Package ffx.potential.bonded

Class AminoAcidUtils

java.lang.Object

ffx.potential.bonded.AminoAcidUtils

public class AminoAcidUtils
extends Object

Utilities for creating Amino Acid residues.

Since:

1.0

Author:

Michael Schnieders

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	AminoAcidUtils.AA	The 20 standard amino acids.
static enum	AminoAcidUtils.AIB	Constant AIB
static enum	AminoAcidUtils.ALA	Constant ALA
static enum	AminoAcidUtils.AminoAcid1	Single letter amino acid codes (need to
static enum	AminoAcidUtils.AminoAcid3
static enum	AminoAcidUtils.AminoAcidBackboneAtoms	Constant AminoAcidBackboneAtoms
static enum	AminoAcidUtils.ARG	Constant ARG
static enum	AminoAcidUtils.ASD	Constant ASD
static enum	AminoAcidUtils.ASH	Constant ASH
static enum	AminoAcidUtils.ASN	Constant ASN
static enum	AminoAcidUtils.ASP	Constant ASP
static enum	AminoAcidUtils.CYD	Constant CYD
static enum	AminoAcidUtils.CYS	Constant CYS
static enum	AminoAcidUtils.CYX	Constant CYS
static enum	AminoAcidUtils.GLD	Constant GLD
static enum	AminoAcidUtils.GLH	Constant GLH
static enum	AminoAcidUtils.GLN	Constant GlutamineAtomNames
static enum	AminoAcidUtils.GLU	Constant GLU
static enum	AminoAcidUtils.GLY	Constant GLY
static enum	AminoAcidUtils.GlycineBackboneAtoms	Constant GlycineBackboneAtoms
static enum	AminoAcidUtils.HID	Constant HID
static enum	AminoAcidUtils.HIE	Constant HIE
static enum	AminoAcidUtils.HIS	Constant HistidineAtoms
static enum	AminoAcidUtils.ILE	Constant ILE
static enum	AminoAcidUtils.LEU	Constant LEU
static enum	AminoAcidUtils.LYD	Constant LYD
static enum	AminoAcidUtils.LYS	Constant LYS
static enum	AminoAcidUtils.MET	Constant MethionineAtomNames
static enum	AminoAcidUtils.ORN	Constant ORN
static enum	AminoAcidUtils.PCA	Constant PCA
static enum	AminoAcidUtils.PHE	Constant PHE
static enum	AminoAcidUtils.PRO	Constant PRO
static enum	AminoAcidUtils.ProlineBackboneAtoms	Constant ProlineBackboneAtoms
static enum	AminoAcidUtils.ResiduePosition	The location of a residue within a chain.
static enum	AminoAcidUtils.SER	Constant SER
static interface	AminoAcidUtils.SideChainType	This interface is used by the "Build" routines.
static enum	AminoAcidUtils.THR	Constant THR
static enum	AminoAcidUtils.TRP	Constant TRP
static enum	AminoAcidUtils.TYD	Constant TYD
static enum	AminoAcidUtils.TYR	Constant TYR
static enum	AminoAcidUtils.VAL	Constant VAL

Field Summary

Fields

Modifier and Type	Field	Description
static final int[][]	AA_C	Constant AA_C
static final int[][]	AA_CA	Constant AA_CA
static final int[]	AA_CB	Constant AA_CB
static final int[][]	AA_HA	Constant AA_HA
static final int[][]	AA_HN	Constant AA_HN
static final int[][]	AA_N	Biotype keys for amino acid backbone atom types.
static final int[][]	AA_O	Constant AA_O
static final HashMap<AminoAcidUtils.AminoAcid1,AminoAcidUtils.AminoAcid3>	AA1toAA3	Constant AA1toAA3
static final int[]	AAPATTERN	Repeating atomic numbers of an amino acid chain.
static final List<AminoAcidUtils.AminoAcid1>	aminoAcid1List	List of values from the AminoAcid1 enum.
static final List<AminoAcidUtils.AminoAcid3>	aminoAcidList	Constant aminoAcidList
static final HashMap<String,String>	sidechainStoichiometry	Stoichiometry of side chains can be used for identification, accept for a couple cases:

Method Summary

Modifier and Type	Method	Description
static void	assignAminoAcidAtomTypes(Residue residue, Residue previousResidue, Residue nextResidue, ForceField forceField, List<Bond> bondList)	assignAminoAcidAtomTypes.
static void	assignAminoAcidAtomTypes(List<Residue> residues, ForceField forceField, List<Bond> bondList)	Assign atom types to an amino acid polymer.
static Residue	buildAIB(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAIB.
static Residue	buildAlanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAlanine.
static Residue	buildArginine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildArginine.
static Residue	buildAsparagine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAsparagine.
static Residue	buildAspartate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAspartate.
static Residue	buildCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCysteine.
static Residue	buildCystine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCystine.
static Residue	buildDeprotonatedCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedCysteine.
static Residue	buildDeprotonatedLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedLysine.
static Residue	buildDeprotonatedTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedTyrosine.
static Residue	buildGlutamate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamate.
static Residue	buildGlutamine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamine.
static Residue	buildGlycine(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildGlycine.
static Residue	buildHistidine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildHistidine.
static Residue	buildIsoleucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildIsoleucine.
static Residue	buildLeucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLeucine.
static Residue	buildLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLysine.
static Residue	buildMethionine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildMethionine.
static Residue	buildNeutralAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralAsparticAcid.
static Residue	buildNeutralGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralGlutamicAcid.
static Residue	buildNeutralHistidineD(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineD.
static Residue	buildNeutralHistidineE(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineE.
static Residue	buildOrnithine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildOrnithine.
static Residue	buildPCA(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPCA.
static Residue	buildPhenylalanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPhenylalanine.
static Residue	buildProline(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildProline.
static Residue	buildSerine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildSerine.
static Residue	buildThreonine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildThreonine.
static Residue	buildTryptophan(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildTryptophan.
static Residue	buildTwoProtonAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonAsparticAcid.
static Residue	buildTwoProtonGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonGlutamicAcid.
static Residue	buildTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTyrosine.
static Residue	buildValine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildValine.
static void	copyResidue(Residue fromResidue, Residue toResidue)	copyResidue.
static AminoAcidUtils.AminoAcid3	getAminoAcid(String residueName)	getAminoAcid.
static AminoAcidUtils.AminoAcid3	getAminoAcid3From1(String residueName)	This method takes a one letter amino acid code and converts it to a three letter amino acid code.
static int	getAminoAcidNumber(String residueName)	getAminoAcidNumber.
static String[]	getNames(Class<? extends Enum<?>> e)	Turn an Enum into String array.
static void	removeH1_H2_H3(AminoAcidUtils.AminoAcid3 aminoAcid, Residue residue)	Only the first nitrogen should have H1, H2 and H3 atoms, unless it's an NME cap.
static void	removeOXT_OT2(Residue residue)	Only the last residue in a chain should have an OXT/OT2 atom.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

AAPATTERN

public static final int[] AAPATTERN

Repeating atomic numbers of an amino acid chain.

AA1toAA3

public static final HashMap<AminoAcidUtils.AminoAcid1,AminoAcidUtils.AminoAcid3> AA1toAA3

Constant AA1toAA3

aminoAcid1List

public static final List<AminoAcidUtils.AminoAcid1> aminoAcid1List

List of values from the AminoAcid1 enum.

aminoAcidList

public static final List<AminoAcidUtils.AminoAcid3> aminoAcidList

Constant aminoAcidList

sidechainStoichiometry

public static final HashMap<String,String> sidechainStoichiometry

Stoichiometry of side chains can be used for identification, accept for a couple cases:

1. Proline and Valine

2. (Iso)Leucine

3. DNA Guanine/RNA Adenine.

This Hashtable returns the 3-letter name for amino acids, a single character for nucleic acids, or an integer indicating a special case.

AA_N

public static final int[][] AA_N

Biotype keys for amino acid backbone atom types. These are consistent with parameter files from TINKER v. 6.1 (June 2012).
xType[0][..] are for N-terminal residues.
xType[1][..] are mid-chain residues.
xType[2][..] are for C-terminal residues.

GLY ALA VAL LEU ILE SER THR CYS CYX CYD PRO PHE TYR TYD TRP HIS HID HIE ASP ASH ASD ASN GLU GLH GLD GLN MET LYS LYD ARG ORN AIB PCA H2N FOR ACE COH NH2 NME UNK

AA_CA

public static final int[][] AA_CA

Constant AA_CA

GLY ALA VAL LEU ILE SER THR CYS CYX CYD PRO PHE TYR TYD TRP HIS HID HIE ASP ASH ASD ASN GLU GLH GLD GLN MET LYS LYD ARG ORN AIB PCA H2N FOR ACE COH NH2 NME UNK

AA_C

public static final int[][] AA_C

Constant AA_C

GLY ALA VAL LEU ILE SER THR CYS CYX CYD PRO PHE TYR TYD TRP HIS HID HIE ASP ASH ASD ASN GLU GLH GLD GLN MET LYS LYD ARG ORN AIB PCA H2N FOR ACE COH NH2 NME UNK

AA_HN

public static final int[][] AA_HN

Constant AA_HN

GLY ALA VAL LEU ILE SER THR CYS CYX CYD PRO PHE TYR TYD TRP HIS HID HIE ASP ASH ASD ASN GLU GLH GLD GLN MET LYS LYD ARG ORN AIB PCA H2N FOR ACE COH NH2 NME UNK

AA_O

public static final int[][] AA_O

Constant AA_O

GLY ALA VAL LEU ILE SER THR CYS CYX CYD PRO PHE TYR TYD TRP HIS HID HIE ASP ASH ASD ASN GLU GLH GLD GLN MET LYS LYD ARG ORN AIB PCA H2N FOR ACE COH NH2 NME UNK

AA_HA

public static final int[][] AA_HA

Constant AA_HA

GLY ALA VAL LEU ILE SER THR CYS CYX CYD PRO PHE TYR TYD TRP HIS HID HIE ASP ASH ASD ASN GLU GLH GLD GLN MET LYS LYD ARG ORN AIB PCA H2N FOR ACE COH NH2 NME UNK

AA_CB

public static final int[] AA_CB

Constant AA_CB

GLY ALA VAL LEU ILE SER THR CYS CYX CYD PRO PHE TYR TYD TRP HIS HID HIE ASP ASH ASD ASN GLU GLH GLD GLN MET LYS LYD ARG ORN AIB PCA H2N FOR ACE COH NH2 NME UNK

Method Details

getNames

public static String[] getNames(Class<? extends Enum<?>> e)

Turn an Enum into String array.

Parameters:

e - The enum class.

Returns:

A String array with all the enum values.

assignAminoAcidAtomTypes

public static void assignAminoAcidAtomTypes(List<Residue> residues,
 ForceField forceField,
 List<Bond> bondList)
                                     throws BondedUtils.MissingHeavyAtomException,
BondedUtils.MissingAtomTypeException

Assign atom types to an amino acid polymer.

Parameters:

residues - The residues to assign atom types to.

forceField - The ForceField to apply.

bondList - Created bonds are added to this List.

Throws:

BondedUtils.MissingHeavyAtomException - A needed heavy atom was not found.

BondedUtils.MissingAtomTypeException - An atom type could not be found.

Since:

1.0

assignAminoAcidAtomTypes

public static void assignAminoAcidAtomTypes(Residue residue,
 Residue previousResidue,
 Residue nextResidue,
 ForceField forceField,
 List<Bond> bondList)
                                     throws BondedUtils.MissingHeavyAtomException,
BondedUtils.MissingAtomTypeException

assignAminoAcidAtomTypes.

Parameters:

residue - a Residue object.

previousResidue - a Residue object.

nextResidue - a Residue object.

forceField - a ForceField object.

bondList - a List object.

Throws:

BondedUtils.MissingHeavyAtomException - if any.

BondedUtils.MissingAtomTypeException - if any.

buildAIB

public static Residue buildAIB(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildAIB.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildGlycine

public static Residue buildGlycine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 AminoAcidUtils.ResiduePosition position,
 ForceField ff,
 List<Bond> bonds)

buildGlycine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

position - AminoAcidUtils.ResiduePosition object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildAlanine

public static Residue buildAlanine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildAlanine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildArginine

public static Residue buildArginine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildArginine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildAsparagine

public static Residue buildAsparagine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildAsparagine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildAspartate

public static Residue buildAspartate(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildAspartate.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildCysteine

public static Residue buildCysteine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildCysteine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildCystine

public static Residue buildCystine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildCystine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildDeprotonatedCysteine

public static Residue buildDeprotonatedCysteine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildDeprotonatedCysteine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildDeprotonatedLysine

public static Residue buildDeprotonatedLysine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildDeprotonatedLysine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildDeprotonatedTyrosine

public static Residue buildDeprotonatedTyrosine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildDeprotonatedTyrosine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildGlutamate

public static Residue buildGlutamate(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildGlutamate.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildGlutamine

public static Residue buildGlutamine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildGlutamine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildHistidine

public static Residue buildHistidine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildHistidine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildIsoleucine

public static Residue buildIsoleucine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildIsoleucine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildLeucine

public static Residue buildLeucine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildLeucine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildLysine

public static Residue buildLysine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildLysine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildMethionine

public static Residue buildMethionine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bond)

buildMethionine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bond - a List object.

Returns:

a Residue object.

buildNeutralAsparticAcid

public static Residue buildNeutralAsparticAcid(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildNeutralAsparticAcid.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildTwoProtonAsparticAcid

public static Residue buildTwoProtonAsparticAcid(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildTwoProtonAsparticAcid.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildNeutralGlutamicAcid

public static Residue buildNeutralGlutamicAcid(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildNeutralGlutamicAcid.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildTwoProtonGlutamicAcid

public static Residue buildTwoProtonGlutamicAcid(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildTwoProtonGlutamicAcid.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildNeutralHistidineD

public static Residue buildNeutralHistidineD(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildNeutralHistidineD.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildNeutralHistidineE

public static Residue buildNeutralHistidineE(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildNeutralHistidineE.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildOrnithine

public static Residue buildOrnithine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildOrnithine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildPCA

public static Residue buildPCA(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildPCA.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildPhenylalanine

public static Residue buildPhenylalanine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildPhenylalanine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildProline

public static Residue buildProline(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 AminoAcidUtils.ResiduePosition position,
 ForceField ff,
 List<Bond> bonds)

buildProline.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

position - a AminoAcidUtils.ResiduePosition object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildSerine

public static Residue buildSerine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildSerine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildThreonine

public static Residue buildThreonine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildThreonine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildTryptophan

public static Residue buildTryptophan(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bond)

buildTryptophan.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bond - a List object.

Returns:

a Residue object.

buildTyrosine

public static Residue buildTyrosine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildTyrosine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

buildValine

public static Residue buildValine(Residue res,
 Atom CA,
 Atom N,
 Atom C,
 ForceField ff,
 List<Bond> bonds)

buildValine.

Parameters:

res - a Residue object.

CA - a Atom object.

N - a Atom object.

C - a Atom object.

ff - a ForceField object.

bonds - a List object.

Returns:

a Residue object.

copyResidue

public static void copyResidue(Residue fromResidue,
 Residue toResidue)

copyResidue.

Parameters:

fromResidue - a Residue object.

toResidue - a Residue object.

removeH1_H2_H3

public static void removeH1_H2_H3(AminoAcidUtils.AminoAcid3 aminoAcid,
 Residue residue)

Only the first nitrogen should have H1, H2 and H3 atoms, unless it's an NME cap.

Parameters:

aminoAcid - 3-letter amino acid name.

residue - the amino acid Residue.

removeOXT_OT2

public static void removeOXT_OT2(Residue residue)

Only the last residue in a chain should have an OXT/OT2 atom.

Parameters:

residue - the amino acid residue.

getAminoAcid

public static AminoAcidUtils.AminoAcid3 getAminoAcid(String residueName)

getAminoAcid.

Parameters:

residueName - a String object.

Returns:

a AminoAcidUtils.AminoAcid3 object.

getAminoAcid3From1

public static AminoAcidUtils.AminoAcid3 getAminoAcid3From1(String residueName)

This method takes a one letter amino acid code and converts it to a three letter amino acid code. This method relies on the AminoAcid1 and AminoAcid3 enums having amino acids in exactly the same order.

Parameters:

residueName - The one letter amino acid code.

Returns:

The three letter amino acid code.

getAminoAcidNumber

public static int getAminoAcidNumber(String residueName)

getAminoAcidNumber.

Parameters:

residueName - a String object.

Returns:

The index of the amino acid in the aminoAcidlist.