• RE: Extract names of molecules in crystal.

    @Anonymous  Similar to conquest, the CSD API may be instructed to export the molecules present as a SMILES string, e.g. pyridine as c1ccccn1 .  If there are multiple different molecules to consider (think hydrates, or co-crystals in general), they may be described with concatenation by a period / a full stop.  The CSD API documentation presents an example e.g., here. It is up to you to either write a separate string function to separate these entries, or to iterate with the CSD API tools to split them into individual entries per line.

    But eventually, you may submit this string about an individual molecule (or, a file containing a list of multiple SMILES strings) to the PubChem's Identifier Exchange Service . Among the outputs available is a listing with the input SMILES in the first column, and the then added IUPAC name in the second.  If suitable for you, you equally may elect Inchis / InchiKeys as a descriptor, or toggle on/off a compression of the output list.


  • RE: Is there any script for converting .cif files too good old ,pdb format?

    If you missed exporting the results of your search in conquest as .pdb, give OpenBabel, e.g by instruction

    obabel *.cif -opdb -m

    a chance.  It is a program freely available for Windows, Mac, and Linux (source).  Its actions may be scripted, like the CSD API, with Python; yet other languages are your disposition, too.  For the occasional conversion of a single .cif, you may opt for either the CLI

    obabel -icif input.cif -opdb -O output.pdb

    or run the GUI of the program (obgui, if running Linux).

    Contrasting to openbabel.org -- in its description still often about old version 2.4, the current documentation is hosted on readthedocs.io . Including many examples, the manual may be downloaded as .html, .pdf, or .epub file.