diff --git a/src/USER-PTM/ptm_polar.cpp b/src/USER-PTM/ptm_polar.cpp index fa199ca656..6996d8dfef 100644 --- a/src/USER-PTM/ptm_polar.cpp +++ b/src/USER-PTM/ptm_polar.cpp @@ -1,5 +1,5 @@ /******************************************************************************* - * -/_|:|_|_\- + * -/_|:|_|_\- * * This code is a modification of D.L. Theobald's QCP rotation code. * It has been adapted to calculate the polar decomposition of a 3x3 matrix @@ -14,7 +14,7 @@ * USA * * dtheobald@brandeis.edu - * + * * Pu Liu * Johnson & Johnson Pharmaceutical Research and Development, L.L.C. * 665 Stockton Drive @@ -22,7 +22,7 @@ * USA * * pliu24@its.jnj.com - * + * * * If you use this QCP rotation calculation method in a publication, please * reference: @@ -33,7 +33,7 @@ * Acta Crystallographica A 61(4):478-480. * * Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2009) - * "Fast determination of the optimal rotational matrix for macromolecular + * "Fast determination of the optimal rotational matrix for macromolecular * superpositions." * Journal of Computational Chemistry 31(7):1561-1563. * @@ -63,7 +63,7 @@ * 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. + * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * * Source: started anew. * @@ -82,7 +82,7 @@ * * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix, * for use in Polyhedral Template Matching. - * + * ******************************************************************************/ #include @@ -326,7 +326,7 @@ void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coord A[6] += z1 * x2; A[7] += z1 * y2; - A[8] += z1 * z2; + A[8] += z1 * z2; } } diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp index 7eb4cd3d84..055a2bf3b0 100644 --- a/src/USER-PTM/ptm_structure_matcher.cpp +++ b/src/USER-PTM/ptm_structure_matcher.cpp @@ -308,7 +308,7 @@ static void check_graphs_graphene( const refdata_t* s, int num_points, const double (*ideal_points)[3], double (*normalized)[3], - int8_t* mapping, + int8_t* mapping, result_t* res) { double G1 = 0, G2 = 0; diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp index 87db58fe30..65ad8b3324 100644 --- a/src/USER-PTM/ptm_voronoi_cell.cpp +++ b/src/USER-PTM/ptm_voronoi_cell.cpp @@ -4,19 +4,19 @@ Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved. Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: +modification, are permitted provided that the following conditions are met: (1) Redistributions of source code must retain the above copyright notice, this -list of conditions and the following disclaimer. +list of conditions and the following disclaimer. (2) 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. +and/or other materials provided with the distribution. (3) Neither the name of the University of California, Lawrence Berkeley National Laboratory, U.S. Dept. of Energy nor the names of its contributors may be used to endorse or promote products derived from this software without -specific prior written permission. +specific prior written permission. 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 @@ -27,7 +27,7 @@ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 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. +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h index 007e36f8b7..8137aa3340 100644 --- a/src/USER-PTM/ptm_voronoi_cell.h +++ b/src/USER-PTM/ptm_voronoi_cell.h @@ -4,19 +4,19 @@ Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved. Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: +modification, are permitted provided that the following conditions are met: (1) Redistributions of source code must retain the above copyright notice, this -list of conditions and the following disclaimer. +list of conditions and the following disclaimer. (2) 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. +and/or other materials provided with the distribution. (3) Neither the name of the University of California, Lawrence Berkeley National Laboratory, U.S. Dept. of Energy nor the names of its contributors may be used to endorse or promote products derived from this software without -specific prior written permission. +specific prior written permission. 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 @@ -27,7 +27,7 @@ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 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. +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code diff --git a/src/USER-PTM/ptm_voronoi_config.h b/src/USER-PTM/ptm_voronoi_config.h index d0718a3630..ca5dcd9559 100644 --- a/src/USER-PTM/ptm_voronoi_config.h +++ b/src/USER-PTM/ptm_voronoi_config.h @@ -4,19 +4,19 @@ Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved. Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: +modification, are permitted provided that the following conditions are met: (1) Redistributions of source code must retain the above copyright notice, this -list of conditions and the following disclaimer. +list of conditions and the following disclaimer. (2) 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. +and/or other materials provided with the distribution. (3) Neither the name of the University of California, Lawrence Berkeley National Laboratory, U.S. Dept. of Energy nor the names of its contributors may be used to endorse or promote products derived from this software without -specific prior written permission. +specific prior written permission. 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 @@ -27,7 +27,7 @@ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 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. +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code