SBResidue

See also

SAMSON SDK: SBMStructuralModelNodeResidue

class samson.SBResidue(*args, **kwargs)

Bases: SBStructuralGroup

This class describes a residue in a structural model.

Overloaded function.

1. __init__(self: samson.SBResidue) -> None

Constructs a residue.

2. __init__(self: samson.SBResidue, name: str) -> None

Constructs a residue with the given name.

class HydrophobicityScale(self: samson.SBResidue.HydrophobicityScale, value: int)

Bases: pybind11_object

Members:

KyteDoolittle1982 : A hydrophobicity scale of Kyte J, Doolittle RF, A simple method for displaying the hydropathic character of a protein, J Mol Biol. 1982.

SeredaEtAl1994 : A hydrophobicity scale of Sereda TJ et al. 1994.

MoneraEtAl1995 : A hydrophobicity scale of Monera et al. 1995.

WimleyWhite1996 : A hydrophobicity scale of Wimley WC, White SH, Experimentally determined hydrophobicity scale for proteins at membrane interfaces, Nat Struct Biol. 1996.

HessaEtAl2005 : A hydrophobicity scale of Hessa T et al. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature. 2005.

ZhaoLondon2006 : A hydrophobicity scale of Zhao G, London E. An amino acid transmembrane tendency scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices : relationship to biological hydrophobicity. Protein Sci. 2006.

MoonFleming2011 : A hydrophobicity scale of Moon CP, Fleming KG. Side chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers. Proc Natl Acad Sci USA. 2011.

HessaEtAl2005 = <HydrophobicityScale.HessaEtAl2005: 4>

KyteDoolittle1982 = <HydrophobicityScale.KyteDoolittle1982: 0>

MoneraEtAl1995 = <HydrophobicityScale.MoneraEtAl1995: 2>

MoonFleming2011 = <HydrophobicityScale.MoonFleming2011: 6>

SeredaEtAl1994 = <HydrophobicityScale.SeredaEtAl1994: 1>

WimleyWhite1996 = <HydrophobicityScale.WimleyWhite1996: 3>

ZhaoLondon2006 = <HydrophobicityScale.ZhaoLondon2006: 5>

property name

property value

class ResidueType(self: samson.SBResidue.ResidueType, value: int)

Bases: pybind11_object

Members:

Undefined : Undefined residue type

ALA : Alanine

ARG : Arginine

ASP : Aspartic acid

ASN : Asparagine

VAL : Valine

HIS : Histidine

GLY : Glycine

GLU : Glutamic acid

GLN : Glutamine

ILE : Isoleucine

LEU : Leucine

LYS : Lysine

MET : Methionine

PRO : Proline

SER : Serine

TYR : Tyrosine

THR : Threonine

TRP : Tryptophan

PHE : Phenylalanine

CYS : Cysteine

ASX : ASN or ASP (Asparagine or Aspartic acid)

GLX : GLN or GLU (Glutamine or Glutamic acid)

XLE : LEU or ILE (Leucine or Isoleucine)

XAA : Unknown residue type

SEC : Selenocysteine

PYL : Pyrrolysine

A : Adenosine-5’-monophosphate

C : Cytidine-5’-monophosphate

G : Guanosine-5’-monophosphate

U : Uridine-5’-monophosphate

I : Inosinic acid

DA : 2’-deoxyadenosine-5’-monophosphate

DC : 2’-deoxycytidine-5’-monophosphate

DG : 2’-deoxyguanosine-5’-monophosphate

DT : Thymidine-5’-monophosphate

DI : 2’-deoxyinosine-5’-monophosphate

A = <ResidueType.A: 27>

ALA = <ResidueType.ALA: 1>

ARG = <ResidueType.ARG: 2>

ASN = <ResidueType.ASN: 4>

ASP = <ResidueType.ASP: 3>

ASX = <ResidueType.ASX: 21>

C = <ResidueType.C: 28>

CYS = <ResidueType.CYS: 20>

DA = <ResidueType.DA: 32>

DC = <ResidueType.DC: 33>

DG = <ResidueType.DG: 34>

DI = <ResidueType.DI: 36>

DT = <ResidueType.DT: 35>

G = <ResidueType.G: 29>

GLN = <ResidueType.GLN: 9>

GLU = <ResidueType.GLU: 8>

GLX = <ResidueType.GLX: 22>

GLY = <ResidueType.GLY: 7>

HIS = <ResidueType.HIS: 6>

I = <ResidueType.I: 31>

ILE = <ResidueType.ILE: 10>

LEU = <ResidueType.LEU: 11>

LYS = <ResidueType.LYS: 12>

MET = <ResidueType.MET: 13>

PHE = <ResidueType.PHE: 19>

PRO = <ResidueType.PRO: 14>

PYL = <ResidueType.PYL: 26>

SEC = <ResidueType.SEC: 25>

SER = <ResidueType.SER: 15>

THR = <ResidueType.THR: 17>

TRP = <ResidueType.TRP: 18>

TYR = <ResidueType.TYR: 16>

U = <ResidueType.U: 30>

Undefined = <ResidueType.Undefined: 0>

VAL = <ResidueType.VAL: 5>

XAA = <ResidueType.XAA: 24>

XLE = <ResidueType.XLE: 23>

property name

property value

class SecondaryStructureType(self: samson.SBResidue.SecondaryStructureType, value: int)

Bases: pybind11_object

Members:

Unstructured : Unstructured secondary structure element

Alpha : Alpha helix secondary structure element

Beta : Beta strand/sheet secondary structure element

Alpha = <SecondaryStructureType.Alpha: 1>

Beta = <SecondaryStructureType.Beta: 2>

Unstructured = <SecondaryStructureType.Unstructured: 0>

property name

property value

class SideChainCharge(self: samson.SBResidue.SideChainCharge, value: int)

Bases: pybind11_object

Members:

UndefinedSideChainCharge : Undefined side chain charge

Negative : Residue has a side chain with negative charge

Neutral : Residue has a side chain with neutral charge

Positive : Residue has a side chain with positive charge

Negative = <SideChainCharge.Negative: 1>

Neutral = <SideChainCharge.Neutral: 2>

Positive = <SideChainCharge.Positive: 3>

UndefinedSideChainCharge = <SideChainCharge.UndefinedSideChainCharge: 0>

property name

property value

class SideChainPolarity(self: samson.SBResidue.SideChainPolarity, value: int)

Bases: pybind11_object

Members:

UndefinedSideChainPolarity : Undefined side chain polarity

Nonpolar : Residue has a nonpolar side chain

Polar : Residue has a polar side chain

AcidicPolar : Residue has a side chain with acidic polarity

BasicPolar : Residue has a side chain with basic polarity

AcidicPolar = <SideChainPolarity.AcidicPolar: 3>

BasicPolar = <SideChainPolarity.BasicPolar: 4>

Nonpolar = <SideChainPolarity.Nonpolar: 1>

Polar = <SideChainPolarity.Polar: 2>

UndefinedSideChainPolarity = <SideChainPolarity.UndefinedSideChainPolarity: 0>

property name

property value

addHydrogensByResidueType(self: samson.SBResidue) → int

Adds hydrogen atoms based on the residue type.

computeAminoAcidChi1Angle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the chi1 angle (in degrees) for the amino acid residue’s side chain.

computeAminoAcidChi2Angle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the chi2 angle (in degrees) for the amino acid residue’s side chain.

computeAminoAcidChi3Angle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the chi3 angle (in degrees) for the amino acid residue’s side chain.

computeAminoAcidChi4Angle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the chi4 angle (in degrees) for the amino acid residue’s side chain.

computeAminoAcidChi5Angle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the chi5 angle (in degrees) for the amino acid residue’s side chain.

computeAminoAcidPhiAngle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the phi dihedral angle (in degrees) for the amino acid residue’s backbone.

computeAminoAcidPsiAngle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the psi dihedral angle (in degrees) for the amino acid residue’s backbone.

computeNucleicAcidAlphaAngle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the alpha (O3’(i-1)-P-O5’-C5’) dihedral angle (in degrees) for the nucleic acid’s backbone.

computeNucleicAcidBetaAngle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the beta (P-O5’-C5’-C4’) dihedral angle (in degrees) for the nucleic acid’s backbone.

computeNucleicAcidChiAngle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the chi dihedral angle (in degrees) for the nucleic acid’s backbone.

computeNucleicAcidDeltaAngle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the delta (C5’-C4’-C3’-O3’) dihedral angle (in degrees) for the nucleic acid’s backbone.

computeNucleicAcidEpsilonAngle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the epsilon (C4’-C3’-O3’-P(i+1)) dihedral angle (in degrees) for the nucleic acid’s backbone.

computeNucleicAcidGammaAngle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the gamma (O5’-C5’-C4’-C3’) dihedral angle (in degrees) for the nucleic acid’s backbone.

computeNucleicAcidZetaAngle(self: samson.SBResidue) → samson.SBQuantity.unitsSI

Computes the zeta (C3’-O3’-P(i+1)-O5’(i+1)) dihedral angle (in degrees) for the nucleic acid’s backbone.

createCovalentBondsByResidueType(self: samson.SBResidue) → int

Sets the order of covalent bonds for the atoms belonging to the residue according to the residue type, regardless of inter-atomic distances.

static getAminoAcidOneLetterCode(residueType: SBMStructuralModelNodeResidue::ResidueType) → str

Returns one letter code of the amino acid residue residueType.

getBackbone(self: samson.SBResidue) → samson.SBBackbone

Returns the residue’s backbone.

static getDissociationConstant1(residueType: SBMStructuralModelNodeResidue::ResidueType) → float

Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for the residue residueType.

static getDissociationConstant2(residueType: SBMStructuralModelNodeResidue::ResidueType) → float

Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for the residue residueType.

getHydrophobicity(*args, **kwargs)

Overloaded function.

1. getHydrophobicity(self: samson.SBResidue) -> float

Returns the residue’s hydrophobicity in the current hydrophobicity scale.

2. getHydrophobicity(self: samson.SBResidue, hydrophobicityScale: samson.SBResidue.HydrophobicityScale) -> float

Returns the residue’s hydrophobicity in the given hydrophobicity scale hydrophobicityScale.

static getHydrophobicityForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType, hydrophobicityScale: samson.SBResidue.HydrophobicityScale) → float

Returns the hydrophobicity value for the residue residueType in the hydrophobicity scale hydrophobicityScale.

static getHydrophobicityScaleString(hydrophobicityScale: samson.SBResidue.HydrophobicityScale) → str

Returns the hydrophobicity scale hydrophobicityScale as a string.

static getIsoelectricPointPH(residueType: SBMStructuralModelNodeResidue::ResidueType) → float

Returns the pI value (the pH at the isoelectric point) for the residue residueType.

getNextAminoAcid(self: samson.SBResidue) → samson.SBResidue

getNextNucleicAcid(self: samson.SBResidue) → samson.SBResidue

getNextResidue(self: samson.SBResidue) → samson.SBResidue

getPreviousAminoAcid(self: samson.SBResidue) → samson.SBResidue

getPreviousNucleicAcid(self: samson.SBResidue) → samson.SBResidue

getPreviousResidue(self: samson.SBResidue) → samson.SBResidue

static getResidueTypeFromAminoAcidOneLetterCode(code: str) → SBMStructuralModelNodeResidue::ResidueType

Returns the amino acid residue type from the one letter code, code, of an amino acid residue.

static getResidueTypeFromString(residueTypeString: str) → SBMStructuralModelNodeResidue::ResidueType

Returns the residue’s type based on the given string.

static getResidueTypeFullName(residueType: SBMStructuralModelNodeResidue::ResidueType) → str

Returns the full name of the residue type residueType.

static getResidueTypeString(residueType: SBMStructuralModelNodeResidue::ResidueType) → str

Returns the string representation of the residue type residueType.

getSecondaryStructureTypeString(self: samson.SBResidue, secondaryStructureType: SBMStructuralModelNodeResidue::SecondaryStructureType) → str

Returns the secondary structure type secondaryStructureType as a string.

getSideChain(self: samson.SBResidue) → SBMStructuralModelNodeSideChain

Returns the residue’s side chain.

static getSideChainCharge(residueType: SBMStructuralModelNodeResidue::ResidueType) → samson.SBResidue.SideChainCharge

Returns the residue’s side chain charge for the residue residueType.

static getSideChainChargeString(sideChainCharge: samson.SBResidue.SideChainCharge) → str

Returns the side chain charge sideChainCharge as a string.

static getSideChainPolarity(residueType: SBMStructuralModelNodeResidue::ResidueType) → samson.SBResidue.SideChainPolarity

Returns the residue’s side chain polarity for the residue residueType.

static getSideChainPolarityString(sideChainPolarity: samson.SBResidue.SideChainPolarity) → str

Returns the side chain polarity sideChainPolarity as a string.

hasAminoAcidChi1Angle(self: samson.SBResidue) → bool

Returns True if it is an amino acid and has chi1 angle.

static hasAminoAcidChi1AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if the residue type residueType is an amino acid and has chi1 angle.

hasAminoAcidChi2Angle(self: samson.SBResidue) → bool

Returns True if it is an amino acid and has chi2 angle.

static hasAminoAcidChi2AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if the residue type residueType is an amino acid and has chi2 angle.

hasAminoAcidChi3Angle(self: samson.SBResidue) → bool

Returns True if it is an amino acid and has chi3 angle.

static hasAminoAcidChi3AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if the residue type residueType is an amino acid and has chi3 angle.

hasAminoAcidChi4Angle(self: samson.SBResidue) → bool

Returns True if it is an amino acid and has chi4 angle.

static hasAminoAcidChi4AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if the residue type residueType is an amino acid and has chi4 angle.

hasAminoAcidChi5Angle(self: samson.SBResidue) → bool

Returns True if it is an amino acid and has chi5 angle.

static hasAminoAcidChi5AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if the residue type residueType is an amino acid and has chi5 angle.

static hasDissociationConstantForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for the residue residueType.

static hasHydrophobicityForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if for the residue type residueType the hydrophobicity is defined

static hasSideChainChargeForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if for the residue type residueType the side chain charge is defined.

static hasSideChainPolarityForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if for the residue type residueType the side chain polarity is defined.

hasStandardResidueName(self: samson.SBResidue) → bool

Returns True if and only if the residue name corresponds to one of the standard PDB residue names.

static isAminoAcidResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if and only if the given residue type is of amino acid.

static isNucleicAcidResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns True if and only if the given residue type is of nucleic acid.

static isStandardAminoAcidName(name: str) → bool

Returns True if and only if the name name corresponds to one of the standard PDB amino acid residue names.

static isStandardNucleicAcidName(name: str) → bool

Returns True if and only if the name name corresponds to one of the standard PDB nucleic acid residue names.

static isStandardResidueName(name: str) → bool

Returns True if and only if the name name corresponds to one of the standard PDB amino or nucleic acid residue names.

orientAminoAcidSideChain(self: samson.SBResidue, chi1: samson.SBQuantity.unitsSI, chi2: samson.SBQuantity.unitsSI = 0(dimensionless), chi3: samson.SBQuantity.unitsSI = 0(dimensionless), chi4: samson.SBQuantity.unitsSI = 0(dimensionless), chi5: samson.SBQuantity.unitsSI = 0(dimensionless)) → bool

Rotates the amino acid’s side chain to orient it according to given dihedral angles chi1, chi2, chi3, chi4, chi5 (in degrees). Returns True if at least the chi1 rotation was performed.

setName(self: samson.SBResidue, arg0: str) → None

Sets the name of the residue, and updates accordingly names for its backbone and side chain, if any.

A = <ResidueType.A: 27>

ALA = <ResidueType.ALA: 1>

ARG = <ResidueType.ARG: 2>

ASN = <ResidueType.ASN: 4>

ASP = <ResidueType.ASP: 3>

ASX = <ResidueType.ASX: 21>

AcidicPolar = <SideChainPolarity.AcidicPolar: 3>

Alpha = <SecondaryStructureType.Alpha: 1>

BasicPolar = <SideChainPolarity.BasicPolar: 4>

Beta = <SecondaryStructureType.Beta: 2>

C = <ResidueType.C: 28>

CYS = <ResidueType.CYS: 20>

DA = <ResidueType.DA: 32>

DC = <ResidueType.DC: 33>

DG = <ResidueType.DG: 34>

DI = <ResidueType.DI: 36>

DT = <ResidueType.DT: 35>

G = <ResidueType.G: 29>

GLN = <ResidueType.GLN: 9>

GLU = <ResidueType.GLU: 8>

GLX = <ResidueType.GLX: 22>

GLY = <ResidueType.GLY: 7>

HIS = <ResidueType.HIS: 6>

HessaEtAl2005 = <HydrophobicityScale.HessaEtAl2005: 4>

I = <ResidueType.I: 31>

ILE = <ResidueType.ILE: 10>

KyteDoolittle1982 = <HydrophobicityScale.KyteDoolittle1982: 0>

LEU = <ResidueType.LEU: 11>

LYS = <ResidueType.LYS: 12>

MET = <ResidueType.MET: 13>

MoneraEtAl1995 = <HydrophobicityScale.MoneraEtAl1995: 2>

MoonFleming2011 = <HydrophobicityScale.MoonFleming2011: 6>

Negative = <SideChainCharge.Negative: 1>

Neutral = <SideChainCharge.Neutral: 2>

Nonpolar = <SideChainPolarity.Nonpolar: 1>

PHE = <ResidueType.PHE: 19>

PRO = <ResidueType.PRO: 14>

PYL = <ResidueType.PYL: 26>

Polar = <SideChainPolarity.Polar: 2>

Positive = <SideChainCharge.Positive: 3>

SEC = <ResidueType.SEC: 25>

SER = <ResidueType.SER: 15>

SeredaEtAl1994 = <HydrophobicityScale.SeredaEtAl1994: 1>

THR = <ResidueType.THR: 17>

TRP = <ResidueType.TRP: 18>

TYR = <ResidueType.TYR: 16>

U = <ResidueType.U: 30>

Undefined = <ResidueType.Undefined: 0>

UndefinedSideChainCharge = <SideChainCharge.UndefinedSideChainCharge: 0>

UndefinedSideChainPolarity = <SideChainPolarity.UndefinedSideChainPolarity: 0>

Unstructured = <SecondaryStructureType.Unstructured: 0>

VAL = <ResidueType.VAL: 5>

WimleyWhite1996 = <HydrophobicityScale.WimleyWhite1996: 3>

XAA = <ResidueType.XAA: 24>

XLE = <ResidueType.XLE: 23>

ZhaoLondon2006 = <HydrophobicityScale.ZhaoLondon2006: 5>

property aminoAcidOneLetterCode

Returns one letter code of the amino acid residue. A read-only property.

property dissociationConstant1

Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for this residue. A read-only property.

property dissociationConstant2

Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for this residue. A read-only property.

property hasCompleteAminoAcidBackbone

Returns True if and only if the residue has a complete amino acid backbone. A read-only property.

property hasDissociationConstant

Returns True if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for this residue. A read-only property.

property hasHydrophobicity

Returns True if the residue’s hydrophobicity is defined. A read-only property.

property hasSideChainCharge

Returns True if the residue’s side chain charge is defined. A read-only property.

property hasSideChainPolarity

Returns True if the residue’s side chain polarity is defined. A read-only property.

property hydrophobicityScale

The current residue’s hydrophobicity scale

property hydrophobicityScaleString

Returns the current hydrophobicity scale as a string. A read-only property.

property isAminoAcid

Returns True if and only if the residue is an amino acid. A read-only property.

property isNucleicAcid

Returns True if and only if the residue is a nucleic acid. A read-only property.

property isTerminal

Returns True if and only if the residue is terminal. A read-only property.

property isoelectricPointPH

Returns the pI value (the pH at the isoelectric point) for this residue. A read-only property.

property residueType

property residueTypeFullName

Returns the full name of the residue’s type. A read-only property.

property residueTypeString

property secondaryStructureType

Returns the most probable secondary structure based on bonds parameters and residue geometry

property secondaryStructureTypeString

The secondary structure type as a string. A read-only property.

property sideChainCharge

Returns the residue’s side chain charge. A read-only property.

property sideChainChargeString

Returns the residue’s side chain charge as a string. A read-only property.

property sideChainPolarity

Returns the residue’s side chain polarity. A read-only property.

property sideChainPolarityString

Returns the residue’s side chain polarity as a string. A read-only property.