util.hh File Reference

Utilities for interacting with the RDKit library. More...

#include <core/chemical/Bond.fwd.hh>
#include <core/chemical/rdkit/RDKit.fwd.hh>
#include <core/chemical/AtomRefMapping.hh>
#include <core/types.hh>
#include <map>
#include <rdkit/GraphMol/Bond.h>
#include <rdkit/GraphMol/Substruct/SubstructMatch.h>

Namespaces
	core
	A class for reading in the atom type properties.
	core::chemical
	core::chemical::rdkit

Typedefs
typedef std::vector< std::pair< ::RDKit::RWMolOP, int > >	core::chemical::rdkit::ChargeTransformList

Functions
void	core::chemical::rdkit::initialize_rdkit_random (int seed)
	Initialize the RDKit random number generator. More...
void	core::chemical::rdkit::initialize_rdkit_tracers ()
	Initialize the RDKit output levels with the Rosetta commandline settings. More...
::RDKit::Bond::BondType	core::chemical::rdkit::convert_to_rdkit_bondtype (core::chemical::BondName bondtype, bool aro2double=false)
	Convert a Rosetta BondName enum to an RDKit BondType value. More...
core::chemical::BondName	core::chemical::rdkit::convert_from_rdkit_bondtype (::RDKit::Bond::BondType bondtype)
	Convert an RDKit BondType value to a Rosetta BondName enum. More...
std::string	core::chemical::rdkit::get_name (::RDKit::ROMol const &mol)
	Get the name of the RDMol. More...
bool	core::chemical::rdkit::has_physical_Hs (::RDKit::ROMol const &mol)
	Does the molecule have physical hydrogens? More...
bool	core::chemical::rdkit::has_explicit_Hs (::RDKit::ROMol const &mol)
	Does the molecule have "explicit" (but not physical) hydrogens? More...
bool	core::chemical::rdkit::has_implicit_Hs (::RDKit::ROMol const &mol)
	Does the molecule have implicit hydrogens? More...
::RDKit::ForceFieldOP	core::chemical::rdkit::get_forcefield (::RDKit::ROMol &mol, int conf_num=-1)
	Load an RDKit forcefield. Will prefer MMFF, but will fall back to UFF. More...
void	core::chemical::rdkit::softSanitize (::RDKit::RWMol &mol)
	Non strict sanitization, useful if working with molecules which aren't 100% acceptable by RDKit (e.g. protonation/kekulization issues) More...
void	core::chemical::rdkit::remove_excess_protons (::RDKit::RWMol &rdmol)
	Remove any excess hydrogens, where "excess" is defined as any which contribute to a positive formal charge (Assumes a graph-hydrogen removed form.) More...
void	core::chemical::rdkit::apply_charge_transforms (::RDKit::RWMol &rdmol, ChargeTransformList const &transforms)
	Reset the charges on particular groups (Assumes a graph-hydrogen removed form.) More...
void	core::chemical::rdkit::reprotonate_rdmol (::RDKit::RWMol &rdmol)
	Change the protonation state on an rdmol to match physiological pH. Will reset the molecule to an graph-explicit hydrogen form. More...
void	core::chemical::rdkit::neutralize_rdmol (::RDKit::RWMol &rdmol, bool addHs=true)
	Remove any pH-dependent charges on the molecule If addHs is true, then the resultant molecule with have hydrogens added. If addHs is false, then the resultant molecule will be without hydrogens. More...
void	core::chemical::rdkit::final_neutralize (RDKit::RWMOL_SPTR const &rdmol)
	Final neutralization process invoked in constructing an RDMol from a piece of a Pose. More...
void	core::chemical::rdkit::label_with_index (::RDKit::ROMol &rdmol, std::string const &index_prop)
	Label a molecule with it's index values (for find_mapping, later) More...
core::chemical::IndexIndexMapping	core::chemical::rdkit::convert_match_vect_to_index_index_map (::RDKit::MatchVectType const &match_vect)
	Convert the MatchVectType to an IndexIndex map, going query->molecule Use -1 as the invalid value, as zero is a valid one. More...
core::chemical::IndexIndexMapping	core::chemical::rdkit::find_mapping (::RDKit::ROMOL_SPTR from, ::RDKit::ROMOL_SPTR to, std::string const &index_prop)
	Find a mapping from one RDMol to another. More...
void	core::chemical::rdkit::load_sdf (std::string const &filename, utility::vector1< ::RDKit::ROMolOP > &mol_vector, bool removeHs)
	Load molecules from file and append them to mol_vector. More...
std::map< std::string, std::string >	core::chemical::rdkit::get_metric_names ()
	Return a set containing all the valid names for the rdkit_metric() function mapped to short descriptions. More...
core::Real	core::chemical::rdkit::rdkit_metric (::RDKit::ROMol const &mol, std::string const &metric)
	Return the value of a given RDKit metric for the given mol. More...

Detailed Description

Utilities for interacting with the RDKit library.

Author

Rocco Moretti (rmore.nosp@m.ttia.nosp@m.se@gm.nosp@m.ail..nosp@m.com)