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Added test to demonstrate bug where AtomPlacer3D().numberOfUnplacedHeavy... #54

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@ghost ghost commented Sep 1, 2014

...Atoms() counts explicit hydrogens as heavy atoms.

…avyAtoms() counts explicit hydrogens as heavy atoms.
mol.addAtom(new Atom("H"));
mol.addAtom(new Atom("H"));

mol.addBond(0, 1, IBond.Order.DOUBLE);
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C(=[H])([H])([H])([H])?

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Hi John,

I'm a victim of cut and paste editing!

Mark

From: John May
Sent: Monday, September 01, 2014 9:12 PM
To: cdk/cdk
Cc: mbv31602
Subject: Re: [cdk] Added test to demonstrate bug where AtomPlacer3D().numberOfUnplacedHeavy... (#54)

In tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3DTest.java:

@@ -104,6 +104,22 @@ private IAtomContainer makeAlphaPinene() {
return mol;
}

  • private IAtomContainer makeMethaneWithExplicitHydrogens() {
  • IAtomContainer mol = new AtomContainer();
    
  • mol.addAtom(new Atom("C")); 
    
  • mol.addAtom(new Atom("H")); 
    
  • mol.addAtom(new Atom("H")); 
    
  • mol.addAtom(new Atom("H")); 
    
  • mol.addAtom(new Atom("H")); 
    
  • mol.addBond(0, 1, IBond.Order.DOUBLE); 
    
    [H]=C([H])([H])([H])?


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Please could you fix it up (Order.SINGLE) before the commit. Many thanks,

M

From: John May
Sent: Monday, September 01, 2014 9:12 PM
To: cdk/cdk
Cc: mbv31602
Subject: Re: [cdk] Added test to demonstrate bug where AtomPlacer3D().numberOfUnplacedHeavy... (#54)

In tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3DTest.java:

@@ -104,6 +104,22 @@ private IAtomContainer makeAlphaPinene() {
return mol;
}

  • private IAtomContainer makeMethaneWithExplicitHydrogens() {
  • IAtomContainer mol = new AtomContainer();
    
  • mol.addAtom(new Atom("C")); 
    
  • mol.addAtom(new Atom("H")); 
    
  • mol.addAtom(new Atom("H")); 
    
  • mol.addAtom(new Atom("H")); 
    
  • mol.addAtom(new Atom("H")); 
    
  • mol.addBond(0, 1, IBond.Order.DOUBLE); 
    
    [H]=C([H])([H])([H])?


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Will do.

@johnmay
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johnmay commented Sep 1, 2014

Applied and pushed - pulled in the fix also but didn't release there was no pull request for it yet, sorry.

@johnmay johnmay closed this Sep 1, 2014
@ghost ghost deleted the builder3d/bugtest branch September 27, 2014 19:29
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