Package net.sf.jniinchi
Class JniInchiStereo0D
- java.lang.Object
-
- net.sf.jniinchi.JniInchiStereo0D
-
public class JniInchiStereo0D extends java.lang.Object
Encapsulates properites of InChI Stereo Parity. See inchi_api.h.
-
-
Field Summary
Fields Modifier and Type Field Description private JniInchiAtom
centralAtom
Central atom.private INCHI_PARITY
disconParity
Second parity (for disconnected systems).private JniInchiAtom[]
neighbors
Neighbouring atoms.static int
NO_ATOM
Indicates non-existent (central) atom.private INCHI_PARITY
parity
Parity.private INCHI_STEREOTYPE
type
Stereo parity type.
-
Constructor Summary
Constructors Constructor Description JniInchiStereo0D(JniInchiAtom atC, JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, int type, int parity)
JniInchiStereo0D(JniInchiAtom atC, JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, INCHI_STEREOTYPE type, INCHI_PARITY parity)
Constructor.
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static JniInchiStereo0D
createNewDoublebondStereo0D(JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, INCHI_PARITY parity)
Convenience method for generating 0D stereo parities at stereogenic double bonds.static JniInchiStereo0D
createNewTetrahedralStereo0D(JniInchiAtom atC, JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, INCHI_PARITY parity)
Convenience method for generating 0D stereo parities at tetrahedral atom centres.void
debug()
Outputs information on stereo parity, for debugging purposes.JniInchiAtom
getCentralAtom()
Returns central atom of stereo parity.java.lang.String
getDebugString()
Generates string representation of information on stereo parity, for debugging purposes.INCHI_PARITY
getDisconnectedParity()
Returns disconnected parity.(package private) int
getInchiParity()
(package private) int
getInchiStereoType()
JniInchiAtom
getNeighbor(int i)
JniInchiAtom[]
getNeighbors()
Returns neighboring atoms of stereo parity.INCHI_PARITY
getParity()
Returns parity.INCHI_STEREOTYPE
getStereoType()
Returns type of stereochemistry.void
setDisconnectedParity(INCHI_PARITY parity)
Set second parity (for disconnected systems)
-
-
-
Field Detail
-
NO_ATOM
public static final int NO_ATOM
Indicates non-existent (central) atom. Value from inchi_api.h.- See Also:
- Constant Field Values
-
neighbors
private JniInchiAtom[] neighbors
Neighbouring atoms.
-
centralAtom
private JniInchiAtom centralAtom
Central atom.
-
type
private INCHI_STEREOTYPE type
Stereo parity type.
-
parity
private INCHI_PARITY parity
Parity.
-
disconParity
private INCHI_PARITY disconParity
Second parity (for disconnected systems).
-
-
Constructor Detail
-
JniInchiStereo0D
public JniInchiStereo0D(JniInchiAtom atC, JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, INCHI_STEREOTYPE type, INCHI_PARITY parity)
Constructor. See inchi_api.h for details of usage.- Parameters:
atC
- Central atomat0
- Neighbour atom 0at1
- Neighbour atom 1at2
- Neighbour atom 2at3
- Neighbour atom 3type
- Stereo parity typeparity
- Parity- See Also:
createNewTetrahedralStereo0D(net.sf.jniinchi.JniInchiAtom,net.sf.jniinchi.JniInchiAtom,net.sf.jniinchi.JniInchiAtom,net.sf.jniinchi.JniInchiAtom,net.sf.jniinchi.JniInchiAtom,net.sf.jniinchi.INCHI_PARITY)
,createNewDoublebondStereo0D(net.sf.jniinchi.JniInchiAtom,net.sf.jniinchi.JniInchiAtom,net.sf.jniinchi.JniInchiAtom,net.sf.jniinchi.JniInchiAtom,net.sf.jniinchi.INCHI_PARITY)
-
JniInchiStereo0D
JniInchiStereo0D(JniInchiAtom atC, JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, int type, int parity)
-
-
Method Detail
-
setDisconnectedParity
public void setDisconnectedParity(INCHI_PARITY parity)
Set second parity (for disconnected systems)- Parameters:
parity
-
-
getCentralAtom
public JniInchiAtom getCentralAtom()
Returns central atom of stereo parity.- Returns:
-
getNeighbors
public JniInchiAtom[] getNeighbors()
Returns neighboring atoms of stereo parity.- Returns:
-
getNeighbor
public JniInchiAtom getNeighbor(int i)
-
getParity
public INCHI_PARITY getParity()
Returns parity.- Returns:
-
getDisconnectedParity
public INCHI_PARITY getDisconnectedParity()
Returns disconnected parity.- Returns:
-
getStereoType
public INCHI_STEREOTYPE getStereoType()
Returns type of stereochemistry.- Returns:
-
getDebugString
public java.lang.String getDebugString()
Generates string representation of information on stereo parity, for debugging purposes.
-
debug
public void debug()
Outputs information on stereo parity, for debugging purposes.
-
createNewTetrahedralStereo0D
public static JniInchiStereo0D createNewTetrahedralStereo0D(JniInchiAtom atC, JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, INCHI_PARITY parity)
Convenience method for generating 0D stereo parities at tetrahedral atom centres.
Usage notes from inchi_api.h:
4 neighbors X neighbor[4] : {#W, #X, #Y, #Z} | central_atom: #A W--A--Y type : INCHI_StereoType_Tetrahedral | Z parity: if (X,Y,Z) are clockwize when seen from W then parity is 'e' otherwise 'o' Example (see AXYZW above): if W is above the plane XYZ then parity = 'e' 3 neighbors Y Y neighbor[4] : {#A, #X, #Y, #Z} / / central_atom: #A X--A (e.g. O=S ) type : INCHI_StereoType_Tetrahedral \ \ Z Z parity: if (X,Y,Z) are clockwize when seen from A then parity is 'e', otherwise 'o' unknown parity = 'u' Example (see AXYZ above): if A is above the plane XYZ then parity = 'e' This approach may be used also in case of an implicit H attached to A. ============================================== Note. Correspondence to CML 0D stereo parities ============================================== a list of 4 atoms corresponds to CML atomRefs4 tetrahedral atom ================ CML atomParity > 0 <=> INCHI_PARITY_EVEN CML atomParity < 0 <=> INCHI_PARITY_ODD | 1 1 1 1 | where xW is x-coordinate of | xW xX xY xZ | atom W, etc. (xyz is a CML atomParity = determinant | yW yX yY yZ | 'right-handed' Cartesian | zW zX xY zZ | coordinate system)
- Parameters:
atC
- Central atomat0
- Neighbour atom 0at1
- Neighbour atom 1at2
- Neighbour atom 2at3
- Neighbour atom 3parity
- Parity
-
createNewDoublebondStereo0D
public static JniInchiStereo0D createNewDoublebondStereo0D(JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, INCHI_PARITY parity)
Convenience method for generating 0D stereo parities at stereogenic double bonds.
Usage notes from inchi_api.h:
============================================= stereogenic bond >A=B< or cumulene >A=C=C=B< ============================================= neighbor[4] : {#X,#A,#B,#Y} in this order X central_atom : NO_ATOM \ X Y type : INCHI_StereoType_DoubleBond A==B \ / \ A==B Y parity= 'e' parity= 'o' unknown parity = 'u' ============================================== Note. Correspondence to CML 0D stereo parities ============================================== stereogenic double bond and (not yet defined in CML) cumulenes ============================================================== CML 'C' (cis) <=> INCHI_PARITY_ODD CML 'T' (trans) <=> INCHI_PARITY_EVEN
- Parameters:
at0
- Neighbour atom 0at1
- Neighbour atom 1at2
- Neighbour atom 2at3
- Neighbour atom 3parity
- Parity- Returns:
-
getInchiStereoType
int getInchiStereoType()
-
getInchiParity
int getInchiParity()
-
-