Package rdkit :: Package Chem :: Module rdchem

Module rdchem

Module containing the core chemistry functionality of the RDKit

Classes

[hide private]

Atom
The class to store Atoms.

AtomMonomerInfo
The class to store monomer information attached to Atoms

AtomMonomerType

AtomPDBResidueInfo
The class to store PDB residue information attached to Atoms

Bond
The class to store Bonds.

BondDir

BondStereo

BondType

ChiralType

CompositeQueryType

Conformer
The class to store 2D or 3D conformation of a molecule

EditableMol
an editable molecule class

HybridizationType

Mol
The Molecule class.

MolBundle
A class for storing gropus of related molecules.

PeriodicTable
A class which stores information from the Periodic Table.

PropertyPickleOptions

QueryAtom
The class to store QueryAtoms.

QueryBond
The class to store QueryBonds.

RWMol
The RW molecule class (read/write)

ResonanceFlags

ResonanceMolSupplier
A class which supplies resonance structures (as mols) from a mol.

RingInfo
contains information about a molecule's rings

_ROAtomSeq
Read-only sequence of atoms, not constructable from Python.

_ROBondSeq
Read-only sequence of bonds, not constructable from Python.

_ROQAtomSeq
Read-only sequence of atoms matching a query, not constructable from Python.

_listPN5RDKit4AtomE

_listPN5RDKit4BondE

Functions

[hide private]

GetAtomAlias(...)
GetAtomAlias( (Atom)atom) -> str : Returns the atom's MDL alias text

GetAtomRLabel(...)
GetAtomRLabel( (Atom)atom) -> int : Returns the atom's MDL AtomRLabel (this is an integer from 0 to 99)

GetAtomValue(...)
GetAtomValue( (Atom)atom) -> str : Returns the atom's MDL alias text

int :

GetDefaultPickleProperties()
Get the current global mol pickler options.

PeriodicTable :

GetPeriodicTable()
Returns the application's PeriodicTable instance.

GetSupplementalSmilesLabel(...)
GetSupplementalSmilesLabel( (Atom)atom) -> str : Gets the supplemental smiles label on an atom, returns an empty string if not present.

LogErrorMsg(...)
LogErrorMsg( (str)arg1) -> None : Log a warning message to the RDKit error logs

LogWarningMsg(...)
LogWarningMsg( (str)arg1) -> None : Log a warning message to the RDKit warning logs

SetAtomAlias(...)
SetAtomAlias( (Atom)atom, (str)rlabel) -> None : Sets the atom's MDL alias text.

SetAtomRLabel(...)
SetAtomRLabel( (Atom)atom, (int)rlabel) -> None : Sets the atom's MDL RLabel (this is an integer from 0 to 99).

SetAtomValue(...)
SetAtomValue( (Atom)atom, (str)rlabel) -> None : Sets the atom's MDL alias text.

SetDefaultPickleProperties(...)
SetDefaultPickleProperties( (int)arg1) -> None : Set the current global mol pickler options.

SetSupplementalSmilesLabel(...)
SetSupplementalSmilesLabel( (Atom)atom, (str)label) -> None : Sets a supplemental label on an atom that is written to the smiles string.

None :

WrapLogs()
Wrap the internal RDKit streams so they go to python's SysStdErr

_HasSubstructMatchStr(...)
_HasSubstructMatchStr( (str)pkl, (Mol)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool : This function is included to speed substructure queries from databases, it's probably not of general interest.

None :

tossit()
C++ signature :...

Variables

[hide private]

ALLOW_CHARGE_SEPARATION = rdkit.Chem.rdchem.ResonanceFlags.ALL...

ALLOW_INCOMPLETE_OCTETS = rdkit.Chem.rdchem.ResonanceFlags.ALL...

AllProps = rdkit.Chem.rdchem.PropertyPickleOptions.AllProps

AtomProps = rdkit.Chem.rdchem.PropertyPickleOptions.AtomProps

BondProps = rdkit.Chem.rdchem.PropertyPickleOptions.BondProps

CHI_OTHER = rdkit.Chem.rdchem.ChiralType.CHI_OTHER

CHI_TETRAHEDRAL_CCW = rdkit.Chem.rdchem.ChiralType.CHI_TETRAHE...

CHI_TETRAHEDRAL_CW = rdkit.Chem.rdchem.ChiralType.CHI_TETRAHED...

CHI_UNSPECIFIED = rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED

COMPOSITE_AND = rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE...

COMPOSITE_OR = rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_OR

COMPOSITE_XOR = rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE...

ComputedProps = rdkit.Chem.rdchem.PropertyPickleOptions.Comput...

KEKULE_ALL = rdkit.Chem.rdchem.ResonanceFlags.KEKULE_ALL

MolProps = rdkit.Chem.rdchem.PropertyPickleOptions.MolProps

NoProps = rdkit.Chem.rdchem.PropertyPickleOptions.NoProps

PrivateProps = rdkit.Chem.rdchem.PropertyPickleOptions.Private...

QueryAtomData = rdkit.Chem.rdchem.PropertyPickleOptions.QueryA...

UNCONSTRAINED_ANIONS = rdkit.Chem.rdchem.ResonanceFlags.UNCONS...

UNCONSTRAINED_CATIONS = rdkit.Chem.rdchem.ResonanceFlags.UNCON...

__package__ = None
hash(x)

Function Details

[hide private]

GetAtomAlias(...)


GetAtomAlias( (Atom)atom) -> str :
    Returns the atom's MDL alias text

    C++ signature :
        std::string GetAtomAlias(RDKit::Atom const*)

GetAtomRLabel(...)


GetAtomRLabel( (Atom)atom) -> int :
    Returns the atom's MDL AtomRLabel (this is an integer from 0 to 99)

    C++ signature :
        int GetAtomRLabel(RDKit::Atom const*)

GetAtomValue(...)


GetAtomValue( (Atom)atom) -> str :
    Returns the atom's MDL alias text

    C++ signature :
        std::string GetAtomValue(RDKit::Atom const*)

GetDefaultPickleProperties()

    Get the current global mol pickler options.

    C++ signature :
        unsigned int GetDefaultPickleProperties()

Returns: int :

GetPeriodicTable()

    Returns the application's PeriodicTable instance.
    
    

    C++ signature :
        RDKit::PeriodicTable* GetPeriodicTable()

Returns: PeriodicTable :

GetSupplementalSmilesLabel(...)


GetSupplementalSmilesLabel( (Atom)atom) -> str :
    Gets the supplemental smiles label on an atom, returns an empty string if not present.

    C++ signature :
        std::string GetSupplementalSmilesLabel(RDKit::Atom const*)

LogErrorMsg(...)


LogErrorMsg( (str)arg1) -> None :
    Log a warning message to the RDKit error logs

    C++ signature :
        void LogErrorMsg(std::string)

LogWarningMsg(...)


LogWarningMsg( (str)arg1) -> None :
    Log a warning message to the RDKit warning logs

    C++ signature :
        void LogWarningMsg(std::string)

SetAtomAlias(...)


SetAtomAlias( (Atom)atom, (str)rlabel) -> None :
    Sets the atom's MDL alias text.
    Setting to an empty string clears the alias.

    C++ signature :
        void SetAtomAlias(RDKit::Atom*,std::string)

SetAtomRLabel(...)


SetAtomRLabel( (Atom)atom, (int)rlabel) -> None :
    Sets the atom's MDL RLabel (this is an integer from 0 to 99).
    Setting to 0 clears the rlabel.

    C++ signature :
        void SetAtomRLabel(RDKit::Atom*,int)

SetAtomValue(...)


SetAtomValue( (Atom)atom, (str)rlabel) -> None :
    Sets the atom's MDL alias text.
    Setting to an empty string clears the alias.

    C++ signature :
        void SetAtomValue(RDKit::Atom*,std::string)

SetDefaultPickleProperties(...)


SetDefaultPickleProperties( (int)arg1) -> None :
    Set the current global mol pickler options.

    C++ signature :
        void SetDefaultPickleProperties(unsigned int)

SetSupplementalSmilesLabel(...)


SetSupplementalSmilesLabel( (Atom)atom, (str)label) -> None :
    Sets a supplemental label on an atom that is written to the smiles string.
    >>> m = Chem.MolFromSmiles("C")
    >>> Chem.SetSupplementalSmilesLabel(m.GetAtomWithIdx(0), '<xxx>')
    >>> Chem.MolToSmiles(m)
    'C<xxx>'
    

    C++ signature :
        void SetSupplementalSmilesLabel(RDKit::Atom*,std::string)

WrapLogs()

    Wrap the internal RDKit streams so they go to python's SysStdErr

    C++ signature :
        void WrapLogs()

Returns: None :

_HasSubstructMatchStr(...)


_HasSubstructMatchStr( (str)pkl, (Mol)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool :
    This function is included to speed substructure queries from databases, 
    it's probably not of
    general interest.
    
      ARGUMENTS:
        - pkl: a Molecule pickle
    
        - query: a Molecule
    
        - recursionPossible: (optional)
    
        - useChirality: (optional)
    
        - useQueryQueryMatches: use query-query matching logic
    
      RETURNS: True or False
    

    C++ signature :
        bool _HasSubstructMatchStr(std::string,RDKit::ROMol [,bool=True [,bool=False [,bool=False]]])

tossit()

    C++ signature :
        void tossit()

Returns: None :

Variables Details

[hide private]

ALLOW_CHARGE_SEPARATION

Value:

rdkit.Chem.rdchem.ResonanceFlags.ALLOW_CHARGE_SEPARATION

ALLOW_INCOMPLETE_OCTETS

Value:

rdkit.Chem.rdchem.ResonanceFlags.ALLOW_INCOMPLETE_OCTETS

CHI_TETRAHEDRAL_CCW

Value:

rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW

CHI_TETRAHEDRAL_CW

Value:

rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW

COMPOSITE_AND

Value:

rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND

COMPOSITE_XOR

Value:

rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_XOR

ComputedProps

Value:

rdkit.Chem.rdchem.PropertyPickleOptions.ComputedProps

PrivateProps

Value:

rdkit.Chem.rdchem.PropertyPickleOptions.PrivateProps

QueryAtomData

Value:

rdkit.Chem.rdchem.PropertyPickleOptions.QueryAtomData

UNCONSTRAINED_ANIONS

Value:

rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_ANIONS

UNCONSTRAINED_CATIONS

Value:

rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_CATIONS