scripps.mol_data
Class ChemUtil

java.lang.Object
  |
  +--scripps.mol_data.ChemUtil

public class ChemUtil

extends java.lang.Object

Field Summary

static int	ATOM
static int	HETATM
static java.lang.String	metalsRE
static java.lang.String	waterRE

Constructor Summary

ChemUtil()

Method Summary

static ResidueSet	filter(ResidueSet a, java.lang.String[] resnumber, java.lang.String[] resname, java.lang.String[] reschain)
static AtomSet	filterByName(AtomSet a, java.lang.String[] atomname)
static ResidueSet	filterByName(ResidueSet a, java.lang.String[] resname)
static ResidueSet	filterByNumber(ResidueSet a, java.lang.String[] resnumber)
static AtomSet	filterByRE(AtomSet aset, java.lang.String sRE)
static AtomSet	filterByRecType(AtomSet aset, int atomType)
static AtomSet	getAtoms(AtomSet aSet)
static AtomSet	getHetAtoms(AtomSet aSet)
static AtomSet	getLigAtoms(Residue r)
static AtomSet	getMetals(AtomSet aSet)
static boolean	hasMetals(Residue res)
static boolean	isLigAtom(Atom a)
static boolean	isMetal(Atom a)
static boolean	isWater(Residue r)

Methods inherited from class java.lang.Object

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

Field Detail

metalsRE

public static java.lang.String metalsRE

waterRE

public static java.lang.String waterRE

ATOM

public static final int ATOM

See Also:

Constant Field Values

HETATM

public static final int HETATM

See Also:

Constant Field Values

Constructor Detail

ChemUtil

public ChemUtil()

Method Detail

filterByRE

public static AtomSet filterByRE(AtomSet aset,
                                 java.lang.String sRE)

isMetal

public static boolean isMetal(Atom a)

getLigAtoms

public static AtomSet getLigAtoms(Residue r)

isLigAtom

public static boolean isLigAtom(Atom a)

isWater

public static boolean isWater(Residue r)

getMetals

public static AtomSet getMetals(AtomSet aSet)

hasMetals

public static boolean hasMetals(Residue res)

getHetAtoms

public static AtomSet getHetAtoms(AtomSet aSet)

getAtoms

public static AtomSet getAtoms(AtomSet aSet)

filterByRecType

public static AtomSet filterByRecType(AtomSet aset,
                                      int atomType)

filterByName

public static ResidueSet filterByName(ResidueSet a,
                                      java.lang.String[] resname)

filterByNumber

public static ResidueSet filterByNumber(ResidueSet a,
                                        java.lang.String[] resnumber)

filter

public static ResidueSet filter(ResidueSet a,
                                java.lang.String[] resnumber,
                                java.lang.String[] resname,
                                java.lang.String[] reschain)

filterByName

public static AtomSet filterByName(AtomSet a,
                                   java.lang.String[] atomname)