def test_typical_omega(self):
size = 1000
trials = 100
threshold = .9
count_typical = 0
for i in range(trials):
poly = Polymer(size)
poly.make_environment()
count_typical += spacevar_typical(poly)
# print count_typical
self.assertTrue(count_typical > threshold*trials)
def test_typical_omega(self):
size = 1000
trials = 100
threshold = .9
count_typical = 0
for i in range(trials):
poly = Polymer(size)
poly.make_environment()
count_typical += spacevar_typical(poly)
# print count_typical
self.assertTrue(count_typical > threshold * trials)
def test_tau(self):
size = 1000
poly = Polymer(size)
poly.make_environment()
poly.compute_actions()
path = poly.compute_path()
end = poly.compute_endpoint()
tau = poly.compute_tau()
self.assertTrue(abs(end) > abs(path[tau - 1]))
def test_action(self):
size = 1000
poly = Polymer(size)
poly.make_environment()
poly.compute_actions()
poly.compute_path()
self.assertEqual(
poly.action_range(1, size) + poly.environment[0][size],
poly.max_action)
def test_action(self):
size = 1000
poly = Polymer(size)
poly.make_environment()
poly.compute_actions()
poly.compute_path()
self.assertEqual(poly.action_range(1, size)+poly.environment[0][size], poly.max_action)
def test_unwrap():
l=10
box = Box([0,0,0],[l,l,l])
P1 = Polymer(N=20,type_bead=1,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[],gconstrain=[box])
for i in range(20):
P1.coords[i][0] = i
if P1.coords[i][0] > l:
P1.coords[i][0] -= l
print P1.coords
P1.unwrap(ref=[0,0,0],box=box)
print P1.coords
assert np.sum(P1.coords[::,0] - np.array(range(20))) < 1e-9
def test_end_discrepancy(self):
size = 1000
exponent = 0.5
constant = 10
poly = Polymer(size)
poly.make_environment()
poly.compute_actions()
path = poly.compute_path()
end = poly.compute_endpoint()
self.assertTrue(
poly.discrepancy(end) < constant * pow(abs(float(end)), -exponent))
def test_endpoint(self):
size = 1000
poly = Polymer(size)
poly.make_environment()
poly.compute_actions()
path = poly.compute_path()
end = poly.compute_endpoint()
self.assertTrue(abs(path[-1] - end) <= 1)
def test_lammps_angle():
Simu = LSimu()
box = Box([0,0,0],[10,10,10])
liaison = {"1-1":[1,1]}
angle_def = {"1-1-1":[20,1]}
P1 = Polymer(N=20,type_bead=1,liaison=liaison,angle_bond=True,angle_def=angle_def,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[],gconstrain=[box])
Simu.add(P1)
Simu.add_box(box)
for idl,value in liaison.iteritems():
R0,idbond = value
idpair1,idpair2=map(int,idl.split("-"))
Simu.add_bond(typeb="harmonic",idbond=idbond,K=80,R0=R0)
Simu.add_pair(typep="lj/cut",idpair1=idpair1,idpair2=idpair2,epsilon=1,sigma=R0,cutoff1=1.15)
for idl,value in angle_def.iteritems():
K,idangle = value
idpair1,idpair2,idpair3=map(int,idl.split("-"))
Simu.add_angle(typea="harmonic",idangle=idangle,K=K,theta=180)
Simu.generate_xyz("test/lp.xyz",Mass="one")
Simu.generate_interactions("test/ainteractions")
Simu.generate_pdb("test/lp.pdb")
Simu.generate_script("test/lp.txt",run_length=10000,samplingrate=10,initconf="test/lp.xyz",
outtraj="test/lp.dcd",outfile="test/lp.xyz",interactions="test/ainteractions",particle="1 2")
Simu.run(script="test/lp.txt")
def test_tau(self):
size = 1000
poly = Polymer(size)
poly.make_environment()
poly.compute_actions()
path = poly.compute_path()
end = poly.compute_endpoint()
tau = poly.compute_tau()
self.assertTrue(abs(end) > abs(path[tau-1]))
def test_end_discrepancy(self):
size = 1000
exponent = 0.5
constant = 10
poly = Polymer(size)
poly.make_environment()
poly.compute_actions()
path = poly.compute_path()
end = poly.compute_endpoint()
self.assertTrue(poly.discrepancy(end) < constant*pow(abs(float(end)), -exponent) )
def test_pinned_path(n):
poly = Polymer(n)
poly.make_environment()
poly.compute_actions()
for i in range(n + 1):
j = random.randint(-i, i)
try:
poly.pinned_path(j, i)
except IndexError:
print "failure at ", j, i
def test_endpoint(self):
size = 1000
poly = Polymer(size)
poly.make_environment()
poly.compute_actions()
path = poly.compute_path()
end = poly.compute_endpoint()
self.assertTrue(abs(path[-1] - end) <= 1)
def test_unwrap():
l = 10
box = Box([0, 0, 0], [l, l, l])
P1 = Polymer(N=20,
type_bead=1,
ptolerance=0,
type_polymer="linear",
start_id=0,
lconstrain=[],
gconstrain=[box])
for i in range(20):
P1.coords[i][0] = i
if P1.coords[i][0] > l:
P1.coords[i][0] -= l
print P1.coords
P1.unwrap(ref=[0, 0, 0], box=box)
print P1.coords
assert np.sum(P1.coords[::, 0] - np.array(range(20))) < 1e-9
def test_pinned_path(n):
poly = Polymer(n)
poly.make_environment()
poly.compute_actions()
for i in range(n+1):
j = random.randint(-i,i)
try:
poly.pinned_path(j, i)
except IndexError:
print "failure at ", j, i
def test_lammps_from_hand_mix():
Simu = LSimu()
box = Box([0,0,0],[10,10,10])
liaison={"1-1":[1,1],"1-2":[1,2],"2-2":[1,3]}
P1 = Polymer(N=20,type_bead=1,liaison=liaison,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[],gconstrain=[box])
P2 = Polymer(N=20,type_bead=2,liaison=liaison,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[],gconstrain=[box])
Simu.add(P1)
Simu.add(P2)
for idl,value in liaison.iteritems():
R0,idbond = value
idpair1,idpair2=map(int,idl.split("-"))
Simu.add_bond(typeb="harmonic",idbond=idbond,K=80,R0=R0)
Simu.add_pair(typep="lj/cut",idpair1=idpair1,idpair2=idpair2,epsilon=1,sigma=R0,cutoff1=1.15)
Simu.add_box(box)
Simu.generate_xyz("test/mix.xyz",Mass="one")
Simu.generate_interactions("test/interactionsm")
Simu.generate_pdb("test/mix.pdb")
Simu.generate_script("test/basic.txt",run_length=1000,samplingrate=10,initconf="test/mix.xyz",
outtraj="test/out.dcd",outfile="test/out.xyz",interactions="test/interactionsm",particle="1 2")
Simu.run(script="test/basic.txt")
def Test(f, name, num):
rules = reg.Rules.get(name)
handlers = reg.Handlers.get(name, [])
ts0 = time.strftime('%H:%M:%S')
numpass = 0
numfail = {
'1': 0,
}
ki = None
try:
for case in Polymer.ModelsChooser(rules, num).Gen():
sentence = ''.join([v[1] for v in case])
ts = time.time()
intent = api.Do(AGENT, USERID, sentence)
if intent.NAME == name:
# TODO: match handlers
#resp = intent.Go()
msg = '{}, {}ms, +pass, {} {}'.format(
time.strftime('%H:%M:%S'),
int((time.time() - ts) * 1000),
name, sentence,
)
numpass += 1
else:
msg = '{}, {}ms, -fail, 1(intent dismatch), {} => {} {}'.format(
time.strftime('%H:%M:%S'),
int((time.time() - ts) * 1000),
name, intent.NAME, sentence,
)
numfail['1'] += 1
f.write(msg+'\n')
print(msg)
except KeyboardInterrupt as e:
ki = e
tfail = 0
for k in numfail:
tfail += numfail[k]
total = numpass+tfail
msg = 'Passed {}, Total {}, {}, {}-{}'.format(
str(round(numpass/total*100, 1))+'%' if total else 'N/A',
total, name,
ts0, time.strftime('%H:%M:%S'),
)
msg = '{}\n{}\n{}'.format(
'---', msg, '---',
)
f.write(msg+'\n')
print(msg)
if ki:
raise ki
return numpass, tfail, numfail
def test_lammps_from_hand():
Simu = LSimu()
box = Box([0,0,0],[10,10,10])
P1 = Polymer(N=20,type_bead=1,ptolerance=0,type_polymer="linear",start_id=0,lconstrain=[],gconstrain=[box])
Simu.add(P1)
Simu.add_box(box)
Simu.add_bond(typeb="harmonic",idbond=1,K=80,R0=1)
Simu.add_pair(typep="lj/cut",idpair1=1,idpair2=1,epsilon=1,sigma=1,cutoff1=1.12)
Simu.generate_xyz("test/mixh.xyz",Mass="one")
Simu.generate_interactions("test/interactionsh")
Simu.generate_pdb("test/mixh.pdb")
Simu.generate_script("test/basich.txt",run_length=1000,samplingrate=10,initconf="test/mixh.xyz",
outtraj="test/out.dcd",outfile="test/out.xyz",interactions="test/interactionsh",particle="1")
Simu.run(script="test/basich.txt")
def read_pdb(self, pdb):
self.clear()
chain_id = '-'
res_num = None
res_insert = ' '
is_last_chain_protein = False
for line in open(pdb, 'r').readlines():
if line.startswith("ATOM"):
atom = AtomFromPdbLine(line)
if not is_last_chain_protein or chain_id != atom.chain_id:
protein = Protein()
protein.id = atom.chain_id
chain_id = protein.id
self.append_chain(protein)
is_last_chain_protein = True
res_num = None
if (res_num != atom.res_num) or (res_insert !=
atom.res_insert):
residue = Residue(atom.res_type, atom.chain_id,
atom.res_num, atom.res_insert)
residue.chain_id = chain_id
protein.append_residue_no_renum(residue)
res_num = atom.res_num
res_insert = atom.res_insert
protein.insert_atom(-1, atom)
if line.startswith("HETATM"):
atom = AtomFromPdbLine(line)
if res_num != atom.res_num or chain_id != atom.chain_id:
mol = Polymer()
residue = Residue(atom.res_type, atom.chain_id,
atom.res_num)
residue.chain_id = atom.chain_id
mol.append_residue_no_renum(residue)
mol.id = atom.chain_id
self.append_chain(mol)
res_num = atom.res_num
chain_id = atom.chain_id
last_chain_is_polymer = False
mol.insert_atom(0, atom)
if line.startswith("TER"):
chain_id = '-'
if line.startswith("ENDMDL"):
break
def create_polymers(self, NP, **kwargs):
"""
create NP polymers
All the option to cleate a polymer are defined in the function
one_polymer in the create module
if a box is specified it will be added in the global constrained of the polymer
"""
if kwargs.has_key("box"):
self.box = kwargs["box"]
kwargs.pop("box")
if kwargs.has_key("gconstrain"):
kwargs["gconstrain"].append(self.box)
else:
kwargs["gconstrain"] = [self.box]
else:
print("must specify a box")
raise
self.molecules = []
for p in range(NP):
self.add(Polymer(**kwargs))
def read_pdb(self, pdb):
self.clear()
chain_id = '-'
res_num = None
res_insert = ' '
is_last_chain_protein = False
for line in open(pdb, 'r').readlines():
if line.startswith("ATOM"):
atom = AtomFromPdbLine(line)
if not is_last_chain_protein or chain_id != atom.chain_id:
protein = Protein()
protein.id = atom.chain_id
chain_id = protein.id
self.append_chain(protein)
is_last_chain_protein = True
res_num = None
if (res_num != atom.res_num) or (res_insert != atom.res_insert):
residue = Residue(atom.res_type, atom.chain_id,
atom.res_num, atom.res_insert)
residue.chain_id = chain_id
protein.append_residue_no_renum(residue)
res_num = atom.res_num
res_insert = atom.res_insert
protein.insert_atom(-1, atom)
if line.startswith("HETATM"):
atom = AtomFromPdbLine(line)
if res_num != atom.res_num or chain_id != atom.chain_id:
mol = Polymer()
residue = Residue(atom.res_type, atom.chain_id, atom.res_num)
residue.chain_id = atom.chain_id
mol.append_residue_no_renum(residue)
mol.id = atom.chain_id
self.append_chain(mol)
res_num = atom.res_num
chain_id = atom.chain_id
last_chain_is_polymer = False
mol.insert_atom(0, atom);
if line.startswith("TER"):
chain_id = '-'
if line.startswith("ENDMDL"):
break
from polymer import Polymer
user_sglq_a = Polymer([
'增加',
'新增',
'新建',
'创建',
'执行',
'处理',
'关注',
'完成',
'标记完成',
'被完成',
])
user_sglq_s = Polymer([
'已经完成',
'已完成',
'未完成',
'待完成',
'没有完成',
'尚未完成',
'还没有完成',
'过期',
'已过期',
'已经过期',
])
user_sglq_w = Polymer([
'刘德华', '张学友',
])
def setUpClass(cls):
buildingBlockTests.itp = Polymer()
from polymer import Polymer
kw_gei = Polymer([
'给', '发给', '送给', '捎给', '给到', '送到',
])
给 = kw_gei
from polymer import Polymer
kw_bei = Polymer([
'被', '需要',
])
被 = kw_bei
# -*- coding: utf-8 -*-
from case.polymer import Polymer
TimeWords = Polymer(
['今天', '明天', '后天'],
Polymer.Range(8, 13),
'点',
)
DriveWords = Polymer(
['开车', '步行', '坐地铁'],
'去',
)
EventWords = Polymer(['吃饭', '上班', '开会'], )
Cases = Polymer(TimeWords, DriveWords.OR(), EventWords)
from polymer import Polymer
from dict.sys_time import sys_time
from dict.sys_period import sys_period
前后 = Polymer([
'前',
'后',
])
几 = Polymer('几', )
日期 = Polymer([
'日',
'天',
'周',
'星期',
'礼拜',
'月',
'年',
])
common = Polymer([
'最近',
'近期',
'最近一段时间',
'近段时间',
'这段时间',
'最近几天',
'这几',
'近几天',
'凌晨',
'早晨',
import reg
from polymer import Polymer
IntentName = 'UPLOAD_FILE2'
# <base>
我想 = Polymer(['我想', '我想要', '我要', '我准备', '我希望'])
上传 = Polymer(['上传', '保存', '添加', '创建', '提交', '上载', '新建', '建', '加', '存'])
文档 = Polymer(['文档', '文件', '文本', '档案'])
一份 = Polymer(['一份', '一个', '一些', '几个', '几份', '几份儿', '一份儿', '个', '份'])
怎么 = Polymer([
'怎么', '怎样', '如何', '该如何', '我应该怎么', '应该怎么', '应该如何', '我该怎么', '我该如何', '我应该如何',
'我如何', '我怎么', '我要怎么', '我要如何'
])
啊 = Polymer(['啊', '呀'])
# </base>
reg.AddRules(
IntentName,
Polymer(我想.OR(), 上传, 一份.OR(), 文档, 啊.OR()),
Polymer(怎么, 上传, 一份.OR(), 文档, 啊.OR()),
)
from polymer import Polymer
kw_inc = Polymer([
'有关于',
'包含有',
'包含',
'包括',
'包涵',
'含有',
'关于',
'有关',
])
包含 = kw_inc
from polymer import Polymer
kw_is = Polymer([
'是',
'就是',
'为',
])
是 = kw_is
def cell(chrlen,chrcen,Ribopos,lp,Radius,mt,liaison,angle_def,angle_bond,special=[]):
"""
chrlen and chrcen are in monomere unit
Ribopos also
lp also
"""
chl = []
chn = []
for l,cen in zip(chrlen,chrcen):
if cen == None:
chl.append(None)
chn.append([None,None,l])
else:
fact = 16
chl.append([np.sqrt(2*fact*lp**2*cen),np.sqrt(2*fact*lp**2*(l-cen))])
chn.append([cen,(l-cen),l])
chl = np.array(chl)
Refs = get_ref_points(snucleus=Radius,smicrotubule=mt,l_len_p=chl)
#print liaison
nucleus = Sphere(position=[0,0,0],radius=Radius)
list_polymer = []
for chromosome,(rep,length,spe) in enumerate(zip(Refs,chn,special)):
#print chromosome,length,chl[chromosome]
#,rep
#print Radius,mt
#print start,middle,end
type_bead = [1 for n in range(length[2])]
for special_beads in spe:
[P,T] = special_beads
type_bead[P] = T
for ch,insert,rlength in Ribopos:
if chromosome == ch-1:
type_bead[insert:insert+rlength] = [3 for _i in range(rlength)]
cm_nuc = insert + int(rlength)/2
if rep != None:
start = Point(index=0,position=rep[0]._v)
middle = Point(index=length[0],position=rep[1]._v)
end = Point(index=length[2],position=rep[2]._v)
lconstrain=[start,middle,end]
else:
lconstrain = []
for ch,insert,rlength in Ribopos:
if chromosome == ch-1:
nucleole = Point(index=cm_nuc,position=(0.66*Radius,0,0))
lconstrain=[start,middle,nucleole,end]
#print liaison
list_polymer.append(Polymer(N=length[2],type_bead=type_bead,liaison=liaison,
angle_bond=angle_bond,
angle_def=angle_def,
ptolerance=0,type_polymer="linear",
lconstrain=lconstrain,gconstrain=[nucleus],
max_trial=300000,rc=1.,virtual_lp=None,
rigid_constrain=False))
return list_polymer
from polymer import Polymer
kw_done = Polymer([
'完成',
'做完',
'执行完',
'做掉',
'完成掉',
'进行',
'执行',
'搞定',
'做',
'开始',
'开始做',
'开始进行',
'必须完成',
'必须做完',
'必须搞定',
'必须做掉',
'必须要完成',
'必须要做完',
'必须要搞定',
'必须要做掉',
'一定要完成',
'一定得完成',
'一定得做完',
])
完成 = kw_done
import reg
from polymer import Polymer
IntentName = 'HELP2'
# <base>
我 = Polymer(['我'])
需要 = Polymer(['需要', '想要', '要'])
我需要 = Polymer(我.OR(), 需要)
一份 = Polymer(['一份', '一个', '份'])
使用 = Polymer(['使用', '操作', '用'])
帮助 = Polymer(['帮助', '说明', '手册', '例句', '操作手册', '操作说明', '帮助文档', '帮助手册', '指导'])
了解 = Polymer(['了解', '知道', '明白', '搞清楚', '弄清楚', '弄明白'])
吧 = Polymer(['吧'])
啊 = Polymer(['啊', '呀'])
给我 = Polymer(['给我', '能给我', '能发我', '发我', '给', '发'])
怎么 = Polymer(['怎么', '怎样', '如何', '该如何', '我应该怎么', '应该怎么', '应该如何', '我该怎么', '我该如何', '我应该如何', '我如何', '我怎么', '我要怎么', '我要如何'])
小助手 = Polymer(['小助手', '机器人', '这', '这东西', '这玩意儿', '这玩意', '这家伙'])
# </base>
reg.AddRules(
IntentName,
Polymer(我需要.OR(), 一份.OR(), 使用.OR(), 帮助, 吧.OR()),
Polymer(我需要.OR(), 了解.OR(), 怎么, 使用, 啊.OR()),
Polymer(小助手, 需要.OR(), 怎么, 使用, 啊.OR()),
Polymer(Polymer(我需要, 了解).OR(), 小助手, 怎么, 使用, 啊.OR()),
def test__path(n):
poly = Polymer(n)
poly.make_environment()
poly.compute_actions()
poly.compute_path()
poly.compute_record_discrepancies()
poly.records
for i in range(n+1):
try:
poly.compute_path(i)
except IndexError:
print "failure at ", i
from polymer import Polymer
kw_gen = Polymer([
'跟',
'对',
'给',
])
跟 = kw_gen
from polymer import Polymer
user_sglq_w = Polymer([
'刘德华',
'张学友',
])
人物 = user_sglq_w
reg.AddRules(
IntentName,
Polymer([
'绑定',
'绑定账号',
'请帮我绑定账号',
'我想要绑定账号',
'绑定一下',
'帮我绑定一下',
'绑定链接',
'有绑定链接吗',
'把绑定链接发我一下',
'怎样绑定',
'怎么绑定',
'怎样绑定账号',
'怎么绑定账号',
'绑定小助手',
'我想绑定小助手',
'我要绑定小助手',
'怎么绑定小助手',
'帮我绑定小助手',
'绑定一下小助手',
'我想要绑定链接',
'绑定账号的链接发我一下',
'绑定链接发我一下',
'怎样绑定呢',
'怎样绑定账号呢',
'怎样才能拿到绑定链接',
]),
)
from polymer import Polymer from dict.user_sglq_asw import * user_db_cr = Polymer(['创建人', '创建者', '创建的人']) 创建er = user_db_cr 二重行为 = 行为 二重状态 = 状态
from polymer import Polymer
ti_event = Polymer([
'去杭州参加云栖大会',
'开会',
'旅游',
'一起去郊游',
'去看电影',
'参加单身排队',
'和刘总讨论节目内容精简的事情',
])
事件 = ti_event
