def setUpClass(self): from moleculekit.home import home from moleculekit.molecule import Molecule import numpy as np import os self.testfolder = home(dataDir='molecule-writers') mol = Molecule(os.path.join(self.testfolder, 'filtered.pdb')) mol.coords = np.tile(mol.coords, (1, 1, 2)) mol.filter('protein and resid 1 to 20') mol.boxangles = np.ones((3, 2), dtype=np.float32) * 90 mol.box = np.ones((3, 2), dtype=np.float32) * 15 mol.step = np.arange(2) mol.time = np.arange(2) * 1E5 mol.fileloc = [mol.fileloc[0], mol.fileloc[0]] self.mol = mol
def setUpClass(self): from moleculekit.home import home from moleculekit.molecule import Molecule import numpy as np import os self.testfolder = home(dataDir="molecule-writers") mol = Molecule(os.path.join(self.testfolder, "filtered.psf")) mol.read(os.path.join(self.testfolder, "filtered.pdb")) mol.coords = np.tile(mol.coords, (1, 1, 2)) mol.filter("protein and resid 1 to 20") mol.boxangles = np.ones((3, 2), dtype=np.float32) * 90 mol.box = np.ones((3, 2), dtype=np.float32) * 15 mol.step = np.arange(2) mol.time = np.arange(2) * 1e5 mol.fileloc = [mol.fileloc[0], mol.fileloc[0]] mol.bondtype[:] = "1" self.mol = mol