"""MDTraj: A modern, open library for the analysis of molecular dynamics trajectories MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories and perform a variety of analyses, including fast RMSD, solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj is the wide variety of molecular dynamics trajectory file formats which are supported, including RCSB pdb, GROMACS xtc, and trr, CHARMM / NAMD dcd, AMBER AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5. """ import sys import versioneer from setuptools import Extension, find_packages, setup from basesetup import ( CompilerDetection, StaticLibrary, build_ext, parse_setuppy_commands, ) DOCLINES = __doc__.split("\n") sys.path.insert(0, ".") try: # add an optional --disable-openmp to disable OpenMP support sys.argv.remove("--disable-openmp") disable_openmp = True except ValueError: disable_openmp = False CLASSIFIERS = """\ Development Status :: 5 - Production/Stable Intended Audience :: Science/Research Intended Audience :: Developers License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) Programming Language :: C Programming Language :: Python Programming Language :: Python :: 3 Topic :: Scientific/Engineering :: Bio-Informatics Topic :: Scientific/Engineering :: Chemistry Operating System :: Microsoft :: Windows Operating System :: POSIX Operating System :: Unix Operating System :: MacOS """ # Global info about compiler compiler = CompilerDetection(disable_openmp) compiler.initialize() extra_cpp_libraries = [] if sys.platform == "win32": extra_cpp_libraries.append("Ws2_32") # For determining if a path is relative (for dtr) extra_cpp_libraries.append("Shlwapi") ################################################################################ # Declaration of the compiled extension modules (cython + c) ################################################################################ def format_extensions(): compiler_args = compiler.compiler_args_warn xtc = Extension( "mdtraj.formats.xtc", sources=[ "mdtraj/formats/xtc/src/xdrfile.c", "mdtraj/formats/xtc/src/xdr_seek.c", "mdtraj/formats/xtc/src/xdrfile_xtc.c", "mdtraj/formats/xtc/xtc.pyx", ], include_dirs=[ "mdtraj/formats/xtc/include/", "mdtraj/formats/xtc/", ], extra_compile_args=compiler_args, ) trr = Extension( "mdtraj.formats.trr", sources=[ "mdtraj/formats/xtc/src/xdrfile.c", "mdtraj/formats/xtc/src/xdr_seek.c", "mdtraj/formats/xtc/src/xdrfile_trr.c", "mdtraj/formats/xtc/trr.pyx", ], include_dirs=[ "mdtraj/formats/xtc/include/", "mdtraj/formats/xtc/", ], extra_compile_args=compiler_args, ) zlib_include_dirs = [] zlib_library_dirs = [] if sys.platform == "win32": # Conda puts the zlib headers in ./Library/... on windows # If you're not using conda, good luck! zlib_include_dirs += [f"{sys.prefix}/Library/include"] zlib_library_dirs += [f"{sys.prefix}/Library/lib"] else: # On linux (and mac(?)) these paths should work for a standard # install of python+zlib or a conda install of python+zlib zlib_include_dirs += [f"{sys.prefix}/include"] zlib_library_dirs += [f"{sys.prefix}/lib"] dcd = Extension( "mdtraj.formats.dcd", sources=[ "mdtraj/formats/dcd/src/dcdplugin.c", "mdtraj/formats/dcd/dcd.pyx", ], include_dirs=[ "mdtraj/formats/dcd/include/", "mdtraj/formats/dcd/", ], extra_compile_args=compiler_args, ) dtr = Extension( "mdtraj.formats.dtr", sources=[ "mdtraj/formats/dtr/src/dtrplugin.cxx", "mdtraj/formats/dtr/dtr.pyx", ], include_dirs=[ "mdtraj/formats/dtr/include/", "mdtraj/formats/dtr/", ], define_macros=[("DESRES_READ_TIMESTEP2", 1)], language="c++", extra_compile_args=compiler_args, libraries=extra_cpp_libraries, ) return [xtc, trr, dcd, dtr] def rmsd_extensions(): compiler_args = ( compiler.compiler_args_openmp + compiler.compiler_args_sse2 + compiler.compiler_args_sse3 + compiler.compiler_args_opt + compiler.compiler_args_warn ) compiler_libraries = compiler.compiler_libraries_openmp define_macros = [("__NO_INTRINSICS", 1)] if compiler.disable_intrinsics else None libtheobald = StaticLibrary( "mdtraj.core.lib.libtheobald", sources=[ "mdtraj/rmsd/src/theobald_rmsd.cpp", "mdtraj/rmsd/src/center.cpp", ], include_dirs=[ "mdtraj/rmsd/include", ], export_include=[ "mdtraj/rmsd/include/theobald_rmsd.h", "mdtraj/rmsd/include/center.h", ], language="c++", # don't enable OpenMP extra_compile_args=(compiler.compiler_args_sse2 + compiler.compiler_args_sse3 + compiler.compiler_args_opt), ) rmsd = Extension( "mdtraj._rmsd", sources=[ "mdtraj/rmsd/src/theobald_rmsd.cpp", "mdtraj/rmsd/src/rotation.cpp", "mdtraj/rmsd/src/center.cpp", "mdtraj/rmsd/_rmsd.pyx", ], include_dirs=["mdtraj/rmsd/include"], define_macros=define_macros, extra_compile_args=compiler_args, libraries=compiler_libraries, language="c++", ) lprmsd = Extension( "mdtraj._lprmsd", sources=[ "mdtraj/rmsd/src/theobald_rmsd.cpp", "mdtraj/rmsd/src/rotation.cpp", "mdtraj/rmsd/src/center.cpp", "mdtraj/rmsd/src/fancy_index.cpp", "mdtraj/rmsd/src/Munkres.cpp", "mdtraj/rmsd/src/euclidean_permutation.cpp", "mdtraj/rmsd/_lprmsd.pyx", ], language="c++", define_macros=define_macros, include_dirs=["mdtraj/rmsd/include"], extra_compile_args=compiler_args, libraries=compiler_libraries + extra_cpp_libraries, ) return rmsd, lprmsd, libtheobald def geometry_extensions(): compiler.initialize() compiler_args = ( compiler.compiler_args_openmp + compiler.compiler_args_sse2 + compiler.compiler_args_sse3 + compiler.compiler_args_opt + compiler.compiler_args_warn ) define_macros = [("__NO_INTRINSICS", 1)] if compiler.disable_intrinsics else None compiler_libraries = compiler.compiler_libraries_openmp + extra_cpp_libraries return [ Extension( "mdtraj.geometry._geometry", sources=[ "mdtraj/geometry/src/sasa.cpp", "mdtraj/geometry/src/dssp.cpp", "mdtraj/geometry/src/geometry.cpp", "mdtraj/geometry/src/_geometry.pyx", ], include_dirs=[ "mdtraj/geometry/include", "mdtraj/geometry/src/kernels", ], depends=[ "mdtraj/geometry/src/kernels/anglekernels.h", "mdtraj/geometry/src/kernels/dihedralkernels.h", "mdtraj/geometry/src/kernels/distancekernels.h", ], define_macros=define_macros, extra_compile_args=compiler_args, libraries=compiler_libraries, language="c++", ), Extension( "mdtraj.geometry.drid", sources=[ "mdtraj/geometry/drid.pyx", "mdtraj/geometry/src/dridkernels.cpp", "mdtraj/geometry/src/moments.cpp", ], include_dirs=["mdtraj/geometry/include"], define_macros=define_macros, extra_compile_args=compiler_args, libraries=compiler_libraries, language="c++", ), Extension( "mdtraj.geometry.neighbors", sources=[ "mdtraj/geometry/neighbors.pyx", "mdtraj/geometry/src/neighbors.cpp", ], include_dirs=["mdtraj/geometry/include"], define_macros=define_macros, extra_compile_args=compiler_args, libraries=compiler_libraries, language="c++", ), Extension( "mdtraj.geometry.neighborlist", sources=[ "mdtraj/geometry/neighborlist.pyx", "mdtraj/geometry/src/neighborlist.cpp", ], include_dirs=["mdtraj/geometry/include"], define_macros=define_macros, extra_compile_args=compiler_args, libraries=compiler_libraries, language="c++", ), ] EXTRAS_REQUIRE = { "tests": [ "pytest", "pytest-rerunfailures", "pytest-xdist", ], "optional": [ "tables", "networkx", "netCDF4", "pandas", ], } metadata = dict( name="mdtraj", author="Robert McGibbon", author_email="rmcgibbo@gmail.com", description=DOCLINES[0], long_description="\n".join(DOCLINES[2:]), version=versioneer.get_version(), license="LGPLv2.1+", url="http://mdtraj.org", download_url="https://github.com/rmcgibbo/mdtraj/releases/latest", platforms=["Linux", "Mac OS-X", "Unix", "Windows"], python_requires=">=3.11", classifiers=CLASSIFIERS.splitlines(), packages=find_packages(), cmdclass={**versioneer.get_cmdclass(), "build_ext": build_ext}, install_requires=[ "numpy>=1.25.0,<3", "scipy", "pyparsing", "packaging", ], extras_require={ "tests": EXTRAS_REQUIRE["tests"], "optional": EXTRAS_REQUIRE["optional"], "all": EXTRAS_REQUIRE["tests"] + EXTRAS_REQUIRE["optional"], }, package_data={"mdtraj.formats.pdb": ["data/*"]}, zip_safe=False, entry_points={ "console_scripts": [ "mdconvert-mdtraj = mdtraj.scripts.mdconvert:entry_point", "mdinspect = mdtraj.scripts.mdinspect:entry_point", ], }, ) if __name__ == "__main__": # Don't use numpy if we are just - non-build actions are required to succeed # without NumPy for example when pip is used to install Scipy when # NumPy is not yet present in the system. run_build = parse_setuppy_commands() if run_build: extensions = format_extensions() extensions.extend(rmsd_extensions()) extensions.extend(geometry_extensions()) # most extensions use numpy, add headers for it. try: import Cython as _c from Cython.Build import cythonize if _c.__version__ < "0.29": raise ImportError("Too old") except ImportError as e: print( "mdtrajs setup depends on Cython (>=0.29). Install it prior invoking setup.py", ) print(e) sys.exit(1) try: import numpy as np except ImportError: print("mdtrajs setup depends on NumPy. Install it prior invoking setup.py") sys.exit(1) for e in extensions: e.include_dirs.append(np.get_include()) metadata["ext_modules"] = cythonize( extensions, language_level=sys.version_info[0], force=True, ) setup(**metadata)