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G

getAbbreviation() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAcid

Returns amino acid abbreviation.

getAbsDihAngle1() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridge

Returns dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of first cysteine.

getAbsDihAngle2() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridge

Returns dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of second cysteine.

getAbsDihAngleSS() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridge

Returns dihedral angle between planes formed by CB1, S1, S2 and S1, S2, CB2 atoms (1 - first cysteine, 2 - second cysteine).

getAcceptor() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns amino acid of participant with acceptor atom.

getAcceptorAntecedentAtom() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns atom preceding hydrogen bond acceptor.

getAcceptorAtom() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns hydrogen bond acceptor.

getAminoAcid() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticRing

Returns amino acid of the aromatic ring.

getAminoAminoAcid() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteraction

Returns amino acid of interaction participant with amino group.

getAngleBtwRings() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticAromaticInteraction

Returns angle between aromatic rings' normal vectors.

getAngleDAAa() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns angle between donor, acceptor and acceptor antecedent.

getAngleDHA() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns angle between donor, hydrogen and acceptor.

getAngleHAAa() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns angle between hydrogen, acceptor and acceptor antecedent.

getAnionicAminoAcid() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.IonicInteraction

Returns negatively charged amino acid.

getAromaticAminoAcid() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteraction

Returns amino acid of aromatic interaction participant.

getAromaticAminoAcid() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteraction

Returns amino acid of aromatic interaction participant.

getAromaticRings() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.PdbStructureParser

Returns aromatic rings present in parsed PDB structure.

getAtoms() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticRing

Returns atoms forming the aromatic ring.

getAtoms(String[]) - Method in class io.github.WeronikaJargielo.protein_interaction_finder.PdbStructureParser

Returns atoms of requested atoms' names present in parsed PDB structure.

getAtoms(String[], List<AminoAcidAbbreviations>) - Method in class io.github.WeronikaJargielo.protein_interaction_finder.PdbStructureParser

Returns atoms of requested atoms' names from allowed amino acids which are present in parsed PDB structure.

getAzimuthalAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteraction

Returns azimuthal angle for aromatic ring and amino group representative.

getCationicAminoAcid() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.IonicInteraction

Returns positively charged amino acid.

getChainId() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAcid

Returns chain ID of amino acid.

getDistanceBtwCAs() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridge

Returns distance between CA atoms of participating cysteines.

getDistanceBtwCAs() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns maximum distance between CA atoms of participating cysteines.

getDistanceBtwCAs() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrophobicInteraction

Returns distance between CA atoms of interaction participants.

getDistanceBtwCationRing() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteraction

Returns distance between aromatic ring centroid and amino group representative.

getDistanceBtwCBs() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridge

Returns distance between CB atoms of participating cysteines.

getDistanceBtwCBs() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns maximum distance between CB atoms of participating cysteines.

getDistanceBtwCentroids() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.IonicInteraction

Returns distance between charged groups' centroids of interaction participants.

getDistanceBtwRings() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticAromaticInteraction

Returns distance between aromatic rings' centroids.

getDistanceBtwRingSulphur() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteraction

Returns distance between aromatic ring centroid and sulphur atom.

getDistanceBtwSS() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridge

Returns distance between sulphur atoms of participating cysteines.

getDistanceDA() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns distance between donor and acceptor.

getDistanceHA() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns distance between hydrogen and acceptor.

getDonor() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns amino acid of participant with donor atom.

getDonorAtom() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns hydrogen bond donor.

getElevationAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteraction

Returns elevation angle for aromatic ring and sulphur atom.

getEquatorialAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteraction

Returns equatorial angle for aromatic ring and sulphur atom.

getFirstAromaticRing() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticAromaticInteraction

Returns aromatic amino acid of first interaction participant.

getFirstInteractee() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridge

Returns first cysteine.

getFirstInteractee() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrophobicInteraction

Returns amino acid of first interaction participant.

getGroup() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticRing

Returns group representing aromatic ring's amino acid.

getHydrogenAtom() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBond

Returns hydrogen atom bound to donor.

getLowerRangeMaxAbsDihAngle1() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns maximum dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of first cysteine in first range.

getLowerRangeMaxAbsDihAngle2() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns maximum dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of second cysteine in first range.

getLowerRangeMinAbsDihAngle1() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns minimum dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of first cysteine in first range.

getLowerRangeMinAbsDihAngle2() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns minimum dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of second cysteine in first range.

getMaxAbsDihAngleSS() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns maximum dihedral angle between planes formed by CB1, S1, S2 and S1, S2, CB2 atoms (1 - first cysteine, 2 - second cysteine).

getMaxAngleBtwRings() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticAromaticInteractionCriteria

Returns maximum angle between aromatic rings' normal vectors.

getMaxAngleDAAa() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns maximum between donor, acceptor and acceptor antecedent.

getMaxAngleDHA() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns maximum angle between donor, hydrogen and acceptor.

getMaxAngleHAAa() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns maximum between hydrogen, acceptor and acceptor antecedent.

getMaxAzimuthalAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteractionCriteria

Returns maximum azimuthal angle for aromatic ring and amino group representative.

getMaxDistanceBtwCationRing() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteractionCriteria

Returns maximum distance between aromatic ring centroid and amino group representative.

getMaxDistanceBtwCentroids() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.IonicInteractionCriteria

Returns maximum distance between charged groups' centroids of interaction participants.

getMaxDistanceBtwRings() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticAromaticInteractionCriteria

Returns maximum distance between aromatic rings' centroids.

getMaxDistanceBtwRingSulphur() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteractionCriteria

Returns maximum distance between aromatic ring centroid and sulphur atom.

getMaxDistanceBtwSulphurs() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns maximum distance between sulphur atoms of participating cysteines.

getMaxDistanceCAs() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrophobicInteractionCriteria

Returns maximum distance between CA atoms of interaction participants.

getMaxDistanceDA() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns maximum distance between donor and acceptor.

getMaxDistanceHA() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns maximum distance between hydrogen and acceptor.

getMaxElevationAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteractionCriteria

Returns maximum elevation angle for aromatic ring and sulphur atom.

getMaxEquatorialAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteractionCriteria

Returns maximum equatorial angle for aromatic ring and sulphur atom.

getMaxPolarAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteractionCriteria

Returns maximum polar angle for aromatic ring and amino group representative.

getMinAbsDihAngleSS() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns minimum dihedral angle between planes formed by CB1, S1, S2 and S1, S2, CB2 atoms (1 - first cysteine, 2 - second cysteine).

getMinAngleBtwRings() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticAromaticInteractionCriteria

Returns minimum angle between aromatic rings' normal vectors.

getMinAngleDAAa() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns minimum between donor, acceptor and acceptor antecedent.

getMinAngleDHA() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns minimum angle between donor, hydrogen and acceptor.

getMinAngleHAAa() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns minimum between hydrogen, acceptor and acceptor antecedent.

getMinAzimuthalAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteractionCriteria

Returns minimum azimuthal angle for aromatic ring and amino group representative.

getMinDistanceBtwCationRing() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteractionCriteria

Returns minimum distance between aromatic ring centroid and amino group representative.

getMinDistanceBtwCentroids() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.IonicInteractionCriteria

Returns minimum distance between charged groups' centroids of interaction participants.

getMinDistanceBtwRings() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticAromaticInteractionCriteria

Returns minimum distance between aromatic rings' centroids.

getMinDistanceBtwRingSulphur() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteractionCriteria

Returns minimum distance between aromatic ring centroid and sulphur atom.

getMinDistanceBtwSulphurs() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns minimum distance between sulphur atoms of participating cysteines.

getMinDistanceCAs() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrophobicInteractionCriteria

Returns minimum distance between CA atoms of interaction participants.

getMinDistanceDA() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns minimum distance between donor and acceptor.

getMinDistanceHA() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrogenBondCriteria

Returns minimum distance between hydrogen and acceptor.

getMinElevationAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteractionCriteria

Returns minimum elevation angle for aromatic ring and sulphur atom.

getMinEquatorialAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteractionCriteria

Returns minimum equatorial angle for aromatic ring and sulphur atom.

getMinPolarAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteractionCriteria

Returns minimum polar angle for aromatic ring and amino group representative.

getNormalVector() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticRing

Returns normal vector to aromatic ring plane.

getPdbStructureParser() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.ProteinInteractionFinder

Returns PdbStructureParser created in constructor.

getPolarAngle() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAromaticInteraction

Returns polar angle for aromatic ring and amino group representative.

getPosition() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AminoAcid

Returns amino acid position in protein chain.

getProteinStructure() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.PdbStructureParser

Returns parsed protein structure.

getRingCentroid() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticRing

Returns ring centroid.

getSecondAromaticRing() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.AromaticAromaticInteraction

Returns aromatic amino acid of second interaction participant.

getSecondInteractee() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridge

Returns second cysteine.

getSecondInteractee() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.HydrophobicInteraction

Returns amino acid of second interaction participant.

getSulphurAminoAcid() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.SulphurAromaticInteraction

Returns amino acid with sulphur atom.

getUpperRangeMaxAbsDihAngle1() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns maximum dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of first cysteine in second range.

getUpperRangeMaxAbsDihAngle2() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns maximum dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of second cysteine in second range.

getUpperRangeMinAbsDihAngle1() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns minimum dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of first cysteine in second range.

getUpperRangeMinAbsDihAngle2() - Method in class io.github.WeronikaJargielo.protein_interaction_finder.DisulphideBridgeCriteria

Returns minimum dihedral angle between planes formed by N, CA, CB and CA, CB, S atoms of second cysteine in second range.

GLN - io.github.WeronikaJargielo.protein_interaction_finder.AminoAcidAbbreviations

Glutamine

GLU - io.github.WeronikaJargielo.protein_interaction_finder.AminoAcidAbbreviations

Glutamic acid

GLY - io.github.WeronikaJargielo.protein_interaction_finder.AminoAcidAbbreviations

Glycine

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