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protocols::ligand_docking::ga_ligand_dock::ConstraintInfo Class Reference

Constraint information about AtomProperties and/or Pharmacophores. More...

#include <LigandAligner.hh>

Public Member Functions

 ConstraintInfo ()
 
 ConstraintInfo (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, bool use_pharmacophore, bool report_phore_info=false)
 
 ConstraintInfo (utility::vector1< numeric::xyzVector< core::Real > > density_points)
 
 ConstraintInfo (core::pose::Pose const &pose, GridScorerOP gridscore, bool const simple=false)
 
void init_from_ligand (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids)
 use a (non-identical) target ligand (for reference ligand matching) More...
 
void init_from_map (utility::vector1< numeric::xyzVector< core::Real > > density_points)
 
void init_from_ligand_pharmacophore (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, bool report_phore_info)
 defines pharmacophore partners in ligand (for pharmacophore matching) More...
 
void init_from_receptor (core::pose::Pose const &pose, GridScorerOP gridscore, bool const simple)
 
core::Size natoms () const
 
numeric::xyzVector< core::Real > const & coord (core::Size i) const
 
AtomProperties const & properties (core::Size i) const
 
core::id::AtomID const & atomid (core::Size i) const
 
core::Real limit ()
 
core::Real weight ()
 
core::Real polar_scale ()
 
bool pharmacophores_defined () const
 
utility::vector1< Pharmacophore > const & phores () const
 
core::Size n_phore_match () const
 
void select_phore_match (core::Size const run_index)
 selects a phore_match and updates current_phore_match_ More...
 
void align_to_current_phore_match (core::pose::Pose &pose, ConstraintInfo const &recinfo, utility::vector1< core::Size > const &ligids, utility::vector1< std::pair< core::Size, core::Size > > &marked_pairs, utility::vector1< core::Size > &SrcPriorIDs, utility::vector1< core::Size > &TgtPriorIDs)
 try aligning to the phore defined by current_phore_match_ (defined by select_phore_match) More...
 
void map_phores (utility::vector1< Pharmacophore > const &receptor_phores, bool const update, core::Size const nmax=100)
 matches ligand phores (==own) to provided receptor phores and stores at phore_match_ More...
 

Private Member Functions

void set_default ()
 
void define_active_virtual_sites (core::pose::Pose const &pose, GridScorerOP gridscore, utility::vector1< std::pair< core::Real, core::Size > > &Vdonor_sort, utility::vector1< std::pair< core::Real, core::Size > > &Vacceptor_sort, core::Size const nneigh_cut_for_exposed_sc, core::Size const nneigh_cut_for_exposed_bb, bool const report=false)
 findes all virtual sites (for h-bonding candidates) in receptor More...
 
void append_metal_vsites (core::pose::Pose const &pose, core::Size const &ires, utility::vector1< std::pair< core::Real, core::Size > > &Vacceptor_sort, bool report=false)
 
void build_Dmtrx ()
 
void define_all_ligand_phores (core::Size const minsize, bool report_phore_info)
 defines all ligand phores More...
 
void define_ligand_multibody_phores (bool report_phore_info)
 defines all ligand phores More...
 
bool phore_overlaps_with_existing (Pharmacophore const &phore_i, core::Size &jphore) const
 
void define_receptor_phores (utility::vector1< std::pair< core::Real, core::Size > > &Vdonor_sort, utility::vector1< std::pair< core::Real, core::Size > > &Vacceptor_sort, core::Size const nmin=10, bool report_phore_info=false)
 defines receptor phores More...
 
void update_ligand_coord (core::pose::Pose const &pose)
 

Private Attributes

utility::vector1< core::id::AtomIDatmids_
 
utility::vector1< numeric::xyzVector< core::Real > > coords_
 
utility::vector1< AtomPropertiesproperties_
 
core::Real limit_
 
core::Real weight_
 
core::Real polar_scale_
 
bool is_ligand_
 
core::Real phore_dcut_
 
core::Size n_match_per_ligand_motif_
 
core::Size NNEIGH_CUT_FOR_EXPOSED_SC
 
core::Size NNEIGH_CUT_FOR_EXPOSED_BB
 
core::Size RECEPTOR_PHORE_MIN
 
core::Size RECEPTOR_PHORE_MAX
 
utility::vector1< utility::vector1< core::Real > > Dmtrx_
 
utility::vector1< Pharmacophorephores_
 
utility::vector1< Pharmacophoremultibody_phores_
 
utility::vector1< std::pair< core::Size, Pharmacophore > > phore_match_
 
std::pair< core::Size, Pharmacophorecurrent_phore_match_
 
bool debug_
 

Detailed Description

Constraint information about AtomProperties and/or Pharmacophores.

includes constrained xyzs & important properties we do not use a residue type (which already has this info) because in "pharmicophore mode" we generate virtual sites from the protein side. we want targets generated in both ways to run through the same machinery therefore, we instead we have two initialization routines:

Constructor & Destructor Documentation

◆ ConstraintInfo() [1/4]

protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( )
inline

◆ ConstraintInfo() [2/4]

protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  ligids,
bool  use_pharmacophore,
bool  report_phore_info = false 
)
inline

◆ ConstraintInfo() [3/4]

protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( utility::vector1< numeric::xyzVector< core::Real > >  density_points)
inline

◆ ConstraintInfo() [4/4]

protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( core::pose::Pose const &  pose,
GridScorerOP  gridscore,
bool const  simple = false 
)
inline

Member Function Documentation

◆ align_to_current_phore_match()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::align_to_current_phore_match ( core::pose::Pose pose,
ConstraintInfo const &  recinfo,
utility::vector1< core::Size > const &  ligids,
utility::vector1< std::pair< core::Size, core::Size > > &  marked_pairs,
utility::vector1< core::Size > &  SrcPriorIDs,
utility::vector1< core::Size > &  TgtPriorIDs 
)

◆ append_metal_vsites()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites ( core::pose::Pose const &  pose,
core::Size const &  ires,
utility::vector1< std::pair< core::Real, core::Size > > &  Vacceptor_sort,
bool  report = false 
)
private

◆ atomid()

core::id::AtomID const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::atomid ( core::Size  i) const
inline

◆ build_Dmtrx()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::build_Dmtrx ( )
private

◆ coord()

numeric::xyzVector< core::Real > const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coord ( core::Size  i) const
inline

◆ define_active_virtual_sites()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites ( core::pose::Pose const &  pose,
GridScorerOP  gridscore,
utility::vector1< std::pair< core::Real, core::Size > > &  Vdonor_sort,
utility::vector1< std::pair< core::Real, core::Size > > &  Vacceptor_sort,
core::Size const  nneigh_cut_for_exposed_sc,
core::Size const  nneigh_cut_for_exposed_bb,
bool const  report = false 
)
private

◆ define_all_ligand_phores()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_all_ligand_phores ( core::Size const  minsize,
bool  report_phore_info 
)
private

◆ define_ligand_multibody_phores()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_ligand_multibody_phores ( bool  report_phore_info)
private

◆ define_receptor_phores()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores ( utility::vector1< std::pair< core::Real, core::Size > > &  Vdonor_sort,
utility::vector1< std::pair< core::Real, core::Size > > &  Vacceptor_sort,
core::Size const  nmin = 10,
bool  report_phore_info = false 
)
private

◆ init_from_ligand()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  ligids 
)

◆ init_from_ligand_pharmacophore()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  ligids,
bool  report_phore_info 
)

◆ init_from_map()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_map ( utility::vector1< numeric::xyzVector< core::Real > >  density_points)

References coords_, properties_, and set_default().

◆ init_from_receptor()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_receptor ( core::pose::Pose const &  pose,
GridScorerOP  gridscore,
bool const  simple 
)

◆ limit()

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::limit ( )
inline

◆ map_phores()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores ( utility::vector1< Pharmacophore > const &  receptor_phores,
bool const  update,
core::Size const  nmax = 100 
)

◆ n_phore_match()

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::n_phore_match ( ) const
inline

◆ natoms()

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::natoms ( ) const
inline

◆ pharmacophores_defined()

bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::pharmacophores_defined ( ) const
inline

◆ phore_overlaps_with_existing()

bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_overlaps_with_existing ( Pharmacophore const &  phore_i,
core::Size jphore 
) const
private

◆ phores()

utility::vector1< Pharmacophore > const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phores ( ) const
inline

◆ polar_scale()

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::polar_scale ( )
inline

◆ properties()

AtomProperties const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::properties ( core::Size  i) const
inline

◆ select_phore_match()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::select_phore_match ( core::Size const  run_index)

◆ set_default()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::set_default ( )
private

◆ update_ligand_coord()

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::update_ligand_coord ( core::pose::Pose const &  pose)
private

◆ weight()

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::weight ( )
inline

Member Data Documentation

◆ atmids_

utility::vector1< core::id::AtomID > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::atmids_
private

◆ coords_

utility::vector1< numeric::xyzVector< core::Real > > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coords_
private

◆ current_phore_match_

std::pair< core::Size, Pharmacophore > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::current_phore_match_
private

◆ debug_

bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::debug_
private

◆ Dmtrx_

utility::vector1< utility::vector1< core::Real > > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::Dmtrx_
private

◆ is_ligand_

bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::is_ligand_
private

◆ limit_

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::limit_
private

Referenced by set_default().

◆ multibody_phores_

utility::vector1< Pharmacophore > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::multibody_phores_
private

◆ n_match_per_ligand_motif_

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::n_match_per_ligand_motif_
private

Referenced by map_phores(), and set_default().

◆ NNEIGH_CUT_FOR_EXPOSED_BB

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::NNEIGH_CUT_FOR_EXPOSED_BB
private

Referenced by init_from_receptor(), and set_default().

◆ NNEIGH_CUT_FOR_EXPOSED_SC

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::NNEIGH_CUT_FOR_EXPOSED_SC
private

Referenced by init_from_receptor(), and set_default().

◆ phore_dcut_

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_dcut_
private

◆ phore_match_

utility::vector1< std::pair< core::Size, Pharmacophore > > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_match_
private

Referenced by map_phores(), and select_phore_match().

◆ phores_

utility::vector1< Pharmacophore > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phores_
private

◆ polar_scale_

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::polar_scale_
private

Referenced by set_default().

◆ properties_

utility::vector1< AtomProperties > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::properties_
private

◆ RECEPTOR_PHORE_MAX

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::RECEPTOR_PHORE_MAX
private

Referenced by init_from_receptor(), and set_default().

◆ RECEPTOR_PHORE_MIN

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::RECEPTOR_PHORE_MIN
private

Referenced by init_from_receptor(), and set_default().

◆ weight_

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::weight_
private

Referenced by set_default().


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