net.sf.jniinchi
Class JniInchiStereo0D

java.lang.Object
  net.sf.jniinchi.JniInchiStereo0D

public class JniInchiStereo0D
extends Object

Encapsulates properites of InChI Stereo Parity. See inchi_api.h.

Author:

Sam Adams

Field Summary

static int

NO_ATOM Indicates non-existent (central) atom.

Constructor Summary

JniInchiStereo0D(JniInchiAtom atC, JniInchiAtom at0, JniInchiAtom at1, JniInchiAtom at2, JniInchiAtom at3, INCHI_STEREOTYPE type, INCHI_PARITY parity)
Constructor.

Method Summary

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.
String	getDebugString() Generates string representation of information on stereo parity, for debugging purposes.
INCHI_PARITY	getDisconnectedParity() Returns disconnected parity.
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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

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 atom

at0 - Neighbour atom 0

at1 - Neighbour atom 1

at2 - Neighbour atom 2

at3 - Neighbour atom 3

type - Stereo parity type

parity - Parity

See Also:

createNewTetrahedralStereo0D(), createNewDoublebondStereo0D()

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 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 atom

at0 - Neighbour atom 0

at1 - Neighbour atom 1

at2 - Neighbour atom 2

at3 - Neighbour atom 3

parity - 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 0

at1 - Neighbour atom 1

at2 - Neighbour atom 2

at3 - Neighbour atom 3

parity - Parity

Returns: