/usr/include/mmdb/mmdb_graph.h is in libmmdb-dev 1.25.5-2.
This file is owned by root:root, with mode 0o644.
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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.
//
// =================================================================
//
// 08.07.08 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : mmdb_graph <interface>
// ~~~~~~~~~
// **** Classes : CVertex ( graph vertex )
// ~~~~~~~~~ CEdge ( graph edge )
// CGraph ( structural graph )
// CMatch ( match of structural graphs )
// CGraphMatch ( CSIA algorithms for graphs matching )
//
// (C) E. Krissinel 2000-2008
//
// When used, please cite:
//
// Krissinel, E. and Henrick, K. (2004)
// Common subgraph isomorphism detection by backtracking search.
// Software - Practice and Experience, 34, 591-607.
//
// =================================================================
//
#ifndef __MMDB_Graph__
#define __MMDB_Graph__
#ifndef __TIME_H
#include <time.h>
#endif
#ifndef __MMDB_Atom__
#include "mmdb_atom.h"
#endif
// ========================== CVertex ============================
DefineClass(CVertex);
#define CHIRAL_RIGHT 0x10000000
#define CHIRAL_LEFT 0x20000000
#define ATOM_LEAVING 0x40000000
#define HYDROGEN_BOND 0x0F000000
#define SYMREL_MASK 0x00FF0000
#define CHIRAL_MASK 0xCFFFFFFF
#define TYPE_MASK 0x00FFFFFF
class CVertex : public CStream {
friend class CGraph;
friend class CGraphMatch;
friend class CSBase0;
public:
CVertex ();
CVertex ( RPCStream Object );
CVertex ( int vtype, cpstr vname );
CVertex ( int vtype );
CVertex ( cpstr chem_elem );
CVertex ( cpstr chem_elem, cpstr name );
~CVertex();
void SetVertex ( cpstr chem_elem );
void SetVertex ( int vtype, cpstr vname );
void SetVertex ( int vtype );
void SetType ( int vtype );
void SetTypeExt ( int typeExt );
void RemoveChirality();
void LeaveChirality ( int eltype );
void SetName ( cpstr vname );
void SetProperty ( int vprop );
void SetID ( int vid );
void SetUserID ( int vid ) { user_id = vid; }
void AddBond ();
void CopyNBonds ( PCVertex V );
int GetProperty () { return property; }
int GetID () { return id; }
int GetUserID () { return user_id; }
cpstr GetName () { return name; }
int GetType () { return type; }
int GetTypeExt () { return type_ext; }
int GetNBonds ();
void SaveType (); // in userid
void RestoreType (); // from userid
void CopyType ( PCVertex V );
virtual void Print ( int PKey );
virtual void Copy ( PCVertex V );
void read ( RCFile f );
void write ( RCFile f );
void mem_read ( cpstr S, int & l );
void mem_write ( pstr S, int & l );
protected:
pstr name; // name may be general, "C", "Hg", "Cl" etc.
int type; // type of vertex, see comments in mmdb_graph.cpp
int type_ext; // vertex type extention
int property; // flagwise properties -- user-defined
int id; // a graph-defined vertex id
int user_id; // a user-defined vertex id
void InitVertex();
};
DefineStreamFunctions(CVertex);
// =========================== CEdge =============================
#define BOND_SINGLE 1
#define BOND_DOUBLE 2
#define BOND_AROMATIC 3
#define BOND_TRIPLE 4
DefineClass(CEdge);
class CEdge : public CStream {
friend class CGraph;
friend class CGMatch;
friend class CSBase0;
public:
CEdge ();
CEdge ( RPCStream Object );
CEdge ( int vx1, int vx2, int btype ); // vx1,vx2 are numbered
// as 1,2,3 on and refer
// to vertices in the order
// as they were added to
// the graph; btype>0
~CEdge();
void SetEdge ( int vx1, int vx2, cpstr btype );
void SetEdge ( int vx1, int vx2, int btype ); // btype>0
void SetType ( int btype );
void SetProperty ( int eprop );
void SaveType (); // in property
void RestoreType (); // from property
inline int GetVertex1 () { return v1; }
inline int GetVertex2 () { return v2; }
inline int GetType () { return type; }
inline int GetProperty () { return property; }
virtual void Print ( int PKey );
virtual void Copy ( PCEdge G );
void read ( RCFile f );
void write ( RCFile f );
void mem_read ( cpstr S, int & l );
void mem_write ( pstr S, int & l );
protected:
int v1,v2; // >=1
int type;
int property;
void InitEdge();
};
DefineStreamFunctions(CEdge);
// ========================== CGraph ============================
#define MKGRAPH_Ok 0
#define MKGRAPH_NoAtoms -1
#define MKGRAPH_ChangedAltLoc 1
#define MKGRAPH_MaxOccupancy 2
DefineClass(CGraph);
class CGraph : public CStream {
friend class CGraphMatch;
friend class CSBase0;
public :
CGraph ();
CGraph ( PCResidue R, cpstr altLoc=NULL );
CGraph ( RPCStream Object );
~CGraph();
void Reset ();
void SetName ( cpstr gname );
pstr GetName () { return name; }
// AddVertex(..) and AddEdge(..) do not copy the objects, but
// take them over. This means that application should forget
// about pointers to V and G once they were given to CGraph.
// Vertices and edges must be allocated newly prior each call
// to AddVertex(..) and AddEdge(..).
void AddVertex ( PCVertex V );
void AddEdge ( PCEdge G );
void SetVertices ( PPCVertex V, int vlen );
void SetEdges ( PPCEdge G, int glen );
void RemoveChirality();
void LeaveChirality ( int eltype );
// MakeGraph(..) makes a graph corresponding to residue R.
// The graphs vertices then correspond to the residue's atoms
// (CVertex::userid points to atom R->atom[CVertex::userid]),
// edges are calculated as chemical bonds between atoms basing
// on the table of cut-off distances.
// altCode specifies a particular conformation that should be
// used for making the graph. If it is set to "" or NULL ("empty"
// altcode) but the residue does not have conformation which
// contains *only* ""-altcode atoms, a conformation corresponding
// to maximal occupancy will be used. The same will happen if
// altcode information in residue is not correct, whatever altCode
// is specified.
// After making the graph, Build(..) should be called as usual
// before graph matching.
// Non-negative return means that graph has been made.
// MakeGraph(..) may return:
// MKGRAPH_Ok everything is Ok
// MKGRAPH_NoAtoms residue does not have atoms, graph
// is not made
// MKGRAPH_ChangedAltLoc a different altcode was used because
// the residue has only one altcode and
// that is different of
// MKGRAPH_MaxOccupancy a maximal-occupancy conformation has
// been chosen because of default
// ""-altcode supplied or incorrect
// altcode information in the residue
int MakeGraph ( PCResidue R, cpstr altLoc=NULL );
int MakeGraph ( PPCAtom atom, int nAtoms );
void HideType ( int bond_vx_type );
void ExcludeType ( int type );
void MakeSymmetryRelief ( Boolean noCO2 );
void IdentifyRings ();
int IdentifyConnectedComponents(); // returns their number >= 1
int Build ( Boolean bondOrder ); // returns 0 if Ok
void MakeVertexIDs (); // simply numbers vertices as 1.. on
int GetVertexID ( int vertexNo );
int GetVertexNo ( cpstr vname );
// GetBondedVertexID(..) works after MoveType(..)
int GetNBondedVertices ( int vertexNo );
int GetBondedVertexID ( int vertexNo, int bond_vx_type,
int bondNo );
PCVertex GetVertex ( int vertexNo ); // 1<=vertexNo<=nVertices
inline int GetNofVertices() { return nVertices; }
PCEdge GetEdge ( int edgeNo ); // 1<=edgeNo<=nEdges
inline int GetNofEdges() { return nEdges; }
void GetVertices ( PPCVertex & V, int & nV );
void GetEdges ( PPCEdge & E, int & nE );
virtual void Print();
void Print1();
virtual void Copy ( PCGraph G );
void read ( RCFile f );
void write ( RCFile f );
void mem_read ( cpstr S, int & l );
void mem_write ( pstr S, int & l );
protected :
pstr name;
int nVertices,nEdges, nAllVertices,nAllEdges;
PPCVertex Vertex;
PPCEdge Edge;
imatrix graph;
void InitGraph ();
void FreeMemory();
void markConnected ( int vno, int cno );
private :
int nVAlloc,nEAlloc,nGAlloc;
};
DefineStreamFunctions(CGraph);
// ========================== CMatch ============================
DefineClass(CMatch);
DefineStreamFunctions(CMatch);
class CMatch : public CStream {
friend class CGraphMatch;
public :
CMatch ();
CMatch ( RPCStream Object );
CMatch ( ivector FV1, ivector FV2, int nv, int n, int m );
~CMatch();
// FV1[] and FV2[] are copied into internal buffers
void SetMatch ( ivector FV1, ivector FV2, int nv, int n, int m );
Boolean isMatch ( ivector FV1, ivector FV2, int nv );
Boolean isCombination ( ivector FV1, ivector FV2, int nv );
// do not allocate or dispose FV1 and FV2 in application!
void GetMatch ( ivector & FV1, ivector & FV2, int & nv,
realtype & p1, realtype & p2 );
void read ( RCFile f );
void write ( RCFile f );
void mem_read ( cpstr S, int & l );
void mem_write ( pstr S, int & l );
protected :
int n1,n2,mlength;
ivector F1,F2;
void InitMatch();
private :
int nAlloc;
};
// ======================= CGraphMatch =========================
#define _UseRecursion
#define GMF_UniqueMatch 0x00000001
#define GMF_NoCombinations 0x00000002
#define EXTTYPE_Ignore 0
#define EXTTYPE_Equal 1
#define EXTTYPE_AND 2
#define EXTTYPE_OR 3
#define EXTTYPE_XOR 4
#define EXTTYPE_NotEqual 5
#define EXTTYPE_NotAND 6
#define EXTTYPE_NotOR 7
DefineClass(CGraphMatch);
class CGraphMatch : public CStream {
public :
CGraphMatch ();
CGraphMatch ( RPCStream Object );
~CGraphMatch();
void SetFlag ( word flag );
void RemoveFlag ( word flag );
void SetMaxNofMatches ( int maxNofMatches, Boolean stopOnMaxN );
void SetTimeLimit ( int maxTimeToRun=0 );
Boolean GetStopSignal () { return Stop; }
void Reset();
// MatchGraphs looks for maximal common subgraphs of size
// not less than minMatch. The number of found subgraphs
// is returned by GetNofMatches(), the subgraph vertices
// are returned by GetMatch(..). Control parameters:
// vertexType True if vertex type should be taken
// into account and False otherwise
// vertexExt key to use extended vertex types (defined
// as type_ext in CVertex).
void MatchGraphs ( PCGraph Gh1, PCGraph Gh2, int minMatch,
Boolean vertexType=True,
int vertexExt=EXTTYPE_Ignore );
void PrintMatches ();
int GetNofMatches () { return nMatches; }
int GetMaxMatchSize() { return maxMatch; }
// do not allocate or dispose FV1 and FV2 in application!
// FV1/p1 will always correspond to Gh1, and FV2/p2 -
// to Gh2 as specified in MatchGraphs(..)
void GetMatch ( int MatchNo, ivector & FV1, ivector & FV2,
int & nv, realtype & p1, realtype & p2 );
void read ( RCFile f );
void write ( RCFile f );
void mem_read ( cpstr S, int & l );
void mem_write ( pstr S, int & l );
protected :
PCGraph G1,G2;
PPCVertex V1;
PPCVertex V2;
imatrix c1,c2;
Boolean swap;
#ifndef _UseRecursion
ivector jj;
#endif
int n,m;
imatrix3 P;
imatrix iF1;
ivector F1,F2,ix;
int nMatches,maxNMatches;
PPCMatch Match;
Boolean wasFullMatch,Stop,stopOnMaxNMathches;
word flags;
int maxMatch,timeLimit;
void InitGraphMatch();
void FreeMemory ();
void FreeRecHeap ();
void GetMemory ();
void GetRecHeap ();
int Initialize ( Boolean vertexType, int vertexExt );
#ifdef _UseRecursion
void Backtrack ( int i ); // exact matching
#else
void Ullman ();
#endif
void Backtrack1 ( int i, int k0 ); // exact/partial matching
void CollectMatch ( int nm );
private :
int nAlloc,mAlloc,nMAlloc;
time_t startTime;
};
DefineStreamFunctions(CGraphMatch);
extern void SetGraphAllocPortion ( int alloc_portion );
/*
extern void TestGraphMatch();
*/
#endif
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