/usr/include/ssm/ssm_graph.h is in libssm-dev 1.3-2.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// =================================================================
//
// 10.04.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : ssm_graph <interface>
// ~~~~~~~~~
// **** Classes : ssm::Graph ( secondary structure graph )
// ~~~~~~~~~
//
// E. Krissinel 2002-2013
//
// =================================================================
//
#ifndef __SSM_Graph__
#define __SSM_Graph__
#include "mmdb/mmdb_manager.h"
#include "ssm_vxedge.h"
namespace ssm {
// ========================== Graph ===========================
DefineClass(Graph);
DefineStreamFunctions(Graph)
class Graph : public CStream {
friend class GraphMatch;
public :
Graph ();
Graph ( RPCStream Object );
~Graph();
void Reset(); // must be called before building a graph
// The sequence of calls is:
// Graph.Reset();
// for (....) {
// V = new CSSVertex();
// .....
// SSGraph.AddVertex ( V );
// }
// SSGraph.Build();
void SetGraphName ( cpstr gname );
void SelectCalphas ( PCMMDBManager MMDB, int & selHnd,
cpstr selstring );
// AddVertex(..) do not copy the objects, but take them over.
// This means that application should forget about pointers to
// V once they were given to CSSGraph. All vertices must be
// allocated newly prior each call to AddVertex(..).
void AddVertex ( PVertex Vx );
int MakeGraph ( PCMMDBManager MMDB );
void CalcVertexOrder();
void RepairSS ( PCMMDBManager MMDB );
// BuildGraph() calculates all edges and builds the graph.
void BuildGraph();
Boolean isBuild ();
void calcVTypes(); // calculates nHelices and nStrands only
// ReleaseEdges() deallocates all graph edges and
// the connectivity matrix
void ReleaseEdges();
void RemoveShortVertices ( int nmin_hx, int nmin_sd );
// LeaveVertices(..) removes all vertices from the graph
// except those having numbers listed in vector vlist. Thus,
// if vlist[i]=j, 1<=i<=vllen, 1<=j, then jth vertex will
// not be removed.
void LeaveVertices ( ivector vlist, int vllen );
// LeaveVertices(..) removes all vertices from the graph
// except those found in the specified range. 'select' is of
// the following format:
// "*", "(all)" - take all file
// "-" - take chain without chain ID
// "a:Ni-Mj,b:Kp-Lq,..." - take chain a residue number N
// insertion code i to residue number M
// insertion code j plus chain b
// residue number K insertion code p to
// residue number L insertion code q and
// so on.
// "a:,b:..." - take whole chains a and b and so on
// "a:,b:Kp-Lq,..." - any combination of the above.
void LeaveVertices ( cpstr select, PCMMDBManager M );
// LeaveVertices ( selHnd,MMDB ) leaves only vertices that are
// covered by the given selection. selHnd may refer to the
// selection of atoms, residues or chains.
void LeaveVertices ( int selHnd, PCMMDBManager M );
void RemoveVertex ( int vertex_no ); // 1..nVertices
Boolean inRange ( cpstr chainID, int initPos, int endPos );
inline cpstr GetGraphName () { return name; }
inline cpstr GetDevChain () { return devChain; }
pstr GetChainList ( pstr S );
inline int GetNofVertices () { return nVertices; }
inline PPVertex GetVertices () { return V; }
inline int GetNofEdges () { return nEdges; }
inline int GetNofHelices () { return nHelices; }
inline int GetNofStrands () { return nStrands; }
void GetAllChains ( PChainID & chain, int & nchains );
int GetNofChains ();
Boolean GetEdgeDirection ( int v1, int v2, vect3 & v );
VERTEX_TYPE GetVertexType ( int vertex_no ); // 1..nVertices
int GetVertexClass ( int vertex_no ); // 1..nVertices
Boolean GetVertexDirection ( int vertex_no, vect3 & v );
int GetSeqLength ( int vertex_no ); // 1..nVertices
realtype GetMass ( int vertex_no ); // 1..nVertices
PVertex GetGraphVertex ( int vertex_no ); // 1..nVertices
pstr GetVertexChainID ( int vertex_no ); // 1..nVertices
pstr GetVertexInitRes ( int vertex_no ); // 1..nVertices
pstr GetVertexEndRes ( int vertex_no ); // 1..nVertices
void GetVertexRange ( int vertex_no, // 1..nVertices
ChainID chID,
int & initSeqNum,
InsCode initICode,
int & endSeqNum,
InsCode endICode );
void GetVertexRange ( int vertex_no, // 1..nVertices
ChainID chID,
int & initPos,
int & endPos );
VERTEX_TYPE GetSSEType ( pstr chainID, int atomPos );
VERTEX_TYPE GetSSEType ( PCAtom A );
PEdge GetGraphEdge ( int edge_no ); // 1..nEdges
PEdge GetGraphEdge ( int v1, int v2 ); // 1..nVertices
realtype CalcCombinations ( ivector F, int nm );
void DevelopChainGraphs ( PPGraph & G, int & nGraphs );
// Superpose(..) returns TMatrix - a transformation matrix for
// G's coordinates, such that TMatrix*{G} ~= {this}
// F1 is for 'this' graph, F2 = for G.
void Superpose ( PGraph G, ivector F1, ivector F2,
int nMatch, mat44 & TMatrix );
void Copy ( PGraph G );
void read ( RCFile f );
void write ( RCFile f );
protected :
pstr name; // graph name
ChainID devChain; // chain of a developed graph
int nVertices,nEdges;
int nHelices,nStrands;
PPVertex V;
PPEdge E;
imatrix graph;
void InitGraph ();
void FreeMemory ();
void _leaveVertices ( PCMMDBManager M, int selHnd1 );
// CompareEdges(..) compares edge (ij) of the graph with
// edge (kl) of graph G. i may be either less or greater
// than j, same about k and l. If edges compare, the function
// returns 0. Edges with equal indices (i.e. (ii) and (kk))
// are considered as comparable (returns 0).
// The function may be used only after both graphs have
// been built.
int CompareEdges ( int i, int j, PGraph G, int k, int l );
int CheckEdgeConnectivity ( int i, int j, PGraph G, int k, int l );
private :
int nVAlloc,nEAlloc,nGAlloc;
};
// ==================================================================
// In SelectDomain(..) and CutOutDomain(..), select is of the
// following format:
// "*", "(all)" - take all file
// "-" - take chain without chain ID
// "a:Ni-Mj,b:Kp-Lq,..." - take chain a residue number N
// insertion code i to residue number M
// insertion code j plus chain b
// residue number K insertion code p to
// residue number L insertion code q and
// so on.
// "a:,b:..." - take whole chains a and b and so on
// "a:,b:Kp-Lq,..." - any combination of the above.
extern int SelectDomain ( PCMMDBManager MMDB, int & selHnd,
cpstr select, int selType );
extern int CutOutDomain ( PCMMDBManager MMDB, cpstr select );
extern PGraph GetSSGraph ( PCMMDBManager M, int selHnd, int & rc );
extern void DisposeGraphs ( PPGraph & G, int & nGraphs );
extern int SuperposeGraphs ( PGraph G1, ivector F1,
PGraph G2, ivector F2,
int matchlen,
mat44 & TMatrix );
}
/*
extern realtype GetTorsion ( rvector U, rvector W, rvector V );
// U W V
// o<----o----->o----->o
//
extern realtype GetAngle ( rvector v1, rvector v2 );
// returns angle between v1 and v2
extern void CalcCombinations ( rvector & combs, int & vlen,
PCSSGraph G1, PCSSGraph G2 );
*/
#endif
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