The outage for Sunday 24th November has been cancelled.
Bioplib
Protein Structure C Library
 All Data Structures Files Functions Variables Typedefs Macros Pages
deprecated.h
Go to the documentation of this file.
1 /************************************************************************/
2 /**
3 
4  \file deprecated.h
5 
6  \version v1.5
7  \date 24.10.14
8  \brief Redirect calls to deprecated functions.
9 
10  \copyright (c) UCL / Dr. Andrew C. R. Martin 2014
11  \author Dr. Andrew C. R. Martin
12  \par
13  Institute of Structural & Molecular Biology,
14  University College London,
15  Gower Street,
16  London.
17  WC1E 6BT.
18  \par
19  andrew@bioinf.org.uk
20  andrew.martin@ucl.ac.uk
21 
22 **************************************************************************
23 
24  This code is NOT IN THE PUBLIC DOMAIN, but it may be copied
25  according to the conditions laid out in the accompanying file
26  COPYING.DOC.
27 
28  The code may be modified as required, but any modifications must be
29  documented so that the person responsible can be identified.
30 
31  The code may not be sold commercially or included as part of a
32  commercial product except as described in the file COPYING.DOC.
33 
34 **************************************************************************
35 
36  Description:
37  ============
38 
39  Allows code utilising BiopLib to compile without modification to use
40  function names with the 'bl' prefix.(The 'bl' prefix was introduced in
41  July 2014.)
42 
43  Contains prototypes for all deprecated functions.
44 
45  Contains the DEPRECATED() macro which prints a warning message when a
46  call is made to a deprecated function.
47 
48  Allows use of deprecated functions that took a single character for the
49  PDB chain identifier or insert value.
50 
51  Used by the following header files:
52 
53 - pdb.h
54 - general.h
55 - BuffInp.h
56 - ErrStack.h
57 - MathUtil.h
58 - WindIO.h
59 - aalist.h
60 - angle.h
61 - array.h
62 - cssr.h
63 - fit.h
64 - hbond.h
65 - help.h
66 - hpgl.h
67 - matrix.h
68 - parse.h
69 - plotting.h
70 - ps.h
71 - safemem.h
72 - seq.h
73 - eigen.h
74 - regression.h
75 
76 
77 \par Documentation
78  Doxygen is not set to document deprecated functions. To document
79  deprecated functions, add "deprecated" to the ENABLED SECTIONS tag in
80  the Doxygen config file:
81  bioplib/doc/doxygen/Doxyfile
82 
83 
84 **************************************************************************
85 
86 
87  Usage:
88  ======
89 
90  The deprecated.h header file is included at the end of a header file
91  with deprecated functions. This is to ensure that data structures are
92  defined _before_ the prototypes that use them are declared in
93  deprecated.h. For example, the PDB data structure must be defined
94  before declaring the prototypes for the functions returning a PDB
95  linked list.
96 
97  Prototypes for the deprecated functions for each header file are
98  enclosed within compiler directives to ensure that functions are not
99  declared using undefined data structures.
100 
101 
102 **************************************************************************
103 
104  Revision History:
105  =================
106 
107 - V1.0 07.05.14 Original By: CTP
108 - V1.1 07.07.14 Rename functions with 'bl' prefix. By: CTP
109 - V1.2 31.07.14 Rewrite of deprecation system. Moved deprecated function
110  code to deprecated.c By: CTP
111 - V1.3 14.08.14 Moved deprecated function prototypes to deprecated.h
112  By: CTP
113 - V1.4 26.08.14 Added blSetMDMScoreWeight() By: ACRM
114  PDB2Seq macros give deprecation message. By: CTP
115 - V1.5 24.10.14 Added regression and eigen By: ACRM
116  Added NODEPRECATION check
117  Added ExtractZoneSpecPDB
118 
119 *************************************************************************/
120 #ifndef NODEPRECATION
121 # ifndef _DEPRECATED_H
122 # define _DEPRECATED_H
123 
124 /* Includes
125 */
126 # include <stdio.h>
127 # include <stdlib.h>
128 # include <string.h>
129 # include "macros.h"
130 
131 
132 /************************************************************************/
133 /* Defines and macros
134 */
135 
136 
137 /************************************************************************/
138 /*>DEPRECATED(s, t)
139  ----------------
140 *//**
141 
142  The DEPRECATED macro gives a warning message if a function is
143  deprecated and indicates the replacement function.
144 
145  The default option is to give a warning message unless an environment
146  variable, BIOPLIB_DEPRECATED_QUIET, is set.
147 
148  Alternatively the compile options: -D BIOPLIB_DEPRECATED_CHECK or
149  -D BIOPLIB_DEPRECATED_QUIET will set the DEPRECATED macro to ignore the
150  BIOPLIB_DEPRECATED_QUIET environment variable.
151 
152  -D BIOPLIB_DEPRECATED_CHECK will display the warning message.
153  -D BIOPLIB_DEPRECATED_QUIET will always silence the warning message.
154 
155 - 29.04.14 Original By: CTP
156 */
157 # if(defined BIOPLIB_DEPRECATED_CHECK || defined BIOPLIB_DEPRECATED_QUIET)
158 # ifndef BIOPLIB_DEPRECATED_QUIET
159 # define DEPRECATED(s, t) \
160  fprintf(stderr, \
161  "This code uses %s which is now deprecated!\n" \
162  " Use %s instead\n", (s), (t))
163 # else
164 # define DEPRECATED(s, t)
165 # endif
166 # else
167 # define DEPRECATED(s, t) \
168  { \
169  if(!getenv("BIOPLIB_DEPRECATED_QUIET")) \
170  fprintf(stderr, \
171  "This code uses %s which is now deprecated!\n" \
172  " Use %s instead\n" \
173  " Set the BIOPLIB_DEPRECATED_QUIET environment \
174 variable to silence this message\n" , (s), (t)); \
175  }
176 # endif
177 
178 
179 /************************************************************************/
180 /* Globals
181 */
182 
183 /************************************************************************/
184 /* Prototypes
185 */
186 
187 # endif /* _DEPRECATED_H */
188 
189 /************************************************************************/
190 /** \cond deprecated */
191 /************************************************************************/
192 /* Deprecated functions: general.h */
193 
194 # ifdef _GENERAL_H_DEPRECATED
195 # undef _GENERAL_H_DEPRECATED
196 
197 void StringToLower(char *string1, char *string2);
198 void StringToUpper(char *string1, char *string2);
199 char *KillLeadSpaces(char *string);
200 void KillLine(FILE *fp);
201 void SetExtn(char *File, char *Ext);
202 int chindex(char *string, char ch);
203 void Word(char *string1, char *string2);
204 void WordN(char *string1, char *string2, int MaxChar);
205 void padterm(char *string, int length); /* defined in cssr.h */
206 void padchar(char *string, int length, char ch);
207 BOOL CheckExtn(char *string, char *ext);
208 char *ftostr(char *str, int maxlen, REAL x, int precision);
209 
210 void GetFilestem(char *filename, char *stem);
211 int upstrcmp(char *word1, char *word2);
212 int upstrncmp(char *word1, char *word2, int ncomp);
213 char *GetWord(char *buffer, char *word, int maxsize);
214 BOOL OpenStdFiles(char *infile, char *outfile, FILE **in, FILE **out);
215 FILE *OpenFile(char *filename, char *envvar, char *mode, BOOL *noenv);
216 int countchar(char *string, char ch);
217 char *fgetsany(FILE *fp);
218 char *strcatalloc(char *instr, char *catstr);
219 
220 STRINGLIST *StoreString(STRINGLIST *StringList, char *string);
221 BOOL InStringList(STRINGLIST *StringList, char *string);
222 void FreeStringList(STRINGLIST *StringList);
223 
224 char *QueryStrStr(char *string, char *substring);
225 
226 void IndexReal(REAL *arrin, int *indx, int n);
227 
228 FILE *OpenOrPipe(char *filename);
229 int CloseOrPipe(FILE *fp);
230 
231 BOOL WrapString(char *in, char *out, int maxlen);
232 BOOL WrapPrint(FILE *out, char *string);
233 void RightJustify(char *string);
234 char *GetWordNC(char *buffer, char *word, int maxlen);
235 void getfield(char *buffer, int start, int width, char *str);
236 
237 # endif /* _GENERAL_H_DEPRECATED */
238 
239 /************************************************************************/
240 /* Deprecated functions: pdb.h */
241 
242 # ifdef _PDB_H_DEPRECATED
243 # undef _PDB_H_DEPRECATED
244 
245 char *GetPDBChainLabels(PDB *pdb);
246 PDB *ReadPDB(FILE *fp, int *natom);
247 PDB *ReadPDBAll(FILE *fp, int *natom);
248 PDB *ReadPDBAtoms(FILE *fp, int *natom);
249 PDB *ReadPDBOccRank(FILE *fp, int *natom, int OccRank);
250 PDB *ReadPDBAtomsOccRank(FILE *fp, int *natom, int OccRank);
251 PDB *doReadPDB(FILE *fp, int *natom, BOOL AllAtoms, int OccRank,
252  int ModelNum);
253 PDB *doReadPDBML(FILE *fp, int *natom, BOOL AllAtoms, int OccRank,
254  int ModelNum);
255 BOOL CheckFileFormatPDBML(FILE *fp);
256 
257 void WritePDB(FILE *fp, PDB *pdb);
258 void WriteAsPDB(FILE *fp, PDB *pdb);
259 void WriteAsPDBML(FILE *fp, PDB *pdb);
260 BOOL FormatCheckWritePDB(PDB *pdb);
261 void WriteWholePDB(FILE *fp, WHOLEPDB *wpdb);
262 void WriteWholePDBHeader(FILE *fp, WHOLEPDB *wpdb);
263 void WriteWholePDBTrailer(FILE *fp, WHOLEPDB *wpdb);
264 
265 void WritePDBRecord(FILE *fp, PDB *pdb);
266 void WritePDBRecordAtnam(FILE *fp, PDB *pdb);
267 void WriteGromosPDB(FILE *fp, PDB *pdb);
268 void WriteGromosPDBRecord(FILE *fp, PDB *pdb);
269 void GetCofGPDB(PDB *pdb, VEC3F *cg);
270 void GetCofGPDBRange(PDB *start, PDB *stop, VEC3F *cg);
271 void GetCofGPDBSCRange(PDB *start, PDB *stop, VEC3F *cg);
272 void OriginPDB(PDB *pdb);
273 void RotatePDB(PDB *pdb, REAL rm[3][3]);
274 void TranslatePDB(PDB *pdb, VEC3F tvect);
275 BOOL FitPDB(PDB *ref_pdb, PDB *fit_pdb, REAL rm[3][3]);
276 BOOL FitCaPDB(PDB *ref_pdb, PDB *fit_pdb, REAL rm[3][3]);
277 BOOL FitNCaCPDB(PDB *ref_pdb, PDB *fit_pdb, REAL rm[3][3]);
278 BOOL FitCaCbPDB(PDB *ref_pdb, PDB *fit_pdb, REAL rm[3][3]);
279 REAL CalcRMSPDB(PDB *pdb1, PDB *pdb2);
280 int GetPDBCoor(PDB *pdb, COOR **coor);
281 BOOL FindZonePDB(PDB *pdb, int start, char startinsert, int stop,
282  char stopinsert, char chain, int mode,
283  PDB **pdb_start, PDB **pdb_stop);
284 int HAddPDB(FILE *fp, PDB *pdb);
285 int ReadPGP(FILE *fp);
286 FILE *OpenPGPFile(char *pgpfile, BOOL AllHyd);
287 PDB *SelectAtomsPDB(PDB *pdbin, int nsel, char **sel, int *natom);
288 PDB *StripHPDB(PDB *pdbin, int *natom);
289 SECSTRUC *ReadSecPDB(FILE *fp, int *nsec);
290 void RenumAtomsPDB(PDB *pdb);
291 PDB *FindEndPDB(PDB *start);
292 PDB *FixOrderPDB(PDB *pdb, BOOL Pad, BOOL Renum);
293 PDB *ShuffleResPDB(PDB *start, PDB *end, BOOL Pad);
294 BOOL GetAtomTypes(char *resnam, char **AtomTypes);
295 PDB *KillPDB(PDB *pdb, PDB *prev);
296 void CopyPDB(PDB *out, PDB *in);
297 BOOL MovePDB(PDB *move, PDB **from, PDB **to);
298 PDB *AppendPDB(PDB *first, PDB *second);
299 PDB *ShuffleBB(PDB *pdb);
300 REAL CalcChi(PDB *pdb, int type);
301 PDB *GetPDBByN(PDB *pdb, int n);
302 void SetChi(PDB *pdb, PDB *next, REAL chi, int type);
303 BOOL KillSidechain(PDB *ResStart, PDB *NextRes, BOOL doCB);
304 void SetResnam(PDB *ResStart, PDB *NextRes, char *resnam, int resnum,
305  char *insert, char *chain);
306 void ApplyMatrixPDB(PDB *pdb, REAL matrix[3][3]);
307 BOOL GetResolPDB(FILE *fp, REAL *resolution, REAL *RFactor,
308  int *StrucType);
309 BOOL GetExptl(FILE *fp, REAL *resolution, REAL *RFactor, REAL *FreeR,
310  int *StrucType);
311 BOOL GetExptlOld(FILE *fp, REAL *resolution, REAL *RFactor, REAL *FreeR,
312  int *StrucType);
313 char *ReportStructureType(int type);
314 PDB **IndexPDB(PDB *pdb, int *natom);
315 DISULPHIDE *ReadDisulphidesPDB(FILE *fp, BOOL *error);
316 BOOL ParseResSpec(char *spec, char *chain, int *resnum, char *insert);
317 BOOL ParseResSpecNoUpper(char *spec, char *chain, int *resnum, char *insert);
318 BOOL DoParseResSpec(char *spec, char *chain, int *resnum, char *insert,
319  BOOL uppercaseresspec);
320 BOOL RepSChain(PDB *pdb, char *sequence, char *ChiTable, char *RefCoords);
321 PDB *FindNextChainPDB(PDB *pdb);
322 BOOL FixCterPDB(PDB *pdb, int style);
323 BOOL CalcCterCoords(PDB *p, PDB *ca_p, PDB *c_p, PDB *o_p);
324 int CalcTetraHCoords(PDB *nter, COOR *coor);
325 int AddNTerHs(PDB **ppdb, BOOL Charmm);
326 char *FNam2PDB(char *filename);
327 PDB *TermPDB(PDB *pdb, int length);
328 PDB *FindHetatmResidueSpec(PDB *pdb, char *resspec);
329 PDB *FindResidueSpec(PDB *pdb, char *resspec);
330 PDB *FindNextResidue(PDB *pdb);
331 PDB *DupePDB(PDB *in);
332 BOOL CopyPDBCoords(PDB *out, PDB *in);
333 void CalcCellTrans(VEC3F UnitCell, VEC3F CellAngles,
334  VEC3F *xtrans, VEC3F *ytrans, VEC3F *ztrans);
335 int GetCrystPDB(FILE *fp, VEC3F *UnitCell, VEC3F *CellAngles,
336  char *spacegroup,
337  REAL OrigMatrix[3][4], REAL ScaleMatrix[3][4]);
338 void WriteCrystPDB(FILE *fp, VEC3F UnitCell, VEC3F CellAngles,
339  char *spacegroup,
340  REAL OrigMatrix[3][4], REAL ScaleMatrix[3][4]);
341 PDB *ExtractZonePDB(PDB *inpdb, char *chain1, int resnum1, char *insert1,
342  char *chain2, int resnum2, char *insert2);
343 PDB *ExtractZoneSpecPDB(PDB *pdb, char *firstRes, char *lastRes);
344 PDB *FindResidue(PDB *pdb, char chain, int resnum, char insert);
345 PDB *FindHetatmResidue(PDB *pdb, char chain, int resnum, char insert);
346 PDB *FindAtomInRes(PDB *pdb, char *atnam);
347 BOOL InPDBZone(PDB *p, char chain, int resnum1, char insert1,
348  int resnum2, char insert2);
349 BOOL InPDBZoneSpec(PDB *p, char *resspec1, char *resspec2);
350 BOOL AtomNameMatch(char *atnam, char *spec, BOOL *ErrorWarn);
351 BOOL AtomNameRawMatch(char *atnam, char *spec, BOOL *ErrorWarn);
352 BOOL LegalAtomSpec(char *spec);
353 BOOL RepOneSChain(PDB *pdb, char *ResSpec, char aa, char *ChiTable,
354  char *RefCoords);
355 void EndRepSChain(void);
356 char **ReadSeqresPDB(FILE *fp, int *nchains);
357 PDB *SelectCaPDB(PDB *pdb);
358 char *FixAtomName(char *name, REAL occup);
359 
360 void FreeWholePDB(WHOLEPDB *wpdb);
361 WHOLEPDB *ReadWholePDB(FILE *fpin);
362 WHOLEPDB *ReadWholePDBAtoms(FILE *fpin);
363 BOOL AddCBtoGly(PDB *pdb);
364 BOOL AddCBtoAllGly(PDB *pdb);
365 PDB *StripGlyCB(PDB *pdb);
366 PDB *RemoveAlternates(PDB *pdb);
367 PDB *BuildAtomNeighbourPDBList(PDB *pdb, PDB *pRes, REAL NeighbDist);
368 PDB *FindAtomWildcardInRes(PDB *pdb, char *pattern);
369 PDB *DupeResiduePDB(PDB *in);
370 PDB *StripWatersPDB(PDB *pdbin, int *natom);
371 PDBSTRUCT *AllocPDBStructure(PDB *pdb);
372 PDB *FindNextChain(PDB *pdb);
373 void FreePDBStructure(PDBSTRUCT *pdbstruct);
374 void SetElementSymbolFromAtomName(char *element, char * atom_name);
375 
376 # endif /* _PDB_H_DEPRECATED */
377 
378 /************************************************************************/
379 /* Deprecated functions: BuffInp.h */
380 
381 # ifdef _BUFFINPUT_H_DEPRECATED
382 # undef _BUFFINPUT_H_DEPRECATED
383 
384 INBUFFER *OpenBufferedFile(char *filename, int maxstr);
385 BOOL ReadBufferedFile(INBUFFER *bfp, char *string, int length);
386 BOOL ProbeBufferedFile(INBUFFER *bfp, char *string, int length);
387 
388 # endif /* _BUFFINPUT_H_DEPRECATED */
389 
390 /************************************************************************/
391 /* Deprecated functions: ErrStack.h */
392 # ifdef _ERRSTACK_H_DEPRECATED
393 # undef _ERRSTACK_H_DEPRECATED
394 
395 void StoreError(char *routine, char *error);
396 void ShowErrors(void *PrintRoutine(char *), BOOL Trace);
397 
398 # endif /* _ERRSTACK_H_DEPRECATED */
399 
400 /************************************************************************/
401 /* Deprecated functions: MathUtil.h */
402 
403 # ifdef _MATHUTIL_H_DEPRECATED
404 # undef _MATHUTIL_H_DEPRECATED
405 
406 void CalcSD(REAL val, int action, REAL *mean, REAL *SD);
407 void CalcExtSD(REAL val, int action, REAL *Sx, REAL *SxSq,
408  int *NValues, REAL *mean, REAL *SD);
409 REAL pearson(REAL *x, REAL *y, int NItem);
410 REAL pearson1(REAL *x, REAL *y, int NItem);
411 
412 void CrossProd3(VEC3F *Out, VEC3F In1, VEC3F In2);
413 void VecSub3(VEC3F *Out, VEC3F In1, VEC3F In2);
414 void VecAdd3(VEC3F *Out, VEC3F In1, VEC3F In2);
415 REAL VecLen3(VEC3F Vec);
416 REAL DistPtVect(VEC3F Point, VEC3F End1, VEC3F End2);
417 REAL blDistPtVect(VEC3F Point, VEC3F End1, VEC3F End2);
418 REAL PointLineDistance(REAL Px, REAL Py, REAL Pz,
419  REAL P1x, REAL P1y, REAL P1z,
420  REAL P2x, REAL P2y, REAL P2z,
421  REAL *Rx, REAL *Ry, REAL *Rz,
422  REAL *frac);
423 ULONG factorial(int n);
424 ULONG Factdiv(int n1, int n2);
425 ULONG NPerm(int n, int r);
426 ULONG NComb(int n, int r);
427 
428 # endif /* _MATHUTIL_H_DEPRECATED */
429 
430 /************************************************************************/
431 /* Deprecated functions: WindIO.h */
432 
433 # ifdef _WINDIO_H_DEPRECATED
434 # undef _WINDIO_H_DEPRECATED
435 
436 void screen(char *string);
437 void prompt(char *string);
438 void RePrompt(void);
439 void GetKybdString(char *string, int maxlen);
440 void PagingOn(void);
441 void PagingOff(void);
442 void WindowMode(BOOL mode);
443 void WindowInteractive(BOOL mode);
444 int YorN(char deflt);
445 
446 # endif /* _WINDIO_H_DEPRECATED */
447 
448 /************************************************************************/
449 /* Deprecated functions: aalist.h */
450 
451 # ifdef _AALIST_H_DEPRECATED
452 # undef _AALIST_H_DEPRECATED
453 
454 AA *InsertNextResiduesInAAList(AA *a, char res, int nres);
455 AA *InsertNextResidueInAAList(AA *a, char res);
456 char *BuildSeqFromAAList(AA *aa);
457 AA *InsertResidueInAAListAt(AA *aa, char res, int pos);
458 AA *InsertResiduesInAAListAt(AA *aa, char res, int nres, int pos);
459 AA *BuildAAList(char *seq);
460 int FindAAListOffsetByResnum(AA *aa, int resnum);
461 AA *FindAAListItemByResnum(AA *aa, int resnum);
462 void SetAAListFlagByResnum(AA *aa, int resnum);
463 char *BuildFlagSeqFromAAList(AA *aa, char ch);
464 int GetAAListLen(AA *aa);
465 
466 # endif /* _AALIST_H_DEPRECATED */
467 
468 /************************************************************************/
469 /* Deprecated functions: angle.h */
470 
471 # ifdef _ANGLE_H_DEPRECATED
472 # undef _ANGLE_H_DEPRECATED
473 
474 REAL angle(REAL xi, REAL yi, REAL zi, REAL xj, REAL yj, REAL zj,
475  REAL xk, REAL yk, REAL zk);
476 REAL phi(REAL xi, REAL yi, REAL zi, REAL xj, REAL yj, REAL zj,
477  REAL xk, REAL yk, REAL zk, REAL xl, REAL yl, REAL zl);
478 REAL simpleangle(REAL ang);
479 REAL TrueAngle(REAL opp, REAL adj);
480 BOOL TorToCoor(VEC3F ant1, VEC3F ant2, VEC3F ant3,
481  REAL bond, REAL theta, REAL torsion,
482  VEC3F *coords);
483 
484 # endif /* _ANGLE_H_DEPRECATED */
485 
486 /************************************************************************/
487 /* Deprecated functions: array.h */
488 
489 # ifdef _ARRAY_H_DEPRECATED
490 # undef _ARRAY_H_DEPRECATED
491 
492 char **Array2D(int size, int dim1, int dim2);
493 void FreeArray2D(char **array, int dim1, int dim2);
494 char ***Array3D(int size, int dim1, int dim2, int dim3);
495 void FreeArray3D(char ***array, int dim1, int dim2, int dim3);
496 
497 # endif /* _ARRAY_H_DEPRECATED */
498 
499 /************************************************************************/
500 /* Deprecated functions: cssr.h */
501 
502 
503 # ifdef _CSSR_H_DEPRECATED
504 # undef _CSSR_H_DEPRECATED
505 
506 CSSR *ReadCSSR(FILE *fp, int *natom, char *name, char *title);
507 PDB *ReadCSSRasPDB(FILE *fp, int *natom);
508 void NormaliseCSSR(CSSR *cssr, REAL cell[3], REAL alpha, REAL beta,
509  REAL gamma);
510 void NormalisePDB(PDB *pdb, REAL cell[3], REAL alpha, REAL beta,
511  REAL gamma);
512 void ortho(REAL cell[3], REAL alpha, REAL beta, REAL gamma,
513  REAL amatrx[3][3], int isw, int ncode);
514 void WriteCSSR(FILE *fp, CSSR *cssr, char *name, char *title);
515 
516 # endif /* _CSSR_H_DEPRECATED */
517 
518 /************************************************************************/
519 /* Deprecated functions: fit.h */
520 
521 # ifdef _FIT_H_DEPRECATED
522 # undef _FIT_H_DEPRECATED
523 
524 
525 BOOL matfit(COOR *x1, COOR *x2, REAL rm[3][3], int n, REAL *wt1,
526  BOOL column);
527 
528 # endif /* _FIT_H_DEPRECATED */
529 
530 /************************************************************************/
531 /* Deprecated functions: hbond.h */
532 
533 # ifdef _HBOND_H_DEPRECATED
534 # undef _HBOND_H_DEPRECATED
535 
536 int IsHBonded(PDB *res1, PDB *res2, int type);
537 BOOL ValidHBond(PDB *AtomH, PDB *AtomD, PDB *AtomA, PDB *AtomP);
538 int IsMCDonorHBonded(PDB *res1, PDB *res2, int type);
539 int IsMCAcceptorHBonded(PDB *res1, PDB *res2, int type);
540 
541 # endif /* _HBOND_H_DEPRECATED */
542 
543 /************************************************************************/
544 /* Deprecated functions: help.h */
545 
546 # ifdef _HELP_H_DEPRECATED
547 # undef _HELP_H_DEPRECATED
548 
549 void Help(char *string, char *HelpFile);
550 void DoHelp(char *string, char *HelpFile);
551 
552 # endif /* _HELP_H_DEPRECATED */
553 
554 /************************************************************************/
555 /* Deprecated functions: hpgl.h */
556 
557 # ifdef _HPGL_H_DEPRECATED
558 # undef _HPGL_H_DEPRECATED
559 
560 BOOL HPGLInit(char *filename, char *AltFont, REAL xmargin, REAL ymargin);
561 void HPGLPen(int num);
562 void HPGLMove(REAL x, REAL y);
563 void HPGLDraw(REAL x, REAL y);
564 void HPGLSetDash(int style);
565 void HPGLFont(int font, REAL size);
566 void HPGLLText(REAL x, REAL y, char *string);
567 void HPGLCBText(REAL x, REAL y, REAL offset, char *text);
568 void HPGLROffText(REAL x, REAL y, REAL offset, char *text);
569 void HPGLLCText(REAL x, REAL y, char *text);
570 void HPGLCTText(REAL x, REAL y, REAL offset, char *text);
571 void HPGLVText(REAL x, REAL y, REAL xoff, char *text, int TitleFont,
572  REAL TitleSize, char *label, int LabelFont, REAL LabelSize);
573 void HPGLEnd(void);
574 void HPGLShowText(char *text, BOOL orientation, int XBase, int YBase);
575 
576 # endif /* _HPGL_H_DEPRECATED */
577 
578 /************************************************************************/
579 /* Deprecated functions: matrix.h */
580 
581 # ifdef _MATRIX_H_DEPRECATED
582 # undef _MATRIX_H_DEPRECATED
583 
584 void MatMult3_33(VEC3F vecin, REAL matin[3][3], VEC3F *vecout);
585 void MatMult33_33(REAL a[3][3], REAL b[3][3], REAL out[3][3]);
586 void invert33(REAL s[3][3], REAL ss[3][3]);
587 void CreateRotMat(char direction, REAL angle, REAL matrix[3][3]);
588 REAL VecDist(REAL *a, REAL *b, int len);
589 
590 # endif /* _MATRIX_H_DEPRECATED */
591 
592 /************************************************************************/
593 /* Deprecated functions: parse.h */
594 
595 # ifdef _PARSE_H_DEPRECATED
596 # undef _PARSE_H_DEPRECATED
597 
598 int parse(char *comline, int nkeys, KeyWd *keywords, REAL *REALparam,
599  char **strparam);
600 int mparse(char *comline, int nkeys, MKeyWd *keywords, REAL *REALparam,
601  char **strparam, int *nparams);
602 int match(char *comstring, char *string2, int *nletters);
603 int GetString(char *command, char *strparam);
604 int GetParam(char *command, REAL *value, int *nletters);
605 
606 # endif /* _PARSE_H_DEPRECATED */
607 
608 /************************************************************************/
609 /* Deprecated functions: plotting.h */
610 
611 # ifdef _PLOTTING_H_DEPRECATED
612 # undef _PLOTTING_H_DEPRECATED
613 
614 BOOL AMInitPlot(char *filename, char *title, int dest, REAL OutXSize,
615  REAL OutYSize, REAL OutXOff, REAL OutYOff,
616  char *AltFont, REAL xmargin, REAL ymargin,
617  REAL DataXMin, REAL DataYMin, REAL DataXMax,
618  REAL DataYMax);
619 void AMSetPen(int dest, int pen);
620 void AMMove(int dest, REAL x, REAL y);
621 void AMDraw(int dest, REAL x, REAL y);
622 void AMSetLineStyle(int dest, int style);
623 void AMEndLine(int dest);
624 void AMSetFont(int dest, char *PSFontName, REAL FontSize);
625 void AMText(int dest, REAL x, REAL y, char *text);
626 void AMCBText(int dest, REAL x, REAL y, char *text);
627 void AMRText(int dest, REAL x, REAL y, REAL offset, char *text);
628 void AMLCText(int dest, REAL x, REAL y, char *text);
629 void AMCTText(int dest, REAL x, REAL y, REAL CTOffset, char *text);
630 void AMEndPlot(int dest);
631 int PS2HPGLFont(char *font);
632 char *SimplifyText(char *string);
633 
634 # endif /* _PLOTTING_H_DEPRECATED */
635 
636 /************************************************************************/
637 /* Deprecated functions: ps.h */
638 
639 # ifdef _PS_H_DEPRECATED
640 # undef _PS_H_DEPRECATED
641 
642 BOOL PSInit(char *FName, char *creator, char *AltFont);
643 void PSThick(REAL thickness);
644 void PSMove(REAL X, REAL Y);
645 void PSDraw(REAL X, REAL Y);
646 void PSSetDash(char *linepatt);
647 void PSClearDash(void);
648 void PSStroke(void);
649 void PSFont(char *fontname, REAL size);
650 void PSLText(REAL X, REAL Y, char *label);
651 void PSCBText(REAL X, REAL Y, REAL Offset, char *label);
652 void PSROffText(REAL X, REAL Y, REAL offset, char *label);
653 void PSLCText(REAL X, REAL Y, char *label);
654 void PSCTText(REAL X, REAL Y, REAL Offset, char *label);
655 void PSVText(REAL x, REAL y, REAL xoff, char *text, char *font, REAL size,
656  char *label, char *lfont, REAL lsize);
657 void PSShowText(char *text);
658 void PSEnd(void);
659 char *PSCorrectCase(char *font);
660 
661 # endif /* _PS_H_DEPRECATED */
662 
663 /************************************************************************/
664 /* Deprecated functions: safemem.h */
665 
666 # ifdef _SAFEMEM_H_DEPRECATED
667 # undef _SAFEMEM_H_DEPRECATED
668 
669 void *safemalloc(int nbytes);
670 BOOL safefree(void *ptr);
671 void safeleaks(void);
672 
673 # endif /* _SAFEMEM_H_DEPRECATED */
674 
675 /************************************************************************/
676 /* Deprecated macros: seq.h */
677 
678 # ifdef _SEQ_H_DEPRECATED
679 # undef _SEQ_H_DEPRECATED
680 
681 #define PDB2Seq(x) DoPDB2Seq((x), FALSE, FALSE, FALSE)
682 #define PDB2SeqX(x) DoPDB2Seq((x), TRUE, FALSE, FALSE)
683 #define PDB2SeqNoX(x) DoPDB2Seq((x), FALSE, FALSE, TRUE)
684 #define PDB2SeqXNoX(x) DoPDB2Seq((x), TRUE, FALSE, TRUE)
685 
686 #define PDBProt2Seq(x) DoPDB2Seq((x), FALSE, TRUE, FALSE)
687 #define PDBProt2SeqX(x) DoPDB2Seq((x), TRUE, TRUE, FALSE)
688 #define PDBProt2SeqNoX(x) DoPDB2Seq((x), FALSE, TRUE, TRUE)
689 #define PDBProt2SeqXNoX(x) DoPDB2Seq((x), TRUE, TRUE, TRUE)
690 
691 /************************************************************************/
692 /* Deprecated functions: seq.h */
693 
694 char throne(char *three);
695 char thronex(char *three);
696 char *onethr(char one);
697 char *DoPDB2Seq(PDB *pdb, BOOL DoAsxGlx, BOOL ProtOnly, BOOL NoX);
698 int SplitSeq(char *LinearSeq, char **seqs);
699 int ReadSimplePIR(FILE *fp, int maxres, char **seqs);
700 int ReadPIR(FILE *fp, BOOL DoInsert, char **seqs, int maxchain,
701  SEQINFO *seqinfo, BOOL *punct, BOOL *error);
702 int ReadRawPIR(FILE *fp, char **seqs, int maxchain, BOOL upcase,
703  SEQINFO *seqinfo, BOOL *error);
704 int align(char *seq1, int length1, char *seq2, int length2,
705  BOOL verbose, BOOL identity, int penalty,
706  char *align1, char *align2, int *align_len);
707 int affinealign(char *seq1, int length1, char *seq2, int length2,
708  BOOL verbose, BOOL identity, int penalty, int penext,
709  char *align1, char *align2, int *align_len);
710 int CalcMDMScore(char resa, char resb);
711 int affinealignuc(char *seq1, int length1, char *seq2, int length2,
712  BOOL verbose, BOOL identity, int penalty, int penext,
713  char *align1, char *align2, int *align_len);
714 int CalcMDMScoreUC(char resa, char resb);
715 BOOL ReadMDM(char *mdmfile);
716 int ZeroMDM(void);
717 char DNAtoAA(char *dna);
718 int TrueSeqLen(char *sequence);
719 int KnownSeqLen(char *sequence);
720 BOOL NumericReadMDM(char *mdmfile);
721 int NumericCalcMDMScore(int resa, int resb);
722 int NumericAffineAlign(int *seq1, int length1, int *seq2, int length2,
723  BOOL verbose, BOOL identity, int penalty,
724  int penext, int *align1, int *align2,
725  int *align_len);
726 void SetMDMScoreWeight(char resa, char resb, REAL weight);
727 
728 # endif /* _SEQ_H_DEPRECATED */
729 
730 /************************************************************************/
731 /* Deprecated functions: eigen.h */
732 
733 # ifdef _EIGEN_H_DEPRECATED
734 # undef _EIGEN_H_DEPRECATED
735 
736 int eigen(REAL **M, REAL **Vectors, REAL *lambda, int n);
737 
738 # endif /* _EIGEN_H_DEPRECATED */
739 
740 /************************************************************************/
741 /* Deprecated functions: regression.h */
742 # ifdef _REGRESSION_H_DEPRECATED
743 # undef _REGRESSION_H_DEPRECATED
744 
745 BOOL CalculateBestFitLine(double **coordinates, int numberOfPoints,
746  int numberOfDimensions, double *centroid,
747  double *eigenVector);
748 void FindCentroid(REAL **coordinates, int numberOfPoints,
749  int numberOfDimensions, REAL *centroid);
750 BOOL CalculateCovarianceMatrix(REAL **x, int numX, int numY, REAL **cov);
751 
752 # endif /* _REGRESSION_H_DEPRECATED */
753 
754 
755 /************************************************************************/
756 #endif /* NODEPRECATION */
757 
758 /************************************************************************/
759 /** \endcond */
760 /************************************************************************/
_stringlist
Definition: general.h:82
BOOL
short BOOL
Definition: SysDefs.h:64
pdb_entry
Definition: pdb.h:298
cssr_entry::atnam
char atnam[8]
Definition: cssr.h:71
_wholepdb
Definition: pdb.h:372
cssr_entry::x
REAL x
Definition: cssr.h:66
SEQINFO
Definition: seq.h:90
macros.h
Useful macros.
aa
Definition: aalist.h:70
VEC3F
Definition: MathType.h:69
MKeyWd
Definition: parse.h:92
ULONG
unsigned long ULONG
Definition: SysDefs.h:66
REAL
double REAL
Definition: MathType.h:67
cssr_entry
Definition: cssr.h:63
KeyWd
Definition: parse.h:86
PDBSTRUCT
Definition: pdb.h:349
cssr_entry::next
struct cssr_entry * next
Definition: cssr.h:67
cssr_entry::y
REAL y
Definition: cssr.h:66
_disulphide
Definition: pdb.h:439
sec_entry
Definition: pdb.h:360
Generated on Tue Oct 24 2017 10:57:05 for Bioplib by   doxygen 1.8.8