IMP-dev November 2008

imp-dev@salilab.org

7 participants
23 discussions

cross module dependencies
by Daniel Russel 03 Dec '08

03 Dec '08

How are cross-module python dependencies handled in the current build system? If I just %import core.i in misc.i then swig tries to load a module IMP_core rather than IMP.core. Changing the module name to IMP.core in core.i doesn't work since swig declares macros using the name and macros can't have "." in then.

3 7

Re: [IMP-dev] [IMP-commits] r903 - in trunk/modules/misc: include pyext src test/transformation
by Daniel Russel 29 Nov '08

29 Nov '08

Couple quick comments: - we are mostly avoiding abbreviations, so get_trans should probably be "get_translation". It is a bit weird just having that (and no get_matrix or "get_rotation") - The function on Rotation3D shouldn't be mult (since it isn't necessarily multiplication as it is not necessarily a matrix). "transform" taken from Transformation3D or "rotate" are probably the best options. - I still don't like exposing the various methods on Matrix3D having to do with rotation. I think they should be hidden (and some classes made friends if outside classes need them). Otherwise, looks good. THanks. On Nov 29, 2008, at 6:14 PM, Notification of IMP commits wrote: > Author: kerenl(a)SALILAB.ORG > Date: 2008-11-29 18:14:37 -0800 (Sat, 29 Nov 2008) > New Revision: 903 > > Modified: > trunk/modules/misc/include/Rotation3D.h > trunk/modules/misc/include/Transformation3D.h > trunk/modules/misc/pyext/misc.i > trunk/modules/misc/src/SConscript > trunk/modules/misc/test/transformation/ > test_particles_transformation.py > trunk/modules/misc/test/transformation/test_rigid_transformation.py > Log: > Update interface for Rotation3D class > > Modified: trunk/modules/misc/include/Rotation3D.h > =================================================================== > --- trunk/modules/misc/include/Rotation3D.h 2008-11-29 04:49:09 UTC > (rev 902) > +++ trunk/modules/misc/include/Rotation3D.h 2008-11-30 02:14:37 UTC > (rev 903) > @@ -9,122 +9,98 @@ > #define IMPMISC_ROTATION_3D_H > > #include "misc_exports.h" > - > -#include "Matrix3D.h" > +#include "IMP/Vector3D.h" > +#include <iostream> > IMPMISC_BEGIN_NAMESPACE > > //! 3D rotation class. > -/** Holds a 3-dimensional rotation compactly using a quaternions (4 > numbers). > - For a given axis and angle, one can easily construct the > corresponding > - quaternion, and conversely, for a given quaternion one can > easily read > - off the axis and the angle. > - Another advantage is robustness to rounding errors. > - The quaternions representation does not harm the performance > too much. > +/** Holds a three dimensional rotation compactly using a quaternion > (4 numbers). > + Advantages using quaternion: > + 1. Easy convertion between axis/angle to quaternion reprsentation > + 2. Robustness to rounding errors. > + 3. Is not subject to "Gimbal lock" (i.e. attempts to rotate an > + object fail to appear as expected, due to the order in which > the > + rotations are performed) like Euler angles. > + 4. Can be interpolated > + 5. The quaternions representation does not harm the performance > too much. > + http://www.euclideanspace.com/maths/algebra/matrix/orthogonal/rotation/inde… > + > + Currently the rotation can be initialized from either: > + XYZ Euler angles > + Rotation Matrix > + Quaternion > */ > > class IMPMISCEXPORT Rotation3D { > public: > - Rotation3D(){ > - } > - //! Initialize a rotation in x-y-z order from three angles > - /** \param[in] xr Rotation around the X axis in radians > - \param[in] yr Rotation around the Y axis in radians > - \param[in] zr Rotation around the Z axis in radians > - */ > - Rotation3D(Float xr, Float yr, Float zr) { > - init_angles(xr,yr,zr); > + Rotation3D():a_(0.0),b_(0.0),c_(0.0),d_(0.0) {} > + Rotation3D(Float a, Float b, Float c, Float d){ > + a_=a;b_=b;c_=c;d_=d; > } > - //! Initialize a rotation in x-y-z order from three identical > angles > - /** \param[in] e_angle Rotation around first the X axis, Y axis > and Z axis > - in radians > - */ > - Rotation3D(Float e_angle){ > - init_angles(e_angle, e_angle, e_angle); > + //! Rotation by vector multiplication > + Vector3D mult(const Vector3D &o) const { > + return Vector3D((a_*a_+b_*b_-c_*c_-d_*d_)*o[0] + > + 2*(b_*c_-a_*d_)*o[1] + 2*(b_*d_+a_*c_)*o[2], > + 2*(b_*c_+a_*d_)*o[0] + > + (a_*a_-b_*b_+c_*c_-d_*d_)*o[1] + 2*(c_*d_- > a_*b_)*o[2], > + 2*(b_*d_-a_*c_)*o[0] + > + 2*(c_*d_+a_*b_)*o[1] + (a_*a_-b_*b_-c_*c_ > +d_*d_)*o[2]); > } > - Matrix3D get_matrix() const { > - const Float a = quat_[0]; > - const Float b = quat_[1]; > - const Float c = quat_[2]; > - const Float d = quat_[3]; > - return Matrix3D(a*a+b*b-c*c-d*d, 2*(b*c-a*d) , 2*(b*d+a*c), > - 2*(b*c+a*d) , a*a-b*b+c*c-d*d, 2*(c*d-a*b), > - 2*(b*d-a*c) , 2*(c*d+a*b) , a*a-b*b-c*c+d*d); > + void show(std::ostream& out = std::cout) const { > + out <<a_<<"|"<<b_<<"|"<<c_<<"|"<<d_<<'\n'; > } > - //! Rotation by vector multiplication > - Vector3D operator*(const Vector3D &o) const { > - const Float a = quat_[0]; > - const Float b = quat_[1]; > - const Float c = quat_[2]; > - const Float d = quat_[3]; > - return Vector3D((a*a+b*b-c*c-d*d)*o[0] + 2*(b*c-a*d)*o[1] + 2*(b*d > +a*c)*o[2], > - 2*(b*c+a*d)*o[0] + (a*a-b*b+c*c-d*d)*o[1] + > 2*(c*d-a*b)*o[2], > - 2*(b*d-a*c)*o[0] + 2*(c*d+a*b)*o[1] + (a*a-b*b-c*c > +d*d)*o[2]); > - } > - //! Returns the rotation around the x-axis for a rotational > matrix assuming > - //! rotations are performed in the order of x-y-z. > - Float rotX() const{ > - return atan2(matrix32(), matrix33()); > - } > +private: > + Float a_,b_,c_,d_; > +}; > > - //! Returns the rotation around the y-axis for a rotational > matrix assuming > - //! rotations are performed in the order of x-y-z. > - Float rotY() const{ > - return atan2(matrix31(), sqrt(sqr(matrix21())+sqr(matrix11()))); > - } > > - //! Returns the rotation around the z-axis for a rotational > matrix assuming > - //! rotations are performed in the order of x-y-z. > - Float rotZ() const{ > - return atan2(matrix21(), matrix11()); > - } > +//! Initialize a rotation in x-y-z order from three angles > +/** \param[in] xr Rotation around the X axis in radians > + \param[in] yr Rotation around the Y axis in radians > + \param[in] zr Rotation around the Z axis in radians > + \note The three rotations are represented in the original > (fixed) > + coordinate frame. http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles > +*/ > +inline Rotation3D rotation_from_fixed_xyz(Float xr,Float yr, Float > zr) > +{ > + Float a,b,c,d; > + Float cx = cos(xr); Float cy = cos(yr); Float cz = cos(zr); > + Float sx = sin(xr); Float sy = sin(yr); Float sz = sin(zr); > + Float m00 = cz*cy; > + Float m11 = -sy*sx*sz + cx*cz; > + Float m22 = cy*cx; > + a = sqrt(1+m00+m11+m22)/2.0; > + b = sqrt(1+m00-m11-m22)/2.0; > + c = sqrt(1-m00+m11-m22)/2.0; > + d = sqrt(1-m00-m11+m22)/2.0; > + if (cy*sx + sy*cx*sz + sx*cz < 0.0) b = -b; > + if (sz*sx - sy*cx*cz - sy < 0.0) c = -c; > + if (sz*cy + sy*sx*cz + sz*cx < 0.0) d = -d; > + return Rotation3D(a,b,c,d); > +} > > -private: > - void init_angles(Float xr, Float yr, Float zr) { > - Float cx = cos(xr); Float cy = cos(yr); Float cz = cos(zr); > - Float sx = sin(xr); Float sy = sin(yr); Float sz = sin(zr); > - Float m00 = cz*cy; > - Float m11 = -sy*sx*sz + cx*cz; > - Float m22 = cy*cx; > - quat_[0] = sqrt(1+m00+m11+m22)/2.0; > - quat_[1] = sqrt(1+m00-m11-m22)/2.0; > - quat_[2] = sqrt(1-m00+m11-m22)/2.0; > - quat_[3] = sqrt(1-m00-m11+m22)/2.0; > - if (cy*sx + sy*cx*sz + sx*cz < 0.0) quat_[1] = -quat_[1]; > - if (sz*sx - sy*cx*cz - sy < 0.0) quat_[2] = -quat_[2]; > - if (sz*cy + sy*sx*cz + sz*cx < 0.0) quat_[3] = -quat_[3]; > - } > +inline Rotation3D rotation_from_mat(Float m11,Float m12,Float m13, > + Float m21,Float m22,Float m23, > + Float m31,Float m32,Float m33) { > + Float a,b,c,d; > + a = fabs(1+m11+m22+m33)/4; > + b = fabs(1+m11-m22-m33)/4; > + c = fabs(1-m11+m22-m33)/4; > + d = fabs(1-m11-m22+m33)/4; > > - Float matrix11() const { > - return sqr(quat_[0]) + sqr(quat_[1]) - sqr(quat_[2]) - > sqr(quat_[3]); > - } > - Float matrix12() const { > - return 2*(quat_[1]*quat_[2] - quat_[0]*quat_[3]); > - } > - Float matrix13() const{ > - return 2*(quat_[2]*quat_[3] + quat_[0]*quat_[2]); > - } > - Float matrix21() const { > - return 2*(quat_[1]*quat_[2] + quat_[0]*quat_[3]); > - } > - Float matrix22() const { > - return sqr(quat_[0]) - sqr(quat_[1]) + sqr(quat_[2]) - > sqr(quat_[3]); > - } > - Float matrix23() const { > - return 2*(quat_[2]*quat_[3] - quat_[0]*quat_[1]); > - } > - Float matrix31() const { > - return 2*(quat_[1]*quat_[3] - quat_[0]*quat_[2]); > - } > - Float matrix32() const { > - return 2*(quat_[2]*quat_[3] + quat_[0]*quat_[1]); > - } > - Float matrix33() const { > - return sqr(quat_[0]) - sqr(quat_[1]) - sqr(quat_[2]) + > sqr(quat_[3]); > - } > + // make sure quat is normalized. > + Float sum = a+b+c+d; > + a = sqrt(a/sum); > + b = sqrt(b/sum); > + c = sqrt(c/sum); > + d = sqrt(d/sum); > > -private: > - Float sqr(Float a)const{return a*a;} > - Float quat_[4]; > -}; > + if (m32-m23 < 0.0) b=-b; > + if (m13-m31 < 0.0) c=-c; > + if (m21-m12 < 0.0) d=-d; > +} > +/* > +Rotation3D rotation_from_axis_angle(Vector3D axis, Float a){} > +*/ > IMPMISC_END_NAMESPACE > #endif /* IMPMISC_ROTATION_3D_H */ > > Modified: trunk/modules/misc/include/Transformation3D.h > =================================================================== > --- trunk/modules/misc/include/Transformation3D.h 2008-11-29 > 04:49:09 UTC (rev 902) > +++ trunk/modules/misc/include/Transformation3D.h 2008-11-30 > 02:14:37 UTC (rev 903) > @@ -23,24 +23,23 @@ > public: > // public for swig > typedef Transformation3D This; > - Transformation3D():rot_(1.0),trans_(){ > + Transformation3D():rot_(),trans_(){ > } > - > Transformation3D(const Rotation3D& r, const Vector3D& t) > - : rot_(r.get_matrix()), trans_(t){} > + : rot_(r), trans_(t){} > //! transform > Vector3D transform(const Vector3D &o) const { > - return (rot_ * o) + trans_; > + return rot_.mult(o) + trans_; > } > Vector3D get_trans()const{return trans_;} > - Matrix3D get_mat()const{return rot_;} > + // Matrix3D get_mat()const{return rot_;} > void show(std::ostream& out = std::cout) const { > rot_.show(out); > out<<" || "<<trans_<<"\n"; > } > private: > Vector3D trans_; //tranlation > - Matrix3D rot_; //rotation > + Rotation3D rot_; //rotation > }; > > IMPMISC_END_NAMESPACE > > Modified: trunk/modules/misc/pyext/misc.i > =================================================================== > --- trunk/modules/misc/pyext/misc.i 2008-11-29 04:49:09 UTC (rev 902) > +++ trunk/modules/misc/pyext/misc.i 2008-11-30 02:14:37 UTC (rev 903) > @@ -1,11 +1,11 @@ > %module(directors="1") IMP_misc > > %{ > -#include "IMP/misc.h" > -#include "IMP/core.h" > #include "IMP.h" > +#include "IMP/misc.h" > %} > > + > %include "kernel/pyext/IMP_macros.i" > %include "kernel/pyext/IMP_exceptions.i" > > @@ -17,7 +17,6 @@ > > /* Get definitions of kernel base classes (but do not wrap) */ > %import "kernel/pyext/IMP.i" > -%import "modules/core/pyext/core.i" > > namespace IMP { > typedef VectorD<3> Vector3D; > @@ -37,8 +36,6 @@ > %include "IMP/misc/RefineOncePairScore.h" > %include "IMP/misc/TunnelSingletonScore.h" > %include "IMP/misc/LowestRefinedPairScore.h" > -%include "IMP/misc/Matrix3D.h" > %include "IMP/misc/Rotation3D.h" > %include "IMP/misc/Transformation3D.h" > -%include "IMP/misc/ParticleFunction.h" > -%include "IMP/misc/TransformationFunction.h" > +%include "IMP/misc/TransformationFunction.h" > \ No newline at end of file > > Modified: trunk/modules/misc/src/SConscript > =================================================================== > --- trunk/modules/misc/src/SConscript 2008-11-29 04:49:09 UTC (rev > 902) > +++ trunk/modules/misc/src/SConscript 2008-11-30 02:14:37 UTC (rev > 903) > @@ -4,11 +4,11 @@ > files = [ > 'ChildrenParticleRefiner.cpp', > 'LowestRefinedPairScore.cpp', > - 'Matrix3D.cpp', > 'RefineOncePairScore.cpp', > 'Rotation3D.cpp', > 'Transformation3D.cpp', > 'TunnelSingletonScore.cpp', > + 'Rotation3D.cpp','Transformation3D.cpp' > ] > > # Build and install the shared library: > > Modified: trunk/modules/misc/test/transformation/ > test_particles_transformation.py > =================================================================== > --- trunk/modules/misc/test/transformation/ > test_particles_transformation.py 2008-11-29 04:49:09 UTC (rev 902) > +++ trunk/modules/misc/test/transformation/ > test_particles_transformation.py 2008-11-30 02:14:37 UTC (rev 903) > @@ -27,7 +27,8 @@ > > 82.603,46.874,76.53)) > def test_transformation(self): > """Test the TransformationFunction class""" > - > t > = > IMP > .misc > .Transformation3D > (IMP.misc.Rotation3D(0.2,0.8,-0.4),IMP.Vector3D(20.0,-12.4,18.6)) > + r = IMP.misc.rotation_from_fixed_xyz(0.2,0.8,-0.4) > + t=IMP.misc.Transformation3D(r,IMP.Vector3D(20.0,-12.4,18.6)) > tf=IMP.misc.TransformationFunction(t) > r = tf.apply(self.particles) > tp=[] > > Modified: trunk/modules/misc/test/transformation/ > test_rigid_transformation.py > =================================================================== > --- trunk/modules/misc/test/transformation/ > test_rigid_transformation.py 2008-11-29 04:49:09 UTC (rev 902) > +++ trunk/modules/misc/test/transformation/ > test_rigid_transformation.py 2008-11-30 02:14:37 UTC (rev 903) > @@ -16,7 +16,8 @@ > > def test_transformation(self): > """Check that the rotation function is ok""" > - > t > = > IMP > .misc > .Transformation3D > (IMP.misc.Rotation3D(0.2,0.8,-0.4),IMP.Vector3D(20.0,-12.4,18.6)) > + rt = IMP.misc.rotation_from_fixed_xyz(0.2,0.8,-0.4) > + t=IMP.misc.Transformation3D(rt,IMP.Vector3D(20.0,-12.4,18.6)) > v1_t = t.transform(self.v1) > v2_t = t.transform(self.v2) > v1_t_res=IMP.Vector3D(-62.517,86.209, 41.139) > > _______________________________________________ > IMP-commits mailing list > IMP-commits(a)salilab.org > https://salilab.org/mailman/listinfo/imp-commits

2 2

TransformationModifier
by Keren Lasker 29 Nov '08

29 Nov '08

hi, Trying to implement misc.TransformationModifier that inherits from core.SingletonModifier #include "misc_exports.h" #include "internal/misc_version_info.h" ... #include "IMP/core/SingletonModifier.h" IMPMISC_BEGIN_NAMESPACE class IMPMISCEXPORT TransformationModifier : public SingletonModifier The compiler can not recognize SingletonModifier, specifically I get: g++ -pthread -o modules/misc/pyext/misc_wrap.os -c -g -fPIC -fno- strict-aliasing -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -- param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC - Ibuild/include -I/usr/include/python2.5 modules/misc/pyext/misc_wrap.cc In file included from build/include/IMP/misc.h:22, from modules/misc/pyext/misc_wrap.cc:3236: should I change something in the SConsript file of mics/include? thank you, Keren.

2 4

Protecting destructors
by Daniel Russel 26 Nov '08

26 Nov '08

In order to avoid issues like the one I patched in the angle restraint, this class protects the destructors of the ref counted bases classes. These classes should always be controlled through ref counted pointers and so should never be directly deleted.

1 0

Request to simplify IMP config
by Daniel Russel 26 Nov '08

26 Nov '08

Having once again spent a reasonably large amount of time screwing with various bits of the IMP configure scripts in order to get things to work on a mac, I would really like us to simplify things. I suggest the configure options simply be extra_lib_paths="a//b/lib c/d/lib" extra_include_paths="a/b/include c/d/include" python_path="a/b/lib/python-2.5/..." which get parsed and prepended to the scon environment before any tests are performed and get added to all build environments. (I am not sure if space is the best delimiter, but that can be solved later, perhaps by using python syntax "['a/b/include', 'c/d/include']"). The cgal, boost, em, modeller etc arguments can then be removed and configure can then simply test if it can build against modeller, em, cgal, boost etc and not worry about making sure all the paths are added in the right places. We then only have to worry about adding the correct library dependencies to link commands and otherwise ignore dependencies in the build scripts. This also makes it clear that all libraries are searched for in all locations. Keren, Javi and I have all at various points been confused and frustrated by imp picking up copies of libimp in the diva modeller build when neither the imp config arguments nor the directory name (/ diva1/home/modeller-SVN) gave us any clue that such could happen. This also removes the distinction between setups which we happen to have encoded into our config system (which work magically) and setups which differ in some way from what is encoded (which can't be easily made to work). There is currently no way for a user to tell whether things will work, what to do to fix them if they don't and no simple way to document what will work. And we can't ship prebuilt mac binaries for C++ programmers since the boost versions have to match, so we have to support the large number of different ways things can be set up on macs at the very least. Any better suggestions?

3 8

IMP configure cleanup
by Daniel Russel 26 Nov '08

26 Nov '08

Here is a patch which cleans up a bunch of issues with the current IMP config and runtime setup. The only change that people are likely to see up front is that on a mac with macports installed in /opt/local you need to add "include=/opt/local" to your scons command line or your config.py. First, the normal dependencies (boost and cgal) no longer take a path as the value, instead the configure just searches for them in the provided include and link paths. Modeller might be too much of a mess to move to a normal installation, but embed probably should at some point (once someone writes an install script for it). Second, the patch fixes a bunch of places where the internal paths were Appended rather than Prepended, resulting in external headers/ libs being used instead of internal ones. Internal paths should always be searched before external ones. This change includes imppy.sh, so, in theory, once should be able to use modeller on diva again with IMP, but I have not tested this. We also need to be very careful that the library search paths (both link time and dynamic) are always in the same order. Third, the CGAL check checks for linking since it needs some special compiler arguments sometimes. The link check uses Scons.SConf which is not used elsewhere. Since it is been part of scons for several years now (and is part of the 1.0 release of SCons), it seems a bit silly not to use it. Fourth, it adds a way of adding compilation and link arguments to make it easier to handle eccentric setups (such as pre-release versions of CGAL). Fifth, it make the python libraries only link against the corresponding C++ libraries as that is all that is needed (since the C+ + library will pull in the external dependencies) and Mac OS complains about linking against something twice. Finally, the patch adds the external lib search paths to the linked library rpaths on linux (and removes them from imppy.sh on all patforms). There are several reasons to do this - first the LD_LIBRARY_PATH used in the imppy.sh overrides the internal library search paths for other peoples libraries and can result in linking problems if there are multiple libraries on your system with the same name. For example, on my mac there are a large number of libJPEG.dylibs. Adding /opt/local/lib to the LD_LIBRARY_PATH causes the one located there to be used in preference to any found on the internal search paths of the platform SDK libraries and results in link failures. - second, it makes it more likely that IMP is linked against the same libraries at run time and compile time since the two sets of search paths are the same. Various of us have run into nasty problems with this. - on macos the full paths to properly built libraries are embedded in the library upon linking so we don't need LD_LIBRARY_PATH analogs except for getting python started. Another note, the build/lib directory is not added as an rpath since that would change once the libraries are installed (and once they are installed, things that link against the installed libraries are responsible to make sure that imp). I would like to be able to add to the path from the command line but can't figure out how to do it early enough that SWIG is found using the new path.

1 0

module descriptions
by Daniel Russel 25 Nov '08

25 Nov '08

For an eventual IMP release, each module needs some sort of description page giving an overview of the module. I checked in files modules/core/src/core.dox (and a misc version) which provide a first crack at this. So far the page contains: - an overview which includes the namespace containing the code - a list of authors - a list of publications to cite when using the code - the license that the code is released under Anything more that should go in there?

3 4

Containers and Modifiers
by Daniel Russel 24 Nov '08

24 Nov '08

Following my proposal for share containers for particles, I have checked in a set of containers, restraints and score states which allow sets of particles to be shared between different objects. There are versions for Particles and pairs of Particles and there will be version for triplets as soon as Ben checks in the patch to the kernel. All the code is generated from common templates, so supporting different types is easy. The general idea is that you create an appropriate container of particles: say you just have a list of particles, then you create a ListSingletonContainer and put your particles in there. If you want to create a restraint by applying a score to each singleton, you create a SingletonsRestraint and pass the score and the container to the Restraint. If you want to find the close pairs, you create a ClosePairsScoreState and pass it your container. It fills a PairsContainer with all close pairs. You pass that pairs container to a PairsRestraint (just like if you made a ListPairsContainer yourself). Since the container is shared, when the ClosePairsScoreState updates its contents, the PairsRestraint will get the new contents. We also have a new set of base classes called Modifiers which change a particle (or pair of particles) in some way. These can be coupled with a PairsScoreState, for example, to apply the modifier to all of the pairs each time evaluate is called. This provides a way of enforcing hard symmetry constraints (by making one Particle a transformed version of another). Containers can be joined to make another container: i.e. a SingletonContainerSet is a SingletonContainer (just like the ListSingletonContainer above) that contains all the particles container in several SingletonContainers. My intent is to gradually move away from the following classes as their functionality is duplicated in a more flexible way by the new classes using less code: NonbondedRestraint BondedListScoreState SingletonListRestraint PairListRestraint MaxChangeScoreState PairChainRestraint BipartititeNBL AllNBL BondDecoratorListScoreState TripletChainRestraint PairChainRestraint BondDecoratorListRestraint Any comments would be appreciated. A list of the new classes can be found at <http://salilab.org/~drussel/imp/group__restraint.html>

1 0

xcode and imp
by Daniel Russel 24 Nov '08

24 Nov '08

Is anyone else interested in using xcode (the apple IDE) and IMP? I have found it an improvement over emacs (and Aquaemacs) for handling building and editing and debugging on my mac. If others are interested I can maintain an xcode project in the IMP repository. It uses the existing scons build system, it just requires keeping the list of files up to date (so that you can easily get to them in the editor).

2 4

Instantiation of boost code
by Javier Ángel Velázquez Muriel 19 Nov '08

19 Nov '08

Hi there I have a problem trying to use a template class based on Boost in Python. Here is the thing. I write this template: template<typename T> class IMPDLLEXPORT MultiArray: public boost::multi_array<T,MULTIARRAY_DIM> { bla, bla .... } The problem is that I am not able to get this class in Python. The only solution that I have found is to create another class that specifically instantiate the first one: class IMPDLLEXPORT sillyclass { public: MultiArray<Float> data_; }; I've also tried this more clever solution, trying to add this line to kernel/pyext/IMP.i : %template(MultiArrayF) IMP::MultiArray<Float>; but the compiler or SWIG (I don't know which one) complaints with: kernel/pyext/IMP.i:114: Warning(401): Nothing known about base class 'boost::multi_array<float,3 >'. Ignored. kernel/pyext/IMP.i:114: Warning(401): Maybe you forgot to instantiate 'boost::multi_array<float,3 >' using %template. Something that I don't know to fix. Help, please. Javi

1 0

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IMP-dev November 2008