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Rosetta
2021.16
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Rosetta
2021.16
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Utilities for interacting with the RDKit library. More...
#include <core/chemical/rdkit/util.hh>#include <core/chemical/AtomRefMapping.hh>#include <core/types.hh>#include <utility/io/izstream.hh>#include <utility/exit.hh>#include <basic/Tracer.hh>#include <rdkit/RDGeneral/utils.h>#include <rdkit/GraphMol/FileParsers/MolSupplier.h>#include <rdkit/ForceField/ForceField.h>#include <rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>#include <rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.h>#include <rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h>#include <rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.h>#include <rdkit/GraphMol/SmilesParse/SmilesWrite.h>#include <rdkit/GraphMol/Substruct/SubstructMatch.h>#include <rdkit/GraphMol/FMCS/FMCS.h>#include <rdkit/GraphMol/SmilesParse/SmilesParse.h>#include <rdkit/GraphMol/SmilesParse/SmartsWrite.h>#include <rdkit/GraphMol/FileParsers/FileParsers.h>#include <rdkit/GraphMol/Descriptors/MolDescriptors.h>#include <rdkit/GraphMol/MolPickler.h>Namespaces | |
| core | |
| A class for reading in the atom type properties. | |
| core::chemical | |
| core::chemical::rdkit | |
Functions | |
| static basic::Tracer | core::chemical::rdkit::TR ("core.chemical.rdkit.util") |
| static basic::Tracer | core::chemical::rdkit::TR_RDKit ("RDKit") |
| 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) |
| 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::remove_most_charges (::RDKit::RWMol &rdmol) |
| 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::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... | |
Utilities for interacting with the RDKit library.
1.8.7