如何使用ChemDraw / Python从InChI创建.cdx文件？ [英] How to create a .cdx file from InChI with ChemDraw/Python?

问题描述

我想用Python从InChI创建ChemDraw .cdx文件。
此答案为 cdx->提供了一种解决方案。 InChI 。

I would like to create a ChemDraw .cdx file from an InChI with Python. This answer gives a solution for cdx --> InChI.

cdx_to_inchi 下面的最小示例很好用，但
我不知道如何使 inchi_to_cdx 正常工作。

The minimal example below cdx_to_inchi works fine, but I could not figure out how I can get inchi_to_cdx to work.

import comtypes.client as w32

def cdx_to_inchi(cdx):
    ChemDraw = w32.CreateObject("ChemDraw.Application")
    ChemDraw.Visible = False
    Compound = ChemDraw.Documents.Open(cdx)            # opens existing file
    inchi = Compound.Objects.Data("chemical/x-inchi")
    print(inchi)
    ChemDraw.Quit()

def inchi_to_cdx(inchi):
    ChemDraw = w32.CreateObject("ChemDraw.Application")
    ChemDraw.Visible = False

    Compound = ChemDraw.Documents.Open("Emtpy.cdx")   # opens existing file
    # ChemDraw.Documents.New("NewFile.cdx")           # How to create a new file?

    # Compound.Objects.SetData(inchi)                 # How to paste InChi data?
    # ChemDraw.Documents.Save()                       # How to save?
    # ChemDraw.Documents.SaveAs("MyMolecule.cdx")     # How to save under different name?
    ChemDraw.Quit()

cdx = r'C:\Data\Test.cdx'
inchi = '1S/C6H6/c1-2-4-6-5-3-1/h1-6H'

cdx_to_inchi(cdx)
inchi_to_cdx(inchi)

推荐答案

以下至少是某种可行的解决方案。它基本上是通过按键来模仿人类用户。改编自此处。缺点是：

The following is at least a somehow working solution. It basically "mimics" a human user with keypresses. It is adapted from here. The drawbacks are:

1. 它似乎是Windows特定的


2. ChemDraw必须是活动应用程序，即无法在后台运行


3. 其他延迟会减慢整个过程。

1. it seems to be Windows specific
2. ChemDraw has to be the active application, i.e. will not work in the background
3. additional delays slow down the whole procedure. a few 10'000 molecules would take about a day (well, better than by hand ;-)

这些问题仍然存在： p>

These questions remain:

1. 如何使其独立于平台？


2. 如何使其在后台运行？


3. 如何避免额外的延迟，或者延迟多久才能使其仍然可靠地工作？

代码：

### create a ChemDraw .cdx file from an InChI string
import win32com.client as win32
import win32clipboard
import time

def sleep():
    time.sleep(0.5)   # wait for 0.5 seconds that script is not too fast for ChemDraw

def sleep_short():
    time.sleep(0.25)  # wait for 0.25 seconds between key presses

# initialize windows shell (so we can send keyboard commands)
shell = win32.Dispatch("WScript.Shell")

def hit_keys(keys): # function to wait, then send a keypress signal
    sleep_short()
    shell.SendKeys(keys,1)

# initialize ChemDraw
chemdraw = win32.gencache.EnsureDispatch('ChemDraw.Application') # connect to ChemDraw
chemdraw.Visible = True  # window needs to be visible otherwise keypresses will not work
sleep()

doc = chemdraw.Documents.Add()    # create a new document
doc.Activate()
sleep()

# ChemDraw must be the active application, so it can receive keyboard commands
shell.AppActivate("ChemDraw Prime") # name of the ChemDraw window bar
sleep()

inchi = 'InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H'
# set clipboard data
win32clipboard.OpenClipboard()
win32clipboard.EmptyClipboard()
win32clipboard.SetClipboardText(inchi)
win32clipboard.CloseClipboard()
sleep()     # not sure whether a delay is needed here

hit_keys("%e") # edit
hit_keys("s")  # paste special
hit_keys("i")  # pase as inchi
sleep()

ffname = r'C:\Users\Test\Scripts\MyMolecule.cdx'  # full filename
doc.SaveAs(ffname)   # save the file
doc.Close()
chemdraw.Quit()    # close ChemDraw
### end of code

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