1 /* 2 * This file is part of the GROMACS molecular simulation package. 3 * 4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands. 5 * Copyright (c) 2001-2004, The GROMACS development team. 6 * Copyright (c) 2010,2014,2015,2016,2018 by the GROMACS development team. 7 * Copyright (c) 2019,2020, by the GROMACS development team, led by 8 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, 9 * and including many others, as listed in the AUTHORS file in the 10 * top-level source directory and at http://www.gromacs.org. 11 * 12 * GROMACS is free software; you can redistribute it and/or 13 * modify it under the terms of the GNU Lesser General Public License 14 * as published by the Free Software Foundation; either version 2.1 15 * of the License, or (at your option) any later version. 16 * 17 * GROMACS is distributed in the hope that it will be useful, 18 * but WITHOUT ANY WARRANTY; without even the implied warranty of 19 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 20 * Lesser General Public License for more details. 21 * 22 * You should have received a copy of the GNU Lesser General Public 23 * License along with GROMACS; if not, see 24 * http://www.gnu.org/licenses, or write to the Free Software Foundation, 25 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 26 * 27 * If you want to redistribute modifications to GROMACS, please 28 * consider that scientific software is very special. Version 29 * control is crucial - bugs must be traceable. We will be happy to 30 * consider code for inclusion in the official distribution, but 31 * derived work must not be called official GROMACS. Details are found 32 * in the README & COPYING files - if they are missing, get the 33 * official version at http://www.gromacs.org. 34 * 35 * To help us fund GROMACS development, we humbly ask that you cite 36 * the research papers on the package. Check out http://www.gromacs.org. 37 */ 38 #ifndef GMX_MATH_DO_FIT_H 39 #define GMX_MATH_DO_FIT_H 40 41 #include "gromacs/math/vectypes.h" 42 #include "gromacs/utility/basedefinitions.h" 43 #include "gromacs/utility/real.h" 44 45 real calc_similar_ind(gmx_bool bRho, int nind, const int* index, const real mass[], rvec x[], rvec xp[]); 46 /* Returns RMSD or Rho (depending on bRho) over all atoms in index */ 47 48 real rmsdev_ind(int nind, int index[], real mass[], rvec x[], rvec xp[]); 49 /* Returns the RMS Deviation betweem x and xp over all atoms in index */ 50 51 real rmsdev(int natoms, real mass[], rvec x[], rvec xp[]); 52 /* Returns the RMS Deviation betweem x and xp over all atoms */ 53 54 real rhodev_ind(int nind, int index[], real mass[], rvec x[], rvec xp[]); 55 /* Returns size-independent Rho similarity parameter over all atoms in index 56 * Maiorov & Crippen, PROTEINS 22, 273 (1995). 57 */ 58 59 real rhodev(int natoms, real mass[], rvec x[], rvec xp[]); 60 /* Returns size-independent Rho similarity parameter over all atoms 61 * Maiorov & Crippen, PROTEINS 22, 273 (1995). 62 */ 63 64 void calc_fit_R(int ndim, int natoms, const real* w_rls, const rvec* xp, rvec* x, matrix R); 65 /* Calculates the rotation matrix R for which 66 * sum_i w_rls_i (xp_i - R x_i).(xp_i - R x_i) 67 * is minimal. ndim=3 gives full fit, ndim=2 gives xy fit. 68 * This matrix is also used do_fit. 69 * x_rotated[i] = sum R[i][j]*x[j] 70 */ 71 72 void do_fit_ndim(int ndim, int natoms, real* w_rls, const rvec* xp, rvec* x); 73 /* Do a least squares fit of x to xp. Atoms which have zero mass 74 * (w_rls[i]) are not taken into account in fitting. 75 * This makes is possible to fit eg. on Calpha atoms and orient 76 * all atoms. The routine only fits the rotational part, 77 * therefore both xp and x should be centered round the origin. 78 */ 79 80 void do_fit(int natoms, real* w_rls, const rvec* xp, rvec* x); 81 /* Calls do_fit with ndim=3, thus fitting in 3D */ 82 83 void reset_x_ndim(int ndim, int ncm, const int* ind_cm, int nreset, const int* ind_reset, rvec x[], const real mass[]); 84 /* Put the center of mass of atoms in the origin for dimensions 0 to ndim. 85 * The center of mass is computed from the index ind_cm. 86 * When ind_cm!=NULL the COM is determined using ind_cm. 87 * When ind_cm==NULL the COM is determined for atoms 0 to ncm. 88 * When ind_reset!=NULL the coordinates indexed by ind_reset are reset. 89 * When ind_reset==NULL the coordinates up to nreset are reset. 90 */ 91 92 void reset_x(int ncm, const int* ind_cm, int nreset, const int* ind_reset, rvec x[], const real mass[]); 93 /* Calls reset_x with ndim=3, thus resetting all dimesions */ 94 95 #endif 96