/* SeqCalc.h						David Wagner */
/* This program attempts to calculate a sequence of amino acids    */
/* that may form a protein given information about its main chain. */
/* This is similar to the problem addressed by Mayo in his paper   */
/* He uses an energy function, but here we will use statistical    */
/* data to derive a Hidden Markov Model for the sequence.          */
/* At the start of this experiment, I do not know if this model    */
/* is applicable.  Thus the primary objective is to determine if   */
/* this model is useful for solving this problem.                  */

#define  ALA  0
#define  CYS  1
#define  ASP  2
#define  GLU  3
#define  PHE  4
#define  GLY  5
#define  HIS  6
#define  ILE  7
#define  LYS  8
#define  LEU  9
#define  MET  10
#define  ASN  11
#define  PRO  12
#define  GLN  13
#define  ARG  14
#define  SER  15
#define  THR  16
#define  VAL  17
#define  TRP  18
#define  TYR  19

#define NUMRESTYPES 20
#define NUMPHIANGLES 20
#define NUMPSIANGLES 20

#define PR_NAME 0
#define PR_PHI 1
#define PR_PSI 2
#define PR_BETA 3
#define PR_PRED 4

#define CM_REPORT 0
#define CM_TRAIN 1
#define CM_PREDICT 2

#define TRAINING_FILE "trainHMM.txt"

#define START_NODE_NUM 20

typedef char boolean;

typedef struct atomLoc {
	double x;
	double y;
	double z;
} AtomLoc;

typedef struct aaInfo {
        int aaType;
        char aaCode[4];
        int predictedType;

        AtomLoc N;
        AtomLoc CA;
        AtomLoc C;
        AtomLoc O;
        AtomLoc CB;

	boolean Nbool;
	boolean CAbool;
	boolean Cbool;
	boolean Obool;
	boolean CBbool;

        double psi;     // The angle between the two surrounding N's
        double phi;     // The angle between the two surrounding C's
        double beta;    // An angle I invented to represent whether the
                        // C-beta points toward the center, hopefully
                        // this is a measure of hydrophobicity

        struct aaInfo* next;
        struct aaInfo* prev;
} AAInfo;

typedef struct aaChain {
        AAInfo* aaChainHead;
        AAInfo* aaChainTail;
        struct aaChain* next;
} AAChain;


typedef struct node {
	double prob[NUMPSIANGLES][NUMPHIANGLES];
	int total[NUMPSIANGLES][NUMPHIANGLES];
} Node;

typedef struct edge {
	int start;
	int end;
	double prob;
	int total;
} Edge;

typedef struct hmm {
	Node nodeList[NUMRESTYPES+1];
	Edge edgeList[NUMRESTYPES+1][NUMRESTYPES];
} HMM;

	

FILE* openfile(char* filename);
int countAtoms(FILE* fname);

void parseLines(FILE *fname);
void parseLine(char * theLine, int residueNum);

void addAtom(char *atomName, int residueNum, char chainID, int resSeqNum, 
		                double x, double y, double z);
void addChain(AAChain ** currChain);
void addResidue(AAInfo ** currAA, AAChain * currChain);
void addAtomInfo(AAInfo * currAA, char * atomName, int residueNum, 
			double x, double y, double z);
void addPrevAtomAngles(AAInfo * currAA);

void trainChains(FILE * fname);
void trainChain(FILE * fname, AAChain * theChain);
void trainAAInfo(FILE * fname, AAInfo * theInfo);

void printChains();
void printChain(AAChain * theChain, int item);
void printAAInfo(AAInfo * theInfo, int item);
void printAACode(AAInfo * theInfo);

double findAngle(AtomLoc * p1, AtomLoc * p2, AtomLoc * p3, AtomLoc * p4);

void initHMM();
void trainHMM(FILE * fname);
void adjustHMM();
void printHMM();

void runViterbi(AAChain * theChain);