// // ccealign -- structural alignment plugin for PyMol // ////////////////////////////////////////////////////////////////////////////// // // Copyright (C) Jason Vertrees. // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // // * Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in // the documentation and/or other materials provided with the // distribution. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS // IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED // TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A // PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER // OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR // PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF // LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // ////////////////////////////////////////////////////////////////////////////// // include the template numerical toolkit #include "tnt/tnt.h" // for reflections #include "jama_lu.h" // for the SVD #include "jama_svd.h" ///////////////////////////////////////////////////////////////////////////// // Structs, typedefs, declarations that need C++ linkage ///////////////////////////////////////////////////////////////////////////// #define TA1 TNT::Array1D #define TA2 TNT::Array2D // tranpose of a matrix TA2<double> transpose( const TA2<double>& v ); // C-linkage declarations #ifdef __cplusplus extern "C" { #endif #include"ce_types.h" #include"os_std.h" #include"os_python.h" #include <math.h> ///////////////////////////////////////////////////////////////////////////// // Function Declarations ///////////////////////////////////////////////////////////////////////////// // Calculates the CE Similarity Matrix double** calcS(double** d1, double** d2, int lenA, int lenB, int wSize); // calculates a simple distance matrix double** calcDM(pcePoint coords, int len); // Converter: Python Object -> C Structs pcePoint getCoords( PyObject* L, int len ); // Optimal path finding algorithm (CE). pathCache findPath(double** S, double** dA, double**dB, int lenA, int lenB, int winSize, int* bufferSize); // filter through the results and find the best PyObject* findBest( pcePoint coordsA, pcePoint coordsB, pathCache paths, int bufferSize, int smaller, int winSize ); #ifdef __cplusplus } #endif