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|
// $Id: mmdb_coormngr.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.
//
// =================================================================
//
// 07.09.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : mmdb_coormngr <interface>
// ~~~~~~~~~
// Project : MacroMolecular Data Base (MMDB)
// ~~~~~~~~~
// **** Classes : mmdb::Brick ( space brick )
// ~~~~~~~~~ mmdb::CoorManager ( MMDB atom coordinate manager )
//
// (C) E. Krissinel 2000-2015
//
// =================================================================
//
#ifndef __MMDB_CoorMngr__
#define __MMDB_CoorMngr__
#include "mmdb_root.h"
namespace mmdb {
// =========================== Brick ==============================
// bricking control
enum BRICK_STATE {
BRICK_ON_1 = 0x00000001,
BRICK_ON_2 = 0x00000002,
BRICK_READY = 0x00000004
};
DefineClass(Brick);
typedef PPBrick * PPPBrick;
class Brick {
public :
int nAtoms; // number of atoms hit into brick
PPAtom atom; // pointers to atoms
ivector id; // atom ids (in present realization, these are
// indices of atoms from the bricked array)
Brick ();
~Brick();
void Clear ();
void AddAtom ( PAtom A, int atomid );
protected :
int nAllocAtoms;
void InitBrick();
};
// =========================== MBrick =============================
// Bricking multiple structures
DefineClass(MBrick);
typedef PPMBrick * PPPMBrick;
class MBrick {
public :
ivector nAtoms; // number of atoms in the brick
PPAtom *atom; // pointers to atoms
imatrix id; // atom ids (in present realization, these are
// indices of atoms from the bricked array)
MBrick ( int nStructures );
~MBrick();
void Clear ();
void AddAtom ( PAtom A, int structNo, int atomid );
protected :
ivector nAlloAtoms;
int nStruct;
void InitMBrick ( int nStructures );
};
// ==================== GenSym ========================
DefineClass(GenSym);
DefineStreamFunctions(GenSym);
class GenSym : public SymOps {
friend class CoorManager;
public :
GenSym ();
GenSym ( io::RPStream Object );
~GenSym();
void FreeMemory();
int AddSymOp ( cpstr XYZOperation );
// the number of just added operation may be obtained as
// Nop = GenSym::GetNofSymOps()-1 .
int AddRenChain ( int Nop, const ChainID ch1, const ChainID ch2 );
void Copy ( PSymOps genSym );
void write ( io::RFile f );
void read ( io::RFile f );
protected :
PChainID * chID1; // pairs of chains to rename from chID1[n][i]
PChainID * chID2; // to chID2[n][i] for each operation n<Nops
ivector nChains; // number of chains to rename for each oper-n
void InitGenSym();
private :
int nOpAlloc; // number of allocated operations
};
// ========================= Contact =============================
DefineStructure(Contact);
struct Contact {
int id1,id2;
long group;
realtype dist;
void Copy ( RContact c );
void Swap ( RContact c );
};
// ======================== MContact =============================
DefineClass(MContact);
class MContact : public io::Stream {
public :
int nStruct,contactID;
ivector nAtoms;
PPAtom * atom;
imatrix id;
MContact ( int nStructures );
~MContact();
void AddContact ( PAtom A, int structNo, int atomid );
protected:
ivector nAlloc;
};
extern void DeleteMContacts ( PPMContact & mcontact, int nContacts );
// ====================== CoorManager =========================
DefineClass(CoorManager);
DefineStreamFunctions(CoorManager);
// ---- Atom extraction return
enum CID_RC {
CID_Ok = 0,
CID_NoModel = 1,
CID_NoChain = 2,
CID_NoResidue = 3,
CID_NoAtom = 4,
CID_WrongPath = 5
};
// ---- generate symmetry mates return codes
enum GSM_RC {
GSM_Ok = 0,
GSM_NoSymOps = 1,
GSM_NoTransfMatrices = 2,
GSM_NoCell = 3
};
class CoorManager : public Root {
public :
int CoorIDCode; // last return from atom extraction procedure
CoorManager ();
CoorManager ( io::RPStream Object );
~CoorManager();
// ----------------------------------------------------------
int SetDefaultCoorID ( cpstr CID );
// ---------------- Bricking ------------------------------
void RemoveBricks ();
bool areBricks () { return (brick!=NULL); }
void MakeBricks ( PPAtom atmvec, int avlen,
realtype Margin, realtype BrickSize=6.0 );
void GetBrickDimension (
int & nxmax, int & nymax, int & nzmax );
void GetBrickCoor ( PAtom A, int & nx, int & ny, int & nz );
void GetBrickCoor ( realtype x, realtype y, realtype z,
int & nx, int & ny, int & nz );
void GetBrickCoor ( vect3 & xyz, int & nx, int & ny, int & nz );
PBrick GetBrick ( int nx, int ny, int nz );
void RemoveMBricks ();
bool areMBricks () { return (mbrick!=NULL); }
void MakeMBricks ( PPAtom * atmvec, ivector avlen,
int nStructures, realtype Margin,
realtype BrickSize=6.0 );
void GetMBrickDimension (
int & nxmax, int & nymax, int & nzmax );
void GetMBrickCoor ( PAtom A, int & nx, int & ny, int & nz );
void GetMBrickCoor ( realtype x, realtype y, realtype z,
int & nx, int & ny, int & nz );
PMBrick GetMBrick ( int nx, int ny, int nz );
// ---------------- Extracting models ---------------------
int GetNumberOfModels () { return nModels; }
int GetFirstModelNum ();
PModel GetFirstDefinedModel();
PModel GetModel ( int modelNo ); // 1<=modelNo<=nModels
PModel GetModel ( cpstr CID );
void GetModelTable ( PPModel & modTable,
int & NumberOfModels );
// ---------------- Deleting models -----------------------
int DeleteModel ( cpstr CID );
int DeleteModel ( int modelNo ); // 1<=modelNo<=nOfModels
// ---------------- Adding/Inserting models ---------------
int AddModel ( PModel mdl );
int InsModel ( PModel mdl, int modelNo );
void RotateModels ( int modelNo1, int modelNo2, int rotdir );
void SwapModels ( int modelNo1, int modelNo2 );
// ---------------- Extracting chains ---------------------
int GetNumberOfChains ( int modelNo );
int GetNumberOfChains ( cpstr CID );
PChain GetChain ( int modelNo, const ChainID chainID );
PChain GetChain ( int modelNo, int chainNo );
PChain GetChain ( cpstr CID );
void GetChainTable ( int modelNo, PPChain & chainTable,
int & NumberOfChains );
void GetChainTable ( cpstr CID, PPChain & chainTable,
int & NumberOfChains );
// ----------------- Deleting chains ----------------------
int DeleteChain ( int modelNo, const ChainID chID );
int DeleteChain ( int modelNo, int chainNo );
int DeleteAllChains ( int modelNo );
int DeleteAllChains ();
// ------------------ Adding chains -----------------------
int AddChain ( int modelNo, PChain chain );
// ---------------- Extracting residues -------------------
int GetNumberOfResidues ( int modelNo, const ChainID chainID );
int GetNumberOfResidues ( int modelNo, int chainNo );
int GetNumberOfResidues ( cpstr CID );
PResidue GetResidue ( int modelNo, const ChainID chainID,
int seqNo, const InsCode insCode );
PResidue GetResidue ( int modelNo, int chainNo,
int seqNo, const InsCode insCode );
PResidue GetResidue ( int modelNo, const ChainID chainID,
int resNo );
PResidue GetResidue ( int modelNo, int chainNo, int resNo );
PResidue GetResidue ( cpstr CID );
int GetResidueNo ( int modelNo, const ChainID chainID,
int seqNo, const InsCode insCode );
int GetResidueNo ( int modelNo, int chainNo,
int seqNo, const InsCode insCode );
void GetResidueTable ( PPResidue & resTable,
int & NumberOfResidues );
void GetResidueTable ( int modelNo, const ChainID chainID,
PPResidue & resTable,
int & NumberOfResidues );
void GetResidueTable ( int modelNo, int chainNo,
PPResidue & resTable,
int & NumberOfResidues );
void GetResidueTable ( cpstr CID, PPResidue & resTable,
int & NumberOfResidues );
// ----------------- Deleting residues -----------------------
int DeleteResidue ( int modelNo, const ChainID chainID,
int seqNo, const InsCode insCode );
int DeleteResidue ( int modelNo, const ChainID chainID,
int resNo );
int DeleteResidue ( int modelNo, int chainNo,
int seqNo, const InsCode insCode );
int DeleteResidue ( int modelNo, int chainNo, int resNo );
int DeleteAllResidues ( int modelNo, const ChainID chainID );
int DeleteAllResidues ( int modelNo, int chainNo );
int DeleteAllResidues ( int modelNo );
int DeleteAllResidues ();
int DeleteSolvent ();
// ------------------- Adding residues -----------------------
int AddResidue ( int modelNo, const ChainID chainID,
PResidue res );
int AddResidue ( int modelNo, int chainNo, PResidue res );
// -------------------- Extracting atoms ----------------------
int GetNumberOfAtoms () { return nAtoms; }
int GetNumberOfAtoms ( int modelNo, const ChainID chainID,
int seqNo, const InsCode insCode );
int GetNumberOfAtoms ( int modelNo, int chainNo,
int seqNo, const InsCode insCode );
int GetNumberOfAtoms ( int modelNo, const ChainID chainID,
int resNo );
int GetNumberOfAtoms ( int modelNo, int chainNo, int resNo );
int GetNumberOfAtoms ( cpstr CID );
PAtom GetAtom (
int modelNo, // model serial number 1...
const ChainID chID, // chain ID
int seqNo, // residue sequence number
const InsCode insCode, // residue insertion code
const AtomName aname, // atom name
const Element elmnt, // chemical element code or '*'
const AltLoc aloc // alternate location indicator
);
PAtom GetAtom (
int modelNo, // model serial number 1...
const ChainID chID, // chain ID
int seqNo, // residue sequence number
const InsCode insCode, // residue insertion code
int atomNo // atom number 0..
);
PAtom GetAtom (
int modelNo, // model serial number 1...
const ChainID chID, // chain ID
int resNo, // residue number 0..
const AtomName aname, // atom name
const Element elmnt, // chemical element code or '*'
const AltLoc aloc // alternate location indicator
);
PAtom GetAtom (
int modelNo, // model serial number 1...
const ChainID chID, // chain ID
int resNo, // residue number 0..
int atomNo // atom number 0..
);
PAtom GetAtom (
int modelNo, // model serial number 1...
int chNo, // chain number 0..
int seqNo, // residue sequence number
const InsCode insCode, // residue insertion code
const AtomName aname, // atom name
const Element elmnt, // chemical element code or '*'
const AltLoc aloc // alternate location indicator
);
PAtom GetAtom (
int modelNo, // model serial number 1...
int chNo, // chain number 0...
int seqNo, // residue sequence number
const InsCode insCode, // residue insertion code
int atomNo // atom number 0...
);
PAtom GetAtom (
int modelNo, // model serial number 1...
int chNo, // chain number 0...
int resNo, // residue number 0...
const AtomName aname, // atom name
const Element elmnt, // chemical element code or '*'
const AltLoc aloc // alternate location indicator
);
PAtom GetAtom (
int modelNo, // model serial number 1...
int chNo, // chain number 0...
int resNo, // residue number 0...
int atomNo // atom number 0...
);
// GetAtom(CID) returns atom answering to the following
// CID pattern:
// /mdl/chn/seq(res).i/atm[elm]:a
// where
// mdl - model number (mandatory); at least model #1 is always
// present
// chn - chain identifier ( mandatory)
// seq - residue sequence number (mandatory)
// (res) - residue name in round brackets (may be omitted)
// .i - insert code after a dot; if '.i' or 'i' is missing
// then residue without an insertion code is looked
// for
// atm - atom name (mandatory)
// [elm] - chemical element code in square brackets; it may
// be omitted but could be helpful for e.g.
// distinguishing C_alpha and CA
// :a - alternate location indicator after colon; if
// ':a' or 'a' is missing then an atom without
// alternate location indicator is looked for.
// All spaces are ignored, all identifiers should be in capital
// letters (comparisons are case-sensitive).
PAtom GetAtom ( cpstr CID );
void GetAtomTable ( PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable ( int modelNo, const ChainID chainID,
int seqNo, const InsCode insCode,
PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable ( int modelNo, int chainNo,
int seqNo, const InsCode insCode,
PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable ( int modelNo, const ChainID chainID, int resNo,
PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable ( int modelNo, int chainNo, int resNo,
PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable ( cpstr CID, PPAtom & atomTable,
int & NumberOfAtoms );
// GetAtomTable1(..) returns atom table without TER atoms and
// without NULL atom pointers. NumberOfAtoms returns the actual
// number of atom pointers in atomTable.
// atomTable is allocated within the function. If it was
// not set to NULL before calling the function, the function will
// attempt to deallocate it first.
// The application is responsible for deleting atomTable,
// however it must not touch atom pointers, i.e. use simply
// "delete atomTable;". Never pass atomTable from GetAtomTable(..)
// into this function, unless you set it to NULL before doing that.
void GetAtomTable1 ( PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable1 ( int modelNo, const ChainID chainID,
int seqNo, const InsCode insCode,
PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable1 ( int modelNo, int chainNo,
int seqNo, const InsCode insCode,
PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable1 ( int modelNo, const ChainID chainID, int resNo,
PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable1 ( int modelNo, int chainNo, int resNo,
PPAtom & atomTable, int & NumberOfAtoms );
void GetAtomTable1 ( cpstr CID, PPAtom & atomTable,
int & NumberOfAtoms );
// -------------------- Deleting atoms -----------------------
int DeleteAtom ( int modelNo,
const ChainID chID,
int seqNo,
const InsCode insCode,
const AtomName aname,
const Element elmnt,
const AltLoc aloc );
int DeleteAtom ( int modelNo,
const ChainID chID,
int seqNo,
const InsCode insCode,
int atomNo );
int DeleteAtom ( int modelNo,
const ChainID chID,
int resNo,
const AtomName aname,
const Element elmnt,
const AltLoc aloc );
int DeleteAtom ( int modelNo, const ChainID chID,
int resNo, int atomNo );
int DeleteAtom ( int modelNo, int chNo, int seqNo,
const InsCode insCode,
const AtomName aname,
const Element elmnt,
const AltLoc aloc );
int DeleteAtom ( int modelNo, int chNo, int seqNo,
const InsCode insCode, int atomNo );
int DeleteAtom ( int modelNo, int chNo, int resNo,
const AtomName aname,
const Element elmnt,
const AltLoc aloc );
int DeleteAtom ( int modelNo, int chNo, int resNo, int atomNo );
int DeleteAllAtoms ( int modelNo, const ChainID chID,
int seqNo, const InsCode insCode );
int DeleteAllAtoms ( int modelNo, const ChainID chID, int resNo );
int DeleteAllAtoms ( int modelNo, const ChainID chID );
int DeleteAllAtoms ( int modelNo, int chNo, int seqNo,
const InsCode insCode );
int DeleteAllAtoms ( int modelNo, int chNo, int resNo );
int DeleteAllAtoms ( int modelNo, int chNo );
int DeleteAllAtoms ( int modelNo );
int DeleteAllAtoms ();
// This function leaves only alternative location with maximal
// occupancy, if those are equal or unspecified, the one with
// "least" alternative location indicator.
// The function returns the number of deleted atoms and optimizes
// the atom index.
int DeleteAltLocs ();
// --------------------- Adding atoms ------------------------
int AddAtom ( int modelNo, const ChainID chID,
int seqNo, const InsCode insCode, PAtom atom );
int AddAtom ( int modelNo, const ChainID chID, int resNo,
PAtom atom );
int AddAtom ( int modelNo, int chNo, int seqNo,
const InsCode insCode, PAtom atom );
int AddAtom ( int modelNo, int chNo, int resNo, PAtom atom );
// -------------------- Transformations -----------------------
int GenerateSymMates ( PGenSym genSym=NULL );
// 1: no Sym operations,
// 2: no fract/orth matrices
// 3: no cell parameters
// 0: Ok
void ApplyTransform ( mat44 & TMatrix ); // simply transforms all
// coordinates by multiplying
// with matrix TMatrix
int BringToUnitCell(); // brings all chains into 0th unit cell
// 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 xfrac, realtype yfrac, realtype zfrac,
realtype & xorth, realtype & yorth, realtype & zorth );
bool Orth2Frac (
realtype xorth, realtype yorth, realtype zorth,
realtype & xfrac, realtype & yfrac, realtype & zfrac );
// 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 );
// ==================== Seeking contacts ======================
void SeekContacts (
PPAtom AIndex, // index of atoms [0..ilen-1]
int ilen, // length of index
int atomNum, // number of 1st contact atom
// in the index. All other atoms
// are checked for contact with
// 1st atom
realtype dist1, // minimal contact distance
realtype dist2, // maximal contact distance
int seqDist, // the sequence distance to neglect.
// If seqDist==0, all atoms are
// checked for contact. If
// seqDist==1, the atoms belonging
// to the same residue as atom
// AIndex[atomNum], are neglected.
// If seqDist>1, all atoms belonging
// to residues closer than
// +/-(seqDist-1) around that of
// atom AIndex[atomNum], are
// neglected. If chain is broken
// (has a gap) on section
// [-(seqDist-1)..seqDist-1], the
// section of neglection is
// shortened to that gap.
RPContact contact, // indices of contacting atoms
// [0..ncontacts-1]. contact[i].id1
// is set to atomNum and
// contact[i].id2 is set to the
// index of 2nd contacting atom
// in vector AIndex
int & ncontacts, // number of contacts found. If
// ncontacts>0 on input, it is
// assumed that new contacts that
// newly found contacts should be
// appended to those already
// existing
int maxlen=0, // if <=0, then vector contact is
// allocated dynamically. If
// contact!=NULL, then it is
// appended with new contacts.
// The application is responsible
// for deallocation of contact
// after use.
// If maxlen>0 then vector contact
// is prohibited of dynamical
// allocation/deallocation. In this
// case, not more than maxlen
// contacts will be returned.
long group=0 // a contact group ID, which will be
// simply stored in contact[i].group
// fields. This ID may be useful
// if contacts are obtained in
// multiple calls of the function
);
void SeekContacts (
PAtom A, // 1st atom in contact
PPAtom AIndex, // index of atoms [0..ilen-1] to
// check for contact with 1st atom
int ilen, // length of index
realtype dist1, // minimal contact distance
realtype dist2, // maximal contact distance
int seqDist, // the sequence distance to neglect.
// If seqDist==0, all atoms are
// checked for contact. If
// seqDist==1, the atoms belonging
// to the same residue as atom
// A, are neglected. If seqDist>1,
// all atoms belonging to residues
// closer than +/-(seqDist-1) around
// that of atom A, are neglected. If
// chain is broken (has a gap) on
// section
// [-(seqDist-1)..seqDist-1], the
// section of neglection is
// shortened to that gap.
RPContact contact, // indices of contacting atoms
// [0..ncontacts-1]. contact[i].id1
// is set to -1, and contact[i].id2
// is set to the index of 2nd
// contacting atom in vector AIndex
int & ncontacts, // number of contacts found. If
// ncontacts>0 on input, it is
// assumed that new contacts that
// newly found contacts should be
// appended those already existing
int maxlen=0, // if <=0, then vector contact is
// allocated dynamically. If
// contact!=NULL, then it is
// appended with new contacts.
// The application is responsible
// for deallocation of contact
// after use.
// If maxlen>0 then vector contact
// is prohibited of dynamical
// allocation/deallocation. In this
// case, not more than maxlen
// contacts will be returned.
long group=0 // a contact group ID, which will be
// simply stored in contact[i].group
// fields. This ID may be useful
// if contacts are obtained in
// multiple calls of the function
);
void SeekContacts (
PPAtom AIndex1, // 1st atom index [0..ilen1-1]
int ilen1, // length of 1st index
PPAtom AIndex2, // 2nd atom index [0..ilen2-1] to
// check for contact with 1st index
int ilen2, // length of 2nd index
realtype dist1, // minimal contact distance
realtype dist2, // maximal contact distance
int seqDist, // the sequence distance to
// neglect.
// If seqDist==0, all atoms are
// checked for contact.
// If seqDist==1, the atoms
// belonging to the same residue
// are neglected.
// If seqDist>1, all atoms
// belonging to residues closer than
// +/-(seqDist-1) to each other,
// are neglected. If chain is broken
// (has a gap) on section
// [-(seqDist-1)..seqDist-1], the
// section of neglection is
// shortened to that gap.
RPContact contact, // indices of contacting atoms
// [0..ncontacts-1]. contact[i].id1
// contains number of atom from 1st
// index, and contact[i].id2
// contains number of atom from 2nd
// index, contacting with the former
// one
int & ncontacts, // number of contacts found. If
// ncontacts>0 on input, it is
// assumed that newly found
// contacts should be appended to
// those already existing
int maxlen=0, // if <=0, then vector contact is
// allocated dynamically. If
// contact!=NULL, then it is
// appended with new contacts.
// The application is responsible
// for deallocation of contact
// after use.
// If maxlen>0 then vector contact
// is prohibited of dynamical
// allocation/deallocation. In this
// case, not more than maxlen
// contacts will be returned.
mat44 * TMatrix=NULL, // transformation matrix for 2nd
// set of atoms (AIndex2)
long group=0, // a contact group ID, which will
// be stored in contact[i].group
// fields. This ID may be useful
// if contacts are obtained in
// multiple calls of the function
int bricking=0, // bricking control; may be a
// combination of BRICK_ON_1 or
// BRICK_ON_2 with BRICK_READY
bool doSqrt=true // if False, then Contact contains
// square distances
);
// Simplified optimized for speed version:
// - no NULL pointers and Ters in AIndex1 and AIndex2
// - no checks for identity atoms in AIndex1 and AIndex2
// - contact must be pre-allocated with at least ilen1*ilen2
// elements
// - contact returns square distances
// - ncontacts is always reset
void SeekContacts (
PPAtom AIndex1, // 1st atom index [0..ilen1-1]
int ilen1, // length of 1st index
PPAtom AIndex2, // 2nd atom index [0..ilen2-1] to
// check for contact with 1st index
int ilen2, // length of 2nd index
realtype contDist, // maximal contact distance
PContact contact, // indices of contacting atoms
// [0..ncontacts-1]. contact[i].id1
// contains number of atom from 1st
// index, and contact[i].id2
// contains number of atom from 2nd
// index, contacting with the former
// one. Must be pre-allocated
int & ncontacts, // number of contacts found
int bricking=0 // bricking control; may be a
// combination of BRICK_ON_1 or
// BRICK_ON_2 with BRICK_READY
);
// Simplified optimized for speed and convenience version:
// - bricking is pre-done
// - contacting set of atoms is given as a bare vect3 (xyz)
// coordinate vector
// - no checks for identity atoms
// - contact must be pre-allocated with at least ilen1*ilen2
// elements
// - contact returns square distances
// - ncontacts is always reset
void SeekContacts (
vect3 * xyz, // 2nd atom index [0..ilen2-1] to
// check for contact with 1st index
// which was used for bricking
int nxyz, // length of 2nd index
realtype contDist, // maximal contact distance
PContact contact, // indices of contacting atoms
// [0..ncontacts-1]. contact[i].id1
// contains number of atom from 1st
// index, and contact[i].id2
// contains number of atom from 2nd
// index, contacting with the former
// one. Must be pre-allocated
int & ncontacts // number of contacts found
);
void SeekContacts (
PPAtom AIndex1, // 1st atom index [0..ilen1-1]
int ilen1, // length of 1st index
PPAtom * AIndex2, // indexes of atoms to be checked
// for contact with each atom from
// Aindex1; dimension
// [0..nStructures-1][0..ilen2[i]-1]
ivector ilen2, // lengths of indexes AIndex2
int nStructures, // number of indexes AIndex2
realtype dist1, // minimal contact distance
realtype dist2, // maximal contact distance
PPMContact & contact, // resulting contacts, one structure
// per each position in AIndex1. If
// AIndex1[i] is NULL, contact[i] is
// also NULL. "contact" is always
// allocated, no re-use or
// re-allocation is attempted.
int bricking=0 // bricking control; may be
// BRICK_READY if AIndex2 does not
// change
);
protected :
// bricks
realtype brick_size, xbrick_0,ybrick_0,zbrick_0;
int nbrick_x,nbrick_y,nbrick_z;
PPPBrick * brick;
realtype mbrick_size, xmbrick_0,ymbrick_0,zmbrick_0;
int nmbrick_x,nmbrick_y,nmbrick_z;
PPPMBrick * mbrick;
// --------------- Stream I/O -----------------------------
void write ( io::RFile f );
void read ( io::RFile f );
void InitMMDBCoorManager();
void ApplySymTransform ( int SymMatrixNo, PGenSym genSym=NULL );
void ResetManager ();
void FindSeqSection ( PAtom atom, int seqDist,
int & seq1, int & seq2 );
bool iContact ( PAtom a1, PAtom a2,
int seq1, int seq2,
realtype dd, realtype d12,
realtype d22, realtype & d2 );
bool iContact ( realtype x, realtype y,
realtype z, PAtom a2,
realtype dd, realtype d12,
realtype d22, realtype & d2 );
};
// ===================================================================
// GetEulerRotMatrix(..) calculates the Euler rotation matrix
// for rotation:
// 1) about z-axis by angle alpha
// 2) about new y-axis by angle beta
// 3) about new z-axis by angle gamma
extern void GetEulerRotMatrix ( mat33 & erm, realtype alpha,
realtype beta, realtype gamma );
// GetEulerTMatrix(..) calculates the Euler rotation-translation
// matrix for rotation:
// 1) about z-axis by angle alpha
// 2) about new y-axis by angle beta
// 3) about new z-axis by angle gamma
// Point (x0,y0,z0) is the center of rotation.
extern void GetEulerTMatrix ( mat44 & erm, realtype alpha,
realtype beta, realtype gamma,
realtype x0, realtype y0, realtype z0 );
// Euler rotation: 1) about z-axis by angle alpha
// 2) about new y-axis by angle beta
// 3) about new z-axis by angle gamma
// Point (x0,y0,z0) is the center of rotation.
extern void EulerRotation ( PPAtom A, int nA,
realtype alpha, realtype beta, realtype gamma,
realtype x0, realtype y0, realtype z0 );
// GetVecRotMatrix(..) calculates the rotation matrix for
// rotation by angle alpha about arbitrary vector directed
// as (vx,vy,vz) = (vx2-vx1,vy2-vy1,vz2-vz1).
extern void GetVecRotMatrix ( mat33 & vrm, realtype alpha,
realtype vx, realtype vy, realtype vz );
// Given the rotation matrix vrm, GetRotParameters(..)
// returns the rotation angle alpha and the normalized
// rotation axis vector (vx,vy,vz).
// The rotation angle and vector are determined up to
// their sign (however correlated, so that being substituted
// into GetVecRotMatrix(..) they yield the same rotation
// matrix).
// The function does not check for vrm to be a valid
// rotation matrix.
extern void GetRotParameters ( mat33 & vrm, realtype & alpha,
realtype & vx, realtype & vy, realtype & vz );
// GetVecTMatrix(..) calculates the rotation-translation matrix
// for rotation by angle alpha about arbitrary vector directed as
// (vx,vy,vz) = (vx2-vx1,vy2-vy1,vz2-vz1). Point (x0,y0,z0) is
// the center of rotation -- actually a point belonging to the
// rotation axis.
extern void GetVecTMatrix ( mat44 & vrm, realtype alpha,
realtype vx, realtype vy, realtype vz,
realtype x0, realtype y0, realtype z0 );
// Vector rotation is rotation by angle alpha about arbitrary
// vector directed as (vx,vy,vz) = (vx2-vx1,vy2-vy1,vz2-vz1).
// Point (x0,y0,z0) is the center of rotation -- actually
// a point belonging to the rotation axis.
extern void VectorRotation ( PPAtom A, int nA, realtype alpha,
realtype vx, realtype vy, realtype vz,
realtype x0, realtype y0, realtype z0 );
extern void GetMassCenter ( PPAtom A, int nA,
realtype & xmc, realtype & ymc, realtype & zmc );
enum SPOSEAT_RC {
SPOSEAT_Ok = 0,
SPOSEAT_NoAtoms = 1,
SPOSEAT_SVD_Fail = 2
};
// Given two sets of atoms, A1 and A2, SuperposeAtoms(...) calculates
// the rotational-translational matrix T such that |T*A1 - A2| is
// minimal in least-square terms.
// If vector C is not given (default), all nA atoms of set A1 are
// considered as corresponding to nA first atoms of set A2,
// A1[i] <-> A2[i], 0<=i<nA .
// If vector C is given, then the correspondence of atoms is
// established as A1[i] <-> A2[C[i]] only for those i that C[i]>=0.
// The default option (C==NULL) is thus identical to C[i]==i, 0<=i<nA.
// Upon normal completion, the procedure returns SPOSEAT_Ok.
extern int SuperposeAtoms ( mat44 & T, PPAtom A1, int nA, PPAtom A2,
ivector C=NULL );
enum CNSORT_DIR {
CNSORT_OFF = 0,
CNSORT_1INC = 1,
CNSORT_1DEC = 2,
CNSORT_2INC = 3,
CNSORT_2DEC = 4,
CNSORT_DINC = 5,
CNSORT_DDEC = 6
};
extern void SortContacts ( PContact contact, int ncontacts,
CNSORT_DIR sortmode );
extern const realtype NO_TORSION;
extern realtype getPhi ( PPAtom A ); // A[0] - A[3] used
extern realtype getPsi ( PPAtom A ); // A[0] - A[2] used
} // namespace mmdb
#endif
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