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
|
#ifndef ATOM_H
#define ATOM_H
#include "basetypes.h"
#include <string>
#include <iostream>
#include "coord3d.h"
namespace PTools{
class Atomproperty {
private:
std::string mAtomType; ///< CA, N, HN1, ...
std::string mAtomElement; ///< C, N, H, O, etc.
std::string mResidType; ///< LEU, ARG, ...
std::string mChainId; ///< A, B, etc.
uint mResidId; ///< residue number
uint mAtomId; ///< atom number
dbl mAtomCharge; ///< charge of the atom
std::string mExtra; ///< extra data
public:
/// default constructor
Atomproperty()
{
mAtomType="X";
mAtomElement="X";
mResidType="XXX";
mChainId="X";
mResidId=1;
mAtomId=1;
mAtomCharge=0.0;
};
/// return atom type (CA, CB, O, N...)
std::string GetType() const {return mAtomType;};
/// define atom type (CA, CB, O, N...)
void SetType(std::string newtype) { mAtomType = newtype;};
/// return residue type (LEU, ARG...)
std::string GetResidType() const {return mResidType;};
/// define residue type (LEU, ARG...)
void SetResidType(std::string residtype){mResidType=residtype;};
/// return atom charge
inline dbl GetAtomCharge() const {return mAtomCharge;};
/// define atom charge
inline void SetAtomCharge(dbl ch) {mAtomCharge=ch;};
/// return chain ID (A, B...)
inline std::string GetChainId() const {return mChainId;};
/// define chain ID (A, B...)
inline void SetChainId(std::string chainid) {mChainId=chainid;};
/// return residue ID (1, 2...)
inline uint GetResidId() const {return mResidId;};
/// define residue ID (1, 2...)
inline void SetResidId(uint id) {mResidId = id;};
/// return atom ID (1, 2...)
inline uint GetAtomId() const {return mAtomId;};
/// define atom ID (1, 2...)
inline void SetAtomId(uint atomnumber) {mAtomId=atomnumber;};
/// set the extra data field
inline void SetExtra(std::string extra){mExtra=extra;};
/// get the extra data field
inline std::string GetExtra() const {return mExtra;};
};
class Atom : public Atomproperty
{
private:
Coord3D mCoords; ///< Atom cartesian coordinates
public:
Atom(Atomproperty ap, Coord3D co)
: Atomproperty(ap), mCoords(co) {};
Coord3D GetCoords() const; ///< return atom coordinates
/// define atom coordinates
inline void SetCoords(const Coord3D& coords) {mCoords=coords;};
/// convert atom (properties and coordinates) to std::string
std::string ToString() const;
/// convert atom (properties and coordinates) to classical PDB-like string
std::string ToPdbString() const ;
/// translation of an atom
void Translate(const Coord3D& tr);
};
/// distance between two atoms
inline dbl Dist(const Atom& at1, const Atom& at2)
{
return Norm(at1.GetCoords()-at2.GetCoords());
}
/// distance**2 between two atoms
inline dbl Dist2(const Atom& at1, const Atom& at2)
{
return Norm2(at1.GetCoords()-at2.GetCoords());
}
}
#endif
|