SBResidue#
See also
SAMSON SDK: SBMStructuralModelNodeResidue
- class samson.SBResidue(*args, **kwargs)#
Bases:
SBStructuralGroup
This class describes a residue in a structural model.
Overloaded function.
__init__(self: samson.SBResidue) -> None
Constructs a residue.
__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.
getHydrophobicity(self: samson.SBResidue) -> float
Returns the residue’s hydrophobicity in the current hydrophobicity scale.
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.