Class Molecule

java.lang.Object
  |
  +--Molecule

public class Molecule

extends java.lang.Object

Molecule.java class for storing information about a molecule read in from a pdb file

Nested Class Summary

class

Molecule.Atom inner class Atom for use in Molecule

Constructor Summary

Molecule()
Constructor

Method Summary

void	addAtom(int serial, java.lang.String name, java.lang.String loc, java.lang.String residue, java.lang.String chain, java.lang.String resid, java.lang.String insertion, float occ, float temp, java.lang.String segmentId, java.lang.String symbol, java.lang.String charge) Adds an Atom to this Molecule
void	addAtom(Molecule.Atom newAtom) Add an Atom to this Molecule
void	addNewPosition(int atomIndex, float[] position) Adds a new position for a new time index for a specified Atom
float	atomRadius(int index) Gets the radius for a specified Atom
static float	atomRadius(java.lang.String atomName) Gets a radius for an atom based on its name gotten from the pdb.
void	calc_minmax() Calculates the minimum and maximum x, y, and z coordinates Stores the values in m_fMinX, m_fMaxX, m_fMinY, m_fMaxY, m_fMinZ, m_fMaxZ
void	createBondList() Creates the neighbor list, listing the neighbors of each atom for drawing bonds It creates a 2D array, where each element contains an array of integers that correspond to the indeces of its neighbors and stores it in m_iaBondList
void	createCAList() Creates a list of atom indeces that are all the C-Alpha (CA) atoms in the molecule Stores result in m_iaCAList
Molecule.Atom	findAtomInResidue(java.lang.String name, int resId) Gets the atom given its name and residue id
java.util.Vector	getAllPositions() Gets all the coordinates for the Atoms in this Molecule, for all times
Molecule.Atom	getAtom(int index) Gets the atom at a specific index
static char	getAtomCharacter(java.lang.String name) Gets a character representing this atom, based on the String name gotten from the pdb.
int[][]	getBondList() Gets the list of bonds between atoms
float[]	getCoords() Gets all the coordinates for each Atom in this Molecule for time 0
float[]	getCoords(int time) Gets all the coordinates for each Atom in this Molecule for a specified timestep
float	getMaxX() Gets maximum x coordinate for this Molecule
float	getMaxY() Gets maximum y coordinate for this Molecule
float	getMaxZ() Gets maximum z coordinate for this Molecule
float	getMinX() Gets minimum x coordinate for this Molecule
float	getMinY() Gets minimum y coordinate for this Molecule
float	getMinZ() Gets minimum z coordinate for this Molecule
float[]	getPosition(int atomIndex) gets the coordinates of an atom position for time 0
float[]	getPosition(int atomIndex, int timeIndex) gets the coordinates of an atom position for a specified time index
int	numAtoms() Returns the number of atoms in the molecule
void	print() Prints information for the Molecule: the serial, name, residue id, and (x,y,z) coordinate for each Atom
void	setPositions(java.util.Vector positions) Sets the coordinates for the Atoms in the Molecule

Methods inherited from class java.lang.Object

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

Constructor Detail

Molecule

public Molecule()

Constructor

Method Detail

numAtoms

public int numAtoms()

Returns the number of atoms in the molecule

addAtom

public void addAtom(Molecule.Atom newAtom)

Add an Atom to this Molecule

getAtom

public Molecule.Atom getAtom(int index)

Gets the atom at a specific index

Parameters:

index - the index for the atom

Returns:

the Atom in the Molecule with the specified index

getCoords

public float[] getCoords()

Gets all the coordinates for each Atom in this Molecule for time 0

Returns:

a float array of the (x,y,z) coordinates for each Atom in the Molecule, i.e. [x1, y1, z1, x2, y2, z2...]

getCoords

public float[] getCoords(int time)

Gets all the coordinates for each Atom in this Molecule for a specified timestep

Parameters:

time - the time position to get the coordinates for

Returns:

a float array of the (x,y,z) coordinates for each Atom in the Molecule, i.e. [x1, y1, z1, x2, y2, z2...]

addAtom

public void addAtom(int serial,
                    java.lang.String name,
                    java.lang.String loc,
                    java.lang.String residue,
                    java.lang.String chain,
                    java.lang.String resid,
                    java.lang.String insertion,
                    float occ,
                    float temp,
                    java.lang.String segmentId,
                    java.lang.String symbol,
                    java.lang.String charge)

Adds an Atom to this Molecule

Parameters:

serial - the serial number

name - the Atom name

loc - the location of the Atom

residue - the residue the Atom is in

chain - the chain the Atom is in

resid - the id for the residue the Atom is in

insertion - the insertion code

occ - the occupancy of the Atom

temp - the temperature of the Atom

segmentId - the id for the segment the Atom is in

symbol - the atomic symbol for the Atom

charge - the charge of the Atom

setPositions

public void setPositions(java.util.Vector positions)

Sets the coordinates for the Atoms in the Molecule

Parameters:

positions - a Vector containing the (x,y,z) coordinates for each Atom for each time index

getAllPositions

public java.util.Vector getAllPositions()

Gets all the coordinates for the Atoms in this Molecule, for all times

Returns:

a Vector containing the (x,y,z) coordinates for each Atom for each time index

getPosition

public float[] getPosition(int atomIndex,
                           int timeIndex)

gets the coordinates of an atom position for a specified time index

Parameters:

atomIndex - the index of the atom in this Molecule's atom vector

timeIndex - the index of the time position for this atom

Returns:

a float array of the x,y,z coordinate for this atom and time

getPosition

public float[] getPosition(int atomIndex)

gets the coordinates of an atom position for time 0

Parameters:

atomIndex - the index of the atom in this Molecule's atom vector

Returns:

a float array of the x,y,z coordinate for this atom and time

calc_minmax

public void calc_minmax()

Calculates the minimum and maximum x, y, and z coordinates Stores the values in m_fMinX, m_fMaxX, m_fMinY, m_fMaxY, m_fMinZ, m_fMaxZ

getMinX

public float getMinX()

Gets minimum x coordinate for this Molecule

getMaxX

public float getMaxX()

Gets maximum x coordinate for this Molecule

getMinY

public float getMinY()

Gets minimum y coordinate for this Molecule

getMaxY

public float getMaxY()

Gets maximum y coordinate for this Molecule

getMinZ

public float getMinZ()

Gets minimum z coordinate for this Molecule

getMaxZ

public float getMaxZ()

Gets maximum z coordinate for this Molecule

addNewPosition

public void addNewPosition(int atomIndex,
                           float[] position)

Adds a new position for a new time index for a specified Atom

Parameters:

atomIndex - the index of the Atom to modify

position - a float array of the (x,y,z) coordinate to add

print

public void print()

Prints information for the Molecule: the serial, name, residue id, and (x,y,z) coordinate for each Atom

atomRadius

public static float atomRadius(java.lang.String atomName)

Gets a radius for an atom based on its name gotten from the pdb.

Returns:

the radius for the atom

atomRadius

public float atomRadius(int index)

Gets the radius for a specified Atom

Parameters:

index - the index of the Atom to get the radius for

Returns:

the radius of the Atom

getAtomCharacter

public static char getAtomCharacter(java.lang.String name)

Gets a character representing this atom, based on the String name gotten from the pdb.

Parameters:

name - the name of the atom gotten from the pdb file

Returns:

the character representing this Atom

createBondList

public void createBondList()

Creates the neighbor list, listing the neighbors of each atom for drawing bonds It creates a 2D array, where each element contains an array of integers that correspond to the indeces of its neighbors and stores it in m_iaBondList

getBondList

public int[][] getBondList()

Gets the list of bonds between atoms

Returns:

a 2d int array representing the neighboring Atom indeces for each Atom

createCAList

public void createCAList()

Creates a list of atom indeces that are all the C-Alpha (CA) atoms in the molecule Stores result in m_iaCAList

findAtomInResidue

public Molecule.Atom findAtomInResidue(java.lang.String name,
                                       int resId)

Gets the atom given its name and residue id

Parameters:

name - the name of the atom ("O", "CA", etc)

resId - the residue id in which you wish to find the atom

Returns:

the Atom in the molecule with the specified residue id and name