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<!doctype html public "-//w3c//dtd html 4.0 transitional//en"><html><head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta name="GENERATOR" content="Mozilla/4.5C-SGI [en] (X11; I; IRIX 6.5 IP22) [Netscape]"> <title> The Bioinformatics Template Library (BTL) Documentation</title></HEADER></head><body bgcolor="#99FFCC"><center><h1><a href="http://www.cryst.bbk.ac.uk/~classlib/"><img SRC="BTL2.gif" ALT="BTL logo" BORDER=0 height=100 width=100 align=CENTER></a>TheBioinformatics Template Library (BTL) <a href="http://www.cryst.bbk.ac.uk/"><img SRC="shield9.gif" ALT="Birkbeck Shield" BORDER=0 height=100 width=100 align=CENTER></a> <br CLEAR=BOTH><br><br><br><br><BR></h1></center><hr SIZE=5><p><b>Version</b> 3.0 alpha<p><b>Description</b><p>The focus of this library is on the <b>data structures and algorithmsused within the fields of bioinformatics and molecular modelling</b>. Theapproach used closely follows that of the Standard Template Library (STL)which is part of ISO/ANSI standard C++. This library uses templates toimplement <b>generic programming</b>. Templates allow the development ofefficient programming modules using compile-time mechanisms. Although theBTL has been designed with biomolecular applications in mind it containsclasses of more general utility. For instance, the matrix container andassociated algorithms could be used for matrix algebra in many contexts.<p><b>Floating Point Precision</b><p>The floating point precision of the library as a whole is defined asthe user defined type BTL_REAL. A typedef statement in the BTL.h. e.g.<p><tt>typedef double BTL_REAL;</tt><p>To change the precision used simply alter this statement and recompileyour code. Of course not all floating point variables in the library areof type BTL_REAL, some, for instance, are fixed at type double to avoidlarge round off errors. In spite of this, setting BTL_REAL to be of typefloat may well result significant round off problems in certain calculationssuch as those used by the eigen_solution() algorithm.<p><b>Debugging Version of Library</b><p>If the DEBUG_VERSION symbol is defined then the library will carry outextra error checking such as some array bounds checking. This checkingwill obviously make the library more robust but will also increase excecutiontimes. Simply comment out the define statement in the <a href="btl/BTL.h">BTL.h</a>file, if the extra checking is not required.<p><a NAME="Classes"></a><h2>Components</h2><ul><li><b><a href="#ATOM_processor">ATOM_processor</a></b> - <i>reads PDB formatfiles and extracts ATOM record data into vectors.</i></li><li><b><a href="#PDBSort">pdb_sort</a></b> - <i>function object (functor) usedfor sorting objects into Protein Data Bank (pdb) format atom order</i></li><li><b><a href="#AminoAcidProperty">amino_acid_property</a></b> - <i>functorthat returns amino acid property values</i></li><li><b><a href="#PIR_processor">PIR_processor</a></b> - <i>simple class forparsing PIR format sequence files</i></li><li><b><a href="#PPM_processor">PPM_processor</a></b> - <i>simple class forparsing ascii PPM format image files</i></li><li><b><a href="#XYZ_processor">XYZ_processor</a></b> - <i>reads xyz formatcoordinate files and puts the data in vectors</i></li><li><b><a href="#needleman_wunsch_similarity">needleman_wunsch_similarity</a></b></li><li><b><a href="#needleman_wusch_align">needleman_wusch_align</a></b></li><li><b><a href="#fourier_transform">fourier_transform</a></b></li><li><b><a href="#mean">mean</a></b></li><li><b><a href="#mean_absolute_deviation">mean_absolute_deviation</a></b></li><li><b><a href="#variance">variance</a></b></li><li><b><a href="#normal_statistics">normal_statistics</a></b></li><li><b><a href="#max_mismatch">max_mismatch</a></b></li><li><b><a href="#max_absolute_mismatch">max_absolute_mismatch</a></b></li><li><b><a href="#min_mismatch">min_mismatch</a></b></li><li><b><a href="#min_absolute_mismatch">min_absolute_mismatch</a></b></li><li><b><a href="#every_less_equal">every_less_equal</a></b></li><li><b><a href="#every_less">every_less</a></b></li><li><b><a href="#less_absolute">less_absolute</a></b></li><li><b><a href="#random_uniform">random_uniform</a></b></li><li><b><a href="#random_normal">random_normal</a></b></li><li><b><a href="#random_exponential">random_exponential</a></b></li><li><b><a href="#numeric_vector">numeric_vector</a></b> - <i>a vector of realnumbers of any size</i></li><li><b><a href="#scalar_product">scalar_product</a></b></li><li><b><a href="#direct_product">direct_product</a></b></li><li><b><a href="#triple_vector_product">triple_vector_product</a></b></li><li><b><a href="#triple_scalar_product">triple_scalar_product</a></b></li><li><b><a href="#separation_squared">separation_squared</a></b></li><li><b><a href="#separation">separation</a></b></li><li><b><a href="#sum">sum</a></b></li><li><b><a href="#sum_precise">sum_precise</a></b></li><li><b><a href="#sum_of_squares">sum_of_squares</a></b></li><li><b><a href="#sum_of_squares_precise">sum_of_squares_precise</a></b></li><li><b><a href="#magnitude">magnitude</a></b></li><li><b><a href="#magnitude_precise">magnitude_precise</a></b></li><li><b><a href="#rotate">rotate</a></b></li><li><b><a href="#translate">translate</a></b></li><li><b><a href="#matrix">matrix</a></b> - <i>a 2-dimensional array of realnumbers of any size</i></li><li><b><a href="#matrix_product">matrix_product</a></b></li><li><b><a href="#matrixtranspose_matrix_product">matrixtranspose_matrix_product</a></b></li><li><b><a href="#matrix_matrixtranspose_product">matrix_matrixtranspose_product</a></b></li><li><b><a href="#transpose">transpose</a></b></li><li><b><a href="#column_means">column_means</a></b></li><li><b><a href="#copy_column">copy_column</a></b></li><li><b><a href="#determinant">determinant</a></b></li><li><b><a href="#minor">minor</a></b></li><li><b><a href="#adjoint">adjoint</a></b></li><li><b><a href="#inverse_square">inverse_square</a></b></li><li><b><a href="#eigen_solution">eigen_solution</a></b></li><li><b><a href="#inverse_cholesy">inverse_cholesy</a></b></li><li><b><a href="#lsqfit_rmsd">lsqfit_rmsd</a></b></li><li><b><a href="#centroid">centroid</a></b></li><li><b><a href="#rotation_from_fit">rotation_from_fit</a></b></li><li><b><a href="#rmsd">rmsd</a></b></li><li><b><a href="#check_3d_data">check_3d_data</a></b></li><li><b><a href="#BTL_VertexWithEdges">BTL_VertexWithEdges</a></b> - <i>templategraph vertex for use with BTL_GraphWithEdges</i></li><li><b><a href="#BTL_Edge">BTL_Edge</a></b> - <i>a template graph edge foruse with BTL_GraphWithEdges</i></li><li><b><a href="#BTL_GraphWithEdges">BTL_GraphWithEdges</a></b> - <i>a templategraph with two template parameters determining the type of vertices andedges</i></li><li><b><a href="#BTL_Vertex">BTL_Vertex</a></b> - <i>a template graph vertexfor use with graph</i></li><li><b><a href="#BTL_Graph">BTL_Graph</a></b> - <i>A template graph with edgesas simple pointers to vertices.</i></li><li><b><a href="#BTL_DFSIterator">BTL_DFSIterator</a></b> - <i>an iteratorfor iterating over a connected sub-graph in depth first order.</i></li><li><b><a href="#BTL_ConstDFSIterator">BTL_ConstDFSIterator</a></b> - <i>theconst version of the BTL_DFSIterator.</i></li><br> <p> <br> <br> <br> <br> <br> <br> </ul><a NAME="Files"></a><h2>Files</h2><ul><li><a href="btl/">The library source code</a></li><li><a href="examples/">Demo programs</a></li></ul><!--END PAGE --><hr><p><a NAME="ATOM_processor"></a><h2>ATOM_processor</h2><p><br>This is simple class for reading ATOM records from clean PDB formatfiles.<br><b>Friends:</b> an output operator<br><b>Authors:</b> M.A.Williams<br><b>Files:</b> <a href="btl/ATOM_processor.h">ATOM_processor.h</a><br><b>Dependencies:</b> None<p><b>Operations</b><br> <br> <ul><li><tt><a href="#ATOM_processorO0">CloseFile</a> -</tt></li><li><tt><a href="#ATOM_processorO1">Alternate</a> -</tt></li><li><tt><a href="#ATOM_processorO2">ATOM_processor</a> - - <i>Default constructor(does nothing)</i></tt></li><li><tt><a href="#ATOM_processorO3">~ATOM_processor</a> - - <i>Default destructor(does nothing)</i></tt></li><li><tt><a href="#ATOM_processorO4">empty</a> - - <i>Returns true if no coordinateshave been read</i></tt></li><li><tt><a href="#ATOM_processorO5">ReadFile</a> - - <i>Read a PDB format filewith the given name, selecting only those chains whose id letter occursin a given string and using the alternate set of coordinates identifiedby the user-supplied character. The default reads records with any chainid and either no alternate id or the first encounterd alternate id.</i></tt></li><li><tt><a href="#ATOM_processorO6">AtomNo</a> - - <i>Return a reference tothe atom number in a STL vector of int.</i></tt></li><li><tt><a href="#ATOM_processorO7">AtomName</a> - - <i>Return a referenceto the atom n in a STL vector of char. Each name is stored as 4 chars.</i></tt></li><li><tt><a href="#ATOM_processorO8">ResidueName</a> - - <i>Return a referenceto the atom names in a STL vector of char. Each name is stored as 3 chars.</i></tt></li><li><tt><a href="#ATOM_processorO9">ResidueNo</a> - - <i>Return a referenceto the residue number in a STL vector of int.</i></tt></li><li><tt><a href="#ATOM_processorO10">ChainName</a> - - <i>Return a referenceto the chain names in a STL vector of char. Each name is stored as a singlechar.</i></tt></li><li><tt><a href="#ATOM_processorO11">Coords</a> - - <i>Return a reference tothe read coordinates in a STL vector of float. Coordinates are stored inthe following order: x,y,z,x,y,z,x,...</i></tt></li><li><tt><a href="#ATOM_processorO12">Occupancy</a> - - <i>Return a referenceto the occupancy in a STL vector of float.</i></tt></li><li><tt><a href="#ATOM_processorO13">BFactor</a> - - <i>Return a referenceto the b_factor in a STL vector of float.</i></tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 height=40 width=40></a><hr><p><a NAME="PDBSort"></a><h2>PDBSort</h2><p><br>This class defines a functor or function object which can be usedby a generic sort routine to sort atoms into the order used in Brookhavenpdb format files. Order is defined by strings, 2 or 3 characters long.<br><b>Authors:</b> W.R.Pitt<br><b>Files:</b> <a href="btl/pdb_sort.h">pdb_sort.h</a><br><b>Dependencies:</b> none<p><b>Operations</b><br> <br> <ul><li><tt><a href="#PDBSortO0">operator()</a> - - <i>Returns true is 1st stringcomes before the 2nd in pdb order. Returns false otherwise</i></tt></li><li><tt><a href="#PDBSortO1">operator()</a> - - <i>The c style string versionof the above function</i></tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="AminoAcidProperty"></a><h2>AminoAcidProperty</h2><p><br>This class defines a function object that will, given an amino acidsingle letter code with return a property value for that residue type.<br><b>Authors:</b> W.R.Pitt<br><b>Files:</b> <a href="btl/amino_acid_property.h">amino_acid_property.h</a><br><b>Dependencies:</b> none<p><b>Operations</b><br> <br> <ul><li><tt><a href="#AminoAcidPropertyO0">AminoAcidProperty</a> - - <i>Defaultconstructor. The default property type is KyteHydropathy.</i></tt></li><li><tt><a href="#AminoAcidPropertyO1">AminoAcidProperty</a> - - <i>Constructfunction object which will return property values of a given type.</i></tt></li><li><tt><a href="#AminoAcidPropertyO2">operator()</a> - - <i>Operator thatwill return a property value given a single letter amino acid code.</i></tt></li></ul><a href="#Classes"><img SRC="leftb.gif" ALT="back" BORDER=0 ></a><hr><p><a NAME="PIR_processor"></a><h2>PIR_processor</h2><p><br>This class is a simple PIR sequence file processor. It is not completeand is only included for use by the demo programs that come with this library.It can parse a PIR format containing any number of sequences and providethe data as a vector<string> or as individual strings.<br><b>Authors:</b> W.R.Pitt<br><b>Files:</b> <a href="btl/PIR_processor.h">PIR_processor.h</a><br><b>Dependencies:</b> none<p><b>Operations</b><br> <br> <ul><li><tt><a href="#PIR_processorO0">PIR_processor</a> - - <i>Default constructor(does nothing)</i></tt></li><li><tt><a href="#PIR_processorO1">empty</a> - - <i>Return true if no sequenceshave been read in, false otherwise.</i></tt></li><li><tt><a href="#PIR_processorO2">ReadFile</a> - - <i>Read a file with a givenname. If this function is called more than once, the new sequences areadded to those already there.</i></tt></li><li><tt><a href="#PIR_processorO3">Seqs</a> - - <i>Return any sequences thatbeen read in.</i></tt></li><li><tt><a href="#PIR_processorO4">Seq</a> - - <i>Return a single sequence,given a valid index number</i></tt></li>⌨️ 快捷键说明
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