public interface IAtom extends IAtomType
IAtomType.Hybridization
Ac, Ag, Al, Am, Ar, As, At, Au, B, Ba, Be, Bh, Bi, Bk, Br, C, Ca, Cd, Ce, Cf, Cl, Cm, Cn, Co, Cr, Cs, Cu, Db, Ds, Dy, Er, Es, Eu, F, Fe, Fl, Fm, Fr, Ga, Gd, Ge, H, He, Hf, Hg, Ho, Hs, I, In, Ir, K, Kr, La, Li, Lr, Lu, Lv, Mc, Md, Mg, Mn, Mo, Mt, N, Na, Nb, Nd, Ne, Nh, Ni, No, Np, O, Og, Os, P, Pa, Pb, Pd, Pm, Po, Pr, Pt, Pu, Ra, Rb, Re, Rf, Rg, Rh, Rn, Ru, S, Sb, Sc, Se, Sg, Si, Sm, Sn, Sr, Ta, Tb, Tc, Te, Th, Ti, Tl, Tm, Ts, U, V, W, Wildcard, Xe, Y, Yb, Zn, Zr
Modifier and Type | Method and Description |
---|---|
Iterable<IBond> |
bonds()
Returns the bonds connected to this atom.
|
IAtom |
clone()
Returns a deep clone of this IChemObject.
|
IBond |
getBond(IAtom atom)
Returns the bond connecting 'this' atom to the provided atom.
|
int |
getBondCount()
Get the number of explicit bonds connected to this atom.
|
Double |
getCharge()
Returns the partial charge of this atom.
|
IAtomContainer |
getContainer()
Access the
IAtomContainer of which this atom is a member of. |
javax.vecmath.Point3d |
getFractionalPoint3d()
Returns a point specifying the location of this
atom in a Crystal unit cell.
|
Integer |
getImplicitHydrogenCount()
Returns the implicit hydrogen count of this atom.
|
int |
getIndex()
Acces the index of an atom in the context of an
IAtomContainer . |
int |
getMapIdx()
Access the map index for this atom.
|
javax.vecmath.Point2d |
getPoint2d()
Returns a point specifying the location of this
atom in a 2D space.
|
javax.vecmath.Point3d |
getPoint3d()
Returns a point specifying the location of this
atom in a 3D space.
|
Integer |
getStereoParity()
Deprecated.
use
IStereoElement s for storing stereochemistry |
boolean |
isAromatic()
Access whether this atom has been marked as aromatic.
|
boolean |
isInRing()
Access whether this atom has been flagged as in a ring.
|
void |
setCharge(Double charge)
Sets the partial charge of this atom.
|
void |
setFractionalPoint3d(javax.vecmath.Point3d point3d)
Sets a point specifying the location of this
atom in a Crystal unit cell.
|
void |
setImplicitHydrogenCount(Integer hydrogenCount)
Sets the implicit hydrogen count of this atom.
|
void |
setIsAromatic(boolean arom)
Mark this atom as being aromatic.
|
void |
setIsInRing(boolean ring)
Mark this atom as being in a ring.
|
void |
setMapIdx(int mapidx)
Set the map index for this atom.
|
void |
setPoint2d(javax.vecmath.Point2d point2d)
Sets a point specifying the location of this
atom in a 2D space.
|
void |
setPoint3d(javax.vecmath.Point3d point3d)
Sets a point specifying the location of this
atom in 3D space.
|
void |
setStereoParity(Integer stereoParity)
Deprecated.
use
IStereoElement s for storing stereochemistry |
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
getBuilder
void setCharge(Double charge)
charge
- The partial chargegetCharge()
Double getCharge()
setCharge(java.lang.Double)
void setImplicitHydrogenCount(Integer hydrogenCount)
hydrogenCount
- The number of hydrogen atoms bonded to this atom.getImplicitHydrogenCount()
Integer getImplicitHydrogenCount()
setImplicitHydrogenCount(java.lang.Integer)
void setPoint2d(javax.vecmath.Point2d point2d)
point2d
- A point in a 2D planegetPoint2d()
void setPoint3d(javax.vecmath.Point3d point3d)
point3d
- A point in a 3-dimensional spacegetPoint3d()
void setFractionalPoint3d(javax.vecmath.Point3d point3d)
point3d
- A point in a 3d fractional unit cell spacegetFractionalPoint3d()
,
Crystal
@Deprecated void setStereoParity(Integer stereoParity)
IStereoElement
s for storing stereochemistrystereoParity
- The stereo parity for this atomfor predefined values.
,
getStereoParity()
javax.vecmath.Point2d getPoint2d()
setPoint2d(javax.vecmath.Point2d)
javax.vecmath.Point3d getPoint3d()
setPoint3d(javax.vecmath.Point3d)
javax.vecmath.Point3d getFractionalPoint3d()
setFractionalPoint3d(javax.vecmath.Point3d)
,
for predefined values.
@Deprecated Integer getStereoParity()
IStereoElement
s for storing stereochemistryCDKConstants
,
setStereoParity(java.lang.Integer)
IAtomContainer getContainer()
IAtomContainer
of which this atom is a member of. Because atoms
can be in multiple molecules this method will only work if the atom has been accessed
in the context of an IAtomContainer
, for example:
IAtomContainer mol = new AtomContainer();
IAtom atom = new Atom(6);
atom.getContainer(); // null
mol.add(atom);
atom.getContainer(); // still null
mol.getAtom(0).getContainer(); // not-null, returns 'mol'
int getIndex()
IAtomContainer
. If the
index is not known, < 0 is returned.Iterable<IBond> bonds()
getIndex()
returns < 0 or getContainer()
returns null.
IAtom atom = ...;
if (atom.getIndex() >= 0) {
for (IBond bond : atom.bonds()) {
}
}
if (atom.getContainer() != null) {
for (IBond bond : atom.bonds()) {
}
}
IAtomContainer mol = ...;
// guaranteed not throw an exception
for (IBond bond : mol.getAtom(i).bonds()) {
}
UnsupportedOperationException
- thrown if the bonds are not knownint getBondCount()
IBond getBond(IAtom atom)
atom
- the other atomUnsupportedOperationException
- thrown if the bonds are not knownboolean isAromatic()
IChemObject.getFlag(int)
,
Aromaticity
void setIsAromatic(boolean arom)
arom
- aromatic statusIChemObject.setFlag(int, boolean)
boolean isInRing()
IChemObject.getFlag(int)
,
RingSearch
void setIsInRing(boolean ring)
ring
- ring statusIChemObject.setFlag(int, boolean)
int getMapIdx()
void setMapIdx(int mapidx)
mapidx
- the new map indexIAtom clone() throws CloneNotSupportedException
clone
in interface IChemObject
CloneNotSupportedException
- if the IChemObject cannot be clonedCopyright © 2021. All rights reserved.