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 0x7500b10226c0>]]]) → 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 0x7500b10226c0>]]])

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 0x7500b1022c00>]) → 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 0x7500b1022c00>])