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Two typo fixes and a few JavaDoc links
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egonw committed Aug 10, 2016
1 parent 0dda78a commit 1938e0b
Showing 1 changed file with 4 additions and 5 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,7 @@
import org.openscience.cdk.interfaces.IPseudoAtom;

/**
* Class with utilities for the <code>AtomType</code> class.
* - changed 21/7/05 by cho: add properties for mmff94 atom type
* Class with utilities for the {@link IAtomType} class.
*
* @author mfe4
* @author egonw
Expand All @@ -40,7 +39,7 @@ public class AtomTypeManipulator {

/**
* Method that assign properties to an atom given a particular atomType.
* An <code>IllegalArgumentException</code> is thrown if the given <code>IAtomType</code>
* An {@link IllegalArgumentException} is thrown if the given {@link IAtomType}
* is null. <b>This method overwrites non-null values.</b>
*
* @param atom Atom to configure
Expand All @@ -58,14 +57,14 @@ public static void configure(IAtom atom, IAtomType atomType) {
// we set the atom type name, but nothing else
atom.setAtomTypeName(atomType.getAtomTypeName());

// configuring aotm type information is not really valid
// configuring atom type information is not really valid
// for pseudo atoms - first because they basically have no
// type information and second because they may have information
// associated with them from another context, which should not be
// overwritten. So we only do the stuff below if we have a non pseudoatom
//
// a side effect of this is that it is probably not valid to get the atom
// type of a peudo atom. I think this is OK, since you can always check
// type of a pseudo atom. I think this is OK, since you can always check
// whether an atom is a pseudo atom without looking at its atom type
if (!(atom instanceof IPseudoAtom)) {
atom.setSymbol(atomType.getSymbol());
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