1 /* 2 * This file is part of the GROMACS molecular simulation package. 3 * 4 * Copyright (c) 2014,2015,2016,2018,2019, by the GROMACS development team, led by 5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, 6 * and including many others, as listed in the AUTHORS file in the 7 * top-level source directory and at http://www.gromacs.org. 8 * 9 * GROMACS is free software; you can redistribute it and/or 10 * modify it under the terms of the GNU Lesser General Public License 11 * as published by the Free Software Foundation; either version 2.1 12 * of the License, or (at your option) any later version. 13 * 14 * GROMACS is distributed in the hope that it will be useful, 15 * but WITHOUT ANY WARRANTY; without even the implied warranty of 16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 17 * Lesser General Public License for more details. 18 * 19 * You should have received a copy of the GNU Lesser General Public 20 * License along with GROMACS; if not, see 21 * http://www.gnu.org/licenses, or write to the Free Software Foundation, 22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 23 * 24 * If you want to redistribute modifications to GROMACS, please 25 * consider that scientific software is very special. Version 26 * control is crucial - bugs must be traceable. We will be happy to 27 * consider code for inclusion in the official distribution, but 28 * derived work must not be called official GROMACS. Details are found 29 * in the README & COPYING files - if they are missing, get the 30 * official version at http://www.gromacs.org. 31 * 32 * To help us fund GROMACS development, we humbly ask that you cite 33 * the research papers on the package. Check out http://www.gromacs.org. 34 */ 35 #ifndef GMX_GMXPREPROCESS_READ_CONFORMATION_H 36 #define GMX_GMXPREPROCESS_READ_CONFORMATION_H 37 38 #include <vector> 39 40 #include "gromacs/utility/real.h" 41 42 class AtomProperties; 43 struct t_atoms; 44 45 /*! \brief Allocate and fill an array of inter-atomic half distances 46 * 47 * These are either scaled VDW radii taken from vdwradii.dat, or the 48 * default value. Used directly and indirectly by solvate and 49 * insert-molecules for deciding whether molecules clash. The return 50 * pointer should be freed by the caller. */ 51 std::vector<real> makeExclusionDistances(const t_atoms* a, AtomProperties* aps, real defaultDistance, real scaleFactor); 52 53 #endif 54