def test_atomtyping(self, mol_name, testfiles_dir=TRAPPE_TESTFILES_DIR): files = glob.glob(os.path.join(testfiles_dir, mol_name, '*')) for mol_file in files: _, ext = os.path.splitext(mol_file) mol2_path = os.path.join(testfiles_dir, mol_name, mol_file) structure = pmd.load_file(mol2_path, structure=True) atomtype(structure, TRAPPE_UA, non_atomistic=True)
def test_atomtyping(self, mol_name, testfiles_dir=OPLS_TESTFILES_DIR): files = glob.glob(os.path.join(testfiles_dir, mol_name, '*')) for mol_file in files: _, ext = os.path.splitext(mol_file) if ext == '.top': top_filename = '{}.top'.format(mol_name) gro_filename = '{}.gro'.format(mol_name) top_path = os.path.join(testfiles_dir, mol_name, top_filename) gro_path = os.path.join(testfiles_dir, mol_name, gro_filename) structure = pmd.load_file(top_path, xyz=gro_path, parametrize=False) elif ext == '.mol2': mol2_path = os.path.join(testfiles_dir, mol_name, mol_file) structure = pmd.load_file(mol2_path, structure=True) atomtype(structure, OPLSAA)
def test_atomtyping(self, mol_name, oplsaa, testfiles_dir=OPLS_TESTFILES_DIR): files = glob.glob(os.path.join(testfiles_dir, mol_name, "*")) for mol_file in files: _, ext = os.path.splitext(mol_file) if ext == ".top": top_filename = "{}.top".format(mol_name) gro_filename = "{}.gro".format(mol_name) top_path = os.path.join(testfiles_dir, mol_name, top_filename) gro_path = os.path.join(testfiles_dir, mol_name, gro_filename) structure = pmd.load_file(top_path, xyz=gro_path, parametrize=False) elif ext == ".mol2": mol2_path = os.path.join(testfiles_dir, mol_name, mol_file) structure = pmd.load_file(mol2_path, structure=True) atomtype(structure, oplsaa)
def test_atomtyping(mol2_file): structure = pmd.load_file(mol2_file, structure=True) atomtype(structure, FORCEFIELD)
from glob import glob import parmed as pmd import pytest from foyer import Forcefield from foyer.tests.utils import atomtype MOL2_FILES = glob('test_molecules/*.mol2') FORCEFIELD_FILES = 'forcefield.xml' FORCEFIELD = Forcefield(forcefield_files=FORCEFIELD_FILES) @pytest.mark.parametrize('mol2_file', MOL2_FILES) def test_atomtyping(mol2_file): structure = pmd.load_file(mol2_file, structure=True) atomtype(structure, FORCEFIELD) if __name__ == "__main__": structure = pmd.load_file(mol2_file, structure=True) atomtype(structure, FORCEFIELD)