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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object chemaxon.struc.CNode chemaxon.struc.MolAtom
Atom object and the properties of the elements. Atom objects are identified by their reference valees.
Field Summary | |
static int |
AAMAP_MASK
Atom map mask in flags. |
static int |
AAMAP_MAX
Maximum atom-atom mapping number. |
static int |
AAMAP_OFF
Atom map offset in flags. |
static int |
ALIPHATIC
Aliphatic query atom. |
static int |
ANY
"Atomic number" of the any atom A. |
static int |
AROMATIC
Aromatic query atom. |
static int |
AROMATIC_OR_ALIPHATIC
Aromatic or aliphatic query atom. |
static int |
ATOM_TYPE_COUNT
Number of atom types in the elements array |
static int |
ATTACH_BOTH
Attachment point on first and second site. |
static int |
ATTACH1
Attachment point on first site. |
static int |
ATTACH2
Attachment point on second site. |
static int |
CHARGED_H
Include charged Hydrogen atom(s). |
static int |
ELEMENT_COUNT
Number of elements in the periodic system |
static int |
EMPTY
Empty atom type. |
static int |
FIX_CHARGE
The charge is fix if this flag is set. |
static int |
HETERO
"Atomic number" of the hetero any atom Q. |
static int |
HS_S
S hybridization state. |
static int |
HS_SP
SP hybridization state. |
static int |
HS_SP2
SP2 hybridization state. |
static int |
HS_SP3
SP3 hybridization state. |
static int |
HS_UNKNOWN
Unknown hybridization state. |
static int |
ISOTOPE_H
Include Hydrogen isotope(s). |
static int |
LIST
"Atomic number" of the inclusive atom list. |
static int |
LONELY_H
Include lonely Hydrogen atom(s). |
static int |
LP
"Atomic number" of the lonely pair. |
static int |
MAPPED_H
Mapped Hydrogen atom(s). |
static int |
NOTLIST
"Atomic number" of the exclusive atom list. |
static int |
PSEUDO
"Atomic number" of a pseudoatom. |
static int |
RAD_COUNT_MASK
Radical's free electron count bits in flags. |
static int |
RAD_MASK
Radical value bits in flags. |
static int |
RAD_OFF
Radical value offset in flags. |
static int |
RAD1
Monovalent radical center. |
static int |
RAD2
Divalent radical center. |
static int |
RAD2_SINGLET
Divalent radical center with singlet electronic configuration. |
static int |
RAD2_TRIPLET
Divalent radical center with triplet electronic configuration. |
static int |
RAD3
Trivalent radical center. |
static int |
RADICAL_H
Include radical Hydrogen atom(s). |
static int |
RESSEQ_MAX
Maximum residue sequence number is currently 8191. |
static int |
RESTYPE_MAX
Maximum residue type is currently 63. |
static int |
RGROUP
"Atomic number" of the Rgroup query "atom". |
static int |
RGROUP_MAX
Maximum R-group index. |
static int |
RXNSTEREO_INVERSION
The stereo configuration of the atom is inverted during the reaction. |
static int |
RXNSTEREO_NONE
The stereo configuration of the atom is not considered during the reaction. |
static int |
RXNSTEREO_RETENTION
The stereo configuration of the atom is retained during the reaction. |
static int |
SETSEQ_MAX
Maximum atom set sequence number is currently 63. |
static int |
SGROUP
"Atomic number" of an Sgroup. |
static int |
SMARTS_H_DAYLIGHT_COMP_MODE
Option flag to express daylight-type smarts atom parsing of H. |
static int |
SMARTS_H_MARVIN_COMP_MODE
Option flag to express marvin-pre-3.5-type smarts atom parsing of H. |
static int |
VALCHK_ATTACH
Deprecated. as of Marvin 3.5, attachment points are always checked |
static int |
VALENCE_CHECKED
Valence checked if this flag is set. |
protected double |
xCoordinate
X coordinate. |
protected double |
yCoordinate
Y coordinate. |
protected double |
zCoordinate
Z coordinate. |
Fields inherited from class chemaxon.struc.CNode |
edges, nedges |
Fields inherited from interface chemaxon.struc.StereoConstants |
ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_MASK, CHIRALITY_R, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, TRANS |
Constructor Summary | |
MolAtom(double x,
double y)
Construct a carbon atom at the specified location. |
|
MolAtom(int z)
Construct an atom of the specified type at the origin. |
|
MolAtom(int zZ,
double x,
double y,
double z)
Construct an atom. |
Method Summary | |
protected void |
add(CEdge b)
Add an edge if it had not been already added. |
void |
bondweights(double[] w,
CTransform3D t)
Calculates the average of the bond unit vectors pointing out of this atom. |
void |
clear()
Clear query properties, charge, and hcount. |
void |
clearExtraLabel()
Clears the extra label. |
void |
clearQProps()
Clears query props. |
java.lang.Object |
clone()
Clones the atom. |
protected void |
copy(CNode node)
Make a copy of this atom. |
protected int |
countAllAtoms()
Counts all atoms represented by this atom. |
static double |
covalentRadiusOf(int z,
int t)
Gets the covalent radius in C-C bond length units. |
static int |
electronegOf(int z)
Gets 10 times the electronegativity value for the specified element. |
java.lang.String |
getAliasstr()
Gets the alias string. |
int |
getAtno()
Gets the atomic number. |
int |
getAtomMap()
Gets the atom-atom mapping number. |
java.lang.String |
getAtomSymbol(int style,
int aflags,
int[] lcenter,
CTransform3D preTransform)
Gets the string representation of the atom symbol. |
int |
getAttach()
Gets attachment point information. |
MolBond |
getBond(int i)
Gets the i-th bond. |
int |
getBondCount()
Gets the number of bonds/ligands. |
int |
getCharge()
Gets the charge. |
int |
getExplicitHcount()
Gets number of hydrogen connections. |
java.lang.String |
getExtraLabel()
Gets the label string: "result" or "result1|result2". |
long |
getExtraLabelColor()
Gets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue). |
int |
getExtraLabelColor(int i)
Gets the extra label color: (alpha<<24 + red<<16 + green<<8 + blue). |
int |
getFlags()
Gets flags. |
int |
getHybridizationState()
Gets the hybridization state. |
int |
getImplicitHcount()
Gets the number of implicit hydrogens attached. |
int[] |
getList()
Gets the atom list. |
DPoint3 |
getLocation()
Gets the coordinates. |
void |
getLocation(DPoint3 p)
Gets the coordinates. |
double |
getMass()
Gets the atomic weight. |
int |
getMassno()
Gets the mass number. |
int |
getMaxRepetitions()
Gets the maximum number of repetitions for a link node. |
int |
getMinRepetitions()
Gets the minimum number of repetitions for a link node. |
java.lang.Object |
getQProp(java.lang.String name)
Gets a query property. |
int |
getQPropAsInt(java.lang.String name)
Gets a query property as an integer. |
int |
getQueryAromaticity()
Gets the aromatic/aliphatic query property. |
java.lang.String |
getQueryLabel()
Gets the string representation of the query atom |
java.lang.String |
getQuerystr()
Gets the query properties. |
int |
getRadical()
Gets the radical value. |
int |
getRadicalCount()
Gets the number of free electrons. |
int |
getReactionStereo()
Gets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction. |
int |
getRealBondCount()
Gets the number of bonds connected to "real" atoms. |
int |
getRelativeNegativity()
Check negativity compared to the neighbors. |
int |
getResidueAtomId()
Gets the residue atom identifier. |
int |
getResidueSeq()
Gets the residue sequence number. |
int |
getResidueType()
Gets the residue type. |
int |
getRgroup()
Gets the R-group index. |
int |
getSetSeq()
Gets the atom set sequence number. |
boolean |
getStereoCare()
Reports double bond stereo care information on the connected bonds. |
int |
getStereoGroupNumber()
Gets the stereochemical group number. |
int |
getStereoGroupType()
Gets the stereochemical group type. |
java.lang.String |
getSymbol()
Gets the element symbol. |
int |
getValence()
Gets the valence. |
int |
getValenceProp()
Gets the valence property. |
double |
getX()
Gets the X coordinate. |
double |
getY()
Gets the Y coordinate. |
double |
getZ()
Gets the Z coordinate. |
boolean |
hasAromaticBond()
Tests whether the atom has aromatic bond. |
boolean |
hasQProps()
Does it have query properties? |
boolean |
hasQueryBonds()
Tests whether the atom has query bonds ("ANY" bonds). |
boolean |
hasSMARTSProps()
Tests whether it is a SMARTS query atom. |
boolean |
hasSMARTSPropsExcluding(java.lang.String exclude)
Tests whether it is a SMARTS query atom. |
boolean |
hasValenceError()
Determines if this atom has a valence error. |
boolean |
haveEqualProperties(CNode node)
Tests if two atoms have the same properties. |
boolean |
insideLabel(double x,
double y)
Tests whether the specified point is inside the atom label. |
static int |
ionChargeOf(int z)
Gets the ion charge. |
boolean |
isArrowEnd()
Tests if this is an arrow endpoint. |
boolean |
isImplicitizableH(int f)
Tests whether the hydrogen atom is implicitizable or not. |
boolean |
isLinkNode()
The atom is a link node if the maximum number of repetitions is nonzero. |
boolean |
isMappable()
Is it a mappable atom? |
boolean |
isNobleGas()
Is it a noble gas? |
static int |
isotopeType(int z,
int a)
Gets the type of an isotope. |
boolean |
isPseudo()
Tests whether if the atom is a pseudo atom. |
boolean |
isQProp()
Tests whether this object represents a query property. |
boolean |
isQuery()
Tests whether it is a query atom. |
static boolean |
isSameParityClass(int i1,
int i2,
int i3,
int i4,
int j1,
int j2,
int j3,
int j4)
Calculates if chirality centers in the structure and the query belong to the same parity class. |
boolean |
isSelected()
Tests whether this atom is selected. |
boolean |
isTerminalAtom()
Determines whether it is a terminal atom or not. |
static java.lang.String |
nameOf(int z)
Gets the name of the specified element. |
static double |
naturalWeightOf(int z)
Gets the natural weight of the element. |
static int |
negOxOf(int z)
Gets the negative oxidation number. |
static int |
numOf(java.lang.String e)
Gets the atomic number of an element. |
static int |
numoxstatesOf(int z)
Gets the number of oxidation states for the specified element. |
static int |
oxstateOf(int z,
int k)
Gets the oxidation states. |
static int |
paritySign(int a,
int b,
int c,
int d)
Calculates the sign of the parity for the specified indexes. |
static int |
posOxOf(int z)
Gets the smallest positive oxidation number. |
void |
qpropCheck()
Query property checking. |
protected void |
removeEdge(int i)
Removes a bond. |
static java.lang.String |
residueSymbolOf(int id)
Gets the name of a residue. |
static int |
residueTypeOf(java.lang.String name)
Gets the residue identifier for a residue name. |
void |
setAliasstr(java.lang.String s)
Sets the alias string. |
void |
setAtno(int z)
Sets the atomic number. |
void |
setAtomMap(int map)
Sets the atom-atom mapping number. |
void |
setAttach(int a)
Sets attachment point information. |
void |
setAttach(int a,
Sgroup sg)
Sets attachment point information for an S-group attachment atom. |
void |
setCharge(int q)
Sets the charge. |
void |
setCorners(double xnw,
double ynw,
double xse,
double yse)
Used internally by MolPainter. |
void |
setExtraLabel(java.lang.String s)
Sets the extra atom label: "label" or "label1|label2". |
void |
setExtraLabelColor(long rgbs)
Sets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue). |
void |
setFlags(int f)
Sets the flags. |
void |
setFlags(int f,
int mask)
Sets the flags. |
void |
setHybridizationState(int h)
Sets the hybridization state. |
void |
setImplicitHcount(int h)
Sets the number of implicit hydrogens. |
void |
setList(int[] l)
Sets the list elements. |
void |
setList(int[] l,
int n)
Sets the list elements. |
void |
setLocation(DPoint3 p)
Sets the coordinates. |
void |
setMassno(int a)
Sets the mass number. |
void |
setMassnoIfKnown(java.lang.String sym)
Sets the atomic weight for deuterium or tricium. |
void |
setMaxRepetitions(int r)
Sets the maximum number of repetitions for a link node. |
void |
setMinRepetitions(int r)
Sets the minimum number of repetitions for a link node. |
void |
setQProp(java.lang.String name,
int v)
Sets a query property as an integer. |
void |
setQProp(java.lang.String name,
java.lang.Object v)
Sets a query property. |
void |
setQueryAromaticity(int x)
Sets the aromatic/aliphatic query property. |
void |
setQuerystr(java.lang.String s)
Assigns the query properties string to this atom while setting all necessary atom and query properties. |
void |
setQuerystr(java.lang.String s,
int options)
Assigns the query properties string to this atom while setting all necessary atom and query properties. |
void |
setRadical(int r)
Sets the radical value. |
void |
setReactionStereo(int r)
Sets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction. |
void |
setResidueAtomId(int id)
Sets the residue atom identifier. |
void |
setResidueSeq(int n)
Sets the residue sequence number. |
void |
setResidueType(int t)
Sets the residue type. |
void |
setRgroup(int r)
Sets the R-group index. |
void |
setSelected(boolean sel)
Selects or unselects this atom. |
void |
setSetSeq(int id)
Sets the atom set sequence number. |
void |
setSMARTS(java.lang.String s)
Sets SMARTS query string data. |
void |
setStereoGroupNumber(int n)
Sets the stereochemical group number. |
void |
setStereoGroupType(int t)
Sets the stereochemical group type. |
void |
setValenceError(boolean v)
Sets or clears the valence error flag. |
void |
setValenceProp(int v)
Sets the valence property. |
void |
setX(double x)
Sets the X coordinate. |
void |
setXY(double x,
double y)
Sets the x and y coordinates. |
void |
setXYZ(double x,
double y,
double z)
Sets the coordinates. |
void |
setY(double y)
Sets the Y coordinate. |
void |
setZ(double z)
Sets the Z coordinate. |
static java.lang.String |
symbolOf(int z)
Gets the element symbol for the specified atomic number. |
java.lang.String |
toString()
Overrides Object.toString() to ease debugging. |
int |
twicesumbonds(boolean countH,
boolean all2)
Calculates the sum of bond orders. |
void |
valenceCheck()
Valence checking. |
void |
valenceCheck(int opts)
Valence checking. |
Methods inherited from class chemaxon.struc.CNode |
getEdge, getEdgeCount, getEdgeTo, getLigand, getLock, getParent, haveSimilarEdges, indexOf, isBoundTo, pack, removeAllEdges, removeEdge, setNode1, setNode2, sringsize |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
public static final int VALCHK_ATTACH
valenceCheck(int)
,
Constant Field Valuespublic static final int LONELY_H
MoleculeGraph.implicitizeHydrogens(int)
,
Constant Field Valuespublic static final int ISOTOPE_H
MoleculeGraph.implicitizeHydrogens(int)
,
Constant Field Valuespublic static final int CHARGED_H
MoleculeGraph.implicitizeHydrogens(int)
,
Constant Field Valuespublic static final int RADICAL_H
MoleculeGraph.implicitizeHydrogens(int)
,
Constant Field Valuespublic static final int MAPPED_H
MoleculeGraph.implicitizeHydrogens(int)
,
Constant Field Valuespublic static final int ELEMENT_COUNT
public static final int ATOM_TYPE_COUNT
public static final int EMPTY
public static final int LIST
public static final int NOTLIST
public static final int LP
public static final int ANY
public static final int HETERO
public static final int RGROUP
public static final int SGROUP
public static final int PSEUDO
public static final int VALENCE_CHECKED
getFlags()
,
Constant Field Valuespublic static final int FIX_CHARGE
getFlags()
,
Constant Field Valuespublic static final int HS_UNKNOWN
getHybridizationState()
,
Constant Field Valuespublic static final int HS_S
getHybridizationState()
,
Constant Field Valuespublic static final int HS_SP
getHybridizationState()
,
Constant Field Valuespublic static final int HS_SP2
getHybridizationState()
,
Constant Field Valuespublic static final int HS_SP3
getHybridizationState()
,
Constant Field Valuespublic static final int RGROUP_MAX
setRgroup(int)
,
Constant Field Valuespublic static final int RAD_OFF
public static final int RAD_MASK
public static final int RAD_COUNT_MASK
public static final int RAD1
public static final int RAD2
public static final int RAD2_SINGLET
public static final int RAD2_TRIPLET
public static final int RAD3
public static final int AAMAP_MAX
setAtomMap(int)
,
Constant Field Valuespublic static final int AAMAP_OFF
public static final int AAMAP_MASK
getAtomMap()
,
getFlags()
,
Constant Field Valuespublic static final int SETSEQ_MAX
setSetSeq(int)
,
Constant Field Valuespublic static final int RESTYPE_MAX
setResidueType(int)
,
Constant Field Valuespublic static final int RESSEQ_MAX
setResidueSeq(int)
,
Constant Field Valuespublic static final int RXNSTEREO_NONE
public static final int RXNSTEREO_INVERSION
public static final int RXNSTEREO_RETENTION
public static final int AROMATIC
getQueryAromaticity()
,
Constant Field Valuespublic static final int ALIPHATIC
getQueryAromaticity()
,
Constant Field Valuespublic static final int AROMATIC_OR_ALIPHATIC
getQueryAromaticity()
,
Constant Field Valuespublic static final int ATTACH1
getAttach()
,
Constant Field Valuespublic static final int ATTACH2
getAttach()
,
Constant Field Valuespublic static final int ATTACH_BOTH
getAttach()
,
Constant Field Valuespublic static final int SMARTS_H_DAYLIGHT_COMP_MODE
setQuerystr(String, int)
,
Constant Field Valuespublic static final int SMARTS_H_MARVIN_COMP_MODE
setQuerystr(String, int)
,
Constant Field Valuesprotected transient double xCoordinate
protected transient double yCoordinate
protected transient double zCoordinate
Constructor Detail |
public MolAtom(int zZ, double x, double y, double z)
zZ
- the atomic numberx
- the x coordinatey
- the y coordinatez
- the z coordinatepublic MolAtom(double x, double y)
x
- the x coordinatey
- the y coordinatepublic MolAtom(int z)
z
- the atomic numberMethod Detail |
public final int getBondCount()
public final MolBond getBond(int i)
i
- bond index
public final int getRealBondCount()
public double getX()
public void setX(double x)
x
- the x coordinate in Angstromspublic double getY()
public void setY(double y)
y
- the y coordinate in Angstromspublic double getZ()
public void setZ(double z)
z
- the z coordinate in Angstromspublic void setXY(double x, double y)
x
- the x coordinate in Angstromsy
- the y coordinate in Angstromspublic void setXYZ(double x, double y, double z)
x
- the x coordinate in Angstromsy
- the y coordinate in Angstromsz
- the z coordinate in Angstromspublic final DPoint3 getLocation()
public final void getLocation(DPoint3 p)
p
- object that will store the locationpublic void setLocation(DPoint3 p)
p
- the locationpublic java.lang.String getSymbol()
public final int getAtno()
public void setAtno(int z)
z
- the atomic numberpublic int getMassno()
public void setMassno(int a)
a
- the mass number or zeropublic void setMassnoIfKnown(java.lang.String sym)
sym
- the atom symbolpublic double getMass()
public boolean isNobleGas()
true
if noble gas, false
otherwisepublic boolean isMappable()
true
if it is a real mappable atom,
false
if it is a lone pairpublic int getRelativeNegativity()
public int getImplicitHcount()
public void setImplicitHcount(int h)
h
- the number of implicit hydrogens
java.lang.IllegalArgumentException
- negative h value specifiedpublic int getCharge()
public void setCharge(int q)
q
- the chargepublic int getRadical()
RAD1
,
RAD2
,
RAD2_SINGLET
,
RAD2_TRIPLET
,
RAD3
public void setRadical(int r)
r
- the radical valueRAD1
,
RAD2
,
RAD2_SINGLET
,
RAD2_TRIPLET
,
RAD3
public int getRadicalCount()
public int getValenceProp()
public void setValenceProp(int v)
v
- the valencepublic int getValence()
public int getExplicitHcount()
public boolean hasQProps()
true
if it has query properties,
false
otherwisepublic java.lang.Object getQProp(java.lang.String name)
getQueryAromaticity()
instead
name
- the property name
public int getQPropAsInt(java.lang.String name)
name
- the property name
getQProp(java.lang.String)
public void setQProp(java.lang.String name, java.lang.Object v)
name
- the property namev
- the valuegetQProp(java.lang.String)
public void setQProp(java.lang.String name, int v)
name
- the property namev
- the valuepublic void clearQProps()
public int getQueryAromaticity()
AROMATIC
, ALIPHATIC
or AROMATIC_OR_ALIPHATIC
public void setQueryAromaticity(int x)
x
- 0, AROMATIC
, ALIPHATIC
or AROMATIC_OR_ALIPHATIC
public int getRgroup()
public void setRgroup(int r)
r
- Rgroup number, between 1 and 32RGROUP_MAX
public int getAttach()
ATTACH1
(first),
ATTACH2
(second) or ATTACH_BOTH
(both)public void setAttach(int a)
a
- 0 (not an attachment point), ATTACH1
(first),
ATTACH2
(second) or ATTACH_BOTH
(both)public void setAttach(int a, Sgroup sg)
a
- 0 (not an attachment point), ATTACH1
(first),
ATTACH2
(second) or ATTACH_BOTH
(both)sg
- the parent S-group or nullpublic int getHybridizationState()
HS_UNKNOWN
,
HS_S
,
HS_SP
,
HS_SP2
,
HS_SP3
public void setHybridizationState(int h)
h
- the hybridization stategetHybridizationState()
public int getAtomMap()
public void setAtomMap(int map)
map
- the map value (positive integer) or 0AAMAP_MAX
public int getSetSeq()
SETSEQ_MAX
public void setSetSeq(int id)
id
- a number between 0 and SETSEQ_MAXSETSEQ_MAX
public static int residueTypeOf(java.lang.String name)
name
- residue name
public static java.lang.String residueSymbolOf(int id)
id
- the residue identifier
public int getResidueType()
RESTYPE_MAX
public void setResidueType(int t)
t
- the residue typeRESTYPE_MAX
public int getResidueSeq()
RESSEQ_MAX
public void setResidueSeq(int n)
n
- the residue sequence numberRESSEQ_MAX
public int getResidueAtomId()
public void setResidueAtomId(int id)
id
- the residue atom identifierpublic int getMinRepetitions()
public void setMinRepetitions(int r)
r
- the minimum number of repetitionspublic int getMaxRepetitions()
public void setMaxRepetitions(int r)
r
- the maximum number of repetitionspublic boolean isLinkNode()
public final boolean isArrowEnd()
true
if this is an arrow endpoint,
false
otherwiseMolBond.isArrow()
public void bondweights(double[] w, CTransform3D t)
w
- 3-element array that will contain the resulting vectort
- the rotation matrixpublic java.lang.String getAtomSymbol(int style, int aflags, int[] lcenter, CTransform3D preTransform)
style
- normal (0), show hydrogen count (1),
SMILES string in [ ] with total H count(2),
show total hydrogen count (3),
don't show mapping (4),
force SMARTS query string (5), or
SMARTS string with A/a property shown always(6).aflags
- atom flagspreTransform
- viewing transformationlcenter
- if not null, then its first two element (index 0-1) will
will be set to the index and the length of the element
symbol substring in the returned string, the element at
at index 2 will be set to +1 if the H label is above,
-1 if below the element symbol or 0 otherwise
public java.lang.String getQueryLabel()
public final boolean isQuery()
true
if it is a query atom,
false
otherwisepublic boolean isQProp()
true
if it is a query property,
false
otherwisepublic boolean isImplicitizableH(int f)
f
- flags specifying special H atom types to include
true
if the hydrogen is implicitizable,
false
otherwiseLONELY_H
,
ISOTOPE_H
,
CHARGED_H
,
RADICAL_H
,
MAPPED_H
,
MoleculeGraph.implicitizeHydrogens(int)
public boolean isPseudo()
true
if the atom is a pseudo atom,
false
otherwisepublic final boolean hasAromaticBond()
true
if it has query bonds,
false
otherwisepublic final boolean hasQueryBonds()
true
if it has query bonds,
false
otherwisepublic final boolean hasSMARTSProps()
true
if it has SMARTS properties,
false
otherwisepublic final boolean hasSMARTSPropsExcluding(java.lang.String exclude)
exclude
- list of SMARTS properties to exclude
true
if it has SMARTS properties,
false
otherwisepublic void setSMARTS(java.lang.String s) throws java.lang.SecurityException
s
- the SMARTS string
java.lang.SecurityException
- the SmilesImport cannot be loaded,
possibly because of a misconfigured firewallpublic java.lang.String getQuerystr()
public void setQuerystr(java.lang.String s)
s
- the query stringpublic void setQuerystr(java.lang.String s, int options)
In daylight smarts H is only considered as H atom when the atom expression has the syntax [<mass>H<charge><map>] (mass, charge and map are optional). If options is SMARTS_H_MARVIN_COMP_MODE and "H" is not in the form [<mass>H<charge><map>] then it may be interpreted as Hydrogen atom, not total H count! It is neccesary for backward compatibility.
s
- the query stringoptions
- Possible values: SMARTS_H_MARVIN_COMP_MODE or
SMARTS_H_DAYLIGHT_COMP_MODE. Instead of using this option, we recommend
using unambigous smarts queries: #1 for H atom and H1 for H count 1.SMARTS_H_DAYLIGHT_COMP_MODE
,
SMARTS_H_MARVIN_COMP_MODE
public void setAliasstr(java.lang.String s)
s
- the aliaspublic java.lang.String getAliasstr()
public void setExtraLabel(java.lang.String s)
s
- the atom labelpublic void setExtraLabelColor(long rgbs)
rgbs
- the color(s)setExtraLabel(String)
public java.lang.String getExtraLabel()
public long getExtraLabelColor()
public int getExtraLabelColor(int i)
i
- is the result index (0 or 1)
public void clearExtraLabel()
public int[] getList()
public void setList(int[] l, int n)
l
- the listn
- number of elements to setpublic void setList(int[] l)
l
- the listpublic int getReactionStereo()
RXNSTEREO_NONE
,
RXNSTEREO_INVERSION
,
RXNSTEREO_RETENTION
public void setReactionStereo(int r)
r
- the reaction stereo propertyRXNSTEREO_NONE
,
RXNSTEREO_INVERSION
,
RXNSTEREO_RETENTION
public void clear()
public java.lang.Object clone()
clone
in class CNode
public java.lang.String toString()
toString
in class CNode
public boolean insideLabel(double x, double y)
x
- the x coordinatey
- the y coordinate
true
if inside, false
if outsidepublic static int numOf(java.lang.String e)
e
- the element name
public static java.lang.String symbolOf(int z)
z
- the atomic number
public static java.lang.String nameOf(int z)
z
- the atomic number
public static int electronegOf(int z)
z
- the atomic number
public static int numoxstatesOf(int z)
z
- the atomic number
public static int oxstateOf(int z, int k)
z
- the atomic numberk
- the oxidation state index
public static int negOxOf(int z)
z
- the atomic number
public static int posOxOf(int z)
z
- the atomic number
public static int ionChargeOf(int z)
z
- the atomic number
public static double covalentRadiusOf(int z, int t)
z
- the atomic numbert
- the bond type (1, 2, 3)
public static double naturalWeightOf(int z)
z
- the atomic number
public static int isotopeType(int z, int a)
z
- atomic numbera
- mass number
public int twicesumbonds(boolean countH, boolean all2)
countH
- also count bonds to explicit hydrogen atomsall2
- calculate (two times) the number of bonds instead of the
sum of bond orders
public void qpropCheck()
public void valenceCheck()
public void valenceCheck(int opts)
opts
- valence checking optionsVALCHK_ATTACH
public void setCorners(double xnw, double ynw, double xse, double yse)
xnw
- north-west corner xynw
- north-west corner yxse
- south-east corner xyse
- south-east corner ypublic int getFlags()
StereoConstants.PARITY_MASK
,
StereoConstants.CHIRALITY_MASK
,
StereoConstants.ATOMSTEREO_MASK
public void setFlags(int f)
f
- new flagspublic void setFlags(int f, int mask)
f
- new flagsmask
- bits to set in flagspublic boolean isSelected()
true
if selected, false
otherwisepublic void setSelected(boolean sel)
sel
- true to select, false to unselectpublic boolean hasValenceError()
public void setValenceError(boolean v)
v
- true to set, false to unsetpublic boolean getStereoCare()
MolBond.getFlags()
,
MolBond.setFlags(int)
public int getStereoGroupType()
StereoConstants.STGRP_NONE
,
StereoConstants.STGRP_ABS
,
StereoConstants.STGRP_OR
,
StereoConstants.STGRP_AND
public void setStereoGroupType(int t)
t
- the stereochemical group typegetStereoGroupType()
public int getStereoGroupNumber()
getStereoGroupType()
,
StereoConstants.STGRP_OR
,
StereoConstants.STGRP_AND
public void setStereoGroupNumber(int n)
n
- the stereochemical group number (positive integer)getStereoGroupNumber()
protected void copy(CNode node)
node
- the target atomprotected void add(CEdge b)
add
in class CNode
b
- the edge to addprotected void removeEdge(int i)
removeEdge
in class CNode
i
- bond indexpublic static int paritySign(int a, int b, int c, int d)
a
- first atom indexb
- second atom indexc
- third atom indexd
- fourth atom index
public static boolean isSameParityClass(int i1, int i2, int i3, int i4, int j1, int j2, int j3, int j4)
paritySign(int, int, int, int)
public boolean isTerminalAtom()
public boolean haveEqualProperties(CNode node)
haveEqualProperties
in class CNode
true
if they have the same properties,
false
otherwiseprotected int countAllAtoms()
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