/*
 * Copyright (C) 1992-1994 Dmitrij Frishman <d.frishman at wzw.tum.de>
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 * 
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */


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);

FILE *efopen(char *file, char *mode, char *progname);

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);

double GetAtomRadius(char *AtomType);

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);

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);