Re: [IMP-dev] Warnings in documentation: isd, integrative_docking, em and multifit
To: List for IMP development <>
Subject: Re: [IMP-dev] Warnings in documentation: isd, integrative_docking, em and multifit
From: Daniel Russel <>
Date: Fri, 3 Aug 2012 11:24:01 -0700
Reply-to: List for IMP development <>
Good question. \< and \>
On Fri, Aug 3, 2012 at 10:56 AM, Dina Schneidman <" target="_blank">> wrote:
is there escape character for '<'?
On Fri, Aug 3, 2012 at 10:45 AM, Daniel Russel <">> wrote:
> 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 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:
> Â 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:
> Â 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:
> Â parameter 'p'
> Â 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:
> Â parameter 'p'
> Â 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:
> Â 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:
> Â 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:
> Â 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:
> Â 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:
> Â 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:
> Â 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:
> Â parameter 'ps'
> Â 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:
> Â parameter 'x'
> Â parameter 'sample_mean'
> Â parameter 'sample_std'
> Â parameter 'n_obs'
> Â parameter 'mean_function'
> Â parameter 'covariance_function'
> Â parameter 'sigma'
> Â 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:
> Â parameter 'FX'
> Â parameter 'JF'
> Â parameter 'FM'
> Â parameter 'Sigma'
> Â 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:
> Â parameter 'Fbar'
> Â parameter 'JF'
> Â parameter 'FM'
> Â parameter 'Nobs'
> Â parameter 'W'
> Â parameter 'Sigma'
> Â 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:
> Â parameter 'dmap'
> Â parameter 'dens_threshold'
> Â parameter 'num_beads'
> Â parameter 'mdl'
> Â 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:
> Â parameter 'mh'
> Â parameter 'num_beads'
> Â parameter 'mdl'
> Â parameter 'bead_radius'
> Â 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:
> Â parameter 'mhs'
> Â parameter 'frag_len'
> Â parameter 'mdl'
> Â parameter 'bead_radius'
> Â 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:
> Â 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:
> Â parameter 'mh'
> Â parameter 'top_sols'
> Â 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:
> Â parameter 'trans'
> Â 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:
> Â 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:
> Â 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=
>