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Remove useless space.
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@njzjz
njzjz committed Jul 20, 2018
1 parent e4b9927 commit 6c24611
Showing 1 changed file with 41 additions and 41 deletions.
82 changes: 41 additions & 41 deletions ReacNetGenerator/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,11 +123,11 @@ def run(self):
else:
print("networkx is not installed. Try \"pip install networkx\".")
raise InstallError("networkx")

if self.runHMM and not hmmlearn_installed:
self.runHMM=False
print("Since you have not installed hmmlearn, HMM cannot be used to filter noise.")

######start#####
print("======Run HMM calculation:======")
timearray=self.printtime([])
Expand Down Expand Up @@ -172,7 +172,7 @@ def draw(self):

#make color
colorsRGB=[(self.start_color+i*(self.end_color-self.start_color) / self.n_color) for i in np.arange(self.n_color)]

G = nx.DiGraph()
for i in range(len(table)):
if name[i] in species and not name[i] in self.filter:
Expand All @@ -190,20 +190,20 @@ def draw(self):
print("The position of the species in the network is:")
print(pos)
print()

for with_labels in ([True] if not self.nolabel else [True,False]):
nx.draw(G,pos = pos,width=widths,node_size=self.node_size,font_size=self.font_size,with_labels=with_labels,edge_color=colors,node_color=self.node_color)

plt.savefig(self.imagefilename if with_labels else "nolabel_"+self.imagefilename)

if self.show:
plt.show()

plt.close()

except Exception as e:
print("Error: cannot draw images. Details:",e)

timearray=self.printtime(timearray)
####### end #######
print()
Expand All @@ -221,15 +221,15 @@ def step1(self):
readstepfunc=self.readlammpsbondstep
elif self.inputfiletype=="lammpscrdfile" or self.inputfiletype=="lammpsdumpfile":
readNfunc=self.readlammpscrdN
readstepfunc=self.readlammpscrdstep
readstepfunc=self.readlammpscrdstep
self.readinputfile(readNfunc,readstepfunc)

def step2(self):
if self.runHMM:
self.initHMM()
self.calhmm()

def step3(self):
def step3(self):
if self.SMILES:
self.printmoleculeSMILESname()
else:
Expand All @@ -241,22 +241,22 @@ def step3(self):
def step4(self,allmoleculeroute):
allroute=self.getallroute(allmoleculeroute)
self.printtable(allroute)

####### functions #######
def printtime(self,timearray):
timearray.append(time.time())
if len(timearray)>1:
print("Step ",len(timearray)-1," has been completed. Time consumed: ",round(timearray[-1]-timearray[-2],3),"s")
return timearray

def union_dict(self,x,y):
def union_dict(self,x,y):
for k, v in y.items():
if k in x.keys():
x[k] += v
else:
x[k] = v
return x

def mo(self,i,bond,level,molecule,done,bondlist): #connect molecule
molecule.append(i)
done[i]=True
Expand All @@ -273,7 +273,7 @@ def mo(self,i,bond,level,molecule,done,bondlist): #connect molecule
def readinputfile(self,readNfunc,readstepfunc):
steplinenum=readNfunc()
self.getdandtimestep(readstepfunc,steplinenum)

def readlammpsbondN(self):
with open(self.inputfilename) as file:
iscompleted=False
Expand All @@ -290,7 +290,7 @@ def readlammpsbondN(self):
atomtype=np.zeros(N+1,dtype=np.int)
else:
s=line.split()
atomtype[int(s[0])]=int(s[1])
atomtype[int(s[0])]=int(s[1])
steplinenum=stepbindex-stepaindex
self.N=N
self.atomtype=atomtype
Expand All @@ -304,15 +304,15 @@ def readlammpsbondstep(self,item):
if line:
if line.startswith("#"):
if line.startswith("# Timestep"):
timestep=step,[int(s) for s in line.split() if s.isdigit()][0]
else:
timestep=step,[int(s) for s in line.split() if s.isdigit()][0]
else:
s=line.split()
for i in range(int(s[2])):
bond[int(s[0])].append(int(s[i+3]))
bondlevel=round(float(s[i+4+int(s[2])]))
if bondlevel==0:
bondlevel=1
level[int(s[0])].append(bondlevel)
level[int(s[0])].append(bondlevel)
d=self.connectmolecule({},step,bond,level)
return d,timestep

Expand Down Expand Up @@ -374,7 +374,7 @@ def readlammpscrdstep(self,item):
return d,timestep

def getdandtimestep(self,readfunc,steplinenum):
d={}
d={}
timestep={}
with open(self.inputfilename) as file,Pool(maxtasksperchild=100) as pool:
semaphore = Semaphore(360)
Expand All @@ -386,8 +386,8 @@ def getdandtimestep(self,readfunc,steplinenum):
semaphore.release()
self.writemoleculetempfile(d)
self.timestep=timestep
self.step=len(timestep)-1
self.step=len(timestep)-1

def connectmolecule(self,d,step,bond,level):
#init
done=np.zeros(self.N+1,dtype=bool)
Expand All @@ -402,14 +402,14 @@ def connectmolecule(self,d,step,bond,level):
else:
d[(tuple(mole),tuple(bondlist))]=[step]
return d

def writemoleculetempfile(self,d):
with open(self.moleculetempfilename,'w') as f:
for item in d.items():
key,value=item
print(",".join([str(x) for x in key[0]]),";".join([",".join([str(y) for y in x]) for x in key[1]]),",".join([str(x) for x in value]),file=f)
def getbondfromcrd(self,atomtype,atomcrd,step,filename="crd"):

def getbondfromcrd(self,atomtype,atomcrd,step,filename="crd"):
xyzfilename=filename+"_"+str(step)+".xyz"
mol2filename=filename+"_"+str(step)+".mol2"
self.convertxyz(atomtype,atomcrd,xyzfilename)
Expand All @@ -421,7 +421,7 @@ def convertxyz(self,atomtype,atomcrd,xyzfilename):
with open(xyzfilename,'w') as f:
print(len(atomcrd),file=f)
print("by ReacNetGenerator",file=f)
for type,(x,y,z) in zip(atomtype,atomcrd):
for type,(x,y,z) in zip(atomtype,atomcrd):
print(self.atomname[type-1],x,y,z,file=f)

def getbondfrommol2(self,atomnumber,mol2filename):
Expand All @@ -447,7 +447,7 @@ def initHMM(self):
self.model.startprob_= self.p
self.model.transmat_= self.a
self.model.emissionprob_= self.b

def produce(self,semaphore, list,parameter):
for item in list:
# Reduce Semaphore by 1 or wait if 0
Expand Down Expand Up @@ -514,7 +514,7 @@ def printatomroute(self,atomeach):
for mroute in moleculeroute:
if not mroute in allmoleculeroute:
allmoleculeroute.append(mroute)
semaphore.release()
semaphore.release()
return allmoleculeroute

def makemoleculegraph(self,atoms,bonds):
Expand Down Expand Up @@ -558,7 +558,7 @@ def printmoleculename(self):
typenumber[self.atomtype[atomnumber]-1]+=1
atomtypes.append((atomnumber,self.atomtype[atomnumber]))
G=self.makemoleculegraph(atomtypes,bonds)
name="".join([self.atomname[i]+(str(typenumber[i] if typenumber[i]>1 else "")) if typenumber[i]>0 else "" for i in range(0,len(self.atomname))])
name="".join([self.atomname[i]+(str(typenumber[i] if typenumber[i]>1 else "")) if typenumber[i]>0 else "" for i in range(0,len(self.atomname))])
if name in d:
for j in range(len(d[name])):
if nx.is_isomorphic(G,d[name][j],em):
Expand Down Expand Up @@ -586,7 +586,7 @@ def calmoleculeSMILESname(self,item):
type[atomnumber]=self.atomname[self.atomtype[atomnumber]-1]
name=self.convertSMILES(atoms,bonds,type)
return name,atoms,bonds

def printmoleculeSMILESname(self):
mname=[]
with open(self.moleculefilename, 'w') as fm,open(self.moleculetemp2filename) as ft,Pool(maxtasksperchild=100) as pool:
Expand All @@ -598,7 +598,7 @@ def printmoleculeSMILESname(self):
print(name,",".join([str(x) for x in atoms]),";".join([",".join([str(y) for y in x]) for x in bonds]),file=fm)
semaphore.release()
self.mname=mname

def convertSMILES(self,atoms,bonds,type):
m = Chem.RWMol(Chem.MolFromSmiles(''))
d={}
Expand All @@ -609,7 +609,7 @@ def convertSMILES(self,atoms,bonds,type):
m.AddBond(d[atom1],d[atom2], Chem.BondType.DOUBLE if level==2 else (Chem.BondType.TRIPLE if level==3 else (Chem.BondType.AROMATIC if level==12 else Chem.BondType.SINGLE)))
name=Chem.MolToSmiles(m)
return name

def getatomeach(self):
atomeach=np.zeros((self.N+1,self.step),dtype=np.int)
with open(self.hmmfilename) as fh,open(self.moleculetemp2filename) as ft:
Expand All @@ -635,7 +635,7 @@ def getallroute(self,allmoleculeroute):
if equation in allroute:
allroute[equation]+=1
else:
allroute[equation]=1
allroute[equation]=1
return allroute

def printtable(self,allroute):
Expand All @@ -648,7 +648,7 @@ def printtable(self,allroute):
reaction=k.split("->")
for i,spec in enumerate(reaction):
if spec in species:
number=species.index(spec)
number=species.index(spec)
elif len(species)<100:
species.append(spec)
number=species.index(spec)
Expand All @@ -673,15 +673,15 @@ def readtable(self):
name.append(line.split()[0])
table.append([int(s) for s in line.split()[1:]])
return table,name

def convertstructure(self,atoms,bonds):
types={}
atomtypes=[]
for atom in enumerate(atoms,start=1):
atomtypes.append((i,self.atomname.index(atom)))
G=self.makemoleculegraph(atomtypes,bonds)
return G

def handlespecies(self,name):
showname={}
n=0
Expand Down Expand Up @@ -718,10 +718,10 @@ def handlespecies(self,name):
showname[specname]=str(n)
print(n,specname)
return species_out,showname

def __enter__(self):return self
def __exit__(self,Type, value, traceback):pass

class InstallError(Exception):
def __init__(self,ErrorInfo):
super().__init__(self)
Expand All @@ -730,10 +730,10 @@ def __str__(self):
return self.errorinfo+" is not installed."

class Placeholder(object):
def __init__(self):pass
def __init__(self):pass
def __enter__(self):return self
def __exit__(self,Type, value, traceback):pass

##### main #####
if __name__ == '__main__':
ReacNetGenerator().runanddraw()
ReacNetGenerator().runanddraw()

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