public class Conformer
extends java.lang.Object
This class contains
a pointer to the owing molecule a vector of 3D points (positions of atoms)
Modifier and Type | Field and Description |
---|---|
protected boolean |
swigCMemOwn |
Modifier | Constructor and Description |
---|---|
|
Conformer() |
|
Conformer(Conformer other) |
|
Conformer(long numAtoms) |
protected |
Conformer(long cPtr,
boolean cMemoryOwn) |
Modifier and Type | Method and Description |
---|---|
void |
canonicalizeConformer() |
void |
canonicalizeConformer(Point3D center) |
void |
canonicalizeConformer(Point3D center,
boolean normalizeCovar) |
void |
canonicalizeConformer(Point3D center,
boolean normalizeCovar,
boolean ignoreHs) |
Transform3D |
computeCanonicalTransform() |
Transform3D |
computeCanonicalTransform(Point3D center) |
Transform3D |
computeCanonicalTransform(Point3D center,
boolean normalizeCovar) |
Transform3D |
computeCanonicalTransform(Point3D center,
boolean normalizeCovar,
boolean ignoreHs) |
Point3D |
computeCentroid() |
Point3D |
computeCentroid(boolean ignoreHs) |
void |
delete() |
protected void |
finalize() |
Point3D |
getAtomPos(long atomId) |
protected static long |
getCPtr(Conformer obj) |
long |
getId() |
long |
getNumAtoms() |
ROMol |
getOwningMol() |
SWIGTYPE_p_std__vectorT_RDGeom__Point3D_t |
getPositions() |
boolean |
hasOwningMol() |
boolean |
is3D() |
void |
reserve(long size) |
void |
resize(long size)
Resize the conformer so that more atoms location can be added.
|
void |
set3D(boolean v) |
void |
setAtomPos(long atomId,
Point3D position) |
void |
setId(long id) |
void |
setSwigCMemOwn(boolean cMemoryOwn) |
void |
transformConformer(Transform3D trans) |
protected Conformer(long cPtr, boolean cMemoryOwn)
public Conformer()
public Conformer(long numAtoms)
public Conformer(Conformer other)
protected static long getCPtr(Conformer obj)
protected void finalize()
finalize
in class java.lang.Object
public void delete()
public void setSwigCMemOwn(boolean cMemoryOwn)
public void resize(long size)
Resize the conformer so that more atoms location can be added. Useful, for e.g., when adding hydrogens
public void reserve(long size)
public boolean hasOwningMol()
public ROMol getOwningMol()
public SWIGTYPE_p_std__vectorT_RDGeom__Point3D_t getPositions()
public Point3D getAtomPos(long atomId)
public void setAtomPos(long atomId, Point3D position)
public long getId()
public void setId(long id)
public long getNumAtoms()
public boolean is3D()
public void set3D(boolean v)
public Point3D computeCentroid(boolean ignoreHs)
public Point3D computeCentroid()
public Transform3D computeCanonicalTransform(Point3D center, boolean normalizeCovar, boolean ignoreHs)
public Transform3D computeCanonicalTransform(Point3D center, boolean normalizeCovar)
public Transform3D computeCanonicalTransform(Point3D center)
public Transform3D computeCanonicalTransform()
public void transformConformer(Transform3D trans)
public void canonicalizeConformer(Point3D center, boolean normalizeCovar, boolean ignoreHs)
public void canonicalizeConformer(Point3D center, boolean normalizeCovar)
public void canonicalizeConformer(Point3D center)
public void canonicalizeConformer()