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

Args:

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

Args:

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

Args:

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()