OEProton Functions

OEAssignPartialCharges

bool OEAssignPartialCharges(OEChem::OEMolBase &mol,
                            unsigned int method=OECharges::Default,
                            bool noHydrogen=false, bool debug=false)
bool OEAssignPartialCharges(OEChem::OEMCMolBase &mol,
                            unsigned int method=OECharges::Default,
                            bool noHydrogen=false, bool debug=false)

This function sets the partial charge value of each atom in a molecule. The molecule to be charged is passed as the first argument. The second argument is the charge model to be used. These values should be selected from the OECharges namespace. The third argument is a boolean for whether the final molecule should have explicit hydrogens. If noHydrogen is set to true, all hydrogens will be made implicit, and the charge on each heavy atom with attached hydrogens will be adjusted to be the sum of it’s original partial charge and all of the attached hydrogen partial charges. The debug flag controls the volume of debug information written to standard error. This function return a boolean value evaluating the success of the calculation.

This function is overloaded to accept an OEMolBase or an OEMCMolBase. Currently, only AM1 and AM1BCC charges have specialized multiconformer implementations in the OEMCMolBase overload. For all other charges, the OEMCMolBase and OEMolBase implementations are identical.

OEEnumerateFormalCharges

unsigned int OEEnumerateFormalCharges(OEChem::OEMolBase &mol,
                                      OEMolFunctionBase &mfb,
                                      bool verbose=false)

This function has three arguments. The first is the non-const molecule whose formal charges are to be enumerated. For details of the enumeration process, please see Pkatyper - Ligand pKa. The second argument is a functor call-back. The functor’s operator() is called with each new protonation state enumerated. The enumeration will continue until the functor returns false or until the enumeration is complete. The third argument determines if verbose atom-type information should be written to standard out. The function will return the total number of states which were enumerated.

OEEnumerateTautomers

unsigned int OEEnumerateTautomers(OEChem::OEMolBase &mol,
                                  OEMolFunctionBase &mfb, unsigned int allflag=0,
                                  bool ch3flag=false)

This function has four arguments. The first argument in a non-const molecule that will be the basis for the tautomer enumeration. For details of the enumeration process, please see Tautomers - Enumeration and Canonicalization. The second argument is a functor call-back. The functor’s operator() is called with each new tautomer state enumerated. The enumeration will continue until the functor returns false or until the enumeration is complete. The third argument is an unsigned int which indicates the maximum acceptable energetic category of enumerated tautomers. The function will return all categories of tautomers from the lowest available up to this cutoff. If the only available level is higher than the cutoff, that single level of tautomers will be enumerated. This control is in addition to the call-back control. Finally, the bool ch3flag argument controls whether tautomer enumeration should include tautomerization of methyl and methylene groups adjacent to a conjugated system. This allows cyclohexa-2,4-dien-1-one, O=C1CC=CC=C1, to be canonicalized as a tautomer of phenol, Oc1ccccc1. Unfortunately, the combinatorial explosion from tautomerizing across the alpha carbon of amino acids means that this option should not be used when enumerating the tautomers of proteins and large peptides. This function returns the total number of tautomers enumerated.

OEQuacPacGetArch

const char *OEQuacPacGetArch()

Returns the architecture on which the release was built

OEQuacPacGetLicensee

bool OEQuacPacGetLicensee(std::string &licensee)

Fills the parameter string &licensee with the licensee of the license file being used

OEQuacPacGetPlatform

const char *OEQuacPacGetPlatform()

Returns the platform on which the release of built

OEQuacPacGetRelease

const char *OEQuacPacGetRelease()

Returns the versions number as a const char* in major.minor.bugfix form

OEQuacPacGetSite

bool OEQuacPacGetSite(std::string &site)

Fills the parameter string &licensee with the site on the license file being used

OEQuacPacGetVersion

unsigned int OEQuacPacGetVersion()

Returns the build date of the release.

OEQuacPacIsLicensed

bool OEQuacPacIsLicensed(const char *feature=0, unsigned int *expdate=0)

Returns a bool indicating if a valid license for QuacPacTK has been set

OESetNeutralpHModel

bool OESetNeutralpHModel(OEChem::OEMolBase &mol)
bool OESetNeutralpHModel(OEChem::OEMCMolBase &mol)

This function will attempt to set mol to the most energetically favorable ionization state for pH=7.4 using a rule-based system.