• Chirality assessment

    Dear developers,

    I have come across an issue that for certain structures non-chiral atoms are assessed as chiral. I have noticed many structures with Z'<1, e.g. BOBDON, BOSMOM, LAWCOC, to name some. When viewed in Mercury, initially all atoms are apparently achiral, however, after performing 'Auto edit structure...' chirality labels appear for some atoms. The same happens if Python API is being used and the routine mol.assign_bond_types() followed by mol.add_hydrogens() is called. (Btw, I hope this is the correct order to make molecules look nice).

    Another structure, which I spotted having half the same problem is HODKER. In Mercury there are no chiral atoms, even after 'Auto edit structure...'. However, in Python API [mol.assign_bond_types() followed by mol.add_hydrogens()] it assigns .is_chiral = True for atom C17, which is not chiral.

     

    Best wishes, 

    Toms Rekis

  • RE: Altering crystal structures

    Thank you! It works. If anybody else at some point looks this up - instead of: new_molecule = molecule.Molecule(original_molecule.identifier) this should be: new_molecule = Molecule(original_molecule.identifier) and of course from ccdc.molecule import Molecule at the top of the script.

  • Altering crystal structures

    Dear experts,

    I am trying to slightly modify crystal structures programmatically. For example, to alter conformation of one component in Z'>1 structures and after that use some features like generating packing shells around that slightly altered molecule etc. I am confused of how to implement my calculated new atomic positions for a specific component. What I am trying is something like this:

    csd = io.EntryReader('CSD')
    entry = csd.entry(some_ref_code)

    print len(entry.molecule.components[0].atoms)
    entry.molecule.components[0].assign_bond_types()
    entry.molecule.components[0].add_hydrogens()
    entry.molecule.components[0].normalise_atom_order()
    entry.molecule.components[0].remove_hydrogens()
    print len(entry.molecule.components[0].atoms) #here it shows the same number as above, so the hydrogens are not being removed? 

    # here mol2 is defined as molecule with all non-hydrogen atoms of entry.molecule.components[0]

    for i, atom in enumerate(entry.molecule.components[0].atoms):
              atom.coordinates = (-mol2.atoms[i].coordinates[0]+2*pseudo_inv[0], -mol2.atoms[i].coordinates[1]+2*pseudo_inv[1], -mol2.atoms[i].coordinates[2]+2*pseudo_inv[2]) #this is the point I want to specify slightly different atomic coordinates for component[0] and after use all packing-based features (search for hydrogen bonds, contacts, etc.)

    What could I do? Should I instead initialize a new Crystal instance with all the essential parameters (unit cell, symmetry) copied from my entry.crystal and then create a molecule object and atom objects with desired coordinates within this new Crystal instance?

  • RE: Python: cannot access atom.occupancy/ General: what is atom.chirality = 'Mixed'?

    Code sample from the terminal:

    >>> entry.molecule.atoms[0].label
    u'S1'
    >>> entry.molecule.atoms[0].occupancy
    Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    AttributeError: 'Atom' object has no attribute 'occupancy'

    I am using the following:

    LSB Version: n/a
    Distributor ID: ManjaroLinux
    Description: Manjaro Linux
    Release: 18.0.2
    Codename: Illyria

     

    Best regards,

    Toms

  • RE: Python: cannot access atom.occupancy/ General: what is atom.chirality = 'Mixed'?

    Thanks!

    I keep getting the same error using the code specified above, but it should be system-related issue then. I am running everything on Arch Linux (Manjaro) for which the product has not been tested. I should switch to another distribution. Interesting, however, that .occupancy seems to be the only one not being recognized, as every other attribute tested returns the corresponding value without any problem.

  • Python: cannot access atom.occupancy/ General: what is atom.chirality = 'Mixed'?

    I am using Python to access the database. So far I have come across an issue I cannot solve:

    Occupancy of an atom is not accessible. Whenever I try to access it, I get the following error: AttributeError: 'Atom' object has no attribute 'occupancy'. However, this attribute has been specified in Molecule API documentation. Everything works well for other attributes, e.g. mymolecule.atoms[0].label gives me the label etc., but mymolecule.atoms[0].occupancy returns error.

    Additional question: How to understand from stereochemistry point of view atom chirality flag valued 'Mixed'? 

     

    Thanks in advance,

    T.