chemaxon.struc
Interface WSmolecule

All Superinterfaces:

Incomplecule, Smolecule

public interface WSmolecule
extends Smolecule

Writable abstract molecule class.

PLEASE DO NOT IMPLEMENT THIS INTERFACE! It may get more abstract methods in later versions.

Since:

Marvin 5.3, 05/21/2009

Version:

5.3, 06/04/2009

Author:

Peter Csizmadia

Field Summary

Fields inherited from interface chemaxon.struc.Smolecule

A_ALL, A_ASTEREO, A_ATOMMAP, A_BOND, A_CHARGE, A_CHIRALITY, A_EXPLH, A_HYBRIDIZATION, A_IMPLH, A_MASSNO, A_PARITY, A_RADICAL, A_RGROUP, A_VALENCE, RGROUP_MAX

Method Summary

void	addAtom(int atno) Adds an atom.
void	addAtom(Smolecule smol, int k) Adds an atom from another Smolecule.
void	addBond(int atom1, int atom2, int type) Adds a bond.
WSmolecule	newInstance(int na, int nb, int aflags) Creates a new WSmolecule instance with the specified capacity.
void	removeAtom(int k) Removes an atom.
void	removeBond(int k) Removes a bond.
void	reset(int aflags) Clears the molecule and sets the array flags.
void	setAtomMap(int atom, int map) Sets the atom-atom mapping number.
void	setAtomStereo(int atom, int stereo) Sets atom stereo properties.
void	setCharge(int atom, int chg) Sets the charge of an ion.
void	setHybridizationState(int atom, int hs) Sets the hybridization state of an atom.
void	setImplicitHcount(int atom, int h) Sets the number of implicit Hydrogens.
void	setMassno(int atom, int m) Sets the mass number.
void	setRadical(int atom, int rad) Sets the radical value of an atom.
void	setRgroupId(int atom, int rgid) Sets the R-group identifier of an atom.
void	setValence(int atom, int v) Sets the valence.

Methods inherited from interface chemaxon.struc.Smolecule

areNeighbors, gearch, getArrayFlags, getAtom1, getAtom2, getAtomMap, getAtomStereo, getAtomType, getBondFlags, getBondIndex, getBondType, getBondType, getCharge, getChirality, getExplicitHcount, getHcount, getHybridizationState, getImplicitHcount, getImplicitHcount, getMassno, getNeighbor, getNeighborCount, getParity, getQPropAsInt, getRadical, getRgroupId, getValence, inAtomList

Methods inherited from interface chemaxon.struc.Incomplecule

getAtomCount, getBondCount, getName, properties

Method Detail

newInstance

WSmolecule newInstance(int na,
                       int nb,
                       int aflags)

Creates a new WSmolecule instance with the specified capacity.

Parameters:

na - the maximum number of atoms

nb - the maximum number of bonds

aflags - arrays to enable, see Smolecule.A_ALL

reset

void reset(int aflags)

Clears the molecule and sets the array flags.

Parameters:

aflags - the array flags

addAtom

void addAtom(Smolecule smol,
             int k)

Adds an atom from another Smolecule.

Parameters:

smol - the other Smolecule

k - atom index in smol

addAtom

void addAtom(int atno)

Adds an atom.

Parameters:

atno - the atomic number

addBond

void addBond(int atom1,
             int atom2,
             int type)

Adds a bond.

Parameters:

atom1 - first atom index

atom2 - second atom index

type - bond type

removeAtom

void removeAtom(int k)

Removes an atom.

Parameters:

k - the atom index

removeBond

void removeBond(int k)

Removes a bond.

Parameters:

k - the bond index

setCharge

void setCharge(int atom,
               int chg)

Sets the charge of an ion.

Parameters:

atom - the atom index

chg - the charge

setRadical

void setRadical(int atom,
                int rad)

Sets the radical value of an atom.

Parameters:

atom - the atom index

rad - the radical value

setHybridizationState

void setHybridizationState(int atom,
                           int hs)

Sets the hybridization state of an atom.

Parameters:

atom - the atom index

hs - the hybridization state

See Also:

HybridizationStateConsts

setMassno

void setMassno(int atom,
               int m)

Sets the mass number.

Parameters:

atom - the atom index

m - the mass number or zero to unset

setValence

void setValence(int atom,
                int v)

Sets the valence.

Parameters:

atom - the atom index

v - the valence

setImplicitHcount

void setImplicitHcount(int atom,
                       int h)

Sets the number of implicit Hydrogens.

Parameters:

atom - the atom index

h - the number of implicit Hydrogens

setRgroupId

void setRgroupId(int atom,
                 int rgid)

Sets the R-group identifier of an atom.

Parameters:

atom - the atom index

rgid - the R-group identifier or 0 to unset

setAtomMap

void setAtomMap(int atom,
                int map)

Sets the atom-atom mapping number.

Parameters:

atom - the atom index

map - the map value (positive integer) or 0

setAtomStereo

void setAtomStereo(int atom,
                   int stereo)

Sets atom stereo properties.

Parameters:

atom - the atom index

stereo - parity | chirality

See Also:

StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, StereoConstants.PARITY_UNSPEC, StereoConstants.PARITY_EITHER, StereoConstants.PARITY_MASK, StereoConstants.CHIRALITY_R, StereoConstants.CHIRALITY_S, StereoConstants.CHIRALITY_MASK