- IMP-dev - salilab.org

Re: [IMP-dev] IMP-dev meeting tomorrow
by Barak Raveh 16 Oct '12

16 Oct '12

Hi Daniel, Could we keep it for lunch as originally planned? We can have it while eating in the group meeting room if it's free, but then 1pm is probably a better hour Barak On Mon, Oct 15, 2012 at 10:54 AM, Daniel Russel <drussel(a)gmail.com> wrote: > Will be in the usual group meeting slot and room, since group meeting took > ours :-) > > > > > > > -- Barak

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Let's restart having imp-dev meetings
by Daniel Russel 09 Oct '12

09 Oct '12

How is Tuesdays at 11, every two weeks, starting next week?

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Multithreaded IMP
by Daniel Russel 20 Sep '12

20 Sep '12

I've been experimenting with using OpenMP for getting IMP to make use of more than one thread during evaluation. At the moment, all that is done is that independent ScoreStates have their update methods called in parallel, and restraints are evaluated in parallel. The speedups look to be pretty good with my benchmarks, but I haven't tested too many things yet. If you want to play with it or get involved in improving it, you can get it from the salilab github repo (http://github.com/salilab/imp)… [View More]

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If you needed more reasons to upgrade to mac os 10.8...
by Daniel Russel 18 Aug '12

18 Aug '12

clang++ The new mac os compiler seems to be a huge improvement over gcc. In addition to much nicer error messages and faster compilation, I can build IMP from scratch in 20 minutes on my 2 year old laptop, keeping all 4 cores busy. And the laptop remains completely usable for other purposes the whole time (as compared to building IMP with gcc which locks up my laptop and linux box for extended periods and tends to spend inordinate amounts of time waiting for I/O).

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CHARMM topology question
by Dina Schneidman 17 Aug '12

17 Aug '12

Hi, I want to add bonds, angles and dihedrals to my structure. It has some missing atoms, but I don't want them there on purpose. When I create the topology, those atoms are automatically added to the structure. Is there a way to tell it not to add any missing atoms? I use the following code: IMP::atom::CHARMMParameters* ff = new IMP::atom::CHARMMParameters(topology_file_name, parameter_file_name); IMP::atom::CHARMMTopology* topology = ff->create_topology(mhd_); topology->… [View More]

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Re: [IMP-dev] [IMP-build] Build system failure, 08/15/2012
by Barak Raveh 16 Aug '12

16 Aug '12

guys, let's try to get one day of TOTALLY clean tests :) can people in charge of* cgal, isd and multifit *(Fast build only)** give a quick look to see if they can quickly solve the test issues (the atom case is known, and if other tests are solved, we'll handle that too). If there's a complicated issue behind these failures, we can temporarily disable those tests until the relevant person get to work on it. B On Wed, Aug 15, 2012 at 7:01 AM, Notification of IMP build failures < imp-build(a)… [View More]

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boost versions and directories.cpp
by Daniel Russel 07 Aug '12

07 Aug '12

Boost has dropped support for filesystem v2 as of 1.49, so directories.cpp needs to be patched. It is already a mess with trying to support the various permutations of things (VC or not, boost < 1.35, boost < 1.36, and now boost filesystem v2 vs v3, no boost file system) so it would be really nice to simplify it. Some options are: 1) only support boost.filesystem v3 (with windows) or no boost.filesystem: the motivation being that this is the way forward and there is no reason on windows … [View More]

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Fwd: on documentation
by Daniel Russel 06 Aug '12

06 Aug '12

---------- Forwarded message ---------- From: Riccardo Pellarin <pellarin.riccardo(a)gmail.com> Date: Mon, Aug 6, 2012 at 12:05 AM Subject: Re: on documentation To: Daniel Russel <drussel(a)gmail.com> Hi Guys, would like to share my thoughts on IMP documentation, maybe repeating what we've already said. I think it is important, though, to share our experience. Let's suppose I want to fit two structures and calculate the Calpha-rmsd, a very simple task. Was typing RMSD in the imp … [View More]manual search field and got 36 entries. 1st problem: the entry titles are uninformative, unless you know exactly what each module is supposed to do (statistic, atom, multifit etc, etc). Knowing a little bit of IMP I could filter the entries and remove all classes belonging to multifit and em modules, for instance. Let's take the first seven entries which might do what I want to do: Member IMP::statistics::ConfigurationSetRMSDMetric:: ConfigurationSetRMSDMetric class IMP::atom::RMSDCalculator Member IMP::atom::RMSDCalculator::RMSDCalculator Member IMP::atom::RMSDCalculator::RMSDCalculators class IMP::statistics::ConfigurationSetRMSDMetric Member IMP::atom::get_pairwise_rmsd_score IMP::atom::get_rmsd 2nd problem: I see a lot of redundancy in the list, and a lot of confusion: classes and members are mixed together... why is that? Wouldn't it be cleaner to separate them in two different lists? Now, let's clean a little bit the list, my eyes go on these candidates: class IMP::atom::RMSDCalculator class IMP::statistics::ConfigurationSetRMSDMetric Member IMP::atom::get_pairwise_rmsd_score IMP::atom::get_rmsd 3rd Problem: there is not a single function that does a simple task as an RMSD calculation, but there are many, with different flavors... Probably many people implemented the same thing many times because they didn't understand what was implemented before? Let's have a look at the functions and see if they do what I want... (as a side note, reading the documentation of IMP functions, I really would like to leave notes on many of them....) Let's start with IMP::atom::RMSDCalculator Detailed Description Fast rmsd calculation. Used to calculate rmsd between multiple transformation that operate on the same particles Well, that is not detailed. What is a "fast rmsd"? No structural fitting I guess? What is the "rmsd between multiple transformations" ? Maybe rigid body transformations? I start to doubt that this rmsd function is calculated between particles at all... Let's try to rewrite it. This is what I would like to read: *Short Description:* Calculates the rmsd of a list of particles. *Detailed Description:* Calculates the root mean square displacement (rmsd) of particles subjected to rigid-body transformations. The rmsd calculation does not perform structural best-fit alignment. *Usage:* 1) construct the class using a list of particles: RMSDCalculator(particles) 2) get the rmsd using the method get_rmsd(trans3D1, trans3D2) where trans3D1 and trans3D2 are rigid body transformations of the reference and displaced configurations, respectively. *Simple Example: ....* * * It would be cool if the short description appears in the search page, along with the class name. Let's go to the second function: IMP::statistics::ConfigurationSetRMSDMetric Detailed Description Compute the RMSD between specified sets of particles in pairs of configurations, within a configuration set this is even more cryptic. Maybe: Calculates the RMSD of a list of particles between all possible configurations pairs in a "configuration set", which is.... Strangely, this class has not get_rmsd(), but get_distance() method.... Is that the same? Let's go to another example: IMP::atom::get_pairwise_rmsd_score The measure quantifies the RMSD between the relative placements of two components compared to a reference relative placement. First, the two compared structures are brought into the same frame of reference by superposing the first pair of equivalent domains (ref1 and mdl1). Next, the RMSD is calculated for the second component What are the components? Maybe subunits? What are the domains? Why the function is called rmsd_score? Is that different from the rmsd? Ok I can go on for almost every function and method in IMP. At the end, I'm completely unsure of what function I should use for my task.... they all look the same. Here's my proposal: Every function documentation must have these entries: *Short Description:* (appears in the search page) *Detailed Description:* [*Algorithm Description:* in some cases] *Usage:* *Simple Example: * The developer might leave these fields empty, of course. When I search something, the first entries should be the ones which are more relevant and documented. Or maybe, the search page should have Documented and Undocumented results. (where Undocumented is a function which is lacking a long documentation page). Of course we cannot force people to write comprehensive documentation, but at least we can give the user the option of choosing the functions which are better documented: that will be bad for developers that write code which is undocumented, since their code will never be used by somebody else. As a user, I will be skeptical using something where the documentation fields are empty! Sorry, that was long. Hope to hear your feedbacks [View Less]

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Warnings in documentation: isd, integrative_docking, em and multifit
by Daniel Russel 03 Aug '12

03 Aug '12

Generating the documentation produces a very large number of warnings. These make it hard to find new problems introduced by changes, as well as, sometimes, representing real problems in the documentation (there are a few warnings that I have not for the life of me been able to figure out what is going on). It would be really nice if people could clean up the warnings in the code they produce. To produce the documentation (and see the warnings), you can do "scons doc". Note, the first time will … [View More]take much longer than subsequent runs (graphs and equations gets cached between runs). And for convenience, I'm including the current set of warnings below. The main offenders are integrative_docking, isd, em, and multifit. Thanks very much. To clarify some of the warnings: - < must be escaped if it is not an html tag - not all files are in the example path (only examples and the example module). This could change, but I'm not sure there is a good reason to build/doxygen/integrative_docking/overview.dox:7: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:7: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:7: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:7: warning: Unsupported xml/html tag <exp_profile_file> found build/doxygen/integrative_docking/overview.dox:10: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:11: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:12: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:21: warning: Unsupported xml/html tag <exp_profile_file> found build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported xml/html tag <image1> found build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported xml/html tag <image2> found build/doxygen/integrative_docking/overview.dox:27: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:27: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:27: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:28: warning: Unsupported xml/html tag <image1> found build/doxygen/integrative_docking/overview.dox:28: warning: Unsupported xml/html tag <image2> found build/doxygen/integrative_docking/overview.dox:31: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:31: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:31: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:31: warning: Unsupported xml/html tag <em_map> found build/doxygen/integrative_docking/overview.dox:34: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:34: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:34: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:35: warning: Unsupported xml/html tag <em_map> found build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported xml/html tag <residue_content_file1> found build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported xml/html tag <residue_content_file2> found build/doxygen/integrative_docking/overview.dox:43: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:43: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:43: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:44: warning: Unsupported xml/html tag <residue_content_file1> found build/doxygen/integrative_docking/overview.dox:45: warning: Unsupported xml/html tag <residue_content_file2> found build/doxygen/integrative_docking/overview.dox:55: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:55: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:55: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:55: warning: Unsupported xml/html tag <cross_links_file> found build/doxygen/integrative_docking/overview.dox:58: warning: Unsupported xml/html tag <pdb1> found build/doxygen/integrative_docking/overview.dox:58: warning: Unsupported xml/html tag <pdb2> found build/doxygen/integrative_docking/overview.dox:58: warning: Unsupported xml/html tag <trans_file> found build/doxygen/integrative_docking/overview.dox:59: warning: Unsupported xml/html tag <cross_links_file> found build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported xml/html tag <file1> found build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported xml/html tag <weight1> found build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported xml/html tag <file2> found build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported xml/html tag <weight2> found build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported xml/html tag <file3> found build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported xml/html tag <weight3> found /usr/local/google/home/drussel/src/imp/imp/modules/librmf/doc/categories.dox:94: warning: Found unknown command `\rmfattribute' /usr/local/google/home/drussel/src/imp/imp/doc/developer_guide.dox:683: warning: explicit link request to 'if' could not be resolved /usr/local/google/home/drussel/src/imp/imp/doc/developer_guide.dox:812: warning: explicit link request to 'include' could not be resolved /usr/local/google/home/drussel/src/imp/imp/doc/developer_guide.dox:850: warning: unable to resolve reference to `close_pairs' for \ref command /usr/local/google/home/drussel/src/imp/imp/doc/history.dox:318: warning: explicit link request to 'RMF::HDF5FloatDataSet2D' could not be resolved /usr/local/google/home/drussel/src/imp/imp/doc/history.dox:167: warning: unable to resolve reference to `nup84_cg' for \ref command /usr/local/google/home/drussel/src/imp/imp/doc/history.dox:167: warning: unable to resolve reference to `nup84_rb' for \ref command /usr/local/google/home/drussel/src/imp/imp/doc/introduction.dox:316: warning: unable to resolve reference to `nup84_cg.py' for \ref command build/doxygen/atom/overview.dox:5: warning: found paragraph command outside of subsubsection context! <unknown>:206: warning: unable to resolve reference to `B' for \ref command build/include/IMP/em/rigid_fitting.h:300: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key(), bool local=false) build/include/IMP/em/rigid_fitting.h:300: warning: The following parameters of IMP::em::compute_fitting_score(const ParticlesTemp &ps, DensityMap *em_map, FloatKey wei_key=atom::Mass::get_mass_key(), bool local=false) are not documented: parameter 'local' build/include/IMP/em/rigid_fitting.h:250: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::compute_fitting_scores(const ParticlesTemp &ps, DensityMap *em_map, const algebra::Transformation3Ds &transformations, bool fast_version=false, bool local_score=false, const FloatKey &wei_key=atom::Mass::get_mass_key()) build/include/IMP/em/rigid_fitting.h:277: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::compute_fitting_scores(DensityMap *em_map, core::RigidBody rb, Refiner *refiner, const algebra::Transformation3Ds &transformations, const FloatKey &=atom::Mass::get_mass_key()) build/include/IMP/em/rigid_fitting.h:277: warning: argument 'wei_key' of command @param is not found in the argument list of IMP::em::compute_fitting_scores(DensityMap *em_map, core::RigidBody rb, Refiner *refiner, const algebra::Transformation3Ds &transformations, const FloatKey &=atom::Mass::get_mass_key()) build/include/IMP/em/density_map_volumetrics.h:29: warning: argument 'only' of command @param is not found in the argument list of IMP::em::get_molecular_mass_at_threshold(DensityMap *m, Float threshold, atom::ProteinDensityReference ref=atom::HARPAZ) build/include/IMP/em/density_map_volumetrics.h:29: warning: argument 'the' of command @param is not found in the argument list of IMP::em::get_molecular_mass_at_threshold(DensityMap *m, Float threshold, atom::ProteinDensityReference ref=atom::HARPAZ) build/include/IMP/em/density_map_volumetrics.h:57: warning: argument 'the' of command @param is not found in the argument list of IMP::em::get_threshold_for_approximate_mass(DensityMap *m, Float desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ) build/include/IMP/em/DensityMap.h:582: warning: argument 'from' of command @param is not found in the argument list of IMP::em::get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) build/include/IMP/em/DensityMap.h:582: warning: The following parameters of IMP::em::get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) are not documented: parameter 'source' build/include/IMP/em/density_map_volumetrics.h:19: warning: argument 'consider' of command @param is not found in the argument list of IMP::em::get_volume_at_threshold(DensityMap *m, Float threshold) build/include/IMP/em/rigid_fitting.h:102: warning: argument 'rb' of command @param is not found in the argument list of IMP::em::local_rigid_fitting_around_point(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false) build/include/IMP/em/rigid_fitting.h:102: warning: argument 'radius_key' of command @param is not found in the argument list of IMP::em::local_rigid_fitting_around_point(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false) build/include/IMP/em/rigid_fitting.h:102: warning: The following parameters of IMP::em::local_rigid_fitting_around_point(Particle *p, Refiner *refiner, const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D &anchor_centroid, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, bool fast=false) are not documented: parameter 'p' parameter 'refiner' build/include/IMP/em/rigid_fitting.h:189: warning: argument 'rb' of command @param is not found in the argument list of IMP::em::local_rigid_fitting_around_points(Particle *p, Refiner *refiner, const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds &anchor_centroids, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3) build/include/IMP/em/rigid_fitting.h:189: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::local_rigid_fitting_around_points(Particle *p, Refiner *refiner, const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds &anchor_centroids, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3) build/include/IMP/em/rigid_fitting.h:189: warning: The following parameters of IMP::em::local_rigid_fitting_around_points(Particle *p, Refiner *refiner, const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds &anchor_centroids, OptimizerStates display_log, Int number_of_optimization_runs=5, Int number_of_mc_steps=10, Int number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3) are not documented: parameter 'p' parameter 'refiner' build/include/IMP/em/rigid_fitting.h:219: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::local_rigid_fitting_grid_search(const ParticlesTemp &ps, const FloatKey &wei_key, DensityMap *dmap, Int max_voxels_translation=2, Int translation_step=1, Float max_angle_in_radians=0.174, Int number_of_rotations=100) build/include/IMP/em/converters.h:73: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::particles2binarized_density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) build/include/IMP/em/converters.h:54: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) build/include/IMP/em/converters.h:101: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::particles2surface(const ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) build/include/IMP/em/CoarseCCatIntervals.h:32: warning: argument 'dvx' of command @param is not found in the argument list of IMP::em::CoarseCCatIntervals::evaluate(DensityMap *em_map, SampledDensityMap *model_map, const algebra::Vector3Ds &deriv, float scalefac, bool lderiv, unsigned long eval_interval) build/include/IMP/em/CoarseCCatIntervals.h:32: warning: argument 'dvy' of command @param is not found in the argument list of IMP::em::CoarseCCatIntervals::evaluate(DensityMap *em_map, SampledDensityMap *model_map, const algebra::Vector3Ds &deriv, float scalefac, bool lderiv, unsigned long eval_interval) build/include/IMP/em/CoarseCCatIntervals.h:32: warning: argument 'dvz' of command @param is not found in the argument list of IMP::em::CoarseCCatIntervals::evaluate(DensityMap *em_map, SampledDensityMap *model_map, const algebra::Vector3Ds &deriv, float scalefac, bool lderiv, unsigned long eval_interval) build/include/IMP/em/CoarseCCatIntervals.h:32: warning: The following parameters of IMP::em::CoarseCCatIntervals::evaluate(DensityMap *em_map, SampledDensityMap *model_map, const algebra::Vector3Ds &deriv, float scalefac, bool lderiv, unsigned long eval_interval) are not documented: parameter 'deriv' build/include/IMP/em/DensityFillingRestraint.h:33: warning: The following parameters of IMP::em::DensityFillingRestraint::DensityFillingRestraint(Particles ps, DensityMap *em_map, Float threshold) are not documented: parameter 'threshold' build/include/IMP/em/DensityMap.h:582: warning: argument 'from' of command @param is not found in the argument list of IMP::em::DensityMap::get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) build/include/IMP/em/DensityMap.h:582: warning: The following parameters of IMP::em::DensityMap::get_transformed_into(const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) are not documented: parameter 'source' build/include/IMP/em/EnvelopePenetrationRestraint.h:33: warning: The following parameters of IMP::em::EnvelopePenetrationRestraint::EnvelopePenetrationRestraint(Particles ps, DensityMap *em_map, Float threshold) are not documented: parameter 'threshold' build/include/IMP/em/FitRestraint.h:37: warning: The following parameters of IMP::em::FitRestraint::FitRestraint(ParticlesTemp ps, DensityMap *em_map, FloatPair norm_factors=FloatPair(0., 0.), FloatKey weight_key=atom::Mass::get_mass_key(), float scale=1, bool use_rigid_bodies=true, KernelType kt=GAUSSIAN) are not documented: parameter 'kt' build/include/IMP/em/ImageHeader.h:60: warning: argument 'in' of command @param is not found in the argument list of IMP::em::ImageHeader::set_image_type(img_type im) build/include/IMP/em/ImageHeader.h:60: warning: The following parameters of IMP::em::ImageHeader::set_image_type(img_type im) are not documented: parameter 'im' build/include/IMP/em/SampledDensityMap.h:74: warning: The following parameters of IMP::em::SampledDensityMap::project(const ParticlesTemp &ps, int x_margin, int y_margin, int z_margin, algebra::Vector3D shift=algebra::Vector3D(0., 0., 0.), FloatKey mass_key=atom::Mass::get_mass_key()) are not documented: parameter 'ps' parameter 'mass_key' build/include/IMP/em/converters.h:73: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::SampledDensityMap::particles2binarized_density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) build/include/IMP/em/converters.h:54: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::SampledDensityMap::particles2density(const ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) build/include/IMP/em/converters.h:101: warning: argument 'rad_key' of command @param is not found in the argument list of IMP::em::SampledDensityMap::particles2surface(const ParticlesTemp &ps, Float apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) build/include/IMP/isd/AmbiguousNOERestraint.h:25: warning: included file AmbiguousNOERestraint.h is not found. Check your EXAMPLE_PATH build/include/IMP/isd/AmbiguousNOERestraint.h:26: warning: included file AmbiguousNOERestraint.cpp is not found. Check your EXAMPLE_PATH build/include/IMP/isd/GaussianProcessInterpolation.h:41: warning: expected whitespace after param command build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, Particle *sigma, double sparse_cutoff=1e-7) build/include/IMP/isd/GaussianProcessInterpolation.h:43: warning: expected whitespace after param command build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, Particle *sigma, double sparse_cutoff=1e-7) build/include/IMP/isd/GaussianProcessInterpolation.h:45: warning: expected whitespace after param command build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, Particle *sigma, double sparse_cutoff=1e-7) build/include/IMP/isd/GaussianProcessInterpolation.h:46: warning: expected whitespace after param command build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, Particle *sigma, double sparse_cutoff=1e-7) build/include/IMP/isd/GaussianProcessInterpolation.h:49: warning: expected whitespace after param command build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, Particle *sigma, double sparse_cutoff=1e-7) build/include/IMP/isd/GaussianProcessInterpolation.h:50: warning: expected whitespace after param command build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, Particle *sigma, double sparse_cutoff=1e-7) build/include/IMP/isd/GaussianProcessInterpolation.h:51: warning: expected whitespace after param command build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, Particle *sigma, double sparse_cutoff=1e-7) build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: The following parameters of IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList x, Floats sample_mean, Floats sample_std, unsigned n_obs, UnivariateFunction *mean_function, BivariateFunction *covariance_function, Particle *sigma, double sparse_cutoff=1e-7) are not documented: parameter 'x' parameter 'sample_mean' parameter 'sample_std' parameter 'n_obs' parameter 'mean_function' parameter 'covariance_function' parameter 'sigma' parameter 'sparse_cutoff' build/include/IMP/isd/GaussianRestraint.h:22: warning: included file GaussianRestraint.h is not found. Check your EXAMPLE_PATH build/include/IMP/isd/GaussianRestraint.h:23: warning: included file GaussianRestraint.cpp is not found. Check your EXAMPLE_PATH build/include/IMP/isd/ISDRestraint.h:28: warning: included file ISDRestraint.h is not found. Check your EXAMPLE_PATH build/include/IMP/isd/LogicalORRestraint.h:24: warning: included file LogicalORRestraint.h is not found. Check your EXAMPLE_PATH build/include/IMP/isd/LogicalORRestraint.h:25: warning: included file LogicalORRestraint.cpp is not found. Check your EXAMPLE_PATH build/include/IMP/isd/LognormalRestraint.h:22: warning: included file LognormalRestraint.h is not found. Check your EXAMPLE_PATH build/include/IMP/isd/LognormalRestraint.h:23: warning: included file LognormalRestraint.cpp is not found. Check your EXAMPLE_PATH build/include/IMP/isd/MarginalHBondRestraint.h:31: warning: included file MarginalHBondRestraint.h is not found. Check your EXAMPLE_PATH build/include/IMP/isd/MarginalHBondRestraint.h:32: warning: included file MarginalHBondRestraint.cpp is not found. Check your EXAMPLE_PATH build/include/IMP/isd/MarginalNOERestraint.h:31: warning: included file MarginalNOERestraint.h is not found. Check your EXAMPLE_PATH build/include/IMP/isd/MarginalNOERestraint.h:32: warning: included file MarginalNOERestraint.cpp is not found. Check your EXAMPLE_PATH build/include/IMP/isd/MultivariateFNormalSufficient.h:52: warning: Found unknown command `\Sigma' build/include/IMP/isd/MultivariateFNormalSufficient.h:118: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:119: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:121: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:122: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:123: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: The following parameters of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, double factor=1) are not documented: parameter 'FX' parameter 'JF' parameter 'FM' parameter 'Sigma' parameter 'factor' build/include/IMP/isd/MultivariateFNormalSufficient.h:129: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd &W, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:130: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd &W, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:132: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd &W, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:133: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd &W, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:134: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd &W, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:135: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd &W, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:136: warning: expected whitespace after param command build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: argument 'in' of command @param is not found in the argument list of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd &W, const MatrixXd &Sigma, double factor=1) build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: The following parameters of IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd &W, const MatrixXd &Sigma, double factor=1) are not documented: parameter 'Fbar' parameter 'JF' parameter 'FM' parameter 'Nobs' parameter 'W' parameter 'Sigma' parameter 'factor' build/include/IMP/isd/NOERestraint.h:27: warning: included file NOERestraint.h is not found. Check your EXAMPLE_PATH build/include/IMP/isd/NOERestraint.h:28: warning: included file NOERestraint.cpp is not found. Check your EXAMPLE_PATH build/include/IMP/multifit/coarse_molecule.h:50: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:50: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius) build/include/IMP/multifit/coarse_molecule.h:51: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:50: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius) build/include/IMP/multifit/coarse_molecule.h:53: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:50: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius) build/include/IMP/multifit/coarse_molecule.h:54: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:50: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius) build/include/IMP/multifit/coarse_molecule.h:55: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:50: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius) build/include/IMP/multifit/coarse_molecule.h:50: warning: The following parameters of IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius) are not documented: parameter 'dmap' parameter 'dens_threshold' parameter 'num_beads' parameter 'mdl' parameter 'bead_radius' build/include/IMP/multifit/coarse_molecule.h:16: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:16: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:17: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:16: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:18: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:16: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:19: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:16: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:20: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:16: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:16: warning: The following parameters of IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool add_conn_restraint=false) are not documented: parameter 'mh' parameter 'num_beads' parameter 'mdl' parameter 'bead_radius' parameter 'add_conn_restraint' build/include/IMP/multifit/coarse_molecule.h:32: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:32: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:33: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:32: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:35: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:32: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:36: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:32: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:37: warning: expected whitespace after param command build/include/IMP/multifit/coarse_molecule.h:32: warning: argument 'input' of command @param is not found in the argument list of IMP::multifit::create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool add_conn_restraint=false) build/include/IMP/multifit/coarse_molecule.h:32: warning: The following parameters of IMP::multifit::create_coarse_molecules_from_molecules(const atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool add_conn_restraint=false) are not documented: parameter 'mhs' parameter 'frag_len' parameter 'mdl' parameter 'bead_radius' parameter 'add_conn_restraint' build/include/IMP/multifit/fft_based_rigid_fitting.h:159: warning: argument 'angle_sampling_interval' of command @param is not found in the argument list of IMP::multifit::fft_based_rigid_fitting(atom::Hierarchy mol2fit, em::DensityMap *dmap, double angle_sampling_interval_rad) build/include/IMP/multifit/fft_based_rigid_fitting.h:159: warning: The following parameters of IMP::multifit::fft_based_rigid_fitting(atom::Hierarchy mol2fit, em::DensityMap *dmap, double angle_sampling_interval_rad) are not documented: parameter 'angle_sampling_interval_rad' build/include/IMP/multifit/fitting_clustering.h:21: warning: argument 'pdb_filename' of command @param is not found in the argument list of IMP::multifit::fitting_clustering(const atom::Hierarchy &mh, const em::FittingSolutions &ts, float spacing, int top_sols, float rmsd) build/include/IMP/multifit/fitting_clustering.h:21: warning: The following parameters of IMP::multifit::fitting_clustering(const atom::Hierarchy &mh, const em::FittingSolutions &ts, float spacing, int top_sols, float rmsd) are not documented: parameter 'mh' parameter 'top_sols' parameter 'rmsd' build/include/IMP/multifit/TransformationClustering.h:79: warning: expected whitespace after param command build/include/IMP/multifit/TransformationClustering.h:75: warning: argument 'in' of command @param is not found in the argument list of IMP::multifit::get_clustered(Particles ps, const algebra::Transformation3Ds &trans, float max_rmsd, float max_angle_diff_in_rad, float max_displace, int min_cluster_size) build/include/IMP/multifit/TransformationClustering.h:75: warning: The following parameters of IMP::multifit::get_clustered(Particles ps, const algebra::Transformation3Ds &trans, float max_rmsd, float max_angle_diff_in_rad, float max_displace, int min_cluster_size) are not documented: parameter 'trans' parameter 'max_displace' build/include/IMP/multifit/pca_based_rigid_fitting.h:28: warning: argument 'rb_refine' of command @param is not found in the argument list of IMP::multifit::pca_based_rigid_fitting(core::RigidBody rb, Refiner *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis()) build/include/IMP/multifit/pca_based_rigid_fitting.h:28: warning: The following parameters of IMP::multifit::pca_based_rigid_fitting(core::RigidBody rb, Refiner *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis()) are not documented: parameter 'rb_refiner' build/include/IMP/multifit/RadiusOfGyrationRestraint.h:31: warning: argument 'the' of command @param is not found in the argument list of IMP::multifit::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(Particles ps, int num_residues, Float scale=1.) build/include/IMP/multifit/RadiusOfGyrationRestraint.h:31: warning: The following parameters of IMP::multifit::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(Particles ps, int num_residues, Float scale=1.) are not documented: parameter 'num_residues' [generated]:0: warning: explicit link request to 'Object' could not be resolved build/include/IMP/saxs/RadiusOfGyrationRestraint.h:31: warning: The following parameters of IMP::saxs::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(const Particles &particles, const Profile &exp_profile, const double end_q_rg= [View Less]

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Trying to make the most surprising aspect of IMP less surprising
by Daniel Russel 03 Aug '12

03 Aug '12

Most people using IMP at some point get tripped up by the fact that ScoreState dependent state is not updated until Model::update() is caller or a Restraint that requires it is evaluated. For example, if you move a bunch of particles, the non-bonded no longer contains the correct pairs until Model::update is called. And similar problems can arrise with rigid bodies. The reason for this is that updating the state can be expensive (imagine moving each of 100 or 1000 particles one at a time and … [View More]

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