- IMP-dev - salilab.org

derivatives of IMP float attributes
by Friedrich Foerster 19 Dec '08

19 Dec '08

hi all, when checking the attributes of my IMP particles i discovered that all float attributes have derivative values. is there any option to switch that off? now i get derivatives for fixed parameters such as radii or mass weights, which are a mere waste of memory. a possible solution would be to distinguish attributes into variables and parameters. thanks frido -- Friedrich Foerster Max-Planck Institut fuer Biochemie Am Klopferspitz 18 D-82152 Martinsried Tel: +49 89 8578 2651 Fax: +49 89 8578 2641 foerster(a)biochem.mpg.de www.tomotronic.org

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TEST_DIRECTORY
by Daniel Russel 18 Dec '08

18 Dec '08

Having it be set in the runalltests script means you cant easily run tests that use it individually, making debugging tests even harder. I would suggest either reverting to using full paths or have imppy.sh set a path to imp and have the test file paths be relative to that.

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ResidueType and AtomType
by Dina Schneidman 17 Dec '08

17 Dec '08

Hi, is there any reason that ResidueTypes and AtomTypes are defined as static variables, rather than enum? what is the best way to map between ResidueType and the PDB residue name string and the same for atoms? thanks! Dina

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ParticleFunction TransformFunction
by Daniel Russel 16 Dec '08

16 Dec '08

Is anyone using these at the moment? From what I understand they are just intermediates until the functionality is moved to the SingletonFunction. If they are not being used, I'll remove them since they spit out swig warnings.

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Re: [IMP-dev] equality tolerance.
by Javier Ángel Velázquez Muriel 16 Dec '08

16 Dec '08

2008/12/15 <imp-dev-owner(a)salilab.org>: > You are not allowed to post to this mailing list, and your message has > been automatically rejected. If you think that your messages are > being rejected in error, contact the mailing list owner at > imp-dev-owner(a)salilab.org. > > > > ---------- Mensaje reenviado ---------- > From: "Javier Ángel Velázquez-Muriel" <javi.velazquez(a)gmail.com> > To: "List for IMP development" <imp-dev(a)salilab.org> > Date: Mon, 15 Dec 2008 17:02:10 -0800 > Subject: equality tolerance. > I am currently using the class vector3D derived from vectorD and I > have noticed that the compare function is very strict. That is, when > checking if a vector is zero, and is for example (0,0,0.00001), I > would probably like that the function returns yes. Same thing with > other vectors, and matrices, and everything that can vary whit > rounding errors. I propose (In fact I have done it already but not > submitted it to SVN) to have a math_macros.h file that defines this > kind of things and specifically here define the macro > EQUALITY_TOLERANCE. I have put a value 1e-6 to it, but maybe you have > different opinions, guys. > >

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VectorD adjustments
by Javier Ángel Velázquez Muriel 15 Dec '08

15 Dec '08

VectorD lacks operators = and -=. Is there any way to perform the operation p = p - v or p-=v then ?

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Re: [IMP-dev] equality tolerance.
by Javier Ángel Velázquez Muriel 15 Dec '08

15 Dec '08

2008/12/15 <imp-dev-owner(a)salilab.org>: > You are not allowed to post to this mailing list, and your message has > been automatically rejected. If you think that your messages are > being rejected in error, contact the mailing list owner at > imp-dev-owner(a)salilab.org. > > > > ---------- Mensaje reenviado ---------- > From: "Javier Ángel Velázquez-Muriel" <javi.velazquez(a)gmail.com> > To: "List for IMP development" <imp-dev(a)salilab.org> > Date: Mon, 15 Dec 2008 17:02:10 -0800 > Subject: equality tolerance. > I am currently using the class vector3D derived from vectorD and I > have noticed that the compare function is very strict. That is, when > checking if a vector is zero, and is for example (0,0,0.00001), I > would probably like that the function returns yes. Same thing with > other vectors, and matrices, and everything that can vary whit > rounding errors. I propose (In fact I have done it already but not > submitted it to SVN) to have a math_macros.h file that defines this > kind of things and specifically here define the macro > EQUALITY_TOLERANCE. I have put a value 1e-6 to it, but maybe you have > different opinions, guys. > >

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VectorD adjustments
by Javier Ángel Velázquez Muriel 15 Dec '08

15 Dec '08

VectorD lacks operators = and -=. Is there any way to perform the operation p = p - v or p-=v then ?

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Karin's lunch
by Daniel Russel 12 Dec '08

12 Dec '08

Let's head out at 12:20. She has to leave relatively early.

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Moving base classes to kernel
by Daniel Russel 12 Dec '08

12 Dec '08

It probably makes sense to move the *Modifier and *Container base classes to the kernel as they are pretty stable and will, hopefully, be used by various modules. Thoughts?

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