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// $Id: mmdb_cryst.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_Cryst <interface>
// ~~~~~~~~~
// **** Project : MacroMolecular Data Base (MMDB)
// ~~~~~~~~~
// **** Classes : mmdb::CrystContainer ( container for cryst. data )
// ~~~~~~~~~ mmdb::NCSMatrix ( non-cryst. symm. matrix class )
// mmdb::TVect ( translation vector class )
// mmdb::Cryst ( MMDB cryst. section class )
//
// (C) E. Krissinel 2000-2013
//
// =================================================================
//
#ifndef __MMDB_Cryst__
#define __MMDB_Cryst__
#include "mmdb_io_stream.h"
#include "mmdb_symop.h"
#include "mmdb_defs.h"
#include "mmdb_utils.h"
namespace mmdb {
// ==================== CrystContainer ======================
DefineClass(CrystContainer);
DefineStreamFunctions(CrystContainer);
class CrystContainer : public ClassContainer {
public :
CrystContainer () : ClassContainer() {}
CrystContainer ( io::RPStream Object )
: ClassContainer ( Object ) {}
~CrystContainer() {}
PContainerClass MakeContainerClass ( int ClassID );
ERROR_CODE AddMTRIXLine ( cpstr S );
};
// ================== NCSMatrix ========================
enum NCSM_SET {
NCSMSET_Matrix1 = 0x00000001,
NCSMSET_Matrix2 = 0x00000002,
NCSMSET_Matrix3 = 0x00000004,
NCSMSET_All = 0x00000007
};
DefineClass(NCSMatrix);
DefineStreamFunctions(NCSMatrix);
class NCSMatrix : public ContainerClass {
friend class Cryst;
public :
int serNum; // serial number
mat33 m; // non-crystallographic symmetry matrix
vect3 v; // translational part of ncs matrix
int iGiven; // iGiven flag (see PDB format)
NCSMatrix ();
NCSMatrix ( cpstr S );
NCSMatrix ( io::RPStream Object );
~NCSMatrix();
bool PDBASCIIDump1 ( io::RFile f );
ERROR_CODE ConvertPDBASCII ( cpstr S );
void MakeCIF ( mmcif::PData CIF, int N );
ERROR_CODE GetCIF ( mmcif::PData CIF, int & n );
CLASS_ID GetClassID () { return ClassID_NCSMatrix; }
void SetNCSMatrix ( int serialNum,
mat33 & ncs_m, vect3 & ncs_v,
int i_Given );
void Copy ( PContainerClass NCSMatrix );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
word WhatIsSet; // mask field
// 0x0001 MTRIX1 was converted
// 0x0002 MTRIX2 was converted
// 0x0004 MTRIX3 was converted
void Init();
};
// ================== TVect ========================
DefineClass(TVect);
DefineStreamFunctions(TVect);
class TVect : public ContainerClass {
public :
int serNum; // serial number
vect3 t; // translation vector
pstr comment; // comment
TVect ();
TVect ( cpstr S );
TVect ( io::RPStream Object );
~TVect();
void PDBASCIIDump ( pstr S, int N );
ERROR_CODE ConvertPDBASCII ( cpstr S );
void MakeCIF ( mmcif::PData CIF, int N );
ERROR_CODE GetCIF ( mmcif::PData CIF, int & n );
CLASS_ID GetClassID () { return ClassID_TVect; }
void Copy ( PContainerClass TVect );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
void Init();
};
// ================= Cryst =======================
DefineClass(Cryst);
DefineStreamFunctions(Cryst);
// constants for the CellCheck field
enum CELL_CHECK {
CCHK_Ok = 0x00000000,
CCHK_NoCell = 0x00000001,
CCHK_Error = 0x00000002,
CCHK_Disagreement = 0x00000004,
CCHK_NoOrthCode = 0x00000008,
CCHK_Translations = 0x00000010,
CCHK_Unchecked = 0x00001000
};
// constants for the WhatIsSet field
enum CELL_SET {
CSET_CellParams1 = 0x00000001,
CSET_CellParams2 = 0x00000002,
CSET_CellParams = 0x00000003,
CSET_SpaceGroup = 0x00000004,
CSET_ZValue = 0x00000008,
CSET_CrystCard = 0x0000000F,
CSET_OrigMatrix1 = 0x00000010,
CSET_OrigMatrix2 = 0x00000020,
CSET_OrigMatrix3 = 0x00000040,
CSET_OrigMatrix = 0x00000070,
CSET_ScaleMatrix1 = 0x00000080,
CSET_ScaleMatrix2 = 0x00000100,
CSET_ScaleMatrix3 = 0x00000200,
CSET_ScaleMatrix = 0x00000380,
CSET_Transforms = 0x00000400,
CSET_DummyCell = 0x00001000
};
extern cpstr OrthCode[6];
class Cryst : public io::Stream {
friend class Channel;
public :
realtype a,b,c; // cell parameters
realtype alpha,beta,gamma; // cell parameters
mat44 RO,RF; // orthogonal-fractional recalculation
// matrices
mat44 ROU,RFU; // ort-frac recalc matrices for
// anisotr. t-fac
mat633 RR; // standard orthogonalizations
realtype Vol; // cell volume
int NCode; // code of orthogonalization matrix
SymGroup spaceGroup; // group of space symmetry as read
// from file
SymGroup spaceGroupFix; // actually used space group
int Z; // Z-value
mat33 o; // orthogonal transformation matrix
vect3 t; // translation orthogonal vector
mat33 s; // scale matrix
vect3 u; // translation part of the scale matrix
word CellCheck; // 0x0000 - Ok
// 0x0001 - no cell stored
// 0x0002 - some error in cell volume
// 0x0004 - disagreement between
// cell and PDB
// 0x0008 - no orth code derived
// 0x0010 - translations also specified
// 0x1000 - the check was not done
word WhatIsSet; // indicator of the fields set
bool ignoreScalei; // flag to ignore SCALEi cards
bool processSG; // flag to process space group at file
// read
bool fixSpaceGroup; // flag to fix space group at file read
Cryst ();
Cryst ( io::RPStream Object );
~Cryst();
void FreeMemory();
void Reset ();
// ConvertPDBString(..) interprets an ASCII PDB line and fills
// the corresponding data fields. It returns zero if the line was
// successfully converted, otherwise returns a non-negative value
// of Error_XXXX.
// PDBString must be not shorter than 81 characters.
ERROR_CODE ConvertPDBString ( pstr PDBString );
// RWBROOKReadPrintout() may be invoked after reading PDB file
// for simulating the old RWBROOK messages and warnings
void RWBROOKReadPrintout();
void SetCell ( realtype cell_a,
realtype cell_b,
realtype cell_c,
realtype cell_alpha,
realtype cell_beta,
realtype cell_gamma,
int OrthCode );
void PutCell ( realtype cell_a,
realtype cell_b,
realtype cell_c,
realtype cell_alpha,
realtype cell_beta,
realtype cell_gamma,
int OrthCode );
void GetCell ( realtype & cell_a,
realtype & cell_b,
realtype & cell_c,
realtype & cell_alpha,
realtype & cell_beta,
realtype & cell_gamma,
realtype & vol );
void GetRCell ( realtype & cell_as,
realtype & cell_bs,
realtype & cell_cs,
realtype & cell_alphas,
realtype & cell_betas,
realtype & cell_gammas,
realtype & vols );
void SetSyminfoLib ( cpstr syminfoLib );
pstr GetSyminfoLib ();
int SetSpaceGroup ( cpstr spGroup );
pstr GetSpaceGroup ();
pstr GetSpaceGroupFix();
// CalcCoordTransforms() should be called once after all data
// relevant to the crystallographic information, are read and
// converted. Field CellCheck will then have bits set if there
// are errors, e.g. bit CCHK_NoCell means that the coordinate
// transformations cannot be performed.
void CalcCoordTransforms();
// A PDB ASCII dump
void PDBASCIIDump ( io::RFile f );
ERROR_CODE GetCIF ( mmcif::PData CIF );
void MakeCIF ( mmcif::PData CIF );
bool areMatrices(); // returns True if the orthogonal-to-
// fractional and fractional-to-orthogonal
// matrices are defined
// Frac2Orth(..) and Orth2Frac(..) transform between fractional
// and orthogonal coordinates, if areMatrices() returns True.
// If the transformation matrices were not set, the functions just
// copy the coordinates. Returns True if the transformation was
// done; False return means that transformation matrices were not
// calculated
bool Frac2Orth (
realtype x, realtype y, realtype z,
realtype & xx, realtype & yy, realtype & zz );
bool Orth2Frac (
realtype x, realtype y, realtype z,
realtype & xx, realtype & yy, realtype & zz );
// Below, F and T are transformation matrices in fractional and
// orthogonal coordinates, respectively.
bool Frac2Orth ( mat44 & F, mat44 & T );
bool Orth2Frac ( mat44 & T, mat44 & F );
// Cryst2Orth(..) and Orth2Cryst(..) transform between fractional
// and orthogonal anisotropic temperature factors, if areMatrices()
// returns True. If the transformation matrices were not set, the
// functions leave the factors unchanged.
// Vector U is composed as follows:
// U[0]=u11 U[1]=u22 U[2]=u33
// U[3]=u12 U[4]=u13 U[5]=u23
// Returns True if the transformation was done; False retuen
// means that transformation matrices were not calculated
bool Cryst2Orth ( rvector U );
bool Orth2Cryst ( rvector U );
void CalcOrthMatrices(); // calculates RR, AC, cella's and Vol
bool isNCSMatrix ();
bool isScaleMatrix ();
bool isCellParameters();
int GetNumberOfSymOps();
pstr GetSymOp ( int Nop );
int GetNumberOfNCSMatrices();
int GetNumberOfNCSMates (); // Returns the number of
// NCS mates not given in
// the file (iGiven==0)
bool GetNCSMatrix ( int NCSMatrixNo, mat33 & ncs_m,
vect3 & ncs_v );
bool GetNCSMatrix ( int NCSMatrixNo, mat44 & ncs_m,
int & iGiven ); // no=0..N-1
int AddNCSMatrix ( mat33 & ncs_m, vect3 & ncs_v, int iGiven );
// 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, PSymOps symOpers=NULL );
// GetUCTMatrix(..) calculates and returns the coordinate
// transformation matrix, which converts orthogonal coordinates
// according to the symmetry operation 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, PSymOps symOpers=NULL );
// 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, PSymOps symOpers=NULL );
// 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 );
void Copy ( PCryst Cryst );
void write ( io::RFile f ); // writes header to PDB binary file
void read ( io::RFile f ); // reads header from PDB binary file
protected :
CrystContainer ncsMatrix; // non-cryst. symm. matrices
CrystContainer tVect; // translation vectors
realtype as,bs,cs; // calculated 'cell parameters'
realtype alphas,betas,gammas; // calculated 'cell parameters'
realtype AC[6];
realtype VolChk,VolErr;
pstr syminfo_lib; // path to syminfo.lib
SymOps symOps; // symmetry operations
void Init ( bool fullInit );
int FixSpaceGroup();
};
extern cpstr getOrthCodeName ( int NCode );
} // namespace mmdb
/*
extern void TestCryst(); // reads from 'in.cryst', writes into
// 'out.cryst' and 'abin.cryst'
*/
#endif
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