def test_load_psf():
top = psf.load_psf(get_fn('ala_ala_ala.psf'))
ref_top = md.load(get_fn('ala_ala_ala.pdb')).topology
eq(top, ref_top)
# Test the XPLOR psf format parsing
top2 = psf.load_psf(get_fn('ala_ala_ala.xpsf'))
eq(top2, ref_top)
def test_load_psf():
top = psf.load_psf(get_fn('ala_ala_ala.psf'))
ref_top = md.load(get_fn('ala_ala_ala.pdb')).topology
eq(top, ref_top)
# Test the XPLOR psf format parsing
top2 = psf.load_psf(get_fn('ala_ala_ala.xpsf'))
eq(top2, ref_top)
def test_load_psf(get_fn):
top = psf.load_psf(get_fn('ala_ala_ala.psf'))
ref_top = md.load(get_fn('ala_ala_ala.pdb')).topology
eq(top, ref_top)
# Test the XPLOR psf format parsing
top2 = psf.load_psf(get_fn('ala_ala_ala.xpsf'))
eq(top2, ref_top)
# Test segment_names are loaded properly
assert next(top.residues).segment_id == "AAL", "Segment id is not being assigned correctly for ala_ala_ala.psf"
assert next(top2.residues).segment_id == "AAL", "Segment id is not being assigned correctly for ala_ala_ala.xpsf"
def test_load_psf():
print('sddsfsfdsdsdf')
top = psf.load_psf(get_fn('ala_ala_ala.psf'))
ref_top = md.load(get_fn('ala_ala_ala.pdb')).topology
eq(top, ref_top)
# Test the XPLOR psf format parsing
top2 = psf.load_psf(get_fn('ala_ala_ala.xpsf'))
eq(top2, ref_top)
# Test segment_names are loaded properly
assert next(top.residues).segment_id == "AAL", "Segment id is not being assigned correctly for ala_ala_ala.psf"
assert next(top2.residues).segment_id == "AAL", "Segment id is not being assigned correctly for ala_ala_ala.xpsf"
def test_multichain_psf():
top = psf.load_psf(get_fn('3pqr_memb.psf'))
# Check that each segment was turned into a chain
eq(top.n_chains, 11)
chain_lengths = [5162, 185, 97, 28, 24, 24, 45, 35742, 72822, 75, 73]
for i, n in enumerate(chain_lengths):
eq(top.chain(i).n_atoms, n)
# There are some non-sequentially numbered residues across chain
# boundaries... make sure resSeq is properly taken from the PSF
eq(top.chain(0).residue(0).resSeq, 1)
eq(top.chain(0).residue(-1).resSeq, 326)
eq(top.chain(1).residue(0).resSeq, 340)
eq(top.chain(1).residue(-1).resSeq, 350)
eq(top.chain(2).residue(0).resSeq, 1)
eq(top.chain(2).residue(-1).resSeq, 4)
eq(top.chain(3).residue(0).resSeq, 1)
eq(top.chain(3).residue(-1).resSeq, 1)
eq(top.chain(4).residue(0).resSeq, 1)
eq(top.chain(4).residue(-1).resSeq, 1)
eq(top.chain(5).residue(0).resSeq, 1)
eq(top.chain(5).residue(-1).resSeq, 1)
eq(top.chain(6).residue(0).resSeq, 1)
eq(top.chain(6).residue(-1).resSeq, 2)
eq(top.chain(7).residue(0).resSeq, 1)
eq(top.chain(7).residue(-1).resSeq, 276)
eq(top.chain(8).residue(0).resSeq, 1)
eq(top.chain(8).residue(-1).resSeq, 24274)
eq(top.chain(9).residue(0).resSeq, 1)
eq(top.chain(9).residue(-1).resSeq, 75)
eq(top.chain(10).residue(0).resSeq, 1)
eq(top.chain(10).residue(-1).resSeq, 73)
def test_multichain_psf():
top = psf.load_psf(get_fn('3pqr_memb.psf'))
# Check that each segment was turned into a chain
eq(top.n_chains, 11)
chain_lengths = [5162, 185, 97, 28, 24, 24, 45, 35742, 72822, 75, 73]
for i, n in enumerate(chain_lengths):
eq(top.chain(i).n_atoms, n)
# There are some non-sequentially numbered residues across chain
# boundaries... make sure resSeq is properly taken from the PSF
eq(top.chain(0).residue(0).resSeq, 1)
eq(top.chain(0).residue(-1).resSeq, 326)
eq(top.chain(1).residue(0).resSeq, 340)
eq(top.chain(1).residue(-1).resSeq, 350)
eq(top.chain(2).residue(0).resSeq, 1)
eq(top.chain(2).residue(-1).resSeq, 4)
eq(top.chain(3).residue(0).resSeq, 1)
eq(top.chain(3).residue(-1).resSeq, 1)
eq(top.chain(4).residue(0).resSeq, 1)
eq(top.chain(4).residue(-1).resSeq, 1)
eq(top.chain(5).residue(0).resSeq, 1)
eq(top.chain(5).residue(-1).resSeq, 1)
eq(top.chain(6).residue(0).resSeq, 1)
eq(top.chain(6).residue(-1).resSeq, 2)
eq(top.chain(7).residue(0).resSeq, 1)
eq(top.chain(7).residue(-1).resSeq, 276)
eq(top.chain(8).residue(0).resSeq, 1)
eq(top.chain(8).residue(-1).resSeq, 24274)
eq(top.chain(9).residue(0).resSeq, 1)
eq(top.chain(9).residue(-1).resSeq, 75)
eq(top.chain(10).residue(0).resSeq, 1)
eq(top.chain(10).residue(-1).resSeq, 73)
