public class Atom
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
Bond[] |
bonds |
javax.vecmath.Point3f |
position |
Constructor and Description |
---|
Atom(Atom_3D originalAtom,
Molecule parentMolecule,
int index,
MembranePackingAlgorithm algo)
!NOT MEANT TO BE USED BY ALGORITHM DEVELOPERS!
|
Modifier and Type | Method and Description |
---|---|
Bond[] |
getAllInternalBonds()
Returns a list of all bond objects associated with this atom.
|
float |
getAtomicMass()
Returns the atomic mass of this atom.
|
java.lang.String |
getAtomName()
Returns the name of this atom in its pdb-file entry
|
java.lang.String |
getChainID()
Returns the id of the atom's peptide chain as specifed in its pdb-file
entry
|
java.lang.String |
getCharge()
Returns the fieldcharge as specifed in the pdb-file entry
|
float |
getCovalentRadiusInAngstrom()
Returns the determined covalent radius of this atom
|
java.lang.String |
getElement()
Returns the field element as specifed in the pdb-file entry
|
double |
getEnergy()
Returns the stored energy value
|
java.lang.String |
getOccupancy()
Returns the field occupancy as specifed in the pdb-file entry
|
java.lang.String |
getParameterKey()
Returns the string that serves as a possible key for parameters.
|
Molecule |
getParentalMolecule()
Returns the molecule instance that hosts this atom
|
java.lang.String |
getParticleID()
Returns the particle identifier of this particle
|
javax.vecmath.Point3f |
getPosition()
Gets a copy of the atom's current position inside the molecule
|
java.lang.String |
getRecordName()
Returns the record name of this atom's pdb-file entry
|
java.lang.String |
getResidueName()
Returns the name of the atom's residue as specifed in its pdb-file entry
|
java.lang.String |
getTempFactor()
Returns the field tempfactor as specifed in the pdb-file entry
|
java.lang.Object |
getUserData()
Returns the object that has been stored by setUserData()
|
float |
getVanDerWaalsRadiusInAngstrom()
Returns the determined Van-der-Waals-radius of this atom
|
boolean |
isCoarseGrainParticle()
Determines, wether this atom is actually a coarse-grain-particle
|
void |
setEnergy(double en)
Can be used to store an energy value for this atom
|
void |
setPosition(javax.vecmath.Point3f position)
Sets and applies a new position to this atom.
|
void |
setUserData(java.lang.Object userData)
Can be used to store any Object to associate it with this atom
|
public javax.vecmath.Point3f position
public Bond[] bonds
public Atom(Atom_3D originalAtom, Molecule parentMolecule, int index, MembranePackingAlgorithm algo)
public void setPosition(javax.vecmath.Point3f position)
position
- the new absolute position of the atom, measured from the
molecule's center pointpublic javax.vecmath.Point3f getPosition()
public Molecule getParentalMolecule()
public java.lang.String getRecordName()
public java.lang.String getAtomName()
public java.lang.String getResidueName()
public java.lang.String getChainID()
public java.lang.String getOccupancy()
public java.lang.String getTempFactor()
public java.lang.String getElement()
public java.lang.String getCharge()
public float getCovalentRadiusInAngstrom()
public float getVanDerWaalsRadiusInAngstrom()
public Bond[] getAllInternalBonds()
public boolean isCoarseGrainParticle()
public java.lang.String getParticleID()
public java.lang.String getParameterKey()
public void setEnergy(double en)
en
- the energy value to storepublic double getEnergy()
public void setUserData(java.lang.Object userData)
userData
- any Objectpublic java.lang.Object getUserData()
public float getAtomicMass()