Richard Sykes CCDC

Hi Puck,

it sounds as if you are trying to write the refcodes directly to the CrystalWriter instance, but this needs a crystal structure.  If you have the refcodes in a list you can create the crystals from the CSD as follows:

csd = io.EntryReader('csd')
for refcode in list_of_refcodes:
    with io.CrystalWriter('/path/to/pdb/directort/%s,pdb' % refcode) as writer:
        writer.write(csd.crystal(refcode))

Alternatively, if you have the refcodes in a file, they can be read through a CrystalReader instance:

with io.CrystalReader('/path/to/refcode/file', format='identifiers') as reader:
    for crystal in reader:
        with io.CrystalWriter('/path/to/pdb/directory/%s.pdb' % crystal.identifier) as writer:
            writer.write(crystal)

Hope this is helpful.  Please let me know if I've misunderstood your problem.

Best wishes
Richard

Hi Hope,

Can you tell me which methods you have used and for which you would like documentation and pseudocode?  Is it the similarity searching that Alex used, where the reference given above should be sufficient?

Best wishes

Richard

Dear Anthony,

I'm very sorry about the long delay in getting back to you.

It sounds as if you need to do a substructure search on the CSD which for 22,000 structures is going to take some time.

This script will do something like what you want.  It will process your target file, search the CSD for structures containing your target molecule and will write the hits to a results file.  The hits will contain matches where your target molecule is a proper substructure of the matched structure; if you need exact matches, then please let me know.

--

import time

from ccdc import io, search, utilities

target_file = '/path/to/your/file/of/structures.mol2'
hit_file = '/path/to/where/you/want/to/put/results.gcd'

def one_search(m):
    searcher = search.SubstructureSearch()
    searcher.add_substructure(search.MoleculeSubstructure(m))
    hits = searcher.search()
    print 'CSD contained %d hits for %s' % (len(hits), m.identifier)
    return [h.identifier for h in hits]

reader = io.MoleculeReader(target_file)
start = time.time()
with open(hit_file, 'w') as gcd_writer:
    for i, m in enumerate(reader):
        gcd_writer.write('\n'.join(one_search(m)))
        utilities.Timer.progress(start, i+1, len(reader), '')
--

As I say, 20,000 structures is a lot of searching.  It may be advisable to split the input file into smaller chunks and process them separately.

Once again, I am terribly sorry about the delay in answering.

If you need any more help, please get back in touch.

Best wishes

Richard

Hi Alex,

similarity searching of the CSD follows the implementation described in:

http://scripts.iucr.org/cgi-bin/paper?S0021889810000452

that is to say by comparing fingerprints of the probe molecule and of a structures from the CSD.

I hope this is enough for your project; if not, please get back to me and I will happily provide more information.

Best wishes

Richard

Hi Martin,

if you want to run scripts which take longer than three minutes, you can invoke python directly from a shell prompt:

C:\Program Files (x86)\CCDC\Python_AP I_2018\miniconda\Scripts\activate

python name_of_your_script.py

This will not need the mercury interface.

Best wishes

Richard

Hi Martin,

There is no direct method in the API to search on spacegroup, so one has to fall back on enumeration of the database.  I believe the following will do what you want:


import time

from ccdc import io, utilities
csd = io.EntryReader('csd')

start = time.time()
hits = []

for i, e in enumerate(csd):
    if i and i % 1000 == 0:
        utilities.Timer.progress(start, i, len(csd), '%d hits' % len(hits))
    if not e.has_3d_structure:
        continue
    c = e.crystal
    if not c.spacegroup_symbol.startswith('R'):
        continue
    hits.append((c.void_volume(), e.identifier))

hits.sort()

This works by rejecting structures with no 3d information (they won't support a void volume calculation) and rejecting structures which do not have a rhombohdral space group.  If you like you can change this line to test different space groups.

At the end you will have a list of void_volume, refcode pairs which you can write in any format you care.

Hope this is helpful,

Best wishes
RIchard

Hi,

there is a workaround to this problem along the lines of:

from ccdc import search

smiles = 'something interesting'

searcher = search.SubstructureSearch()
searcher.add_substructure(search.SMARTSSubstructure(smiles))
hits = [h for h in searcher.search() if len(h.molecule.components) == 1 and h.molecule.smiles = smiles]

Best wishes
Richard

That's good to know, Puck. Feel free to raise any other issues you have with the API.

Best wishes

Richard

Hi Puck,

there are a couple of issues with this script:

Firstly, the no_disorder setting actually has three distinct values corresponding to False (don't check disorder at all), True (check for significant disorder, i.e of heavy atoms), or 'All' (check for any disorder).  Since you have specified True, structures like AARBOX will pass as the disorder is only in the position of the hydrogens.

Secondly, you are checking the crystal for disorder, rather than the entry.  This is a less specific test than that of the entry, as the editorial decisions made for the entry are lost when constructing the crystal, and this is why ABABUB is found.

There is a third problem for which I must apologise: there is a bug in the processing of the test for entries which, coincidentally I fixed today.  This will appear in the next release of the API.  This concerns entries with disorder but where the editors have not suppressed any atoms.

A better check would be:

for entry in io.EntryReader('csd'):
    if settings.test(entry) and not entry.has_disorder and len(entry.molecule.components) == 1:
        refcodes.append(entry.identifier)

Please let me know how you get on with this.

Best wishes

Richard

Dear Gabor,

I'm sorry to say you have come across a bug in the interaction between our licensing and our implementation.  The orth method has inadvertently taken its definition from a library with restrictions.  This will certainly be fixed in a forthcoming release, probably version 1.5.2 in about three months' time.

In the meantime I have provided a 'monkey patch' which will change the use of 'orth' to one in a library without these restrictions.  This should be applied in any script you use to examine the coordinates of a molecule's atoms.

Please let me know if anything is unclear about this, and my apologies for allowing this bug to slip into the release.

Best wishes
Richard Sykes

--

# Monkey-patch around the licence restriction

from ccdc.utilities import _private_importer
with _private_importer():
    import ChemistryLib
    import PackingSimilarityLib
PackingSimilarityLib.Point = ChemistryLib.Point