February 2009 - IMP-dev

Re: [IMP-dev] IMP-dev Digest, Vol 16, Issue 5
by Javier Ángel Velázquez Muriel 03 Feb '09

03 Feb '09

I would suggest something similar to what I have in em/include/EulerOperations.h, if you find it useful. > Given we already have rotation from_fixed_xyz which is a form of euler > angles, this function should probably have a more descriptive name > describing which Euler angles it uses. > > > On Feb 2, 2009, at 10:10 PM, Notification of IMP commits wrote: > > > Author: kerenl(a)SALILAB.ORG > > Date: 2009-02-02 22:10:39 -0800 (Mon, 02 Feb 2009) > > New Revision: 1414 > > > > Modified: > > trunk/modules/algebra/include/Rotation3D.h > > Log: > > add rotation_from_euler > > > > Modified: trunk/modules/algebra/include/Rotation3D.h > > =================================================================== > > --- trunk/modules/algebra/include/Rotation3D.h 2009-02-03 03:11:05 > > UTC (rev 1413) > > +++ trunk/modules/algebra/include/Rotation3D.h 2009-02-03 06:10:39 > > UTC (rev 1414) > > @@ -114,6 +114,24 @@ > > return Rotation3D(a,b,c,d); > > } > > > > +//! Initialize a rotation from euler angles > > +/** > > + \note http://en.wikipedia.org/wiki/ > > + Conversion_between_quaternions_and_Euler_angles > > + \relates Rotation3D > > +*/ > > +inline Rotation3D rotation_from_euler(Float phi, Float theta, Float > > psi) > > +{ > > + Float a,b,c,d; > > + Float c1,c2,c3,s1,s2,s3; > > + c2=cos(theta/2);c1=cos(phi/2);c3=cos(psi/2); > > + s2=sin(theta/2);s1=sin(phi/2);s3=sin(psi/2); > > + a = c1*c2*c3+s1*s2*s3; > > + b = s1*c2*c3-c1*s2*s3; > > + c = c1*s2*c3+s1*c2*s3; > > + d = c1*c2*s3-s1*s2*c3; > > + return Rotation3D(a,b,c,d); > > +} > > //! Generate a Rotation3D object from a rotation matrix > > /** > > \throw ValueException if the rotation is not a rotation matrix. > > > > _______________________________________________ > > IMP-commits mailing list > > IMP-commits(a)salilab.org > > https://salilab.org/mailman/listinfo/imp-commits > >

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lost my paths
by Keren Lasker 03 Feb '09

03 Feb '09

hi, A recent change in r1369 (imppy.sh no longer propagates external LD_LIBRARY_FLAGS and PYTHONPATH) breaks Frido and my assembler code since our pythonpath contains more than just IMP. Can someone please take a look? thanks, Keren.

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Re: [IMP-dev] [IMP-commits] r1414 - trunk/modules/algebra/include
by Daniel Russel 02 Feb '09

02 Feb '09

Given we already have rotation from_fixed_xyz which is a form of euler angles, this function should probably have a more descriptive name describing which Euler angles it uses. On Feb 2, 2009, at 10:10 PM, Notification of IMP commits wrote: > Author: kerenl(a)SALILAB.ORG > Date: 2009-02-02 22:10:39 -0800 (Mon, 02 Feb 2009) > New Revision: 1414 > > Modified: > trunk/modules/algebra/include/Rotation3D.h > Log: > add rotation_from_euler > > Modified: trunk/modules/algebra/include/Rotation3D.h > =================================================================== > --- trunk/modules/algebra/include/Rotation3D.h 2009-02-03 03:11:05 > UTC (rev 1413) > +++ trunk/modules/algebra/include/Rotation3D.h 2009-02-03 06:10:39 > UTC (rev 1414) > @@ -114,6 +114,24 @@ > return Rotation3D(a,b,c,d); > } > > +//! Initialize a rotation from euler angles > +/** > + \note http://en.wikipedia.org/wiki/ > + Conversion_between_quaternions_and_Euler_angles > + \relates Rotation3D > +*/ > +inline Rotation3D rotation_from_euler(Float phi, Float theta, Float > psi) > +{ > + Float a,b,c,d; > + Float c1,c2,c3,s1,s2,s3; > + c2=cos(theta/2);c1=cos(phi/2);c3=cos(psi/2); > + s2=sin(theta/2);s1=sin(phi/2);s3=sin(psi/2); > + a = c1*c2*c3+s1*s2*s3; > + b = s1*c2*c3-c1*s2*s3; > + c = c1*s2*c3+s1*c2*s3; > + d = c1*c2*s3-s1*s2*c3; > + return Rotation3D(a,b,c,d); > +} > //! Generate a Rotation3D object from a rotation matrix > /** > \throw ValueException if the rotation is not a rotation matrix. > > _______________________________________________ > IMP-commits mailing list > IMP-commits(a)salilab.org > https://salilab.org/mailman/listinfo/imp-commits

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Moving Movers to Containers
by Daniel Russel 02 Feb '09

02 Feb '09

As part of the gradual move to using containers, I would like to move the Mover classes (NormalMover and BallMover) to use the container classes. The visible change would be that they would take a non-optional SingletonContainer as the first argument of the constructor instead of an optional list of particles as the last argument. Any reasons not to?

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how can you retrieve the atom index from AtomDecorator ?
by Keren Lasker 02 Feb '09

02 Feb '09

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problems with IMP.modeller.read_pdb
by Keren Lasker 02 Feb '09

02 Feb '09

hey, Reading either the attached files I get: File "../../../utils/transform_mol.py", line 7, in <module> mp= IMP.modeller.read_pdb(sys.argv[1],m) File "/viola1/home/kerenl/bioinformatics/projects/imp/build/lib/IMP/ modeller/__init__.py", line 460, in read_pdb hcp.add_child(hrp) File "/viola1/home/kerenl/bioinformatics/projects/imp/build/lib/IMP/ core/__init__.py", line 1985, in add_child def add_child(*args): return _IMP_core.MolecularHierarchyDecorator_add_child(*args) RuntimeError: Bad key index File "build/include/IMP/internal/AttributeTable.h", line 245 any clue why ? thanks, Keren.

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can I add HETATM to MolecularHierarchyDecorator::Type ?
by Keren Lasker 02 Feb '09

02 Feb '09

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