Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2
Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino.
I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile.
Thanks, Iain
________________________________________ From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] Sent: 12 March 2011 20:00 To: imp-users@salilab.org Subject: IMP-users Digest, Vol 10, Issue 2
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Today's Topics:
1. Re: Symmetry (Daniel Russel)
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Message: 1 Date: Sat, 12 Mar 2011 11:58:04 -0800 From: Daniel Russel drussel@gmail.com Subject: Re: [IMP-users] Symmetry To: Help and discussion for users of IMP imp-users@salilab.org, Keren Lasker kerenlasker@gmail.com Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com Content-Type: text/plain; charset=us-ascii
On Mar 11, 2011, at 12:05 AM, Iain Moal wrote:
> Hi, > I am new to IMP so please fogive naievity! > Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them.
Does that help?
> Also, when reconstructing em maps, such as in particles2density, I get this warning: > WARNING could not find parameters for radius:8.16743 > EM map is using default params > > What does this mean, are the default params ok? Keren will have to answer this.
Daniel
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On Mar 12, 2011, at 5:29 PM, Iain Moal wrote:
> Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. I think an easier way to do this is to set it up as a constraint. That is, let rb0 be your original rigid body and rb1 your symmetry related one (and tr the transform that relates them). Then one can implement a SingletonModifier (which, to be honest we should have already, but don't) called something like TransformedFrom that in its apply call does something like rb1.set_reference_frame(tr*rb0.get_reference_frame().get_transformation_to()) to force rb1 to be in the position defined by rb0. Then you would do trfr= IMP.core.TransformedFrom(rb0, tr) c= IMP.core.SingletonConstraint(trfr, None, rb1) model.add_constraint(c)
See IMP.core.Transform for a class that is very similar to IMP.core.TransformedFrom (but not very useful).
Does that make sense?
> > I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. There are three likely causes: If "import IMP.core" works, but you can't use your new class, then probably you forgot to add the %include and IMP_SWIG_OBJECT lines to the swig.i-in in core/pyext (or didn't add the .cpp and .h to the SConscripts in core).
If "import IMP.core" fails with an error about a missing symbol, then either, IMPCOREEXPORT is missing on the SymmerticalRigidBodyMover or one or more of the required functions for SymmerticalRigidBodyMover is not implemented in the .cpp file.
If you post error message, it might be clearer. There are an unfortunately large number of things that have to be in place to get a class working all the way through to python. I haven't been able to reduce the number much.
> > Thanks, > Iain > > ________________________________________ > From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] > Sent: 12 March 2011 20:00 > To: imp-users@salilab.org > Subject: IMP-users Digest, Vol 10, Issue 2 > > Send IMP-users mailing list submissions to > imp-users@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/imp-users > or, via email, send a message with subject or body 'help' to > imp-users-request@salilab.org > > You can reach the person managing the list at > imp-users-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of IMP-users digest..." > > > Today's Topics: > > 1. Re: Symmetry (Daniel Russel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 12 Mar 2011 11:58:04 -0800 > From: Daniel Russel drussel@gmail.com > Subject: Re: [IMP-users] Symmetry > To: Help and discussion for users of IMP imp-users@salilab.org, > Keren Lasker kerenlasker@gmail.com > Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com > Content-Type: text/plain; charset=us-ascii > > > On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: > >> Hi, >> I am new to IMP so please fogive naievity! >> Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. > I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. > > Does that help? > > >> Also, when reconstructing em maps, such as in particles2density, I get this warning: >> WARNING could not find parameters for radius:8.16743 >> EM map is using default params >> >> What does this mean, are the default params ok? > Keren will have to answer this. > > Daniel > > > ------------------------------ > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > > End of IMP-users Digest, Vol 10, Issue 2 > **************************************** > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
OK. When I tried modifying the core module, I modified modules/core/include/RigidBodyMover.h RigidBodyMover class as follows:
Added to public: RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3,
Float max_translation, Float max_rotation);
Added to private: RigidBody d2_;
RigidBody d3_;
Then, to modules/core/src/RigidBodyMover.cpp, I added the following:
RigidBodyMover::RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3,
Float max_translation, Float max_angle) {
IMP_LOG(VERBOSE,"start RigidBodyMover constructor");
max_translation_=max_translation;
max_angle_ =max_angle;
d_= d;
d2_ = d2;
d3_ = d3;
IMP_LOG(VERBOSE,"finish mover construction" << std::endl);
}
All this does is add a constructor which takes in two extra RigidBody objects and sets d2_ and d3_. IMP compiles without complaining, but when I try and run my script, I get this error:
Traceback (most recent call last):
File "newtest3_test_unchanged_symm.py", line 10, in ?
import IMP.atom
File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 161, in ?
import IMP.core
File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/core/__init__.py", line 28, in ?
import _IMP_core
ImportError: /farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/_IMP_core.so: undefined symbol: _ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd
When I run nm on IMP_core.so, I get
U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, IMP::core::RigidBody, IMP::core::RigidBody, double, double)
U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, double, double)
I haven't a clue why this doesn't work! Because this didn't work, I started again from scratch and attempted to implement a new module called 'symm'. I included only the SConscript files and the following files: in modules/symm/include/ : http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.h http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.h in modules/symm/src/ : http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.cpp http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.cpp
This time, IMP fails to compile. Scons gives this error: scons: warning: Two different environments were specified for target /farm/home/moal01/SOFT/imp-1.0/build/include/IMP/symm/symm_config.h,
but they appear to have the same action: installFunc(target, source, env)
File "/farm/home/moal01/SOFT/imp-1.0/scons_tools/symlinks.py", line 32, in LinkInstall
Just before crashing, it doesn't seem to accept my class name:
Install file: "modules/symm/include/SymmM.h" as "build/include/IMP/symm/SymmM.h"
g++ -o modules/symm/src/SymmM.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fno-strict-aliasing -Wall -Woverloaded-virtual -O2 -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/imp" -DIMP_EXAMPLE_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/doc/imp/examples" -D_USE_MATH_DEFINES -D_USE_MATH_DEFINES -DIMPSYMM_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/usr/local/include modules/symm/src/SymmM.cpp
build/include/IMP/symm/SymmM.h:24: error: expected class-name before '{' token
build/include/IMP/symm/SymmM.h:26: error: expected `)' before 'RigidBody'
build/include/IMP/symm/SymmM.h:36: error: 'RigidBody' does not name a type
build/include/IMP/symm/SymmM.h:37: error: 'RigidBody' does not name a type
build/include/IMP/symm/SymmM.h:38: error: 'RigidBody' does not name a type
modules/symm/src/SymmM.cpp:15: error: expected `)' before 'd'
modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input
modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input
scons: *** [modules/symm/src/SymmM.os] Error 1
scons: building terminated because of errors.
Its very frustrating. I can't make heads nor tails of it! Anyway, I will try your suggestion of implementing the symmetry as a constraint. Hopefully I can do this just in my python scripts without having to delve into any more C++ code.
Thank you again Daniel, I will let you know how I get on with the constraints.
Iain
________________________________________ From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] Sent: 13 March 2011 15:00 To: Help and discussion for users of IMP Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2
On Mar 12, 2011, at 5:29 PM, Iain Moal wrote:
> Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. I think an easier way to do this is to set it up as a constraint. That is, let rb0 be your original rigid body and rb1 your symmetry related one (and tr the transform that relates them). Then one can implement a SingletonModifier (which, to be honest we should have already, but don't) called something like TransformedFrom that in its apply call does something like rb1.set_reference_frame(tr*rb0.get_reference_frame().get_transformation_to()) to force rb1 to be in the position defined by rb0. Then you would do trfr= IMP.core.TransformedFrom(rb0, tr) c= IMP.core.SingletonConstraint(trfr, None, rb1) model.add_constraint(c)
See IMP.core.Transform for a class that is very similar to IMP.core.TransformedFrom (but not very useful).
Does that make sense?
> > I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. There are three likely causes: If "import IMP.core" works, but you can't use your new class, then probably you forgot to add the %include and IMP_SWIG_OBJECT lines to the swig.i-in in core/pyext (or didn't add the .cpp and .h to the SConscripts in core).
If "import IMP.core" fails with an error about a missing symbol, then either, IMPCOREEXPORT is missing on the SymmerticalRigidBodyMover or one or more of the required functions for SymmerticalRigidBodyMover is not implemented in the .cpp file.
If you post error message, it might be clearer. There are an unfortunately large number of things that have to be in place to get a class working all the way through to python. I haven't been able to reduce the number much.
> > Thanks, > Iain > > ________________________________________ > From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] > Sent: 12 March 2011 20:00 > To: imp-users@salilab.org > Subject: IMP-users Digest, Vol 10, Issue 2 > > Send IMP-users mailing list submissions to > imp-users@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/imp-users > or, via email, send a message with subject or body 'help' to > imp-users-request@salilab.org > > You can reach the person managing the list at > imp-users-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of IMP-users digest..." > > > Today's Topics: > > 1. Re: Symmetry (Daniel Russel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 12 Mar 2011 11:58:04 -0800 > From: Daniel Russel drussel@gmail.com > Subject: Re: [IMP-users] Symmetry > To: Help and discussion for users of IMP imp-users@salilab.org, > Keren Lasker kerenlasker@gmail.com > Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com > Content-Type: text/plain; charset=us-ascii > > > On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: > >> Hi, >> I am new to IMP so please fogive naievity! >> Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. > I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. > > Does that help? > > >> Also, when reconstructing em maps, such as in particles2density, I get this warning: >> WARNING could not find parameters for radius:8.16743 >> EM map is using default params >> >> What does this mean, are the default params ok? > Keren will have to answer this. > > Daniel > > > ------------------------------ > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > > End of IMP-users Digest, Vol 10, Issue 2 > **************************************** > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
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This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200.
This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it.
E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
To solve the easy problems first: The reason scons complained about your new module is the IMP scons scripts generate files x_config.h and x_config.cpp for module x which have various config things needed by the module. Having files with those names already there confuses things.
The build problems with the new module are due to either needed headers not being included in the SymmM.h or the class not being searched for in the appropriate name space. In order to use IMP::core::RigidBody in a .h file in another module you have have to #include <IMP/core/rigid_bodies.h> and to refer to it as core::RigidBody.
For the harder question: "_ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd" looks like the original constructor for the RigidBodyMover. Are you sure you didn't delete it by accident from the .cpp file, but not from the .h?
On Mar 13, 2011, at 9:10 AM, Iain Moal wrote:
> > OK. When I tried modifying the core module, I modified modules/core/include/RigidBodyMover.h RigidBodyMover class as follows: > > Added to public: > RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_rotation); > > > Added to private: > RigidBody d2_; > > RigidBody d3_; > > > Then, to modules/core/src/RigidBodyMover.cpp, I added the following: > > RigidBodyMover::RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_angle) { > > IMP_LOG(VERBOSE,"start RigidBodyMover constructor"); > > max_translation_=max_translation; > > max_angle_ =max_angle; > > d_= d; > > d2_ = d2; > > d3_ = d3; > > IMP_LOG(VERBOSE,"finish mover construction" << std::endl); > > } > > > All this does is add a constructor which takes in two extra RigidBody objects and sets d2_ and d3_. IMP compiles without complaining, but when I try and run my script, I get this error: > > Traceback (most recent call last): > > File "newtest3_test_unchanged_symm.py", line 10, in ? > > import IMP.atom > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 161, in ? > > import IMP.core > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/core/__init__.py", line 28, in ? > > import _IMP_core > > ImportError: /farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/_IMP_core.so: undefined symbol: _ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd > > > When I run nm on IMP_core.so, I get > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, IMP::core::RigidBody, IMP::core::RigidBody, double, double) > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, double, double) > > > > > I haven't a clue why this doesn't work! Because this didn't work, I started again from scratch and attempted to implement a new module called 'symm'. I included only the SConscript files and the following files: > in modules/symm/include/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.h > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.h > in modules/symm/src/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.cpp > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.cpp > > > This time, IMP fails to compile. Scons gives this error: > scons: warning: Two different environments were specified for target /farm/home/moal01/SOFT/imp-1.0/build/include/IMP/symm/symm_config.h, > > but they appear to have the same action: installFunc(target, source, env) > > File "/farm/home/moal01/SOFT/imp-1.0/scons_tools/symlinks.py", line 32, in LinkInstall > > > > Just before crashing, it doesn't seem to accept my class name: > > Install file: "modules/symm/include/SymmM.h" as "build/include/IMP/symm/SymmM.h" > > g++ -o modules/symm/src/SymmM.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fno-strict-aliasing -Wall -Woverloaded-virtual -O2 -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/imp" -DIMP_EXAMPLE_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/doc/imp/examples" -D_USE_MATH_DEFINES -D_USE_MATH_DEFINES -DIMPSYMM_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/usr/local/include modules/symm/src/SymmM.cpp > > build/include/IMP/symm/SymmM.h:24: error: expected class-name before '{' token > > build/include/IMP/symm/SymmM.h:26: error: expected `)' before 'RigidBody' > > build/include/IMP/symm/SymmM.h:36: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:37: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:38: error: 'RigidBody' does not name a type > > modules/symm/src/SymmM.cpp:15: error: expected `)' before 'd' > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > scons: *** [modules/symm/src/SymmM.os] Error 1 > > scons: building terminated because of errors. > > > > Its very frustrating. I can't make heads nor tails of it! Anyway, I will try your suggestion of implementing the symmetry as a constraint. Hopefully I can do this just in my python scripts without having to delve into any more C++ code. > > Thank you again Daniel, I will let you know how I get on with the constraints. > > Iain > > > ________________________________________ > From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] > Sent: 13 March 2011 15:00 > To: Help and discussion for users of IMP > Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2 > > On Mar 12, 2011, at 5:29 PM, Iain Moal wrote: > >> Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. > I think an easier way to do this is to set it up as a constraint. That is, let rb0 be your original rigid body and rb1 your symmetry related one (and tr the transform that relates them). Then one can implement a SingletonModifier (which, to be honest we should have already, but don't) called something like TransformedFrom that in its apply call does something like rb1.set_reference_frame(tr*rb0.get_reference_frame().get_transformation_to()) to force rb1 to be in the position defined by rb0. Then you would do > trfr= IMP.core.TransformedFrom(rb0, tr) > c= IMP.core.SingletonConstraint(trfr, None, rb1) > model.add_constraint(c) > > See IMP.core.Transform for a class that is very similar to IMP.core.TransformedFrom (but not very useful). > > Does that make sense? > >> >> I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. > There are three likely causes: > If "import IMP.core" works, but you can't use your new class, then probably you forgot to add the %include and IMP_SWIG_OBJECT lines to the swig.i-in in core/pyext (or didn't add the .cpp and .h to the SConscripts in core). > > If "import IMP.core" fails with an error about a missing symbol, then either, IMPCOREEXPORT is missing on the SymmerticalRigidBodyMover or one or more of the required functions for SymmerticalRigidBodyMover is not implemented in the .cpp file. > > If you post error message, it might be clearer. There are an unfortunately large number of things that have to be in place to get a class working all the way through to python. I haven't been able to reduce the number much. > > >> >> Thanks, >> Iain >> >> ________________________________________ >> From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] >> Sent: 12 March 2011 20:00 >> To: imp-users@salilab.org >> Subject: IMP-users Digest, Vol 10, Issue 2 >> >> Send IMP-users mailing list submissions to >> imp-users@salilab.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://salilab.org/mailman/listinfo/imp-users >> or, via email, send a message with subject or body 'help' to >> imp-users-request@salilab.org >> >> You can reach the person managing the list at >> imp-users-owner@salilab.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of IMP-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Symmetry (Daniel Russel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sat, 12 Mar 2011 11:58:04 -0800 >> From: Daniel Russel drussel@gmail.com >> Subject: Re: [IMP-users] Symmetry >> To: Help and discussion for users of IMP imp-users@salilab.org, >> Keren Lasker kerenlasker@gmail.com >> Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com >> Content-Type: text/plain; charset=us-ascii >> >> >> On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: >> >>> Hi, >>> I am new to IMP so please fogive naievity! >>> Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. >> I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. >> >> Does that help? >> >> >>> Also, when reconstructing em maps, such as in particles2density, I get this warning: >>> WARNING could not find parameters for radius:8.16743 >>> EM map is using default params >>> >>> What does this mean, are the default params ok? >> Keren will have to answer this. >> >> Daniel >> >> >> ------------------------------ >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> >> End of IMP-users Digest, Vol 10, Issue 2 >> **************************************** >> >> This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. >> >> This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. >> >> E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
Hi Daniel,
Removing the symm_config.cpp and .h files eliminated the scons multiple environment warning. With #include <IMP/core/rigid_bodies.h> and referring to RigidBody as core::RigidBody in SymmM.cpp and SymmM.h, most the errors have gone, but I am still left with this one:
build/include/IMP/symm/SymmM.h:22: error: expected class-name before '{' token
With regards to the other approach, in which I modified IMP::core:RigidBodyMover, both the original constructor and the overloaded constructor appear in both RigidBodyMover.h and RigidBodyMover.cpp.
Iain ________________________________________ From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] Sent: 13 March 2011 16:56 To: Help and discussion for users of IMP Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2
To solve the easy problems first: The reason scons complained about your new module is the IMP scons scripts generate files x_config.h and x_config.cpp for module x which have various config things needed by the module. Having files with those names already there confuses things.
The build problems with the new module are due to either needed headers not being included in the SymmM.h or the class not being searched for in the appropriate name space. In order to use IMP::core::RigidBody in a .h file in another module you have have to #include <IMP/core/rigid_bodies.h> and to refer to it as core::RigidBody.
For the harder question: "_ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd" looks like the original constructor for the RigidBodyMover. Are you sure you didn't delete it by accident from the .cpp file, but not from the .h?
On Mar 13, 2011, at 9:10 AM, Iain Moal wrote:
> > OK. When I tried modifying the core module, I modified modules/core/include/RigidBodyMover.h RigidBodyMover class as follows: > > Added to public: > RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_rotation); > > > Added to private: > RigidBody d2_; > > RigidBody d3_; > > > Then, to modules/core/src/RigidBodyMover.cpp, I added the following: > > RigidBodyMover::RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_angle) { > > IMP_LOG(VERBOSE,"start RigidBodyMover constructor"); > > max_translation_=max_translation; > > max_angle_ =max_angle; > > d_= d; > > d2_ = d2; > > d3_ = d3; > > IMP_LOG(VERBOSE,"finish mover construction" << std::endl); > > } > > > All this does is add a constructor which takes in two extra RigidBody objects and sets d2_ and d3_. IMP compiles without complaining, but when I try and run my script, I get this error: > > Traceback (most recent call last): > > File "newtest3_test_unchanged_symm.py", line 10, in ? > > import IMP.atom > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 161, in ? > > import IMP.core > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/core/__init__.py", line 28, in ? > > import _IMP_core > > ImportError: /farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/_IMP_core.so: undefined symbol: _ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd > > > When I run nm on IMP_core.so, I get > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, IMP::core::RigidBody, IMP::core::RigidBody, double, double) > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, double, double) > > > > > I haven't a clue why this doesn't work! Because this didn't work, I started again from scratch and attempted to implement a new module called 'symm'. I included only the SConscript files and the following files: > in modules/symm/include/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.h > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.h > in modules/symm/src/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.cpp > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.cpp > > > This time, IMP fails to compile. Scons gives this error: > scons: warning: Two different environments were specified for target /farm/home/moal01/SOFT/imp-1.0/build/include/IMP/symm/symm_config.h, > > but they appear to have the same action: installFunc(target, source, env) > > File "/farm/home/moal01/SOFT/imp-1.0/scons_tools/symlinks.py", line 32, in LinkInstall > > > > Just before crashing, it doesn't seem to accept my class name: > > Install file: "modules/symm/include/SymmM.h" as "build/include/IMP/symm/SymmM.h" > > g++ -o modules/symm/src/SymmM.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fno-strict-aliasing -Wall -Woverloaded-virtual -O2 -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/imp" -DIMP_EXAMPLE_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/doc/imp/examples" -D_USE_MATH_DEFINES -D_USE_MATH_DEFINES -DIMPSYMM_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/usr/local/include modules/symm/src/SymmM.cpp > > build/include/IMP/symm/SymmM.h:24: error: expected class-name before '{' token > > build/include/IMP/symm/SymmM.h:26: error: expected `)' before 'RigidBody' > > build/include/IMP/symm/SymmM.h:36: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:37: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:38: error: 'RigidBody' does not name a type > > modules/symm/src/SymmM.cpp:15: error: expected `)' before 'd' > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > scons: *** [modules/symm/src/SymmM.os] Error 1 > > scons: building terminated because of errors. > > > > Its very frustrating. I can't make heads nor tails of it! Anyway, I will try your suggestion of implementing the symmetry as a constraint. Hopefully I can do this just in my python scripts without having to delve into any more C++ code. > > Thank you again Daniel, I will let you know how I get on with the constraints. > > Iain > > > ________________________________________ > From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] > Sent: 13 March 2011 15:00 > To: Help and discussion for users of IMP > Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2 > > On Mar 12, 2011, at 5:29 PM, Iain Moal wrote: > >> Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. > I think an easier way to do this is to set it up as a constraint. That is, let rb0 be your original rigid body and rb1 your symmetry related one (and tr the transform that relates them). Then one can implement a SingletonModifier (which, to be honest we should have already, but don't) called something like TransformedFrom that in its apply call does something like rb1.set_reference_frame(tr*rb0.get_reference_frame().get_transformation_to()) to force rb1 to be in the position defined by rb0. Then you would do > trfr= IMP.core.TransformedFrom(rb0, tr) > c= IMP.core.SingletonConstraint(trfr, None, rb1) > model.add_constraint(c) > > See IMP.core.Transform for a class that is very similar to IMP.core.TransformedFrom (but not very useful). > > Does that make sense? > >> >> I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. > There are three likely causes: > If "import IMP.core" works, but you can't use your new class, then probably you forgot to add the %include and IMP_SWIG_OBJECT lines to the swig.i-in in core/pyext (or didn't add the .cpp and .h to the SConscripts in core). > > If "import IMP.core" fails with an error about a missing symbol, then either, IMPCOREEXPORT is missing on the SymmerticalRigidBodyMover or one or more of the required functions for SymmerticalRigidBodyMover is not implemented in the .cpp file. > > If you post error message, it might be clearer. There are an unfortunately large number of things that have to be in place to get a class working all the way through to python. I haven't been able to reduce the number much. > > >> >> Thanks, >> Iain >> >> ________________________________________ >> From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] >> Sent: 12 March 2011 20:00 >> To: imp-users@salilab.org >> Subject: IMP-users Digest, Vol 10, Issue 2 >> >> Send IMP-users mailing list submissions to >> imp-users@salilab.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://salilab.org/mailman/listinfo/imp-users >> or, via email, send a message with subject or body 'help' to >> imp-users-request@salilab.org >> >> You can reach the person managing the list at >> imp-users-owner@salilab.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of IMP-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Symmetry (Daniel Russel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sat, 12 Mar 2011 11:58:04 -0800 >> From: Daniel Russel drussel@gmail.com >> Subject: Re: [IMP-users] Symmetry >> To: Help and discussion for users of IMP imp-users@salilab.org, >> Keren Lasker kerenlasker@gmail.com >> Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com >> Content-Type: text/plain; charset=us-ascii >> >> >> On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: >> >>> Hi, >>> I am new to IMP so please fogive naievity! >>> Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. >> I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. >> >> Does that help? >> >> >>> Also, when reconstructing em maps, such as in particles2density, I get this warning: >>> WARNING could not find parameters for radius:8.16743 >>> EM map is using default params >>> >>> What does this mean, are the default params ok? >> Keren will have to answer this. >> >> Daniel >> >> >> ------------------------------ >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> >> End of IMP-users Digest, Vol 10, Issue 2 >> **************************************** >> >> This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. >> >> This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. >> >> E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
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This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200.
This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it.
E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
Right, I've managed to get it to compile by changing 'public : Mover' to 'public : core::Mover'. This is very good! However, now import IMP.symm in python gives 'ImportError: No module named symm'. I have the following in my ./modules/symm/pyext/swig.i-in :
/* Wrap our own classes */ %include "IMP/symm/SymmM.h"
namespace IMP { namespace symm { IMP_SWIG_OBJECT(SymmM) } }
________________________________________ From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] Sent: 13 March 2011 16:56 To: Help and discussion for users of IMP Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2
To solve the easy problems first: The reason scons complained about your new module is the IMP scons scripts generate files x_config.h and x_config.cpp for module x which have various config things needed by the module. Having files with those names already there confuses things.
The build problems with the new module are due to either needed headers not being included in the SymmM.h or the class not being searched for in the appropriate name space. In order to use IMP::core::RigidBody in a .h file in another module you have have to #include <IMP/core/rigid_bodies.h> and to refer to it as core::RigidBody.
For the harder question: "_ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd" looks like the original constructor for the RigidBodyMover. Are you sure you didn't delete it by accident from the .cpp file, but not from the .h?
On Mar 13, 2011, at 9:10 AM, Iain Moal wrote:
> > OK. When I tried modifying the core module, I modified modules/core/include/RigidBodyMover.h RigidBodyMover class as follows: > > Added to public: > RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_rotation); > > > Added to private: > RigidBody d2_; > > RigidBody d3_; > > > Then, to modules/core/src/RigidBodyMover.cpp, I added the following: > > RigidBodyMover::RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_angle) { > > IMP_LOG(VERBOSE,"start RigidBodyMover constructor"); > > max_translation_=max_translation; > > max_angle_ =max_angle; > > d_= d; > > d2_ = d2; > > d3_ = d3; > > IMP_LOG(VERBOSE,"finish mover construction" << std::endl); > > } > > > All this does is add a constructor which takes in two extra RigidBody objects and sets d2_ and d3_. IMP compiles without complaining, but when I try and run my script, I get this error: > > Traceback (most recent call last): > > File "newtest3_test_unchanged_symm.py", line 10, in ? > > import IMP.atom > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 161, in ? > > import IMP.core > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/core/__init__.py", line 28, in ? > > import _IMP_core > > ImportError: /farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/_IMP_core.so: undefined symbol: _ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd > > > When I run nm on IMP_core.so, I get > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, IMP::core::RigidBody, IMP::core::RigidBody, double, double) > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, double, double) > > > > > I haven't a clue why this doesn't work! Because this didn't work, I started again from scratch and attempted to implement a new module called 'symm'. I included only the SConscript files and the following files: > in modules/symm/include/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.h > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.h > in modules/symm/src/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.cpp > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.cpp > > > This time, IMP fails to compile. Scons gives this error: > scons: warning: Two different environments were specified for target /farm/home/moal01/SOFT/imp-1.0/build/include/IMP/symm/symm_config.h, > > but they appear to have the same action: installFunc(target, source, env) > > File "/farm/home/moal01/SOFT/imp-1.0/scons_tools/symlinks.py", line 32, in LinkInstall > > > > Just before crashing, it doesn't seem to accept my class name: > > Install file: "modules/symm/include/SymmM.h" as "build/include/IMP/symm/SymmM.h" > > g++ -o modules/symm/src/SymmM.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fno-strict-aliasing -Wall -Woverloaded-virtual -O2 -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/imp" -DIMP_EXAMPLE_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/doc/imp/examples" -D_USE_MATH_DEFINES -D_USE_MATH_DEFINES -DIMPSYMM_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/usr/local/include modules/symm/src/SymmM.cpp > > build/include/IMP/symm/SymmM.h:24: error: expected class-name before '{' token > > build/include/IMP/symm/SymmM.h:26: error: expected `)' before 'RigidBody' > > build/include/IMP/symm/SymmM.h:36: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:37: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:38: error: 'RigidBody' does not name a type > > modules/symm/src/SymmM.cpp:15: error: expected `)' before 'd' > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > scons: *** [modules/symm/src/SymmM.os] Error 1 > > scons: building terminated because of errors. > > > > Its very frustrating. I can't make heads nor tails of it! Anyway, I will try your suggestion of implementing the symmetry as a constraint. Hopefully I can do this just in my python scripts without having to delve into any more C++ code. > > Thank you again Daniel, I will let you know how I get on with the constraints. > > Iain > > > ________________________________________ > From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] > Sent: 13 March 2011 15:00 > To: Help and discussion for users of IMP > Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2 > > On Mar 12, 2011, at 5:29 PM, Iain Moal wrote: > >> Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. > I think an easier way to do this is to set it up as a constraint. That is, let rb0 be your original rigid body and rb1 your symmetry related one (and tr the transform that relates them). Then one can implement a SingletonModifier (which, to be honest we should have already, but don't) called something like TransformedFrom that in its apply call does something like rb1.set_reference_frame(tr*rb0.get_reference_frame().get_transformation_to()) to force rb1 to be in the position defined by rb0. Then you would do > trfr= IMP.core.TransformedFrom(rb0, tr) > c= IMP.core.SingletonConstraint(trfr, None, rb1) > model.add_constraint(c) > > See IMP.core.Transform for a class that is very similar to IMP.core.TransformedFrom (but not very useful). > > Does that make sense? > >> >> I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. > There are three likely causes: > If "import IMP.core" works, but you can't use your new class, then probably you forgot to add the %include and IMP_SWIG_OBJECT lines to the swig.i-in in core/pyext (or didn't add the .cpp and .h to the SConscripts in core). > > If "import IMP.core" fails with an error about a missing symbol, then either, IMPCOREEXPORT is missing on the SymmerticalRigidBodyMover or one or more of the required functions for SymmerticalRigidBodyMover is not implemented in the .cpp file. > > If you post error message, it might be clearer. There are an unfortunately large number of things that have to be in place to get a class working all the way through to python. I haven't been able to reduce the number much. > > >> >> Thanks, >> Iain >> >> ________________________________________ >> From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] >> Sent: 12 March 2011 20:00 >> To: imp-users@salilab.org >> Subject: IMP-users Digest, Vol 10, Issue 2 >> >> Send IMP-users mailing list submissions to >> imp-users@salilab.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://salilab.org/mailman/listinfo/imp-users >> or, via email, send a message with subject or body 'help' to >> imp-users-request@salilab.org >> >> You can reach the person managing the list at >> imp-users-owner@salilab.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of IMP-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Symmetry (Daniel Russel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sat, 12 Mar 2011 11:58:04 -0800 >> From: Daniel Russel drussel@gmail.com >> Subject: Re: [IMP-users] Symmetry >> To: Help and discussion for users of IMP imp-users@salilab.org, >> Keren Lasker kerenlasker@gmail.com >> Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com >> Content-Type: text/plain; charset=us-ascii >> >> >> On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: >> >>> Hi, >>> I am new to IMP so please fogive naievity! >>> Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. >> I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. >> >> Does that help? >> >> >>> Also, when reconstructing em maps, such as in particles2density, I get this warning: >>> WARNING could not find parameters for radius:8.16743 >>> EM map is using default params >>> >>> What does this mean, are the default params ok? >> Keren will have to answer this. >> >> Daniel >> >> >> ------------------------------ >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> >> End of IMP-users Digest, Vol 10, Issue 2 >> **************************************** >> >> This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. >> >> This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. >> >> E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
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This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200.
This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it.
E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
Hi again Daniel. I made a silly mistake and didn't have an SConscript file in pyext. However, now I do, but python still crashes:
Traceback (most recent call last): File "newtest3_test_unchanged_symm.py", line 15, in ? import IMP.symm File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/symm/__init__.py", line 28, in ? import _IMP_symm ImportError: libimp_symm.so: cannot open shared object file: No such file or directory
I do have a copy of libimp_symm.so in my /bin/imp-1.0/imp64. I don't want to bother you any more with my problems, but I'm so close to getting this thing working!
Thanks, Iain
________________________________________ From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] Sent: 13 March 2011 16:56 To: Help and discussion for users of IMP Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2
To solve the easy problems first: The reason scons complained about your new module is the IMP scons scripts generate files x_config.h and x_config.cpp for module x which have various config things needed by the module. Having files with those names already there confuses things.
The build problems with the new module are due to either needed headers not being included in the SymmM.h or the class not being searched for in the appropriate name space. In order to use IMP::core::RigidBody in a .h file in another module you have have to #include <IMP/core/rigid_bodies.h> and to refer to it as core::RigidBody.
For the harder question: "_ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd" looks like the original constructor for the RigidBodyMover. Are you sure you didn't delete it by accident from the .cpp file, but not from the .h?
On Mar 13, 2011, at 9:10 AM, Iain Moal wrote:
> > OK. When I tried modifying the core module, I modified modules/core/include/RigidBodyMover.h RigidBodyMover class as follows: > > Added to public: > RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_rotation); > > > Added to private: > RigidBody d2_; > > RigidBody d3_; > > > Then, to modules/core/src/RigidBodyMover.cpp, I added the following: > > RigidBodyMover::RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_angle) { > > IMP_LOG(VERBOSE,"start RigidBodyMover constructor"); > > max_translation_=max_translation; > > max_angle_ =max_angle; > > d_= d; > > d2_ = d2; > > d3_ = d3; > > IMP_LOG(VERBOSE,"finish mover construction" << std::endl); > > } > > > All this does is add a constructor which takes in two extra RigidBody objects and sets d2_ and d3_. IMP compiles without complaining, but when I try and run my script, I get this error: > > Traceback (most recent call last): > > File "newtest3_test_unchanged_symm.py", line 10, in ? > > import IMP.atom > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 161, in ? > > import IMP.core > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/core/__init__.py", line 28, in ? > > import _IMP_core > > ImportError: /farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/_IMP_core.so: undefined symbol: _ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd > > > When I run nm on IMP_core.so, I get > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, IMP::core::RigidBody, IMP::core::RigidBody, double, double) > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, double, double) > > > > > I haven't a clue why this doesn't work! Because this didn't work, I started again from scratch and attempted to implement a new module called 'symm'. I included only the SConscript files and the following files: > in modules/symm/include/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.h > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.h > in modules/symm/src/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.cpp > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.cpp > > > This time, IMP fails to compile. Scons gives this error: > scons: warning: Two different environments were specified for target /farm/home/moal01/SOFT/imp-1.0/build/include/IMP/symm/symm_config.h, > > but they appear to have the same action: installFunc(target, source, env) > > File "/farm/home/moal01/SOFT/imp-1.0/scons_tools/symlinks.py", line 32, in LinkInstall > > > > Just before crashing, it doesn't seem to accept my class name: > > Install file: "modules/symm/include/SymmM.h" as "build/include/IMP/symm/SymmM.h" > > g++ -o modules/symm/src/SymmM.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fno-strict-aliasing -Wall -Woverloaded-virtual -O2 -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/imp" -DIMP_EXAMPLE_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/doc/imp/examples" -D_USE_MATH_DEFINES -D_USE_MATH_DEFINES -DIMPSYMM_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/usr/local/include modules/symm/src/SymmM.cpp > > build/include/IMP/symm/SymmM.h:24: error: expected class-name before '{' token > > build/include/IMP/symm/SymmM.h:26: error: expected `)' before 'RigidBody' > > build/include/IMP/symm/SymmM.h:36: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:37: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:38: error: 'RigidBody' does not name a type > > modules/symm/src/SymmM.cpp:15: error: expected `)' before 'd' > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > scons: *** [modules/symm/src/SymmM.os] Error 1 > > scons: building terminated because of errors. > > > > Its very frustrating. I can't make heads nor tails of it! Anyway, I will try your suggestion of implementing the symmetry as a constraint. Hopefully I can do this just in my python scripts without having to delve into any more C++ code. > > Thank you again Daniel, I will let you know how I get on with the constraints. > > Iain > > > ________________________________________ > From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] > Sent: 13 March 2011 15:00 > To: Help and discussion for users of IMP > Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2 > > On Mar 12, 2011, at 5:29 PM, Iain Moal wrote: > >> Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. > I think an easier way to do this is to set it up as a constraint. That is, let rb0 be your original rigid body and rb1 your symmetry related one (and tr the transform that relates them). Then one can implement a SingletonModifier (which, to be honest we should have already, but don't) called something like TransformedFrom that in its apply call does something like rb1.set_reference_frame(tr*rb0.get_reference_frame().get_transformation_to()) to force rb1 to be in the position defined by rb0. Then you would do > trfr= IMP.core.TransformedFrom(rb0, tr) > c= IMP.core.SingletonConstraint(trfr, None, rb1) > model.add_constraint(c) > > See IMP.core.Transform for a class that is very similar to IMP.core.TransformedFrom (but not very useful). > > Does that make sense? > >> >> I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. > There are three likely causes: > If "import IMP.core" works, but you can't use your new class, then probably you forgot to add the %include and IMP_SWIG_OBJECT lines to the swig.i-in in core/pyext (or didn't add the .cpp and .h to the SConscripts in core). > > If "import IMP.core" fails with an error about a missing symbol, then either, IMPCOREEXPORT is missing on the SymmerticalRigidBodyMover or one or more of the required functions for SymmerticalRigidBodyMover is not implemented in the .cpp file. > > If you post error message, it might be clearer. There are an unfortunately large number of things that have to be in place to get a class working all the way through to python. I haven't been able to reduce the number much. > > >> >> Thanks, >> Iain >> >> ________________________________________ >> From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] >> Sent: 12 March 2011 20:00 >> To: imp-users@salilab.org >> Subject: IMP-users Digest, Vol 10, Issue 2 >> >> Send IMP-users mailing list submissions to >> imp-users@salilab.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://salilab.org/mailman/listinfo/imp-users >> or, via email, send a message with subject or body 'help' to >> imp-users-request@salilab.org >> >> You can reach the person managing the list at >> imp-users-owner@salilab.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of IMP-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Symmetry (Daniel Russel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sat, 12 Mar 2011 11:58:04 -0800 >> From: Daniel Russel drussel@gmail.com >> Subject: Re: [IMP-users] Symmetry >> To: Help and discussion for users of IMP imp-users@salilab.org, >> Keren Lasker kerenlasker@gmail.com >> Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com >> Content-Type: text/plain; charset=us-ascii >> >> >> On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: >> >>> Hi, >>> I am new to IMP so please fogive naievity! >>> Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. >> I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. >> >> Does that help? >> >> >>> Also, when reconstructing em maps, such as in particles2density, I get this warning: >>> WARNING could not find parameters for radius:8.16743 >>> EM map is using default params >>> >>> What does this mean, are the default params ok? >> Keren will have to answer this. >> >> Daniel >> >> >> ------------------------------ >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> >> End of IMP-users Digest, Vol 10, Issue 2 >> **************************************** >> >> This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. >> >> This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. >> >> E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
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This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it.
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First, make sure that "import IMP" is really importing the version of IMP in the directory with the libimp_symm. This is a bit tricky to do with the 1.0 release though (you have to make sure there are no other copies of IMP that could be loading via your PYTHONPATH, or just move it out of the directory and make sure that breaks importing IMP). If not, get that working.
Second, well, I can't think of a second thing to try at the moment.
Do you run IMP using tools/imppy.sh or via PYTHONPATH and LD_LIBRARY_PATH that you set yourself? It looks like the latter, but I just want to make sure.
On Mar 13, 2011, at 12:13 PM, Iain Moal wrote:
> Hi again Daniel. > I made a silly mistake and didn't have an SConscript file in pyext. However, now I do, but python still crashes: > > Traceback (most recent call last): > File "newtest3_test_unchanged_symm.py", line 15, in ? > import IMP.symm > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/symm/__init__.py", line 28, in ? > import _IMP_symm > ImportError: libimp_symm.so: cannot open shared object file: No such file or directory > > I do have a copy of libimp_symm.so in my /bin/imp-1.0/imp64. I don't want to bother you any more with my problems, but I'm so close to getting this thing working! > > Thanks, > Iain > > > ________________________________________ > From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] > Sent: 13 March 2011 16:56 > To: Help and discussion for users of IMP > Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2 > > To solve the easy problems first: > The reason scons complained about your new module is the IMP scons scripts generate files x_config.h and x_config.cpp for module x which have various config things needed by the module. Having files with those names already there confuses things. > > The build problems with the new module are due to either needed headers not being included in the SymmM.h or the class not being searched for in the appropriate name space. In order to use IMP::core::RigidBody in a .h file in another module you have have to > #include <IMP/core/rigid_bodies.h> > and to refer to it as core::RigidBody. > > > For the harder question: > "_ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd" looks like the original constructor for the RigidBodyMover. Are you sure you didn't delete it by accident from the .cpp file, but not from the .h? > > > On Mar 13, 2011, at 9:10 AM, Iain Moal wrote: > >> >> OK. When I tried modifying the core module, I modified modules/core/include/RigidBodyMover.h RigidBodyMover class as follows: >> >> Added to public: >> RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, >> >> Float max_translation, Float max_rotation); >> >> >> Added to private: >> RigidBody d2_; >> >> RigidBody d3_; >> >> >> Then, to modules/core/src/RigidBodyMover.cpp, I added the following: >> >> RigidBodyMover::RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, >> >> Float max_translation, Float max_angle) { >> >> IMP_LOG(VERBOSE,"start RigidBodyMover constructor"); >> >> max_translation_=max_translation; >> >> max_angle_ =max_angle; >> >> d_= d; >> >> d2_ = d2; >> >> d3_ = d3; >> >> IMP_LOG(VERBOSE,"finish mover construction" << std::endl); >> >> } >> >> >> All this does is add a constructor which takes in two extra RigidBody objects and sets d2_ and d3_. IMP compiles without complaining, but when I try and run my script, I get this error: >> >> Traceback (most recent call last): >> >> File "newtest3_test_unchanged_symm.py", line 10, in ? >> >> import IMP.atom >> >> File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 161, in ? >> >> import IMP.core >> >> File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/core/__init__.py", line 28, in ? >> >> import _IMP_core >> >> ImportError: /farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/_IMP_core.so: undefined symbol: _ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd >> >> >> When I run nm on IMP_core.so, I get >> >> U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, IMP::core::RigidBody, IMP::core::RigidBody, double, double) >> >> U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, double, double) >> >> >> >> >> I haven't a clue why this doesn't work! Because this didn't work, I started again from scratch and attempted to implement a new module called 'symm'. I included only the SConscript files and the following files: >> in modules/symm/include/ : >> http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.h >> http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.h >> in modules/symm/src/ : >> http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.cpp >> http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.cpp >> >> >> This time, IMP fails to compile. Scons gives this error: >> scons: warning: Two different environments were specified for target /farm/home/moal01/SOFT/imp-1.0/build/include/IMP/symm/symm_config.h, >> >> but they appear to have the same action: installFunc(target, source, env) >> >> File "/farm/home/moal01/SOFT/imp-1.0/scons_tools/symlinks.py", line 32, in LinkInstall >> >> >> >> Just before crashing, it doesn't seem to accept my class name: >> >> Install file: "modules/symm/include/SymmM.h" as "build/include/IMP/symm/SymmM.h" >> >> g++ -o modules/symm/src/SymmM.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fno-strict-aliasing -Wall -Woverloaded-virtual -O2 -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/imp" -DIMP_EXAMPLE_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/doc/imp/examples" -D_USE_MATH_DEFINES -D_USE_MATH_DEFINES -DIMPSYMM_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/usr/local/include modules/symm/src/SymmM.cpp >> >> build/include/IMP/symm/SymmM.h:24: error: expected class-name before '{' token >> >> build/include/IMP/symm/SymmM.h:26: error: expected `)' before 'RigidBody' >> >> build/include/IMP/symm/SymmM.h:36: error: 'RigidBody' does not name a type >> >> build/include/IMP/symm/SymmM.h:37: error: 'RigidBody' does not name a type >> >> build/include/IMP/symm/SymmM.h:38: error: 'RigidBody' does not name a type >> >> modules/symm/src/SymmM.cpp:15: error: expected `)' before 'd' >> >> modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input >> >> modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input >> >> scons: *** [modules/symm/src/SymmM.os] Error 1 >> >> scons: building terminated because of errors. >> >> >> >> Its very frustrating. I can't make heads nor tails of it! Anyway, I will try your suggestion of implementing the symmetry as a constraint. Hopefully I can do this just in my python scripts without having to delve into any more C++ code. >> >> Thank you again Daniel, I will let you know how I get on with the constraints. >> >> Iain >> >> >> ________________________________________ >> From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] >> Sent: 13 March 2011 15:00 >> To: Help and discussion for users of IMP >> Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2 >> >> On Mar 12, 2011, at 5:29 PM, Iain Moal wrote: >> >>> Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. >> I think an easier way to do this is to set it up as a constraint. That is, let rb0 be your original rigid body and rb1 your symmetry related one (and tr the transform that relates them). Then one can implement a SingletonModifier (which, to be honest we should have already, but don't) called something like TransformedFrom that in its apply call does something like rb1.set_reference_frame(tr*rb0.get_reference_frame().get_transformation_to()) to force rb1 to be in the position defined by rb0. Then you would do >> trfr= IMP.core.TransformedFrom(rb0, tr) >> c= IMP.core.SingletonConstraint(trfr, None, rb1) >> model.add_constraint(c) >> >> See IMP.core.Transform for a class that is very similar to IMP.core.TransformedFrom (but not very useful). >> >> Does that make sense? >> >>> >>> I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. >> There are three likely causes: >> If "import IMP.core" works, but you can't use your new class, then probably you forgot to add the %include and IMP_SWIG_OBJECT lines to the swig.i-in in core/pyext (or didn't add the .cpp and .h to the SConscripts in core). >> >> If "import IMP.core" fails with an error about a missing symbol, then either, IMPCOREEXPORT is missing on the SymmerticalRigidBodyMover or one or more of the required functions for SymmerticalRigidBodyMover is not implemented in the .cpp file. >> >> If you post error message, it might be clearer. There are an unfortunately large number of things that have to be in place to get a class working all the way through to python. I haven't been able to reduce the number much. >> >> >>> >>> Thanks, >>> Iain >>> >>> ________________________________________ >>> From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] >>> Sent: 12 March 2011 20:00 >>> To: imp-users@salilab.org >>> Subject: IMP-users Digest, Vol 10, Issue 2 >>> >>> Send IMP-users mailing list submissions to >>> imp-users@salilab.org >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://salilab.org/mailman/listinfo/imp-users >>> or, via email, send a message with subject or body 'help' to >>> imp-users-request@salilab.org >>> >>> You can reach the person managing the list at >>> imp-users-owner@salilab.org >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of IMP-users digest..." >>> >>> >>> Today's Topics: >>> >>> 1. Re: Symmetry (Daniel Russel) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Sat, 12 Mar 2011 11:58:04 -0800 >>> From: Daniel Russel drussel@gmail.com >>> Subject: Re: [IMP-users] Symmetry >>> To: Help and discussion for users of IMP imp-users@salilab.org, >>> Keren Lasker kerenlasker@gmail.com >>> Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com >>> Content-Type: text/plain; charset=us-ascii >>> >>> >>> On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: >>> >>>> Hi, >>>> I am new to IMP so please fogive naievity! >>>> Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. >>> I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. >>> >>> Does that help? >>> >>> >>>> Also, when reconstructing em maps, such as in particles2density, I get this warning: >>>> WARNING could not find parameters for radius:8.16743 >>>> EM map is using default params >>>> >>>> What does this mean, are the default params ok? >>> Keren will have to answer this. >>> >>> Daniel >>> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >>> >>> >>> End of IMP-users Digest, Vol 10, Issue 2 >>> **************************************** >>> >>> This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. >>> >>> This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. >>> >>> E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >> >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. >> >> This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. >> >> E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
Hi Again Daniel. Scrap my previous comments. I've made it work. Thanks again for your help.
Iain ________________________________________ From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] Sent: 13 March 2011 16:56 To: Help and discussion for users of IMP Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2
To solve the easy problems first: The reason scons complained about your new module is the IMP scons scripts generate files x_config.h and x_config.cpp for module x which have various config things needed by the module. Having files with those names already there confuses things.
The build problems with the new module are due to either needed headers not being included in the SymmM.h or the class not being searched for in the appropriate name space. In order to use IMP::core::RigidBody in a .h file in another module you have have to #include <IMP/core/rigid_bodies.h> and to refer to it as core::RigidBody.
For the harder question: "_ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd" looks like the original constructor for the RigidBodyMover. Are you sure you didn't delete it by accident from the .cpp file, but not from the .h?
On Mar 13, 2011, at 9:10 AM, Iain Moal wrote:
> > OK. When I tried modifying the core module, I modified modules/core/include/RigidBodyMover.h RigidBodyMover class as follows: > > Added to public: > RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_rotation); > > > Added to private: > RigidBody d2_; > > RigidBody d3_; > > > Then, to modules/core/src/RigidBodyMover.cpp, I added the following: > > RigidBodyMover::RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, > > Float max_translation, Float max_angle) { > > IMP_LOG(VERBOSE,"start RigidBodyMover constructor"); > > max_translation_=max_translation; > > max_angle_ =max_angle; > > d_= d; > > d2_ = d2; > > d3_ = d3; > > IMP_LOG(VERBOSE,"finish mover construction" << std::endl); > > } > > > All this does is add a constructor which takes in two extra RigidBody objects and sets d2_ and d3_. IMP compiles without complaining, but when I try and run my script, I get this error: > > Traceback (most recent call last): > > File "newtest3_test_unchanged_symm.py", line 10, in ? > > import IMP.atom > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 161, in ? > > import IMP.core > > File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/core/__init__.py", line 28, in ? > > import _IMP_core > > ImportError: /farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/_IMP_core.so: undefined symbol: _ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd > > > When I run nm on IMP_core.so, I get > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, IMP::core::RigidBody, IMP::core::RigidBody, double, double) > > U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, double, double) > > > > > I haven't a clue why this doesn't work! Because this didn't work, I started again from scratch and attempted to implement a new module called 'symm'. I included only the SConscript files and the following files: > in modules/symm/include/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.h > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.h > in modules/symm/src/ : > http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.cpp > http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.cpp > > > This time, IMP fails to compile. Scons gives this error: > scons: warning: Two different environments were specified for target /farm/home/moal01/SOFT/imp-1.0/build/include/IMP/symm/symm_config.h, > > but they appear to have the same action: installFunc(target, source, env) > > File "/farm/home/moal01/SOFT/imp-1.0/scons_tools/symlinks.py", line 32, in LinkInstall > > > > Just before crashing, it doesn't seem to accept my class name: > > Install file: "modules/symm/include/SymmM.h" as "build/include/IMP/symm/SymmM.h" > > g++ -o modules/symm/src/SymmM.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fno-strict-aliasing -Wall -Woverloaded-virtual -O2 -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/imp" -DIMP_EXAMPLE_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/doc/imp/examples" -D_USE_MATH_DEFINES -D_USE_MATH_DEFINES -DIMPSYMM_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/usr/local/include modules/symm/src/SymmM.cpp > > build/include/IMP/symm/SymmM.h:24: error: expected class-name before '{' token > > build/include/IMP/symm/SymmM.h:26: error: expected `)' before 'RigidBody' > > build/include/IMP/symm/SymmM.h:36: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:37: error: 'RigidBody' does not name a type > > build/include/IMP/symm/SymmM.h:38: error: 'RigidBody' does not name a type > > modules/symm/src/SymmM.cpp:15: error: expected `)' before 'd' > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input > > scons: *** [modules/symm/src/SymmM.os] Error 1 > > scons: building terminated because of errors. > > > > Its very frustrating. I can't make heads nor tails of it! Anyway, I will try your suggestion of implementing the symmetry as a constraint. Hopefully I can do this just in my python scripts without having to delve into any more C++ code. > > Thank you again Daniel, I will let you know how I get on with the constraints. > > Iain > > > ________________________________________ > From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] > Sent: 13 March 2011 15:00 > To: Help and discussion for users of IMP > Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2 > > On Mar 12, 2011, at 5:29 PM, Iain Moal wrote: > >> Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. > I think an easier way to do this is to set it up as a constraint. That is, let rb0 be your original rigid body and rb1 your symmetry related one (and tr the transform that relates them). Then one can implement a SingletonModifier (which, to be honest we should have already, but don't) called something like TransformedFrom that in its apply call does something like rb1.set_reference_frame(tr*rb0.get_reference_frame().get_transformation_to()) to force rb1 to be in the position defined by rb0. Then you would do > trfr= IMP.core.TransformedFrom(rb0, tr) > c= IMP.core.SingletonConstraint(trfr, None, rb1) > model.add_constraint(c) > > See IMP.core.Transform for a class that is very similar to IMP.core.TransformedFrom (but not very useful). > > Does that make sense? > >> >> I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. > There are three likely causes: > If "import IMP.core" works, but you can't use your new class, then probably you forgot to add the %include and IMP_SWIG_OBJECT lines to the swig.i-in in core/pyext (or didn't add the .cpp and .h to the SConscripts in core). > > If "import IMP.core" fails with an error about a missing symbol, then either, IMPCOREEXPORT is missing on the SymmerticalRigidBodyMover or one or more of the required functions for SymmerticalRigidBodyMover is not implemented in the .cpp file. > > If you post error message, it might be clearer. There are an unfortunately large number of things that have to be in place to get a class working all the way through to python. I haven't been able to reduce the number much. > > >> >> Thanks, >> Iain >> >> ________________________________________ >> From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] >> Sent: 12 March 2011 20:00 >> To: imp-users@salilab.org >> Subject: IMP-users Digest, Vol 10, Issue 2 >> >> Send IMP-users mailing list submissions to >> imp-users@salilab.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://salilab.org/mailman/listinfo/imp-users >> or, via email, send a message with subject or body 'help' to >> imp-users-request@salilab.org >> >> You can reach the person managing the list at >> imp-users-owner@salilab.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of IMP-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Symmetry (Daniel Russel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sat, 12 Mar 2011 11:58:04 -0800 >> From: Daniel Russel drussel@gmail.com >> Subject: Re: [IMP-users] Symmetry >> To: Help and discussion for users of IMP imp-users@salilab.org, >> Keren Lasker kerenlasker@gmail.com >> Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com >> Content-Type: text/plain; charset=us-ascii >> >> >> On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: >> >>> Hi, >>> I am new to IMP so please fogive naievity! >>> Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. >> I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. >> >> Does that help? >> >> >>> Also, when reconstructing em maps, such as in particles2density, I get this warning: >>> WARNING could not find parameters for radius:8.16743 >>> EM map is using default params >>> >>> What does this mean, are the default params ok? >> Keren will have to answer this. >> >> Daniel >> >> >> ------------------------------ >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> >> End of IMP-users Digest, Vol 10, Issue 2 >> **************************************** >> >> This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. >> >> This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. >> >> E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
_______________________________________________ IMP-users mailing list IMP-users@salilab.org https://salilab.org/mailman/listinfo/imp-users
This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200.
This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it.
E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
Excellent.
BTW, I had forgotten to send one message before: The IMP_SWIG_OBJECT call needs to look like the other IMP_SWIG_OBJECT calls (otherwise swig tends to silently ignore it). Something like IMP_SWIG_OBJECT(IMP::symm, SymmM, SymmMs); See the example module.
On Mar 13, 2011, at 12:35 PM, Iain Moal wrote:
> Hi Again Daniel. > Scrap my previous comments. I've made it work. > Thanks again for your help. > > Iain > ________________________________________ > From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] > Sent: 13 March 2011 16:56 > To: Help and discussion for users of IMP > Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2 > > To solve the easy problems first: > The reason scons complained about your new module is the IMP scons scripts generate files x_config.h and x_config.cpp for module x which have various config things needed by the module. Having files with those names already there confuses things. > > The build problems with the new module are due to either needed headers not being included in the SymmM.h or the class not being searched for in the appropriate name space. In order to use IMP::core::RigidBody in a .h file in another module you have have to > #include <IMP/core/rigid_bodies.h> > and to refer to it as core::RigidBody. > > > For the harder question: > "_ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd" looks like the original constructor for the RigidBodyMover. Are you sure you didn't delete it by accident from the .cpp file, but not from the .h? > > > On Mar 13, 2011, at 9:10 AM, Iain Moal wrote: > >> >> OK. When I tried modifying the core module, I modified modules/core/include/RigidBodyMover.h RigidBodyMover class as follows: >> >> Added to public: >> RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, >> >> Float max_translation, Float max_rotation); >> >> >> Added to private: >> RigidBody d2_; >> >> RigidBody d3_; >> >> >> Then, to modules/core/src/RigidBodyMover.cpp, I added the following: >> >> RigidBodyMover::RigidBodyMover(RigidBody d, RigidBody d2, RigidBody d3, >> >> Float max_translation, Float max_angle) { >> >> IMP_LOG(VERBOSE,"start RigidBodyMover constructor"); >> >> max_translation_=max_translation; >> >> max_angle_ =max_angle; >> >> d_= d; >> >> d2_ = d2; >> >> d3_ = d3; >> >> IMP_LOG(VERBOSE,"finish mover construction" << std::endl); >> >> } >> >> >> All this does is add a constructor which takes in two extra RigidBody objects and sets d2_ and d3_. IMP compiles without complaining, but when I try and run my script, I get this error: >> >> Traceback (most recent call last): >> >> File "newtest3_test_unchanged_symm.py", line 10, in ? >> >> import IMP.atom >> >> File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 161, in ? >> >> import IMP.core >> >> File "/farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/IMP/core/__init__.py", line 28, in ? >> >> import _IMP_core >> >> ImportError: /farm/home/moal01/bin/imp-1.0/lib64/python2.4/site-packages/_IMP_core.so: undefined symbol: _ZN3IMP4core14RigidBodyMoverC1ENS0_9RigidBodyES2_S2_dd >> >> >> When I run nm on IMP_core.so, I get >> >> U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, IMP::core::RigidBody, IMP::core::RigidBody, double, double) >> >> U IMP::core::RigidBodyMover::RigidBodyMover(IMP::core::RigidBody, double, double) >> >> >> >> >> I haven't a clue why this doesn't work! Because this didn't work, I started again from scratch and attempted to implement a new module called 'symm'. I included only the SConscript files and the following files: >> in modules/symm/include/ : >> http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.h >> http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.h >> in modules/symm/src/ : >> http://bmm.cancerresearchuk.org/~moal01/IMP/symm_config.cpp >> http://bmm.cancerresearchuk.org/~moal01/IMP/SymmM.cpp >> >> >> This time, IMP fails to compile. Scons gives this error: >> scons: warning: Two different environments were specified for target /farm/home/moal01/SOFT/imp-1.0/build/include/IMP/symm/symm_config.h, >> >> but they appear to have the same action: installFunc(target, source, env) >> >> File "/farm/home/moal01/SOFT/imp-1.0/scons_tools/symlinks.py", line 32, in LinkInstall >> >> >> >> Just before crashing, it doesn't seem to accept my class name: >> >> Install file: "modules/symm/include/SymmM.h" as "build/include/IMP/symm/SymmM.h" >> >> g++ -o modules/symm/src/SymmM.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fno-strict-aliasing -Wall -Woverloaded-virtual -O2 -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/imp" -DIMP_EXAMPLE_DIRECTORY="/farm/home/moal01/bin/imp-1.0/share/doc/imp/examples" -D_USE_MATH_DEFINES -D_USE_MATH_DEFINES -DIMPSYMM_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/usr/local/include modules/symm/src/SymmM.cpp >> >> build/include/IMP/symm/SymmM.h:24: error: expected class-name before '{' token >> >> build/include/IMP/symm/SymmM.h:26: error: expected `)' before 'RigidBody' >> >> build/include/IMP/symm/SymmM.h:36: error: 'RigidBody' does not name a type >> >> build/include/IMP/symm/SymmM.h:37: error: 'RigidBody' does not name a type >> >> build/include/IMP/symm/SymmM.h:38: error: 'RigidBody' does not name a type >> >> modules/symm/src/SymmM.cpp:15: error: expected `)' before 'd' >> >> modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input >> >> modules/symm/src/SymmM.cpp:64: error: expected `}' at end of input >> >> scons: *** [modules/symm/src/SymmM.os] Error 1 >> >> scons: building terminated because of errors. >> >> >> >> Its very frustrating. I can't make heads nor tails of it! Anyway, I will try your suggestion of implementing the symmetry as a constraint. Hopefully I can do this just in my python scripts without having to delve into any more C++ code. >> >> Thank you again Daniel, I will let you know how I get on with the constraints. >> >> Iain >> >> >> ________________________________________ >> From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of Daniel Russel [drussel@gmail.com] >> Sent: 13 March 2011 15:00 >> To: Help and discussion for users of IMP >> Subject: Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2 >> >> On Mar 12, 2011, at 5:29 PM, Iain Moal wrote: >> >>> Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. >> I think an easier way to do this is to set it up as a constraint. That is, let rb0 be your original rigid body and rb1 your symmetry related one (and tr the transform that relates them). Then one can implement a SingletonModifier (which, to be honest we should have already, but don't) called something like TransformedFrom that in its apply call does something like rb1.set_reference_frame(tr*rb0.get_reference_frame().get_transformation_to()) to force rb1 to be in the position defined by rb0. Then you would do >> trfr= IMP.core.TransformedFrom(rb0, tr) >> c= IMP.core.SingletonConstraint(trfr, None, rb1) >> model.add_constraint(c) >> >> See IMP.core.Transform for a class that is very similar to IMP.core.TransformedFrom (but not very useful). >> >> Does that make sense? >> >>> >>> I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. >> There are three likely causes: >> If "import IMP.core" works, but you can't use your new class, then probably you forgot to add the %include and IMP_SWIG_OBJECT lines to the swig.i-in in core/pyext (or didn't add the .cpp and .h to the SConscripts in core). >> >> If "import IMP.core" fails with an error about a missing symbol, then either, IMPCOREEXPORT is missing on the SymmerticalRigidBodyMover or one or more of the required functions for SymmerticalRigidBodyMover is not implemented in the .cpp file. >> >> If you post error message, it might be clearer. There are an unfortunately large number of things that have to be in place to get a class working all the way through to python. I haven't been able to reduce the number much. >> >> >>> >>> Thanks, >>> Iain >>> >>> ________________________________________ >>> From: imp-users-bounces@salilab.org [imp-users-bounces@salilab.org] On Behalf Of imp-users-request@salilab.org [imp-users-request@salilab.org] >>> Sent: 12 March 2011 20:00 >>> To: imp-users@salilab.org >>> Subject: IMP-users Digest, Vol 10, Issue 2 >>> >>> Send IMP-users mailing list submissions to >>> imp-users@salilab.org >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://salilab.org/mailman/listinfo/imp-users >>> or, via email, send a message with subject or body 'help' to >>> imp-users-request@salilab.org >>> >>> You can reach the person managing the list at >>> imp-users-owner@salilab.org >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of IMP-users digest..." >>> >>> >>> Today's Topics: >>> >>> 1. Re: Symmetry (Daniel Russel) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Sat, 12 Mar 2011 11:58:04 -0800 >>> From: Daniel Russel drussel@gmail.com >>> Subject: Re: [IMP-users] Symmetry >>> To: Help and discussion for users of IMP imp-users@salilab.org, >>> Keren Lasker kerenlasker@gmail.com >>> Message-ID: 2093665D-E853-471A-9F1D-2641669FC29E@gmail.com >>> Content-Type: text/plain; charset=us-ascii >>> >>> >>> On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: >>> >>>> Hi, >>>> I am new to IMP so please fogive naievity! >>>> Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. >>> I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. >>> >>> Does that help? >>> >>> >>>> Also, when reconstructing em maps, such as in particles2density, I get this warning: >>>> WARNING could not find parameters for radius:8.16743 >>>> EM map is using default params >>>> >>>> What does this mean, are the default params ok? >>> Keren will have to answer this. >>> >>> Daniel >>> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >>> >>> >>> End of IMP-users Digest, Vol 10, Issue 2 >>> **************************************** >>> >>> This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. >>> >>> This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. >>> >>> E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >> >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> >> This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. >> >> This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. >> >> E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
participants (2)
-
Daniel Russel -
Iain Moal