• searching for likely interactions with a fragment

    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

  • RE: Searching the database based on structure void space

    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:


        "options": {
            "interface_version": 3,
            "identifier": "AABHTZ",
            "selected_atoms": [

            "distances": [

            "angles": [

            "torsions": [

            "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",
            "working_directory_path": "C:\\Users\\lpb16197\\Desktop\\CSD_void/AABHTZ/void_space/2018_04_25_22_14_44",
            "output_base": "C:\\Users\\lpb16197\\Desktop\\CSD_void/AABHTZ/void_space/2018_04_25_22_14_44/AABHTZ_void_space",
            "conquest_path": "C:\\Program Files (x86)\\CCDC\\CSD_2018\\ConQuest\\exe\\csds.exe"

  • RE: Searching the database based on structure void space

    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

  • RE: Searching the database based on structure void space

    Dear Richard,


    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>
    import tempfile
    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'

  • Searching the database based on structure void space

    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?



    Many thanks