def __init__(self,
paper,
type="normal",
points=[],
shape=(8, 10, 3),
pin=1,
spline=0,
package=None,
fill="#000"):
meta_enabled.__init__(self, standard=paper.standard)
drawable.__init__(self)
with_line.__init__(self)
line_colored.__init__(self)
self.paper = paper
self.type = type
self.points = []
self.spline = spline
self.paper = paper
self.shape = shape
self.items = []
self.pin = 1
if points:
for p in points:
pnt = point(self.paper, xy=p, arrow=self)
self.points.append(pnt)
self.reaction = reaction()
self.reaction.arrows.append(self)
if package:
self.read_package(package)
def read_text( self, text):
# reaction support
if ">" in text:
if text.count(">") != 2:
raise oasa_exceptions.oasa_smiles_error( "Only two '>' characters are supported in SMILES reactions. %d present" % text.count(">"))
parts = text.split( ">")
res = []
for part in parts:
res.append( self._read_string( part))
if not self.last_status == self.STATUS_OK:
res = []
break
if not res:
self.result = []
return []
else:
react = reaction.reaction()
for p in res[0]:
react.reactants.append( reaction.reaction_component( p))
for p in res[2]:
react.products.append( reaction.reaction_component( p))
for p in res[1]:
react.reagents.append( reaction.reaction_component( p))
self.result = [react]
return self.result
else:
return self._read_string( text)
def __init__( self, paper, type="normal", points=[], shape=(8,10,3), pin=1, spline=0, package=None, fill="#000"):
meta_enabled.__init__( self, standard=paper.standard)
drawable.__init__( self)
with_line.__init__( self)
line_colored.__init__( self)
self.paper = paper
self.type = type
self.points = []
self.spline = spline
self.paper = paper
self.shape = shape
self.items = []
self.pin = 1
if points:
for p in points:
pnt = point( self.paper, xy=p, arrow=self)
self.points.append( pnt)
self.reaction = reaction()
self.reaction.arrows.append( self)
if package:
self.read_package( package)
from reaction import reaction
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import os
import sys
if sys.platform != 'win32':
os.chdir(os.path.dirname(sys.argv[0]))
r = reaction()
# equ. 1
r.add_equation('fs+e->f1f2s+e', 'k0')
r.add_equation('fps+e->f1pf2ps+e', 'k0')
# equ. 2
r.add_equation('f1f2s+i->if2s+f1', 'k1')
r.add_equation('f1pf2ps+i->if2ps+f1p', 'k1')
# equ. 3
r.add_equation('if2s+f->fs+i+f2', 'k2')
r.add_equation('if2ps+f->fs+i+f2p', 'k2')
# reverse reaction of equ. 2
r.add_equation('if2s+f1->f1f2s+i', 'kr')
r.add_equation('if2ps+f1p->f1pf2ps+i', 'kr')
# additional equ.
r.add_equation('f1p+if2s->f1pf2s+i', 'kr')
r.add_equation('f1+if2ps->f1f2ps+i', 'kr')
# the forward reaction of additional equ.
#r.add_equation('f1pf2s+i->f1p+if2s', 'k1')
def test_reaction_parameters1():
try:
reaction.reaction([10],[1,2,1],[[1,2,0],[0,0,2]],[[0,0,1],[1,2,0]])
except ValueError as err:
assert(type(err) == ValueError)
def test_reaction_result():
assert reaction.reaction([10,10],[1,2,1],[[1,2,0],[0,0,2]],[[0,0,1],[1,2,0]]) == [-30, -60, 20]