#include <Reprotonate.hh>

Inheritance diagram for core::chemical::modifications::Reprotonate:

Public Member Functions
	Reprotonate ()

void	apply (MutableResidueType &res) override
	Search the provided ResidueType for protons which should be added/removed in order to conform to the protonation state in neutral (pH 7-ish) aqueous solution. This is done heuristically, assuming that protons have already been added. The geometry of any existing hydrogen atoms will be adjusted, but not any heavy atoms. More...

core::chemical::VDVDMapping	get_mapping () const override
	Get the vertex mapping that was used for the last apply() or get_additional_output() This is a mapping FROM the vds in the BEFORE MutableResidueType TO the vds in the AFTER MutableResidueType. The base class implementation defaults to an identity mapping. More...

Public Member Functions inherited from core::chemical::modifications::ChemistryBase
	ChemistryBase (std::string const &name)

std::string	name () const
	Return the name of this Chemistry object. More...

virtual bool	has_additional_output () const
	Are there alternate ResidueTypes which are availible from the last time we called apply? (That is, will get_addtional_output() return non-null?) More...

virtual core::chemical::MutableResidueTypeOP	get_additional_output ()
	Get additional generated ResidueTypes, if any. This allows for 1-to-many Chemistries. More...

ChemistryStatus	get_last_status () const
	What was the status of the last call to apply()/get_additional_output() More...

void	set_last_status (ChemistryStatus setting)
	Set the status of the chemistry object. More...

Static Public Member Functions
static std::string	class_name ()

Private Member Functions
VD	find_electron_sink (MutableResidueType const &restype, VD neighbor) const
	Find a doubly-bonded oxygen or sulfur attached to neighbor. More...

bool	is_conjugatable (MutableResidueType const &restype, VD atom) const
	Is the provided able to participate in conjugation? More...

core::Size	remove_hydrogens (MutableResidueType &restype, VD atom)
	Remove hydrogens from specified atom. Returns the number of hydrogens removed. More...

Private Attributes
core::chemical::VDVDMapping	mapping_

Constructor & Destructor Documentation

◆ Reprotonate()

core::chemical::modifications::Reprotonate::Reprotonate ( )

inline

Member Function Documentation

◆ apply()

void core::chemical::modifications::Reprotonate::apply ( MutableResidueType & res )

overridevirtual

Search the provided ResidueType for protons which should be added/removed in order to conform to the protonation state in neutral (pH 7-ish) aqueous solution. This is done heuristically, assuming that protons have already been added. The geometry of any existing hydrogen atoms will be adjusted, but not any heavy atoms.

The current targets are: Deprotonation:

Carboxylates
Thiocarboxylates ( C(=O)-SH as well as C(=S)-OH, if existant)
Sulfates/Phosphates/Nitrates/etc (as well as thio equivalents)
NOT Phenols

Protonation

(aliphatic) Amines
NOT Amides, anilines, or conjugated amines

Protonation/deprotonation will not happen on atoms with existing formal charges. The appropriate formal charge will be added to the reprotonated atom.

Implements core::chemical::modifications::ChemistryBase.

◆ class_name()

std::string core::chemical::modifications::Reprotonate::class_name ( )

static

◆ find_electron_sink()

VD core::chemical::modifications::Reprotonate::find_electron_sink	(	MutableResidueType const &	restype,
		VD	neighbor
	)		const

private

Find a doubly-bonded oxygen or sulfur attached to neighbor.

References core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::bond(), core::chemical::DoubleBondOrder, core::chemical::Atom::element(), core::chemical::MutableResidueType::graph(), core::chemical::MutableResidueType::null_vertex, core::chemical::element::O, core::chemical::Bond::order(), and core::chemical::element::S.

Referenced by apply().

◆ get_mapping()

core::chemical::VDVDMapping core::chemical::modifications::Reprotonate::get_mapping ( ) const

inlineoverridevirtual

Get the vertex mapping that was used for the last apply() or get_additional_output() This is a mapping FROM the vds in the BEFORE MutableResidueType TO the vds in the AFTER MutableResidueType. The base class implementation defaults to an identity mapping.

Get the vertex mapping that was used for the last apply() The base class implementation defaults to an identity mapping.

Reimplemented from core::chemical::modifications::ChemistryBase.

References mapping_.

◆ is_conjugatable()

bool core::chemical::modifications::Reprotonate::is_conjugatable	(	MutableResidueType const &	restype,
		VD	atom
	)		const

private

Is the provided able to participate in conjugation?

Is the provided atom able to participate in conjugation?

References core::chemical::Bond::aromaticity(), core::chemical::MutableResidueType::bond(), core::chemical::DoubleBondOrder, core::chemical::MutableResidueType::graph(), core::chemical::IsAromaticBond, core::chemical::Bond::order(), protocols::forge::methods::order(), and core::chemical::TripleBondOrder.

Referenced by apply().

◆ remove_hydrogens()

core::Size core::chemical::modifications::Reprotonate::remove_hydrogens	(	MutableResidueType &	restype,
		VD	atom
	)

private

Remove hydrogens from specified atom. Returns the number of hydrogens removed.

References core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::bonded_neighbor_iterators(), core::chemical::MutableResidueType::delete_atom(), core::chemical::Atom::element(), core::chemical::element::H, core::chemical::AtomRefMapping< FromRef, ToRef >::invalidate(), and mapping_.

Referenced by apply().

Member Data Documentation

◆ mapping_

core::chemical::VDVDMapping core::chemical::modifications::Reprotonate::mapping_

private

Referenced by apply(), get_mapping(), and remove_hydrogens().

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

src/core/chemical/modifications/Reprotonate.hh
src/core/chemical/modifications/Reprotonate.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ Reprotonate()

Member Function Documentation

◆ apply()

◆ class_name()

◆ find_electron_sink()

◆ get_mapping()

◆ is_conjugatable()

◆ remove_hydrogens()

Member Data Documentation

◆ mapping_