rdkit.Chem.rdDetermineBonds module

Module containing a C++ implementation of the xyz2mol algorithm. This is based on xyz2mol: https://github.com/jensengroup/xyz2mol

rdkit.Chem.rdDetermineBonds.DetermineBondOrders((Mol)mol[, (int)charge=0[, (bool)allowChargedFragments=True[, (bool)embedChiral=True[, (bool)useAtomMap=False]]]]) → None :

Assigns atomic connectivity to a molecule using atomic coordinates, disregarding pre-existing bonds

Parameters:

• mol – the molecule of interest; it must have a 3D conformer

• charge – (optional) the charge of the molecule; it must be provided if the Hueckel method is used and charge is non-zero

• allowChargedFragments – (optional) if this is true, formal charges will be placed on atoms according to their valency; otherwise, radical electrons will be placed on the atoms

• embedChiral – (optional) if this is true, chirality information will be embedded into the molecule; the function calls sanitizeMol() when this is true

• useAtomMap – (optional) if this is true, an atom map will be created for the molecule

C++ signature :

void DetermineBondOrders(RDKit::ROMol {lvalue} [,int=0 [,bool=True [,bool=True [,bool=False]]]])

rdkit.Chem.rdDetermineBonds.DetermineBonds((Mol)mol[, (bool)useHueckel=False[, (int)charge=0[, (float)covFactor=1.3[, (bool)allowChargedFragments=True[, (bool)embedChiral=True[, (bool)useAtomMap=False[, (bool)useVdw=False]]]]]]]) → None :

Assigns atomic connectivity to a molecule using atomic coordinates, disregarding pre-existing bonds

Parameters:

• mol – the molecule of interest; it must have a 3D conformer

• useHueckel – (optional) if this is true, extended Hueckel theory will be used to determine connectivity rather than the van der Waals or connect-the-dots methods

• charge – (optional) the charge of the molecule; it must be provided if the Hueckel method is used and charge is non-zero

• covFactor – (optional) the factor with which to multiply each covalent radius if the van der Waals method is used

• allowChargedFragments – (optional) if this is true, formal charges will be placed on atoms according to their valency; otherwise, radical electrons will be placed on the atoms

• embedChiral – (optional) if this is true, chirality information will be embedded into the molecule; the function calls sanitizeMol() when this is true

• useAtomMap – (optional) if this is true, an atom map will be created for the molecule

• useVdw – (optional) if this is false, the connect-the-dots method will be used instead of the van der Waals method

C++ signature :

void DetermineBonds(RDKit::ROMol {lvalue} [,bool=False [,int=0 [,double=1.3 [,bool=True [,bool=True [,bool=False [,bool=False]]]]]]])

rdkit.Chem.rdDetermineBonds.DetermineConnectivity((Mol)mol[, (bool)useHueckel=False[, (int)charge=0[, (float)covFactor=1.3[, (bool)useVdw=False]]]]) → None :

Assigns atomic connectivity to a molecule using atomic coordinates, disregarding pre-existing bonds

Parameters:

• mol – the molecule of interest; it must have a 3D conformer

• useHueckel – (optional) if this is c true, extended Hueckel theory will be used to determine connectivity rather than the van der Waals or connect-the-dots methods

• charge – (optional) the charge of the molecule; it must be provided if the Hueckel method is used and charge is non-zero

• covFactor – (optional) the factor with which to multiply each covalent radius if the van der Waals method is used

• useVdw – (optional) if this is false, the connect-the-dots method will be used instead of the van der Waals method

C++ signature :

void DetermineConnectivity(RDKit::ROMol {lvalue} [,bool=False [,int=0 [,double=1.3 [,bool=False]]]])

rdkit.Chem.rdDetermineBonds.hueckelEnabled() → bool :

whether or not the RDKit was compiled with YAeHMOP support

C++ signature :

bool hueckelEnabled()