rdkit.Chem.rdFreeSASA module

Module containing rdFreeSASA classes and functions.

rdkit.Chem.rdFreeSASA.CalcSASA((Mol)mol, (AtomPairsParameters)radii[, (int)confIdx=-1[, (Atom)query=None[, (SASAOpts)opts=<rdkit.Chem.rdFreeSASA.SASAOpts object at 0x74618f8cb680>]]]) → float :

Compute the Solvent Accessible Surface Area using the FreeSASA library ARGUMENTS:

  • mol: The molecule to compute.

  • radii: A list of atom raddii where radii[atom.GetIdx()] is the radius of the atom

    These can be passed in or calculated with classifyAtoms for some proteins

  • confIdx: Specify the conformer to use for the 3D geometry [default -1]

  • query: Pass along a query atom to compute the SASA for a subset of atoms.

    precanned query atoms can be made with MakeFreeSasaPolarAtomQuery and MakeFreeSasaAPolarAtomQuery for classified polar and apolar atoms respectively.

  • opts: a SASAOpts class specifying the algorithm to use

RETURNS: The computed solvent accessible surface area.

C++ signature :

double CalcSASA(RDKit::ROMol,boost::python::api::object [,int=-1 [,RDKit::Atom const*=None [,FreeSASA::SASAOpts=<rdkit.Chem.rdFreeSASA.SASAOpts object at 0x74618f8cb680>]]])

rdkit.Chem.rdFreeSASA.MakeFreeSasaAPolarAtomQuery() → QueryAtom :

Returns an APolar atom query for use with CalcSASA. An apolar atom has the SASAClass and SASAClassName set to the APOLAR class. (see classifyAtoms)

C++ signature :

RDKit::QueryAtom const* MakeFreeSasaAPolarAtomQuery()

rdkit.Chem.rdFreeSASA.MakeFreeSasaPolarAtomQuery() → QueryAtom :

Returns a polar atom query for use with CalcSASA. An polar atom has the SASAClass and SASAClassName set to the POLAR class. (see classifyAtoms)

C++ signature :

RDKit::QueryAtom const* MakeFreeSasaPolarAtomQuery()

class rdkit.Chem.rdFreeSASA.SASAAlgorithm

Bases: enum

LeeRichards = rdkit.Chem.rdFreeSASA.SASAAlgorithm.LeeRichards
ShrakeRupley = rdkit.Chem.rdFreeSASA.SASAAlgorithm.ShrakeRupley
names = {'LeeRichards': rdkit.Chem.rdFreeSASA.SASAAlgorithm.LeeRichards, 'ShrakeRupley': rdkit.Chem.rdFreeSASA.SASAAlgorithm.ShrakeRupley}
values = {0: rdkit.Chem.rdFreeSASA.SASAAlgorithm.LeeRichards, 1: rdkit.Chem.rdFreeSASA.SASAAlgorithm.ShrakeRupley}
class rdkit.Chem.rdFreeSASA.SASAClass

Bases: enum

APolar = rdkit.Chem.rdFreeSASA.SASAClass.APolar
Polar = rdkit.Chem.rdFreeSASA.SASAClass.Polar
Unclassified = rdkit.Chem.rdFreeSASA.SASAClass.Unclassified
names = {'APolar': rdkit.Chem.rdFreeSASA.SASAClass.APolar, 'Polar': rdkit.Chem.rdFreeSASA.SASAClass.Polar, 'Unclassified': rdkit.Chem.rdFreeSASA.SASAClass.Unclassified}
values = {0: rdkit.Chem.rdFreeSASA.SASAClass.Unclassified, 1: rdkit.Chem.rdFreeSASA.SASAClass.APolar, 2: rdkit.Chem.rdFreeSASA.SASAClass.Polar}
class rdkit.Chem.rdFreeSASA.SASAClassifier

Bases: enum

NACCESS = rdkit.Chem.rdFreeSASA.SASAClassifier.NACCESS
OONS = rdkit.Chem.rdFreeSASA.SASAClassifier.OONS
Protor = rdkit.Chem.rdFreeSASA.SASAClassifier.Protor
names = {'NACCESS': rdkit.Chem.rdFreeSASA.SASAClassifier.NACCESS, 'OONS': rdkit.Chem.rdFreeSASA.SASAClassifier.OONS, 'Protor': rdkit.Chem.rdFreeSASA.SASAClassifier.Protor}
values = {0: rdkit.Chem.rdFreeSASA.SASAClassifier.Protor, 1: rdkit.Chem.rdFreeSASA.SASAClassifier.NACCESS, 2: rdkit.Chem.rdFreeSASA.SASAClassifier.OONS}
class rdkit.Chem.rdFreeSASA.SASAOpts((object)self)

Bases: instance

Constructor takes no arguments

C++ signature :

void __init__(_object*)

__init__( (object)self, (SASAAlgorithm)alg, (SASAClassifier)cls) -> None :

C++ signature :

void __init__(_object*,FreeSASA::SASAOpts::Algorithm,FreeSASA::SASAOpts::Classifier)

__init__( (object)self, (SASAAlgorithm)alg, (SASAClassifier)cls, (float)pr) -> None :

C++ signature :

void __init__(_object*,FreeSASA::SASAOpts::Algorithm,FreeSASA::SASAOpts::Classifier,double)

property algorithm
property classifier
property probeRadius
rdkit.Chem.rdFreeSASA.classifyAtoms((Mol)mol[, (SASAOpts)options=<rdkit.Chem.rdFreeSASA.SASAOpts object at 0x74618f8cb7d0>]) → object :

Classify the atoms in the molecule returning their radii if possible. ARGUMENTS:

  • mol: molecule to classify

  • options: FreeSASA options class specifying the classification method.

    Current classifiers are Protor, NACCESS and OONS classification is stored as atom property ‘SASAClass’ for the integer value

    and ‘SASAClassName’ for the string name of the class, Polar, APolar…

RETURNS:

list of radii where radii[atom.GetIdx()] is the radii of the atom. If classification fails, NONE is returned

C++ signature :

boost::python::api::object classifyAtoms(RDKit::ROMol {lvalue} [,FreeSASA::SASAOpts=<rdkit.Chem.rdFreeSASA.SASAOpts object at 0x74618f8cb7d0>])