Hi, some comments here:
1) I am writing the 2D classes for vector, matrix , image, and image
headers these days. image and imageheader will be part of the em
module. the others,
wherever you suggest. If you plan to do something similar, Keren, let me know.
2) It doesn't seem logical to me why transformations, rotations and
matrices are not part of the kernel, or at least of a math module.
Misc is an inappropriate module.
2008/11/11 <>:
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> Today's Topics:
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> 1. Comments on transformation stuff (Daniel Russel)
> 2. Re: Comments on transformation stuff (Keren Lasker)
> 3. Re: Comments on transformation stuff (Daniel Russel)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 11 Nov 2008 05:58:36 -0800
> From: Daniel Russel <>
> Subject: [IMP-dev] Comments on transformation stuff
> To: List for IMP development <>
> Message-ID: <>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Rotation3D:
> - the protected methods should probably be private as nothing is
> likely to inherit from Rotation3D and doxygen skips documenting
> private methods and the methods are not general purpose
> - it would be nice to be able to initialize from a vector and an angle
> - the current constructor should probably say Euler angle somewhere in
> its docs.
>
> Matrix3D:
> - why are there the rotation methods there? A cleaner interface would
> probably be to have a method is_rotation() and another get_rotation()
> so you can check is is close to a rotation and then get the rotation3D
> object out directly. Having to go through intermediates of some sort
> is messy.
> - it needs an operator[] which returns a vector3D (with appropriate
> bounds checking and all that).
> - I would suggest using \brief to define multi-line brief comments
>
> ParticleFunction:
> - Why does ParticleFunction take Particles? If you want that it should
> be ParticlesFunction, but it seems to me what we really want is for it
> to only take one particle and then use apply methods if we want to
> apply it to more than one. Otherwise we will be creating Particles
> with one Particle everywhere.
> - apply should be pure virtual so that you can tell if you got the
> name or signature wrong when overriding it.
> - at least one of the methods needs to be defined in a .cpp to get
> linking and casting right when using multiple libraries
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 11 Nov 2008 16:12:03 -0500
> From: Keren Lasker <>
> Subject: Re: [IMP-dev] Comments on transformation stuff
> To: List for IMP development <>
> Message-ID: <>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Daniel - thanks for your good review!
> I'll make the suggested changes.
> I agree with everything on Rotation3D and Matrix3D.
> Regarding ParticleFunction - see discussion below.
> On Nov 11, 2008, at 8:58 AM, Daniel Russel wrote:
>
>> Rotation3D:
>> - the protected methods should probably be private as nothing is
>> likely to inherit from Rotation3D and doxygen skips documenting
>> private methods and the methods are not general purpose
>>
>> - it would be nice to be able to initialize from a vector and an angle
>> - the current constructor should probably say Euler angle somewhere in
>> its docs.
>
>
>>
>>
>> Matrix3D:
>> - why are there the rotation methods there? A cleaner interface would
>> probably be to have a method is_rotation() and another get_rotation()
>> so you can check is is close to a rotation and then get the rotation3D
>> object out directly. Having to go through intermediates of some sort
>> is messy.
>> - it needs an operator[] which returns a vector3D (with appropriate
>> bounds checking and all that).
>> - I would suggest using \brief to define multi-line brief comments
>>
>> ParticleFunction:
>> - Why does ParticleFunction take Particles? If you want that it should
>> be ParticlesFunction, but it seems to me what we really want is for it
>> to only take one particle and then use apply methods if we want to
>> apply it to more than one. Otherwise we will be creating Particles
>> with one Particle everywhere.
> yes ... , but then I'll have to do a loop each time I want to rotate a
> molecule.
> maybe it would be better to have MolecularHierarchyDecoratorFunction ?
> So I could just give as input the root of the molecule?
>>
>> - apply should be pure virtual so that you can tell if you got the
>> name or signature wrong when overriding it.
> sure.
>>
>> - at least one of the methods needs to be defined in a .cpp to get
>> linking and casting right when using multiple libraries
> For some reason python can not find the function implementation if it
> is in the cpp file. It happened to Joerg as well - is there anything
> else other than updating the include/Sconscript, ,src/Sconscript and
> pyext/misc.i ?
>>
>> _______________________________________________
>> IMP-dev mailing list
>>
>> https://salilab.org/mailman/listinfo/imp-dev
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>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 11 Nov 2008 06:21:15 -0800
> From: Daniel Russel <>
> Subject: Re: [IMP-dev] Comments on transformation stuff
> To: List for IMP development <>
> Message-ID: <>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>>> ParticleFunction:
>>> - Why does ParticleFunction take Particles? If you want that it
>>> should
>>> be ParticlesFunction, but it seems to me what we really want is for
>>> it
>>> to only take one particle and then use apply methods if we want to
>>> apply it to more than one. Otherwise we will be creating Particles
>>> with one Particle everywhere.
>> yes ... , but then I'll have to do a loop each time I want to rotate a
>> molecule.
> Write a method to apply it to a molecule. And another to apply it to a
> Particles.
>>
>> maybe it would be better to have MolecularHierarchyDecoratorFunction ?
>> So I could just give as input the root of the molecule?
> If it takes a single particle it is easy enough to have a method which
> traverses the hierarchy and applies it to each atom, for example. This
> is annoying to do with the current definition.
>
>
>>
>>>
>>> - apply should be pure virtual so that you can tell if you got the
>>> name or signature wrong when overriding it.
>> sure.
>>>
>>> - at least one of the methods needs to be defined in a .cpp to get
>>> linking and casting right when using multiple libraries
>> For some reason python can not find the function implementation if it
>> is in the cpp file. It happened to Joerg as well - is there anything
>> else other than updating the include/Sconscript, ,src/Sconscript and
>> pyext/misc.i ?
> I'm not quite sure what you mean. What exactly happens? And what were
> you doing? See UnaryFunction as an example of how it should be.
>
> As it stands now, each library which uses ParticleFunction will have
> its own definition of the base class and they will not be
> interconvertible (i.e. a ParticleFunction defined in IMP.core cannot
> be used in something in Kernel which expects a particlefunction).
>
>
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