def test_read_one(self):
reader = Reader().readThisFile('data/amber_mini.pdb')
coordinates = reader.read()
self.assertEqual(148, reader.numberOfAtoms)
self.assertEqual(3, reader.numberOfFrames)
numpy.testing.assert_almost_equal(testPdbReader.mini_all_coords,
coordinates, 12)
def test_read_multiple_only_CA(self):
reader = Reader().readThisFile('data/amber_mini.pdb').andThisOtherFile('data/amber_mini.pdb').gettingOnlyCAs()
coordinates = reader.read()
self.assertEqual(9, reader.numberOfAtoms)
self.assertEqual(6, reader.numberOfFrames)
coord_shape = coordinates.shape
self.assertEqual(coord_shape[0]*coord_shape[1]*coord_shape[2],9*6*3)
numpy.testing.assert_almost_equal(numpy.reshape(self.mini_CA_coords,3*9*3), numpy.reshape(coordinates,6*9*3)[0:9*3*3], 10)
numpy.testing.assert_almost_equal(numpy.reshape(self.mini_CA_coords,3*9*3), numpy.reshape(coordinates,6*9*3)[9*3*3:], 10)
def test_read_multiple(self):
reader = Reader().readThisFile('data/amber_mini.pdb').andThisOtherFile('data/amber_mini.pdb')
coordinates = reader.read()
self.assertEqual(148, reader.numberOfAtoms)
self.assertEqual(6, reader.numberOfFrames)
coord_shape = coordinates.shape
self.assertEqual(coord_shape[0]*coord_shape[1]*coord_shape[2],148*6*3)
numpy.testing.assert_almost_equal(numpy.reshape(self.mini_all_coords,3*148*3), numpy.reshape(coordinates,148*6*3)[0:148*3*3], 10)
numpy.testing.assert_almost_equal(numpy.reshape(self.mini_all_coords,3*148*3), numpy.reshape(coordinates,148*6*3)[148*3*3:], 10)
def test_read_multiple_only_CA(self):
reader = Reader().readThisFile('data/amber_mini.pdb').andThisOtherFile(
'data/amber_mini.pdb').gettingOnlyCAs()
coordinates = reader.read()
self.assertEqual(9, reader.numberOfAtoms)
self.assertEqual(6, reader.numberOfFrames)
coord_shape = coordinates.shape
self.assertEqual(coord_shape[0] * coord_shape[1] * coord_shape[2],
9 * 6 * 3)
numpy.testing.assert_almost_equal(
numpy.reshape(self.mini_CA_coords, 3 * 9 * 3),
numpy.reshape(coordinates, 6 * 9 * 3)[0:9 * 3 * 3], 10)
numpy.testing.assert_almost_equal(
numpy.reshape(self.mini_CA_coords, 3 * 9 * 3),
numpy.reshape(coordinates, 6 * 9 * 3)[9 * 3 * 3:], 10)
def test_read_multiple(self):
reader = Reader().readThisFile('data/amber_mini.pdb').andThisOtherFile(
'data/amber_mini.pdb')
coordinates = reader.read()
self.assertEqual(148, reader.numberOfAtoms)
self.assertEqual(6, reader.numberOfFrames)
coord_shape = coordinates.shape
self.assertEqual(coord_shape[0] * coord_shape[1] * coord_shape[2],
148 * 6 * 3)
numpy.testing.assert_almost_equal(
numpy.reshape(self.mini_all_coords, 3 * 148 * 3),
numpy.reshape(coordinates, 148 * 6 * 3)[0:148 * 3 * 3], 10)
numpy.testing.assert_almost_equal(
numpy.reshape(self.mini_all_coords, 3 * 148 * 3),
numpy.reshape(coordinates, 148 * 6 * 3)[148 * 3 * 3:], 10)
def test_read_one_only_CA(self):
reader = Reader().readThisFile('data/amber_mini.pdb').gettingOnlyCAs()
coordinates = reader.read()
self.assertEqual(9, reader.numberOfAtoms)
self.assertEqual(3, reader.numberOfFrames)
numpy.testing.assert_almost_equal(self.mini_CA_coords, coordinates, 10)
def test_read_one(self):
reader = Reader().readThisFile('data/amber_mini.pdb')
coordinates = reader.read()
self.assertEqual(148, reader.numberOfAtoms)
self.assertEqual(3, reader.numberOfFrames)
numpy.testing.assert_almost_equal(testPdbReader.mini_all_coords, coordinates, 12)
def test_read_one_only_CA(self):
reader = Reader().readThisFile('data/amber_mini.pdb').gettingOnlyCAs()
coordinates = reader.read()
self.assertEqual(9, reader.numberOfAtoms)
self.assertEqual(3, reader.numberOfFrames)
numpy.testing.assert_almost_equal(self.mini_CA_coords, coordinates, 10)
import os
import bz2
from pyRMSD.utils.proteinReading import Reader
if __name__ == '__main__':
using_cuda = "QCP_CUDA_CALCULATOR" in pyRMSD.RMSDCalculator.availableCalculators()
######################
# BENCHMARKING
######################
print "Loading file..."
t1 = time.time()
print "\tUncompressing..."
open("tmp_amber_long.pdb","w").write(bz2.BZ2File("data/amber_long.pdb.tar.bz2").read())
print "\tLoading..."
reader = Reader().readThisFile('tmp_amber_long.pdb').gettingOnlyCAs()
coordsets = reader.read()
number_of_atoms = reader.numberOfAtoms
number_of_conformations = reader.numberOfFrames
os.system("rm tmp_amber_long.pdb")
print "\tDeleting temporary file"
t2 = time.time()
print 'Loading took %0.3f s' % (t2-t1)
#######################
# CALCULATION
#######################
types = pyRMSD.RMSDCalculator.availableCalculators()
DEFAULT_PRECISSION = 1e-8
precissions = collections.defaultdict(lambda:DEFAULT_PRECISSION)
