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Re: [IMP-dev] Build system failure, 12/04/2008
by Daniel Russel 04 Dec '08

04 Dec '08

How come we get this failure message when the web page is all green? On Dec 4, 2008, at 7:00 AM, build-system(a)salilab.org wrote: > Build system failed on 12/04/2008. > Failed components: IMP. > Please see https://salilab.org/internal/imp/tests.html for full > details. > _______________________________________________ > IMP-dev mailing list > IMP-dev(a)salilab.org > https://salilab.org/mailman/listinfo/imp-dev

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Re: [IMP-dev] [IMP-commits] r940 - in trunk/modules: core/include core/src core/test core/test/transformation misc/include misc/src misc/test
by Keren Lasker 03 Dec '08

03 Dec '08

Ben - actually Matrix3D is dead since we decided it should inherit from MultiArray . I am not using it for the transformation and you can remove it. On Dec 3, 2008, at 9:26 PM, Notification of IMP commits wrote: > Author: ben(a)SALILAB.ORG > Date: 2008-12-03 12:26:15 -0800 (Wed, 03 Dec 2008) > New Revision: 940 > > Added: > trunk/modules/core/include/Matrix3D.h > trunk/modules/core/include/ParticleFunction.h > trunk/modules/core/include/Rotation3D.h > trunk/modules/core/include/Transformation3D.h > trunk/modules/core/include/TransformationFunction.h > trunk/modules/core/src/Matrix3D.cpp > trunk/modules/core/src/Rotation3D.cpp > trunk/modules/core/src/Transformation3D.cpp > trunk/modules/core/test/transformation/ > Removed: > trunk/modules/misc/include/Matrix3D.h > trunk/modules/misc/include/ParticleFunction.h > trunk/modules/misc/include/Rotation3D.h > trunk/modules/misc/include/Transformation3D.h > trunk/modules/misc/include/TransformationFunction.h > trunk/modules/misc/src/Matrix3D.cpp > trunk/modules/misc/src/Rotation3D.cpp > trunk/modules/misc/src/Transformation3D.cpp > trunk/modules/misc/test/transformation/ > Modified: > trunk/modules/core/include/SConscript > trunk/modules/core/src/SConscript > trunk/modules/core/test/transformation/ > test_particles_transformation.py > trunk/modules/core/test/transformation/test_rigid_transformation.py > trunk/modules/misc/include/SConscript > trunk/modules/misc/src/SConscript > Log: > Move transformation classes from misc to core, since they are of > general > utility. > > > Copied: trunk/modules/core/include/Matrix3D.h (from rev 939, trunk/ > modules/misc/include/Matrix3D.h) > =================================================================== > --- trunk/modules/core/include/Matrix3D.h > (rev 0) > +++ trunk/modules/core/include/Matrix3D.h 2008-12-03 20:26:15 UTC > (rev 940) > @@ -0,0 +1,96 @@ > +/** > + * \file Matrix3D.h \brief 3D matrix class. > + * > + * Copyright 2007-8 Sali Lab. All rights reserved. > + * > + */ > + > +#ifndef IMPCORE_MATRIX_3D_H > +#define IMPCORE_MATRIX_3D_H > + > +#include "core_exports.h" > + > +#include "IMP/Vector3D.h" > +#include <math.h> > + > +IMPCORE_BEGIN_NAMESPACE > + > +//! 3D matrix class. > +/** \ingroup helper > +*/ > +class IMPCOREEXPORT Matrix3D > +{ > +public: > + //! Default constructor. All cells of the matrix are 0 > + Matrix3D() { > + vrow[0] = vrow[1] = vrow[2] = Vector3D(0, 0, 0); > + } > + > + //! Initializes a matrix with explicit values > + Matrix3D(Float a11, Float a12, Float a13, > + Float a21, Float a22, Float a23, > + Float a31, Float a32, Float a33) { > + vrow[0] = Vector3D(a11, a12, a13); > + vrow[1] = Vector3D(a21, a22, a23); > + vrow[2] = Vector3D(a31, a32, a33); > + } > + //! Constructs a matrix with d's in the diagonal and 0's else > where. > + /** \param[in] d the value of the diagonal cells > + */ > + Matrix3D(Float d){ > + vrow[0] = Vector3D(d, 0, 0); > + vrow[1] = Vector3D(0, d, 0); > + vrow[2] = Vector3D(0, 0, d); > + } > + > + Vector3D operator*(const Vector3D &o) const { > + return Vector3D(vrow[0]*o, vrow[1]*o, vrow[2]*o); > + } > + > + //! Returns the rotation around the x-axis for a rotational > matrix assuming > + //! rotations are performed in the order of x-y-z. > + /** \note the output is meaningless if the matrix is not a > rotational matrix. > + */ > + Float rotX() const { > + return atan2(element(3,2), element(3,3)); > + } > + //! Returns the rotation around the y-axis for a rotational > matrix assuming > + //! rotations are performed in the order of x-y-z. > + /** \note the output is meaningless if the matrix is not a > rotational matrix. > + */ > + Float rotY() const { > + return atan2(element(3,1), > + > sqrt(element(2,1)*element(2,1)+element(1,1)*element(1,1))); > + } > + > + //! Returns the rotation around the z-axis for a rotational > matrix assuming > + //! rotations are performed in the order of x-y-z. > + /** \note the output is meaningless if the matrix is not a > rotational matrix. > + */ > + Float rotZ() const { > + return atan2(element(2,1), element(1,1)); > + } > + > + //! Returns 3 rotation angles assuming > + //! rotations are performed in the order of x-y-z. > + /** \note the output is meaningless if the matrix is not a > rotational matrix. > + */ > + Vector3D rot() const { > + return Vector3D(rotX(), rotY(), rotZ()); > + } > + > + void show(std::ostream& out = std::cout) const { > + out <<vrow[0]<<'\n'<<vrow[1]<<'\n'<<vrow[2]<<'\n'; > + } > + > +private: > + //! Returns the numerical value at position row, col in the 3X3 > matrix > + //! row, col should be within the range of 1..3 or run time > errors may occur. > + Float element(const unsigned short r, const unsigned short col) > const { > + return vrow[r-1][col-1]; > + } > + Vector3D vrow[3]; // 3 columns of the matrix are held in 3 > vectors > +}; > + > +IMPCORE_END_NAMESPACE > +#endif /* IMPCORE_MATRIX_3D_H */ > > > Property changes on: trunk/modules/core/include/Matrix3D.h > ___________________________________________________________________ > Added: svn:mergeinfo > + > > Copied: trunk/modules/core/include/ParticleFunction.h (from rev 939, > trunk/modules/misc/include/ParticleFunction.h) > =================================================================== > --- trunk/modules/core/include/ > ParticleFunction.h (rev 0) > +++ trunk/modules/core/include/ParticleFunction.h 2008-12-03 > 20:26:15 UTC (rev 940) > @@ -0,0 +1,32 @@ > +/** > + * \file ParticleFunction.h \brief Apply a function on a > particle > + * > + * Copyright 2007-8 Sali Lab. All rights reserved. > + * > + */ > + > +#ifndef IMPCORE_PARTICLE_FUNCTION_H > +#define IMPCORE_PARTICLE_FUNCTION_H > + > +#include "core_exports.h" > + > +#include <IMP/Particle.h> > + > +IMPCORE_BEGIN_NAMESPACE > + > +//! Virtual class for applying a function on Particles > +/** > + */ > +class ParticleFunction > +{ > +public: > + //! Initialize the particle function > + ParticleFunction(){} > + virtual ~ParticleFunction(){} > + //! Apply a function on a particle > + virtual void apply(Particles ps){} > +}; > + > +IMPCORE_END_NAMESPACE > + > +#endif /* IMPCORE_PARTICLE_FUNCTION_H */ > > > Property changes on: trunk/modules/core/include/ParticleFunction.h > ___________________________________________________________________ > Added: svn:mergeinfo > + > > Copied: trunk/modules/core/include/Rotation3D.h (from rev 939, trunk/ > modules/misc/include/Rotation3D.h) > =================================================================== > --- trunk/modules/core/include/Rotation3D.h > (rev 0) > +++ trunk/modules/core/include/Rotation3D.h 2008-12-03 20:26:15 UTC > (rev 940) > @@ -0,0 +1,107 @@ > +/** > + * \file Rotation3D.h \brief Simple 3D rotation class. > + * > + * Copyright 2007-8 Sali Lab. All rights reserved. > + * > + */ > + > +#ifndef IMPCORE_ROTATION_3D_H > +#define IMPCORE_ROTATION_3D_H > + > +#include "core_exports.h" > +#include "IMP/Vector3D.h" > +#include <iostream> > +IMPCORE_BEGIN_NAMESPACE > + > +//! 3D rotation class. > +/** 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 IMPCOREEXPORT Rotation3D { > +public: > + 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; > + } > + //! 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]); > + } > + void show(std::ostream& out = std::cout) const { > + out <<a_<<"|"<<b_<<"|"<<c_<<"|"<<d_<<'\n'; > + } > +private: > + Float a_,b_,c_,d_; > +}; > + > + > +//! 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); > +} > + > +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; > + > + // 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); > + > + if (m32-m23 < 0.0) b=-b; > + if (m13-m31 < 0.0) c=-c; > + if (m21-m12 < 0.0) d=-d; > + return Rotation3D(a,b,c,d); > +} > +/* > +Rotation3D rotation_from_axis_angle(Vector3D axis, Float a){} > +*/ > +IMPCORE_END_NAMESPACE > +#endif /* IMPCORE_ROTATION_3D_H */ > > > Property changes on: trunk/modules/core/include/Rotation3D.h > ___________________________________________________________________ > Added: svn:mergeinfo > + > > Modified: trunk/modules/core/include/SConscript > =================================================================== > --- trunk/modules/core/include/SConscript 2008-12-03 03:57:02 UTC > (rev 939) > +++ trunk/modules/core/include/SConscript 2008-12-03 20:26:15 UTC > (rev 940) > @@ -42,6 +42,7 @@ > 'Linear.h', > 'ListPairContainer.h', > 'ListSingletonContainer.h', > + 'Matrix3D.h', > 'MaxChangeScoreState.h', > 'MaximumChangeScoreState.h', > 'MaximumPairScoreRestraint.h', > @@ -65,10 +66,12 @@ > 'PairModifier.h', > 'PairsRestraint.h', > 'PairsScoreState.h', > + 'ParticleFunction.h', > 'PropagateBondDerivativesSingletonModifier.h', > 'QuadraticClosePairsFinder.h', > 'ResidueDecorator.h', > 'RestraintSet.h', > + 'Rotation3D.h', > 'SingletonContainer.h', > 'SingletonContainerSet.h', > 'SingletonListRestraint.h', > @@ -77,6 +80,8 @@ > 'SingletonsScoreState.h', > 'SphereDistancePairScore.h', > 'SteepestDescent.h', > + 'Transformation3D.h', > + 'TransformationFunction.h', > 'TransformedDistancePairScore.h', > 'TripletChainRestraint.h', > 'TypedPairScore.h', > > Copied: trunk/modules/core/include/Transformation3D.h (from rev 939, > trunk/modules/misc/include/Transformation3D.h) > =================================================================== > --- trunk/modules/core/include/ > Transformation3D.h (rev 0) > +++ trunk/modules/core/include/Transformation3D.h 2008-12-03 > 20:26:15 UTC (rev 940) > @@ -0,0 +1,47 @@ > +/** > + * \file Transformation3D.h \brief Simple 3D transformation class. > + * > + * Copyright 2007-8 Sali Lab. All rights reserved. > + * > + */ > + > +#ifndef IMPCORE_TRANSFORMATION_3D_H > +#define IMPCORE_TRANSFORMATION_3D_H > + > +#include "core_exports.h" > + > +#include "IMP/Vector3D.h" > +#include "IMP/core/Rotation3D.h" > + > +IMPCORE_BEGIN_NAMESPACE > + > +//! Simple 3D transformation class > +/** \ingroup helper > +*/ > +class IMPCOREEXPORT Transformation3D > +{ > +public: > + // public for swig > + typedef Transformation3D This; > + Transformation3D():rot_(),trans_(){ > + } > + Transformation3D(const Rotation3D& r, const Vector3D& t) > + : rot_(r), trans_(t){} > + //! transform > + Vector3D transform(const Vector3D &o) const { > + return rot_.mult(o) + trans_; > + } > + Vector3D get_trans()const{return trans_;} > + // Matrix3D get_mat()const{return rot_;} > + void show(std::ostream& out = std::cout) const { > + rot_.show(out); > + out<<" || "<<trans_<<"\n"; > + } > +private: > + Vector3D trans_; //tranlation > + Rotation3D rot_; //rotation > +}; > + > +IMPCORE_END_NAMESPACE > + > +#endif /* IMPCORE_TRANSFORMATION_3D_H */ > > > Property changes on: trunk/modules/core/include/Transformation3D.h > ___________________________________________________________________ > Added: svn:mergeinfo > + > > Copied: trunk/modules/core/include/TransformationFunction.h (from > rev 939, trunk/modules/misc/include/TransformationFunction.h) > =================================================================== > --- trunk/modules/core/include/ > TransformationFunction.h (rev 0) > +++ trunk/modules/core/include/TransformationFunction.h 2008-12-03 > 20:26:15 UTC (rev 940) > @@ -0,0 +1,50 @@ > +/** > + * \file TransformationFunction.h > + * \brief Transforms a vector of Particles > + * > + * Copyright 2007-8 Sali Lab. All rights reserved. > + */ > + > +#ifndef IMPCORE_TRANSFORMATION_FUNCTION_H > +#define IMPCORE_TRANSFORMATION_FUNCTION_H > + > +#include "core_exports.h" > + > +#include <IMP/core/ParticleFunction.h> > +#include "IMP/core/Transformation3D.h" > +#include "IMP/core/MolecularHierarchyDecorator.h" > +#include "IMP/core/XYZDecorator.h" > +#include <iostream> > + > +IMPCORE_BEGIN_NAMESPACE > +//! This class transforms a vector of particles > +/** > + */ > +class TransformationFunction : public ParticleFunction > +{ > +public: > + TransformationFunction(Transformation3D t) > + { > + t_=t; > + } > + ~TransformationFunction() > + { > + } > + //! Apply the transformation on all of the particle-leaves of > + //! the input particle. > + void apply(Particles ps) > + { > + IMP::core::XYZDecorator xyz; > + Vector3D v; > + for(Particles::iterator it = ps.begin(); it != ps.end();it++) { > + xyz = IMP::core::XYZDecorator::cast(*it); > + v = xyz.get_coordinates(); > + xyz.set_coordinates(t_.transform(v)); > + } > + } > +private: > + Transformation3D t_; > +}; > + > +IMPCORE_END_NAMESPACE > +#endif /* IMPCORE_TRANSFORMATION_FUNCTION_H */ > > > Property changes on: trunk/modules/core/include/ > TransformationFunction.h > ___________________________________________________________________ > Added: svn:mergeinfo > + > > Copied: trunk/modules/core/src/Matrix3D.cpp (from rev 939, trunk/ > modules/misc/src/Matrix3D.cpp) > =================================================================== > --- trunk/modules/core/src/Matrix3D.cpp (rev > 0) > +++ trunk/modules/core/src/Matrix3D.cpp 2008-12-03 20:26:15 UTC (rev > 940) > @@ -0,0 +1,10 @@ > +/** > + * \file Matrix3D.cpp \brief 3D matrix class. > + * > + * Copyright 2007-8 Sali Lab. All rights reserved. > + * > + */ > +#include "IMP/core/Matrix3D.h" > +IMPCORE_BEGIN_NAMESPACE > + > +IMPCORE_END_NAMESPACE > > > Property changes on: trunk/modules/core/src/Matrix3D.cpp > ___________________________________________________________________ > Added: svn:mergeinfo > + > > Copied: trunk/modules/core/src/Rotation3D.cpp (from rev 939, trunk/ > modules/misc/src/Rotation3D.cpp) > =================================================================== > --- trunk/modules/core/src/Rotation3D.cpp > (rev 0) > +++ trunk/modules/core/src/Rotation3D.cpp 2008-12-03 20:26:15 UTC > (rev 940) > @@ -0,0 +1,10 @@ > +/** > + * \file Rotation3D.cpp \brief Simple 3D rotation class. > + * > + * Copyright 2007-8 Sali Lab. All rights reserved. > + * > + */ > +#include "IMP/core/Rotation3D.h" > +IMPCORE_BEGIN_NAMESPACE > + > +IMPCORE_END_NAMESPACE > > > Property changes on: trunk/modules/core/src/Rotation3D.cpp > ___________________________________________________________________ > Added: svn:mergeinfo > + > > Modified: trunk/modules/core/src/SConscript > =================================================================== > --- trunk/modules/core/src/SConscript 2008-12-03 03:57:02 UTC (rev > 939) > +++ trunk/modules/core/src/SConscript 2008-12-03 20:26:15 UTC (rev > 940) > @@ -38,6 +38,7 @@ > 'HierarchyDecorator.cpp', > 'ListPairContainer.cpp', > 'ListSingletonContainer.cpp', > + 'Matrix3D.cpp', > 'MaxChangeScoreState.cpp', > 'MaximumChangeScoreState.cpp', > 'MaximumPairScoreRestraint.cpp', > @@ -64,6 +65,7 @@ > 'QuadraticClosePairsFinder.cpp', > 'ResidueDecorator.cpp', > 'RestraintSet.cpp', > + 'Rotation3D.cpp', > 'SingletonContainer.cpp', > 'SingletonContainerSet.cpp', > 'SingletonListRestraint.cpp', > @@ -72,6 +74,7 @@ > 'SingletonsScoreState.cpp', > 'SphereDistancePairScore.cpp', > 'SteepestDescent.cpp', > + 'Transformation3D.cpp', > 'TransformedDistancePairScore.cpp', > 'TripletChainRestraint.cpp', > 'TypedPairScore.cpp', > > Copied: trunk/modules/core/src/Transformation3D.cpp (from rev 939, > trunk/modules/misc/src/Transformation3D.cpp) > =================================================================== > --- trunk/modules/core/src/ > Transformation3D.cpp (rev 0) > +++ trunk/modules/core/src/Transformation3D.cpp 2008-12-03 20:26:15 > UTC (rev 940) > @@ -0,0 +1,12 @@ > +/** > + * \file Transformation3D.cpp > + * \brief Simple 3D transformation class. > + * > + * Copyright 2007-8 Sali Lab. All rights reserved. > + */ > +#include "IMP/core/Transformation3D.h" > +#include "IMP/core/XYZDecorator.h" > + > +IMPCORE_BEGIN_NAMESPACE > + > +IMPCORE_END_NAMESPACE > > > Property changes on: trunk/modules/core/src/Transformation3D.cpp > ___________________________________________________________________ > Added: svn:mergeinfo > + > > > Property changes on: trunk/modules/core/test/transformation > ___________________________________________________________________ > Added: svn:ignore > + *.pyc > > Added: svn:mergeinfo > + > > Modified: trunk/modules/core/test/transformation/ > test_particles_transformation.py > =================================================================== > --- trunk/modules/misc/test/transformation/ > test_particles_transformation.py 2008-12-03 03:57:02 UTC (rev 939) > +++ trunk/modules/core/test/transformation/ > test_particles_transformation.py 2008-12-03 20:26:15 UTC (rev 940) > @@ -1,6 +1,5 @@ > import unittest > import IMP.utils > -import IMP.misc > import IMP.core > import IMP.test, IMP > > @@ -27,9 +26,9 @@ > > 82.603,46.874,76.53)) > def test_transformation(self): > """Test the TransformationFunction class""" > - 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 = IMP.core.rotation_from_fixed_xyz(0.2,0.8,-0.4) > + t=IMP.core.Transformation3D(r,IMP.Vector3D(20.0,-12.4,18.6)) > + tf=IMP.core.TransformationFunction(t) > r = tf.apply(self.particles) > tp=[] > tp.append(IMP.Vector3D(47.948, -86.769, 118.648)) > > Modified: trunk/modules/core/test/transformation/ > test_rigid_transformation.py > =================================================================== > --- trunk/modules/misc/test/transformation/ > test_rigid_transformation.py 2008-12-03 03:57:02 UTC (rev 939) > +++ trunk/modules/core/test/transformation/ > test_rigid_transformation.py 2008-12-03 20:26:15 UTC (rev 940) > @@ -2,7 +2,6 @@ > import IMP > import IMP.utils > import IMP.test > -import IMP.misc > > class RigidTransformationTests(IMP.test.TestCase): > """Test particles""" > @@ -16,8 +15,8 @@ > > def test_transformation(self): > """Check that the rotation function is ok""" > - 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)) > + rt = IMP.core.rotation_from_fixed_xyz(0.2,0.8,-0.4) > + t=IMP.core.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) > > Modified: trunk/modules/misc/include/SConscript > =================================================================== > --- trunk/modules/misc/include/SConscript 2008-12-03 03:57:02 UTC > (rev 939) > +++ trunk/modules/misc/include/SConscript 2008-12-03 20:26:15 UTC > (rev 940) > @@ -3,12 +3,7 @@ > files = [ > 'ChildrenParticleRefiner.h', > 'LowestRefinedPairScore.h', > - 'Matrix3D.h', > - 'ParticleFunction.h', > 'RefineOncePairScore.h', > - 'Rotation3D.h', > - 'Transformation3D.h', > - 'TransformationFunction.h', > 'TunnelSingletonScore.h', > 'WormLikeChain.h', > ] > > Modified: trunk/modules/misc/src/SConscript > =================================================================== > --- trunk/modules/misc/src/SConscript 2008-12-03 03:57:02 UTC (rev > 939) > +++ trunk/modules/misc/src/SConscript 2008-12-03 20:26:15 UTC (rev > 940) > @@ -4,10 +4,7 @@ > files = [ > 'ChildrenParticleRefiner.cpp', > 'LowestRefinedPairScore.cpp', > - 'Matrix3D.cpp', > 'RefineOncePairScore.cpp', > - 'Rotation3D.cpp', > - 'Transformation3D.cpp', > 'TunnelSingletonScore.cpp', > ] > > > _______________________________________________ > IMP-commits mailing list > IMP-commits(a)salilab.org > https://salilab.org/mailman/listinfo/imp-commits

2 2

maximum diameter restraints
by Friedrich Foerster 03 Dec '08

03 Dec '08

hi impians, for the 26s project i would like to use a maximum diameter restraint on the shape of proteins. so it'd be a restraint similar to the connectivity restraint: all distances in a protein are evaluated and if the largest distance is above a specified threshold, a harmonic restraint would be applied on the respective pair. did anybody already put something like that into imp? and if no, is anybody familiar with the core also interested in that and willing to code it? it'd take me ages and the code would be ugly ;) 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

4 13

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

kernel and modules
by Daniel Russel 03 Dec '08

03 Dec '08

The current setup with kernel and modules doesn't make any sense. - the different modules (misc and core) are not well defined - kernel is useless by itself and it is the only place where we can easily put things that are widely used as base classes or arguments, so having it be less convenient to contribute to doesn't make sense - since it is so hard to patch the kernel, bug fixes take much longer (for example, it took a week for the tiny changes needed to fix the windows build to be made), the documentation is worse (see the bug tracker) and there are more outstanding bugs than in IMP.core (ditto, see the bug tracker). This is a bit silly. - since it is such a pain to work with code in the kernel, lots of things get put into suboptimal places (such as the transforms in IMP.misc and the modifier base classes in IMP.core) where they be easily put into svn and made visible to others. The same goes for docs (for example introduction.dox is currently in core as that was the only place it could be put while still being easily modified). - if core fails the tests, the daily build is just as broken as if the kernel fails - the current setup increases the amount of work for Ben since only he can fix problems in the kernel and the difficulty in patching the kernel means that that average patch size he has to look at is much larger than if changes could be checked in directly. As before, I advocate, removing acls on the kernel and docs and dividing things into clearer modules such as - kernel (base classes and things that are commonly passed as arguments to functions) - core - geometry (restraints and things which work directly on geometry, just since core is getting awfully big, we don't have to have this though- geometry could depend on CGAL if available as that provides improved functionality) - experimental (code which is just testing things) - em - domino - saxs

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improved imp documentation...
by Daniel Russel 02 Dec '08

02 Dec '08

is available at <https://salilab.org/~drussel/imp/index.html>. There are more examples and things have been cleaned up a lot compared to the documentation in svn. Let me know what more examples would be useful and please send me any interesting examples you have. Note that this documentation does not include any internal or undocumented methods or classes. If you have a or method whose documentation is missing and you want it in there, document it and it will get picked up next time I rebuild. If you want to look at doxygen documentation of the internals of IMP, go to the wiki page linked from the dox main page and click on "Internal Documentation". This is a doxygen build that documents everything (and as a result it is hard to find anything if you don't know what you are looking for). The idea is for the doxygen docs and the wiki pages to replace the docbook documentation (which probably no one else has read other than Ben and I :-) And that the linked wiki page will eventually become the main IMP page. Likewise, it would be good to have pages like modules/core/doc/core.dox for the other modules.

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minor change to move things to internal headers
by Daniel Russel 02 Dec '08

02 Dec '08

This just moves code in internal namespaces to internal headers (or into the IMP namespace as appropriate). The point is to make doxygen docs cleaner.

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cleanup to kernel documentation
by Daniel Russel 01 Dec '08

01 Dec '08

Some minor cleanup of kernel documentation. It includes some changes from the last patch (since 7 copies of IMP are enough to maintain already :-)

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SVN server now fixed
by Ben Webb 01 Dec '08

01 Dec '08

If you continue to run into problems with it, please let me know. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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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

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