I know that each atom only has one valency for this reason I thought that it should be a good idea if I create other file xml on other hand. and I used still the AtomTypeFactory.java class. Into this xml there is only one elementType of H, one of C, one of N and so one and there aren't value for maxBondOrder, bondOrderSum, formalNeighbourCount. I created it so because I think it should be better than AtomValenceDescriptor.java which is a Hashtable.
On Mon, 2005-03-21 at 15:19, Egon Willighagen wrote:
At this moment, the AtomType has three related fields:
They are related but don't match fully...
Take nitrogen... depending on the atom type (think formal charge),
the bond order sum is 3 or 4... they valency is always 5.
On Mon, 2005-03-21 at 11:58, Miguel Rojas Cherto wrote:
> Due to the necessidad to find I number of lone pair orbitals into an
> Atom, I have found a algorithm that try to find a SIMPLE WAY the
> molecular geometry for following from Valence Shell ElectronPair
> Reupulsion or VSEPR model and at the same time its hybridization of
> atoms in a molecule. The basic premise of the model is that the
> electrons are paired in a molecule and that the molecule geometry is
> determined only by the repulsion between the pairs. The geomtry
> adopted by a molecule is then the one in which the reulsions are
> I have created a new Class HybridizationStateVSEPRMatcher.java into
> atomType file together with HybridizationStateMatcher.java. I believe
> that hier is correct. It gives you the hybridization as CDK.Constant.
> public int getHybridization(Atom atom, AtomContainer container) throws
> CDKException .
> This class is an experimental alternative to the
> HybridizationStateMatcher.java. I think its not complet and gives
> incorrect solutions. (exemple for one Test).
> * #pairs on hybridization geomtry number for CDK.Constants
> * an atom of the atom
> * 2 sp linear 1
> * 3 sp^2 trigonal planar 2
> * 4 sp^3 tetrahedral 3
> * 5 sp^3d trigonal bipyramid 4
> * 6 sp^3d^2 octahedral 5
> * 7 sp^3d^3 pentagonal bipyramid 6
> This class only works if the central atom is a s-block or p-block
> element (groups IIA trhough VIIIA), not a transition metal.
> It needed the valency of an atom. For this I created a
> hybridizationVSEPR_atomtypes.xml with the valency of all atoms with
> exception of the transition metals. It is practicaler than with
> <atomType id="H">
> <atom elementType="H">
> <scalar dataType="xsd:integer" dictRef="cdk:valency">1</scalar>
> At the same time I have had to modify AtomTypeHandler Into endElement
> and startElement one paar line more (
> atomType.setValency(Integer.parseInt(currentChars)); )
> Also I have had to introduce into AtomType one methode for valency.
> With its getValency und setVelency
> * Sets the the exact electron valency of the AtomType object.
> * @param electronValency The new electronValency value
> public void setValency(int valency)
> this.electronValency = valency;
> and by I complete with into CDK.Contanst the rest of possibilities
> with its hybridization sp^3d^1 (int 4) , sp^3d^2 ( int 5) , and
> sp^3d^3 (int 6).
> And naturally a test for each thing.
> I think it will interessant in order to extend the capacity with
> hybridization and geometry to work.
Adding Valency seems reasonable to me... thoughts?
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