def __init__(self,dcd=None,psf=None,first=0,last=-1,stride=1,waitfor=-1,pdb=None):
self.molID=0
if psf is not None:
self.psf = psf
self.molID=molecule.load('psf',psf)
if (pdb is None) and (dcd is not None):
try:
self.dcd = dcd
self.molID=molecule.new('new')
self.molID=molecule.load('psf',self.psf) # load trajectory
molecule.read(self.molID,'dcd',self.dcd,stride=stride,first=first,last=last,waitfor=waitfor)
print ("DCD file detected id ",self.molID)
except IOError:
print ("Could not read dcd file or psf:", dcd)
raise Exception()
else:
try:
self.molID=molecule.new('pdb')
self.pdb=pdb
molecule.read(molid=self.molID,filetype ='pdb',filename=self.pdb,first=0,last=0)
print ("pdb file detected id ",self.molID)
except IOError:
print ("Could not read dcd file or psf:",pdb)
raise Exception()
def test_create():
m = molecule.new(name="test", natoms=3000)
assert molecule.name(m) == "test"
assert molecule.numatoms(m) == 3000
with pytest.raises(ValueError):
m = molecule.new("test2", -2000)
molecule.delete(m)
def test_create():
m = molecule.new(name="test", natoms=3000)
assert molecule.name(m) == "test"
assert molecule.numatoms(m) == 3000
with pytest.raises(ValueError):
m = molecule.new("test2", -2000)
molecule.delete(m)
def test_materials():
mid = molecule.new(name="Test")
graphics.materials(molid=mid, on=True)
graphics.material(molid=mid, name="AOShiny")
rc = graphics.sphere(molid=mid, center=(1,1,1), radius=5.1, resolution=8)
assert graphics.info(mid, rc) == "sphere {1.000000 1.000000 1.000000} " +\
"radius 5.100000 resolution 8"
with pytest.raises(ValueError):
graphics.sphere(molid=mid, center=(1,1))
rc = graphics.text(mid, (0,0,0), "hello world", size=4.0, width=2.0)
with pytest.raises(ValueError):
graphics.text(mid, 0, "oops")
assert graphics.info(mid, rc) == "text {0.000000 0.000000 0.000000} " + \
"{hello world} size 4.000000 thickness 2.000000"
with pytest.raises(ValueError):
graphics.info(mid+1, 3)
with pytest.raises(IndexError):
graphics.info(mid, 3000)
graphics.delete(mid, rc)
with pytest.raises(IndexError):
graphics.info(mid, rc)
molecule.delete(mid)
def __setstate__(self, state):
name, files, types, reps = state
self.id = molecule.new(name, 0)
for file, type in zip(files, types):
self.load(file, type)
self.clearReps()
for rep in reps:
self.addRep(rep)
def pdb(self,pdb,psf=None):
#sobrecarga para leer pdbs y no dcd
try:
self.molID=molecule.new('pdb')
self.pdb=pdb
if psf is not None:
self.molID=molecule.load('psf',psf)
self.psf=psf # add psf
molecule.read(molid=self.molID,filetype ='pdb',filename=self.pdb,first=0,last=0)
print (self.molID)
except IOError:
print ("Could not read dcd file or psf:",pdb)
raise Exception()
def dcd(self,dcd,psf,first=0,last=-1,stride=1,waitfor=-1):
self.psf = psf
self.dcd = dcd
self.molID=0
try:
self.molID=molecule.new('new')
self.molID=molecule.load('psf',self.psf) # load trajectory
molecule.read(self.molID,'dcd',self.dcd,stride=stride,first=first,last=last,waitfor=waitfor)
print (self.molID)
except IOError:
print ("Could not read dcd file or psf:", dcd)
raise Exception()
def test_colors():
mid = molecule.new(name="colortest")
graphics.color(mid, 1)
graphics.color(mid, "blue2")
with pytest.raises(ValueError):
graphics.color(mid, -1)
with pytest.raises(ValueError):
graphics.color(mid, "not a color")
with pytest.raises(TypeError):
graphics.color(mid, 32.0)
molecule.delete(mid)
def __init__(self, name=None, id=None, atoms=0):
"""
Creating a new Molecule instance with no arguments will create a new
empty molecule in VMD. Passing a valid molecule id will make the
Molecule instance mirror the state of the corresponding molecule in VMD.
If id is None, and a name is given, the new molecule will have that name.
"""
if id is None:
if name is None:
name = "molecule"
self.id = molecule.new(name, atoms)
else:
self.id = id
self.atoms = molecule.numatoms(self.id)
if not molecule.exists(self.id):
raise ValueError("Molecule with id %d does not exist." % self.id)
def test_mol_descstrs(file_3frames):
m1 = molecule.load("pdb", file_3frames)
m2 = molecule.new(name="empty")
# Filenames
assert "ala_nma_3frames.pdb" in molecule.get_filenames(molid=m1)[0]
assert molecule.get_filenames(m2) == []
with pytest.raises(ValueError):
molecule.get_filenames(m2 + 1)
# File types
assert molecule.get_filetypes(molid=m1) == ["pdb"]
assert molecule.get_filetypes(m2) == []
with pytest.raises(ValueError):
molecule.get_filetypes(m2 + 1)
# Databases
assert molecule.get_databases(molid=m1) == ["PDB"]
assert molecule.get_databases(m2) == []
with pytest.raises(ValueError):
molecule.get_databases(m2 + 1)
# Accessions
assert molecule.get_accessions(molid=m1) == ["TEST"]
assert molecule.get_accessions(m2) == []
with pytest.raises(ValueError):
molecule.get_accessions(m2 + 1)
# Remarks
assert molecule.get_remarks(molid=m1) == ["REMARK 1 remark 1\nREMARK 2" \
" also remark 2\n"]
assert molecule.get_remarks(m2) == []
with pytest.raises(ValueError):
molecule.get_remarks(m2 + 1)
molecule.delete(m1)
molecule.delete(m2)
def test_mol_descstrs(file_3frames):
m1 = molecule.load("pdb", file_3frames)
m2 = molecule.new(name="empty")
# Filenames
assert "ala_nma_3frames.pdb" in molecule.get_filenames(molid=m1)[0]
assert molecule.get_filenames(m2) == []
with pytest.raises(ValueError):
molecule.get_filenames(m2+1)
# File types
assert molecule.get_filetypes(molid=m1) == ["pdb"]
assert molecule.get_filetypes(m2) == []
with pytest.raises(ValueError):
molecule.get_filetypes(m2+1)
# Databases
assert molecule.get_databases(molid=m1) == ["PDB"]
assert molecule.get_databases(m2) == []
with pytest.raises(ValueError):
molecule.get_databases(m2+1)
# Accessions
assert molecule.get_accessions(molid=m1) == ["TEST"]
assert molecule.get_accessions(m2) == []
with pytest.raises(ValueError):
molecule.get_accessions(m2+1)
# Remarks
assert molecule.get_remarks(molid=m1) == ["REMARK 1 remark 1\nREMARK 2" \
" also remark 2\n"]
assert molecule.get_remarks(m2) == []
with pytest.raises(ValueError):
molecule.get_remarks(m2+1)
molecule.delete(m1)
molecule.delete(m2)
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)