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: 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=