/usr/include/ghemical/bond.h is in libghemical-dev 3.0.0-2ubuntu1.
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 | // BOND.H : the bond-related classes.
// Copyright (C) 1998 Tommi Hassinen.
// This package is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
// This package 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 General Public License for more details.
// You should have received a copy of the GNU General Public License
// along with this package; if not, write to the Free Software
// Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
/*################################################################################################*/
#ifndef BOND_H
#define BOND_H
#include "libghemicaldefine.h"
class bondtype;
class bond;
/*################################################################################################*/
class atom; // atom.h
#include "typedef.h"
#include <list>
#include <vector>
using namespace std;
/*################################################################################################*/
#define BONDTYPE_CNJGTD 0
#define BONDTYPE_SINGLE 1
#define BONDTYPE_DOUBLE 2
#define BONDTYPE_TRIPLE 3
//////////////////////////////////////////////////////
//#define BONDTYPE_QUADRP 4 // never needed!!!
//////////////////////////////////////////////////////
/// A bondtype class.
class bondtype
{
private:
i32s type;
static const char * string[4];
static const char symbol1[4];
static const char symbol2[4];
public:
static bondtype current_bondtype; ///< This is the current element that user has selected.
public:
bondtype(void);
bondtype(char); ///< By symbols.
bondtype(i32s); ///< By number codes.
~bondtype(void);
const char * GetString(void) const;
i32s GetValue(void) const;
char GetSymbol1(void) const;
char GetSymbol2(void) const;
void operator++(void);
void operator--(void);
// friend ostream & operator<<(ostream &, bondtype &); this is not needed...
};
/*################################################################################################*/
#define BOND_NFLAGS 3 // the number of flags can be increased if needed...
// ABOUT FLAGS:
// ^^^^^^^^^^^^
// 0 is used generally in typerule tests.
// 1 is also used in "RingSize" and "Ring" typerule tests.
// 2 is used by sequencebuilder::FindPath() at least...
/// A bond class.
/** Will store information about a bond, including the atoms that the bond connects,
and bondtype information. */
class bond
{
// protected:
public: // TODO : not properly divided in public/protected data.
atom * atmr[2];
bondtype bt;
vector<bool> flags;
/// A temporary variable used when creating molecular mechanics energy terms.
/** This variable is not otherwise used or initialized, and it is not saved. */
i32s tmp_bt1_index;
bool do_not_render_TSS_fixmelater; ///< this is only for visualize breaking bonds in TSS!!!
public:
bond(void);
bond(atom *, atom *, bondtype);
bond(const bond &);
~bond(void);
bool operator<(const bond &) const; ///< Using molecule numbers.
bool operator==(const bond &) const; ///< Using atom pointers.
};
/*################################################################################################*/
typedef list<bond>::iterator iter_bl; // bl = bond list
typedef bond * ref_bond;
/*################################################################################################*/
#endif // BOND_H
// eof
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