def addRep(self, rep):
""" Add the given rep to the molecule. Modifications to the rep will
affect all molecules to which the rep has been added."""
if rep.molecules.has_key(self.id):
raise ValueError("This molecule already has this rep")
molrep.addrep(self.id, style=rep.style, color=rep.color, selection=rep.selection, material=rep.material)
repid = molrep.num(self.id)-1
repname = molrep.get_repname(self.id, repid)
rep.assign_molecule(self.id, repname)
def test_add_representation(file_3nob):
m = molecule.load("mae", file_3nob)
assert molrep.num(m) == 1
with pytest.raises(ValueError):
molrep.num(m+1)
with pytest.raises(ValueError):
molrep.addrep(molid=m, style="Invalid")
with pytest.raises(ValueError):
molrep.addrep(m, style="NewCartoon", color="Invalid")
with pytest.raises(ValueError):
molrep.addrep(m, "NewCartoon", "Type", selection="unparseable")
with pytest.raises(ValueError):
molrep.addrep(m, "NewCartoon", "Type", "protein", material="Invalid")
r = molrep.addrep(style="NewCartoon", color="ResID", selection="protein",
material="AOShiny", molid=m)
assert r == 1
with pytest.raises(ValueError):
molrep.delrep(m+1, 0)
with pytest.raises(ValueError):
molrep.delrep(m, rep=r+1)
molrep.delrep(rep=r, molid=m)
assert molrep.num(m) == 1
molecule.delete(m)
def test_snapshot(tmpdir, file_3nob):
from vmd import molecule, molrep, display
m = molecule.load("mae", file_3nob)
molrep.addrep(m, "NewCartoon")
display.set(size=(512, 512))
tmpdir = str(tmpdir)
render.render("snapshot", os.path.join(tmpdir, "test.tga"))
# If it's an empty header, the file size will be way too small here
assert os.path.getsize(os.path.join(tmpdir, "test.tga")) == 786450
def test_colorscale(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(color="User2", selection="lipid", molid=m)
assert molrep.get_scaleminmax(m, r) == pytest.approx((0., 0.))
with pytest.raises(ValueError):
molrep.get_scaleminmax(m+1, 0)
with pytest.raises(ValueError):
molrep.get_scaleminmax(m, r+1)
molrep.set_scaleminmax(molid=m, rep=r, scale_min=-10., scale_max=200.)
assert molrep.get_scaleminmax(m, r) == pytest.approx((-10., 200.))
with pytest.raises(ValueError):
molrep.set_scaleminmax(m+1, 0, 0, 12)
with pytest.raises(ValueError):
molrep.set_scaleminmax(m, r+1, 12, 13)
with pytest.raises(RuntimeError):
molrep.set_scaleminmax(m, r, scale_min=100, scale_max=0)
# Test reset
molrep.reset_scaleminmax(molid=m, rep=r)
assert molrep.get_scaleminmax(m, r) == pytest.approx((-10., 200.))
with pytest.raises(ValueError):
molrep.reset_scaleminmax(m+1, 0)
with pytest.raises(ValueError):
molrep.reset_scaleminmax(m, r+1)
# Test changing with modrep
assert molrep.modrep(m, r, scaleminmax=(2.0, 3.0))
assert molrep.get_scaleminmax(m, r) == pytest.approx((2.0, 3.0))
assert molrep.modrep(m, r, scaleminmax=[-10., -5.])
assert molrep.get_scaleminmax(m, r) == pytest.approx((-10., -5.))
molecule.delete(m)
def test_autoupdates(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(color="User", selection="all", molid=m)
# Color update
assert not molrep.get_colorupdate(m, r)
with pytest.raises(ValueError):
molrep.get_colorupdate(m+1, 0)
with pytest.raises(ValueError):
molrep.get_colorupdate(m, r+1)
molrep.set_colorupdate(m, rep=r, autoupdate=True)
assert molrep.get_colorupdate(rep=r, molid=m)
with pytest.raises(ValueError):
molrep.set_colorupdate(m+1, 0, False)
with pytest.raises(ValueError):
molrep.set_colorupdate(m, r+1, False)
# Selection update
assert not molrep.get_autoupdate(molid=m, rep=r)
with pytest.raises(ValueError):
molrep.get_autoupdate(m+1, 0)
with pytest.raises(ValueError):
molrep.get_autoupdate(m, r+1)
molrep.set_autoupdate(m, rep=r, autoupdate=True)
assert molrep.get_autoupdate(rep=r, molid=m)
with pytest.raises(ValueError):
molrep.set_autoupdate(m+1, 0, False)
with pytest.raises(ValueError):
molrep.set_autoupdate(m, r+1, False)
molecule.delete(m)
def test_colorscale(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(color="User2", selection="lipid", molid=m)
assert molrep.get_scaleminmax(m, r) == pytest.approx((0., 0.))
with pytest.raises(ValueError):
molrep.get_scaleminmax(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_scaleminmax(m, r + 1)
molrep.set_scaleminmax(molid=m, rep=r, scale_min=-10., scale_max=200.)
assert molrep.get_scaleminmax(m, r) == pytest.approx((-10., 200.))
with pytest.raises(ValueError):
molrep.set_scaleminmax(m + 1, 0, 0, 12)
with pytest.raises(ValueError):
molrep.set_scaleminmax(m, r + 1, 12, 13)
with pytest.raises(RuntimeError):
molrep.set_scaleminmax(m, r, scale_min=100, scale_max=0)
# Test reset
molrep.reset_scaleminmax(molid=m, rep=r)
assert molrep.get_scaleminmax(m, r) == pytest.approx((-10., 200.))
with pytest.raises(ValueError):
molrep.reset_scaleminmax(m + 1, 0)
with pytest.raises(ValueError):
molrep.reset_scaleminmax(m, r + 1)
# Test changing with modrep
assert molrep.modrep(m, r, scaleminmax=(2.0, 3.0))
assert molrep.get_scaleminmax(m, r) == pytest.approx((2.0, 3.0))
assert molrep.modrep(m, r, scaleminmax=[-10., -5.])
assert molrep.get_scaleminmax(m, r) == pytest.approx((-10., -5.))
molecule.delete(m)
def test_modrep(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(style="Licorice",
color="ResID",
selection="noh",
material="AOEdgy",
molid=m)
with pytest.raises(ValueError):
molrep.modrep(m + 1, 0)
with pytest.raises(ValueError):
molrep.modrep(m, r + 1)
assert molrep.get_style(m, r) == "Licorice"
assert molrep.modrep(m, r, style="Lines")
assert molrep.get_style(m, r) == "Lines"
assert not molrep.modrep(m, r, style="Invalid")
assert molrep.get_style(m, r) == "Lines"
assert molrep.modrep(m,
r,
color="ColorID 0",
selection="resname TIP3",
material="Transparent")
assert molrep.get_selection(m, r) == "resname TIP3"
assert molrep.get_material(m, r) == "Transparent"
assert molrep.get_color(m, r) == "ColorID 0"
molecule.delete(m)
def test_autoupdates(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(color="User", selection="all", molid=m)
# Color update
assert not molrep.get_colorupdate(m, r)
with pytest.raises(ValueError):
molrep.get_colorupdate(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_colorupdate(m, r + 1)
molrep.set_colorupdate(m, rep=r, autoupdate=True)
assert molrep.get_colorupdate(rep=r, molid=m)
with pytest.raises(ValueError):
molrep.set_colorupdate(m + 1, 0, False)
with pytest.raises(ValueError):
molrep.set_colorupdate(m, r + 1, False)
# Selection update
assert not molrep.get_autoupdate(molid=m, rep=r)
with pytest.raises(ValueError):
molrep.get_autoupdate(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_autoupdate(m, r + 1)
molrep.set_autoupdate(m, rep=r, autoupdate=True)
assert molrep.get_autoupdate(rep=r, molid=m)
with pytest.raises(ValueError):
molrep.set_autoupdate(m + 1, 0, False)
with pytest.raises(ValueError):
molrep.set_autoupdate(m, r + 1, False)
molecule.delete(m)
def test_rep_attributes(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(style="NewCartoon",
color="ResID",
selection="protein",
material="AOShiny",
molid=m)
# Query name
assert molrep.get_repname(molid=m, rep=r) == "rep1"
with pytest.raises(ValueError):
molrep.get_repname(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_repname(m, r + 1)
# Query ID
assert molrep.repindex(m, "rep1") == r
assert molrep.repindex(m, "nonexistent") is None
with pytest.raises(ValueError):
molrep.repindex(m + 1, "wrong")
# Query style
assert molrep.get_style(m, r) == "NewCartoon"
with pytest.raises(ValueError):
molrep.get_style(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_style(m, r + 1)
# Query selection
assert molrep.get_selection(m, r) == "protein"
with pytest.raises(ValueError):
molrep.get_selection(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_selection(m, r + 1)
# Query color
assert molrep.get_color(m, r) == "ResID"
with pytest.raises(ValueError):
molrep.get_color(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_color(m, r + 1)
# Query material
assert molrep.get_material(m, r) == "AOShiny"
with pytest.raises(ValueError):
molrep.get_material(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_material(m, r + 1)
molecule.delete(m)
def __init__(self,
pdb_file,
load_data=None,
style=None,
name='my_molecule',
flush_pdb_frame=False,
align=True,
center=True):
self.molid = mol.new(name)
mol.rename(self.molid, name)
self.name = name
mol.read(self.molid, 'pdb', pdb_file, beg=0, end=0, skip=1, waitfor=-1)
self.all_atoms = atomsel("all")
if flush_pdb_frame:
mol.delframe(self.molid) # flush trivial frame
if load_data:
self.load_data(load_data, align=align)
if style:
# delete the default representation
molrep.delrep(self.molid, 0)
for rep in style:
molrep.addrep(self.molid, **rep)
def test_rep_attributes(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(style="NewCartoon", color="ResID", selection="protein",
material="AOShiny", molid=m)
# Query name
assert molrep.get_repname(molid=m, rep=r) == "rep1"
with pytest.raises(ValueError):
molrep.get_repname(m+1, 0)
with pytest.raises(ValueError):
molrep.get_repname(m, r+1)
# Query ID
assert molrep.repindex(m, "rep1") == r
assert molrep.repindex(m, "nonexistent") is None
with pytest.raises(ValueError):
molrep.repindex(m+1, "wrong")
# Query style
assert molrep.get_style(m, r) == "NewCartoon"
with pytest.raises(ValueError):
molrep.get_style(m+1, 0)
with pytest.raises(ValueError):
molrep.get_style(m, r+1)
# Query selection
assert molrep.get_selection(m, r) == "protein"
with pytest.raises(ValueError):
molrep.get_selection(m+1, 0)
with pytest.raises(ValueError):
molrep.get_selection(m, r+1)
# Query color
assert molrep.get_color(m, r) == "ResID"
with pytest.raises(ValueError):
molrep.get_color(m+1, 0)
with pytest.raises(ValueError):
molrep.get_color(m, r+1)
# Query material
assert molrep.get_material(m, r) == "AOShiny"
with pytest.raises(ValueError):
molrep.get_material(m+1, 0)
with pytest.raises(ValueError):
molrep.get_material(m, r+1)
molecule.delete(m)
def test_add_representation(file_3nob):
m = molecule.load("mae", file_3nob)
assert molrep.num(m) == 1
with pytest.raises(ValueError):
molrep.num(m + 1)
with pytest.raises(ValueError):
molrep.addrep(molid=m, style="Invalid")
with pytest.raises(ValueError):
molrep.addrep(m, style="NewCartoon", color="Invalid")
with pytest.raises(ValueError):
molrep.addrep(m, "NewCartoon", "Type", selection="unparseable")
with pytest.raises(ValueError):
molrep.addrep(m, "NewCartoon", "Type", "protein", material="Invalid")
r = molrep.addrep(style="NewCartoon",
color="ResID",
selection="protein",
material="AOShiny",
molid=m)
assert r == 1
with pytest.raises(ValueError):
molrep.delrep(m + 1, 0)
with pytest.raises(ValueError):
molrep.delrep(m, rep=r + 1)
molrep.delrep(rep=r, molid=m)
assert molrep.num(m) == 1
molecule.delete(m)
def test_visible_and_smoothing(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(material="AOChalky", selection="name C", molid=m)
# Get visible
assert molrep.get_visible(m, r)
with pytest.raises(ValueError):
molrep.get_visible(m+1, 0)
with pytest.raises(ValueError):
molrep.get_visible(m, r+1)
# Set visible
molrep.set_visible(m, r, True)
assert molrep.get_visible(m, r)
molrep.set_visible(m, r, visible=False)
assert not molrep.get_visible(m, r)
with pytest.raises(ValueError):
molrep.set_visible(m+1, 0, False)
with pytest.raises(ValueError):
molrep.set_visible(m, r+1, True)
# Get smoothing
assert molrep.get_smoothing(molid=m, rep=r) == 0
with pytest.raises(ValueError):
molrep.get_smoothing(m+1, 0)
with pytest.raises(ValueError):
molrep.get_smoothing(m, r+1)
# Set smoothing
molrep.set_smoothing(m, r, 10)
assert molrep.get_smoothing(rep=r, molid=m) == 10
molrep.set_smoothing(rep=r, molid=m, smoothing=1)
assert molrep.get_smoothing(rep=r, molid=m) == 1
with pytest.raises(ValueError):
molrep.set_smoothing(m, r, -1)
with pytest.raises(ValueError):
molrep.set_smoothing(m+1, 0, 12)
with pytest.raises(ValueError):
molrep.set_smoothing(m, r+1, 2)
molecule.delete(m)
def test_visible_and_smoothing(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(material="AOChalky", selection="name C", molid=m)
# Get visible
assert molrep.get_visible(m, r)
with pytest.raises(ValueError):
molrep.get_visible(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_visible(m, r + 1)
# Set visible
molrep.set_visible(m, r, True)
assert molrep.get_visible(m, r)
molrep.set_visible(m, r, visible=False)
assert not molrep.get_visible(m, r)
with pytest.raises(ValueError):
molrep.set_visible(m + 1, 0, False)
with pytest.raises(ValueError):
molrep.set_visible(m, r + 1, True)
# Get smoothing
assert molrep.get_smoothing(molid=m, rep=r) == 0
with pytest.raises(ValueError):
molrep.get_smoothing(m + 1, 0)
with pytest.raises(ValueError):
molrep.get_smoothing(m, r + 1)
# Set smoothing
molrep.set_smoothing(m, r, 10)
assert molrep.get_smoothing(rep=r, molid=m) == 10
molrep.set_smoothing(rep=r, molid=m, smoothing=1)
assert molrep.get_smoothing(rep=r, molid=m) == 1
with pytest.raises(ValueError):
molrep.set_smoothing(m, r, -1)
with pytest.raises(ValueError):
molrep.set_smoothing(m + 1, 0, 12)
with pytest.raises(ValueError):
molrep.set_smoothing(m, r + 1, 2)
molecule.delete(m)
def test_modrep(file_3nob):
m = molecule.load("mae", file_3nob)
r = molrep.addrep(style="Licorice", color="ResID", selection="noh",
material="AOEdgy", molid=m)
with pytest.raises(ValueError):
molrep.modrep(m+1, 0)
with pytest.raises(ValueError):
molrep.modrep(m, r+1)
assert molrep.get_style(m, r) == "Licorice"
assert molrep.modrep(m, r, style="Lines")
assert molrep.get_style(m, r) == "Lines"
assert not molrep.modrep(m, r, style="Invalid")
assert molrep.get_style(m, r) == "Lines"
assert molrep.modrep(m, r, color="ColorID 0", selection="resname TIP3",
material="Transparent")
assert molrep.get_selection(m, r) == "resname TIP3"
assert molrep.get_material(m, r) == "Transparent"
assert molrep.get_color(m, r) == "ColorID 0"
molecule.delete(m)
