sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2096dbbd74a0e0b2253ca96ad0363d3ab7810442ce80b7669a6b588ce7035a16 | C/C++ | 31,113 | 1,172 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
16aa28d6b585a28776c4a0905db17c79443bb3f68b378c87b00ed5484e7116cb | C/C++ | 31,332 | 714 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009-2010 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License version 3 as published by t... |
bf4b48d8aa6e9844dab793a2e07f32592703018fc42e606d23171bd87e616987 | C/C++ | 31,344 | 811 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
886f1ab57edd26b2c6d356881bea8b991b4e624f813bf8f288fc86a920edad5c | C/C++ | 31,394 | 514 | /*
* Copyright (c) 2003, 2007-14 Matteo Frigo
* Copyright (c) 2003, 2007-14 Massachusetts Institute of Technology
*
* The following statement of license applies *only* to this header file,
* and *not* to the other files distributed with FFTW or derived therefrom:
*
* Redistribution and use in source and binary f... |
ef40fe7047690488a900da0d832470a7d98487c32054b8a4bbed84a66b01d200 | C/C++ | 31,776 | 483 | //=====================================================================================================================
//
// readcxdata.h : Constant and type definitions for MATLAB MEX function readcxdata().
//
// ****** FOR DESCRIPTION, REVISION HISTORY, ETC, SEE IMPLEMENTATION FILE ******
//
//======================... |
d1e1081929add857445d7b789d67fe8015cada3eb21e054b42e6f5471f44fab1 | C/C++ | 31,878 | 731 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms o... |
47605b700a8e3739686547a4e841fd731ee1b682a37865a2c9dacc0d37f76e9c | C/C++ | 32,120 | 686 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
0e504f500be1cefe459794737151ff5b7e271a2c38b86e6ef2a7928587b0630e | C/C++ | 32,129 | 491 | //=====================================================================================================================
//
// readcxdata.h : Constant and type definitions for MATLAB MEX function readcxdata().
//
// ****** FOR DESCRIPTION, REVISION HISTORY, ETC, SEE IMPLEMENTATION FILE ******
//
//======================... |
b53476f5d79db009114945fd6140e7c725b9189f231b0ade89e9701444f349b8 | C/C++ | 32,393 | 826 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
1664976319f9a65b8b92631d480df19b498f157941a511900c402bc803198716 | C/C++ | 32,738 | 1,090 | // matrix.h --- matrix class. Includes interfaces to some BLAS and LAPACK routines
// Copyright (C) 2006-2008 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Sof... |
dd319617a52be72cd7b108366125b1a5a7abfbd149971add69b28e36855d2440 | C/C++ | 32,888 | 828 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
ee60d8c6c1b74b2837a2828d6aa73a53dc4bc9db342a3fb5b1fcc7f1b433e7ba | C/C++ | 33,060 | 846 | // profasi_hydrogen_bond --- PROFASI backbone-backbone and sidechain-backbone hydrogen bonding energy term
// Copyright (C) 2010-2011 Pengfei Tian, Wouter Boomsma, Jes Frellsen, Jesper Ferkinghoff-Borg
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under... |
e751414b936ce365c4e73d67a67ae2b7fa7ad661dc5ff76d94d7776771113e67 | C/C++ | 33,084 | 1,014 | // optimize.h --- Brent and Powell function minimizers
// Copyright (C) 2006-2008 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either vers... |
aa6d528c598211c4708102b21496f825d906980473fa5f47ea14a39bcdc5cfee | C/C++ | 33,117 | 889 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
1331c6f1337e72499371a4feec2bfdb85e3bc08c920a06174e044fadc4122c9f | C/C++ | 33,658 | 750 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
68ddca8547f5c24295b96b6baf36ee5d46e83dbb5261eff7c08a2bce170d774d | C/C++ | 34,028 | 917 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
c0f2e276c4a18a8969a5730ec6aeb491f1f6b901a60631b16792547218ecfdce | C/C++ | 34,076 | 1,152 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
c72c79300ea2999142cb87fc1d56b347a50541d12b11338f0fa7deabdfafd90e | C/C++ | 34,327 | 896 | // move_bgs.h --- Biased Gaussian Step move
// Reference: Monte Carlo update for chain molecules: biased Gaussian steps in torsional space
// G. Favrin, A. Irbäck and F. Sjunnesson, Journal of Chemical Physics, 2001
// Copyright (C) 2006-2010 Wouter Boomsma, Sandro Bottaro, Jesp... |
6ed35c3d0ae974fe7615e483de0d222df0894d3076f4666687eadb3f9a8c151f | C/C++ | 34,630 | 790 | /*
* -----------------------------------------------------------------
* $Revision: 1.13 $
* $Date: 2010/12/01 22:10:38 $
* -----------------------------------------------------------------
* Programmer(s): Scott D. Cohen, Alan C. Hindmarsh, Radu Serban
* and Dan Shumaker @ LLNL
* ---------------... |
dd86aad4149c7b26fec51c4b616118abe2989ad5731e5940208f45457bbe6ce6 | C/C++ | 34,875 | 765 | /*
* -----------------------------------------------------------------
* $Revision: 1.7 $
* $Date: 2010/12/01 22:16:17 $
* -----------------------------------------------------------------
* Programmer(s): Allan Taylor, Alan Hindmarsh, Radu Serban, and
* Aaron Collier @ LLNL
* --------------------... |
1f4f46d3f65904e39e8ca987b9dde9c3926c9f184f41097fa89071c69b46b239 | C/C++ | 35,233 | 905 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008-2010 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2008-2009 Benoit Jacob <jacob.benoit.1@gmail.com>
// Copyright (C) 2009 Kenneth Riddile <kfriddile@yahoo.com>
// Copyright (C) 2010 Hauke Hei... |
972859b61247792e43c8fafe850ba629ae1c49edeaeb1eb9126cb934c7fa18cf | C/C++ | 35,246 | 776 | // move_crankshaft.h --- Crankshaft move: Rotate atoms around an axis defined by two Calpha atoms
// References: [1] Betancourt (2005) Efficient monte carlo trial moves for
// polypeptide simulations, J Chem Phys, 123, 174905
// ... |
3eccb5eaa5429be1474c69ce3a4ea72af8418e80e2c58996329c651d5efdaa24 | C/C++ | 35,335 | 1,078 | /*
* Copyright (c) 2020-2022, NVIDIA CORPORATION. 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 ... |
d259677e5886867da95b714977e793ac0e05c43d988288f59ac0c94a48f2248c | C/C++ | 35,565 | 1,178 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
5fe44b0205392ed919b5cbab2ece8212e5be2b881d09fe5aa9ecab99dfd3a74c | C/C++ | 35,681 | 757 | // definitions.h --- Values and enums used by proteins
// Copyright (C) 2006-2011 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either vers... |
5a95d936b6e8d53223c1ab24c4c6e34a1a1b7d53f2097f9736a24787b3683eb1 | C/C++ | 35,752 | 936 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008-2010 Gael Guennebaud <gael.guennebaud@inria.fr>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License version 3 as published b... |
d8c1e1dcaf74eb198b54694a82e6ba9ce71208b2b598034eebf5068edc0cec3d | C/C++ | 35,756 | 827 | // sphere.h --- Sphere class for calculating visible volume derived measures
// Copyright (C) 2011-2013 Kristoffer Enøe Johansson
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Fre... |
d4133955ad2b5dade258b5de2f6321483ad796a40a1d37d43077ef64a1d28768 | C/C++ | 36,011 | 1,345 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
a56559bdf977f547f56e9e4991dcda11696657e9094bac3ae3858b06c0ef05ee | C/C++ | 36,706 | 587 | /*M///////////////////////////////////////////////////////////////////////////////////////
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
// By downloading, copying, installing or using the software you agree to this license.
// If you do not agree to this license, do not download, instal... |
387d84aeb9a070fd978128c6c6ff7221013e9e1357af0dd89611642989e4f98a | C/C++ | 36,815 | 917 | /** \file playback.h
* Copyright (c) Microsoft Corporation. All rights reserved.
* Licensed under the MIT License.
* Kinect For Azure Recording Playback SDK.
*/
#ifndef K4A_PLAYBACK_H
#define K4A_PLAYBACK_H
#include <k4arecord/types.h>
#include <k4arecord/k4arecord_export.h>
#ifdef __cplusplus
extern "C" {
#end... |
c6b576194a7abc0f6ebdf2afbc468fc2de99906b52665ae1b3d14a8d9fd0647c | C/C++ | 37,041 | 1,171 | /***********************************************************************
* Software License Agreement (BSD License)
*
* Copyright 2008-2009 Marius Muja (mariusm@cs.ubc.ca). All rights reserved.
* Copyright 2008-2009 David G. Lowe (lowe@cs.ubc.ca). All rights reserved.
*
* THE BSD LICENSE
*
* Redistribution an... |
0f9f66c35495ab5863f6b10618fa9e988325c419385b27ce4b888ea414063753 | C/C++ | 37,105 | 1,101 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
163b6d3d09afdc7bce104d90c20ad2a588fc3d32254d1a145e9536da7833fb7e | C/C++ | 37,115 | 912 | /*============================================================================*/
/* DIAdem Connectivity Library */
/*----------------------------------------------------------------------------*/
/* Copyright (c) National Instruments 2004-2010. All Rights Reserved. ... |
6e6086fd60a00eb9a41eb460299e3f1e189200ffbfc3253b9ad16990db25523c | C/C++ | 37,407 | 912 | /*============================================================================*/
/* DIAdem Connectivity Library */
/*----------------------------------------------------------------------------*/
/* Copyright (c) National Instruments 2004-2010. All Rights Reserved. ... |
a6d4506c878c10383734e1ec803177a2c92ba5e693180037e67e87966a7177a9 | C/C++ | 37,628 | 1,135 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
651b5a6b8335c75bb8a901f4bbebd349f4a1ff7bd3e3b27f02a62e7bbc7b327c | C/C++ | 38,009 | 1,811 | #ifndef ReadDataIn_H_
#define ReadDataIn_H_
#include "./FilterGenotype.h"
using namespace std;
int GetBestBase (string Genotype, map <string ,char > SNP_Allele , map <string,string > & SNP_back_Allele , vector <BaseType> & Base_list)
{
vector<string> Base1 ;
split(Genotype, Base1," \t");
map <char,int > Coun... |
80cb5cceb0947fb57a9d9ec884b1fe5cf1581abe5ba6aaa78ae3fc7fdad266cd | C/C++ | 38,374 | 1,087 | // vectorMatrix_3D.h --- 3D vector and matrix classes
// Copyright (C) 2006-2008 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either versi... |
eeeecdfaf1e19a8917bdd54ef576f69d828bec31ef733e081d1e9fb32cf07ff1 | C/C++ | 38,494 | 496 | //=====================================================================================================================
//
// cxfilefmt_mex.h : Data structs defining format of data records in Maestro/Cntrlx trial- and cont-mode data files.
//
// AUTHOR: saruffner, sglisberger, et al.
//
// DESCRIPTION:
// This is a m... |
78ebd660f9bc4e8b823def3602db7924f19d5ee6c39b58277ef49d84af9a912a | C/C++ | 39,250 | 1,048 | /**
* Copyright (c) 1996-2023, SR Research Ltd., All Rights Reserved
*
* For use by SR Research licencees only. Redistribution and use in source
* and binary forms, with or without modification, are NOT permitted.
*
* Redistributions in binary form must reproduce the above copyright
* notice, this list of... |
8104cbcdbae0a9f83273a20b05cd91b9231e25ed91da4b298da04c759c10aab1 | C/C++ | 40,338 | 615 | /**
* (C) Copyright 2026 IBM. All Rights Reserved.
*
* Licensed under the MIT license. See LICENSE file in the project root for details.
*/
#pragma once
#include "bit_line_maker.h"
#include "chopped_weight_output.h"
#include "cuda_util.h"
#include "pwu_kernel.h"
#include "pwu_kernel_parameter_base.h"
#include "rp... |
6a99e95d416a7ee689d4fb755057f1f5b9d795e02da38cc7af9a65d39abdc68e | C/C++ | 41,108 | 617 | /**
* (C) Copyright 2020, 2021, 2022, 2023, 2024 IBM. All Rights Reserved.
*
* This code is licensed under the Apache License, Version 2.0. You may
* obtain a copy of this license in the LICENSE.txt file in the root directory
* of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
*
* Any modific... |
1e8be1451608b5fe2537e42dfa86a920f29f6d838efca6af2eccf2513b0f6407 | C/C++ | 41,218 | 1,782 | /*
* mdarray.h
*
* Copyright (C) 2008, Martin Paluszewski, The Bioinformatics Centre, University of Copenhagen.
*
* This file is part of Mocapy++.
*
* Mocapy++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free S... |
e14aecd057667cb1b98e23903d3b5b5ffcdb3013498857678fc09f75d864d157 | C/C++ | 41,367 | 1,045 | // montecarlo.h --- Base class for optimization and simulation code
// Copyright (C) 2006-2009 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundatio... |
38ba564792baacbeaa91efe06a931a1b0e28439e94c6348319374f53d8c23e30 | C/C++ | 41,986 | 892 | // profasi_sidechain_charge.h --- PROFASI side chain charged interaction energy term
// Copyright (C) 2010 Pengfei Tian, Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// th... |
7b6ddd4f75e184e354f6001cb9a77c751940a83872d352ef874c0cb075fd3b17 | C/C++ | 42,368 | 554 | //=====================================================================================================================
//
// cxfilefmt_mex.h : Data structs defining format of data records in Maestro/Cntrlx trial- and cont-mode data files.
//
// AUTHOR: saruffner, sglisberger, et al.
//
// DESCRIPTION:
// This is a m... |
3f7ebd9f3505b15d1bdec8238574ab88c9e21e9281a4d493dbc49c8d17fc5b33 | C/C++ | 42,446 | 507 | /*
* Copyright (c) 2020-2022, NVIDIA CORPORATION. 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 ... |
79aa549f44cefa376c0bbbae64f73d1dfb3e08e5de7202b796bd2a92f21eda6c | C/C++ | 42,522 | 1,633 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
072193b88b8dee894ccedbccb16ac0dbb11098436ab5d1c51be2a1cd3a0745a8 | C/C++ | 43,286 | 1,271 | /** \file k4atypes.h
* Copyright (c) Microsoft Corporation. All rights reserved.
* Licensed under the MIT License.
* Kinect For Azure SDK Type definitions.
*/
#ifndef K4ATYPES_H
#define K4ATYPES_H
#ifdef __cplusplus
#include <cinttypes>
#include <cstddef>
#include <cstring>
#else
#include <inttypes.h>
#include <s... |
546126c5755ea6b0374a1a2f5475adfb436b8041a7581ec25f82504212939d66 | C/C++ | 43,529 | 1,279 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License version 3 as published b... |
44cafe4184515aff8774265bf90cfde87992d4b4f984100d3c9554fb04801209 | C/C++ | 43,537 | 1,273 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
ccc18a26e01618896db2f5ac3ce56f5032e54105fd9b783271c54d16e74579ac | C/C++ | 43,691 | 1,599 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
f52d863e5062a2baa20b472ce86c488ff9c172a71fc5c78b67fcc9deb977f939 | C/C++ | 44,573 | 1,055 | /*
* -----------------------------------------------------------------
* $Revision: 1.23 $
* $Date: 2011/04/27 20:39:34 $
* -----------------------------------------------------------------
* Programmer(s): Radu Serban @ LLNL
* -----------------------------------------------------------------
* Copyright (c) 20... |
6a59f2a3c17926b229f651748dcaa509fe6f7f5daa5bd09b3e79713536df1699 | C/C++ | 44,574 | 1,055 | /*
* -----------------------------------------------------------------
* $Revision: 1.23 $
* $Date: 2011/04/27 20:39:34 $
* -----------------------------------------------------------------
* Programmer(s): Radu Serban @ LLNL
* -----------------------------------------------------------------
* Copyright (c) 20... |
aed74c49fc8da340b3d74fbf3e4fd07c117edeee8201b57f11bdb057e5e26081 | C/C++ | 44,585 | 1,496 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
0cb9057d2ebdde650e67e9926c513d448631c286510340c31f7e8c426841f8d7 | C/C++ | 44,738 | 822 | // Copyright (C) 2014-2015 by Anders S. Christensen, Anders S. Larsen, Lars A. Bratholm
//
// This file is part of PHAISTOS
//
// PHAISTOS free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the... |
b1fafa35031b61060d6c56ea9538524b835105528ce1fd49e0c5305c89c85f2d | C/C++ | 45,071 | 1,454 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
d97d0869905356abf32e59337d68a34a3f93d2547874b70a802ac7598f7e5633 | C/C++ | 45,469 | 1,557 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
99e377ed0894ec9f1266a3a994a8fb83b37bf38faea87172aeae454c0558f256 | C/C++ | 45,812 | 1,179 | // atomData.h --- Protein input data
// Copyright (C) 2006-2008 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the Licen... |
88e9ed20decc1215f34133232eb3a3db1480e6f4be9e57ffcf918fd79bf07cfa | C/C++ | 46,128 | 991 | // saxs.h --- Small Angle X-ray scattering energy function
// Copyright (C) 2008-2009 Christian Andreetta, Kasper Stovgaard, Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
/... |
ee8f02068118e2dd207bee069740f3c4f70cf769fb514a375bc31d4ea1b475ae | C/C++ | 46,649 | 1,368 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
e3eb010e2b066ae07058d447d722845aa421fc716e5617639ae33e98377b722e | C/C++ | 47,504 | 1,088 | /*
* -----------------------------------------------------------------
* $Revision: 1.21 $
* $Date: 2007/11/26 16:19:59 $
* -----------------------------------------------------------------
* Programmer(s): Radu Serban @ LLNL
* -----------------------------------------------------------------
* Copyright (c) 20... |
5a7644d960c749c68f1e55da4a9ed39880abf50d0ec2fd6f8546539355041b12 | C/C++ | 47,505 | 1,088 | /*
* -----------------------------------------------------------------
* $Revision: 1.21 $
* $Date: 2007/11/26 16:19:59 $
* -----------------------------------------------------------------
* Programmer(s): Radu Serban @ LLNL
* -----------------------------------------------------------------
* Copyright (c) 20... |
8677981f9a16e6494687a623ba741e746097f4e7d532ee88f79f2ca182e725dc | C/C++ | 47,992 | 1,041 | // Copyright (C) 2014-2014 by Anders S. Christensen, Anders S. Larsen, Lars A. Bratholm
//
// This file is part of PHAISTOS
//
// PHAISTOS free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the... |
1f8f179949eb1a193e724ce316f44a74c199ad9b38054f1aebb8cb8ca10b59ff | C/C++ | 48,147 | 1,174 | #ifndef MODEL_H
#define MODEL_H
#include <assert.h>
#include <algorithm>
#include <iostream>
#include <fstream>
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <string>
#include <vector>
#include "logging.h"
using std::vector;
using std::string;
/**
@brief Enumeration to choose a time stepping schem... |
1ac74205f0067672229da3d203c4bfd2b2b5c44e1f590308d7b9bbc1b78020ed | C/C++ | 48,857 | 622 | //=====================================================================================================================
//
// rmvideo_common.h : Constants and structure definitions shared by Remote Maestro Video and its Maestro counterpart.
//
// REVISION HISTORY:
// 22feb2006-- Target types RMV_SINEGRAT and RMV_SQUARE... |
c438be8477d25897d9a8fbce26ac3f5ee7ec3fbfed5d2bf4193e5c61e1e4000e | C/C++ | 49,016 | 1,190 | /*----------------------------------------------------------------------------*/
/* CP2K: A general program to perform molecular dynamics simulations */
/* Copyright 2000-2022 CP2K developers group <https://cp2k.org> */
/* ... |
6f03d9bf783188a629ed14ee0d528691b409727216d45356ed182331a1134c49 | C/C++ | 49,203 | 1,526 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
f2937443d9102674cf1f2d395e50b54c4755814bc03e0b97300a9f4f22df5711 | C/C++ | 49,519 | 938 | /*
* -----------------------------------------------------------------
* $Revision: 1.14 $
* $Date: 2010/12/01 22:14:08 $
* -----------------------------------------------------------------
* Programmer(s): Allan G. Taylor, Alan C. Hindmarsh, Radu Serban,
* and Aaron Collier @ LLNL
* ------------... |
236b6f2fcbe298dd4d97693e88018ea7a1c710a4d1843591eb78369aabdb624b | C/C++ | 49,675 | 1,233 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribut... |
c016f5bc60fa07abc5103a7d80af57dcfd0f9f8550c1b9d18cd2d7623722f1f2 | C/C++ | 49,880 | 1,877 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ... |
59b6e94ef6dc4b13b2d2f8c0021bc01aeabad2e84773824ddd35a3c5b582130a | C/C++ | 50,102 | 1,402 | /*
* Copyright (c) 2020-2022, NVIDIA CORPORATION. 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 ... |
3cfe280c0caa67ac7d30ba919a7b678c9b48e081eb672874ab073fb9775a7761 | C/C++ | 50,880 | 1,557 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
a7739069a5e3cfdb3dfd8df2fea5d545fc665362074a241cb4d50a1f37710a45 | C/C++ | 52,012 | 1,095 | // matint.h
/*
Copyright (C) Cambridge Electronic Design Limited 2014
Author: James Thompson
Web: www.ced.co.uk email: james@ced.co.uk, softhelp@ced.co.uk
This file is part of CEDS64ML, a MATLAB interface to the SON64 library.
CEDS64ML is free software: you can redistribute it and/or modify
it... |
028a1d8cc47d6067402a249e24f185a28feb2f3241401d85cede2d18cec5779e | C/C++ | 52,083 | 1,486 | #ifndef GFF_H
#define GFF_H
//#define CUFFLINKS 1
#include "GBase.h"
#include "gdna.h"
#include "codons.h"
#include "GFaSeqGet.h"
#include "GList.hh"
#include "GHashMap.hh"
#include "GBitVec.h"
#ifdef CUFFLINKS
#include <boost/crc.hpp> // for boost::crc_32_type
#endif
//reserved Gffnames::feats entries -- basic fe... |
46f8125da371f35be37532756e5d1901b447e29dcee7536b36784cd4d32ad402 | C/C++ | 52,490 | 1,209 | /*M///////////////////////////////////////////////////////////////////////////////////////
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
// By downloading, copying, installing or using the software you agree to this license.
// If you do not agree to this license, do not download, instal... |
6af30fd6bbd5727da0d23b2b04429f8d3a5ea144d51b7b395b823bf17ebe3f91 | C/C++ | 53,032 | 1,390 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
// Copyright (C) 2010 Hauke Heibel <hauke.heibel@gmail.com>
//
// Eigen is free software; you can red... |
ae9fa7fa38f55fd9dbd84126e9cec74e7ee64db49a8d06cc740800c5d804471f | C/C++ | 54,984 | 781 | //=====================================================================================================================
//
// cxobj_ifc_mex.h : CNTRLX object-related defines that are shared among two or more CNTRLX classes.
//
// AUTHOR: saruffner
//
// DESCRIPTION:
// This is a modified version of the CNTRLX/CXDRIVER... |
f8e591a850acca1fdaa493dbf03d3663dc7f7f983c00ace94a2dbff075f5b4e7 | C/C++ | 55,409 | 1,921 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
d000f9d8bdb1d3b07c95149b35a218f1da77839af1260016988718eb7e14e13b | C/C++ | 56,053 | 797 | //=====================================================================================================================
//
// cxobj_ifc_mex.h : CNTRLX object-related defines that are shared among two or more CNTRLX classes.
//
// AUTHOR: saruffner
//
// DESCRIPTION:
// This is a modified version of the CNTRLX/CXDRIVER... |
5c0279439cd74e76d269353b5e858b816a81be5f6d9ca38712d07cd1f2a7247b | C/C++ | 56,120 | 1,316 | // move_priors.h --- Priors used by various moves
// Copyright (C) 2006-2010 Wouter Boomsma, Sandro Bottaro, Jesper Ferkinghoff-Borg
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the F... |
f053a9050b58269bbb02c81c947c6289e5d1db4bd7d8420496d1a2b41dd73b24 | C/C++ | 56,228 | 716 | //=====================================================================================================================
//
// rmvideo_common.h : Constants and structure definitions shared by Remote Maestro Video and its Maestro counterpart.
//
// REVISION HISTORY:
// 22feb2006-- Target types RMV_SINEGRAT and RMV_SQUARE... |
014802783c76d94b6b29b69fdb8a2a3678bb55c1db4bc5ba2bd2d26d1dec315d | C/C++ | 56,503 | 1,262 | // gbsa.h --- GBSA implicit solvation energy term
// Copyright (C) 2009-2011 Sandro Bottaro, Kristoffer Enøe Johansson, Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the... |
cec9ddf57f2f647688ea4465b0ec51ceb3c884a61e356a692f55f558fd5ed2f9 | C/C++ | 56,656 | 2,134 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
9fd17d23ab067a14a263f5b50b6b59a124042f15e9c6df24f2f3d1cdd26ea954 | C/C++ | 57,455 | 1,134 | // move_sidechain_local.h --- Move: Local updates of sidechain chi angles using constraints on hydrogen-bond donors and acceptors
// Copyright (C) 2006-2010 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General ... |
cd95c6b9bdbd6d0ecab45085254ae16ad6b401d3ade6b16a1012f9239697cea9 | C/C++ | 58,681 | 1,761 | // TArray.h
// Copyright (c) 2010-2012 Jes Frellsen
//
// This file is part of Muninn.
//
// Muninn is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License version 3 as
// published by the Free Software Foundation.
//
// Muninn is distributed in the hope that it w... |
b11671f4d085fdcdc667089fcb74da7dcc14b212c05affcacb3b22b83017cc58 | C/C++ | 59,097 | 1,717 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
447159f45bac5dbcf1542d75090ff5e9cbc466854fec3a626538740ce1fd9a57 | C/C++ | 61,026 | 1,837 | /*M///////////////////////////////////////////////////////////////////////////////////////
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
// By downloading, copying, installing or using the software you agree to this license.
// If you do not agree to this license, do not download, instal... |
d1da5fd3dcb8aaa3fdf178aa670fe50427db16c6275cbe3f13b09ef76b76774b | C/C++ | 61,629 | 1,884 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
100d00899e0825efc951d911e20edac43cfdd076106ec745b7580948f187f5c2 | C/C++ | 62,771 | 1,829 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
a07317bc8fde792711ca21d9ac00e2155dd021fb53460b9f7a6de9743c1f15ba | C/C++ | 65,857 | 1,782 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
3195a3f28af1064f6acc9eb4b357bca68df4344e04510ae45b88754a12d13eb6 | C/C++ | 69,414 | 1,975 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistr... |
cea732d8e8f985f85a4ce5bbd8c04968ebc9b235073e318e80aa8208849749c4 | C/C++ | 70,032 | 1,716 | // move_crisp.h --- Concerted Rotation Integrating Structural Priors
// Copyright (C) 2006-2010 Wouter Boomsma, Sandro Bottaro, Jesper Ferkinghoff-Borg
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as pu... |
a72756a3faeefe4101fc5686ff90a834acb62156d3ee6f3f5f24e1b9786f7266 | C/C++ | 70,379 | 1,642 | /**
* (C) Copyright 2026 IBM. All Rights Reserved.
*
* Licensed under the MIT license. See LICENSE file in the project root for details.
*/
#pragma once
#include "cuda_fp16_util.h"
#include "cuda_math_util.h"
#include <algorithm>
#include <chrono>
#include <cmath>
#include <iostream>
#include <memory>
#include <... |
6288956fb9bd6ac5f5fe82b18a34b53fa4ed1d84043588252b5c9e25f97c4e5d | C/C++ | 70,498 | 1,644 | /**
* (C) Copyright 2020, 2021, 2022, 2023, 2024 IBM. All Rights Reserved.
*
* This code is licensed under the Apache License, Version 2.0. You may
* obtain a copy of this license in the LICENSE.txt file in the root directory
* of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
*
* Any modific... |
86fc974385be2380b99de794233014c0668b4460193ac92f9e15366593be16b0 | C/C++ | 71,694 | 557 | // default_parameters_torus_dbn.h --- Default parameters for the TorusDbn model
// Copyright (C) 2008-2010 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Softwar... |
17f339e7582ff4d4d56e40b0e87d77eda8d8f8e62806278ddf8fcf0b8b3d9a84 | C/C++ | 72,945 | 1,724 | /* stb_image_write - v1.16 - public domain - http://nothings.org/stb
writes out PNG/BMP/TGA/JPEG/HDR images to C stdio - Sean Barrett 2010-2015
no warranty implied; use at your own risk
Before #including,
#define STB_IMAGE_WRITE_IMPLEMENTATION
in the file ... |
39f37bbf800a90e833613c67979184d1d5de841ea0dcc868c6686053df6e5042 | C/C++ | 77,484 | 1,801 | // program_option_parser.h --- Utility classes for parsing command lines and config files
// Copyright (C) 2006-2010 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the F... |
65c53ed5d61b3fd22d75d71b255edbfc8ec4aeab4d9233af961751cdf6b94eb5 | C/C++ | 77,579 | 2,446 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
421799cb0dcbbdfee549a31c64221dd6be9dfdad5784a664211430067199be01 | C/C++ | 77,926 | 2,181 | /***************************************************************************************************
* Copyright (c) 2017-2021, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions ar... |
e39373f6bd4bb9d3e2a16793c69e94dcc08b333e4db3fbb6b0c9683cd85d9c02 | C/C++ | 78,586 | 518 | // default_parameters_fb5_dbn.h --- Default parameters for the Fb5Dbn model
// Copyright (C) 2008-2010 Wouter Boomsma
//
// This file is part of Phaistos
//
// Phaistos is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Fo... |
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