[Cdk-devel] [ cdk-Bugs-636618 ] SaturationChecker.saturateWithHydrogens

[<no...@so...>]

Bugs item #636618, was opened at 2002-11-11 14:30
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=120024&aid=636618&group_id=20024

Category: org.openscience.cdk.tools
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Peter Murray-Rust (petermr)
Assigned to: Nobody/Anonymous (nobody)
Summary: SaturationChecker.saturateWithHydrogens

Initial Comment:
In tryin to use this I keep getting nullPointers, possibly 
because of AtomTypeFactory. I have added a few debug 
prints (AT, ATT) so the line numbers may be 1-2 offset: I 
hope the stacktrace gives clues. I can upload files if 
required.

Peter

In trying to use staurateWithHydrogens() the following types 
of nullPointer occur:

COc1ccc6c(c1)nc3c6CCN4CC5CC(OC(=O)c2cc(OC)c
(OC)c(c2)OC)C(OC)C(C(=O)OC)C5CC34
ATOMTYPES: [[0]H: exact mass = 0.0; relative natural 
abundance = 0.0, [0]C: exac
t mass = 0.0; relative natural abundance = 0.0, [0]N: exact 
mass = 0.0; relative
 natural abundance = 0.0, [0]N: exact mass = 0.0; relative 
natural abundance = 0
.0, [0]O: exact mass = 0.0; relative natural abundance = 
0.0, [0]S: exact mass =
 0.0; relative natural abundance = 0.0, [0]F: exact mass = 
0.0; relative natural
 abundance = 0.0, [0]Cl: exact mass = 0.0; relative natural 
abundance = 0.0, [0]
Br: exact mass = 0.0; relative natural abundance = 0.0, [0]I: 
exact mass = 0.0;
relative natural abundance = 0.0]
AT10
ATT0
ATT1
O [0]C: exact mass = 0.0; relative natural abundance = 0.0
F null
java.lang.NullPointerException
        at org.openscience.cdk.ChemObject.clone
(ChemObject.java:262)
        at org.openscience.cdk.Element.clone
(Element.java:171)
        at org.openscience.cdk.Isotope.clone
(Isotope.java:144)
        at 
org.openscience.cdk.tools.AtomTypeFactory.getAtomTypes
(AtomTypeFactor
y.java:127)
        at 
org.openscience.cdk.tools.SaturationChecker.saturateWithH
ydrogen(Satu
rationChecker.java:251)
        at org.xmlcml.cdk.test.TestCDK.test(TestCDK.java:188)
        at org.xmlcml.cdk.test.TestCDK.main
(TestCDK.java:296)
ATT2
ATT3
ATT4
ATT5
ATT6
ATT7
ATT8
ATT9
Z[Lorg.openscience.cdk.AtomType;@472d48
DAnull
java.lang.NullPointerException
        at 
org.openscience.cdk.tools.SaturationChecker.saturateWithH
ydrogen(Satu
rationChecker.java:256)
        at org.xmlcml.cdk.test.TestCDK.test(TestCDK.java:188)
        at org.xmlcml.cdk.test.TestCDK.main
(TestCDK.java:296)

*** I have put some debug prints (AT and ATT) in 
AtomTypeFactory and tried to print out the atomTypes. As 
seen above these seem to have uninitialised values. 

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