A class representing a substitution of a molecule from an original molecule through a pair of matched templates to a substituted molecule. More...

#include <substitution_support.hh>

Public Member Functions
	MoleculeSubstitution ()

	MoleculeSubstitution (::RDKit::ROMolOP mol)
	Construct a MoleculeSubstitution from an RDKit molecule (The source molecule.) More...

void	add_template (::RDKit::ROMolOP templt, ::RDKit::MatchVectType const &pairings)
	Add a template to this MoleculeSubstitution. More...

::RDKit::MatchVectType	make_match_vector () const
	Reconstitute the original pairings. This is a vector of pairs of (tdx, mdx) More...

core::chemical::IndexIndexMapping	find_mdx_to_ndx_mapping () const
	Create a mapping from mdx to ndx. More...

MoleculeSubstitutionOP	add_replacement (::RDKit::ROMolOP replacement, std::map< unsigned int, unsigned int > &r_to_t_mapping) const
	Make a new MoleculeSubstitution class with the replacement information. More...

void	add_newmol (::RDKit::RWMolOP newmol)

::RDKit::ROMolOP	get_romol (MoleculeSelection sele)

::RDKit::ROMolOP	mol ()

::RDKit::ROMolOP	templt ()

::RDKit::ROMolOP	replace ()

::RDKit::RWMolOP	newmol ()

AtomSubstitution &	substitution_for_idx (MoleculeSelection sele, unsigned int idx)

AtomSubstitution &	substitution_for_mdx (unsigned int idx)

AtomSubstitution &	substitution_for_tdx (unsigned int idx)

AtomSubstitution &	substitution_for_rdx (unsigned int idx)

bool	tdx_is_dummy (unsigned int tdx) const

bool	rdx_is_dummy (unsigned int rdx) const

utility::vector1< unsigned int > const &	template_dummies () const
	The indexes for dummy atoms on the matching template. More...

utility::vector1< unsigned int > const &	replace_dummies () const
	The indexes for dummy atoms on the replacement template. More...

Private Attributes
::RDKit::ROMolOP	mol_

::RDKit::ROMolOP	templt_

::RDKit::ROMolOP	replace_

::RDKit::RWMolOP	newmol_

std::map< unsigned int, AtomSubstitutionOP >	by_mdx_

std::map< unsigned int, AtomSubstitutionOP >	by_tdx_

std::map< unsigned int, AtomSubstitutionOP >	by_rdx_

utility::vector1< unsigned int >	template_dummies_
	What idx's correspond to dummy atoms? More...

utility::vector1< unsigned int >	replace_dummies_

utility::vector1< AtomSubstitutionOP >	atom_substitutions_
	Storage for the individual atom substitutions. More...

Detailed Description

A class representing a substitution of a molecule from an original molecule through a pair of matched templates to a substituted molecule.

The MoleculeSubstitution can be made progressively from molecule outwards. It should contain an indexed entry for each item in all four molecules (At least for those molecules which it's currently aware of.)

Constructor & Destructor Documentation

◆ MoleculeSubstitution() [1/2]

protocols::drug_design::MoleculeSubstitution::MoleculeSubstitution ( )

inline

◆ MoleculeSubstitution() [2/2]

protocols::drug_design::MoleculeSubstitution::MoleculeSubstitution ( ::RDKit::ROMolOP mol )

Construct a MoleculeSubstitution from an RDKit molecule (The source molecule.)

References atom_substitutions_, by_mdx_, and mol().

Member Function Documentation

◆ add_newmol()

void protocols::drug_design::MoleculeSubstitution::add_newmol ( ::RDKit::RWMolOP newmol )

inline

References newmol(), and newmol_.

◆ add_replacement()

MoleculeSubstitutionOP protocols::drug_design::MoleculeSubstitution::add_replacement	(	::RDKit::ROMolOP	replacement,
		std::map< unsigned int, unsigned int > &	r_to_t_mapping
	)		const

Make a new MoleculeSubstitution class with the replacement information.

Make a new AtomSubstitution class with the replacement information.

Assumes that the new (post-replacement) molecule hasn't been set.

References atom_substitutions_, protocols::drug_design::find_dummies(), mol_, template_dummies_, and templt_.

◆ add_template()

void protocols::drug_design::MoleculeSubstitution::add_template	(	::RDKit::ROMolOP	templt,
		::RDKit::MatchVectType const &	pairings
	)

Add a template to this MoleculeSubstitution.

References by_mdx_, by_tdx_, protocols::drug_design::find_dummies(), template_dummies_, templt(), and templt_.

◆ find_mdx_to_ndx_mapping()

core::chemical::IndexIndexMapping protocols::drug_design::MoleculeSubstitution::find_mdx_to_ndx_mapping ( ) const

Create a mapping from mdx to ndx.

References atom_substitutions_, and protocols::drug_design::AtomSubstitution::invalid_index.

◆ get_romol()

RDKit::ROMolOP protocols::drug_design::MoleculeSubstitution::get_romol ( MoleculeSelection sele )

References mol(), protocols::drug_design::NewMol, protocols::drug_design::OriginalMol, replace(), protocols::drug_design::ReplaceMol, protocols::drug_design::TemplateMol, and templt().

Referenced by protocols::drug_design::copy_attached_atoms().

◆ make_match_vector()

RDKit::MatchVectType protocols::drug_design::MoleculeSubstitution::make_match_vector ( ) const

Reconstitute the original pairings. This is a vector of pairs of (tdx, mdx)

References atom_substitutions_, and protocols::drug_design::AtomSubstitution::invalid_index.

◆ mol()

::RDKit::ROMolOP protocols::drug_design::MoleculeSubstitution::mol ( )

inline

References mol_.

Referenced by get_romol(), and MoleculeSubstitution().

◆ newmol()

::RDKit::RWMolOP protocols::drug_design::MoleculeSubstitution::newmol ( )

inline

References newmol_.

Referenced by add_newmol(), and protocols::drug_design::copy_attached_atoms().

◆ rdx_is_dummy()

bool protocols::drug_design::MoleculeSubstitution::rdx_is_dummy ( unsigned int rdx ) const

References protocols::drug_design::is_dummy(), and replace_.

◆ replace()

::RDKit::ROMolOP protocols::drug_design::MoleculeSubstitution::replace ( )

inline

References replace_.

Referenced by get_romol().

◆ replace_dummies()

utility::vector1< unsigned int > const& protocols::drug_design::MoleculeSubstitution::replace_dummies ( ) const

inline

The indexes for dummy atoms on the replacement template.

References replace_dummies_.

◆ substitution_for_idx()

AtomSubstitution & protocols::drug_design::MoleculeSubstitution::substitution_for_idx	(	MoleculeSelection	sele,
		unsigned int	idx
	)

References protocols::drug_design::NewMol, protocols::drug_design::OriginalMol, protocols::drug_design::ReplaceMol, substitution_for_mdx(), substitution_for_rdx(), substitution_for_tdx(), and protocols::drug_design::TemplateMol.

Referenced by protocols::drug_design::copy_attached_atoms().

◆ substitution_for_mdx()

AtomSubstitution & protocols::drug_design::MoleculeSubstitution::substitution_for_mdx ( unsigned int idx )

References by_mdx_.

Referenced by substitution_for_idx().

◆ substitution_for_rdx()

AtomSubstitution & protocols::drug_design::MoleculeSubstitution::substitution_for_rdx ( unsigned int idx )

References by_rdx_.

Referenced by substitution_for_idx().

◆ substitution_for_tdx()

AtomSubstitution & protocols::drug_design::MoleculeSubstitution::substitution_for_tdx ( unsigned int idx )

References by_tdx_.

Referenced by substitution_for_idx().

◆ tdx_is_dummy()

bool protocols::drug_design::MoleculeSubstitution::tdx_is_dummy ( unsigned int tdx ) const

References protocols::drug_design::is_dummy(), and templt_.

◆ template_dummies()

utility::vector1< unsigned int > const& protocols::drug_design::MoleculeSubstitution::template_dummies ( ) const

inline

The indexes for dummy atoms on the matching template.

References template_dummies_.

◆ templt()

::RDKit::ROMolOP protocols::drug_design::MoleculeSubstitution::templt ( )

inline

References templt_.

Referenced by add_template(), and get_romol().

Member Data Documentation

◆ atom_substitutions_

utility::vector1< AtomSubstitutionOP > protocols::drug_design::MoleculeSubstitution::atom_substitutions_

private

Storage for the individual atom substitutions.

Referenced by add_replacement(), find_mdx_to_ndx_mapping(), make_match_vector(), and MoleculeSubstitution().

◆ by_mdx_

std::map< unsigned int, AtomSubstitutionOP > protocols::drug_design::MoleculeSubstitution::by_mdx_

private

Referenced by add_template(), MoleculeSubstitution(), and substitution_for_mdx().

◆ by_rdx_

std::map< unsigned int, AtomSubstitutionOP > protocols::drug_design::MoleculeSubstitution::by_rdx_

private

Referenced by substitution_for_rdx().

◆ by_tdx_

std::map< unsigned int, AtomSubstitutionOP > protocols::drug_design::MoleculeSubstitution::by_tdx_

private

Referenced by add_template(), and substitution_for_tdx().

◆ mol_

::RDKit::ROMolOP protocols::drug_design::MoleculeSubstitution::mol_

private

Referenced by add_replacement(), and mol().

◆ newmol_

::RDKit::RWMolOP protocols::drug_design::MoleculeSubstitution::newmol_

private

Referenced by add_newmol(), and newmol().

◆ replace_

::RDKit::ROMolOP protocols::drug_design::MoleculeSubstitution::replace_

private

Referenced by rdx_is_dummy(), and replace().

◆ replace_dummies_

utility::vector1< unsigned int > protocols::drug_design::MoleculeSubstitution::replace_dummies_

private

Referenced by replace_dummies().

◆ template_dummies_

utility::vector1< unsigned int > protocols::drug_design::MoleculeSubstitution::template_dummies_

private

What idx's correspond to dummy atoms?

Referenced by add_replacement(), add_template(), and template_dummies().

◆ templt_

::RDKit::ROMolOP protocols::drug_design::MoleculeSubstitution::templt_

private

Referenced by add_replacement(), add_template(), tdx_is_dummy(), and templt().

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MoleculeSubstitution() [1/2]

◆ MoleculeSubstitution() [2/2]

Member Function Documentation

◆ add_newmol()

◆ add_replacement()

◆ add_template()

◆ find_mdx_to_ndx_mapping()

◆ get_romol()

◆ make_match_vector()

◆ mol()

◆ newmol()

◆ rdx_is_dummy()

◆ replace()

◆ replace_dummies()

◆ substitution_for_idx()

◆ substitution_for_mdx()

◆ substitution_for_rdx()

◆ substitution_for_tdx()

◆ tdx_is_dummy()

◆ template_dummies()

◆ templt()

Member Data Documentation

◆ atom_substitutions_

◆ by_mdx_

◆ by_rdx_

◆ by_tdx_

◆ mol_

◆ newmol_

◆ replace_

◆ replace_dummies_

◆ template_dummies_

◆ templt_