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Draw_Energy_Diagram_XML.py
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Draw_Energy_Diagram_XML.py
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# -*- coding: utf-8 -*-
__author__ = 'LiYuanhe'
# 自动防止重叠（改成非贪心）
# Num tag 在同一行时Tag的加粗
# 支持MECP画点
# 支持纵轴切掉一部分
from Python_Lib.My_Lib_PyQt import *
import sys
import os
import math
import copy
import shutil
import re
import time
import subprocess
from openpyxl import load_workbook
import random
from datetime import datetime
import ctypes
number_font_size = 17
tag_font_size = 17
matplotlib.rcParams.update({'font.family': 'Times New Roman'})
temp_folder = os.path.join(filename_class(sys.argv[0]).path,'TEMP')
if not os.path.isdir(temp_folder):
os.mkdir(temp_folder)
# possible_ChemDraw_program_locations =\
# [r"C:\Program Files (x86)\PerkinElmerInformatics\ChemOffice2017\ChemDraw\ChemDraw.exe",
# r"C:\Program Files (x86)\PerkinElmerInformatics\ChemOffice2016\ChemDraw\ChemDraw.exe",
# r"C:\Program Files (x86)\CambridgeSoft\ChemOffice2015\ChemDraw\ChemDraw.exe",
# r"C:\Program Files (x86)\CambridgeSoft\ChemOffice2014\ChemDraw\ChemDraw.exe",
# r"C:\Program Files (x86)\CambridgeSoft\ChemOffice2013\ChemDraw\ChemDraw.exe"]
if __name__ == '__main__':
pyqt_ui_compile('Draw_Energy_Diagram_UI_XML.py')
from UI.Draw_Energy_Diagram_UI_XML import Ui_Draw_Energy_Diagram_Form
if os.name == 'nt':
APPID = 'LYH.DrawEnergyDiagram.3.4'
ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(APPID)
Application = Qt.QApplication(sys.argv)
Application.setWindowIcon(Qt.QIcon('UI/Draw_Energy_Diagram_Icon.png'))
# doc header
default_document = '''<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
<CDXML
CreationProgram="ChemDraw 17.0.0.206"
Name="temp.cdxml"
BoundingBox="226.92 96.70 607.08 337.20"
WindowPosition="0 0"
WindowSize="-2147483648 -2147483648"
WindowIsZoomed="yes"
LabelFont="3"
LabelSize="10"
LabelFace="96"
CaptionFont="4"
CaptionSize="10"
HashSpacing="2.49"
MarginWidth="1.59"
LineWidth="0.60"
BoldWidth="2.01"
BondLength="14.40"
BondSpacing="18"
PrintMargins="99.21 70.87 99.21 70.87"
color="0"
bgcolor="1"
>'''
# font table, id is in the ChemDraw program, cannot be changed, ignore the change font function
default_fonts = '''<fonttable>
<font id="3" charset="iso-8859-1" name="Arial"/>
<font id="4" charset="iso-8859-1" name="Times New Roman"/>'''
default_fonts_end = '''</fonttable>'''
fonts_template = '''<font id="[Font_ID]" charset="[Font_CharSet]" name="[Font_Name]"/>'''
# color table, r.g.b with a maximum of one
colors_list = '''<colortable>
<color r="1" g="1" b="1"/>
<color r="0" g="0" b="0"/>
<color r="1" g="0" b="0"/>
<color r="1" g="1" b="0"/>
<color r="0" g="1" b="0"/>
<color r="0" g="1" b="1"/>
<color r="0" g="0" b="1"/>
<color r="1" g="0" b="1"/>'''.splitlines()
default_colors_end = '''</colortable>'''
# 似乎它的index是从colortable从2开始数的
colors_translate = {'b': 8, 'g': 6, 'r': 4, 'c': 7, 'm': 9, 'y': 5, 'k': 3, 'w': 2}
# add a color, return the proper color index. If the color doesn't exist in the color table, add it, then return the index
def add_color(r, g=None, b=None):
'''
:param colors_list:
:param color_translate:
:param r: in 0~1 float
:param g:
:param b:
:return: a index, pointing to the newly built color
'''
global colors_translate
global colors_list
if r.replace('TAG',"") in colors_translate:
if g!=None and b!=None:
alert_UI("Add_color function error. Report bug.",'Add_color function error')
return colors_translate[r]
if r.startswith('#'):
# in the format of #DDEEFF
if g != None and b != None:
alert_UI("Add_color function error. Report bug.", 'Add_color function error')
r=r.replace('#','0x')
#XXXXXX --> (0.XX, 0.XX, 0.XX)
b=(eval(r)%0x100)/0x100
g=(int(eval(r)/0x100)%0x100)/0x100
r=(int(eval(r)/0x10000))/0x100
if (r,g,b) in colors_translate:
return colors_translate[(r,g,b)]
color_template = '''<color r="[R_Value]" g="[G_Value]" b="[B_Value]"/>''' # in 0~1 float
insert_line = color_template.replace("[R_Value]", str(r)).replace("[G_Value]", str(g)).replace("[B_Value]", str(b))
colors_list.append(insert_line)
colors_translate[(r, g, b)] = len(colors_list)
return len(colors_list)
default_document_end = '''</CDXML>'''
# doesn't matter, 3*3 page is large enough
page_template = '''<page
id="[ID]"
BoundingBox="0 0 [Page_Height_Pixel] [Page_Width_Pixel]"
HeaderPosition="36"
FooterPosition="36"
PrintTrimMarks="yes"
HeightPages="[Page_Height_Page_Count]"
WidthPages="[Page_Width_Page_Count]"
>'''
def add_page(page_height_count,page_width_count):
height = 1930.48/3*page_height_count
width = 1360.76/3*page_width_count
return page_template.replace("[Page_Height_Pixel]",str(height))\
.replace("[Page_Width_Pixel]",str(width))\
.replace("[Page_Height_Page_Count]",str(page_height_count))\
.replace('[ID]', str(random.randint(1000000, 2000000))) \
.replace("[Page_Width_Page_Count]",str(page_width_count))
page_template_end = '''</page>'''
# add fragment only to bond connections, do not add it to graphic and texts
fragment_template = '''<fragment
id="45600"
BoundingBox="0 0 0 0"
Z="28"
>'''
# add a group, with integral-yes, then the user cannot move each elements before de-frooze it
group_template = '''<group
id="453612182"
BoundingBox="156.80 154.98 531.20 261.66"
Z="[Z]"
Integral="yes"
>'''
# the Z determines which element will cover which one, and which bond is broken if overlapped
def add_group(Z):
group_template = '''<group
id="453612182"
BoundingBox="156.80 154.98 531.20 261.66"
Z="[Z]"
Integral="yes"
>'''
return group_template.replace('[Z]',str(Z))
group_template_end = "</group>"
# add an atom, then a bond can be made between atoms
def add_node(id, X, Y, Z):
node_template = '''<n
id="[ID]"
p="[X] [Y]"
Z="[Z]"
AS="N"
/>'''
return node_template.replace('[ID]', str(id)).replace('[X]', str(X)).replace('[Y]', str(Y)).replace('[Z]', str(Z))
# add a bold, horizonal bond between two atoms,
def add_state_Bond(color_index, begin_index, Z, end_index=None):
state_line_template = '''<b
id="[ID]"
Z="[Z]"
color="[Color_index]"
B="[Begin_index]"
E="[End_index]"
Display="Bold"
BS="N"
/>'''
bond_id = str(random.randint(2000000,3000000))
if end_index == None:
end_index = begin_index + 1
return state_line_template.replace('[Color_index]', str(color_index)) \
.replace('[Begin_index]', str(begin_index)) \
.replace('[ID]', str(bond_id)) \
.replace('[End_index]', str(end_index)) \
.replace('[Z]', str(Z))
# add a dashed bond between two bonded states
def add_dash_link_Bond(color_index, begin_index, Z, end_index=None):
link_line_dash_template = '''<b
id="[ID]"
Z="[Z]"
color="[Color_index]"
B="[Begin_index]"
E="[End_index]"
Display="Dash"
BS="N"
/>'''
if end_index == None:
end_index = begin_index + 1
return link_line_dash_template.replace('[Color_index]', str(color_index)) \
.replace('[Begin_index]', str(begin_index)) \
.replace('[ID]', str(random.randint(3000000, 4000000))) \
.replace('[End_index]', str(end_index)) \
.replace('[Z]', str(Z))
# add a solid bond between two bonded states
def add_solid_link_Bond(color_index, begin_index, Z, end_index=None):
link_line_single_template = '''<b
id="[ID]"
Z="[Z]"
color="[Color_index]"
B="[Begin_index]"
E="[End_index]"
BS="N"
/>'''
if end_index == None:
end_index = begin_index + 1
return link_line_single_template.replace('[Color_index]', str(color_index)) \
.replace('[Begin_index]', str(begin_index)) \
.replace('[End_index]', str(end_index)) \
.replace('[ID]', str(random.randint(4000000, 5000000))) \
.replace('[Z]', str(Z))
def add_text(text, X, Y, Z, font_index, size, color_index, face_index,vertical=False,right_align=False):
'''
add text, at x, y, Z
:param text:
:param X:
:param Y:
:param Z:
:param font_index:
:param size:
:param color_index:
:param face_index:
:param vertical: for Y axis label
:param right_align: for Y axis number
:return:
'''
if text == None:
return ""
text = str(text)
if text.strip()=="":
return ""
#似乎当text只有一个字母的时候总是向右偏一点
if len(text)==1:
X-=3
faces = {'Bold': 1, "Normal": 0}
if face_index in faces:
face_index = faces[face_index]
text_template = '''<t
id="[ID]"
p="[X] [Y]"
BoundingBox="0 0 110 110"
Z="[Z]"
CaptionJustification="Center"
Justification="Center"
[vertical]
LineHeight="auto"
><s font="[Font_index]" size="[Size]" color="[Color_index]" face="[Face_index]">[Text]</s></t>'''
if vertical:
text_template = text_template.replace('[vertical]','RotationAngle="17694720"')
else:
text_template = text_template.replace('[vertical]\n','')
if right_align:
text_template = text_template.replace('"Center"\n','"Right"\n')
return text_template.replace('[X]', str(X)) \
.replace('[Y]', str(Y)) \
.replace('[Z]', str(Z)) \
.replace('[Font_index]', str(font_index)) \
.replace('[Size]', str(size)) \
.replace('[ID]', str(random.randint(5000000, 6000000))) \
.replace('[Color_index]', str(color_index)) \
.replace('[Face_index]', str(face_index)) \
.replace('[Text]', text)
# add an ancher point, also serve as a water mark
def test(start_x, start_y, Z=0):
# a water mark pointing right up
x2 = start_x
x1=x2+1.2
y2 = start_y
y1=y2-1.2
# x2,x1 = x1,x2
# y2,y1 = y1,y2
template = '''<graphic
id="453611"
BoundingBox="[x1] [y1] [x2] [y2]"
Z="[Z]"
GraphicType="Orbital"
OrbitalType="lobeFilled"
/>'''
return template.replace('[x1]',str(x1))\
.replace('[x2]',str(x2))\
.replace('[y1]',str(y1))\
.replace('[y2]',str(y2))\
.replace('[Z]',str(Z))
# add graphic line of states (bold), and dashed/non-dashed links
def add_graphic_line(x1,x2,y1,y2,Z,color_index=3,dash=False,bold=False,width=0.6):
arrow_id = str(random.randint(6000000,7000000))
# these two elements must exist in order to be able to freeze it using Integral group
graphic_line_template='''<graphic
id="'''+str(random.randint(7000000,8000000))+'''"
SupersededBy="'''+arrow_id+'''"
BoundingBox="481.66 244.50 306 244.50"
Z="[Z]"
[Line_type]
GraphicType="Line"
/>
<arrow
id="'''+arrow_id+'''"
BoundingBox="226 296.43 423 297.56"
Z="[Z]"
FillType="None"
ArrowheadType="Solid"
color="[Color_Index]"
Head3D="[x2] [y2] 0"
LineWidth="[Width]"
Tail3D="[x1] [y1] 0"
Center3D="538.50 445.75 0"
MajorAxisEnd3D="735.50 445.75 0"
MinorAxisEnd3D="538.50 642.75 0"
[Line_type]
/>'''
if bold==False and dash==False:
graphic_line_template = graphic_line_template.replace(' [Line_type]\n',"")
elif bold:
graphic_line_template = graphic_line_template.replace('[Line_type]', 'LineType="Bold"')
elif dash:
graphic_line_template = graphic_line_template.replace('[Line_type]', 'LineType="Dashed"')
return graphic_line_template.replace('[x2]',str(x2))\
.replace('[x1]',str(x1))\
.replace('[y1]',str(y1))\
.replace('[y2]',str(y2))\
.replace('[Z]',str(Z))\
.replace('[Color_Index]',str(color_index))\
.replace('[Width]',str(width))\
fragment_template_end = '''</fragment>'''
class State_Line:
def __init__(self, state, x_center, span=0.6, style='-', color='k', width=4):
# print(state)
# if color==None:
# color = 'k'
self.tag = state[0]
self.energy = state[1]
self.x_center = x_center
self.span = span
self.width = width
self.style = style
self.color = color
self.x_start = self.x_center - self.span / 2
self.x_end = self.x_center + self.span / 2
self.x = (self.x_start, self.x_end)
self.y = (self.energy, self.energy)
self.annotate = True # annotate(energy label) required
def __hash__(self):
return hash((self.x, self.y, self.span, self.style, self.width))
def __eq__(self, other):
return hash(self) == hash(other)
class Connecting_Line:
def __init__(self, state_line1: State_Line, state_line2: State_Line, style='-', color='k', width=1):
if state_line1.x_center > state_line2.x_center: # swap 1 & 2 if reversed order
state_line1, state_line2 = state_line2, state_line1
# if color==None:
# color = 'k'
self.state_line1 = state_line1
self.state_line2 = state_line2
# the connecting line will intrude the state line due to line width
self.x_start = self.state_line1.x_end + 0.02
self.x_end = self.state_line2.x_start - 0.01
self.y_start = self.state_line1.energy
self.y_end = self.state_line2.energy
self.x = (self.x_start, self.x_end)
self.y = (self.y_start, self.y_end)
self.style = style
self.color = color
self.width = width
self.annotate = False # not annotate required
def __hash__(self):
return hash((self.x_start, self.x_end, self.y_start, self.y_end, self.style, self.width))
def __eq__(self, other):
return hash(self) == hash(other)
class Collision_Box:
def __init__(self, xcenter=None, xlength=None, xleft=None, xright=None,
ycenter=None, yheight=None, ybottom=None, ytop=None):
self.xleft = xleft
self.xright = xright
self.ybottom = ybottom
self.ytop = ytop
if xcenter != None and xlength != None:
self.xleft = xcenter - xlength / 2
self.xright = xcenter + xlength / 2
if ycenter != None and yheight != None:
self.ybottom = ycenter - yheight / 2
self.ytop = ycenter + yheight / 2
if ybottom != None and yheight != None:
self.ybottom = ybottom
self.ytop = ybottom + yheight
def collide(self, other):
if other.xleft > self.xright:
return False
if other.xright < self.xleft:
return False
if other.ytop < self.ybottom:
return False
if other.ybottom > self.ytop:
return False
return True
class MpWidget_Energy_Diagram(Qt.QWidget):
def __init__(self, parent=None, y=[]):
super(MpWidget_Energy_Diagram, self).__init__()
self.setParent(parent)
self.dpi = 24
self.fig = MpPyplot.figure(figsize=(2, 2), dpi=self.dpi, )
self.diagram_subplot = MpPyplot.subplot(1, 1, 1)
self.fig.subplots_adjust(wspace=0.12, left=0.04, right=0.98)
self.canvas = MpFigureCanvas(self.fig)
self.canvas.setParent(self)
self.diagram_subplot.clear()
self.diagram_subplot.plot(range(len(y)), y, 'r')
self.canvas.draw()
self.mpl_toolbar = MpNavToolBar(self.canvas, self)
self.mpl_toolbar.setIconSize(Qt.QSize(18, 18))
self.mpl_toolbar.layout().setSpacing(6)
self.hLayout = Qt.QHBoxLayout()
self.hLayout.addWidget(self.mpl_toolbar)
self.vLayout = Qt.QVBoxLayout()
self.vLayout.addWidget(self.canvas)
self.vLayout.addLayout(self.hLayout)
self.vLayout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.vLayout)
self.diagram_data = []
self.fluctuation_warned = False
self.diagram_limit = (-1, 0)
self.occupied_spaces = [] # list of previous collision boxes
self.initiate()
self.printed_states=[]
def diagram_Update(self, diagram_states, x_span, y_span, state_line_span, color='k', num_with_tag=False):
'''
:param diagram_states: the Energy contains Tag and Energy like: [('S', 0), ('TS1', 183), ('IM1', 75), ('P', 24)]
:param style: set style of line, default None, meaning 'k'
:return:
'''
# if color==None:
# color = 'k'
if 'TAG' in color:
return None
if diagram_states not in self.printed_states:
print(diagram_states)
self.printed_states.append(diagram_states)
self.x_span = x_span
self.y_span = y_span
self.collision_boxes = []
self.annotate_objects = []
self.xs_for_adjust_text = []
self.ys_for_adjust_text = []
# verify data
invalid_data = [x[1] for x in diagram_states if not (isinstance(x[1], float) or isinstance(x[1], int) or x[1] == None)]
if invalid_data:
Qt.QMessageBox.critical(self, 'Invalid Data Found.', 'Invalid Data Found:\n' + str(invalid_data) + '\n'
'Only numbers was allowed in the data section.\n'
'Remove formula by Ctrl+Alt+V if used.\n'
'Program Terminating...',
Qt.QMessageBox.Abort)
# print(self.x_span)
self.diagram_subplot.set_xlim(*self.x_span)
self.diagram_subplot.set_ylim(*self.y_span)
self.canvas.draw()
# self.diagram_subplot.clear()
self.diagram_data = copy.deepcopy(diagram_states)
self.current_states = []
for count, state in enumerate(diagram_states):
if state[1] != None: # 不能用 if not state[1]
state_line = State_Line(state, count, color=color, span=state_line_span)
self.draw_line(state_line, num_with_tag=num_with_tag)
self.current_states.append(state_line)
self.paths.append(self.current_states)
if 'tag' not in color.lower():
for count in range(len(self.current_states) - 1):
connecting_line = Connecting_Line(self.current_states[count], self.current_states[count + 1], color=color)
self.draw_line(connecting_line)
self.connecting_lines.append(connecting_line)
self.diagram_subplot.tick_params(axis='x', labelbottom='off')
self.diagram_subplot.tick_params(axis='y')
if os.path.isfile("Energy_Diagram_Y_Axis_Text.txt"):
with open('Energy_Diagram_Y_Axis_Text.txt') as text_file:
y_axis_text = text_file.readline()
else:
with open('Energy_Diagram_Y_Axis_Text.txt', 'w') as text_file:
y_axis_text = "Solvated Free Energy (kJ/mol)"
text_file.write(y_axis_text)
MpPyplot.ylabel(y_axis_text,
fontsize='xx-large',
weight='normal')
MpPyplot.subplots_adjust(left=0.12, right=0.93, top=0.95)
self.canvas.draw()
def initiate(self):
self.diagram_subplot.clear()
self.paths = []
self.connecting_lines = []
self.diagram_subplot.tick_params(axis='x', labelbottom='off')
self.diagram_subplot.tick_params(axis='y',
labelsize='xx-large')
if os.path.isfile("Energy_Diagram_Y_Axis_Text.txt"):
with open('Energy_Diagram_Y_Axis_Text.txt') as text_file:
y_axis_text = text_file.readline()
else:
with open('Energy_Diagram_Y_Axis_Text.txt', 'w') as text_file:
y_axis_text = "Solvated Free Energy (kJ/mol)"
text_file.write(y_axis_text)
MpPyplot.ylabel(y_axis_text,
fontsize='xx-large',
weight='bold')
MpPyplot.xticks(np.arange(5),[])
MpPyplot.subplots_adjust(left=0.12, right=0.93, top=0.95)
def max_steps(self):
return max([len(x) for x in self.paths])
def all_states(self):
return sum(self.paths, [])
def draw_line(self, line_object: State_Line, num_with_tag=False):
assume_figure_length = 60 # assume the figure span 60 characters
assume_figure_height = 20 # assume the figure span 20 lines
renderer = MpPyplot.gca().get_figure().canvas.get_renderer() # for BBox
fig = plt.gcf()
size = fig.get_size_inches() * fig.dpi
# print(size)
if line_object in sum(self.paths, []) + self.connecting_lines:
return None
if isinstance(line_object, State_Line):
self.xs_for_adjust_text += [line_object.x[0], line_object.x[1]]
self.ys_for_adjust_text += [line_object.y[0], line_object.y[1]]
if 'tag' not in line_object.color.lower(): # independent tag 用color做了标记
self.diagram_subplot.plot(line_object.x,
line_object.y,
line_object.style,
color=line_object.color,
lw=line_object.width)
if 'tag' not in line_object.color.lower(): # independent tag 用color做了标记
if line_object.annotate:
text = "{:.1f}".format(line_object.energy)
if num_with_tag: # number和tag一起显示
if hasattr(line_object, 'tag') and line_object.tag:
text = str(line_object.tag) + ' ' + text
energy_annotate = self.diagram_subplot.annotate(text,
(line_object.x_center, line_object.energy + 3),
fontsize=number_font_size,
verticalalignment='bottom',
horizontalalignment='center',
color=line_object.color,weight='normal')
self.annotate_objects.append(energy_annotate)
# energy_annotate.draggable()
if not num_with_tag or 'tag' in line_object.color.lower(): # 如果要求num和tag一起显示，这里就用不着了；但是如果是用tag标记的independent tag，仍然从这里显示
if hasattr(line_object, 'tag') and line_object.tag:
tag = self.diagram_subplot.annotate(line_object.tag,
(line_object.x_center, line_object.energy),
verticalalignment='top',
horizontalalignment='center',
xytext=(0, -8), textcoords='offset points',
fontsize=tag_font_size,
color=line_object.color.lower().replace("tag", ""), # independent tag 用color做了标记
weight='bold')
# tag.draggable()
self.annotate_objects.append(tag)
class myWidget(Ui_Draw_Energy_Diagram_Form, Qt.QWidget, Qt_Widget_Common_Functions):
def __init__(self):
super(self.__class__, self).__init__()
self.setupUi(self)
self.energy_diagram = MpWidget_Energy_Diagram()
self.energy_diagram.setSizePolicy(Qt.QSizePolicy.Preferred, Qt.QSizePolicy.Preferred)
# self.drag_drop_textEdit = Drag_Drop_TextEdit()
# self.data_tableWidget.hide()
# self.horizontalLayout.setStretch(0, 1)
self.verticalLayout.insertWidget(1,self.energy_diagram, 1)
# self.verticalLayout.insertWidget(4, self.drag_drop_textEdit, 2)
self.open_config_file()
connect_once(self.load_file_pushButton, self.choose_xlsx)
connect_once(self.update_file_pushButton, self.update_xlsx)
# connect_once(self.drag_drop_textEdit.drop_accepted_signal, self.xlsx_dropped)
connect_once(self.x_lower_limit_spinBox, self.x_limits_change)
connect_once(self.x_upper_limit_spinBox, self.x_limits_change)
connect_once(self.Y_lower_limit_spinBox, self.y_limits_change)
connect_once(self.Y_upper_limit_spinBox, self.y_limits_change)
connect_once(self.num_with_tag_checkBox, self.update_xlsx)
connect_once(self.save_cdx_pushButton, self.save_cdxml)
connect_once(self.Y_label_lineEdit.textChanged,self.store_Y_label_to_file)
connect_once(self.Y_tick_auto_checkBox.clicked,self.toggle_auto_Y_tick)
connect_once(self.save_cdx_pushButton_2,self.save_cdx_pushButton.click)
self.dash_solid_button_group = Qt.QButtonGroup()
self.dash_solid_button_group.addButton(self.dash_line_radioButton)
self.dash_solid_button_group.addButton(self.solid_line_radioButton)
self.line_bond_button_group = Qt.QButtonGroup()
self.line_bond_button_group.addButton(self.use_lines_radioButton)
self.line_bond_button_group.addButton(self.use_bonds_radioButton)
self.state_precision_spinBox.setValue(self.load_config('State Precision Digits', 1))
self.state_line_span_doubleSpinBox.setValue(self.load_config('State Line Span', 0.6))
self.Auto_collision_avoidance_checkBox.setChecked(self.load_config('Auto_collision_avoidance', True))
self.allow_overlap_states_checkBox.setChecked(self.load_config('allow_overlap_states_checkBox', False))
self.num_with_tag_checkBox.setChecked(self.load_config('Num with Tag', False))
self.solid_line_radioButton.setChecked(self.load_config('Use Solid Link', True))
self.dash_line_radioButton.setChecked(not self.load_config('Use Solid Link', True))
self.use_lines_radioButton.setChecked(self.load_config('Use Lines', True))
self.use_bonds_radioButton.setChecked(not self.load_config('Use Lines', True))
self.Y_tick_auto_checkBox.setChecked(self.load_config('Y_tick_auto_checkBox', True))
self.Y_label_precision_spinBox.setValue(self.load_config('Y_label_precision_spinBox', 0))
self.Y_label_lineEdit.setText(self.load_config('Y_label_lineEdit', "Solvated Free Energy (kJ/mol)"))
self.use_temp_file_checkBox.setChecked(self.load_config('use_temp_file_checkBox', True))
self.with_MECP_checkBox.hide()
self.X_tick_checkBox.setChecked(self.load_config('X_tick_checkBox',True))
self.Y_tick_checkBox.setChecked(self.load_config('Y_tick_checkBox', True))
self.resize(self.load_config('Draw_energy_diagram_window_width',1011),
self.load_config('Draw_energy_diagram_window_height',580))
self.x_limits_changed = False
self.y_limits_changed = False
self.toggle_auto_Y_tick()
self.center_the_widget()
update_UI()
# if os.path.isfile('Draw_Energy_Diagram_XML_CheckUpdate.exe'):
# subprocess.Popen(['Draw_Energy_Diagram_XML_CheckUpdate.exe'])
# else:
# subprocess.Popen(['python','Draw_Energy_Diagram_XML_CheckUpdate.py'])
def toggle_auto_Y_tick(self):
self.Y_tick_doubleSpinBox.setEnabled(not self.Y_tick_auto_checkBox.isChecked())
self.Y_number_doubleSpinBox.setEnabled(not self.Y_tick_auto_checkBox.isChecked())
self.Y_label_precision_spinBox.setEnabled(not self.Y_tick_auto_checkBox.isChecked())
def store_Y_label_to_file(self):
with open(os.path.join(filename_class(sys.argv[0]).path,'Energy_Diagram_Y_Axis_Text.txt'),'w') as Y_axis_text_file:
Y_axis_text_file.write(self.Y_label_lineEdit.text())
def x_limits_change(self):
if self.x_upper_limit_spinBox.value() > self.x_lower_limit_spinBox.value():
self.x_limits_changed = True
else:
self.x_limits_changed = False
self.update_xlsx()
def y_limits_change(self):
if self.Y_upper_limit_spinBox.value() > self.Y_lower_limit_spinBox.value():
self.y_limits_changed = True
else:
self.y_limits_changed = False
self.update_xlsx()
def choose_xlsx(self):
# self.xlsx_dropped(r"C:\Users\LiYuanhe\Desktop\temp.xlsx")
# self.save_cdxml()
xlsx_filename = Qt.QFileDialog.getOpenFileName(self, 'Choose Input XLSX file', self.load_config('Energy Diagram Last Path'),
filter="xlsx File (*.xlsx)")
if xlsx_filename:
xlsx_filename = xlsx_filename[0]
self.xlsx_dropped(xlsx_filename)
def update_xlsx(self):
if self.xlsx_file_lineEdit.text():
self.energy_diagram.initiate()
self.xlsx_dropped(self.xlsx_file_lineEdit.text(), called_from_update=True)
def xlsx_dropped(self, xlsx_filename, called_from_update=False):
'''
read xlsx data. The first column can be the format setting, e.g. 'r'
'''
# 防止因为改变x, y limit 触发多次limit changed. 在函数末尾重新 connect
disconnect_all(self.x_lower_limit_spinBox, self.x_limits_change)
disconnect_all(self.x_upper_limit_spinBox, self.x_limits_change)
disconnect_all(self.Y_lower_limit_spinBox, self.y_limits_change)
disconnect_all(self.Y_upper_limit_spinBox, self.y_limits_change)
if isinstance(xlsx_filename, list): # drop area 给出的是一个list，可以接受多个文件
xlsx_filename = xlsx_filename[0]
if filename_class(xlsx_filename).append != 'xlsx':
return None
self.energy_diagram.initiate()
self.config['Energy Diagram Last Path'] = filename_class(xlsx_filename).path
self.save_config()
self.xlsx_file_lineEdit.setText(xlsx_filename)
self.xlsx_filename = xlsx_filename
self.load_xlsx(self.xlsx_filename)
# self.table_update()
if [route[0][1] for route in self.routes if not (isinstance(route[0][1], float) or isinstance(route[0][1], int) or route[0][1] == None)]: # 存在格式设定
self.color_of_lines = [route[0][1] for route in self.routes]
# save something like [None,'r']
else:
self.color_of_lines = []
# print(self.routes)
self.x_span = [-1, max([len(route) for route in self.routes])-1]
if not called_from_update:
self.x_limits_changed = False
self.x_lower_limit_spinBox.setValue(self.x_span[0]+2)
self.x_upper_limit_spinBox.setValue(self.x_span[1])
# if not self.color_of_lines:
# self.x_span[1] += 1
else:
if self.x_limits_changed:
self.x_span = [self.x_lower_limit_spinBox.value()-2, self.x_upper_limit_spinBox.value()]
self.x_upper_limit_spinBox.setMinimum(self.x_lower_limit_spinBox.value()+1)
self.x_lower_limit_spinBox.setMaximum(self.x_upper_limit_spinBox.value() - 1)
get_y_range = [state[1] for state in sum(self.routes,[])]
get_y_range = [x for x in get_y_range if is_float(x)]
min_energy = min(get_y_range)
max_energy = max(get_y_range)
y_span = max_energy - min_energy
self.y_span = [min_energy - y_span * 0.3, max_energy + y_span * 0.5]
if not called_from_update:
self.y_limits_changed = False
self.Y_lower_limit_spinBox.setValue(self.y_span[0])
self.Y_upper_limit_spinBox.setValue(self.y_span[1])
else:
if self.y_limits_changed:
self.y_span = [self.Y_lower_limit_spinBox.value(), self.Y_upper_limit_spinBox.value()]
self.paths_for_cdx_drawing = []
self.colors_for_cdx_drawing = []
for count, route in enumerate(self.routes):
if self.color_of_lines: # have format setting
self.energy_diagram.diagram_Update(route[1:], x_span=self.x_span, y_span=self.y_span, color=self.color_of_lines[count],
num_with_tag=self.num_with_tag_checkBox.isChecked(),
state_line_span=self.state_line_span_doubleSpinBox.value())
self.paths_for_cdx_drawing.append(route[1:])
self.colors_for_cdx_drawing.append(self.color_of_lines[count])
else: # doesn't have format setting
self.energy_diagram.diagram_Update(route, x_span=self.x_span, y_span=self.y_span, num_with_tag=self.num_with_tag_checkBox.checked(),
state_line_span=self.state_line_span_doubleSpinBox.value())
self.paths_for_cdx_drawing.append(route)
self.colors_for_cdx_drawing.append('k')
connect_once(self.x_lower_limit_spinBox, self.x_limits_change)
connect_once(self.x_upper_limit_spinBox, self.x_limits_change)
connect_once(self.Y_lower_limit_spinBox, self.y_limits_change)
connect_once(self.Y_upper_limit_spinBox, self.y_limits_change)
self.center_the_widget()
self.show()
def save_cdxml(self):
# 保存各种设置
self.config['State Precision Digits'] = self.state_precision_spinBox.value()
self.config['State Line Span'] = self.state_line_span_doubleSpinBox.value()
self.config['Auto_collision_avoidance']=self.Auto_collision_avoidance_checkBox.isChecked()
self.config['allow_overlap_states_checkBox']=self.allow_overlap_states_checkBox.isChecked()
self.config['Num with Tag'] = self.num_with_tag_checkBox.isChecked()
self.config['Use Solid Link'] = self.solid_line_radioButton.isChecked()
self.config['Use Lines'] = self.use_lines_radioButton.isChecked()
# print(self.config['Use Lines'])
self.config['X_tick_checkBox'] = self.X_tick_checkBox.isChecked()
self.config['Y_tick_checkBox'] = self.Y_tick_checkBox.isChecked()
self.config['Y_tick_auto_checkBox'] = self.Y_tick_auto_checkBox.isChecked()
self.config['Y_label_precision_spinBox'] = self.Y_label_precision_spinBox.value()
self.config['Y_label_lineEdit'] = self.Y_label_lineEdit.text()
self.config['Draw_energy_diagram_window_width']= self.width()
self.config['Draw_energy_diagram_window_height']=self.height()
self.config['use_temp_file_checkBox']=self.use_temp_file_checkBox.isChecked()
self.save_config()
if self.xlsx_file_lineEdit.text() == "":
self.choose_xlsx()
fonts_list = [default_fonts, default_fonts_end]
#获得Energy diagram 与ChemDraw 文档的坐标对应关系
x_range = self.energy_diagram.diagram_subplot.get_xlim() # the x coordinate range
y_range = self.energy_diagram.diagram_subplot.get_ylim() # the y coordinate range
width = self.energy_diagram.canvas.width() # height of diagram in pixels
height = self.energy_diagram.canvas.height() # height of diagram in pixels
x_offset = 200 # spaces left on the left in cdxml
y_offset = 100 # spaces left on the top in cdxml
factor = 0.6 # factor from the pixel in matplotlib to chemdraw
text_line_height = 10 # how many ChemDraw pixels are one line of text took
#两个轴的Matplotlib-->ChemDraw转换函数
x_mapping = lambda x: width / (x_range[1] - x_range[0]) * x * factor+x_offset # map function coordinate to pixel
y_mapping = lambda y: height / (y_range[1] - y_range[0]) * (y_range[1]-y) * factor+y_offset # map function coordinate to pixel
# Z轴编号从多少开始，无所谓，足够大就行
z_start = 50
# 确定Excel第一行的Independent text该相当于放在哪个坐标
x_length = max([len(x) for x_count,x in enumerate(self.paths_for_cdx_drawing) if 'TAG' not in self.colors_for_cdx_drawing[x_count]])
maximum_ys = [-float('inf') for x in range(x_length)]
minimum_ys = [float('inf') for x in range(x_length)]
for route_count,route_content in enumerate(self.paths_for_cdx_drawing):
if 'TAG' not in self.colors_for_cdx_drawing[route_count]:
for column_count, item in enumerate(route_content):
if item[1]==None:
continue
maximum_ys[column_count] = max(maximum_ys[column_count],item[1])
minimum_ys[column_count] = min(minimum_ys[column_count], item[1])
# independent tag wants to be at "two lines" below the state line, to stay below the minimum tag
tags_y_position = [y_mapping(minimum_ys[i])+text_line_height*2+2 for i in range(x_length)]
state_line_span = self.state_line_span_doubleSpinBox.value() # the length of each state line, 1 is full
num_with_tag = self.num_with_tag_checkBox.isChecked()
nodes = [] # a list of notes, for counting ID and counting Z
nodes_id_start = 2000 #足够大就可以了
state_lines = [] # for Z counting
link_lines = [] # for Z counting
texts = [] # for Z counting
current_texts = [] # for text of current route
avoidance = [] # remember each of previous collision box (x,y_start,y_end) for Greedy collision avoidance
font_index = 4 #目前没法换其他的font
size_of_tag = 10
line_width_avoidance = 3 # how many ChemDraw pixels are needed to put a text on top a line
size_of_number = 10
remember_drawn_states = [] # list of tuples (x_count, state_tuple[1]) to avoid draw one line exactly on top of another
face_of_tag = 'Bold'
face_of_number = 'Normal'
#现在的Z轴该用多少
def current_z():
return z_start + len(nodes) + len(state_lines) + len(link_lines) + len(texts)
def get_avoidance_text_position(avoidance, current_x, current_y):
'''
# using greedy algorithm to do text avoidance