安装chemscript

###########基础知识点###########################

WriteFile(file, format=None)Write StructureData or Reaction into a file with file format indicated by *format*.
If *format* is not specified, the file extension is used.
*format* can be a full mime type, or the second part of a mime type (e.g. "cdx" short for "chemical/x-cdx").
Call StructureData.MimeTypes() to list all supported file formats.
Example:
>>>  m = StructureData.LoadData('CCC')
>>>  m.WriteFile('output.cdx')

>>>  m.ReadFile('output.cdx', 'cdx')

#################第一步把sdf拆分成cdx###########################

# Example 003

from sys import *

from os import *
from os.path import *

from ChemScript12 import *

if not exists('Output'):
  mkdir('Output')

# Make an SD reader object for the output file
reader = SDFileReader('./Input/input.sdf')

fileNumber = 1
m = reader.ReadNext()

while m != None:

  filename = './Output/out%02d' % fileNumber + '.cdxml'
 
  m.WriteFile(filename, 'text/xml')
 
  fileNumber += 1
 
  m = reader.ReadNext()


# close reader
reader.Close()

################第二部把cdx保存为sdf#############################

from ChemScript12 import *
reader=SDFileReader("DWF-14.sdf")
mol=reader.ReadNext()
output=SDFileWriter("./3d.sdf")
while(mol != None):
   mol.ConvertTo3DStructure()
   output.WriteStructure(mol)
   mol=reader.ReadNext()

#####################最后的脚本#####################################

###################bug:  2d的sdf转cdx的时候丢失了注释信息#####################################

from ChemScript12 import *

reader=SDFileReader('total264chiral.sdf')

m=reader.ReadNext()
filebasename=0;
output=SDFileWriter('./3dtotal.sdf')
while(m !=None):
   filebasename+=1
   filename=str(filebasename)+'.cdx'
   m.WriteFile(filename,'cdx')
   mol2=StructureData()
   mol2.ReadFile(filename)
   mol2.ConvertTo3DStructure()
   output.WriteStructure(mol2)
   m=reader.ReadNext()

reader.Close()

########添加了MOLNAME的注释信息，但是又发现了新的问题sdf转cdx的时候，结构扁平化#########

from ChemScript12 import *

reader=SDFileReader('total264chiral.sdf')

m=reader.ReadNext()
filebasename=0;
output=SDFileWriter('./3dtotal.sdf')
while(m !=None):
   filebasename+=1
   filename=str(filebasename)+'.cdx'
   m.WriteFile(filename,'cdx')
   mol2=StructureData()
   mol2.ReadFile(filename)
   mol2.ConvertTo3DStructure()
   mol2["MOLNAME"]=m["MOLNAME"]
   output.WriteStructure(mol2)
   m=reader.ReadNext()

reader.Close()

#############################2dsdftocdx#############################################

 

 

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