starfish.chemistry.io
Class PDB

java.lang.Object
  starfish.chemistry.io.PDB

public class PDB
extends java.lang.Object

Constructor Summary

PDB()

Method Summary

boolean	addResidue(tcl.lang.Interp interp, java.lang.String fileName, Residue residue, java.lang.String coordSetName)
static void	capPolymer(Polymer polymer)
int	checkPDBType(tcl.lang.Interp interp, java.lang.String fileName)
static java.lang.String	getReslibDir()
static boolean	isIUPACMode()
void	Nv_ReadPSF(tcl.lang.Interp interp, java.lang.String fileName)
void	readPDB(tcl.lang.Interp interp, java.lang.String fileName, boolean writeAble)
void	readPDBSeq(tcl.lang.Interp interp, java.lang.String fileName)
void	readPDBXYZ(tcl.lang.Interp interp, java.lang.String fileName, int structureNumber)
void	readSD(tcl.lang.Interp interp, java.lang.String fileName, java.lang.String fileContent)
void	readSDResidue(tcl.lang.Interp interp, java.lang.String fileName, java.lang.String fileContent, Molecule molecule, java.lang.String coordSetName)
void	readSeq(tcl.lang.Interp interp, java.lang.String polymerFile, tcl.lang.TclObject seqName, boolean fileMode)

Methods inherited from class java.lang.Object

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

Constructor Detail

PDB

public PDB()

Method Detail

isIUPACMode

public static boolean isIUPACMode()

getReslibDir

public static java.lang.String getReslibDir()

readPDB

public void readPDB(tcl.lang.Interp interp,
                    java.lang.String fileName,
                    boolean writeAble)
             throws tcl.lang.TclException

Throws:

tcl.lang.TclException

Nv_ReadPSF

public void Nv_ReadPSF(tcl.lang.Interp interp,
                       java.lang.String fileName)
                throws tcl.lang.TclException

Throws:

tcl.lang.TclException

readSD

public void readSD(tcl.lang.Interp interp,
                   java.lang.String fileName,
                   java.lang.String fileContent)
            throws tcl.lang.TclException

Throws:

tcl.lang.TclException

readSDResidue

public void readSDResidue(tcl.lang.Interp interp,
                          java.lang.String fileName,
                          java.lang.String fileContent,
                          Molecule molecule,
                          java.lang.String coordSetName)
                   throws tcl.lang.TclException

Throws:

tcl.lang.TclException

capPolymer

public static void capPolymer(Polymer polymer)

readSeq

public void readSeq(tcl.lang.Interp interp,
                    java.lang.String polymerFile,
                    tcl.lang.TclObject seqName,
                    boolean fileMode)
             throws tcl.lang.TclException

Throws:

tcl.lang.TclException

readPDBSeq

public void readPDBSeq(tcl.lang.Interp interp,
                       java.lang.String fileName)
                throws tcl.lang.TclException

Throws:

tcl.lang.TclException

checkPDBType

public int checkPDBType(tcl.lang.Interp interp,
                        java.lang.String fileName)
                 throws tcl.lang.TclException

Throws:

tcl.lang.TclException

readPDBXYZ

public void readPDBXYZ(tcl.lang.Interp interp,
                       java.lang.String fileName,
                       int structureNumber)
                throws tcl.lang.TclException

Throws:

tcl.lang.TclException

addResidue

public boolean addResidue(tcl.lang.Interp interp,
                          java.lang.String fileName,
                          Residue residue,
                          java.lang.String coordSetName)
                   throws tcl.lang.TclException

Throws:

tcl.lang.TclException