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|
// $Id: mmdb_title.h $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
// Copyright (C) Eugene Krissinel 2000-2013.
//
// 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.
//
// =================================================================
//
// 12.09.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : MMDB_Title <interface>
// ~~~~~~~~~
// **** Project : MacroMolecular Data Base (MMDB)
// ~~~~~~~~~
// **** Classes : mmdb::TitleContainer (container of title classes)
// ~~~~~~~~~ mmdb::ObsLine
// mmdb::TitleLine
// mmdb::Caveat
// mmdb::Compound
// mmdb::Source
// mmdb::KeyWords
// mmdb::ExpData
// mmdb::MdlType
// mmdb::Author
// mmdb::RevData
// mmdb::Supersede
// mmdb::Journal
// mmdb::Remark
// mmdb::Biomolecule
// mmdb::Title ( MMDB title section )
//
// (C) E. Krissinel 2000-2013
//
// =================================================================
//
#ifndef __MMDB_Title__
#define __MMDB_Title__
#include "mmdb_io_stream.h"
#include "mmdb_defs.h"
#include "mmdb_utils.h"
#include "mmdb_mmcif_.h"
namespace mmdb {
// ====================== TitleContainer =======================
DefineClass(TitleContainer);
DefineStreamFunctions(TitleContainer);
class TitleContainer : public ClassContainer {
public :
TitleContainer () : ClassContainer() {}
TitleContainer ( io::RPStream Object )
: ClassContainer ( Object ) {}
~TitleContainer() {}
PContainerClass MakeContainerClass ( int ClassID );
};
// ================== ObsLine ========================
DefineClass(ObsLine);
DefineStreamFunctions(ObsLine);
class ObsLine : public ContainerClass {
public :
Date repDate; // date of replacement
IDCode idCode; // ID code of replaced entry
IDCode rIdCode[8]; // ID codes of entries that replaced this one
ObsLine ();
ObsLine ( cpstr S );
ObsLine ( io::RPStream Object );
~ObsLine();
void PDBASCIIDump ( pstr S, int N );
void MakeCIF ( mmcif::PData CIF, int N );
ERROR_CODE ConvertPDBASCII ( cpstr S );
ERROR_CODE GetCIF ( mmcif::PData CIF, int & n );
CLASS_ID GetClassID () { return ClassID_ObsLine; }
void Copy ( PContainerClass ObsLine );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitObsLine();
};
// ==================== TitleLine =====================
DefineClass(TitleLine);
DefineStreamFunctions(TitleLine);
class TitleLine : public ContString {
public :
TitleLine ();
TitleLine ( cpstr S );
TitleLine ( io::RPStream Object );
~TitleLine();
ERROR_CODE ConvertPDBASCII ( cpstr S );
void PDBASCIIDump ( pstr S, int N );
bool PDBASCIIDump1 ( io::RFile ) { return false; }
CLASS_ID GetClassID () { return ClassID_TitleLine; }
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitTitleLine();
};
// ==================== Caveat =====================
DefineClass(Caveat);
DefineStreamFunctions(Caveat);
class Caveat : public ContString {
public :
IDCode idCode; // ID code of the entry
Caveat ();
Caveat ( cpstr S );
Caveat ( io::RPStream Object );
~Caveat();
void PDBASCIIDump ( pstr S, int N );
bool PDBASCIIDump1 ( io::RFile ) { return false; }
void MakeCIF ( mmcif::PData CIF, int N );
ERROR_CODE ConvertPDBASCII ( cpstr S );
// virtual void GetCIF1 ( mmcif::PData CIF, ERROR_CODE & Signal,
// int & pos );
CLASS_ID GetClassID () { return ClassID_CAVEAT; }
void Copy ( PContainerClass Caveat );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitCaveat();
};
// ==================== Compound =====================
DefineClass(Compound);
DefineStreamFunctions(Compound);
class Compound : public ContString {
public :
Compound ();
Compound ( cpstr S );
Compound ( io::RPStream Object );
~Compound();
void PDBASCIIDump ( pstr S, int N );
bool PDBASCIIDump1 ( io::RFile ) { return false; }
ERROR_CODE ConvertPDBASCII ( cpstr S );
CLASS_ID GetClassID () { return ClassID_Compound; }
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitCompound();
};
// ==================== Source =====================
DefineClass(Source);
DefineStreamFunctions(Source);
class Source : public ContString {
public :
Source ();
Source ( cpstr S );
Source ( io::RPStream Object );
~Source();
void PDBASCIIDump ( pstr S, int N );
bool PDBASCIIDump1 ( io::RFile ) { return false; }
ERROR_CODE ConvertPDBASCII ( cpstr S );
CLASS_ID GetClassID () { return ClassID_Source; }
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitSource();
};
// ==================== KeyWords =====================
DefineClass(KeyWords);
DefineStreamFunctions(KeyWords);
class KeyWords : public io::Stream {
public :
int nKeyWords; // number of key words
psvector KeyWord; // key word array
KeyWords ();
KeyWords ( cpstr S );
KeyWords ( io::RPStream Object );
~KeyWords();
void Delete ();
void PDBASCIIDump ( io::RFile f );
void MakeCIF ( mmcif::PData CIF );
int ConvertPDBASCII ( cpstr S );
void GetCIF ( mmcif::PData CIF );
void Copy ( PKeyWords KeyWords );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
bool Cont;
void Init();
};
// ==================== ExpData =====================
DefineClass(ExpData);
DefineStreamFunctions(ExpData);
class ExpData : public ContString {
public :
ExpData ();
ExpData ( cpstr S );
ExpData ( io::RPStream Object );
~ExpData();
void PDBASCIIDump ( pstr S, int N );
bool PDBASCIIDump1 ( io::RFile ) { return false; }
ERROR_CODE ConvertPDBASCII ( cpstr S );
CLASS_ID GetClassID () { return ClassID_ExpData; }
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitExpData();
};
// ==================== MdlType =====================
DefineClass(MdlType);
DefineStreamFunctions(MdlType);
class MdlType : public ContString {
public :
MdlType ();
MdlType ( cpstr S );
MdlType ( io::RPStream Object );
~MdlType();
void PDBASCIIDump ( pstr S, int N );
bool PDBASCIIDump1 ( io::RFile ) { return false; }
ERROR_CODE ConvertPDBASCII ( cpstr S );
CLASS_ID GetClassID () { return ClassID_MdlType; }
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitMdlType();
};
// ==================== Author =====================
DefineClass(Author);
DefineStreamFunctions(Author);
class Author : public ContString {
public :
Author ();
Author ( cpstr S );
Author ( io::RPStream Object );
~Author();
void PDBASCIIDump ( pstr S, int N );
bool PDBASCIIDump1 ( io::RFile ) { return false; }
ERROR_CODE ConvertPDBASCII ( cpstr S );
CLASS_ID GetClassID () { return ClassID_Author; }
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitAuthor();
};
// ==================== RevData =====================
DefineClass(RevData);
DefineStreamFunctions(RevData);
enum REVDAT_WARNING {
REVDAT_WARN_MODNUM = 0x00000001,
REVDAT_WARN_MODTYPE = 0x00000002
};
class RevData : public ContainerClass {
public :
int modNum;
Date modDate;
char modId[13];
int modType;
RecName record[4];
word Warning;
RevData ();
RevData ( cpstr S );
RevData ( io::RPStream Object );
~RevData();
void PDBASCIIDump ( pstr S, int N );
void MakeCIF ( mmcif::PData CIF, int N );
ERROR_CODE ConvertPDBASCII ( cpstr S );
ERROR_CODE GetCIF ( mmcif::PData CIF, int & n );
CLASS_ID GetClassID () { return ClassID_RevData; }
void Copy ( PContainerClass RevData );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitRevData();
};
// ================== Supersede ========================
DefineClass(Supersede);
DefineStreamFunctions(Supersede);
class Supersede : public ContainerClass {
public :
Date sprsdeDate; // date of supersede
IDCode idCode; // ID code of the entry
IDCode sIdCode[8]; // ID codes of superseded entries
Supersede ();
Supersede ( cpstr S );
Supersede ( io::RPStream Object );
~Supersede();
void PDBASCIIDump ( pstr S, int N );
void MakeCIF ( mmcif::PData CIF, int N );
ERROR_CODE ConvertPDBASCII ( cpstr S );
ERROR_CODE GetCIF ( mmcif::PData CIF, int & n );
CLASS_ID GetClassID () { return ClassID_Supersede; }
void Copy ( PContainerClass Supersede );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitSupersede();
};
// ==================== Journal =====================
DefineClass(Journal);
DefineStreamFunctions(Journal);
class Journal : public ContString {
public :
Journal ();
Journal ( cpstr S );
Journal ( io::RPStream Object );
~Journal();
void PDBASCIIDump ( pstr S, int N );
bool PDBASCIIDump1 ( io::RFile ) { return false; }
ERROR_CODE ConvertPDBASCII ( cpstr S );
CLASS_ID GetClassID () { return ClassID_Journal; }
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitJournal();
};
// ==================== Remark =====================
DefineClass(Remark);
DefineStreamFunctions(Remark);
class Remark : public ContainerClass {
public :
int remarkNum; // remark id
pstr remark; // remark line
Remark ();
Remark ( cpstr S );
Remark ( io::RPStream Object );
~Remark();
void PDBASCIIDump ( pstr S, int N );
void MakeCIF ( mmcif::PData CIF, int N );
ERROR_CODE ConvertPDBASCII ( cpstr S );
ERROR_CODE GetCIF ( mmcif::PData CIF, int & n );
CLASS_ID GetClassID () { return ClassID_Remark; }
void Copy ( PContainerClass RemarkClass );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitRemark();
};
// ================= Biomolecule =====================
DefineClass(BMApply);
DefineStreamFunctions(BMApply);
class BMApply : public io::Stream {
public :
PChainID chain;
int nChains;
pmat44 tm;
int nMatrices;
BMApply ();
BMApply ( io::RPStream Object );
~BMApply();
void FreeMemory();
int addChains ( int & i, RPRemark rem, RTitleContainer Remark );
int addMatrices ( int & i, RPRemark rem, RTitleContainer Remark );
void Copy ( PBMApply BMA ); // if BMA is NULL, then empties
// the class
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitBMApply();
};
DefineClass(Biomolecule);
DefineStreamFunctions(Biomolecule);
class Biomolecule : public io::Stream {
public :
PPBMApply bmApply;
int nBMAs;
Biomolecule ();
Biomolecule ( io::RPStream Object );
~Biomolecule();
void FreeMemory();
PBMApply addBMApply();
int Size();
bool checkComposition ( PChainID chID, ivector occ,
ivector wocc, int n );
void Copy ( PBiomolecule B ); // if B is NULL, then empties
// the class
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void InitBiomolecule();
};
// ================= Title =======================
DefineClass(Title);
DefineStreamFunctions(Title);
class Title : public io::Stream {
friend class Model;
friend class Chain;
friend class Root;
public :
Title ();
Title ( io::RPStream Object );
~Title();
void FreeMemory ( bool 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.
ERROR_CODE 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 );
PTitleContainer GetObsData () { return &obsData; }
PTitleContainer GetCaveat () { return &caveat; }
PTitleContainer GetCompound() { return &compound; }
PTitleContainer GetSource () { return &source; }
PKeyWords GetKeyWords() { return &keyWords; }
PTitleContainer GetExpData () { return &expData; }
PTitleContainer GetMdlType () { return &mdlType; }
PTitleContainer GetRemarks () { return &remark; }
PTitleContainer GetJournal () { return &journal; }
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 ( PPBiomolecule & BM, int & nBMs );
PBiomolecule GetBiomolecule ( int bmNo ); // bmno=0,1,..
// returns NULL if bmNo is incorrect
void PDBASCIIDump ( io::RFile f );
void MakeCIF ( mmcif::PData CIF );
// GetCIF(..) returns the same code as ConvertPDBString(..)
// save for Error_WrongSection
ERROR_CODE GetCIF ( mmcif::PData CIF );
inline pstr GetIDCode() { return idCode; }
inline bool GetCol73 () { return col73; }
void TrimInput ( pstr PDBString );
void Copy ( PTitle TS ); // if TS is NULL, then empties
// the class
void write ( io::RFile f ); // writes header to PDB binary file
void read ( io::RFile 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
bool col73; // True if columns 73-80 contain PDB ID
TitleContainer obsData; // obsoletion data
TitleContainer title; // title data
TitleContainer caveat; // error data
TitleContainer compound; // compound data
TitleContainer source; // source
KeyWords keyWords; // key words
TitleContainer expData; // experimental data
TitleContainer mdlType; // model descriptions
TitleContainer author; // author data
TitleContainer revData; // revision data
TitleContainer supersede; // supersede records
TitleContainer journal; // journal records
TitleContainer remark; // remark records
PPBiomolecule biomolecule;
int nBiomolecules;
void Init();
void FreeBiomolecules();
PBiomolecule addBiomolecule();
};
extern void TestHeader();
extern void TestTitle (); // reads PDB title from file 'in.title'
// and rewrites it into 'out.title' and
// 'abin.title'
} // namespace mmdb
#endif
|