#include <DrugDesignMover.hh>

Inheritance diagram for protocols::drug_design::DrugDesignMover:

[legend]

Public Member Functions
	DrugDesignMover ()
	default constructor More...

	~DrugDesignMover () override
	destructor More...

protocols::moves::MoverOP	clone () const override
	create copy constructor More...

protocols::moves::MoverOP	fresh_instance () const override
	create this type of objectt More...

void	apply (core::pose::Pose &pose) override
	apply DrugDesignMover More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

protocols::moves::MoverCOP	redocker () const
	Return the redocker being used. More...

protocols::filters::FilterCOP	scorer () const
	Return the scoring filter. More...

core::Real	temperature () const
	Return the scoring temperature. More...

core::Size	maxtrials () const
	Returns maximum number of trials. More...

char	chain () const
	What chain is the ligand supposed to be? More...

std::string	debug_prefix () const
	What's the prefix of the filename to which intermediate debug structures are dumped? More...

void	add_chemistry (protocols::chemistries::ChemistryOP chemistry, core::Real weight=1.0)
	Add a chemistry to use. More...

void	add_before_chemistry (protocols::chemistries::ChemistryOP chemistry)
	Add a chemistry to use. More...

void	add_after_chemistry (protocols::chemistries::ChemistryOP chemistry)
	Add a chemistry to use. More...

void	redocker (protocols::moves::MoverOP const &mover)
	set redocking mover More...

void	scorer (protocols::filters::FilterOP const &scorer)
	Set the scoring filter in use. More...

void	prefilter (protocols::filters::FilterOP const &setting)
	Set the filter to use before redocking. More...

void	postfilter (protocols::filters::FilterOP const &setting)
	Set the filter to use after redocking. More...

void	temperature (core::Real const temp)
	set temperature More...

void	maxtrials (core::Size const ntrial)
	set max trials of MC trials More...

void	chain (char chain)
	set the ligand chain to use for design More...

void	debug_prefix (std::string const &setting)
	What's the prefix of the filename to which intermediate debug structures are dumped? More...

bool	check_design_position (core::pose::Pose const &pose, core::Size n)
	Is position n a valid designable residue according to the settings. More...

core::Size	find_design_position (core::pose::Pose const &pose)
	Determine which residue on this pose should be designed. More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	parse xml file More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

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

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions
std::string	get_jobname () const
	Return a unique string representing which job this is. More...

utility::vector1< protocols::chemistries::ChemistryOP > &	chemistries ()
	Subclass access to the chemistries. More...

bool	pre_process_restype (core::chemical::MutableResidueTypeOP restype, core::chemical::IndexVDMapping &index_vd_mapping, core::pose::Pose const &pose)
	Pre-process the ResidueType. More...

bool	post_process_restype (core::chemical::MutableResidueTypeOP restype, core::chemical::IndexVDMapping &index_vd_mapping, std::string const &new_name, core::pose::Pose const &pose)
	Post-process the residuetype. More...

bool	emplace_residue_type (core::pose::Pose &pose, core::chemical::MutableResidueTypeOP restype, core::chemical::IndexVDMapping const &index_VD_mapping)
	Take a new residuetype, place it on the pose, and see if it passes filters. More...

void	compute_scores_for_logfile (core::Real score, core::chemical::MutableResidueTypeOP restype, core::Real &raw_score, core::Real &LE_score) const
	Helper function for calculating raw -> LE or LE -> raw score. More...

std::string	find_new_res_name (std::string original_name, core::Size iteration, core::Size subiteration=0) const
	Find a new residue name, if the name already exists in the residue type set. More...

void	dump_molecule (core::chemical::MutableResidueType const &restype, std::string const &stage) const
	Dump the ligand to the given file (appending) More...

void	dump_molecule (core::conformation::Residue const &residue, std::string const &stage) const
	Dump the ligand to the given file (appending) More...

protocols::chemistries::ChemistryOP	chemistry_from_subtag (utility::tag::TagCOP const subtag, basic::datacache::DataMap &data) const

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Private Attributes
utility::vector1< protocols::chemistries::ChemistryOP >	chemistries_
	What chemistries can be done in the design. More...

utility::vector1< core::Real >	weights_
	The weight to use each chemistry at. More...

utility::vector1< protocols::chemistries::ChemistryOP >	before_chemistries_
	What chemistries are always applied before the randomly chosen one. More...

utility::vector1< protocols::chemistries::ChemistryOP >	after_chemistries_
	What chemistries are always applied after the randomly chosen one. More...

protocols::moves::MoverOP	redocker_
	Mover which is used for redocking. More...

protocols::filters::FilterOP	scorer_
	The filter used to do scoring. More...

bool	lig_efficiency_
	if set true, a ligand efficiency interface score will be used for MC acceptance More...

bool	output_logfile_
	if set true, output log files to the output path More...

core::Real	temperature_
	acceptance criterion temperature More...

bool	simulated_annealing_
	if set true, temperature varies throughout MC trials More...

utility::vector1< core::Real >	temperature_params_
	parameters for simulated annealing, in the order: min, max, step, OFF_after_n_trials More...

core::Real	maxtrials_
	the number of MC trials to run in the complete run. More...

char	chain_
	What chain is the ligand? More...

protocols::filters::FilterOP	prefilter_
	The pass/fail filter to use prior to redocking. More...

protocols::filters::FilterOP	postfilter_
	The pass/fail filter to use after redocking. More...

std::string	debug_prefix_
	If non-empty, dump intermediate structures to files based on this prefix. More...

utility::vector1< core::chemical::ResidueTypeCOP >	restypes_
	TODO: HACK - needed to make sure that restypes don't go out of scope. Need to handle this better. More...

core::chemical::PoseResidueTypeSetOP	restypeset_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Constructor & Destructor Documentation

◆ DrugDesignMover()

protocols::drug_design::DrugDesignMover::DrugDesignMover ( )

default constructor

Referenced by clone(), and fresh_instance().

◆ ~DrugDesignMover()

protocols::drug_design::DrugDesignMover::~DrugDesignMover ( )

override

destructor

Member Function Documentation

◆ add_after_chemistry()

void protocols::drug_design::DrugDesignMover::add_after_chemistry ( protocols::chemistries::ChemistryOP chemistry )

Add a chemistry to use.

References after_chemistries_.

Referenced by parse_my_tag().

◆ add_before_chemistry()

void protocols::drug_design::DrugDesignMover::add_before_chemistry ( protocols::chemistries::ChemistryOP chemistry )

Add a chemistry to use.

References before_chemistries_.

Referenced by parse_my_tag().

◆ add_chemistry()

void protocols::drug_design::DrugDesignMover::add_chemistry	(	protocols::chemistries::ChemistryOP	chemistry,
		core::Real	weight = `1.0`
	)

Add a chemistry to use.

References chemistries_, and weights_.

Referenced by parse_my_tag().

◆ apply()

void protocols::drug_design::DrugDesignMover::apply ( core::pose::Pose & pose )

overridevirtual

apply DrugDesignMover

Implements protocols::moves::Mover.

Reimplemented in protocols::drug_design::DrugPolishMover.

◆ chain() [1/2]

char protocols::drug_design::DrugDesignMover::chain ( ) const

inline

What chain is the ligand supposed to be?

References chain_.

Referenced by chain().

◆ chain() [2/2]

void protocols::drug_design::DrugDesignMover::chain ( char chain )

inline

set the ligand chain to use for design

References chain(), and chain_.

◆ check_design_position()

bool protocols::drug_design::DrugDesignMover::check_design_position	(	core::pose::Pose const &	pose,
		core::Size	n
	)

Is position n a valid designable residue according to the settings.

References chain_, and core::pose::Pose::pdb_info().

◆ chemistries()

utility::vector1< protocols::chemistries::ChemistryOP >& protocols::drug_design::DrugDesignMover::chemistries ( )

inlineprotected

Subclass access to the chemistries.

References chemistries_.

◆ chemistry_from_subtag()

protocols::chemistries::ChemistryOP protocols::drug_design::DrugDesignMover::chemistry_from_subtag	(	utility::tag::TagCOP const	subtag,
		basic::datacache::DataMap &	data
	)		const

protected

Referenced by parse_my_tag().

◆ clone()

MoverOP protocols::drug_design::DrugDesignMover::clone ( ) const

overridevirtual

create copy constructor

clone this object

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::drug_design::DrugPolishMover.

References DrugDesignMover().

◆ compute_scores_for_logfile()

void protocols::drug_design::DrugDesignMover::compute_scores_for_logfile	(	core::Real	score,
		core::chemical::MutableResidueTypeOP	restype,
		core::Real &	raw_score,
		core::Real &	LE_score
	)		const

protected

Helper function for calculating raw -> LE or LE -> raw score.

References lig_efficiency_, and protocols::hybridization::score.

Referenced by apply().

◆ debug_prefix() [1/2]

std::string protocols::drug_design::DrugDesignMover::debug_prefix ( ) const

inline

What's the prefix of the filename to which intermediate debug structures are dumped?

References debug_prefix_.

◆ debug_prefix() [2/2]

void protocols::drug_design::DrugDesignMover::debug_prefix ( std::string const & setting )

inline

What's the prefix of the filename to which intermediate debug structures are dumped?

References debug_prefix_.

◆ dump_molecule() [1/2]

void protocols::drug_design::DrugDesignMover::dump_molecule	(	core::chemical::MutableResidueType const &	restype,
		std::string const &	stage
	)		const

protected

Dump the ligand to the given file (appending)

References debug_prefix_, protocols::abinitio::filename(), get_jobname(), core::conformation::membrane::out, and core::chemical::sdf::MolWriter::output_residue().

Referenced by apply(), emplace_residue_type(), and post_process_restype().

◆ dump_molecule() [2/2]

void protocols::drug_design::DrugDesignMover::dump_molecule	(	core::conformation::Residue const &	residue,
		std::string const &	stage
	)		const

protected

Dump the ligand to the given file (appending)

References debug_prefix_, protocols::abinitio::filename(), get_jobname(), core::conformation::membrane::out, and core::chemical::sdf::MolWriter::output_residue().

◆ emplace_residue_type()

bool protocols::drug_design::DrugDesignMover::emplace_residue_type	(	core::pose::Pose &	pose,
		core::chemical::MutableResidueTypeOP	restype,
		core::chemical::IndexVDMapping const &	index_VD_mapping
	)

protected

Take a new residuetype, place it on the pose, and see if it passes filters.

Differs from place_residue_type() in that it also filters

References core::chemical::AtomRefMapping< FromRef, ToRef >::downstream_combine(), dump_molecule(), find_design_position(), protocols::drug_design::place_new_restype(), postfilter_, prefilter_, redocker_, core::pose::Pose::residue(), restypes_, restypeset_, and protocols::drug_design::TR().

Referenced by apply().

◆ find_design_position()

Size protocols::drug_design::DrugDesignMover::find_design_position ( core::pose::Pose const & pose )

Determine which residue on this pose should be designed.

References chain_, core::pose::Pose::pdb_info(), and protocols::drug_design::TR().

Referenced by apply(), and emplace_residue_type().

◆ find_new_res_name()

std::string protocols::drug_design::DrugDesignMover::find_new_res_name	(	std::string	original_name,
		core::Size	iteration,
		core::Size	subiteration = `0`
	)		const

protected

Find a new residue name, if the name already exists in the residue type set.

References get_jobname(), restypeset_, and core::id::to_string().

Referenced by apply().

◆ fresh_instance()

MoverOP protocols::drug_design::DrugDesignMover::fresh_instance ( ) const

overridevirtual

create this type of objectt

create this type of object

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::drug_design::DrugPolishMover.

References DrugDesignMover().

◆ get_jobname()

std::string protocols::drug_design::DrugDesignMover::get_jobname ( ) const

protected

Return a unique string representing which job this is.

References protocols::jd2::JobDistributor::current_output_name(), and protocols::jd2::JobDistributor::get_instance().

Referenced by apply(), dump_molecule(), and find_new_res_name().

◆ get_name()

std::string protocols::drug_design::DrugDesignMover::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Reimplemented in protocols::drug_design::DrugPolishMover.

References mover_name().

◆ maxtrials() [1/2]

core::Size protocols::drug_design::DrugDesignMover::maxtrials ( ) const

inline

Returns maximum number of trials.

References maxtrials_.

◆ maxtrials() [2/2]

void protocols::drug_design::DrugDesignMover::maxtrials ( core::Size const ntrial )

inline

set max trials of MC trials

References maxtrials_.

◆ mover_name()

std::string protocols::drug_design::DrugDesignMover::mover_name ( )

static

Referenced by get_name(), protocols::drug_design::DrugDesignMoverCreator::keyname(), parse_my_tag(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::drug_design::DrugDesignMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml file

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::drug_design::DrugPolishMover.

References add_after_chemistry(), add_before_chemistry(), add_chemistry(), chain_, chemistry_from_subtag(), debug_prefix_, lig_efficiency_, maxtrials_, mover_name(), output_logfile_, protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), postfilter(), prefilter(), redocker(), scorer(), simulated_annealing_, temperature_, and temperature_params_.

◆ post_process_restype()

bool protocols::drug_design::DrugDesignMover::post_process_restype	(	core::chemical::MutableResidueTypeOP	restype,
		core::chemical::IndexVDMapping &	index_vd_mapping,
		std::string const &	new_name,
		core::pose::Pose const &	pose
	)

protected

Post-process the residuetype.

Apply the always chemistries
Fix up some after issues

References after_chemistries_, core::chemical::AtomRefMapping< FromRef, ToRef >::begin(), core::chemical::combine(), dump_molecule(), core::chemical::AtomRefMapping< FromRef, ToRef >::end(), core::chemical::element::H, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_entry(), core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_key(), protocols::rna::denovo::possible_root(), core::chemical::reroot_restype(), core::chemical::AtomRefMapping< FromRef, ToRef >::reverse_lookup(), core::chemical::modifications::SUCCESS, and protocols::drug_design::TR().

Referenced by apply().

◆ postfilter()

void protocols::drug_design::DrugDesignMover::postfilter ( protocols::filters::FilterOP const & setting )

Set the filter to use after redocking.

References postfilter_.

Referenced by parse_my_tag().

◆ pre_process_restype()

bool protocols::drug_design::DrugDesignMover::pre_process_restype	(	core::chemical::MutableResidueTypeOP	restype,
		core::chemical::IndexVDMapping &	index_vd_mapping,
		core::pose::Pose const &	pose
	)

protected

Pre-process the ResidueType.

Apply the always chemistries

References before_chemistries_, core::chemical::combine(), core::chemical::modifications::SUCCESS, and protocols::drug_design::TR().

Referenced by apply().

◆ prefilter()

void protocols::drug_design::DrugDesignMover::prefilter ( protocols::filters::FilterOP const & setting )

Set the filter to use before redocking.

References prefilter_.

Referenced by parse_my_tag().

◆ provide_xml_schema()

void protocols::drug_design::DrugDesignMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::drug_design::DrugDesignMoverCreator::provide_xml_schema().

◆ redocker() [1/2]

MoverCOP protocols::drug_design::DrugDesignMover::redocker ( ) const

Return the redocker being used.

References redocker_.

Referenced by parse_my_tag().

◆ redocker() [2/2]

void protocols::drug_design::DrugDesignMover::redocker ( protocols::moves::MoverOP const & mover )

set redocking mover

set redocker

References redocker_.

◆ scorer() [1/2]

FilterCOP protocols::drug_design::DrugDesignMover::scorer ( ) const

Return the scoring filter.

References scorer_.

Referenced by parse_my_tag(), and scorer().

◆ scorer() [2/2]

void protocols::drug_design::DrugDesignMover::scorer ( protocols::filters::FilterOP const & scorer )

Set the scoring filter in use.

set scoring filter

References scorer(), and scorer_.

◆ temperature() [1/2]

core::Real protocols::drug_design::DrugDesignMover::temperature ( ) const

inline

Return the scoring temperature.

References temperature_.

Referenced by apply().

◆ temperature() [2/2]

void protocols::drug_design::DrugDesignMover::temperature ( core::Real const temp )

inline

set temperature

References temperature_.

Member Data Documentation

◆ after_chemistries_

utility::vector1< protocols::chemistries::ChemistryOP > protocols::drug_design::DrugDesignMover::after_chemistries_

private

What chemistries are always applied after the randomly chosen one.

Referenced by add_after_chemistry(), and post_process_restype().

◆ before_chemistries_

utility::vector1< protocols::chemistries::ChemistryOP > protocols::drug_design::DrugDesignMover::before_chemistries_

private

What chemistries are always applied before the randomly chosen one.

Referenced by add_before_chemistry(), and pre_process_restype().

◆ chain_

char protocols::drug_design::DrugDesignMover::chain_

private

What chain is the ligand?

Referenced by chain(), check_design_position(), find_design_position(), and parse_my_tag().

◆ chemistries_

utility::vector1< protocols::chemistries::ChemistryOP > protocols::drug_design::DrugDesignMover::chemistries_

private

What chemistries can be done in the design.

Referenced by add_chemistry(), apply(), and chemistries().

◆ debug_prefix_

std::string protocols::drug_design::DrugDesignMover::debug_prefix_

private

If non-empty, dump intermediate structures to files based on this prefix.

Referenced by debug_prefix(), dump_molecule(), and parse_my_tag().

◆ lig_efficiency_

bool protocols::drug_design::DrugDesignMover::lig_efficiency_

private

if set true, a ligand efficiency interface score will be used for MC acceptance

Referenced by compute_scores_for_logfile(), and parse_my_tag().

◆ maxtrials_

core::Real protocols::drug_design::DrugDesignMover::maxtrials_

private

the number of MC trials to run in the complete run.

Referenced by apply(), maxtrials(), and parse_my_tag().

◆ output_logfile_

bool protocols::drug_design::DrugDesignMover::output_logfile_

private

if set true, output log files to the output path

Referenced by apply(), and parse_my_tag().

◆ postfilter_

protocols::filters::FilterOP protocols::drug_design::DrugDesignMover::postfilter_

private

The pass/fail filter to use after redocking.

Referenced by emplace_residue_type(), and postfilter().

◆ prefilter_

protocols::filters::FilterOP protocols::drug_design::DrugDesignMover::prefilter_

private

The pass/fail filter to use prior to redocking.

Referenced by emplace_residue_type(), and prefilter().

◆ redocker_

protocols::moves::MoverOP protocols::drug_design::DrugDesignMover::redocker_

private

Mover which is used for redocking.

Referenced by apply(), emplace_residue_type(), and redocker().

◆ restypes_

utility::vector1< core::chemical::ResidueTypeCOP > protocols::drug_design::DrugDesignMover::restypes_

private

TODO: HACK - needed to make sure that restypes don't go out of scope. Need to handle this better.

Referenced by emplace_residue_type().

◆ restypeset_

core::chemical::PoseResidueTypeSetOP protocols::drug_design::DrugDesignMover::restypeset_

private

Referenced by emplace_residue_type(), and find_new_res_name().

◆ scorer_

protocols::filters::FilterOP protocols::drug_design::DrugDesignMover::scorer_

private

The filter used to do scoring.

Referenced by apply(), and scorer().

◆ simulated_annealing_

bool protocols::drug_design::DrugDesignMover::simulated_annealing_

private

if set true, temperature varies throughout MC trials

Referenced by apply(), and parse_my_tag().

◆ temperature_

core::Real protocols::drug_design::DrugDesignMover::temperature_

private

acceptance criterion temperature

Referenced by parse_my_tag(), and temperature().

◆ temperature_params_

utility::vector1< core::Real > protocols::drug_design::DrugDesignMover::temperature_params_

private

parameters for simulated annealing, in the order: min, max, step, OFF_after_n_trials

Referenced by apply(), and parse_my_tag().

◆ weights_

utility::vector1< core::Real > protocols::drug_design::DrugDesignMover::weights_

private

The weight to use each chemistry at.

Referenced by add_chemistry(), and apply().

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

src/protocols/drug_design/DrugDesignMover.hh
src/protocols/drug_design/DrugDesignMover.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ DrugDesignMover()

◆ ~DrugDesignMover()

Member Function Documentation

◆ add_after_chemistry()

◆ add_before_chemistry()

◆ add_chemistry()

◆ apply()

◆ chain() [1/2]

◆ chain() [2/2]

◆ check_design_position()

◆ chemistries()

◆ chemistry_from_subtag()

◆ clone()

◆ compute_scores_for_logfile()

◆ debug_prefix() [1/2]

◆ debug_prefix() [2/2]

◆ dump_molecule() [1/2]

◆ dump_molecule() [2/2]

◆ emplace_residue_type()

◆ find_design_position()

◆ find_new_res_name()

◆ fresh_instance()

◆ get_jobname()

◆ get_name()

◆ maxtrials() [1/2]

◆ maxtrials() [2/2]

◆ mover_name()

◆ parse_my_tag()

◆ post_process_restype()

◆ postfilter()

◆ pre_process_restype()

◆ prefilter()

◆ provide_xml_schema()

◆ redocker() [1/2]

◆ redocker() [2/2]

◆ scorer() [1/2]

◆ scorer() [2/2]

◆ temperature() [1/2]

◆ temperature() [2/2]

Member Data Documentation

◆ after_chemistries_

◆ before_chemistries_

◆ chain_

◆ chemistries_

◆ debug_prefix_

◆ lig_efficiency_

◆ maxtrials_

◆ output_logfile_

◆ postfilter_

◆ prefilter_

◆ redocker_

◆ restypes_

◆ restypeset_

◆ scorer_

◆ simulated_annealing_

◆ temperature_

◆ temperature_params_

◆ weights_