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 read_molecule(r):
""" (reader) -> Molecule
Read a single molecule from r and return it,
or return None to signal end of file.
"""
# If there isn't 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 read_moleculer(r: TextIO) -> Molecule:
""" Read a single molecule from r and return it,
or return None to signal end of file.
"""
#If there isn't 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()
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(int(num), kind, float(x), float(y), float(z)))
return molecule
def read_molecule(r: TextIO) -> Molecule:
"""r로부터 분자 하나를 읽어 반환하거나 파일 끝에 도달하면 None을 반환한다.
"""
# 더 이상 줄이 없으면 파일 끝에 도달한 것이다.
line = r.readline()
if not line:
return None
# 분자명: "COMPND name"
key, name = line.split()
# 그 밖에 줄은 "END" 또는 "ATOM num kind x y z"이다.
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(int(num), kind, float(x), float(y), float(z)))
return molecule
class Particle(types.KX_GameObject):
def __init__(self, obj):
self.damping = 20
if self.name == "Lone Pair":
self.repulsionfactor = 1.25
self.lengthfactor = 10
else:
self.repulsionfactor = 1
self.lengthfactor = 20
self.maxdistance = 100
self.distancefactor = 100
self.strengthfactor = 100
self.totalforce = Vector([0, 0, 0])
##from bond.py
self.bond = Bond(self)
self.molecule = None
if "doubles" in self:
self.charge = self.get_charge()
self.formalCharge = self.get_formal_charge()
########linking and unlinking
def self_destruct(self):
self.state = 2
def get_charge(self):
return 4 - (len(self["bonds"]) + 2 * len(self["doubles"]) +
3 * bool(self["triple"]))
def get_formal_charge(self):
lonepairs = [bond.name for bond in self["bonds"]].count("Lone Pair")
return valence[self.name] - (len(self["bonds"]) +
2 * len(self["doubles"]) +
3 * bool(self["triple"])) - lonepairs
def add_glow(self, type=1):
if type == 1:
type = "Glow"
else:
type = "Glow2"
self["glow"] = self.scene.addObject(type, self)
self["glow"].setParent(self)
def remove_glow(self):
self["glow"].endObject()
del self["glow"]
#links
def unlink(self, other):
if other in self["bonds"]:
self.remove_bond(other, "bonds")
elif "doubles" in self:
if other in self["doubles"]:
self.remove_bond(other, "doubles")
elif other is self["triple"]:
self.remove_bond(other, "triple")
self.molecule.split(self, other)
def link(self, other):
self.add_bond(other, "bonds")
self.form_molecule(other)
#molecules
def form_molecule(self, other):
if self.molecule:
if other.molecule:
if other.molecule != self.molecule:
self.molecule.merge(other.molecule)
return
self.molecule.add(other)
elif other.molecule:
other.molecule.add(self)
else:
self.molecule = Molecule(self)
self.molecule.add(other)
#more linking
def remove_bond(self, other, type):
if type is not "triple":
self[type].discard(other)
other[type].discard(self)
else:
self[type] = None
other[type] = None
def add_bond(self, other, type):
if type is not "triple":
self[type].add(other)
other[type].add(self)
else:
self[type] = other
other[type] = self
def get_bonds(self):
bonds = self["bonds"].copy()
if "doubles" in self:
bonds.update(self["doubles"])
if self["triple"]:
bonds.add(self["triple"])
return bonds
####bond forces
def reset(self):
self.totalforce.zero()
def get_repulsion(self, other):
#repel force
if other.name == "Lone Pair":
repulsion = other.repulsionfactor
else:
repulsion = self.repulsionfactor
distance, uvector, lvector = self.getVectTo(other)
distance /= self.distancefactor
return uvector * repulsion / pow(distance, 2)
def spring_force(self, other):
#spring with damping
if other.name == "Lone Pair":
length = other.lengthfactor
else:
length = self.lengthfactor
distance, uvector, lvector = self.getVectTo(other)
velocity = self.getLinearVelocity().project(uvector)
return uvector * (
distance - length) * self.strengthfactor - velocity * self.damping
def repel_p_bond(self, other):
distance, uvector, lvector = self.getVectTo(other)
if not other.bond.inverted:
pbond = other.getAxisVect((0, 1, 0))
else:
pbond = other.getAxisVect((1, 0, 0))
vector = distance * uvector
projection = vector.project(pbond)
return projection
def repel_p_bond2(self, other):
distance, uvector, lvector = self.getVectTo(other)
pbond = other.getAxisVect((0, 0, 1))
vector = distance * uvector
projection = vector.project(pbond)
return vector - projection
####formation
def find_atoms(self, type):
for other in gdict["free"][type]:
if other is self:
continue
elif other in self.get_bonds():
##see if you can double or triple bond
if self.multiply_bonds(other):
return True
continue
distance = self.getDistanceTo(other)
if distance < self.maxdistance:
self.link(other)
if self.get_charge() == 0:
return True
def form_bonds(self):
for type in ["Hydrogen", "Carbon", "Oxygen", "Bromine"]:
if self.find_atoms(type):
return
def multiply_bonds(self, other):
if self["triple"]:
return
try:
min_charge = min(other.get_charge(), self.get_charge())
except KeyError:
return
if min_charge == 1:
##single to double
if other in self["bonds"]:
self.remove_bond(other, "bonds")
self.add_bond(other, "doubles")
#double to triple
elif other in self["doubles"]:
self.remove_bond(other, "doubles")
self.add_bond(other, "triple")
#single to triple
elif min_charge > 1 and other in self["bonds"]:
self.remove_bond(other, "bonds")
self.add_bond(other, "triple")
self.molecule.refresh()
if self.get_charge() == 0:
return True #charge gone
"""
# If there isn't another line, we're at the end of the file.
line = r.readlne()
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
ammonia = Molecule("AMMONIA")
ammonia.add(Atom(1, "N", 0.257, -0.363, 0.0))
ammonia.add(Atom(2, "H", 0.257, 0.727, 0.0))
ammonia.add(Atom(3, "H", 0.771, -0.727, 0.890))
ammonia.add(Atom(4, "H", 0.771, -0.727, -0.890))
ammonia.translate(0, 0, 0.2)