I would like to search for likely hydrogen-bonded coformers for a polymer fragment that I wish to study.
there is no crystal structure for the polymer or the monomer, but I can ofcourse draw the monomer molcule or the likely accessible functionality of the polymer for searching against.
I am not aware of a way to do this with the CSD suite, or with the API, but any sugestions will be gladly received
Many thanks yet again for your help.
I am running the code from Mercury - I have tried running from a python IDE, but encounters an import error tryign to load CCDC module. Should I be using something other than Mercury?
I apologise for what are likely basic questions - if there is a good reference that might help me get up and running with this rather than continually pestering this forum a recommendation would be greatfully received
The script now appears to complete and outputs a .m2a file. I can open this in a text editor, but doest contain useful information, an example is shown below:
"database_path": "C:/Program Files (x86)/CCDC/CSD_2018/CSD_539/as539be_ASER.sqlite",
"program_executable_path": "C:/Program Files (x86)/CCDC/CSD_2018/Mercury/mercury.exe",
"conquest_path": "C:\\Program Files (x86)\\CCDC\\CSD_2018\\ConQuest\\exe\\csds.exe"
Many thanks Paul, the script now runs, but it does suffer a time-out after 180 seconds of running. I will need to investigate further before starting to grab the data I am looking to source
As you may tell, this is the first time I have started to look at using the Python API
Many thanks for this, I will hopefully be able to get this running soon after figuring out what my issue (below) is. Looks to be python related rather than the script/CCDC system.
Many thanks again
Traceback (most recent call last):
File "C:/Users/lpb16197/Desktop/CSD_void/void_space.py", line 3, in <module>
from ccdc import io, utilities
File "C:\Program Files (x86)\CCDC\Python_API_2018\miniconda\lib\site-packages\csd_python_api-1.5.1-py2.7.egg\ccdc\io.py", line 87, in <module>
from ccdc.entry import Entry
File "C:\Program Files (x86)\CCDC\Python_API_2018\miniconda\lib\site-packages\csd_python_api-1.5.1-py2.7.egg\ccdc\entry.py", line 50, in <module>
from ccdc.crystal import Crystal
File "C:\Program Files (x86)\CCDC\Python_API_2018\miniconda\lib\site-packages\csd_python_api-1.5.1-py2.7.egg\ccdc\crystal.py", line 39, in <module>
from ccdc.molecule import Molecule, _file_object_factory
File "C:\Program Files (x86)\CCDC\Python_API_2018\miniconda\lib\site-packages\csd_python_api-1.5.1-py2.7.egg\ccdc\molecule.py", line 73, in <module>
from ccdc.utilities import UncertainValue, nested_class, bidirectional_dict, _detect_format
File "C:\Program Files (x86)\CCDC\Python_API_2018\miniconda\lib\site-packages\csd_python_api-1.5.1-py2.7.egg\ccdc\utilities.py", line 33, in <module>
File "C:\Program Files (x86)\CCDC\Python_API_2018\miniconda\lib\tempfile.py", line 35, in <module>
from random import Random as _Random
File "C:\Program Files (x86)\CCDC\Python_API_2018\miniconda\lib\random.py", line 49, in <module>
import hashlib as _hashlib
File "C:\Program Files (x86)\CCDC\Python_API_2018\miniconda\lib\hashlib.py", line 138, in <module>
AttributeError: 'module' object has no attribute 'openssl_md_meth_names'
I would like to find a way to search the CCDC database structures and rank them in order of % void space. I have been a thread discussing this based on Rhombohedral space groups only. Is it possible for me to perform such a search on the entire database, or might there even be a .py script out there for such a task?