protocols::drug_design::ChemicalReaction Class Reference

#include <ChemicalReaction.hh>

Inheritance diagram for protocols::drug_design::ChemicalReaction:

Public Member Functions
	ChemicalReaction (std::string const &reaction_dir, std::string const &reaction_name, std::string const &reaction_smirks)
	ChemicalReaction (std::string const &reaction_name, std::string const &reaction_smirks)
	~ChemicalReaction () override
bool	reaction_valid () const
	Is the reaction valid, or was there an error loading the reaction? (Doesn't look at reactants.) More...
bool	is_reaction_usable ()
	is the reaction valid, with usable reaction list (deprecated) More...
std::string const &	reaction_name () const
core::Size	nreagents () const
core::Size	n_availible_reagents (core::Size reag_no)
::RDKit::ROMolOP	reagent (core::Size reag_no, core::Size reag_index)
::RDKit::ROMolOP	representative_prod ()
	Return a representative product structure. More...
void	load_reagents ()
::RDKit::RWMolOP	reaction_result (::RDKit::MOL_SPTR_VECT const &reagents) const
::RDKit::ChemicalReactionOP const &	get_reaction () const

Private Member Functions
bool	cleanup_product (::RDKit::RWMol &prod) const

Static Private Member Functions
static utility::vector1< std::string >	load_file (std::string const &reaction_dir, std::string const &filename)

Private Attributes
std::string	dir_
std::string	name_
::RDKit::ChemicalReactionOP	rxn_
utility::vector1< utility::vector1< std::string > >	reagent_smiles_
utility::vector1< utility::vector1< ::RDKit::RWMolOP > >	reagents_
bool	reagents_bad_ = false

Constructor & Destructor Documentation

ChemicalReaction() [1/2]

protocols::drug_design::ChemicalReaction::ChemicalReaction	(	std::string const &	reaction_dir,
		std::string const &	reaction_name,
		std::string const &	reaction_smirks
	)

References rxn_, and protocols::drug_design::TR().

ChemicalReaction() [2/2]

protocols::drug_design::ChemicalReaction::ChemicalReaction	(	std::string const &	reaction_name,
		std::string const &	reaction_smirks
	)

~ChemicalReaction()

protocols::drug_design::ChemicalReaction::~ChemicalReaction ( )

overridedefault

Member Function Documentation

cleanup_product()

bool protocols::drug_design::ChemicalReaction::cleanup_product ( ::RDKit::RWMol &  prod ) const

private

Referenced by reaction_result().

get_reaction()

RDKit::ChemicalReactionOP const & protocols::drug_design::ChemicalReaction::get_reaction

(

)

const

References rxn_.

is_reaction_usable()

bool protocols::drug_design::ChemicalReaction::is_reaction_usable

(

)

is the reaction valid, with usable reaction list (deprecated)

References load_reagents(), nreagents(), reagent_smiles_, reagents_bad_, and rxn_.

load_file()

utility::vector1< std::string > protocols::drug_design::ChemicalReaction::load_file ( std::string const &  reaction_dir, std::string const &  filename  )

staticprivate

References protocols::abinitio::filename(), and protocols::drug_design::TR().

Referenced by load_reagents().

load_reagents()

void protocols::drug_design::ChemicalReaction::load_reagents

(

)

References dir_, load_file(), name_, nreagents(), reagent_smiles_, reagents_bad_, rxn_, core::id::to_string(), and protocols::drug_design::TR().

Referenced by is_reaction_usable(), n_availible_reagents(), and reagent().

n_availible_reagents()

core::Size protocols::drug_design::ChemicalReaction::n_availible_reagents

(

core::Size

reag_no

)

References load_reagents(), and reagent_smiles_.

nreagents()

core::Size protocols::drug_design::ChemicalReaction::nreagents

(

)

const

References rxn_.

Referenced by is_reaction_usable(), and load_reagents().

reaction_name()

std::string const& protocols::drug_design::ChemicalReaction::reaction_name ( ) const

inline

References name_.

reaction_result()

RDKit::RWMolOP protocols::drug_design::ChemicalReaction::reaction_result

(

::RDKit::MOL_SPTR_VECT const &

reagents

)

const

Do the corresponding reaction, and return the result. The passed parameter is the selection for each reagent. Can return a nullptr if the reaction doesn't work.

References cleanup_product(), rxn_, and protocols::drug_design::TR().

reaction_valid()

bool protocols::drug_design::ChemicalReaction::reaction_valid

(

)

const

Is the reaction valid, or was there an error loading the reaction? (Doesn't look at reactants.)

Is the reaction valid, or was there an error loading the reaction?

References rxn_.

reagent()

RDKit::ROMolOP protocols::drug_design::ChemicalReaction::reagent	(	core::Size	reag_no,
		core::Size	reag_index
	)

References load_reagents(), reagent_smiles_, reagents_, and protocols::drug_design::TR().

representative_prod()

::RDKit::ROMolOP protocols::drug_design::ChemicalReaction::representative_prod

(

)

Return a representative product structure.

Member Data Documentation

dir_

std::string protocols::drug_design::ChemicalReaction::dir_

private

Referenced by load_reagents().

name_

std::string protocols::drug_design::ChemicalReaction::name_

private

Referenced by load_reagents(), and reaction_name().

reagent_smiles_

utility::vector1< utility::vector1< std::string > > protocols::drug_design::ChemicalReaction::reagent_smiles_

private

Referenced by is_reaction_usable(), load_reagents(), n_availible_reagents(), and reagent().

reagents_

utility::vector1< utility::vector1< ::RDKit::RWMolOP > > protocols::drug_design::ChemicalReaction::reagents_

private

Referenced by reagent().

reagents_bad_

bool protocols::drug_design::ChemicalReaction::reagents_bad_ = false

private

Referenced by is_reaction_usable(), and load_reagents().

rxn_

::RDKit::ChemicalReactionOP protocols::drug_design::ChemicalReaction::rxn_

private

Referenced by ChemicalReaction(), get_reaction(), is_reaction_usable(), load_reagents(), nreagents(), reaction_result(), and reaction_valid().

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

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