def test_delete():
"""
Tests removing atoms
"""
from psfgen import PsfGen
os.chdir(dir)
gen = PsfGen(output=os.devnull)
gen.read_topology("top_all36_caps.rtf")
gen.read_topology("top_all36_prot.rtf")
gen.add_segment(segid="P0", pdbfile="psf_protein_P0.pdb")
gen.read_coords(segid="P0", filename="psf_protein_P0.pdb")
# Delete a specific atom
assert "CAY" in gen.get_atom_names(segid="P0", resid=1)
gen.delete_atoms(segid="P0", resid=1, atomname="CAY")
assert "CAY" not in gen.get_atom_names(segid="P0", resid=1)
# Try deleting a capping group
assert gen.get_resids("P0") == [str(_) for _ in range(1, 26)]
gen.delete_atoms(segid="P0", resid=1)
assert gen.get_resids("P0") == [str(_) for _ in range(2, 26)]
# Add and then delete a segment
gen.add_segment(segid="DELETE", pdbfile="psf_protein_P1.pdb")
assert gen.get_segids() == ["P0", "DELETE"]
gen.delete_atoms(segid="DELETE")
assert gen.get_segids() == ["P0"]
def test_set():
"""
Tests that setters work correctly
"""
from psfgen import PsfGen
os.chdir(dir)
gen = PsfGen(output=os.devnull)
gen.read_topology("top_all36_caps.rtf")
gen.read_topology("top_all36_prot.rtf")
gen.add_segment(segid="P", pdbfile="psf_protein_P1.pdb")
assert gen.get_segids() == ["P"]
# Set segid
gen.set_segid(segid="P", new_segid="P1")
assert gen.get_segids() == ["P1"]
gen.read_coords(segid="P1", filename="psf_protein_P1.pdb")
# Set resname
assert gen.get_resname(segid="P1", resid="1") == "ASP"
gen.set_resname(segid="P1", resid="1", new_resname="ASH")
assert gen.get_resname(segid="P1", resid="1") == "ASH"
# Set charge
gen.set_charge(segid="P1", resid="1", atomname="O", charge=-1.)
assert -1.0 in gen.get_charges(segid="P1", resid="1")
# Set atom name
gen.set_atom_name(segid="P1", resid="1", atomname="N", new_atomname="NO")
assert "N" not in gen.get_atom_names(segid="P1", resid="1")
assert "NO" in gen.get_atom_names(segid="P1", resid="1")
# Set coord
gen.set_position(segid="P1",
resid="1",
atomname="HN",
position=(0., 0., -1.))
assert (0., 0., -1.) in gen.get_coordinates(segid="P1", resid="1")
# Set velocity
gen.set_velocity(segid="P1",
resid="1",
atomname="NO",
velocity=(
5.,
5.,
3.,
))
assert (
5.,
5.,
3.,
) in gen.get_velocities(segid="P1", resid="1")
def test_alias():
"""
Tests atom and residue aliases, either at the topology or the PDB level
"""
from psfgen import PsfGen
os.chdir(dir)
gen = PsfGen(output=os.devnull)
gen.read_topology("top_all36_caps.rtf")
gen.read_topology("top_all36_prot.rtf")
gen.alias_residue(top_resname="LEU", pdb_resname="LEX")
gen.alias_residue(top_resname="ARG", pdb_resname="AAA")
gen.alias_atom(top_atomname="N", pdb_atomname="NOOO", resname="PHE")
gen.add_segment(segid="P", pdbfile="protein_newnames.pdb")
gen.read_coords(segid="P", filename="psf_protein_P0.pdb")
assert gen.get_resname(segid="P", resid=2) == "LEU"
assert gen.get_resname(segid="P", resid=5) == "ALA"
assert "N" in gen.get_atom_names(segid="P", resid=23)
def test_query():
"""
Tests that query functions work correctly
"""
from psfgen import PsfGen
gen = PsfGen(output=os.devnull)
os.chdir(dir)
gen.read_topology("top_all36_caps.rtf")
gen.read_topology("top_all36_prot.rtf")
gen.add_segment(segid="P0", pdbfile="psf_protein_P0.pdb")
gen.read_coords(segid="P0", filename="psf_protein_P0.pdb")
gen.add_segment(segid="P1", pdbfile="psf_protein_P1.pdb")
gen.read_coords(segid="P1", filename="psf_protein_P1.pdb")
gen.patch(patchname="DISU", targets=[("P0", "10"), ("P0", "15")])
assert gen.get_topologies() == ["top_all36_caps.rtf", "top_all36_prot.rtf"]
# Check residue names query
resnames = gen.get_residue_types()
assert len(resnames) == 26
assert "CYS" in resnames
assert "TIP3" not in resnames
# Check patches query
patches = gen.get_patches(list_all=True)
assert len(patches) == 25
assert "CYSD" in patches
assert "SEP" not in patches
# Check segids query
assert gen.get_segids() == ["P0", "P1"]
# Check resids query
assert gen.get_resids("P0") == [str(_) for _ in range(1, 26)]
assert gen.get_resids("P1") == [str(_) for _ in range(0, 31)]
# Check resname query, with str or int
assert gen.get_resname(segid="P0", resid="2") == "LEU"
assert gen.get_resname(segid="P1", resid=29) == "SER"
# Check applied patches query
assert gen.get_patches() == [("DISU", "P0", "10"), ("DISU", "P0", "15")]
assert gen.get_first(segid="P0") is None
assert gen.get_last(segid="P1") is None
# Check atom queries
assert gen.get_atom_names(segid="P0", resid="10") \
== ['N', 'HN', 'CA', 'HA', 'CB', 'HB1', 'HB2', 'SG', 'C', 'O']
assert set(gen.get_masses(segid="P0", resid=1)) == {1.008, 12.011, 15.999}
assert gen.get_atom_indices(segid="P1", resid=0) == list(range(1, 7))
assert set(gen.get_charges(segid="P0", resid="10")) \
== {-0.47, 0.07, 0.09, 0.31, -0.1, -0.08, 0.51, -0.51}
# Check coordinates and velocities
assert len(gen.get_coordinates(segid="P1", resid=25)) == 17
assert set(gen.get_velocities(segid="P1", resid=1)) == {(0., 0., 0.)}