# undef _I_I_I_I /* +++++++++ */ # define _I_I_I_I "pdbio.c" /* +++++++++ */ /* ======= */ int nrd_pdb /* ======= */ (FILE *stream, PDB_data *P, double xx[], double yy[], double zz[]) ; /* ====== */ int rd_pdb /* ====== */ (FILE *stream, int iser[], char atnam[][5], char resnam[][5], char chnnam[], int iresn[], double xx[], double yy[], double zz[], double occ[], double b[], char segid[][5]) ; /* ======== */ void pdbdebug /* ======== */ (int iser[], char atnam[][5], char resnam[][5], char chnnam[], int iresn[], double xx[], double yy[], double zz[], double occ[], double b[], char segid[][5], int natom, char *buf) ; /* =========== */ void nprt_pdbrec /* =========== */ (PDB_data *P,double xx[], double yy[], double zz[],int i) ; /* ======== */ void nwrt_pdb /* ======== */ (FILE *stream, PDB_data *P, double xx[], double yy[], double zz[]) ; /* ======== */ void nwrt_dia /* ======== */ (FILE *stream, PDB_data *P, double xx[], double yy[], double zz[]) ; /* ======= */ void wrt_pdb /* ======= */ (FILE *stream, int iser[], char atnam[][5], char resnam[][5], char chnnam[], int iresn[], double xx[], double yy[], double zz[], double occ[], double b[], char segid[][5], int natom) ; /* =========== */ void nwrt_pdbsel /* =========== */ (FILE *stream, PDB_data *P, double xx[], double yy[], double zz[], int sel[]) ; /* ========== */ void wrt_pdbsel /* ========== */ (FILE *stream, int iser[], char atnam[][5], char resnam[][5], char chnnam[], int iresn[], double xx[], double yy[], double zz[], double occ[], double b[], char segid[][5], int natom, int sel[]) ; /* ============= */ int SimpleWrtAtom /* ============= */ (FILE *stream, int iresn, double v[3]) ; /* ============== */ int SimpleWrtAtom2 /* ============== */ (FILE *stream, int iresn, char * resnam, double v[3]) ; /* ======= */ int Nselect (PDB_data *P,int sel[]) /* ======= */ ; /* ========== */ void pdb_select(int argc, char *argv[]) /* ========== */ ; /* ================ */ void pdb2vectcentroid (int argc, char *argv[]) /* ================ */ ; # undef _I_I_I_I /* ++++++++ */ # define _I_I_I_I "util.c" /* ++++++++ */ /* ==== */ void swap (char * a, char * b,int s) /* ==== */ ; /* ==== */ int push (char * a, int s) /* ==== */ ; /* === */ int pop (char * a, int s) /* === */ ; /* ==== */ double ranf(double from, double to) /* ==== */ ; /* ========= */ void old_fillarray(double *arr, double *arrn, double v) /* ========= */ ; /* ========= */ void fillarray (double arr[], const int size, const double v) /* ========= */ ; /* ================ */ void sleep_while_file (char stopfile[], int sleeptime) /* ================ */ ; /* ======== */ void prt_time (FILE *stream) /* ======== */ ; # undef _I_I_I_I /* +++++++++++ */ # define _I_I_I_I "hohvect.c" /* +++++++++++ */ /* ========= */ int mkfrathoh /* ========= */ (int NATOM, int WATBEG, int WATEND, int freeat[]) ; /* ======== */ void pdbtohoh(int i, double xx[], double yy[], double zz[], Water_ptr hoh) /* ======== */ ; /* ======== */ void hohtopdb(int i, double xx[], double yy[], double zz[], Water_ptr hoh) /* ======== */ ; /* ======= */ void hoh2xyz /* ======= */ (Water *hoharr,int watbeg, int watend, double xx[], double yy[], double zz[]) ; /* ======= */ void xyz2hoh /* ======= */ (Water *hoharr,int watbeg, int watend, double xx[], double yy[], double zz[], PDB_data *P) ; /* ============= */ void hohstereochem( vector9 hoh, vector9 bondlen) /* ============= */ ; /* ========= */ double * translate(vector9 v, vector9 u) /* ========= */ ; /* ============ */ double * vectsubtract (Vector9 v, Vector9 u) /* ============ */ ; /* ===== */ double *mkmat /* ===== */ (double rc11, double rc12, double rc13, double rc21, double rc22, double rc23, double rc31, double rc32, double rc33, Matrix R) ; /* ================ */ double *rotate_to_z_axis(Matrix R, vector9 N0) /* ================ */ ; /* ====== */ double *rotate(Matrix R, vector9 v0) /* ====== */ ; /* ======= */ double *qrotate(Vector9 Q, Vector9 v0) /* ======= */ ; /* ===== */ double *scale(vector9 v, double c) /* ===== */ ; /* ======== */ void prt_vect(vector9 v, char *name) /* ======== */ ; /* ======= */ void prt_hoh(Water v, char *name) /* ======= */ ; /* ====== */ float hypot3(float x, float y, float z) /* ====== */ ; /* ======= */ double ndistsq /* ======= */ (double xi, double yi, double zi, double xj, double yj, double zj) ; /* ========== */ void origin_rot(Matrix R, Vector9 origin, Vector9 v) /* ========== */ ; /* ======== */ double *mkrotmat(vector9 v0, double theta, vector9 R) /* ======== */ ; /* ========= */ double *xmkrotmat(vector9 v0, double theta, vector9 R) /* ========= */ ; /* =============== */ double cos_from_z_axis (const Vector9 head, const Vector9 tail) /* =============== */ ; /* ====== */ double dotcos (const Vector9 v, const Vector9 u) /* ====== */ ; /* ================== */ void hohdipole_rad_proj /* ================== */ (const int natom, double xx[], double yy[], double zz[], const int sel[], PDB_data *P, const double x0, const double y0, double rpp[]) ; /* ===== */ bool ishoh(PDB_data *P, int i0) /* ===== */ ; /* ========= */ void hohdipole(const Water hoh, Vector9 p) /* ========= */ ; /* ======= */ double *randlmn(Vector9 v) /* ======= */ ; # undef _I_I_I_I /* ++++++++++++++++ */ # define _I_I_I_I "richards_RAD.c" /* ++++++++++++++++ */ /* ========== */ int * select_all(int sel[MXPDB]) /* ========== */ ; /* ====================== */ int rd_richards_RAD_volume /* ====================== */ (FILE *stream, int ncalc[MXPDB],int i[MXPDB],int numchn[MXPDB],int numfil[MXPDB], char atm[MXPDB][10],char res3[MXPDB][10], int seqnum[MXPDB],double x[MXPDB],double y[MXPDB],double z[MXPDB], double rvdw[MXPDB],double rcov[MXPDB], double volume[MXPDB],int ns[MXPDB] ) ; /* ========================== */ void wrtsel_richards_RAD_volume /* ========================== */ (FILE *stream, int ncalc[MXPDB],int i[MXPDB],int numchn[MXPDB],int numfil[MXPDB], char atm[MXPDB][10],char res3[MXPDB][10], int seqnum[MXPDB],double x[MXPDB],double y[MXPDB],double z[MXPDB], double rvdw[MXPDB],double rcov[MXPDB], double volume[MXPDB],int ns[MXPDB], int natom, int sel[MXPDB]) ; /* ==================== */ int rd_richards_RAD_area /* ==================== */ (FILE *stream, int ncalc[MXPDB],int i[MXPDB],int numchn[MXPDB],int numfil[MXPDB], char atm[MXPDB][10],char res3[MXPDB][10], int seqnum[MXPDB],double x[MXPDB],double y[MXPDB],double z[MXPDB], double rvdw[MXPDB],double rcov[MXPDB], double aarea[MXPDB],double carea[MXPDB],double frcacc[MXPDB]) ; /* ======================== */ void wrtsel_richards_RAD_area /* ======================== */ (FILE *stream, int ncalc[MXPDB],int i[MXPDB],int numchn[MXPDB],int numfil[MXPDB], char atm[MXPDB][10],char res3[MXPDB][10], int seqnum[MXPDB],double x[MXPDB],double y[MXPDB],double z[MXPDB], double rvdw[MXPDB],double rcov[MXPDB], double aarea[MXPDB],double carea[MXPDB],double frcacc[MXPDB], int natom, int sel[MXPDB]) ; /* =============== */ int sum_per_residue /* =============== */ (int seqnum[MXPDB],double prop[MXPDB],int natom,double sum_out[MXPDB]) ; /* ======================== */ int sum_per_residue_prop1000 /* ======================== */ (int seqnum[MXPDB],double prop[MXPDB],int natom,double sum_out[MXPDB]) ; # undef _I_I_I_I /* ++++++++++ */ # define _I_I_I_I "nrvect.c" /* ++++++++++ */ /* ========== */ void FreeVector(double v[3]) /* ========== */ ; /* =========== */ void dump_matrix (double ** m) /* =========== */ ; /* ========= */ double * argv2dvect (int *argc, char ***argv,char *s) /* ========= */ ; /* ====================== */ double ** rotate_v_around_z_to_x (double * u) /* ====================== */ ; /* ===================== */ double * direction_from_2vects (double * nterm,double * cterm) /* ===================== */ ; /* ========= */ double * normalize (double * u) /* ========= */ ; /* ====== */ double * nrcopy (double * u) /* ====== */ ; /* ===== */ double * nrsum (double * v, double * u) /* ===== */ ; /* ======== */ double * midpoint (double * v, double * u) /* ======== */ ; /* ======= */ double * nrscale (double a, double * u) /* ======= */ ; /* ===== */ double * nrrot (double ** R, double * u) /* ===== */ ; /* ========= */ double ** matmult33 (double ** R, double ** S) /* ========= */ ; /* ========== */ double ** nrmkrotmat (double * v0, double theta) /* ========== */ ; /* =================== */ double ** nr_rotate_to_z_axis (double * N0) /* =================== */ ; /* =========== */ void dump_vector (double * v) /* =========== */ ; /* ===================== */ void GraphicsVector3dCross (double * v, double L) /* ===================== */ ; /* ========================= */ void GraphicsVectorKludgeArrow (double * v, double *u) /* ========================= */ ; /* ================ */ void graphics_vectors (double * v, double * u) /* ================ */ ; /* =========== */ void atom_vector /* =========== */ (double * v, char * resnam, int iresn, double b) ; /* ============== */ double angle_on_plane (double * norm, double * u, double * v) /* ============== */ ; /* ============= */ double dist_on_plane (double * norm, double * u, double * v) /* ============= */ ; /* ================= */ double * second_from_first (double * u, double * v) /* ================= */ ; /* ==== */ double * vect (double a, double b, double c) /* ==== */ ; /* ================== */ double * ProjectPtToSegment (double * Pt, double * Seg1,double * Seg2) /* ================== */ ; /* ==== */ bool nreq (double * v, double * w) /* ==== */ ; /* ========= */ double ** PtsOnLine (double * u, double * v, int n) /* ========= */ ; # undef _I_I_I_I /* +++++++++ */ # define _I_I_I_I "myawk.c" /* +++++++++ */ /* =================== */ FILE * NarrowFileBetwStrgs(FILE * in, char * s1, char * s2) /* =================== */ ; /* ===== */ bool StrEq (char * a, char * b) /* ===== */ ; /* ========== */ char * SaveString (char * s) /* ========== */ ; /* ========== */ TokenizeData * InitTokens (TokenizeData * d, char * filename) /* ========== */ ; /* ========= */ bool InitLexer (TokenizeData * d) /* ========= */ ; /* ====================== */ char * ConvertUnixControlChar(char * s) /* ====================== */ ; /* =============== */ int StreqWithSpaces(const char * s1, const char * s2) /* =============== */ ; /* ============= */ char * StringOfIndex (int i, StringIndex ** SI) /* ============= */ ; /* =============== */ char * fgets_WithDelim(char *s,int n, FILE * iop, char ws[]) /* =============== */ ; /* ============= */ int IndexOfString(char s[], StringIndex ** SIP) /* ============= */ ; /* ================= */ int LastIndexOfString(StringIndex * SI) /* ================= */ ; /* ============== */ bool InSymbolTableP (char * s, StringIndex * SI) /* ============== */ ; /* ===================== */ int SymbolTableIndexNoAdd (char * s, StringIndex * SI) /* ===================== */ ; /* =================== */ void PrintIndexedStrings(StringIndex * SI) /* =================== */ ; /* =========== */ void PrintTokens(char * T[],FILE *stream) /* =========== */ ; /* ============ */ void PrintTokens2(TokenizeData * d, FILE * stream) /* ============ */ ; /* ============= */ double * ToksToDoubles(char *T[], double *D) /* ============= */ ; /* ============ */ char ** TokenizeLine(TokenizeData * d) /* ============ */ ; /* ============ */ int TokenizeFile /* ============ */ (void (*function)(), TokenizeData * d) ; /* ============ */ bool TrueBetweenP(bool OnMatch, bool OffMatch, int i ) /* ============ */ ; /* ======= */ bool OnBetwP(bool OnMatch, bool OffMatch, int * flag ) /* ======= */ ; /* ================ */ bool InclusiveOnBetwP(bool OnMatch, bool OffMatch, int * flag ) /* ================ */ ; /* =========== */ bool OnBetwStrgs(TokenizeData * d, char * s1, char * s2) /* =========== */ ; /* ============ */ bool OnBetwStrgs2(TokenizeData * d, char * s1, char * s2, int n) /* ============ */ ; /* ==================== */ bool InclusiveOnBetwStrgs(TokenizeData * d, char * s1, char * s2, int n) /* ==================== */ ; /* ==================== */ bool InclusiveOnAfterStrg(TokenizeData * d, char * s1) /* ==================== */ ; /* ===================== */ bool InclusiveTrueBetweenP(bool OnMatch, bool OffMatch, int i ) /* ===================== */ ; # undef _I_I_I_I /* +++++++++++++++++ */ # define _I_I_I_I "HandleOptions.c" /* +++++++++++++++++ */ /* =============== */ char * ReturnArgvMatch(int argc, char ** argv, char *Option) /* =============== */ ; /* ========= */ int ArgvMatch(int argc, char ** argv, char *Option) /* ========= */ ; /* =============== */ FILE * FileAfterOption /* =============== */ (int argc, char ** argv, char * Option, char * TheDefault, char * type) ; /* ================= */ char * StringAfterOption /* ================= */ (int argc, char ** argv, char * Option, char * TheDefault) ; /* ================= */ double DoubleAfterOption /* ================= */ (int argc, char ** argv, char * Option, double TheDefault) ; /* ================== */ char * StringAfterKeyInDB /* ================== */ (TokenizeData * d, char * key, char * TheDefault) ; /* ================== */ double DoubleAfterKeyInDB /* ================== */ (TokenizeData * d, char * key, double TheDefault) ; /* ============= */ char * GetEnvAndJoin(char *EnvVar, char *JoinTo) /* ============= */ ; /* =============== */ char * Expand1stEnvVar(char * s) /* =============== */ ;