src/mmdb_title.h
Go to the documentation of this file.
00001 // $Id: mmdb_title.h $ 00002 // ================================================================= 00003 // 00004 // CCP4 Coordinate Library: support of coordinate-related 00005 // functionality in protein crystallography applications. 00006 // 00007 // Copyright (C) Eugene Krissinel 2000-2013. 00008 // 00009 // This library is free software: you can redistribute it and/or 00010 // modify it under the terms of the GNU Lesser General Public 00011 // License version 3, modified in accordance with the provisions 00012 // of the license to address the requirements of UK law. 00013 // 00014 // You should have received a copy of the modified GNU Lesser 00015 // General Public License along with this library. If not, copies 00016 // may be downloaded from http://www.ccp4.ac.uk/ccp4license.php 00017 // 00018 // This program is distributed in the hope that it will be useful, 00019 // but WITHOUT ANY WARRANTY; without even the implied warranty of 00020 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00021 // GNU Lesser General Public License for more details. 00022 // 00023 // ================================================================= 00024 // 00025 // 12.09.13 <-- Date of Last Modification. 00026 // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 00027 // ----------------------------------------------------------------- 00028 // 00029 // **** Module : MMDB_Title <interface> 00030 // ~~~~~~~~~ 00031 // **** Project : MacroMolecular Data Base (MMDB) 00032 // ~~~~~~~~~ 00033 // **** Classes : mmdb::TitleContainer (container of title classes) 00034 // ~~~~~~~~~ mmdb::ObsLine 00035 // mmdb::TitleLine 00036 // mmdb::Caveat 00037 // mmdb::Compound 00038 // mmdb::Source 00039 // mmdb::KeyWords 00040 // mmdb::ExpData 00041 // mmdb::MdlType 00042 // mmdb::Author 00043 // mmdb::RevData 00044 // mmdb::Supersede 00045 // mmdb::Journal 00046 // mmdb::Remark 00047 // mmdb::Biomolecule 00048 // mmdb::Title ( MMDB title section ) 00049 // 00050 // (C) E. Krissinel 2000-2013 00051 // 00052 // ================================================================= 00053 // 00054 00055 #ifndef __MMDB_Title__ 00056 #define __MMDB_Title__ 00057 00058 #include "mmdb_io_stream.h" 00059 #include "mmdb_defs.h" 00060 #include "mmdb_utils.h" 00061 #include "mmdb_mmcif_.h" 00062 00063 namespace mmdb { 00064 00065 // ====================== TitleContainer ======================= 00066 00067 DefineClass(TitleContainer); 00068 DefineStreamFunctions(TitleContainer); 00069 00070 class TitleContainer : public ClassContainer { 00071 00072 public : 00073 00074 TitleContainer () : ClassContainer() {} 00075 TitleContainer ( io::RPStream Object ) 00076 : ClassContainer ( Object ) {} 00077 ~TitleContainer() {} 00078 00079 PContainerClass MakeContainerClass ( int ClassID ); 00080 00081 }; 00082 00083 00084 // ================== ObsLine ======================== 00085 00086 DefineClass(ObsLine); 00087 DefineStreamFunctions(ObsLine); 00088 00089 class ObsLine : public ContainerClass { 00090 00091 public : 00092 00093 Date repDate; // date of replacement 00094 IDCode idCode; // ID code of replaced entry 00095 IDCode rIdCode[8]; // ID codes of entries that replaced this one 00096 00097 ObsLine (); 00098 ObsLine ( cpstr S ); 00099 ObsLine ( io::RPStream Object ); 00100 ~ObsLine(); 00101 00102 void PDBASCIIDump ( pstr S, int N ); 00103 void MakeCIF ( mmcif::PData CIF, int N ); 00104 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00105 ERROR_CODE GetCIF ( mmcif::PData CIF, int & n ); 00106 CLASS_ID GetClassID () { return ClassID_ObsLine; } 00107 00108 void Copy ( PContainerClass ObsLine ); 00109 00110 void write ( io::RFile f ); 00111 void read ( io::RFile f ); 00112 00113 protected : 00114 00115 void InitObsLine(); 00116 00117 }; 00118 00119 00120 // ==================== TitleLine ===================== 00121 00122 DefineClass(TitleLine); 00123 DefineStreamFunctions(TitleLine); 00124 00125 class TitleLine : public ContString { 00126 00127 public : 00128 00129 TitleLine (); 00130 TitleLine ( cpstr S ); 00131 TitleLine ( io::RPStream Object ); 00132 ~TitleLine(); 00133 00134 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00135 void PDBASCIIDump ( pstr S, int N ); 00136 bool PDBASCIIDump1 ( io::RFile ) { return false; } 00137 CLASS_ID GetClassID () { return ClassID_TitleLine; } 00138 00139 void write ( io::RFile f ); 00140 void read ( io::RFile f ); 00141 00142 protected : 00143 00144 void InitTitleLine(); 00145 00146 }; 00147 00148 00149 // ==================== Caveat ===================== 00150 00151 DefineClass(Caveat); 00152 DefineStreamFunctions(Caveat); 00153 00154 class Caveat : public ContString { 00155 00156 public : 00157 00158 IDCode idCode; // ID code of the entry 00159 00160 Caveat (); 00161 Caveat ( cpstr S ); 00162 Caveat ( io::RPStream Object ); 00163 ~Caveat(); 00164 00165 void PDBASCIIDump ( pstr S, int N ); 00166 bool PDBASCIIDump1 ( io::RFile ) { return false; } 00167 void MakeCIF ( mmcif::PData CIF, int N ); 00168 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00169 00170 // virtual void GetCIF1 ( mmcif::PData CIF, ERROR_CODE & Signal, 00171 // int & pos ); 00172 00173 CLASS_ID GetClassID () { return ClassID_CAVEAT; } 00174 00175 void Copy ( PContainerClass Caveat ); 00176 00177 void write ( io::RFile f ); 00178 void read ( io::RFile f ); 00179 00180 protected : 00181 00182 void InitCaveat(); 00183 00184 }; 00185 00186 00187 // ==================== Compound ===================== 00188 00189 DefineClass(Compound); 00190 DefineStreamFunctions(Compound); 00191 00192 class Compound : public ContString { 00193 00194 public : 00195 00196 Compound (); 00197 Compound ( cpstr S ); 00198 Compound ( io::RPStream Object ); 00199 ~Compound(); 00200 00201 void PDBASCIIDump ( pstr S, int N ); 00202 bool PDBASCIIDump1 ( io::RFile ) { return false; } 00203 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00204 CLASS_ID GetClassID () { return ClassID_Compound; } 00205 00206 void write ( io::RFile f ); 00207 void read ( io::RFile f ); 00208 00209 protected : 00210 00211 void InitCompound(); 00212 00213 }; 00214 00215 00216 // ==================== Source ===================== 00217 00218 DefineClass(Source); 00219 DefineStreamFunctions(Source); 00220 00221 class Source : public ContString { 00222 00223 public : 00224 00225 Source (); 00226 Source ( cpstr S ); 00227 Source ( io::RPStream Object ); 00228 ~Source(); 00229 00230 void PDBASCIIDump ( pstr S, int N ); 00231 bool PDBASCIIDump1 ( io::RFile ) { return false; } 00232 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00233 CLASS_ID GetClassID () { return ClassID_Source; } 00234 00235 void write ( io::RFile f ); 00236 void read ( io::RFile f ); 00237 00238 protected : 00239 00240 void InitSource(); 00241 00242 }; 00243 00244 00245 // ==================== KeyWords ===================== 00246 00247 DefineClass(KeyWords); 00248 DefineStreamFunctions(KeyWords); 00249 00250 class KeyWords : public io::Stream { 00251 00252 public : 00253 int nKeyWords; // number of key words 00254 psvector KeyWord; // key word array 00255 00256 KeyWords (); 00257 KeyWords ( cpstr S ); 00258 KeyWords ( io::RPStream Object ); 00259 ~KeyWords(); 00260 00261 void Delete (); 00262 00263 void PDBASCIIDump ( io::RFile f ); 00264 void MakeCIF ( mmcif::PData CIF ); 00265 00266 int ConvertPDBASCII ( cpstr S ); 00267 void GetCIF ( mmcif::PData CIF ); 00268 00269 void Copy ( PKeyWords KeyWords ); 00270 00271 void write ( io::RFile f ); 00272 void read ( io::RFile f ); 00273 00274 protected : 00275 bool Cont; 00276 00277 void Init(); 00278 00279 }; 00280 00281 00282 // ==================== ExpData ===================== 00283 00284 DefineClass(ExpData); 00285 DefineStreamFunctions(ExpData); 00286 00287 class ExpData : public ContString { 00288 00289 public : 00290 00291 ExpData (); 00292 ExpData ( cpstr S ); 00293 ExpData ( io::RPStream Object ); 00294 ~ExpData(); 00295 00296 void PDBASCIIDump ( pstr S, int N ); 00297 bool PDBASCIIDump1 ( io::RFile ) { return false; } 00298 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00299 CLASS_ID GetClassID () { return ClassID_ExpData; } 00300 00301 void write ( io::RFile f ); 00302 void read ( io::RFile f ); 00303 00304 protected : 00305 00306 void InitExpData(); 00307 00308 }; 00309 00310 00311 // ==================== MdlType ===================== 00312 00313 DefineClass(MdlType); 00314 DefineStreamFunctions(MdlType); 00315 00316 class MdlType : public ContString { 00317 00318 public : 00319 00320 MdlType (); 00321 MdlType ( cpstr S ); 00322 MdlType ( io::RPStream Object ); 00323 ~MdlType(); 00324 00325 void PDBASCIIDump ( pstr S, int N ); 00326 bool PDBASCIIDump1 ( io::RFile ) { return false; } 00327 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00328 CLASS_ID GetClassID () { return ClassID_MdlType; } 00329 00330 void write ( io::RFile f ); 00331 void read ( io::RFile f ); 00332 00333 protected : 00334 00335 void InitMdlType(); 00336 00337 }; 00338 00339 00340 // ==================== Author ===================== 00341 00342 DefineClass(Author); 00343 DefineStreamFunctions(Author); 00344 00345 class Author : public ContString { 00346 00347 public : 00348 00349 Author (); 00350 Author ( cpstr S ); 00351 Author ( io::RPStream Object ); 00352 ~Author(); 00353 00354 void PDBASCIIDump ( pstr S, int N ); 00355 bool PDBASCIIDump1 ( io::RFile ) { return false; } 00356 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00357 CLASS_ID GetClassID () { return ClassID_Author; } 00358 00359 void write ( io::RFile f ); 00360 void read ( io::RFile f ); 00361 00362 protected : 00363 00364 void InitAuthor(); 00365 00366 }; 00367 00368 00369 // ==================== RevData ===================== 00370 00371 DefineClass(RevData); 00372 DefineStreamFunctions(RevData); 00373 00374 enum REVDAT_WARNING { 00375 REVDAT_WARN_MODNUM = 0x00000001, 00376 REVDAT_WARN_MODTYPE = 0x00000002 00377 }; 00378 00379 class RevData : public ContainerClass { 00380 00381 public : 00382 int modNum; 00383 Date modDate; 00384 char modId[13]; 00385 int modType; 00386 RecName record[4]; 00387 word Warning; 00388 00389 RevData (); 00390 RevData ( cpstr S ); 00391 RevData ( io::RPStream Object ); 00392 ~RevData(); 00393 00394 void PDBASCIIDump ( pstr S, int N ); 00395 void MakeCIF ( mmcif::PData CIF, int N ); 00396 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00397 ERROR_CODE GetCIF ( mmcif::PData CIF, int & n ); 00398 CLASS_ID GetClassID () { return ClassID_RevData; } 00399 00400 void Copy ( PContainerClass RevData ); 00401 00402 void write ( io::RFile f ); 00403 void read ( io::RFile f ); 00404 00405 protected : 00406 00407 void InitRevData(); 00408 00409 }; 00410 00411 00412 // ================== Supersede ======================== 00413 00414 DefineClass(Supersede); 00415 DefineStreamFunctions(Supersede); 00416 00417 class Supersede : public ContainerClass { 00418 00419 public : 00420 Date sprsdeDate; // date of supersede 00421 IDCode idCode; // ID code of the entry 00422 IDCode sIdCode[8]; // ID codes of superseded entries 00423 00424 Supersede (); 00425 Supersede ( cpstr S ); 00426 Supersede ( io::RPStream Object ); 00427 ~Supersede(); 00428 00429 void PDBASCIIDump ( pstr S, int N ); 00430 void MakeCIF ( mmcif::PData CIF, int N ); 00431 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00432 ERROR_CODE GetCIF ( mmcif::PData CIF, int & n ); 00433 CLASS_ID GetClassID () { return ClassID_Supersede; } 00434 00435 void Copy ( PContainerClass Supersede ); 00436 00437 void write ( io::RFile f ); 00438 void read ( io::RFile f ); 00439 00440 protected : 00441 00442 void InitSupersede(); 00443 00444 }; 00445 00446 00447 // ==================== Journal ===================== 00448 00449 DefineClass(Journal); 00450 DefineStreamFunctions(Journal); 00451 00452 class Journal : public ContString { 00453 00454 public : 00455 00456 Journal (); 00457 Journal ( cpstr S ); 00458 Journal ( io::RPStream Object ); 00459 ~Journal(); 00460 00461 void PDBASCIIDump ( pstr S, int N ); 00462 bool PDBASCIIDump1 ( io::RFile ) { return false; } 00463 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00464 CLASS_ID GetClassID () { return ClassID_Journal; } 00465 00466 void write ( io::RFile f ); 00467 void read ( io::RFile f ); 00468 00469 protected : 00470 00471 void InitJournal(); 00472 00473 }; 00474 00475 00476 // ==================== Remark ===================== 00477 00478 DefineClass(Remark); 00479 DefineStreamFunctions(Remark); 00480 00481 class Remark : public ContainerClass { 00482 00483 public : 00484 00485 int remarkNum; // remark id 00486 pstr remark; // remark line 00487 00488 Remark (); 00489 Remark ( cpstr S ); 00490 Remark ( io::RPStream Object ); 00491 ~Remark(); 00492 00493 void PDBASCIIDump ( pstr S, int N ); 00494 void MakeCIF ( mmcif::PData CIF, int N ); 00495 ERROR_CODE ConvertPDBASCII ( cpstr S ); 00496 ERROR_CODE GetCIF ( mmcif::PData CIF, int & n ); 00497 CLASS_ID GetClassID () { return ClassID_Remark; } 00498 00499 void Copy ( PContainerClass RemarkClass ); 00500 00501 void write ( io::RFile f ); 00502 void read ( io::RFile f ); 00503 00504 protected : 00505 00506 void InitRemark(); 00507 00508 }; 00509 00510 // ================= Biomolecule ===================== 00511 00512 DefineClass(BMApply); 00513 DefineStreamFunctions(BMApply); 00514 00515 class BMApply : public io::Stream { 00516 00517 public : 00518 PChainID chain; 00519 int nChains; 00520 pmat44 tm; 00521 int nMatrices; 00522 00523 BMApply (); 00524 BMApply ( io::RPStream Object ); 00525 ~BMApply(); 00526 00527 void FreeMemory(); 00528 00529 int addChains ( int & i, RPRemark rem, RTitleContainer Remark ); 00530 int addMatrices ( int & i, RPRemark rem, RTitleContainer Remark ); 00531 00532 void Copy ( PBMApply BMA ); // if BMA is NULL, then empties 00533 // the class 00534 void write ( io::RFile f ); 00535 void read ( io::RFile f ); 00536 00537 protected : 00538 void InitBMApply(); 00539 00540 }; 00541 00542 00543 DefineClass(Biomolecule); 00544 DefineStreamFunctions(Biomolecule); 00545 00546 class Biomolecule : public io::Stream { 00547 00548 public : 00549 PPBMApply bmApply; 00550 int nBMAs; 00551 00552 Biomolecule (); 00553 Biomolecule ( io::RPStream Object ); 00554 ~Biomolecule(); 00555 00556 void FreeMemory(); 00557 00558 PBMApply addBMApply(); 00559 00560 int Size(); 00561 bool checkComposition ( PChainID chID, ivector occ, 00562 ivector wocc, int n ); 00563 00564 void Copy ( PBiomolecule B ); // if B is NULL, then empties 00565 // the class 00566 void write ( io::RFile f ); 00567 void read ( io::RFile f ); 00568 00569 protected : 00570 void InitBiomolecule(); 00571 00572 }; 00573 00574 // ================= Title ======================= 00575 00576 DefineClass(Title); 00577 DefineStreamFunctions(Title); 00578 00579 class Title : public io::Stream { 00580 00581 friend class Model; 00582 friend class Chain; 00583 friend class Root; 00584 00585 public : 00586 00587 Title (); 00588 Title ( io::RPStream Object ); 00589 ~Title(); 00590 00591 void FreeMemory ( bool keepBiomolecules ); 00592 00593 // Fills the PDB file header 00594 void SetHeader ( cpstr Classification, // any length is Ok 00595 cpstr DepDate, // DD-MMM-YYYY 00596 cpstr ID_Code ); // not more than 11 chars 00597 00598 // Interprets the ASCII PDB line belonging to the title section 00599 // and fills the corresponding fields. 00600 // Returns zero if the line was converted, otherwise returns a 00601 // non-negative value of Error_XXXX. 00602 // PDBString must be not shorter than 81 characters. 00603 ERROR_CODE ConvertPDBString ( pstr PDBString ); 00604 00605 // MakePDBString() makes the ASCII PDB HEADER line from the 00606 // class data. PDBString must be not shorter than 81 characters. 00607 void MakePDBHeaderString ( pstr PDBString ); 00608 00609 // GetStructureTitle() returns the contents of TITLE record 00610 // unfolded into single line. If Title is missing, returns 00611 // contents of COMPND(:MOLECULE). If COMPND is missing, returns 00612 // HEADER. If Header is missing, returns PDB code. If no PDB 00613 // code is there, returns "Not available". 00614 pstr GetStructureTitle ( pstr & S ); 00615 00616 PTitleContainer GetObsData () { return &obsData; } 00617 PTitleContainer GetCaveat () { return &caveat; } 00618 PTitleContainer GetCompound() { return &compound; } 00619 PTitleContainer GetSource () { return &source; } 00620 PKeyWords GetKeyWords() { return &keyWords; } 00621 PTitleContainer GetExpData () { return &expData; } 00622 PTitleContainer GetMdlType () { return &mdlType; } 00623 PTitleContainer GetRemarks () { return &remark; } 00624 PTitleContainer GetJournal () { return &journal; } 00625 00626 realtype GetResolution(); // -1.0 mean no resolution record in file 00627 00628 int ParseBiomolecules(); // returns the number of biomolecules, 00629 // -2 for general format error 00630 // -3 for errors in BIOMT records 00631 00632 int GetNofBiomolecules(); 00633 void GetBiomolecules ( PPBiomolecule & BM, int & nBMs ); 00634 PBiomolecule GetBiomolecule ( int bmNo ); // bmno=0,1,.. 00635 // returns NULL if bmNo is incorrect 00636 00637 void PDBASCIIDump ( io::RFile f ); 00638 void MakeCIF ( mmcif::PData CIF ); 00639 00640 // GetCIF(..) returns the same code as ConvertPDBString(..) 00641 // save for Error_WrongSection 00642 ERROR_CODE GetCIF ( mmcif::PData CIF ); 00643 00644 inline pstr GetIDCode() { return idCode; } 00645 inline bool GetCol73 () { return col73; } 00646 void TrimInput ( pstr PDBString ); 00647 00648 void Copy ( PTitle TS ); // if TS is NULL, then empties 00649 // the class 00650 00651 void write ( io::RFile f ); // writes header to PDB binary file 00652 void read ( io::RFile f ); // reads header from PDB binary file 00653 00654 protected : 00655 00656 // Header data 00657 pstr classification; // classification of the molecule 00658 Date depDate; // deposition date DD-MMM-YYYY 00659 IDCode idCode; // unique PDB identifier 00660 realtype resolution; // resolution 00661 bool col73; // True if columns 73-80 contain PDB ID 00662 00663 TitleContainer obsData; // obsoletion data 00664 TitleContainer title; // title data 00665 TitleContainer caveat; // error data 00666 TitleContainer compound; // compound data 00667 TitleContainer source; // source 00668 KeyWords keyWords; // key words 00669 TitleContainer expData; // experimental data 00670 TitleContainer mdlType; // model desctiptions 00671 TitleContainer author; // author data 00672 TitleContainer revData; // revision data 00673 TitleContainer supersede; // supersede records 00674 TitleContainer journal; // journal records 00675 TitleContainer remark; // remark records 00676 00677 PPBiomolecule biomolecule; 00678 int nBiomolecules; 00679 00680 void Init(); 00681 void FreeBiomolecules(); 00682 00683 PBiomolecule addBiomolecule(); 00684 00685 }; 00686 00687 extern void TestHeader(); 00688 extern void TestTitle (); // reads PDB title from file 'in.title' 00689 // and rewrites it into 'out.title' and 00690 // 'abin.title' 00691 00692 } // namespace mmdb 00693 00694 00695 #endif 00696
