/usr/include/ssm/ssm_vxedge.h is in libssm-dev 1.3-2.2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 | // $Id: ssm_vxedge.h,v 1.1.1.1 2004/11/23 16:24:37 keb Exp $
// =================================================================
//
// 05.04.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : ssm_vxedge <interface>
// ~~~~~~~~~
// **** Classes : ssm::Vertex ( secondary structure graph vertex )
// ~~~~~~~~~ ssm::Edge ( secondary structure graph edge )
//
// E. Krissinel 2002-2013
//
// =================================================================
//
#ifndef __SSM_VxEdge__
#define __SSM_VxEdge__
#include "mmdb/mmdb_manager.h"
#include "ssm_defs.h"
// ========================== Tune-up ============================
namespace ssm {
extern int hx_min_len;
extern int sd_min_len;
extern void InitGraph(); // should be called on top of application
extern void SetMatchPrecision ( PRECISION prec );
extern void writeMatchParameters ( cpstr FileName );
extern int readMatchParameters ( cpstr FileName );
extern void SetConnectivityCheck ( CONNECTIVITY checkMode );
// ========================= CSSVertex ===========================
DefineClass(Vertex);
DefineStreamFunctions(Vertex)
class Vertex : public CStream {
friend class Edge;
friend class Graph;
public :
Vertex ();
Vertex ( RPCStream Object );
~Vertex();
int SetVertex ( PCMMDBManager MMDB, PCHelix Helix );
int SetVertex ( PCMMDBManager MMDB, PCStrand Strand );
int SetVertex ( PCMMDBManager MMDB, VERTEX_TYPE v_type,
int sNum, int iclass, ChainID chID,
int seqNum1, InsCode iCode1,
int seqNum2, InsCode iCode2 );
inline void SetID ( int vid ) { id = vid; }
realtype GetAngle ( PVertex v );
realtype GetCosine ( PVertex v );
realtype GetAngle ( realtype vx, realtype vy, realtype vz );
pstr GetShortVertexDesc ( pstr S );
pstr GetFullVertexDesc ( pstr S );
Boolean Compare ( PVertex v ); // True if vertices compare
realtype GetLengthDeviation ( PVertex v );
void GetDirection ( vect3 & v );
void GetPosition ( vect3 & p );
void GetPosition ( realtype & vx0, realtype & vy0,
realtype & vz0 );
inline realtype GetLength () { return length; }
inline int GetSeqLength () { return nres; }
inline realtype GetMass () { return mass; }
inline realtype GetX1 () { return x1; };
inline realtype GetX2 () { return x2; };
inline realtype GetY1 () { return y1; };
inline realtype GetY2 () { return y2; };
inline realtype GetZ1 () { return z1; };
inline realtype GetZ2 () { return z2; };
Boolean inRange ( cpstr chID, int Pos1, int Pos2 );
inline int GetVertexType () { return type; }
inline int GetVertexChainNo() { return VNo; }
inline cpstr GetChainID () { return chainID; }
void GetVertexRange ( ChainID chID,
ResName name1,
int & seqNum1,
InsCode insCode1,
ResName name2,
int & seqNum2,
InsCode insCode2 );
void Copy ( PVertex v );
void read ( RCFile f );
void write ( RCFile f );
protected :
// matching info
int id; //!< unique identifier that MUST be the vertex
/// number starting from 1 on
VERTEX_TYPE type; //!< a V_XXXXX constant
int classID; //!< class ID for helices
int nres; //!< number of residues
realtype x0,y0,z0; //!< center of mass
realtype mass; //!< the mass
realtype ex,ey,ez; //!< direction vector
realtype dalpha; //!< uncertainty angle
realtype length; //!< vertex length
// identification info
pstr name; //!< composed name for short identification
int serNum; //!< helix serial number
int strandNo; //!< strand number
maxMMDBName vertexID; //!< helix ID or sheet ID
ChainID chainID; //!< chain ID (only for identification)
ResName initResName; //!< name of the strand's initial residue
int initSeqNum; //!< sequence number of the initial residue
int initPos; //!< sequence position of the initial residue
InsCode initICode; //!< insertion code of the initial residue
ResName endResName; //!< name of the strand's terminal residue
int endSeqNum; //!< sequence number of the terminal residue
int endPos; //!< sequence position of the terminal residue
InsCode endICode; //!< insertion code of the terminal residue
int VNo; //!< number of vertex in the chain
realtype x1,x2; //!< coordinates
realtype y1,y2; /// SSE
realtype z1,z2; /// ends
void InitVertex ();
void FreeMemory ();
void CalcGeometry ( PPCAtom CA );
int GetPositions ( PCMMDBManager MMDB, int minlen );
realtype GetCoor1 ( PPCAtom CA, int coor_key );
realtype GetCoor2 ( PPCAtom CA, int coor_key );
};
// ========================== CSSEdge ============================
DefineClass(Edge);
DefineStreamFunctions(Edge)
class Edge : public CStream {
friend class Graph;
friend class GraphMatch;
public :
Edge ();
Edge ( RPCStream Object );
~Edge();
void SetEdge ( PVertex v1, PVertex v2 );
realtype GetAngle ( PVertex v ); // returns angle between
// the edge and vertex
realtype GetCosine ( PEdge E ); // returns cosine angle between
// the edges
realtype GetAngle ( rvector V1, rvector V2 );
// Compare(..) returns 0 if edges compare, that is:
// 1. edge lengths compare within relative precision
// edge_len_tol
// 2. angles alpha1, alpha2 and alpha3 compare within
// absolute deviations edge_alphaX_tol .
int Compare ( Boolean swap_this, PEdge edge,
Boolean swap_edge );
int CheckConnectivity ( Boolean swap_this, PEdge edge,
Boolean swap_edge );
void GetDirection ( vect3 & v );
inline realtype GetLength () { return length; }
void read ( RCFile f );
void write ( RCFile f );
protected :
int id1,id2; //!< linked vertices
int vtype1; //!< type of 1st linked vertex
int vtype2; //!< type of 2nd linked vertex
int bdir; //!< bond direction along the chain
realtype length; //!< length of edge (between v1 and v2 mass centers)
realtype ex,ey,ez; //!< direction vector from v1 to v2
realtype alpha1; //!< angle V1E between v1 and the edge
realtype alpha2; //!< angle V2E between v2 and the edge
realtype alpha3; //!< angle V1V2 between v1 and v2
realtype alpha4; //!< torsion angle V1EV2 of v1, edge and v2
realtype dalpha1; //!< uncertainty in alpha1
realtype dalpha2; //!< uncertainty in alpha2
realtype dalpha3; //!< uncertainty in alpha3
realtype dalpha4; //!< uncertainty in alpha4
realtype dr12;
Boolean GoodTorsion; //!< True if the VEV torsion angle is well defined
void InitEdge();
};
}
#endif
|