChain, COMMAND *Cmd); |
| int ReadPhiPsiMap(char *MapFile, float ***PhiPsiMap, COMMAND *Cmd); |
| int Replace(char *String, char From, char To); |
| int ResInSecondStr(int ResNumb, int (*Bound)[2], int N, int *StrNumb); |
| int RightSide(int LnkA, int LnkD, int I1A, int I1D, int I2A, int I2D ); |
| int RightSide2(int L_A1, int L_D1, int LnkD, int LnkA, int I1A, int I1D, int I2A, int I2D); |
| int RightSidePar(int LnkA, int LnkD, int I1A, int I1D, int I2A, int I2D ); |
| int SplitString(char *Buffer, char **Fields, int MaxField); |
| int SSBond(CHAIN **Chain, int NChain); |
| int TorsBracket(float Torsion, float Min, float Max); |
| int TurnCondition(float Phi2,float Phi2S,float Psi2,float Psi2S, |
| float Phi3,float Phi3S,float Psi3,float Psi3S, |
| float Range1,float Range2); |
| int Uniq(char **List, int ListLength); |
| void Alias(int *D1,int *A1,int *D2,int *A2,char *D1Cn,char *A1Cn,char *D2Cn,char *A2Cn, |
| PATTERN *Pat); |
| void AllocChain(CHAIN **Chain); |
| void Area(CHAIN **Chain, int NChain, COMMAND *Cmd); |
| void BackboneAngles(CHAIN **Chain, int NChain); |
| void BetaTurn(CHAIN **Chain, int Cn); |
| void Bridge(char *Asn1, char *Asn2, CHAIN **Chain, int Cn1, int Cn2, PATTERN **Pat, int NPat); |
| void *ckalloc(size_t bytes); |
| void ContactOrder(CHAIN **Chain, int NChain, COMMAND *Cmd); |
| void ContactMap(CHAIN **Chain, int NChain, COMMAND *Cmd); |
| void CorrectAsn(char *Asn, int Length, char SecStrType, char EditChar, int MaxLength); |
| void CorrectAsnDouble(char *Asn1, char *Asn2, char *KnownAsn, int Length, |
| char SecStrType, char EditChar); |
| void DeallocAcc(DONOR **Acc, int AccNumber); |
| void DeallocDnr(DONOR **Dnr, int DonNumber); |
| void DefaultCmd(COMMAND *Cmd); |
| void die(char *format, ... ); |
| void DiscrPhiPsi(CHAIN **Chain, int NChain, COMMAND *Cmd); |
| void DistMatrix(CHAIN *Chain); |
| void DSSP_Energy(float *Dummy, float *C, float *O, float *H, float *N, COMMAND *Cmd, |
| HBOND *HBond); |
| void ExcludeObvious(char *Asn1, char *Asn2, char *KnownAsn, int Length); |
| void ExtractAsn(CHAIN **Chain, int Cn, char *Asn); |
| void ExtractPdbAsn(CHAIN **Chain, int Cn, char *Asn); |
| void ExtractDsspAsn(CHAIN **Chain, int Cn, char *Asn); |
| void FillAsnAntiPar(char *Asn1, char *Asn2, CHAIN **Chain, int Cn1, int Cn2, |
| PATTERN **Pat, int NPat, COMMAND *Cmd); |
| void FillAsnPar(char *Asn1, char *Asn2, CHAIN **Chain, int Cn1, int Cn2, |
| PATTERN **Pat, int NPat, COMMAND *Cmd); |
| void FilterAntiPar(PATTERN **Pat, int NPat); |
| void FilterPar(PATTERN **Pat, int NPat); |
| void FreeCharMatrix(char **Matrix, int M); |
| void FreeFloatMatrix(float **Matrix, int M); |
| void FreeIntMatrix(int **Matrix, int M); |
| void GammaTurn(CHAIN **Chain, int Cn, HBOND **HBond); |
| void GetFileNameFromPath(char *Path, char *FileName); |
| void GetDsspAsn(CHAIN **Chain, int NChain, COMMAND *Cmd); |
| void GetPdbAsn(CHAIN **Chain, int NChain); |
| void Glue(char *String1, char *String2, FILE *Out); |
| void GRID_Energy(float *CA2, float *C, float *O, float *H, float *N, COMMAND *Cmd, HBOND *HBond); |
| void Helix(CHAIN **Chain, int Cn, HBOND **HBond, COMMAND *Cmd, float **PhiPsiMap); |
| void HBondToBins(HBOND **HBond, int NHBond, COMMAND *Cmd); |
| void InitAsn(CHAIN **Chain, int NChain); |
| void InitChain(CHAIN **Chain); |
| void InsertFirst(DSSP *Dssp, CHAIN *Chain); |
| void InsertLast(DSSP *Dssp, CHAIN *Chain); |
| void JoinNeighb(PATTERN **Nei, PATTERN *Pat, int *MinDB2, int DB, int *MinDW2, int DW); |
| void JoinNeighbours(int *Lnk1A, int Res1, int *Lnk1D, int Res2, PATTERN **Nei, |
| PATTERN *Pat, int *MinDB1, int DB, int *MinDW1, int DW, int *Min, int j); |
| void Measure(CHAIN **Chain, int NChain, int El, COMMAND *Cmd, FILE *Out); |
| void MergePatternsPar(PATTERN **Pat, int NPat); |
| void MergePatternsAntiPar(PATTERN **Pat, int NPat); |
| int NotValid(CHAIN *Chain, char *Message); |
| void OMEGA(CHAIN *Chain, int Res); |
| void PHI(CHAIN *Chain, int Res); |
| void Place123_X(float *Coord1, float *Coord2, float *Coord3, float Dist3X, float Ang23X, |
| float *CoordX); |
| void PrepareBuffer(BUFFER Bf, CHAIN **Chain); |
| void PrintHydrBond(char *Text, HBOND *HBond); |
| void PrintPatterns(PATTERN **Pat, int NPat, CHAIN **Chain, int Cn1, int Cn2); |
| void PrintStrideHelp(COMMAND *Cmd); |
| void ProcessStrideOptions(char **List, int ListLength, COMMAND *Cmd); |
| void Project4_123(float *Coord1, float *Coord2, float *Coord3, float *Coord4, |
| float *Coord_Proj4_123); |
| void PSI(CHAIN *Chain, int Res); |
| void Report(CHAIN **Chain, int NChain, HBOND **HBond, COMMAND *Cmd); |
| void ReportDetailed(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd); |
| void ReportGeneral(CHAIN **Chain, FILE *Out); |
| void ReportHydrBonds(CHAIN **Chain, int NChain, HBOND **HBond, |
| FILE *Out, COMMAND *Cmd); |
| void ReportShort(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd); |
| void ReportSSBonds(CHAIN **Chain, FILE *Out); |
| void ReportSummary(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd); |
| void ReportTurnTypes(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd); |
| void Sheet(CHAIN **Chain, int Cn1, int Cn2, HBOND **HBond, COMMAND *Cmd, float **PhiPsiMap); |
| void StringSort(char **Strings, int left, int right, int StrLen); |
| void StripPathFromLastExtention(char *Path, char *StrippedPath); |
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