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214 lines
11 KiB
C
214 lines
11 KiB
C
/*
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* Copyright (C) 1992-1994 Dmitrij Frishman <d.frishman at wzw.tum.de>
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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* THE SOFTWARE.
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*/
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BOOLEAN ChInStr(char *String, char Char);
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BOOLEAN ExistsSecStr(CHAIN **Chain, int NChain);
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BOOLEAN ExistSSBond(CHAIN **Chain,int NChain,int Cn1,int Cn2,char *Res1,char *Res2);
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BOOLEAN IsHydrogen(char *AtomName) ;
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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);
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char **CharMatrix(int M, int N);
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char *OneToThree(char One);
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char SpaceToDash(char Id);
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char *Tim(void);
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char ThreeToOne(char *Three);
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char *tolostr(char *InputString);
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char *Translate(char Code);
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double GetAtomRadius(char *AtomType);
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float Ang(float *Coord1, float *Coord2, float *Coord3);
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float **DefaultHelixMap(COMMAND *Cmd);
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float **DefaultSheetMap(COMMAND *Cmd);
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float Dist(float *Coord1, float *Coord2);
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float ***FloatCube(int M, int N, int K);
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float **FloatMatrix(int M, int N);
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float PercentCorrect(char *TestAsn, char *KnownAsn, int Length);
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float SecStrContent(CHAIN *Chain, int *HelAlp, int *HelPI, int *Hel310, int *Sheet, int *Turn);
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float Torsion(float *Coord1, float *Coord2, float *Coord3, float *Coord4);
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float VectorProduct(float *Vector1, float *Vector2, float *Product);
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float factrl(int n);
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int AssessCorr(QUALITY *Qual);
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int AssessPerc(QUALITY *Qual);
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int Boundaries(char *Asn, int L, char SecondStr, int (*Bound)[2]);
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int CheckAtom(char *At);
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int CheckChain(CHAIN *Chain, COMMAND *Cmd);
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int CheckRes(char *Res);
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int CompareElements(char *Asn1, char *Asn2, char *Asn3, int Length,
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char SecStrType, int *Better, int *Worse);
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int CompPdbDssp(CHAIN *Chain, DSSP *Dssp);
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int CollectOptions(char **List, int ListLength, int Stream, int *Options);
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int DefineAcceptor(CHAIN *Chain, ACCEPTOR **Acc, int *ac, int Res, enum HYBRID Hybrid,
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enum GROUP Group, float HB_Radius, int N);
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int DefineDnr(CHAIN *Chain, DONOR **Dnr, int *dc, int Res, enum HYBRID Hybrid,
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enum GROUP Group, float HB_Radius, int N);
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int Delete(char *String, char From);
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int Difference(char *TestAsn, char *KnownAsn, int Length, char SecStrType, QUALITY *Qual);
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int escape(int RetVal, char *format, ... );
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int FindAcc(CHAIN *Chain, ACCEPTOR **Acc, int *NAcc, COMMAND *Cmd);
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int FindAtom(CHAIN *Chain, int ResNumb, char *Atom, int *AtNumb);
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int FindBnd(HBOND **HBond, RESIDUE *Res1, RESIDUE *Res2);
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int FindChain(CHAIN **Chain, int NChain, char ChainId);
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int FindDnr(CHAIN *Chain, DONOR **Dnr, int *NDnr, COMMAND *Cmd);
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int FindHydrogenBonds(CHAIN **Chain, int NChain, HBOND **HBond, COMMAND *Cmd);
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int FindPolInt(HBOND **HBond, RESIDUE *Res1, RESIDUE *Res2);
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int FullElement(char *Asn1, char *Asn2, char *Asn3, int Length, char SecStrType,
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int ElemLength, char EditChar, int *YYN, int *NYY, int *YNN, int *NNY);
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int GetPdbChain(CHAIN **Chain, FILE *Db, long int Start);
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int ***IntCube(int M, int N, int K);
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int **IntMatrix(int M, int N);
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int Link(HBOND **HBond, CHAIN **Chain, int Cn1, int Cn2, RESIDUE *Res1_1,
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RESIDUE *Res1_2, RESIDUE *Res2_2, RESIDUE *Res2_1, RESIDUE *CRes1, RESIDUE *CRes2,
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float **PhiPsiMap, PATTERN **Pattern, int *NumPat, char *Text, float Treshold,
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COMMAND *Cmd, int Test);
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int MakeEnds(int *Beg1, int ResBeg1, int NeiBeg1, char *Beg1Cn, char ResBeg1Cn,
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int *End1, int ResEnd1, int NeiEnd1, char ResEnd1Cn, int *Beg2,
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int ResBeg2, int NeiBeg2, char *Beg2Cn, char ResBeg2Cn, int *End2,
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int ResEnd2, int NeiEnd2, char ResEnd2Cn, PATTERN **Pat, int NPat);
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int MolScript(CHAIN **Chain, int NChain, COMMAND *Cmd);
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int Near(int Res1, int Res2, int Res3, int Res4, int Res5, int Res6, int Res7, int Res8,
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char Cn1, char Cn2, char Cn3, char Cn4, int *DistBest, int *DistWorst);
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int NearPar(int Res1, int Res2, int Res3, int Res4, int Res5, int Res6, int Res7, int Res8,
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char Cn1, char Cn2, char Cn3, char Cn4, int *DistBest, int *DistWorst);
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int NoDoubleHBond(HBOND **HBond, int NHBond);
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int OutSeq(CHAIN **Chain, int NChain, COMMAND *Cmd);
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int Parse(char **List, int ListLength, char *Option);
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int PdbN2SeqN(CHAIN *Chain, char *PdbN, int *SeqN);
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int PlaceHydrogens(CHAIN *Chain);
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int Presnell(char *Asn1, int L1, char *Asn2, int L2, char SecStr, float Threshold,
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float *Q2, float *O);
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int Process_ATOM(BUFFER Buffer, CHAIN **Chain, int *ChainNumber,
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BOOLEAN *First_ATOM, COMMAND *Cmd);
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int Process_COMPND(BUFFER Buffer, enum METHOD *Method);
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int Process_ENDMDL(BUFFER Buffer, CHAIN **Chain, int *ChainNumber);
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int Process_EXPDTA(BUFFER Buffer, enum METHOD *Method);
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int Process_HELIX(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd);
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int Process_JRNL(BUFFER Buffer, BOOLEAN *Published);
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int Process_MODEL(enum METHOD *Method);
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int Process_REMARK(BUFFER Buffer, enum METHOD *Method, float *Resolution, BOOLEAN *DsspAssigned);
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int Process_SHEET(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd);
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int Process_SSBOND(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd);
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int Process_TER(BUFFER Buffer, CHAIN **Chain, int *ChainNumber);
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int Process_TURN(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd);
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int ReadDSSP(CHAIN **Chain, DSSP **Dssp, COMMAND *Cmd);
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int ReadPDBFile(CHAIN **Chain, int *NChain, COMMAND *Cmd);
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int ReadPhiPsiMap(char *MapFile, float ***PhiPsiMap, COMMAND *Cmd);
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int Replace(char *String, char From, char To);
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int ResInSecondStr(int ResNumb, int (*Bound)[2], int N, int *StrNumb);
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int RightSide(int LnkA, int LnkD, int I1A, int I1D, int I2A, int I2D );
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int RightSide2(int L_A1, int L_D1, int LnkD, int LnkA, int I1A, int I1D, int I2A, int I2D);
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int RightSidePar(int LnkA, int LnkD, int I1A, int I1D, int I2A, int I2D );
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int SplitString(char *Buffer, char **Fields, int MaxField);
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int SSBond(CHAIN **Chain, int NChain);
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int TorsBracket(float Torsion, float Min, float Max);
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int TurnCondition(float Phi2,float Phi2S,float Psi2,float Psi2S,
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float Phi3,float Phi3S,float Psi3,float Psi3S,
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float Range1,float Range2);
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int Uniq(char **List, int ListLength);
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void Alias(int *D1,int *A1,int *D2,int *A2,char *D1Cn,char *A1Cn,char *D2Cn,char *A2Cn,
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PATTERN *Pat);
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void AllocChain(CHAIN **Chain);
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void Area(CHAIN **Chain, int NChain, COMMAND *Cmd);
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void BackboneAngles(CHAIN **Chain, int NChain);
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void BetaTurn(CHAIN **Chain, int Cn);
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void Bridge(char *Asn1, char *Asn2, CHAIN **Chain, int Cn1, int Cn2, PATTERN **Pat, int NPat);
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void *ckalloc(size_t bytes);
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void ContactOrder(CHAIN **Chain, int NChain, COMMAND *Cmd);
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void ContactMap(CHAIN **Chain, int NChain, COMMAND *Cmd);
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void CorrectAsn(char *Asn, int Length, char SecStrType, char EditChar, int MaxLength);
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void CorrectAsnDouble(char *Asn1, char *Asn2, char *KnownAsn, int Length,
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char SecStrType, char EditChar);
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void DeallocAcc(DONOR **Acc, int AccNumber);
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void DeallocDnr(DONOR **Dnr, int DonNumber);
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void DefaultCmd(COMMAND *Cmd);
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void die(char *format, ... );
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void DiscrPhiPsi(CHAIN **Chain, int NChain, COMMAND *Cmd);
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void DistMatrix(CHAIN *Chain);
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void DSSP_Energy(float *Dummy, float *C, float *O, float *H, float *N, COMMAND *Cmd,
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HBOND *HBond);
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void ExcludeObvious(char *Asn1, char *Asn2, char *KnownAsn, int Length);
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void ExtractAsn(CHAIN **Chain, int Cn, char *Asn);
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void ExtractPdbAsn(CHAIN **Chain, int Cn, char *Asn);
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void ExtractDsspAsn(CHAIN **Chain, int Cn, char *Asn);
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void FillAsnAntiPar(char *Asn1, char *Asn2, CHAIN **Chain, int Cn1, int Cn2,
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PATTERN **Pat, int NPat, COMMAND *Cmd);
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void FillAsnPar(char *Asn1, char *Asn2, CHAIN **Chain, int Cn1, int Cn2,
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PATTERN **Pat, int NPat, COMMAND *Cmd);
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void FilterAntiPar(PATTERN **Pat, int NPat);
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void FilterPar(PATTERN **Pat, int NPat);
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void FreeCharMatrix(char **Matrix, int M);
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void FreeFloatMatrix(float **Matrix, int M);
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void FreeIntMatrix(int **Matrix, int M);
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void GammaTurn(CHAIN **Chain, int Cn, HBOND **HBond);
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void GetFileNameFromPath(char *Path, char *FileName);
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void GetDsspAsn(CHAIN **Chain, int NChain, COMMAND *Cmd);
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void GetPdbAsn(CHAIN **Chain, int NChain);
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void Glue(char *String1, char *String2, FILE *Out);
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void GRID_Energy(float *CA2, float *C, float *O, float *H, float *N, COMMAND *Cmd, HBOND *HBond);
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void Helix(CHAIN **Chain, int Cn, HBOND **HBond, COMMAND *Cmd, float **PhiPsiMap);
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void HBondToBins(HBOND **HBond, int NHBond, COMMAND *Cmd);
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void InitAsn(CHAIN **Chain, int NChain);
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void InitChain(CHAIN **Chain);
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void InsertFirst(DSSP *Dssp, CHAIN *Chain);
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void InsertLast(DSSP *Dssp, CHAIN *Chain);
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void JoinNeighb(PATTERN **Nei, PATTERN *Pat, int *MinDB2, int DB, int *MinDW2, int DW);
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void JoinNeighbours(int *Lnk1A, int Res1, int *Lnk1D, int Res2, PATTERN **Nei,
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PATTERN *Pat, int *MinDB1, int DB, int *MinDW1, int DW, int *Min, int j);
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void Measure(CHAIN **Chain, int NChain, int El, COMMAND *Cmd, FILE *Out);
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void MergePatternsPar(PATTERN **Pat, int NPat);
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void MergePatternsAntiPar(PATTERN **Pat, int NPat);
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int NotValid(CHAIN *Chain, char *Message);
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void OMEGA(CHAIN *Chain, int Res);
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void PHI(CHAIN *Chain, int Res);
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void Place123_X(float *Coord1, float *Coord2, float *Coord3, float Dist3X, float Ang23X,
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float *CoordX);
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void PrepareBuffer(BUFFER Bf, CHAIN **Chain);
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void PrintHydrBond(char *Text, HBOND *HBond);
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void PrintPatterns(PATTERN **Pat, int NPat, CHAIN **Chain, int Cn1, int Cn2);
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void PrintStrideHelp(COMMAND *Cmd);
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void ProcessStrideOptions(char **List, int ListLength, COMMAND *Cmd);
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void Project4_123(float *Coord1, float *Coord2, float *Coord3, float *Coord4,
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float *Coord_Proj4_123);
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void PSI(CHAIN *Chain, int Res);
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void Report(CHAIN **Chain, int NChain, HBOND **HBond, COMMAND *Cmd);
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void ReportDetailed(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd);
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void ReportGeneral(CHAIN **Chain, FILE *Out);
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void ReportHydrBonds(CHAIN **Chain, int NChain, HBOND **HBond,
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FILE *Out, COMMAND *Cmd);
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void ReportShort(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd);
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void ReportSSBonds(CHAIN **Chain, FILE *Out);
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void ReportSummary(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd);
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void ReportTurnTypes(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd);
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void Sheet(CHAIN **Chain, int Cn1, int Cn2, HBOND **HBond, COMMAND *Cmd, float **PhiPsiMap);
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void StringSort(char **Strings, int left, int right, int StrLen);
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void StripPathFromLastExtention(char *Path, char *StrippedPath);
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