/usr/include/mmdb/mmdb_title.h is in libmmdb-dev 1.25.5-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
// Copyright (C) Eugene Krissinel 2000-2008.
//
// This library is free software: you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License version 3, modified in accordance with the provisions
// of the license to address the requirements of UK law.
//
// You should have received a copy of the modified GNU Lesser
// General Public License along with this library. If not, copies
// may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
// =================================================================
//
// 23.06.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : MMDB_Title <interface>
// ~~~~~~~~~
// **** Project : MacroMolecular Data Base (MMDB)
// ~~~~~~~~~
// **** Classes : CTitleContainer (container of title classes)
// ~~~~~~~~~ CObsLine
// CTitleLine
// CCaveat
// CCompound
// CSource
// CKeyWords
// CExpData
// CMdlType
// CAuthor
// CRevData
// CSupersede
// CJournal
// CRemark
// CBiomolecule
// CMMDBTitle ( MMDB title section )
//
// (C) E. Krissinel 2000-2013
//
// =================================================================
//
#ifndef __MMDB_Title__
#define __MMDB_Title__
#ifndef __Stream__
#include "stream_.h"
#endif
#ifndef __MMDB_Defs__
#include "mmdb_defs.h"
#endif
#ifndef __MMDB_Utils__
#include "mmdb_utils.h"
#endif
#ifndef __MMDB_MMCIF__
#include "mmdb_mmcif.h"
#endif
// ==================== CTitleContainer ======================
DefineClass(CTitleContainer);
DefineStreamFunctions(CTitleContainer);
class CTitleContainer : public CClassContainer {
public :
CTitleContainer () : CClassContainer() {}
CTitleContainer ( RPCStream Object )
: CClassContainer ( Object ) {}
~CTitleContainer () {}
PCContainerClass MakeContainerClass ( int ClassID );
};
// ================== CObsLine ========================
DefineClass(CObsLine);
DefineStreamFunctions(CObsLine);
class CObsLine : public CContainerClass {
public :
Date repDate; // date of replacement
IDCode idCode; // ID code of replaced entry
IDCode rIdCode[8]; // ID codes of entries that replaced this one
CObsLine ();
CObsLine ( cpstr S );
CObsLine ( RPCStream Object );
~CObsLine();
void PDBASCIIDump ( pstr S, int N );
void MakeCIF ( PCMMCIFData CIF, int N );
int ConvertPDBASCII ( cpstr S );
void GetCIF ( PCMMCIFData CIF, int & Signal );
int GetClassID () { return ClassID_ObsLine; }
void Copy ( PCContainerClass ObsLine );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitObsLine();
};
// ==================== CTitleLine =====================
DefineClass(CTitleLine);
DefineStreamFunctions(CTitleLine);
class CTitleLine : public CContString {
public :
CTitleLine ();
CTitleLine ( cpstr S );
CTitleLine ( RPCStream Object );
~CTitleLine();
int ConvertPDBASCII ( cpstr S );
void PDBASCIIDump ( pstr S, int N );
Boolean PDBASCIIDump1 ( RCFile ) { return False; }
int GetClassID () { return ClassID_TitleLine; }
// void GetCIF ( PCMMCIFData CIF, int & Signal );
// void MakeCIF ( PCMMCIFData CIF, int N );
// void Copy ( PCContainerClass TitleLine );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitTitleLine();
};
// ==================== CCaveat =====================
DefineClass(CCaveat);
DefineStreamFunctions(CCaveat);
class CCaveat : public CContString {
public :
IDCode idCode; // ID code of the entry
CCaveat ();
CCaveat ( cpstr S );
CCaveat ( RPCStream Object );
~CCaveat();
void PDBASCIIDump ( pstr S, int N );
Boolean PDBASCIIDump1 ( RCFile ) { return False; }
void MakeCIF ( PCMMCIFData CIF, int N );
int ConvertPDBASCII ( cpstr S );
void GetCIF ( PCMMCIFData CIF, int & Signal );
int GetClassID () { return ClassID_CAVEAT; }
void Copy ( PCContainerClass Caveat );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitCaveat();
};
// ==================== CCompound =====================
DefineClass(CCompound);
DefineStreamFunctions(CCompound);
class CCompound : public CContString {
public :
CCompound ();
CCompound ( cpstr S );
CCompound ( RPCStream Object );
~CCompound();
void PDBASCIIDump ( pstr S, int N );
Boolean PDBASCIIDump1 ( RCFile ) { return False; }
int ConvertPDBASCII ( cpstr S );
int GetClassID () { return ClassID_Compound; }
// void GetCIF ( PCMMCIFData CIF, int & Signal );
// void MakeCIF ( PCMMCIFData CIF, int N );
// void Copy ( PCContainerClass Compound );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitCompound();
};
// ==================== CSource =====================
DefineClass(CSource);
DefineStreamFunctions(CSource);
class CSource : public CContString {
public :
CSource ();
CSource ( cpstr S );
CSource ( RPCStream Object );
~CSource();
void PDBASCIIDump ( pstr S, int N );
Boolean PDBASCIIDump1 ( RCFile ) { return False; }
int ConvertPDBASCII ( cpstr S );
int GetClassID () { return ClassID_Source; }
// void GetCIF ( PCMMCIFData CIF, int & Signal );
// void MakeCIF ( PCMMCIFData CIF, int N );
// void Copy ( PCContainerClass Source );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitSource();
};
// ==================== CKeyWords =====================
DefineClass(CKeyWords);
DefineStreamFunctions(CKeyWords);
class CKeyWords : public CStream {
public :
int nKeyWords; // number of key words
psvector KeyWord; // key word array
CKeyWords ();
CKeyWords ( cpstr S );
CKeyWords ( RPCStream Object );
~CKeyWords();
void Delete ();
void PDBASCIIDump ( RCFile f );
void MakeCIF ( PCMMCIFData CIF );
int ConvertPDBASCII ( cpstr S );
void GetCIF ( PCMMCIFData CIF );
void Copy ( PCKeyWords KeyWords );
void write ( RCFile f );
void read ( RCFile f );
protected :
Boolean Cont;
void Init();
};
// ==================== CExpData =====================
DefineClass(CExpData);
DefineStreamFunctions(CExpData);
class CExpData : public CContString {
public :
CExpData ();
CExpData ( cpstr S );
CExpData ( RPCStream Object );
~CExpData();
void PDBASCIIDump ( pstr S, int N );
Boolean PDBASCIIDump1 ( RCFile ) { return False; }
int ConvertPDBASCII ( cpstr S );
int GetClassID () { return ClassID_ExpData; }
// void GetCIF ( PCMMCIFData CIF, int & Signal );
// void MakeCIF ( PCMMCIFData CIF, int N );
// void Copy ( PCContainerClass ExpData );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitExpData();
};
// ==================== CMdlType =====================
DefineClass(CMdlType);
DefineStreamFunctions(CMdlType);
class CMdlType : public CContString {
public :
CMdlType ();
CMdlType ( cpstr S );
CMdlType ( RPCStream Object );
~CMdlType();
void PDBASCIIDump ( pstr S, int N );
Boolean PDBASCIIDump1 ( RCFile ) { return False; }
int ConvertPDBASCII ( cpstr S );
int GetClassID () { return ClassID_MdlType; }
// void GetCIF ( PCMMCIFData CIF, int & Signal );
// void MakeCIF ( PCMMCIFData CIF, int N );
// void Copy ( PCContainerClass ExpData );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitMdlType();
};
// ==================== CAuthor =====================
DefineClass(CAuthor);
DefineStreamFunctions(CAuthor);
class CAuthor : public CContString {
public :
CAuthor ();
CAuthor ( cpstr S );
CAuthor ( RPCStream Object );
~CAuthor();
void PDBASCIIDump ( pstr S, int N );
Boolean PDBASCIIDump1 ( RCFile ) { return False; }
int ConvertPDBASCII ( cpstr S );
int GetClassID () { return ClassID_Author; }
// void GetCIF ( PCMMCIFData CIF, int & Signal );
// void MakeCIF ( PCMMCIFData CIF, int N );
// void Copy ( PCContainerClass Author );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitAuthor();
};
// ==================== CRevData =====================
DefineClass(CRevData);
DefineStreamFunctions(CRevData);
#define REVDAT_WARN_MODNUM 0x00000001
#define REVDAT_WARN_MODTYPE 0x00000002
class CRevData : public CContainerClass {
public :
int modNum;
Date modDate;
char modId[13];
int modType;
RecName record[4];
word Warning;
CRevData ();
CRevData ( cpstr S );
CRevData ( RPCStream Object );
~CRevData();
void PDBASCIIDump ( pstr S, int N );
void MakeCIF ( PCMMCIFData CIF, int N );
int ConvertPDBASCII ( cpstr S );
void GetCIF ( PCMMCIFData CIF, int & Signal );
int GetClassID () { return ClassID_RevData; }
void Copy ( PCContainerClass RevData );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitRevData();
};
// ================== CSupersede ========================
DefineClass(CSupersede);
DefineStreamFunctions(CSupersede);
class CSupersede : public CContainerClass {
public :
Date sprsdeDate; // date of supersede
IDCode idCode; // ID code of the entry
IDCode sIdCode[8]; // ID codes of superseded entries
CSupersede ();
CSupersede ( cpstr S );
CSupersede ( RPCStream Object );
~CSupersede();
void PDBASCIIDump ( pstr S, int N );
void MakeCIF ( PCMMCIFData CIF, int N );
int ConvertPDBASCII ( cpstr S );
void GetCIF ( PCMMCIFData CIF, int & Signal );
int GetClassID () { return ClassID_Supersede; }
void Copy ( PCContainerClass Supersede );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitSupersede();
};
// ==================== CJournal =====================
DefineClass(CJournal);
DefineStreamFunctions(CJournal);
class CJournal : public CContString {
public :
CJournal ();
CJournal ( cpstr S );
CJournal ( RPCStream Object );
~CJournal();
void PDBASCIIDump ( pstr S, int N );
Boolean PDBASCIIDump1 ( RCFile ) { return False; }
int ConvertPDBASCII ( cpstr S );
int GetClassID () { return ClassID_Journal; }
// void GetCIF ( PCMMCIFData CIF, int & Signal );
// void MakeCIF ( PCMMCIFData CIF, int N );
// void Copy ( PCContainerClass Journal );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitJournal();
};
// ==================== CRemark =====================
DefineClass(CRemark);
DefineStreamFunctions(CRemark);
class CRemark : public CContainerClass {
public :
int remarkNum; // remark id
pstr Remark; // remark line
CRemark ();
CRemark ( cpstr S );
CRemark ( RPCStream Object );
~CRemark();
void PDBASCIIDump ( pstr S, int N );
void MakeCIF ( PCMMCIFData CIF, int N );
int ConvertPDBASCII ( cpstr S );
void GetCIF ( PCMMCIFData CIF, int & Signal );
int GetClassID () { return ClassID_Remark; }
void Copy ( PCContainerClass RemarkClass );
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitRemark();
};
// ================= CBiomolecule =====================
DefineClass(CBMApply);
DefineStreamFunctions(CBMApply);
class CBMApply : public CStream {
public :
PChainID chain;
int nChains;
pmat44 tm;
int nMatrices;
CBMApply ();
CBMApply ( RPCStream Object );
~CBMApply();
void FreeMemory();
int addChains ( int & i, RPCRemark rem, RCTitleContainer Remark );
int addMatrices ( int & i, RPCRemark rem, RCTitleContainer Remark );
void Copy ( PCBMApply BMA ); // if BMA is NULL, then empties
// the class
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitBMApply();
};
DefineClass(CBiomolecule);
DefineStreamFunctions(CBiomolecule);
class CBiomolecule : public CStream {
public :
PPCBMApply BMApply;
int nBMAs;
CBiomolecule ();
CBiomolecule ( RPCStream Object );
~CBiomolecule();
void FreeMemory();
PCBMApply addBMApply();
int Size();
Boolean checkComposition ( PChainID chID, ivector occ,
ivector wocc, int n );
void Copy ( PCBiomolecule B ); // if B is NULL, then empties
// the class
void write ( RCFile f );
void read ( RCFile f );
protected :
void InitBiomolecule();
};
// ================= CMMDBTitle =======================
DefineClass(CMMDBTitle);
DefineStreamFunctions(CMMDBTitle);
class CMMDBTitle : public CStream {
friend class CModel;
friend class CChain;
friend class CMMDBFile;
public :
CMMDBTitle ();
CMMDBTitle ( RPCStream Object );
~CMMDBTitle();
void FreeMemory ( Boolean keepBiomolecules );
// Fills the PDB file header
void SetHeader ( cpstr Classification, // any length is Ok
cpstr DepDate, // DD-MMM-YYYY
cpstr ID_Code ); // not more than 11 chars
// Interprets the ASCII PDB line belonging to the title section
// and fills the corresponding fields.
// Returns zero if the line was converted, otherwise returns a
// non-negative value of Error_XXXX.
// PDBString must be not shorter than 81 characters.
int ConvertPDBString ( pstr PDBString );
// MakePDBString() makes the ASCII PDB HEADER line from the
// class data. PDBString must be not shorter than 81 characters.
void MakePDBHeaderString ( pstr PDBString );
// GetStructureTitle() returns the contents of TITLE record
// unfolded into single line. If Title is missing, returns
// contents of COMPND(:MOLECULE). If COMPND is missing, returns
// HEADER. If Header is missing, returns PDB code. If no PDB
// code is there, returns "Not available".
pstr GetStructureTitle ( pstr & S );
PCTitleContainer GetRemarks();
PCTitleContainer GetJournal();
realtype GetResolution(); // -1.0 mean no resolution record in file
int ParseBiomolecules(); // returns the number of biomolecules,
// -2 for general format error
// -3 for errors in BIOMT records
int GetNofBiomolecules();
void GetBiomolecules ( PPCBiomolecule & BM, int & nBMs );
PCBiomolecule GetBiomolecule ( int bmNo ); // bmno=0,1,..
// returns NULL if bmNo is incorrect
void PDBASCIIDump ( RCFile f );
void MakeCIF ( PCMMCIFData CIF );
// GetCIF(..) returns the same code as ConvertPDBString(..)
// save for Error_WrongSection
int GetCIF ( PCMMCIFData CIF );
pstr GetIDCode() { return idCode; }
Boolean GetCol73() { return col73; }
void TrimInput ( pstr PDBString );
void Copy ( PCMMDBTitle TS ); // if TS is NULL, then empties
// the class
void write ( RCFile f ); // writes header to PDB binary file
void read ( RCFile f ); // reads header from PDB binary file
protected :
// Header data
pstr classification; // classification of the molecule
Date depDate; // deposition date DD-MMM-YYYY
IDCode idCode; // unique PDB identifier
realtype resolution; // resolution
Boolean col73; // True if columns 73-80 contain PDB ID
CTitleContainer ObsData; // obsoletion data
CTitleContainer Title; // title data
CTitleContainer CAVEAT; // error data
CTitleContainer Compound; // compound data
CTitleContainer Source; // source
CKeyWords KeyWords; // key words
CTitleContainer ExpData; // experimental data
CTitleContainer MdlType; // model desctiptions
CTitleContainer Author; // author data
CTitleContainer RevData; // revision data
CTitleContainer Supersede; // supersede records
CTitleContainer Journal; // journal records
CTitleContainer Remark; // remark records
PPCBiomolecule Biomolecule;
int nBiomolecules;
void Init();
void FreeBiomolecules();
PCBiomolecule addBiomolecule();
};
extern void TestHeader();
extern void TestTitle (); // reads PDB title from file 'in.title'
// and rewrites it into 'out.title' and
// 'abin.title'
#endif
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