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Author Topic: cdx file pack?  (Read 90 times)

reDEEMed

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cdx file pack?
« on: June 18, 2011, 04:32:44 AM »
Is there anywhere I can download a good collection of chemdraw files? I don't have chemdraw, but I have the nix equivalent. If anybody here uses linux, any debian based distro in particular, I highly suggest the debian science pack or at least looking at the stuff under 'chemistry for linux'. My favorite is Avogadro so far. It can do 3-d modeling and lets you rotate the model around and it's just really nice to play with. I wish I had a collection of already build molecules, though. Is there any such download? I've googled to no avail and torrent searches also seem futile. Gperiodic is also pretty cool. Lots of stuff for doing the math for you in some of these apps, but for now I'm shying away from that until I feel like I know how to do it myself on paper. I really want me some molecules to look at and play with digitally, though.

Anybody?
"Ego is a structure that is erected by a neurotic individual who is a member of a neurotic culture against the facts of the matter. And culture, which we put on like an overcoat, is the collectivized consensus about what sort of neurotic behaviors are acceptable."
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Wizard X

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Re: cdx file pack?
« Reply #1 on: June 18, 2011, 10:43:19 PM »
If you can't find .cdx files, you can download another chemical format and Converting Between Formats http://en.wikipedia.org/wiki/Chemical_file_format#Converting_Between_Formats

http://chemical-mime.sourceforge.net/chemical-mime-data.html
Albert Einstein - "Great ideas often receive violent opposition from mediocre minds."

reDEEMed

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Re: cdx file pack?
« Reply #2 on: June 21, 2011, 10:54:56 AM »
The format is less important than the files themselves and what they represent. I would like to have a library of molecules I can use for comparison and study. I could always draw them myself, but I wouldn't be confident that they were right. Maybe when I get to the point of actually doing a synthesis I can draw all my reactants and what the product should be. Hmmm, I dunno, I still don't trust my own knowledge lol.
"Ego is a structure that is erected by a neurotic individual who is a member of a neurotic culture against the facts of the matter. And culture, which we put on like an overcoat, is the collectivized consensus about what sort of neurotic behaviors are acceptable."
— Terence McKenna

Wizard X

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Re: cdx file pack?
« Reply #3 on: June 22, 2011, 01:28:40 AM »
CDX is a binary file type created by CambridgeSoft Corporation's ChemDraw chemical structure application. CDXML is the XML and preferred version of this format.

http://en.wikipedia.org/wiki/CDX_Format


I suggest download XDrawChem for Linux. http://xdrawchem.sourceforge.net/

Major features. http://en.wikipedia.org/wiki/XDrawChem

Fixed length and fixed angle drawing
Automatic alignment of figures
Detection of structures, text, and arrows, and their automatic placement
Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in a built-in library
Retrieval of structures from a network database based on CAS number, formula, or name
Retrieval of information on a molecule based on a drawing
Symbols such as partial charge and radicals
Reading MDL Molfiles, CML (Chemical Markup Language), ChemDraw binary format, ChemDraw XML text format
Writing MDL Molfiles, CML, ChemDraw XML text format
Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats.
Image export in Portable Network Graphics (PNG), Windows bitmap, Encapsulated PostScript (EPS), and Scalable Vector Graphics (SVG)
3D structure generation with the help of the external program BUILD3D
Simple spectra predictions, including 13C-NMR, 1H-NMR (based on additive rules and functional group lookup methods), and IR
Simple property estimation, including pKa, octanol-water partition coefficient, and gas-phase enthalpy change.


Albert Einstein - "Great ideas often receive violent opposition from mediocre minds."

reDEEMed

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Re: cdx file pack?
« Reply #4 on: June 22, 2011, 10:53:44 AM »
Thanks Wiz, mang! I already have that app, so this should be easy :D

It was part of the debian science package. I just lean towards avogadro because it's all pretty 3-d molecules that I can rotate and whatnot. I'll have a look at Xchemdraw when I get off work this evening.

Thanks again!
"Ego is a structure that is erected by a neurotic individual who is a member of a neurotic culture against the facts of the matter. And culture, which we put on like an overcoat, is the collectivized consensus about what sort of neurotic behaviors are acceptable."
— Terence McKenna

Wizard X

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Re: cdx file pack?
« Reply #5 on: June 24, 2011, 12:35:33 AM »
You can also download molecular structure files like "Molfile" from sites like https://www.ebi.ac.uk

Example: Voacangine Representations. https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/407575
Albert Einstein - "Great ideas often receive violent opposition from mediocre minds."

reDEEMed

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Re: cdx file pack?
« Reply #6 on: June 24, 2011, 11:19:51 AM »
That's what I wanted. Thanks!
"Ego is a structure that is erected by a neurotic individual who is a member of a neurotic culture against the facts of the matter. And culture, which we put on like an overcoat, is the collectivized consensus about what sort of neurotic behaviors are acceptable."
— Terence McKenna
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