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|
// $Id: mmdb_root.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.
//
// =================================================================
//
// 24.07.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : MMDB_Root <interface>
// ~~~~~~~~~
// Project : MacroMolecular Data Base (MMDB)
// ~~~~~~~~~
// **** Classes : mmdb::Root
// ~~~~~~~~~
//
// (C) E. Krissinel 2000-2015
//
// =================================================================
//
#ifndef __MMDB_Root__
#define __MMDB_Root__
#include "mmdb_io_file.h"
#include "mmdb_uddata.h"
#include "mmdb_title.h"
#include "mmdb_cryst.h"
#include "mmdb_chain.h"
#include "mmdb_model.h"
#include "mmdb_defs.h"
namespace mmdb {
// ======================= Root ===========================
// special effect flags
enum MMDB_READ_FLAG {
MMDBF_AutoSerials = 0x00000001,
MMDBF_NoCoordRead = 0x00000002,
MMDBF_SimRWBROOK = 0x00000004,
MMDBF_PrintCIFWarnings = 0x00000008,
MMDBF_EnforceSpaces = 0x00000010,
MMDBF_IgnoreDuplSeqNum = 0x00000020,
MMDBF_IgnoreSegID = 0x00000040,
MMDBF_IgnoreElement = 0x00000080,
MMDBF_IgnoreCharge = 0x00000100,
MMDBF_IgnoreNonCoorPDBErrors = 0x00000200,
MMDBF_IgnoreUnmatch = 0x00000400,
MMDBF_IgnoreBlankLines = 0x00000800,
MMDBF_IgnoreHash = 0x00001000,
MMDBF_IgnoreRemarks = 0x00002000,
MMDBF_AllowDuplChainID = 0x00004000,
MMDBF_FixSpaceGroup = 0x00008000,
MMDBF_EnforceAtomNames = 0x00010000,
MMDBF_EnforceUniqueChainID = 0x00020000,
MMDBF_DoNotProcessSpaceGroup = 0x00040000,
MMDBF_MakeCompactBinary = 0x00080000
};
// MMDBF_EnforceUniqueChainID will make MMDB to rename chains on
// reading a file such as to maintain chains uniquesness. This
// is supposed to work only with 1-letter chain IDs and only
// if chain names are interchanged in the file. For example,
// if file contains a sequence of chains named
//
// A,B, A,B, A,B, A,B, A,B
//
// and this flag is set on, the resulting chain names in
// MMDB will be:
//
// A,B, A0,B0, A1,B1, A2,B2, A3,B3
//
// file types:
enum MMDB_FILE_TYPE {
MMDB_FILE_Undefined = -1,
MMDB_FILE_PDB = 0,
MMDB_FILE_CIF = 1,
MMDB_FILE_Binary = 2
};
// cleanup flags:
enum PDB_CLEAN_FLAG {
PDBCLEAN_ATNAME = 0x00000001,
PDBCLEAN_TER = 0x00000002,
PDBCLEAN_CHAIN = 0x00000004,
PDBCLEAN_CHAIN_STRONG = 0x00000008,
PDBCLEAN_ALTCODE = 0x00000010,
PDBCLEAN_ALTCODE_STRONG = 0x00000020,
PDBCLEAN_SERIAL = 0x00000040,
PDBCLEAN_SEQNUM = 0x00000080,
PDBCLEAN_CHAIN_ORDER = 0x00000100,
PDBCLEAN_CHAIN_ORDER_IX = 0x00000200,
PDBCLEAN_SOLVENT = 0x00000400,
PDBCLEAN_INDEX = 0x00000800,
PDBCLEAN_ELEMENT = 0x00001000,
PDBCLEAN_ELEMENT_STRONG = 0x00002000
};
// crystallographic info inquery
enum MMDB_CRYST_FLAG {
CRRDY_NotPrecise = 0x00000001,
CRRDY_isTranslation = 0x00000002,
CRRDY_NoOrthCode = 0x00000004,
CRRDY_Complete = 0,
CRRDY_NoTransfMatrices = -1,
CRRDY_Unchecked = -2,
CRRDY_Ambiguous = -3,
CRRDY_NoCell = -4,
CRRDY_NoSpaceGroup = -5
};
DefineClass(Root);
DefineStreamFunctions(Root);
class Root : public UDData {
friend class Model;
friend class Chain;
friend class Residue;
friend class Atom;
public :
Root ();
Root ( io::RPStream Object );
~Root();
void FreeFileMemory();
// --------------- Reading/Writing external files ---------
void SetFlag ( word Flag );
void RemoveFlag ( word Flag );
ERROR_CODE ReadPDBASCII ( cpstr PDBFileName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE ReadPDBASCII1 ( cpstr PDBLFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE ReadPDBASCII ( io::RFile f );
ERROR_CODE ReadCIFASCII ( cpstr CIFFileName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE ReadCIFASCII1 ( cpstr CIFLFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE ReadCIFASCII ( io::RFile f );
ERROR_CODE ReadFromCIF ( mmcif::PData CIFD );
// adds info from PDB file
ERROR_CODE AddPDBASCII1 ( cpstr PDBLFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE AddPDBASCII ( cpstr PDBFileName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
// auto format recognition
ERROR_CODE ReadCoorFile ( cpstr LFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE ReadCoorFile1 ( cpstr CFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE ReadCoorFile ( io::RFile f );
ERROR_CODE WritePDBASCII ( cpstr PDBFileName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE WritePDBASCII1 ( cpstr PDBLFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
void WritePDBASCII ( io::RFile f );
ERROR_CODE WriteCIFASCII ( cpstr CIFFileName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE WriteCIFASCII1 ( cpstr CIFLFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE ReadMMDBF ( cpstr MMDBRootName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE ReadMMDBF1 ( cpstr MMDBLFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE ReadMMDBF ( io::RFile f );
ERROR_CODE WriteMMDBF ( cpstr MMDBRootName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE WriteMMDBF1 ( cpstr MMDBLFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
void WriteMMDBF ( io::RFile f );
void GetInputBuffer ( pstr Line, int & count );
// PutPDBString adds a PDB-keyworded string
// to the existing structure. Note that the string
// is namely added meaning that it will be the
// last REMARK, last JRNL, last ATOM etc. string
// -- always the last one in its group.
ERROR_CODE PutPDBString ( cpstr PDBString );
// PDBCleanup(..) cleans coordinate part to comply with PDB
// standards and MMDB "expectations":
//
// PDBCLEAN_ATNAME pads atom names with spaces to form
// 4-symbol names
// PDBCLEAN_TER inserts TER cards in the end of each chain
// PDBCLEAN_CHAIN generates 1-character chain ids instead of
// those many-character
// PDBCLEAN_CHAIN_STRONG generates 1-character chain ids starting
// from 'A' on for all ids, including the
// single-character ones
// PDBCLEAN_ALTCODE generates 1-character alternative codes
// instead of many-character ones
// PDBCLEAN_ALTCODE_STRONG generates 1-character alternative codes
// from 'A' on for all codes, including the
// single-character ones
// PDBCLEAN_SERIAL puts serial numbers in due order
// PDBCLEAN_SEQNUM renumbers all residues so that they go
// incrementally-by-one without insertion codes
// PDBCLEAN_CHAIN_ORDER puts chains in order of atom's serial
// numbers
// PDBCLEAN_CHAIN_ORDER_IX puts chains in order of atom's
// indices internal to MMDB
// PDBCLEAN_SOLVENT moves solvent chains at the end of each model
//
// Return codes (as bits):
// 0 Ok
// PDBCLEAN_CHAIN too many chains for assigning them
// 1-letter codes
// PDBCLEAN_ATNAME element names were not available
// PDBCLEAN_ALTCODE too many alternative codes encountered.
//
word PDBCleanup ( word CleanKey );
// Makes all atoms in chain 'chainID', in all models, as
// 'Het' atoms if Make is set True, and makes them 'ordinary'
// atoms otherwise. 'Ter' is automatically removed when
// converting to 'Het' atoms, and is automatically added
// when converting to 'ordinary' atoms. This may cause
// disorder in serial numbers -- just call
// PDBClean(PDBCLEAN_SERIAL) when necessary to fix this.
void MakeHetAtoms ( cpstr chainID, bool Make );
// --------------- Working with atoms by serial numbers ---
inline PPAtom GetAtomArray () { return atom; }
inline int GetAtomArrayLength() { return atmLen; } // strictly not for
// use in applications!!
PAtom GetAtomI ( int index ); // returns Atom[index-1]
// PutAtom(..) puts atom with the specified properties
// into the structure. The current model is used; if no model
// is set (crModel==NULL), one is created. Coordinates and
// other parameters of the atom need to be set separately.
// The place, at which the atom is put, is determined by
// index. If index is positive, then it points onto (index-1)th
// element of the Atom array (the index counts 1,2,... and
// generally coincides with the atom's serial number). If
// there is already an atom at this position in the system,
// the new atom will REPLACE it. The corresponding residues
// are automatically updated.
// If index is null (=0), the new atom will be put on
// the top of the structure, i.e. it will be put into
// (index=nAtoms+1)-th position.
// If index is negative, then the new atom is INSERTED
// BEFORE the atom in the (-index)th position. For saving
// the computational efforts, this WILL NOT cause the
// recalculation of all atoms' serial numbers according
// to their actual positions. It will be needed, however,
// for putting the things in order at a certain point,
// especially before writing an output ASCII file. NOTE
// that this ordering is never done automatically.
// In a correct PDB file the serial number (serNum) is always
// equal to its position (index). However here we allow them
// to be different for easing the management of relations,
// particularly the connectivity.
//
// Limitation: if PutAtom implies creating new
// chains/residues, these are always created on the top
// of existing chains/residues.
int PutAtom ( int index,
int serNum,
const AtomName atomName,
const ResName resName,
const ChainID chainID,
int seqNum,
const InsCode insCode,
const AltLoc altLoc,
const SegID segID,
const Element element );
int PutAtom (
int index, // same meaning as above
PAtom A, // pointer to completed atom class
int serNum=0 // 0 means that the serial number
// will be set equal to index.
// Otherwise the serial number
// is set to the specified
// value
);
// RemoveAtom(..) removes atom at the specified index
// in the Atom array. This index is always accessible
// as Atom[index]->index. If this leaves a residue empty,
// the residue is removed. If this leaves an empty chain,
// the chain is removed as well; the same happens to the
// model.
void RemoveAtom ( int index );
int FinishStructEdit();
void TrimModelTable();
// ---------------- Deleting models -----------------------
int DeleteAllModels ();
bool GetNewChainID ( int modelNo, ChainID chID, int length=1 );
// --------------- Enquiring -------------------------------
bool isCompactBinary();
int CrystReady();
// Returns flags:
// CRRDY_Complete if crystallographic information is complete
// CRRDY_NotPrecise if cryst. inf-n is not precise
// CRRDY_isTranslation if cryst. inf-n contains translation
// CRRDY_NoOrthCode no orthogonalization code
// Fatal:
// CRRDY_NoTransfMatrices if transform. matrices were not
// calculated
// CRRDY_Unchecked if cryst. inf-n was not checked
// CRRDY_Ambiguous if cryst. inf-n is ambiguous
// CRRDY_NoCell if cryst. inf-n is unusable
// CRRDY_NoSpaceGroup if space group is not set
bool isCrystInfo (); // cell parameters and space group
bool isCellInfo (); // cell param-s a,b,c, alpha,beta,gamma
bool isSpaceGroup (); // space group on CRYST1 card
bool isTransfMatrix(); // orthogonalizing/fractionalizing
// matrices
bool isScaleMatrix (); // SCALEx PDB records
bool isNCSMatrix (); // MTRIXx PDB records
int GetNumberOfNCSMatrices();
int GetNumberOfNCSMates (); // Returns the number of
// NCS mates not given in
// the file (iGiven==0)
bool GetNCSMatrix ( int NCSMatrixNo, // 0..N-1
mat44 & ncs_m, int & iGiven );
int GetNumberOfSymOps (); // number of symmetry operations
pstr GetSymOp ( int Nop ); // XYZ symmetry operation name
// ------------- User-Defined Data ------------------------
int RegisterUDInteger ( UDR_TYPE udr_type, cpstr UDDataID );
int RegisterUDReal ( UDR_TYPE udr_type, cpstr UDDataID );
int RegisterUDString ( UDR_TYPE udr_type, cpstr UDDataID );
int GetUDDHandle ( UDR_TYPE udr_type, cpstr UDDataID );
// ----------------------------------------------------------
void SetSyminfoLib ( cpstr syminfo_lib );
pstr GetSyminfoLib ();
int SetSpaceGroup ( cpstr spGroup );
pstr GetSpaceGroup ();
pstr GetSpaceGroupFix();
void GetAtomStatistics ( RAtomStat AS );
void SetIgnoreSCALEi ( bool ignoreScalei );
// SetCell(..) is for changing cell parameters
void SetCell ( realtype cell_a,
realtype cell_b,
realtype cell_c,
realtype cell_alpha,
realtype cell_beta,
realtype cell_gamma,
int OrthCode=0 );
// PutCell(..) is for setting cell parameters
void PutCell ( realtype cell_a,
realtype cell_b,
realtype cell_c,
realtype cell_alpha,
realtype cell_beta,
realtype cell_gamma,
int OrthCode=0 );
int GetCell ( realtype & cell_a,
realtype & cell_b,
realtype & cell_c,
realtype & cell_alpha,
realtype & cell_beta,
realtype & cell_gamma,
realtype & vol,
int & OrthCode );
int GetRCell ( realtype & cell_as,
realtype & cell_bs,
realtype & cell_cs,
realtype & cell_alphas,
realtype & cell_betas,
realtype & cell_gammas,
realtype & vols,
int & OrthCode );
void GetROMatrix ( mat44 & RO );
// GetTMatrix(..) calculates and returns the coordinate
// transformation matrix, which converts orthogonal coordinates
// according to the symmetry operation number Nop and places
// them into unit cell shifted by cellshift_a a's, cellshift_b
// b's and cellshift_c c's.
//
// Return 0 means everything's fine,
// 1 there's no symmetry operation Nop defined
// 2 fractionalizing/orthogonalizing matrices were not
// calculated
// 3 cell parameters were not set up.
int GetTMatrix ( mat44 & TMatrix, int Nop,
int cellshift_a, int cellshift_b,
int cellshift_c );
// GetUCTMatrix(..) calculates and returns the coordinate
// transformation matrix, which converts orthogonal coordinates
// according to the symmetry operation number Nop. Translation
// part of the matrix is being chosen such that point (x,y,z)
// has least distance to the center of primary (333) unit cell,
// and then it is shifted by cellshift_a a's, cellshift_b b's and
// cellshift_c c's.
//
// Return 0 means everything's fine,
// 1 there's no symmetry operation Nop defined
// 2 fractionalizing/orthogonalizing matrices were not
// calculated
// 3 cell parameters were not set up.
int GetUCTMatrix ( mat44 & TMatrix, int Nop,
realtype x, realtype y, realtype z,
int cellshift_a, int cellshift_b,
int cellshift_c );
// GetFractMatrix(..) calculates and returns the coordinate
// transformation matrix, which converts fractional coordinates
// according to the symmetry operation number Nop and places them
// into unit cell shifted by cellshift_a a's, cellshift_b b's
// and cellshift_c c's.
//
// Return 0 means everything's fine,
// 1 there's no symmetry operation Nop defined
// 2 fractionalizing/orthogonalizing matrices were not
// calculated
// 3 cell parameters were not set up.
int GetFractMatrix ( mat44 & TMatrix, int Nop,
int cellshift_a, int cellshift_b,
int cellshift_c );
// GetSymOpMatrix(..) returns the transformation matrix for
// Nop-th symmetry operator in the space group
//
// Return 0 means everything's fine,
// 1 there's no symmetry operation Nop defined
// 2 fractionalizing/orthogonalizing matrices were not
// calculated
// 3 cell parameters were not set up.
//
int GetSymOpMatrix ( mat44 & TMatrix, int Nop );
int AddNCSMatrix ( mat33 & ncs_m, vect3 & ncs_v, int iGiven );
int GenerateNCSMates(); // 1: no NCS matrices, 0: Ok
pstr GetEntryID ();
void SetEntryID ( const IDCode idCode );
int GetNofExpDataRecs();
pstr GetExpDataRec ( int recNo ); // 0.. on
int GetNofMdlTypeRecs();
pstr GetMdlTypeRec ( int recNo ); // 0.. on
int GetFileType() { return FType; }
void Copy ( PRoot MMDBRoot );
void SetCompactBinary(); // leaves only coordinates in binary files
// ------- user-defined data handlers
int PutUDData ( int UDDhandle, int iudd );
int PutUDData ( int UDDhandle, realtype rudd );
int PutUDData ( int UDDhandle, cpstr sudd );
int GetUDData ( int UDDhandle, int & iudd );
int GetUDData ( int UDDhandle, realtype & rudd );
int GetUDData ( int UDDhandle, pstr sudd, int maxLen );
int GetUDData ( int UDDhandle, pstr & sudd );
// 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 & L );
PCryst GetCrystData() { return &cryst; }
PClassContainer GetUnparsedA() { return &SA; }
PClassContainer GetUnparsedB() { return &SB; }
PClassContainer GetUnparsedC() { return &SC; }
protected :
word Flags; // special effect flags
int FType; // type of last file operation:
// -1 : none
// 0 : PDB
// 1 : CIF
// 2 : BIN
// encoded as MMDB_FILE_XXXXX above
Title title; // title section
Cryst cryst; // crystallographic information section
UDRegister udRegister; // register of user-defined data
int nModels; // number of models
PPModel model; // array of models [0..nModels-1]
int nAtoms; // number of atoms
int atmLen; // length of Atom array
PPAtom atom; // array of atoms ordered by serial numbers
AtomPath DefPath; // default coordinate path
ClassContainer SA; // string container for unrecognized strings
// which are between the title and the
// crystallographic sections
ClassContainer Footnote; // string container for footnotes
ClassContainer SB; // string container for unrecognized strings
// which are between the crystallographic and
// the coordinate sections
ClassContainer SC; // string container for unrecognized strings
// following the coordinate section
// input buffer
int lcount; // input line counter
char S[500]; // read buffer
mmcif::PData CIF; // CIF file manager
PModel crModel; // current model, used at reading a PDB file
PChain crChain; // current chain, used at reading a PDB file
PResidue crRes; // current residue, used at reading a PDB file
bool Exclude; // used internally
bool ignoreRemarks; // used temporarily
bool allowDuplChID; // used temporarily
bool enforceUniqueChID; // used temporarily
void InitMMDBRoot ();
void FreeCoordMemory ();
void ReadPDBLine ( io::RFile f, pstr L, int maxlen );
ERROR_CODE ReadPDBAtom ( cpstr L );
ERROR_CODE ReadCIFAtom ( mmcif::PData CIFD );
ERROR_CODE CheckAtomPlace ( int index, cpstr L );
ERROR_CODE CheckAtomPlace ( int index, mmcif::PLoop Loop );
ERROR_CODE SwitchModel ( cpstr L );
ERROR_CODE SwitchModel ( int nM );
ERROR_CODE AllocateAtom ( int index,
const ChainID chainID,
const ChainID label_asym_id,
const ResName resName,
const ResName label_comp_id,
int seqNum,
int label_seq_id,
int label_entity_id,
const InsCode insCode,
bool Replace );
void ExpandAtomArray ( int inc );
void AddAtomArray ( int inc );
void ApplyNCSTransform ( int NCSMatrixNo );
virtual void ResetManager();
// --------------- Stream I/O -----------------------------
void write ( io::RFile f );
void read ( io::RFile f );
// don't use _ExcludeModel in your applications!
int _ExcludeModel ( int serNum );
int CheckInAtom ( int index, PAtom A );
int CheckInAtoms ( int index, PPAtom A, int natms );
virtual PMask GetSelMask ( int selHnd );
private :
int modelCnt; // used only at reading files
};
// isMMDBBIN will return
// -1 if file FName does not exist
// 0 if file FName is likely a MMDB BIN (binary) file
// 1 if file FName is not a MMDB BIN (binary) file
// 2 if file FName is likely a MMDB BIN (binary) file,
// but of a wrong edition (i.e. produced by a lower
// version of MMDB).
extern int isMMDBBIN ( cpstr FName, io::GZ_MODE gzipMode=io::GZM_CHECK );
extern int isMMDBBIN ( io::RFile f );
// isPDB will return
// -1 if file FName does not exist
// 0 if file FName is likely a PDB file
// 1 if file FName is not a PDB file
extern int isPDB ( cpstr FName, io::GZ_MODE gzipMode=io::GZM_CHECK,
bool IgnoreBlankLines=false );
extern int isPDB ( io::RFile f, bool IgnoreBlankLines=false );
} // namespace mmdb
#endif
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