Package ffx.potential.bonded

Class NucleicAcidUtils

java.lang.Object

ffx.potential.bonded.NucleicAcidUtils

public class NucleicAcidUtils
extends Object

Utilities for creating Nucleic Acid residues.

Since:

1.0

Author:

Michael Schnieders

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	NucleicAcidUtils.NA	The 4 RNA bases, 4 DNA bases, and mono- di- and triphosphate.
static enum	NucleicAcidUtils.NucleicAcid1
static enum	NucleicAcidUtils.NucleicAcid3	Since enumeration values must start with a letter, an 'M' is added to modified bases whose IUPAC name starts with an integer.

Field Summary

Fields

Modifier and Type	Field	Description
static final int[]	NA_C1	Constant NA_C1
static final int[]	NA_C2	Constant NA_C2
static final int[]	NA_C3	Constant NA_C3
static final int[]	NA_C4	Constant NA_C4
static final int[]	NA_C5	Constant NA_C5
static final int[]	NA_H1	Constant NA_H1
static final int[]	NA_H21	Constant NA_H21
static final int[]	NA_H22	Constant NA_H22
static final int[]	NA_H3	Constant NA_H3
static final int[]	NA_H4	Constant NA_H4
static final int[]	NA_H51	Constant NA_H51
static final int[]	NA_H52	Constant NA_H52
static final int[]	NA_HO3T	Should be NA_HO3' (' replaced by T in the name).
static final int[]	NA_HO5T	Should be NA_HO5' (' replaced by T in the name).
static final int[]	NA_O2	Constant NA_O2
static final int[]	NA_O3	Constant NA_O3
static final int[]	NA_O4	Constant NA_O4
static final int[]	NA_O5	Biotype keys for nucleic acid backbone atom types.
static final int[]	NA_OP	Constant NA_OP
static final int[]	NA_P	Constant NA_P
static final HashMap<NucleicAcidUtils.NucleicAcid1,NucleicAcidUtils.NucleicAcid3>	NA1toNA3	Constant NA1toNA3
static final int[]	NAPATTERN	Repeating atomic numbers of a nucleic acid chain.
static final List<NucleicAcidUtils.NucleicAcid3>	nucleicAcidList	Constant nucleicAcidList

Constructor Summary

Constructors

Constructor	Description
NucleicAcidUtils()

Method Summary

Modifier and Type	Method	Description
static void	assignNucleicAcidAtomTypes(List<Residue> residues, ForceField forceField, List<Bond> bondList)	Assign atom types for a nucleic acid polymer.
static int	getNucleicAcidNumber(String residueName)	getNucleicAcidNumber.

Methods inherited from class java.lang.Object

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

Field Details

NA_O5

public static final int[] NA_O5

Biotype keys for nucleic acid backbone atom types. These are consistent with parameter files from TINKER v. 6.1 (June 2012).

NA_C5

public static final int[] NA_C5

Constant NA_C5

NA_H51

public static final int[] NA_H51

Constant NA_H51

NA_H52

public static final int[] NA_H52

Constant NA_H52

NA_C4

public static final int[] NA_C4

Constant NA_C4

NA_H4

public static final int[] NA_H4

Constant NA_H4

NA_O4

public static final int[] NA_O4

Constant NA_O4

NA_C1

public static final int[] NA_C1

Constant NA_C1

NA_H1

public static final int[] NA_H1

Constant NA_H1

NA_C3

public static final int[] NA_C3

Constant NA_C3

NA_H3

public static final int[] NA_H3

Constant NA_H3

NA_C2

public static final int[] NA_C2

Constant NA_C2

NA_H21

public static final int[] NA_H21

Constant NA_H21

NA_O2

public static final int[] NA_O2

Constant NA_O2

NA_H22

public static final int[] NA_H22

Constant NA_H22

NA_O3

public static final int[] NA_O3

Constant NA_O3

NA_P

public static final int[] NA_P

Constant NA_P

NA_OP

public static final int[] NA_OP

Constant NA_OP

NA_HO5T

public static final int[] NA_HO5T

Should be NA_HO5' (' replaced by T in the name).

Constant NA_HO5T

NA_HO3T

public static final int[] NA_HO3T

Should be NA_HO3' (' replaced by T in the name).

Constant NA_HO3T

nucleicAcidList

public static final List<NucleicAcidUtils.NucleicAcid3> nucleicAcidList

Constant nucleicAcidList

NA1toNA3

public static final HashMap<NucleicAcidUtils.NucleicAcid1,NucleicAcidUtils.NucleicAcid3> NA1toNA3

Constant NA1toNA3

NAPATTERN

public static final int[] NAPATTERN

Repeating atomic numbers of a nucleic acid chain.

Constructor Details

NucleicAcidUtils

public NucleicAcidUtils()

Method Details

assignNucleicAcidAtomTypes

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

Assign atom types for a nucleic acid polymer.

Parameters:

residues - A list of residues that form the nucleic acid polymer.

forceField - The ForceField in use.

bondList - A list of created bonds.

Throws:

BondedUtils.MissingHeavyAtomException - if any.

BondedUtils.MissingAtomTypeException - if any.

getNucleicAcidNumber

public static int getNucleicAcidNumber(String residueName)

getNucleicAcidNumber.

Parameters:

residueName - a String object.

Returns:

The index of the nucleic acid in the nucleicAcidList.