substitution_support.hh File Reference

#include <protocols/drug_design/substitution_support.fwd.hh>
#include <core/chemical/rdkit/RDKit.fwd.hh>
#include <core/chemical/rdkit/util.hh>
#include <core/chemical/AtomRefMapping.hh>
#include <utility/pointer/owning_ptr.hh>
#include <rdkit/GraphMol/ROMol.h>
#include <rdkit/Geometry/Transform3D.h>
#include <rdkit/GraphMol/Substruct/SubstructMatch.h>

Classes
class	protocols::drug_design::AtomSubstitution
	A class representing a substitution of an atom from an original molecule through a pair of matched templates to a substituted molecule. Intended to be used through MoleculeSubstitution. More...
class	protocols::drug_design::MoleculeSubstitution
	A class representing a substitution of a molecule from an original molecule through a pair of matched templates to a substituted molecule. More...

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::drug_design

Enumerations
enum	protocols::drug_design::MoleculeSelection { protocols::drug_design::OriginalMol , protocols::drug_design::TemplateMol , protocols::drug_design::ReplaceMol , protocols::drug_design::NewMol }

Functions
::RDKit::Bond::BondType	protocols::drug_design::get_first_bondtype (::RDKit::ROMol const &mol, ::RDKit::Atom const *atom)
	Get the RDKit bond type of the first bond to atom. More...
::RDKit::Bond::BondType	protocols::drug_design::get_first_bondtype (::RDKit::ROMol const &mol, unsigned int idx)
	Get the RDKit bond type of the first bond to the given atom. More...
::RDKit::Bond const &	protocols::drug_design::get_first_bond (::RDKit::ROMol const &mol, unsigned int idx)
	Get the RDKit bond of the first bond to the given atom. More...
unsigned int	protocols::drug_design::get_bonded_atom (::RDKit::ROMol const &mol, unsigned int idx)
	Get the atom number of the atom bonded to idx (it's the first atom) More...
bool	protocols::drug_design::is_dummy (::RDKit::ROMol const &mol, unsigned int idx)
	Is the given atom a dummy (atom number 0)? More...
void	protocols::drug_design::find_dummies (::RDKit::ROMol const &mol, utility::vector1< unsigned int > &dummy_list)
	Populate the list with the index of all the dummies in the molecule. More...
bool	protocols::drug_design::bond_is_in_ring (::RDKit::ROMol const &rdmol, unsigned int atm1, unsigned int atm2)
	Is the bond between the atoms in a ring? More...
std::map< unsigned int, unsigned int >	protocols::drug_design::convert_matchvect_to_map (::RDKit::MatchVectType const &pairings)
	Convert the RDKit MatcVect into a map (real molecule index to query index) More...
MoleculeSubstitutionOP	protocols::drug_design::pick_template (::RDKit::ROMolOP rdmol, utility::vector1< ::RDKit::ROMolOP > &templates, bool dummy_only)
	Pick a template to use, return it and the atom pairing of template->rdmol. More...
MoleculeSubstitutionOP	protocols::drug_design::test_replacement (MoleculeSubstitutionOP current_molsub, ::RDKit::ROMolOP possible_replacement, core::Real dist_threshold)
	Is the replacement molecule template compatible with the molecule and template in template_frag_infos If the replacement is appropriate, the return value will be a new MoleculeSubstitution which has the appropriate replacement entries set. If the replacement doesn't work, it will return a null pointer. More...
MoleculeSubstitutionOP	protocols::drug_design::pick_replacement (MoleculeSubstitutionOP current_molsub, utility::vector1< ::RDKit::ROMolOP > &possible_replacements, core::Real distance_threshold, std::string weighting_property="")
	Given the molecule and template info in template_frag_infos, pick a possible replacement molecule from possible_replacements. More...
void	protocols::drug_design::copy_attached_atoms (MoleculeSubstitution &molsub, MoleculeSelection source, ::RDGeom::Transform3D const &transform, unsigned int start, unsigned int skip)
	Copies all atom and bonds attached to start in the source molecule to the new molecule. If skip is a valid index, it will be supressed in the source molecule, and will not be counted for copying or for attachment purposes The transform is applied to the coordinates of the atom to get the coordinates of the new atom. More...