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[Cdk-commits] CVS: cdk/src/org/openscience/cdk AtomType.java,1.49,1.50 CDKConstants.java,1.34,1.35
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From: Egon W. <eg...@us...> - 2005-10-11 12:03:32
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32169/src/org/openscience/cdk Modified Files: AtomType.java CDKConstants.java Log Message: Removed cdk.AtomType methods not in the interface Index: AtomType.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/AtomType.java,v retrieving revision 1.49 retrieving revision 1.50 diff -u -r1.49 -r1.50 --- AtomType.java 20 Sep 2005 07:54:56 -0000 1.49 +++ AtomType.java 11 Oct 2005 12:03:39 -0000 1.50 @@ -93,40 +93,7 @@ * includes implicit hydrogens. */ protected int formalNeighbourCount; - - /** - * Property if atom is Lewis or Bronsted acceptor - */ - protected boolean acceptor=false; - - /** - * Property if atom is Lewis or Bronsted donor - */ - protected boolean donor=false; - - /** - * Stores the CDKRingConstant for this atom type. - */ - protected int chemicalGroupConstant=0; - - /** - * Stores the size of the ring to which this atom type belongs. - */ - protected int ringSize=0; - - /** - * Stores the information if this atom type is aromatic. - */ - protected boolean isAromatic=false; - - /** - * Stores the spherical matching code,eg. - * A regular expression for the hose code description of this atom type. - * This is a work around for the missing SMARTS handling. - */ - protected String sphericalMatcher=null; - - + /** * Constructor for the AtomType object. * @@ -386,145 +353,6 @@ { return this.electronValency; } - - /** - * Sets the property of acceptor (Lewis or Bronsted type) type boolean - * @param isAcceptor boolean - * - */ - public void setAcceptor(boolean isAcceptor) - { - this.acceptor = isAcceptor; - notifyChanged(); - } - - /** - * Gets the the acceptor type of the AtomType object. - * - * returns boolean - * - */ - public boolean getAcceptor() - { - return this.acceptor; - } - - /** - * Sets the property of donor (Lewis or Bronsted type) type boolean - * @param isDonor boolean - * - */ - public void setDonor(boolean isDonor) - { - this.donor = isDonor; - notifyChanged(); - } - - /** - * Gets the the donor type of the AtomType object. - * - * returns boolean - * - */ - public boolean getDonor() - { - return this.donor; - } - - /** - * Sets the property to which chemical group (e.g. ring system) the atom type belongs. - * Values can be found in CDKChemicalGroupConstants - * - * @param chemicalGroupCDKConstant int - * - */ - public void setChemicalGroupConstant(int chemicalGroupCDKConstant) - { - this.chemicalGroupConstant = chemicalGroupCDKConstant; - notifyChanged(); - } - - /** - * Gets the property to which ring system the atom type belongs. - * - * returns ringConstant int - * - */ - public int getChemicalGroupConstant() - { - return this.chemicalGroupConstant; - } - - /** - * Sets ring size for which the atom type is defined. - * - * @param sizeOfRingSystem int - * - */ - public void setRingSize(int sizeOfRingSystem) - { - this.ringSize = sizeOfRingSystem; - notifyChanged(); - } - - /** - * Gets the ring size for which the atom type is defined. - * - * returns ringSize int - * - */ - public int getRingSize() - { - return this.ringSize; - } - - /** - * Sets if atom type is aromatic. - * - * @param ISAROMATIC boolean - * - */ - public void setIsAromatic(boolean ISAROMATIC) - { - this.isAromatic = ISAROMATIC; - notifyChanged(); - } - - /** - * Gets if atom type is defined as aromatic. - * - * returns isAromatic boolean - * - */ - public boolean getIsAromatic() - { - return this.isAromatic; - } - - /** - * Sets regular expression/or e.g. hoseCode for the corresponding atom to the atom type, - * (In an atom it stores the e.g. hose code, - * in atomType for AtomtypeFactory it stores the regular expression) - * - * @param description String - * - */ - public void setSphericalMatcher(String description) - { - this.sphericalMatcher = description; - notifyChanged(); - } - - /** - * Gets the regular expression for the hose code of the corresponding atom to the atom type. - * - * returns regularExpression String - * - */ - public String getSphericalMatcher() - { - return this.sphericalMatcher; - } public String toString() { @@ -539,12 +367,6 @@ resultString.append("CR:").append(getCovalentRadius()).append(", "); resultString.append("VDWR:").append(getVanderwaalsRadius()).append(", "); resultString.append("EV:").append(getValency()).append(", "); - resultString.append("A:").append(getAcceptor()).append(", "); - resultString.append("D:").append(getDonor()).append(", "); - resultString.append("ChemicalGroupCode:").append(getChemicalGroupConstant()).append(", "); - resultString.append("RingSize:").append(getRingSize()).append(", "); - resultString.append("Aromatic:").append(getIsAromatic()).append(", "); - resultString.append("SphericalDescriptor:").append(getSphericalMatcher()).append(", "); resultString.append(super.toString()); resultString.append(")"); return resultString.toString(); Index: CDKConstants.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/CDKConstants.java,v retrieving revision 1.34 retrieving revision 1.35 diff -u -r1.34 -r1.35 --- CDKConstants.java 4 May 2005 15:12:00 -0000 1.34 +++ CDKConstants.java 11 Oct 2005 12:03:39 -0000 1.35 @@ -170,6 +170,9 @@ */ public final static int MAPPED = 5; + public final static int IS_HYDROGENBOND_DONOR = 70; + public final static int IS_HYDROGENBOND_ACCEPTOR = 71; + /** * Maximum flags array index. */ @@ -236,6 +239,17 @@ */ public static final String ISOTROPIC_SHIELDING = "IsotropicShielding"; + /**************************************** + * Some predefined property names for * + * AtomTypes * + ****************************************/ + + public static final String PART_OF_RING_OF_SIZE = "Part of ring of size"; + + public static final String CHEMICAL_GROUP_CONSTANT = "Chemical Group"; + + public static final String SPHERICAL_MATCHER = "HOSE code spherical matcher"; + } |