protocols::drug_design::AtomSubstitution Class Reference

A class representing a substitution of an atom from an original molecule through a pair of matched templates to a substituted molecule. Intended to be used through MoleculeSubstitution. More...

#include <substitution_support.hh>

Public Member Functions
	AtomSubstitution (unsigned int mdx=invalid_index, unsigned int tdx=invalid_index, unsigned int rdx=invalid_index, unsigned int ndx=invalid_index)
unsigned int	idx (MoleculeSelection sele) const
unsigned int	mdx () const
	The atom index in the original molecule. More...
unsigned int	tdx () const
	The atom index in the template which matches the original molecule. More...
unsigned int	rdx () const
	The atom index in the replacement template. More...
unsigned int	ndx () const
	The atom index in the new (post-replacement) molecule. More...
void	set_idx (MoleculeSelection sele, unsigned int setting)
void	set_mdx (unsigned int setting)
void	set_tdx (unsigned int setting)
void	set_rdx (unsigned int setting)
void	set_ndx (unsigned int setting)

Static Public Attributes
static unsigned int const	invalid_index =65500

Private Attributes
unsigned int	mdx_
unsigned int	tdx_
unsigned int	rdx_
unsigned int	ndx_

Detailed Description

A class representing a substitution of an atom from an original molecule through a pair of matched templates to a substituted molecule. Intended to be used through MoleculeSubstitution.

Constructor & Destructor Documentation

AtomSubstitution()

protocols::drug_design::AtomSubstitution::AtomSubstitution ( unsigned int  mdx = invalid_index, unsigned int  tdx = invalid_index, unsigned int  rdx = invalid_index, unsigned int  ndx = invalid_index  )

inline

Member Function Documentation

idx()

unsigned int protocols::drug_design::AtomSubstitution::idx

(

MoleculeSelection

sele

)

const

References invalid_index, mdx(), ndx(), protocols::drug_design::NewMol, protocols::drug_design::OriginalMol, rdx(), protocols::drug_design::ReplaceMol, tdx(), and protocols::drug_design::TemplateMol.

mdx()

unsigned int protocols::drug_design::AtomSubstitution::mdx ( ) const

inline

The atom index in the original molecule.

References mdx_.

Referenced by protocols::drug_design::SubstructureReplace::apply(), and idx().

ndx()

unsigned int protocols::drug_design::AtomSubstitution::ndx ( ) const

inline

The atom index in the new (post-replacement) molecule.

References ndx_.

Referenced by protocols::drug_design::SubstructureReplace::apply(), protocols::drug_design::copy_attached_atoms(), and idx().

rdx()

unsigned int protocols::drug_design::AtomSubstitution::rdx ( ) const

inline

The atom index in the replacement template.

References rdx_.

Referenced by protocols::drug_design::SubstructureReplace::apply(), and idx().

set_idx()

void protocols::drug_design::AtomSubstitution::set_idx	(	MoleculeSelection	sele,
		unsigned int	setting
	)

References protocols::drug_design::NewMol, protocols::drug_design::OriginalMol, protocols::drug_design::ReplaceMol, set_mdx(), set_ndx(), set_rdx(), set_tdx(), and protocols::drug_design::TemplateMol.

set_mdx()

void protocols::drug_design::AtomSubstitution::set_mdx ( unsigned int  setting )

inline

References mdx_.

Referenced by set_idx().

set_ndx()

void protocols::drug_design::AtomSubstitution::set_ndx ( unsigned int  setting )

inline

References ndx_.

Referenced by protocols::drug_design::SubstructureReplace::apply(), protocols::drug_design::copy_attached_atoms(), and set_idx().

set_rdx()

void protocols::drug_design::AtomSubstitution::set_rdx ( unsigned int  setting )

inline

References rdx_.

Referenced by set_idx().

set_tdx()

void protocols::drug_design::AtomSubstitution::set_tdx ( unsigned int  setting )

inline

References tdx_.

Referenced by set_idx().

tdx()

unsigned int protocols::drug_design::AtomSubstitution::tdx ( ) const

inline

The atom index in the template which matches the original molecule.

References tdx_.

Referenced by idx().

Member Data Documentation

invalid_index

unsigned int const protocols::drug_design::AtomSubstitution::invalid_index =65500

static

Referenced by protocols::drug_design::SubstituentReplace::apply(), protocols::drug_design::SubstructureReplace::apply(), protocols::drug_design::copy_attached_atoms(), protocols::drug_design::MoleculeSubstitution::find_mdx_to_ndx_mapping(), idx(), protocols::drug_design::MoleculeSubstitution::make_match_vector(), protocols::drug_design::SubstituentReplace::pick_replacement(), and protocols::drug_design::test_replacement().

mdx_

unsigned int protocols::drug_design::AtomSubstitution::mdx_

private

Referenced by mdx(), and set_mdx().

ndx_

unsigned int protocols::drug_design::AtomSubstitution::ndx_

private

Referenced by ndx(), and set_ndx().

rdx_

unsigned int protocols::drug_design::AtomSubstitution::rdx_

private

Referenced by rdx(), and set_rdx().

tdx_

unsigned int protocols::drug_design::AtomSubstitution::tdx_

private

Referenced by set_tdx(), and tdx().

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The documentation for this class was generated from the following files:

• src/protocols/drug_design/substitution_support.hh
• src/protocols/drug_design/substitution_support.cc