BioShell examples¶
The latest BioShell 3.0 distribution provides an extensive set of examples. The purpose to create them is three-fold:
- to facilitate continuous testing of the package (unit and integration tests)
- to provide additional functionality to the package,and
- to serve as coding examples and provide ready-to-use snippets
All the tests, which in practice are small C++ applications, were divided into two broad groups; the tests are named
staring from ap_, ex_ and ww_.
ap_* programs¶
These are integration tests, that besides testing whether the package is bug-free, should also do something usefull.
- ap_BackboneHBondMap
- ap_Crmsd
- ap_Hexbins
- ap_aligned_pdb
- ap_chi1_rotamers_estimation
- ap_contact_map
- ap_fit_VonMises_mixture
- ap_ligand_contacts
- ap_orient_pdb
- ap_shuffled_sequence_alignment
- ap_AAHydrophobicity
- ap_AlignmentPValuesProtocol
- ap_LocalStructureMatch
- ap_MSAColumnConservation
- ap_NWAligner
- ap_OnlineStatistics
- ap_PairwiseCrmsd
- ap_PairwiseSequenceIdentityProtocol
- ap_ProteinArchitecture
- ap_QuickSequenceIdentity
- ap_SWAligner
- ap_SequenceProfile
- ap_SequenceWeightingProtocol
- ap_WeightedOnlineStatistics
- ap_align_profiles
- ap_atom_correlations
- ap_blastxml_to_fasta
- ap_build_crystal
- ap_contact_map_overlap
- ap_docking_crmsd
- ap_download_pdb
- ap_dssp
- ap_dssp_to_ss2
- ap_filter_fasta
- ap_find_in_fasta
- ap_ligand_trajectory
- ap_local_backbone_geometry
- ap_molecule_diffusion
- ap_pdb_to_fasta_ss
- ap_pdb_to_pir
- ap_pir_to_fasta
- ap_reorder_profile_columns
- ap_rescore_alignment
- ap_scorefile_columns
- ap_stacking_interactions
- ap_stiff_docking_crmsd
- ap_superimpose_pdb_by_ligand
ex_* programs¶
These group contain unit test, i.e. programs that tests a single class of a function.
- ex_BinaryTreeNode
- ex_Molecule
- ex_Molecule_Vec3
- ex_NcbiSimilarityMatrixFactory
- ex_SelectChainResidueAtom
- ex_SelectPlanarCAGeometry
- ex_VonMisesDistribution
- ex_bf_by_residue
- ex_chi_correlation
- ex_evaluate_chi
- ex_evaluate_phi_psi
- ex_plot_VonMises_mixture
- ex_Array2DSymmetric
- ex_AtomSelector
- ex_AtomicElement
- ex_BioShellVersion
- ex_BitSet
- ex_BivariateNormal
- ex_BoundedPriorityQueue
- ex_Cart
- ex_CartesianToSpherical
- ex_ChiAnglesDefinition
- ex_Cif
- ex_Combinations
- ex_DsspData
- ex_HierarchicalClustering
- ex_Interpolate1D
- ex_InterpolatePeriodic1D
- ex_InterpolatePeriodic2D
- ex_JsonNode
- ex_KDE_1D
- ex_LBFGS
- ex_Monomer
- ex_NormalDistribution
- ex_OptionParser
- ex_P2QuantileEstimation
- ex_PairwiseAlignment
- ex_PairwiseSequenceAlignment
- ex_Pca3
- ex_Pdb
- ex_PdbLineFilter
- ex_Quaternion
- ex_ReduceSequenceAlphabet
- ex_Remark290
- ex_Residue
- ex_RobustDistributionDecorator
- ex_SelectChainBreaks
- ex_SelectResidueRange
- ex_SemiglobalAligner
- ex_Seqres
- ex_Sequence
- ex_SequenceAlignmentWidget
- ex_Structure
- ex_ThreadPool
- ex_ThreadSafeMap
- ex_ThreeDTree
- ex_TreeNode
- ex_UnionFind
- ex_WebServer
- ex_XML
- ex_alignment_io
- ex_basic_algebra
- ex_benchmark_quick_seq_identity
- ex_chi2_independence_test
- ex_consecutive_find
- ex_count_residues_by_type
- ex_define_rotamer
- ex_expectation_maximization
- ex_find_side_group
- ex_goodman_kruskal_rank_correlation
- ex_greedy_clustering
- ex_intersect_sorted
- ex_k_tuples
- ex_local_BBQ_coordinates
- ex_local_coordinates_three_atoms
- ex_monomer_io
- ex_pdb_to_fasta
- ex_peptide_hydrogen
- ex_protein_peptide_interface
- ex_read_properties_file
- ex_selection_protocols
- ex_seq_io
- ex_set_dihedral
- ex_shared_pointers
- ex_simpson_integration
- ex_split_fasta
- ex_structure_iterators
- ex_test_gzip
- ex_uniquify
- ex_web_client
ww_* programs¶
These group contain test which are displayed in WWW browser.