Added Gromac's Tng lib

recipes/tng/all/CMakeLists.txt

@@ -0,0 +1,7 @@
+cmake_minimum_required(VERSION 3.1)
+project(cmake_wrapper)
+
+include(conanbuildinfo.cmake)
+conan_basic_setup()
+
+add_subdirectory("source_subfolder")

recipes/tng/all/conandata.yml

@@ -0,0 +1,10 @@
+sources:
+  "1.8.2":
+    url: "https://github.com/gromacs/tng/archive/v1.8.2.tar.gz"
+    sha256: "242b2ecab5018a42ba80d8df58528ecb9edf419caa671eca4864234672bf025d"
+patches:
+  "1.8.2":
+    - base_path: "source_subfolder"
+      patch_file: "patches/0001-BuildTNG.patch"
+    - base_path: "source_subfolder"
+      patch_file: "patches/0002-CMakeLists.patch"

recipes/tng/all/conanfile.py

@@ -0,0 +1,82 @@
+from conans import ConanFile, tools, CMake
+import os
+import glob
+
+
+class tngConan(ConanFile):
+    name = "tng"
+    description = "External GROMACS library for loading tng files."
+    license = "BSD-3-Clause"
+    topics = ("conan", "tng", "gromacs")
+    homepage = "https://github.com/gromacs/tng/"
+    url = "https://github.com/conan-io/conan-center-index"
+    exports_sources = ["CMakeLists.txt", "patches/*"]
+    generators = "cmake"
+    settings = "os", "arch", "compiler", "build_type"
+    options = {
+        "shared": [True, False],
+        "fPIC": [True, False]
+    }
+    default_options = {
+        "shared": False,
+        "fPIC": True
+    }
+
+    requires = (
+        "zlib/1.2.11"
+    )
+
+    _cmake = None
+
+    @property
+    def _source_subfolder(self):
+        return "source_subfolder"
+
+    @property
+    def _build_subfolder(self):
+        return "build_subfolder"
+
+    def config_options(self):
+        if self.settings.os == "Windows":
+            del self.options.fPIC
+
+    def configure(self):
+        if self.options.shared:
+            del self.options.fPIC
+        del self.settings.compiler.libcxx
+        del self.settings.compiler.cppstd
+
+    def source(self):
+        tools.get(**self.conan_data["sources"][self.version])
+        url = self.conan_data["sources"][self.version]["url"]
+        extracted_dir = self.name + "-" + self.version
+        os.rename(extracted_dir, self._source_subfolder)
+
+    def build(self):
+        for patch in self.conan_data["patches"][self.version]:
+            tools.patch(**patch)
+        cmake = self._configure_cmake()
+        cmake.build()
+
+    def _configure_cmake(self):
+        if self._cmake:
+            return self._cmake
+        self._cmake = CMake(self)
+        self._cmake.definitions["TNG_BUILD_OWN_ZLIB"] = False
+        self._cmake.definitions["TNG_BUILD_EXAMPLES"] = False
+        self._cmake.definitions["TNG_BUILD_TEST"] = False
+        self._cmake.configure(build_folder=self._build_subfolder)
+        return self._cmake
+
+    def package(self):
+        self.copy("COPYING", dst="licenses", src=self._source_subfolder)
+        cmake = self._configure_cmake()
+        cmake.install()
+        tools.rmdir(os.path.join(self.package_folder, "lib", "cmake"))
+
+    def package_info(self):
+        self.cpp_info.libs = ["tng_io"]
+        if self.settings.os == "Linux":
+            self.cpp_info.system_libs = ["m"]
+        self.cpp_info.names["cmake_find_package"] = "tng_io"
+        self.cpp_info.names["cmake_find_package_multi"] = "tng_io"

recipes/tng/all/patches/0001-BuildTNG.patch

@@ -0,0 +1,14 @@
+--- BuildTNG.cmake
++++ BuildTNG.cmake
+@@ -1,9 +1,9 @@
+ set(TNG_ROOT_SOURCE_DIR ${CMAKE_CURRENT_LIST_DIR})
+-file(RELATIVE_PATH TNG_ROOT_BINARY_DIR ${CMAKE_SOURCE_DIR} ${TNG_ROOT_SOURCE_DIR})
++file(RELATIVE_PATH TNG_ROOT_BINARY_DIR ${PROJECT_SOURCE_DIR} ${TNG_ROOT_SOURCE_DIR})
+ if ("${TNG_ROOT_BINARY_DIR}" MATCHES "^\.\.")
+     set(TNG_ROOT_BINARY_DIR tng)
+ endif()
+-set(TNG_ROOT_BINARY_DIR ${CMAKE_BINARY_DIR}/${TNG_ROOT_BINARY_DIR})
++set(TNG_ROOT_BINARY_DIR ${PROJECT_BINARY_DIR}/${TNG_ROOT_BINARY_DIR})
+
+ set(TNG_MAJOR_VERSION "1")
+ set(TNG_MINOR_VERSION "8")

recipes/tng/all/patches/0002-CMakeLists.patch

@@ -0,0 +1,14 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index bc6f8fd..602630e 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -47,7 +47,8 @@ configure_file(              src/lib/tng_io-configVersion.cmake.in
+ install(TARGETS tng_io
+         EXPORT tng_io
+         LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+-        ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}")
++        ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
++        RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}")
+
+ install(EXPORT tng_io FILE tng_io.cmake
+         NAMESPACE tng_io::

recipes/tng/all/test_package/CMakeLists.txt

@@ -0,0 +1,8 @@
+cmake_minimum_required(VERSION 3.1)
+project(test_package)
+
+include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
+conan_basic_setup()
+
+add_executable(${PROJECT_NAME} example.c)
+target_link_libraries(${PROJECT_NAME} ${CONAN_LIBS})

recipes/tng/all/test_package/conanfile.py

@@ -0,0 +1,16 @@
+import os
+from conans import ConanFile, CMake, tools
+
+class TestPackageConan(ConanFile):
+    settings = "os", "compiler", "build_type", "arch"
+    generators = "cmake"
+
+    def build(self):
+        cmake = CMake(self)
+        cmake.configure()
+        cmake.build()
+
+    def test(self):
+        if not tools.cross_building(self.settings):
+            src = os.path.join(self.source_folder, "tng_example.tng")
+            self.run("{} {}".format(os.path.join("bin", "test_package"), src), run_environment=True)

recipes/tng/all/test_package/example.c

@@ -0,0 +1,152 @@
+/* This code is part of the tng binary trajectory format.
+ *
+ * Written by Magnus Lundborg
+ * Copyright (c) 2012-2013, The GROMACS development team.
+ * check out http://www.gromacs.org for more information.
+ *
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the Revised BSD License.
+ */
+
+#include "tng/tng_io.h"
+
+#ifdef USE_STD_INTTYPES_H
+#include <inttypes.h>
+#endif
+
+#include <stdlib.h>
+#include <stdio.h>
+
+int main(int argc, char **argv)
+{
+    tng_trajectory_t traj;
+    union data_values ***positions = 0; /* A 3-dimensional array to be populated */
+    int64_t n_particles, n_values_per_frame, n_frames, tot_n_frames;
+    char data_type;
+    int i, j;
+    int particle = 0;
+    /* Set a default frame range */
+    int first_frame = 0, last_frame = 50;
+    char atom_name[64], res_name[64], chain_name[64];
+
+    if(argc <= 1)
+    {
+        printf("No file specified\n");
+        printf("Usage:\n");
+        printf("tng_io_read_pos <tng_file> [particle number = %d] "
+               "[first_frame = %d] [last_frame = %d]\n",
+               particle, first_frame, last_frame);
+        exit(1);
+    }
+
+    /* A reference must be passed to allocate memory */
+    if(tng_trajectory_init(&traj) != TNG_SUCCESS)
+    {
+        tng_trajectory_destroy(&traj);
+        exit(1);
+    }
+    tng_input_file_set(traj, argv[1]);
+
+    /* Read the file headers */
+    tng_file_headers_read(traj, TNG_USE_HASH);
+
+    if(argc >= 3)
+    {
+        particle = strtol(argv[2], 0, 10);
+        if(argc >= 4)
+        {
+            first_frame = strtol(argv[3], 0, 10);
+            if(argc >= 5)
+            {
+                last_frame = strtol(argv[4], 0, 10);
+            }
+        }
+    }
+
+    if(tng_num_frames_get(traj, &tot_n_frames) != TNG_SUCCESS)
+    {
+        printf("Cannot determine the number of frames in the file\n");
+        tng_trajectory_destroy(&traj);
+        exit(1);
+    }
+
+    printf("%"PRId64" frames in file\n", tot_n_frames);
+
+    if(last_frame > tot_n_frames - 1)
+    {
+        last_frame = tot_n_frames - 1;
+    }
+
+    n_frames = last_frame - first_frame + 1;
+
+    if(tng_atom_name_of_particle_nr_get(traj, particle, atom_name,
+                                        sizeof(atom_name)) ==
+       TNG_SUCCESS &&
+       tng_residue_name_of_particle_nr_get(traj, particle, res_name,
+                                           sizeof(res_name)) ==
+       TNG_SUCCESS &&
+       tng_chain_name_of_particle_nr_get(traj, particle, chain_name,
+                                         sizeof(chain_name)) ==
+       TNG_SUCCESS)
+    {
+        printf("Particle: %s (%s: %s)\n", atom_name, chain_name, res_name);
+    }
+    else
+    {
+        printf("Particle name not found\n");
+    }
+
+    /* Get the positions of all particles in the requested frame range.
+       The positions are stored in the positions array.
+       N.B. No proper error checks. */
+    if(tng_particle_data_interval_get(traj, TNG_TRAJ_POSITIONS, first_frame,
+       last_frame, TNG_USE_HASH, &positions, &n_particles, &n_values_per_frame,
+       &data_type) == TNG_SUCCESS)
+    {
+        if(particle >= n_particles)
+        {
+            printf("Chosen particle out of range. Only %"PRId64" particles in trajectory.\n", n_particles);
+        }
+        else
+        {
+            /* Print the positions of the wanted particle (zero based) */
+            for(i=0; i<n_frames; i++)
+            {
+                printf("%d", first_frame + i);
+                for(j=0; j<n_values_per_frame; j++)
+                {
+                    switch(data_type)
+                    {
+                    case TNG_INT_DATA:
+                        printf("\t%"PRId64"", positions[i][particle][j].i);
+                        break;
+                    case TNG_FLOAT_DATA:
+                        printf("\t%f", positions[i][particle][j].f);
+                        break;
+                    case TNG_DOUBLE_DATA:
+                        printf("\t%f", positions[i][particle][j].d);
+                        break;
+                    default:
+                        break;
+                    }
+                    printf("\n");
+                }
+            }
+        }
+    }
+    else
+    {
+        printf("Cannot read positions\n");
+    }
+
+    /* Free memory */
+    if(positions)
+    {
+        tng_particle_data_values_free(traj, positions, n_frames, n_particles,
+                                      n_values_per_frame, data_type);
+    }
+    tng_trajectory_destroy(&traj);
+
+    return(0);
+}

recipes/tng/config.yml

@@ -0,0 +1,3 @@
+versions:
+  "1.8.2":
+    folder: all