From: Christoph S. <ste...@ic...> - 2001-10-08 09:20:13
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Egon Willighagen wrote: > > Hi all, > > i've been trying to check if the CML lib is able to read output > from xdrawchem (which looks quite a lot like JChemPaint :), And even uses some code of mine to compute the chemical shifts :-) > Most of the parsing seems to go well, until a SAXException is > thrown... BUT, this expection is "null"... funny and annoying. > Since the exception does not exist, i have absolutely no idea > what the cause of the malfunction is... What should we test? The CDK or JCP-CDK? Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Carl-Zeiss-Promenade 10, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Egon W. <eg...@sc...> - 2001-10-15 16:25:51
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On Saturday 06 October 2001 12:06, Egon Willighagen wrote: > i've been trying to check if the CML lib is able to read output > from xdrawchem (which looks quite a lot like JChemPaint :), > but found that CVS HEAD is not able to read any CML at all... It turned out not to be a problem of the CML filter, but of the changed Atom/AtomType architecture... For at least the sixth time (!!!!) i have to change the Atom code to correctly instantiate variables! This is getting rather annoying... (don't feel guilty... just want to make sure the message arrives ;) Therefore: Constructors are developed to initialize variables. Please use them accordingly. Anyway, the good spin off is that we now have a much better logging mechanism ;) regards, Egon |
From: Christoph S. <ste...@ic...> - 2001-10-15 16:40:59
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Egon Willighagen wrote: > > On Saturday 06 October 2001 12:06, Egon Willighagen wrote: > > i've been trying to check if the CML lib is able to read output > > from xdrawchem (which looks quite a lot like JChemPaint :), > > but found that CVS HEAD is not able to read any CML at all... > > It turned out not to be a problem of the CML filter, but of the > changed Atom/AtomType architecture... > > For at least the sixth time (!!!!) i have to change the Atom code > to correctly instantiate variables! This is getting rather annoying... > (don't feel guilty... just want to make sure the message arrives ;) I'm not quite sure what you mean, but I understand you're angry :-) Could you elaborate a little on the problem? Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Carl-Zeiss-Promenade 10, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Egon W. <eg...@sc...> - 2001-10-16 06:21:45
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On Monday 15 October 2001 18:40, Christoph Steinbeck wrote: > Egon Willighagen wrote: > > For at least the sixth time (!!!!) i have to change the Atom code > > to correctly instantiate variables! This is getting rather annoying..= =2E > > (don't feel guilty... just want to make sure the message arrives ;) > > I'm not quite sure what you mean, but I understand you're angry :-) > Could you elaborate a little on the problem? The SAXException that was thrown by the CML import lib, was actually a NullPointerException which was encapsulated... The NullPointerException was thrown when a 3D coord was added to an Atom... It was thrown because point3d was not initialized... The constructor should have done it, *or* the set3Dx() procedure should check if the point3d var was initialized... (i think the former is the better choice...) The constructor looked like: public Atom(String elementSymbol) { super(elementSymbol); } It now initializes the vars: public Atom(String elementSymbol) { super(elementSymbol); this.point3D =3D new javax.vecmath.Point3d(); this.point2D =3D new javax.vecmath.Point2d(); } Egon |
From: Christoph S. <ste...@ic...> - 2001-10-16 07:25:43
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Egon Willighagen wrote: > > On Monday 15 October 2001 18:40, Christoph Steinbeck wrote: > > Egon Willighagen wrote: > > > For at least the sixth time (!!!!) i have to change the Atom code > > > to correctly instantiate variables! This is getting rather annoying... > > > (don't feel guilty... just want to make sure the message arrives ;) > > > > I'm not quite sure what you mean, but I understand you're angry :-) > > Could you elaborate a little on the problem? > > The SAXException that was thrown by the CML import lib, was actually > a NullPointerException which was encapsulated... > > The NullPointerException was thrown when a 3D coord was added to an > Atom... It was thrown because point3d was not initialized... Well, it was initialized. It was null :-) But honestly, there might be a couple of occasions where I check whether an atom acutally has been assigned meaningful coordinates or not, by cheching for null. Just looking whether the point3d has (0,0,0) certainly doesn't make sense, since this can be a reasonable coordinate setting. In principle, of course, you are completely right with your statements on constructors. We might, however, still want to have a mechanism to see, whether an atom object has (meaningful) coordinates or not. Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Carl-Zeiss-Promenade 10, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Egon W. <eg...@sc...> - 2001-10-08 12:55:35
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On Monday 08 October 2001 11:20, Christoph Steinbeck wrote: > Egon Willighagen wrote: > > Hi all, > > > > i've been trying to check if the CML lib is able to read output > > from xdrawchem (which looks quite a lot like JChemPaint :), > >=20 > > Most of the parsing seems to go well, until a SAXException is > > thrown... BUT, this expection is "null"... funny and annoying. > > Since the exception does not exist, i have absolutely no idea > > what the cause of the malfunction is... > > What should we test? The CDK or JCP-CDK? Both are probably not working, but i have been testing it from JCP-CDK. Egon |