Package net.sf.jniinchi
Class JniInchiStereo0D
java.lang.Object
net.sf.jniinchi.JniInchiStereo0D
Encapsulates properites of InChI Stereo Parity. See inchi_api.h.
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate JniInchiAtom
Central atom.private INCHI_PARITY
Second parity (for disconnected systems).private JniInchiAtom[]
Neighbouring atoms.static final int
Indicates non-existent (central) atom.private INCHI_PARITY
Parity.private INCHI_STEREOTYPE
Stereo parity type. -
Constructor Summary
ConstructorsConstructorDescriptionJniInchiStereo0D
(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
Modifier and TypeMethodDescriptionstatic 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.Returns central atom of stereo parity.Generates string representation of information on stereo parity, for debugging purposes.Returns disconnected parity.(package private) int
(package private) int
getNeighbor
(int i) Returns neighboring atoms of stereo parity.Returns parity.Returns type of stereochemistry.void
setDisconnectedParity
(INCHI_PARITY parity) Set second parity (for disconnected systems)
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Field Details
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NO_ATOM
public static final int NO_ATOMIndicates non-existent (central) atom. Value from inchi_api.h.- See Also:
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neighbors
Neighbouring atoms. -
centralAtom
Central atom. -
type
Stereo parity type. -
parity
Parity. -
disconParity
Second parity (for disconnected systems).
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Constructor Details
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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:
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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)
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JniInchiStereo0D
JniInchiStereo0D(JniInchiAtom atC, JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, int type, int parity)
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Method Details
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setDisconnectedParity
Set second parity (for disconnected systems)- Parameters:
parity
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getCentralAtom
Returns central atom of stereo parity.- Returns:
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getNeighbors
Returns neighboring atoms of stereo parity.- Returns:
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getNeighbor
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getParity
Returns parity.- Returns:
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getDisconnectedParity
Returns disconnected parity.- Returns:
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getStereoType
Returns type of stereochemistry.- Returns:
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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
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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:
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getInchiStereoType
int getInchiStereoType() -
getInchiParity
int getInchiParity()
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