def compositeToBasicRules(self, pred, body, varOrder = None):
variables = set()
rules = []
rule = Rule()
passOperator = ''
for literal in body:
newLiteral = None
if isinstance(literal, string_types):
for literalString in literal.split('^'):
if re.match('[!#]?[a-z]+[_0-9\([a-zA-Z,]+\)]?' , literalString):
newLiteral = Literal.fromString(literalString)
rule.body.append(newLiteral)
variables = variables.union(newLiteral.vars())
elif re.match('[!#]', literalString):
passOperator = literalString
else:
freshPred = freshPredicate()
(newLiteralVars, newLiteralRules) = Rule.compositeToBasicRules(freshPred, literal)
rules += newLiteralRules
newLiteral = Literal.fromString( passOperator + freshPred + '(' + ','.join(newLiteralVars) + ')')
rule.body.append(newLiteral)
variables = variables.union(newLiteral.vars())
passOperator = ''
if varOrder is not None:
rule.head = Atom.fromString(pred + '(' + varOrder + ')')
else:
rule.head = Atom.fromString(pred + '(' + ','.join(map(str, variables)) + ')')
rules.append(rule)
return (variables, rules)
def __init__(self, sequence):
self.atoms = []
initialCoor = coor = (0, 0, 0)
j = 0
for i in sequence:
if j == 0:
newAtom = Atom(initialCoor, 0.3, i)
self.addAtom(newAtom)
else:
if j % 2 == 1:
coor = (j * 1.299, -0.75, 0)
else:
coor = (j * 1.299, 0, 0)
newAtom = Atom(coor, 0.3, i)
self.addAtom(newAtom)
j = j + 1
#config = MKTFLILALL
#self.aminoacids = []
#j = 0
#angledistance = 4/math.sqrt(3)
#for i, val in enumerate(chain):
#for i in chain:
# r=4
#coor = (0,1*(r-1),0)
# if i%2 == 1:
# coor = (angledistance,r*j,0)
# else:
# coor = (0,r*j,0)
# self.aminoacids.append(Aminoacid(val,coor,config[val]["radius"]))
# j = j + 1
self.disulfideBonds = None
def toDatalogRules(self):
if self.body.operator == '':
ruleTop = str(self.head.toDatalog('top')) + ' :- ' + str(self.body.subqueries[0].toDatalog('top'))
ruleBot = str(self.head.toDatalog('bot')) + ' :- ' + str(self.body.subqueries[0].toDatalog('bot'))
return [ruleTop, ruleBot]
elif self.body.operator == '!':
freshAtom = Atom.freshWithArgs(self.body.getArgs())
ruleTop = str(self.head.toDatalog('top')) + ' :- not_exists(' + str(freshAtom.toDatalog('bot')) + ')'
ruleBot = str(self.head.toDatalog('bot')) + ' :- not_exists(' + str(freshAtom.toDatalog('top')) + ')'
subqueryRule = Rule()
subqueryRule.head = freshAtom
subqueryRule.body = self.body.subqueries[0]
return [ruleTop, ruleBot] + subqueryRule.toDatalogRules()
elif self.body.operator == '~':
freshAtom = Atom.freshWithArgs(self.body.getArgs())
ruleTop = str(self.head.toDatalog('top')) + ' :- ' + str(freshAtom.toDatalog('bot'))
ruleBot = str(self.head.toDatalog('bot')) + ' :- ' + str(freshAtom.toDatalog('top'))
subqueryRule = Rule()
subqueryRule.head = freshAtom
subqueryRule.body = self.body.subqueries[0]
return [ruleTop, ruleBot] + subqueryRule.toDatalogRules()
elif self.body.operator == '^':
freshAtoms = []
datalogRules = []
for subquery in self.body.subqueries:
freshAtom = Atom.freshWithArgs(subquery.getArgs())
freshAtoms.append(freshAtom)
newRule = Rule()
newRule.head = freshAtom
newRule.body = subquery
datalogRules += newRule.toDatalogRules()
ruleTop = str(self.head.toDatalog('top')) + ' :- ' + ','.join([str(x.toDatalog('top')) for x in freshAtoms])
ruleBot = str(self.head.toDatalog('bot')) + ' :- ' + ','.join([str(x.toDatalog('bot')) for x in freshAtoms])
datalogRules += [ruleTop, ruleBot]
return datalogRules
def repeat(self,n1,n2,n3):
#...unit vectors to be repeated
self.a1= self.a1*n1
self.a2= self.a2*n2
self.a3= self.a3*n3
n123= n1*n2*n3
nsid= 0
for ai in self.atoms:
nsid= max(nsid,ai.sid)
natm0= self.num_atoms()
atoms0= copy.copy(self.atoms)
self.atoms= []
aid= 0
for i1 in range(n1):
for i2 in range(n2):
for i3 in range(n3):
for ai0 in atoms0:
aid += 1
ai= Atom()
ai.sid= ai0.sid
ai.symbol= ai0.symbol
ai.ifmv= ai0.ifmv
x= ai0.pos[0]/n1 +1.0/n1*i1
y= ai0.pos[1]/n2 +1.0/n2*i2
z= ai0.pos[2]/n3 +1.0/n3*i3
ai.set_pos(x,y,z)
ai.set_vel(ai0.vel[0],ai0.vel[1],ai0.vel[2])
ai.set_id(aid)
self.atoms.append(ai)
def __get__(self):
prop = self.connection.core.GetProperty(False, self,
Atom(self.connection, "WM_TRANSIENT_FOR"),
Atom(self.connection, "WINDOW"),
0, 1).reply()
if prop.value:
return Window(byte_list_to_uint32(prop.value)[0])
def __getattr__(self, name):
attr = None
if self.__cachedir__ and Atom.is_cached(self.__cachedir__, name):
attr = Atom.load(self.__cachedir__,
name,
is_client=self.__is_client__)
setattr(self, name, attr)
return attr
if self.__source__ is None and self.__factory__ is not None:
source = self.__factory__()
self.__source__ = source
#Not really the right place for this.
#if self.__cachedir__ is not None:
# print '%s = %s' % (self.__cachedir__, len(self))
if self.__source__ is not None:
attr = getattr(self.__source__, name)
if attr is not None and self.__index__ is not None:
#Although this is simple and effective it is not very efficienct
# a = Ai(Bi(C[xy])))
#Using this method:
# ax = Cx[Bi][Ai], xy = ay[Bi][Ai]
#A better approach is to calculate the index then apply it
# bai = Bi[Ai], ax = Cx[bai], ay = Cx[bai]
attr = attr[self.__index__]
if attr is not None:
setattr(self, name, attr)
return attr
def __getattr__(self, name):
attr = None
if self.__cachedir__ and Atom.is_cached(self.__cachedir__, name):
attr = Atom.load(self.__cachedir__, name, is_client=self.__is_client__)
setattr(self, name, attr)
return attr
if self.__source__ is None and self.__factory__ is not None:
source = self.__factory__()
self.__source__ = source
#Not really the right place for this.
#if self.__cachedir__ is not None:
# print '%s = %s' % (self.__cachedir__, len(self))
if self.__source__ is not None:
attr = getattr(self.__source__, name)
if attr is not None and self.__index__ is not None:
#Although this is simple and effective it is not very efficienct
# a = Ai(Bi(C[xy])))
#Using this method:
# ax = Cx[Bi][Ai], xy = ay[Bi][Ai]
#A better approach is to calculate the index then apply it
# bai = Bi[Ai], ax = Cx[bai], ay = Cx[bai]
attr = attr[self.__index__]
if attr is not None:
setattr(self, name, attr)
return attr
def setup_atoms(self):
# Load atom images
self.atomImage = pygame.image.load('images/osmos.png')
self.enemyImage = pygame.image.load('images/osmos-enemy.png')
self.atoms = []
add = self.atoms.append
self.playerAtom = Atom(self.worldWidth / 2, self.worldHeight / 2,
self.atomImage.get_width() / 4,
self.atomImage.get_height() / 4, self.atomImage,
True)
add(self.playerAtom)
self.camera.follow(self.playerAtom)
for x in xrange(ENEMY_COUNT):
generalSize = random.randint(20, 45)
multiplier = random.randint(1, 3)
x = random.randint(1, self.worldWidth)
y = random.randint(1, self.worldHeight)
width = (generalSize + random.randint(5, 10)) * multiplier
height = (generalSize + random.randint(5, 10)) * multiplier
atom = Atom(x, y, width, height, self.enemyImage)
self.totalEnemyAtomMass += atom.mass
add(atom)
def __init__(self, file):
fh = open(file, 'rb')
size = os.stat(file).st_size
while fh.tell() < size:
root_atom = Atom( stream=fh, offset=fh.tell() )
root_atom.seek( 0, os.SEEK_END )
self.append( root_atom )
def __init__(self, source=None, factory=None, cachedir=None, index=None,
cnames=None, name=None, columns=None, is_client=True, kw={}):
if cachedir and not os.path.exists(cachedir):
os.makedirs(cachedir)
self.__cachedir__ = cachedir
self.__source__ = source
self.__factory__ = factory
self.__index__ = index
#cnames and source.cnames
def __cnames():
__cnames = None
if cnames:
if hasattr(cnames, '__call__'):
__cnames = cnames(self)
elif isinstance(cnames, str):
__cnames = cnames.split(',')
else:
__cnames = cnames
else:
__cnames = []
if source is not None:
__cnames += source.__cnames__
if kw:
__cnames += [x for x in kw.keys() if x not in __cnames]
return __cnames
self.__cnames__ = __cnames()
if columns is not None:
for name, value in zip(self.__cnames__, columns):
setattr(self, name, value)
if name is None:
if source is not None:
name = source.__name__
else:
name = 'element_%s' % id(self)
self.__name__ = name
self.__columns__ = columns
self.__is_client__ = is_client
for name, value in kw.items():
if isinstance(value, str):
value = getcolumn(self, value)
elif hasattr(value, '__call__'):
value = value(self)
if isinstance(value, list):
value = Atom.fromlist(value)
value = value
if isinstance(value, list):
value = Atom.fromlist(value)
elif isinstance(value, np.ndarray) and not isinstance(value, Atom):
value = Atom(value)
setattr(self, name, value)
if cachedir is not None:
for name in self.__cnames__:
if not Atom.is_cached(cachedir, name):
getattr(self, name).persist(cachedir, name)
def WriteAtomToFile(self, elem: Atom) -> None:
try:
testFile = open(elem.IDType().Get('Name') + '.txt', 'r')
testFile.close()
except (IOError):
auxFile = open(elem.IDType().Get('Name') + '.txt', 'w')
auxFile.write(str(elem))
auxFile.close()
def __init__(self, pos):
self.pos = pos
self.hydrogen = []
self.bondlength = 1
self.central = Atom(self.pos, "carbon")
self.size = 1
self.bonds = 0
self.placehydrogen()
def get_text_property(self, window, atom_name):
prop = self.core.GetProperty(False, window,
Atom(self, atom_name).value,
xcb.xproto.GetPropertyType.Any,
0, 4096).reply()
if prop.type == Atom(self, "UTF8_STRING").value:
return unicode(byte_list_to_str(prop.value), "UTF-8")
elif prop.type == Atom(self, "STRING").value:
return byte_list_to_str(prop.value)
def __init__(self):
if RootWindow._singleton is not None:
raise RootWindow._singleton
self.wid = connection.setup.roots[0].root
Atom.build_cache()
self.windows = set()
self.listen()
def __init__(self, file_name):
'''
Protein class constructor
Receives the file from which it is to be read. It needs to be in pdb or gro formats.
Proteins must be ungapped (all resiude numbers must be consecutive).
Only standard residues are considered.
'''
super(Protein, self).__init__()
ext = file_name.split('.')[-1].lower()
if ext == 'pdb':
with open(fileName, 'r') as f:
fileContent = f.read().split('\n')
for line in fileContent:
if line[0:6] in ['TER ', 'END ']:
return None
elif line[0:6] == 'ATOM ':
index = int(line[6:11])
name = line[12:16].strip()
resName = line[17:20].strip()
if res_name in ['HIP', 'HIE', 'HID']:
res_name = 'HIS'
assert res_name in AMINO_ACID_NAMES, \
"Only standard residues are considered."
resId = int(line[22:26])
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
if resId > 0:
try:
self.addResidue(Residue(resId, resName))
except AssertionError:
pass
self.addAtom(Atom(index, name, x, y, z), resId)
q = [x for x in self if x != None]
assert None not in self[self.index(q[0]):self.index(q[-1])+1], \
"Protein contains gaps."
elif ext == 'gro':
with open(file_name, 'r') as read_file:
file_content = read_file.read().split('\n')
number_of_atoms = int(file_content[1])
for index in range(number_of_atoms):
line = file_content[2 + index].split()
index = int(line[2])
name = line[1]
res_name = line[0][-3:]
res_id = int(line[0][:-3])
pos_x = float(line[3]) * 10
pos_y = float(line[4]) * 10
pos_z = float(line[5]) * 10
try:
self.add_residue(Residue(res_id, res_name))
except AssertionError:
pass
self.add_atom(Atom(index, name, (pos_x, pos_y, pos_z)), res_id)
else:
raise NameError('Unknown file extension')
return None
def set_below(self, below):
self._send_client_event(
Atom.get_atom('_NET_WM_STATE'),
[
1 if below else 0,
Atom.get_atom('_NET_WM_STATE_BELOW'),
]
)
connection.push()
def read_akr(self,fname='akr0000'):
f=open(fname,'r')
# 1st: lattice constant
self.alc= float(f.readline().split()[0])
# 2nd-4th: cell vectors
for i in range(3):
data= f.readline().split()
self.a1[i]= float(data[0])
self.a2[i]= float(data[1])
self.a3[i]= float(data[2])
# 5th: num of atoms
natm= int(f.readline().split()[0])
# 9th-: atom positions
self.atoms= []
symbol = None
for i in range(natm):
data= [float(x) for x in f.readline().split()]
ai= Atom()
ai.set_sid(data[0])
ai.set_pos(data[1],data[2],data[3])
ai.set_vel(data[4],data[5],data[6])
if self.specorder:
symbol = self.specorder[ai.sid-1]
if symbol and ai.symbol != symbol:
ai.set_symbol(symbol)
self.atoms.append(ai)
f.close()
def __get__(self):
prop = self.connection.core.GetProperty(False, self,
Atom(self.connection, "WM_PROTOCOLS"),
Atom(self.connection, "ATOM"),
0, 1024).reply()
atoms = byte_list_to_uint32(prop.value)
if atoms:
protos = set()
for a in atoms:
protos.add(Atom(self.connection, a))
return protos
def __init__(self, join, container, outer, axis, *keys):
self.size = len(container)
self.join = join
self.axis = axis
self.outer = outer
_sort_index = sort_index(container, *keys)
self.columns = getcolumns(container[_sort_index], *keys)
self.bin_counts = rl.encode(*self.columns)
self.unique = [Atom(column, bincounts=[self.bin_counts]).first
for column in self.columns]
self.inverted_index = Atom(_sort_index, bincounts=[self.bin_counts])
def restore(self):
self._send_client_event(
Atom.get_atom('_NET_WM_STATE'),
[
0, # _NET_WM_STATE_REMOVE = 0, _NET_WM_STATE_ADD = 1, _NET_WM_STATE_TOGGLE = 2
Atom.get_atom('_NET_WM_STATE_MAXIMIZED_VERT'),
Atom.get_atom('_NET_WM_STATE_MAXIMIZED_HORZ')
]
)
connection.push()
def takefocus(self):
"""Send a take focus request to a window."""
# XXX Seriously, we need to do some stuff for xpyb about this.
buf = struct.pack("BB2xIIII12x",
33, # XCB_CLIENT_MESSAGE
32, self, Atom(self.connection, "WM_PROTOCOLS"),
Atom(self.connection, "WM_TAKE_FOCUS"),
xcb.xproto.Time.CurrentTime)
self.connection.core.SendEvent(False, self,
xcb.xproto.EventMask.NoEvent,
buf)
def set_text_property(self, window, atom_name, value):
if isinstance(value, unicode):
string_atom = Atom(self, "UTF8_STRING")
value = value.encode("UTF-8")
else:
string_atom = Atom(self, "STRING")
self.core.ChangeProperty(xcb.xproto.Property.NewValue,
window,
Atom(self, atom_name).value,
string_atom,
8, len(value), value)
def test_atom_coordination():
a = Atom(6)
assert a.get_coordination() == 4
with pytest.raises(TypeError):
a.set_coordination(1.0)
with pytest.raises(ValueError):
a.set_coordination(5)
a.set_coordination(3)
assert a.get_coordination() == 3
def test_atomness(self):
foo = Atom("foo")
another_foo = Atom("foo")
bar = Atom("bar")
baz = Atom("baz")
self.assertTrue(foo == foo)
self.assertTrue(foo == another_foo)
self.assertTrue(foo != bar)
self.assertTrue(baz != bar)
self.assertTrue(foo != bar != baz)
def fromString(self, string):
newLiteral = Literal()
if string[0] == '!':
newLiteral.op = '!'
newLiteral.atom = Atom.fromString(string[1:])
elif string[0] == '#':
newLiteral.op = '#'
newLiteral.atom = Atom.fromString(string[1:])
else:
newLiteral.op = None
newLiteral.atom = Atom.fromString(string)
return newLiteral
def remove_decorations(self):
if XROOT.wm() == 'openbox':
self._send_client_event(
Atom.get_atom('_NET_WM_STATE'),
[
1,
Atom.get_atom('_OB_WM_STATE_UNDECORATED')
]
)
else:
self._set_property('_MOTIF_WM_HINTS', [2, 0, 0, 0, 0])
connection.push()
def __get__(self):
prop = self.connection.core.GetProperty(False, self,
Atom(self.connection, "_NET_WM_ICON"),
Atom(self.connection, "CARDINAL"),
# Max icon size is:
# w * h * (rgba)
0, 256*256*4).reply()
if len(prop.value) % 4 == 0:
width, height = byte_list_to_uint32(prop.value[:8])
return Image.frombuffer("RGBA",
(width, height),
byte_list_to_str(prop.value[8:]),
"raw", "ARGB", 0, 1)
def read_POSCAR(self,fname='POSCAR'):
with open(fname,'r') as f:
# 1st line: comment
f.readline()
# 2nd: lattice constant
self.alc= float(f.readline().split()[0])
# 3rd-5th: cell vectors
self.a1= np.array([float(x) for x in f.readline().split()])
self.a2= np.array([float(x) for x in f.readline().split()])
self.a3= np.array([float(x) for x in f.readline().split()])
# 6th: species names or number of each species
buff= f.readline().split()
if not buff[0].isdigit():
spcs = copy.deepcopy(buff)
buff= f.readline().split()
if not self.specorder:
self.specorder = spcs
num_species= np.array([ int(n) for n in buff])
natm= 0
for n in num_species:
natm += n
#print("Number of atoms = {0:5d}".format(natm))
# 7th or 8th line: comment
c7= f.readline()
if c7[0] in ('s','S'):
c8= f.readline()
# Atom positions hereafter
self.atoms= []
for i in range(natm):
buff= f.readline().split()
ai= Atom()
sid= 1
m= 0
sindex=0
symbol = None
for n in num_species:
m += n
if i < m:
if spcs and self.specorder:
sid = self.specorder.index(spcs[sindex]) + 1
symbol = spcs[sindex]
break
sid += 1
sindex += 1
ai.set_id(i+1)
ai.set_sid(sid)
if symbol:
ai.symbol = symbol
ai.set_pos(float(buff[0]),float(buff[1]),float(buff[2]))
ai.set_vel(0.0,0.0,0.0)
self.atoms.append(ai)
def buildProtein(url_target):
backboneList, sidechainList, proteinList = [], [], []
currentPos = 0
currentAminoAcid, currentSeq = "", ""
stream = urllib2.urlopen(url_target)
for line in stream:
#All Lines Indexes are found: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html
if (line[0:4] == "ATOM"):
"""
This check is in here because, PDB Files do not necessarily have to start their amino acid count
at 0. Most proteins will have non-amino acid residues before the start of their chain which is
why the position differs. Additionally, each PDB File defines their amino acids as a single number
representing the residue number. Which is why we can use that number as a way to detect when the
start of a new amino acid occurs.
Therefore, everytime the amino acid residue number changes (and that change is not from 0 to residue
number) we can assume it is the start of a new amino acid residue.
"""
if ((currentPos != int(line[22:26])) and currentPos != 0):
#When a new amino acid is started, append the completed one
#Amino Acid, SEQRES, Position, Backbone Atoms [N][Ca][C], Sidechain Atoms [1]...[n]
proteinList.append(
AminoAcid(currentAminoAcid, currentSeq, currentPos,
list(backboneList), list(sidechainList)))
backboneList, sidechainList = [], [] #Reset the lists to empty
#The index is defined by looking at the PDB Files, they are consistent across all PDB Files
currentAminoAcid = str(line[17:20])
currentSeq = str(line[21:22])
currentPos = int(line[22:26])
atomName = line[12:16].strip()
if (atomName in BACKBONE_ATOMS):
backboneList.append(
Atom(atomName, float(line[31:38]), float(line[39:46]),
float(line[47:54]), str(line[76:78].replace(" ",
""))))
else:
sidechainList.append(
Atom(atomName, float(line[31:38]), float(line[39:46]),
float(line[47:54]), str(line[76:78].replace(" ",
""))))
"""
Because we always add the completed Atom after we detect its completion by examining whether or not the
residue number changed, we need to do one more append for the LAST amino acid, since there won't be a
residue change after the last amino acid has been completed
"""
proteinList.append(
AminoAcid(currentAminoAcid, currentSeq, currentPos, list(backboneList),
list(sidechainList)))
return Protein(list(proteinList))
def _get_property(self, atom_name):
try:
if not Atom.get_type_name(atom_name):
return ''
rsp = connection.get_core().GetProperty(
False,
self.wid,
Atom.get_atom(atom_name),
Atom.get_atom_type(atom_name),
0,
(2 ** 32) - 1
).reply()
if Atom.get_type_name(atom_name) in ('UTF8_STRING', 'STRING'):
if atom_name == 'WM_CLASS':
return Atom.null_terminated_to_strarray(rsp.value)
else:
return Atom.ords_to_str(rsp.value)
elif Atom.get_type_name(atom_name) in ('UTF8_STRING[]', 'STRING[]'):
return Atom.null_terminated_to_strarray(rsp.value)
else:
return list(struct.unpack('I' * (len(rsp.value) / 4), rsp.value.buf()))
except:
pass
def structure2aSys(structure, idoffset=1):
"""
Converts Structure object of pymatgen to NAPSystem object in nap.
Args:
structure (Structure): pymatgen Structure object to be converted
to NAPSystem object..
Returns:
aSys (NAPSystem):
"""
lattice = structure.lattice
alc = 1.0
a1 = np.array(lattice.matrix[0])
a2 = np.array(lattice.matrix[1])
a3 = np.array(lattice.matrix[2])
#... rescale a? vectors
a1 = a1 / alc
a2 = a2 / alc
a3 = a3 / alc
aSys = NAPSystem()
aSys.set_lattice(alc, a1, a2, a3)
for ia in range(structure.num_sites):
ai = Atom()
si = structure[ia]
crd = si.frac_coords
ai.set_pos(crd[0], crd[1], crd[2])
sid = structure.symbol_set.index(si.species_string) + idoffset
ai.set_sid(sid)
ai.set_id(ia + 1)
aSys.add_atom(ai)
return aSys
def _createBranch(self, position, lenBranch):
'''
Erstellt alle Atom-Objekte der Nebenkette. Der Index variiert je nachdem, wo die Nebenkette liegt.
An die Statusabfragen sind genauere Kommentare geschrieben.
Parameter: str position - Position in der Hauptkette, an der die Nebenkette liegen soll.
R�ckgabewerte: Bool/String - nur zur Ueberpruefung von Fehlermeldungen
'''
self._branchNumber += 1
branch = []
position = int(position)
atomA = self._atoms[position - 1]
firstSideCarbon = Atom("C", 4)
branch.append(firstSideCarbon)
if lenBranch > 1 or (position != 3 and position != 7
and position % 4 != 0):
status = self._findStatus(atomA, position)
else:
status = self._statusLastAtom(atomA, position)
if type(status) == str:
return status
indexA = self._universalIndex(atomA)
indexC = self._branchIndex(firstSideCarbon, status)
self._createBond(atomA, firstSideCarbon, indexA, indexC,
1) # C wird an Hauptkette rangehangen
for bPos in range(
0, (lenBranch - 1)): # -1 weil oben schon eins erstellt wurde
atomB = Atom("C", 4)
branch.append(atomB)
atomC = branch[bPos]
if bPos == lenBranch - 2 and (position % 4 == 0 or position == 3
or position == 7):
status2 = self._statusLastAtom(atomA, position)
indexB = self._longBranchIndex(atomB, atomC, status2)
if type(status) == str:
return status
else:
indexB = self._longBranchIndex(atomB, atomC, status)
indexC = self._universalIndex(atomC)
self._createBond(atomC, atomB, indexC, indexB, 1)
self._addHydrogen(branch)
self._description += (
"Zeichne jetzt ueber/unter das " + str(position) +
". 'C' der Hauptkette " + str(lenBranch) +
" weitere/s 'C' und verbinde das 'C', das direkt ueber dem der Hauptkette steht mit diesem."
)
return True
def dipole(self):
self.parameter['dipole'] = []
for k in range(len(self.parameter['e_amp'])):
if self.d1 == 1:
j2 = 1.0 / 2.0
else:
j2 = 3.0 / 2.0
n = self.parameter['n']
tmp = [[0 for i in range(n)] for j in range(n)]
cs = Atom()
for i in range(n):
for j in range(n):
d1 = self.index2lfm(i)
d2 = self.index2lfm(j)
if d1[0] == 0 and d2[0] == 1:
q_arr = self.parameter['e_amp'][k][1]
for q in q_arr:
coef = {
'q': q,
'L1': 0,
'L2': 1,
'F1': d1[1],
'F2': d2[1],
'mf1': d1[2],
'mf2': d2[2] + q,
'J1': 1.0 / 2.0,
'J2': j2,
'I': 7.0 / 2.0
}
tmp[i][j] += cs.dipole_element(**coef)
elif d2[0] == 0 and d1[0] == 1:
q_arr = self.parameter['e_amp'][k][1]
for q in q_arr:
coef = {
'q': q,
'L1': 0,
'L2': 1,
'F1': d2[1],
'F2': d1[1],
'mf1': d2[2],
'mf2': d1[2] + q,
'J1': 1.0 / 2.0,
'J2': j2,
'I': 7.0 / 2.0
}
tmp[i][j] += cs.dipole_element(**coef)
else:
tmp[i][j] = 0.0
self.parameter['dipole'].append(tmp)
def read_xyz(path, name, spg, a, b, c, alpha, beta, gamma):
"""
from C21 database.txt extract infomation to form 21(22) molecules/fragemets
in a unit cell and return a list of them
"""
with open(path, "r") as data:
line = data.readline().strip()
line = data.readline().strip()
line = data.readline().strip()
mol = Molecule()
while line:
info = []
for part in line.split(" "):
if len(part) > 0:
info.append(part)
mol.addAtom(
Atom(typ=info[0],
coordinate=np.array(
[float(info[1]),
float(info[2]),
float(info[3])])))
line = data.readline().strip()
mol.setCellpara(a, b, c, alpha, beta, gamma)
mol.setSpg(spg)
mol.setName(name)
return mol
def make_sc(latconst=1.0):
"""
Make a cell of simple cubic structure.
"""
s= NAPSystem(specorder=_default_specorder)
#...lattice
a1= np.array([ 1.0, 0.0, 0.0 ])
a2= np.array([ 0.0, 1.0, 0.0 ])
a3= np.array([ 0.0, 0.0, 1.0 ])
s.set_lattice(latconst,a1,a2,a3)
p=[0.00, 0.00, 0.00]
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
return s
def fromCompositeString(self, string):
newRule = Rule()
newRule.head = Atom.fromString(string.split(':-')[0])
body = string.split(':-')[1].replace(' ', '')
expressions = nestedExpr('[', ']').parseString(body).asList()
(notused, rules) = Rule.compositeToBasicRules(newRule.head.pred, expressions[0], varOrder = ','.join(newRule.head.args))
return reversed(rules)
def fromElements(self, elements):
query = Query()
query.subqueries = []
if elements[0] == '!':
# negated query
query.operator = '!'
subquery = Query.fromElements(elements[1])
query.subqueries.append(subquery)
elif elements[0] == '~':
# inverted query
query.operator = '~'
subquery = Query.fromElements(elements[1])
query.subqueries.append(subquery)
elif elements[0] == '(':
# infix query
if elements[2] == '^':
# conjunction
query.operator = '^'
for subqueryElements in elements[1:-1:2]:
subquery = Query.fromElements(subqueryElements)
query.subqueries.append(subquery)
elif elements[2] in ['-false->', '-bot->', '-top->', '-true->']:
return Query.fromElements(Query.getOverride(elements[1], elements[2][1:-2], elements[3]))
elif elements[2] == '-plus-':
return Query.fromElements(Query.getPlus(elements[1], elements[3]))
elif elements[2] == '-times-':
return Query.fromElements(Query.getTimes(elements[1], elements[3]))
elif elements[2] == '<':
return Query.fromElements(['!', ['(', ['!', ['(', Query.getEq(elements[3], 'true'), '^', elements[1], ')'] ], '^', ['!', ['(', ['!', Query.getEq(elements[3], 'true')], '^', elements[5], ')'] ], ')' ] ])
else:
# atomic query
query.operator = ''
query.subqueries.append(Atom.fromElements(elements))
return query
def read_from_file(cls, filepath):
"""
Create an instance of Sentences from an input file. This file format is given by the
professor for this class.
Args:
filepath <str>: the filepath to the input file.
Returns:
<sentences.Sentences>: an instance of the Sentences class with the given clauses in the
input file.
"""
clauses = []
f = open(filepath)
# First read in the clauses
for line in f:
clause = []
if line[0] == '0':
break
else:
line = line.strip().split(' ')
for l in line:
clause.append(Atom(l))
clauses.append(Clause(clause))
# Then read in the rest of the input file for the translation
rest_of_input = []
for line in f:
rest_of_input.append(line)
return cls(clauses, rest_of_input)
def read(fileObject):
"""Method to read XYZ files.
atomic coord in Angstroem, atom types in lowercase, format:
<number of atoms>
<comment line>
<atomType x y z>
<atomType x y z>
"""
lines = fileObject.readlines()
atoms = None
if atoms is None:
atoms = []
# by convention the first thing in the xyz is the number of atoms
nat = int(lines[0])
# loop over the nat lines
for line in lines[2:nat + 2]:
# check if new section begins
if line.startswith("$"):
break
else:
symbolRaw, x, y, z = line.split()[:4]
symbolShort = symbolRaw.strip()
atomSymbol = symbolShort[0].upper() + symbolShort[1:].lower()
atomPosition = [float(x) / Bohr, float(y) / Bohr, float(z) / Bohr]
atom = Atom(symbol=atomSymbol, position=atomPosition)
atoms.append(atom)
return atoms
def make_argument(self, conclusion: Atom):
"""
Constructs an argument that leads to conclusion.
:param conclusion: Atom - conclusion
:return: str - string that describes argument
"""
if not (conclusion.is_ground()):
raise ValueError('Invalid conclusion')
else:
query_conclusion_str = ':-' + str(conclusion) + '.'
if self.ask(HornClause.from_str(query_conclusion_str))[0]:
s = ''
known_clauses = self.get_clauses(conclusion.predicate)
for known_clause in known_clauses:
subs_dict = unify(known_clause.conclusion, conclusion)
if subs_dict:
substituted_clause = known_clause.substitute(subs_dict)
query = HornClause(None, substituted_clause.premises)
found, solutions = self.ask(query)
if found:
if solutions:
substituted_query = query.substitute(solutions[0])
else:
substituted_query = query
for p in substituted_query.premises:
s += str(p) + '.\n'
s += str(known_clause) + '\n'
s += '\u2234 ' + str(conclusion)
break
else:
s = 'Argument does not exist.'
return s
def main():
webStr = None
queryString = None
opts, args = getopt.getopt(sys.argv[1:], "i:q:", ["input", "query"])
for o, a in opts:
if o == "-i":
webStr = a
elif o == "-q":
queryString = a
if webStr is None or queryString is None:
print "Incorrect usage"
sys.exit(-1)
xsb = XSB()
try:
webStr = webStr.replace("<newline>", "\n")
polStr = "\n".join([l for l in webStr.split("\n") if ":-" in l])
policy = Policy.fromString(escapeCharacters(polStr))
query = Atom.fromElements(Grammar.parseAtom(escapeCharacters(queryString)))
policy.processPolicy()
policy.checkQuery(query)
xsb.loadPolicy(policy)
print xsb.query(query)
xsb.close()
except Exception as e:
print "Error:", e
xsb.close()
sys.exit(-1)
def _createDoubleO(self, atomA, pos, suffix):
'''
Erstellt eine Doppelbindung zu einem O-Atom-Objekt.
Reduziert die Anzahl der Bindugen, die atomA hat.
Setzt fuer verschiedene Positionen verschiedene 'BondModel' , die in graphicMolecule verwendet werden.
Parameter: instance atomA - Atom-Objekt, an das das O-Objekt mit einer Doppelbindung gebunden wird,
int pos - Position des O-Atoms
str suffix - funktionelle Gruppe
R�ckgabewerte: Bool/String - erfolgreich/Fehlermeldung
'''
atomA.updateBondNumber(3)
if suffix == "al":
if pos == 1:
atomA.updateBondModel(8)
elif pos % 2:
atomA.updateBondModel(4)
else:
atomA.updateBondModel(5)
else:
if pos % 2:
atomA.updateBondModel(7)
else:
atomA.updateBondModel(6)
indexA = self._universalIndex(atomA)
if not indexA == "Error":
atomO = Atom("O", 1)
indexO = 0
self._createBond(atomA, atomO, indexA, indexO, 2)
else:
return "Tut uns Leid. Dieses Molekuel existiert bei uns nicht. Ueberpruefen Sie die Anzahl der Bindungen am " + str(
pos) + ". Atom."
return True
def generate_AF(p, ruleset):
"""Generates the abstract AF given the ruleset. Note that the appropriate pref relationship is invoked via the argument file."""
finished = False
argsOld = set()
#there is a hack going on here; we generate arguments, and then iterate through to generate rebutters and undercutters in multiple iterations as needed.
while not finished:
t = argsOld.union(generate_arguments(p, ruleset, set()))
args = deepcopy(t)
for a in t:
args = args.union(a.subarguments)
t = deepcopy(args)
for a in t:
args = args.union(
generate_arguments(a.toprule.con.neg(), ruleset, set()))
args = args.union(
generate_arguments(Atom(True, a.toprule.name), ruleset, set()))
if args == argsOld:
finished = True
else:
argsOld = args
#still better to generate attacks with arguments
attacks = generate_defeats(args)
return (args, attacks)
def read_molecule(r):
""" (reader) -> Molecule
Read a single molecule from r and return it
or return None to signal end of file
"""
# if there isnt another line, we're at the end of the file
line = r.readline()
if not line:
return None
# name of the molecule: "COMPND name"
key, name = line.split()
# other lines are either "END" or "ATOM num kind x y z"
molecule = Molecule(name)
reading = True
while reading:
line = r.readline()
if line.startswith('END'):
reading = False
else:
key, num, kind, x, y, z = line.split()
molecule.add(Atom(num, kind, float(x), float(y), float(z)))
return molecule
def set_desktop(self, desk):
self._send_client_event(
Atom.get_atom('_NET_WM_DESKTOP'),
[
desk,
2
]
)
def structure2aSys(structure,idoffset=1):
"""
Converts Structure object of pymatgen to NAPSystem object in nap.
Args:
structure (Structure): pymatgen Structure object to be converted
to NAPSystem object..
Returns:
aSys (NAPSystem):
"""
lattice= structure.lattice
alc= 1.0
a1= np.array(lattice.matrix[0])
a2= np.array(lattice.matrix[1])
a3= np.array(lattice.matrix[2])
#... rescale a? vectors
a1= a1/alc
a2= a2/alc
a3= a3/alc
aSys= NAPSystem()
aSys.set_lattice(alc,a1,a2,a3)
for ia in range(structure.num_sites):
ai= Atom()
si= structure[ia]
crd= si.frac_coords
ai.set_pos(crd[0],crd[1],crd[2])
sid= structure.symbol_set.index(si.species_string)+idoffset
ai.set_sid(sid)
ai.set_id(ia+1)
aSys.add_atom(ai)
return aSys
def dipole(self):
self.parameter['dipole'] = []
for k in range(len(self.parameter['e_amp'])):
if self.d1 == 1:
j2 = 1.0/2.0
else:
j2 = 3.0/2.0
n=self.parameter['n']
tmp = [[0 for i in range(n)] for j in range(n)]
cs = Atom()
for i in range(n):
for j in range(n):
d1 = self.index2lfm(i)
d2 = self.index2lfm(j)
if d1[0] == 0 and d2[0] == 1:
q_arr=self.parameter['e_amp'][k][1]
for q in q_arr:
coef = {'q':q,
'L1':0,
'L2':1,
'F1':d1[1],
'F2':d2[1],
'mf1':d1[2],
'mf2':d2[2]+q,
'J1':1.0/2.0,
'J2':j2,
'I':7.0/2.0}
tmp[i][j] += cs.dipole_element(**coef)
elif d2[0] == 0 and d1[0] == 1:
q_arr=self.parameter['e_amp'][k][1]
for q in q_arr:
coef = {'q':q,
'L1':0,
'L2':1,
'F1':d2[1],
'F2':d1[1],
'mf1':d2[2],
'mf2':d1[2]+q,
'J1':1.0/2.0,
'J2':j2,
'I':7.0/2.0}
tmp[i][j] += cs.dipole_element(**coef)
else:
tmp[i][j] = 0.0
self.parameter['dipole'].append(tmp)
def restack(self, below=False):
self._send_client_event(
Atom.get_atom('_NET_RESTACK_WINDOW'),
[
2 if not below else 1,
self.wid,
0
]
)
def make_bcc(latconst=1.0):
"""
Make a cell of bcc structure.
"""
s= NAPSystem(specorder=_default_specorder)
#...lattice
a1= np.array([ 1.0, 0.0, 0.0 ])
a2= np.array([ 0.0, 1.0, 0.0 ])
a3= np.array([ 0.0, 0.0, 1.0 ])
s.set_lattice(latconst,a1,a2,a3)
positions=[(0.00, 0.00, 0.00),
(0.50, 0.50, 0.50)]
for p in positions:
atom= Atom()
atom.set_pos(p[0],p[1],p[2])
atom.set_symbol(_default_specorder[0])
s.add_atom(atom)
return s
def activate(self):
self._send_client_event(
Atom.get_atom('_NET_ACTIVE_WINDOW'),
[
2,
xcb.xcb.CurrentTime,
self.wid
]
)
self.stack(True)
def attrs(self, **new_columns):
cnames = self.__cnames__[:]
new = Element(source=self)
for name, val in new_columns.items():
if isinstance(val, str):
attr = getcolumn(new, val)
elif hasattr(val, '__call__'):
val = val(self)
if isinstance(val, list):
val = Atom.fromlist(val)
attr = val
elif isinstance(val, list):
attr = Atom.fromlist(val)
else:
attr = val
setattr(new, name, attr)
if name not in cnames:
cnames.append(name)
new.__cnames__ = cnames
return new
def main():
bellogFilename = None
queryString = None
datalogFilename = None
opts, args = getopt.getopt(sys.argv[1:], 'i:q:o:', ['input', 'query'])
for o, a in opts:
if o == '-i':
bellogFilename = a
elif o == '-q':
queryString = a
elif o == '-o':
datalogFilename = a
if bellogFilename is None and (queryString is None or datalogFilename is None):
print 'Usage: python', sys.argv[0], '-i <BelLog file> -q <query> [-o <Datalog filename>]'
sys.exit(-1)
fileStr = open(bellogFilename, 'r').read().strip()
polStr = '\n'.join([l for l in fileStr.split('\n') if ':-' in l])
try:
policy = Policy.fromString(escapeCharacters(polStr))
if queryString is not None:
query = Atom.fromElements(Grammar.parseAtom(escapeCharacters(queryString)))
policy.processPolicy()
except Exception as e:
print 'Error parsing the policy:', e
sys.exit(-1)
if queryString is not None:
xsb = XSB()
try:
policy.checkQuery(query)
xsb.loadPolicy(policy)
print 'Query', queryString, ':', xsb.query(query)
xsb.close()
except Exception as e:
print 'Error loading the policy:', e
sys.exit(-1)
xsb.close()
if datalogFilename is not None:
if os.path.isfile(datalogFilename):
msg = 'Override ' + datalogFilename + '?'
shall = True if raw_input("%s (y/N) " % msg).lower() == 'y' else False
if not shall:
sys.exit(-1)
outFile = open(datalogFilename, 'w')
for rule in policy.rules:
for datalogRule in rule.toDatalogRules():
outFile.write(datalogRule + '.\n')
for datalogRule in XSB.STATIC_RULES:
outFile.write(datalogRule + '.\n')
outFile.close()
def close(self):
self._send_client_event(
Atom.get_atom('_NET_CLOSE_WINDOW'),
[
xcb.xproto.Time.CurrentTime,
2,
0,
0,
0
]
)
def doc_to_pos(doc,conf):
"""
Make a pos file, which has pmd format, from a document in MongoDB.
"""
psys= NAPSystem()
matrix=doc['calculations'][-1]['output']['crystal']['lattice']['matrix']
a1= matrix[0]
a2= matrix[1]
a3= matrix[2]
psys.set_lattice(1.0,a1,a2,a3)
species_ids=conf['species_ids']
sites= doc['calculations'][-1]['output']['crystal']['sites']
for site in sites:
ra= site['abc']
ai= Atom()
ai.set_pos(ra[0],ra[1],ra[2])
ai.set_sid(species_ids[site['species'][0]['element']])
psys.add_atom(ai)
return psys
def _set_property(self, atom_name, value):
try:
if isinstance(value, list):
data = struct.pack(len(value) * 'I', *value)
data_len = len(value)
else:
value = str(value)
data_len = len(value)
data = value
connection.get_core().ChangeProperty(
xcb.xproto.PropMode.Replace,
self.wid,
Atom.get_atom(atom_name),
Atom.get_atom_type(atom_name),
Atom.get_atom_length(atom_name),
data_len,
data
)
except:
print traceback.format_exc()
def __init__(self, wsid, x, y, width, height, color=0x000000):
self._root_depth = connection.setup.roots[0].root_depth
self._root_visual = connection.setup.roots[0].root_visual
self._pixel = color
self.wid = connection.conn.generate_id()
connection.get_core().CreateWindow(
self._root_depth,
self.wid,
XROOT.wid,
x,
y,
width,
height,
0,
xcb.xproto.WindowClass.InputOutput,
self._root_visual,
xcb.xproto.CW.BackPixel,
[self._pixel]
)
self._set_property('_NET_WM_NAME', 'Place holder')
self.set_desktop(wsid)
self._set_property('WM_NAME', 'pytyle-internal-window')
self._set_property('WM_PROTOCOLS', [Atom.get_atom('WM_DELETE_WINDOW')])
self._set_property(
'_PYTYLE_TYPE',
[
Atom.get_atom('_PYTYLE_TYPE_PLACE_HOLDER')
]
)
#self.set_override_redirect(True)
connection.get_core().MapWindow(self.wid)
connection.push()
self._moveresize(x, y, width, height)
connection.push()
#self.set_override_redirect(False)
connection.push()
def dipole(parameter):
n = parameter["n"]
parameter["dipole"] = [[0 for i in range(n)] for j in range(n)]
cs = Atom()
for i in range(n):
for j in range(n):
d1 = index2lfm(i)
d2 = index2lfm(j)
if d1[0] == 0 and d2[0] == 1:
coef = {
"q": 0,
"L1": 0,
"L2": 1,
"F1": d1[1],
"F2": d2[1],
"mf1": d1[2],
"mf2": d2[2],
"J1": 1.0 / 2.0,
"J2": 1.0 / 2.0,
"I": 7.0 / 2.0,
}
parameter["dipole"][i][j] = cs.dipole_element(**coef)
elif d2[0] == 0 and d1[0] == 1:
coef = {
"q": 0,
"L1": 0,
"L2": 1,
"F1": d2[1],
"F2": d1[1],
"mf1": d2[2],
"mf2": d1[2],
"J1": 1.0 / 2.0,
"J2": 1.0 / 2.0,
"I": 7.0 / 2.0,
}
parameter["dipole"][i][j] = cs.dipole_element(**coef)
else:
parameter["dipole"][i][j] = 0.0
return parameter
def _moveresize(self, x, y, width, height):
#print self.get_wmname(), x, y, width, height
self._send_client_event(
Atom.get_atom('_NET_MOVERESIZE_WINDOW'),
[
xcb.xproto.Gravity.NorthWest
| 1 << 8 | 1 << 9 | 1 << 10 | 1 << 11 | 1 << 13,
x,
y,
width,
height
],
32,
xcb.xproto.EventMask.StructureNotify
)
connection.push()
def make_residue(key,hydrogens = True):
""" returns a molecule object with
default geometry"""
if not library._aacids.has_key(key):
raise KeyError, "Residue %s not known" % key
m = Molecule()
m.unity = 'A'
m.resname = key
for i, entry in enumerate(library._aacids[key]):
if hydrogens == False and entry[0][0] == 'H':
continue
else:
a = Atom()
a.id = i+1
a.name = entry[0]
a.symbol = a.name[0]
a.x = entry[1]
a.occ = 1.
a.resname = key
a.m = library._atommass[a.symbol]
a.unity = 'A'
m.atoms.append(a)
return m
