/usr/include/BALL/STRUCTURE/disulfidBondProcessor.h is in libball1.4-dev 1.4.3~beta1-3.
This file is owned by root:root, with mode 0o644.
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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 | #ifndef BALL_STRUCTURE_DISULFIDBONDPROCESSOR_H
#define BALL_STRUCTURE_DISULFIDBONDPROCESSOR_H
#ifndef BALL_CONCEPT_PROCESSOR_H
# include <BALL/CONCEPT/processor.h>
#endif
#ifndef BALL_KERNEL_SYSTEM_H
# include <BALL/KERNEL/system.h>
#endif
#include <set>
namespace BALL
{
/** Disulfid Bond Processor
\ingroup StructureMiscellaneous
*/
/** Detection and Computation of disulfid bonds of the atom container.
*/
class BALL_EXPORT DisulfidBondProcessor
: public UnaryProcessor<AtomContainer>
{
public:
/** @name Type definitions
*/
//@{
typedef std::pair<Residue*, Residue*> DisulfidBond;
typedef std::set<DisulfidBond> DisulfidBonds;
//@}
BALL_CREATE(DisulfidBondProcessor);
/** @name Constructors and Destructors
*/
//@{
/// Default Constructor
DisulfidBondProcessor();
/// Destructor
virtual ~DisulfidBondProcessor();
//@}
/** @name Processor-related methods
*/
//@{
/// Processor method which is called before the operator()-call.
virtual bool start();
/** Clears the data structures.
*/
void clear();
/** Operator () for the processor
*/
virtual Processor::Result operator ()(AtomContainer& ac);
/// Processor method which is called after the operator()-call.
virtual bool finish();
//@}
/** @name Accessors.
*/
//@{
/// Return the number of detected disulfid bonds.
Size getNumberOfDetectedDisulfidBonds() {return sulfur_bridges_.size();};
/// Return the vector of disulfid bonds.
DisulfidBonds& getDisulfidBonds() {return sulfur_bridges_;};
/// Return the vector of disulfid bonds, const variant.
const DisulfidBonds& getDisulfidBonds() const {return sulfur_bridges_;};
//@}
/// Connect two sulfurs by disulid bond
bool connect(Atom* atom1, Atom* atom2, bool toggle = false);
/// Connect two residues by disulid bond
bool connect(Residue* residue1, Residue* residue2, bool toggle = false);
/// Connect two atom containers by disulid bond
bool connect(Composite* composite1, Composite* composite2, bool toggle = false);
/// Disconnect a disulid bond
bool disconnect(Atom* atom1, Atom* atom2);
/// Disconnect a disulid bond by its residues
bool disconnect(Residue* residue1, Residue* residue2);
/// Disconnect a disulid bond by its constitutional atom containers
bool disconnect(Composite* composite1, Composite* composite2);
protected:
DisulfidBonds sulfur_bridges_;
};
}
#endif // BALL_STRUCTURE_DISULFIDBONDPROCESSOR_H
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