bugGChemPaint - Bugs: bug #18648, import / export files

 
 

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bug #18648: import / export files

Submitted by:  Francesco Pietra <chiendarret>
Submitted on:  Sat 30 Dec 2006 09:11:53 PM UTC  
 
Category: NoneSeverity: 1 - Wish
Item Group: NoneStatus: Fixed
Privacy: PublicAssigned to: Jean Bréfort <jean_brefort>
Open/Closed: Closed

(Jump to the original submission Jump to the original submission)

Mon 28 May 2007 04:17:45 PM UTC, comment #12:

closed after 0.8.0 release

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Thu 04 Jan 2007 08:29:18 AM UTC, comment #11:

What you call the next major step is mostly already there. Last development version (0.7.5) has this, but is lacking the user interface to change the settings. I plan to have this fully functional in 0.7.6 next month.

New or updated templates are welcome.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Thu 04 Jan 2007 08:00:11 AM UTC, comment #10:

These are good and timely news indeed, thank you.

The next major step toward acceptance of gchempaint as a tool for publishing chemistry should be (in due time) free settings for the line width, bond length, etc., so as to comply fully with requests by the editors. I hope this is no difficult problem.

I see a bright future for gchempaint, which should allow the scientific community to circumvent the wall set by illitterate editors in the area of organic chemistry.

The little I can offer from my side (if useful) is to provide more templates, while checking those already available (most amino acids lack stereochemical notation, and the D series may be accompanied by the L series).

Cheers
francesco pietra

Francesco Pietra <chiendarret>
Wed 03 Jan 2007 09:26:58 PM UTC, comment #9:

I tested with a pubchem xml file and it can be opened. Just this needs some fixes in openbabel (a mime type) and preferably an entry in chemical-mime-data.

While working on this I found that PubChem is indexed by InChI. I added a menu item in the molecule contextual menu to open the PubChem page for the molecule in the default web navigator.

I now consider this bug as fixed in HEAD. I'll not fix in 0.6 because it would be a lot of work and 0.8 should be there soon (march or april).

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Wed 03 Jan 2007 10:21:22 AM UTC, comment #8:

Partially fixed in HEAD. Also added pubchem xml format in default list. Now, not sure it will work, but the problem is mainly an openbabel one.

Btw, I don't understand how comment #5 has been duplicated and replaced #6 from Francesco...

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 02 Jan 2007 04:22:31 PM UTC, comment #7:

About the PubChem xml format, the problem is that there is no mime type at the moment, and GChemPaint is strongly dependent upon mime types.
OpenBabel doc says that the extension is .pc, but when loading a file from PubChem, I get a .xml extension.
It is quite easy to recognize a PubChem xml file by its contents. We just need a mime type definition. chemical-mime-data is where it should be.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 02 Jan 2007 02:40:01 PM UTC, comment #6:

After some thoughts, I came to the following conclusions:
GChemPaint should support as many formats as possible. Requirements are that the format has a mime type (listed in chemical-mime-data) and supported by OpenBabel.
Some types will be hard-coded in GChempaint:

Type .......................... Openbabel-2.1 support
chemical/x-cml ................ yes
chemical/x-mdl-molfile ........ yes
chemical/x-pdb ................ yes
chemical/x-xyz ................ yes
chemical/x-cdx ................ read only
chemical/x-cdxml .............. no
chemical/x-ncbi-asn1 .......... no
chemical/x-ncbi-asn1-binary ... no

On startup, GChemPaint will also check the $HOME/.chempaint/mime-types file and test if mime types listed there (one per line) are supported, so that a user might add some other types. I'll try to write a user interface to populate this file from GChemPaint.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Tue 02 Jan 2007 12:17:27 PM UTC, comment #5:

After some thoughts, I came to the following conclusions:
GChemPaint should support as many formats as possible. Requirements are that the format has a mime type (listed in chemical-mime-data) and supported by OpenBabel.
Some types will be hard-coded in GChempaint:

Type .......................... Openbabel-2.1 support
chemical/x-cml ................ yes
chemical/x-mdl-molfile ........ yes
chemical/x-pdb ................ yes
chemical/x-xyz ................ yes
chemical/x-cdx ................ read only
chemical/x-cdxml .............. no
chemical/x-ncbi-asn1 .......... no
chemical/x-ncbi-asn1-binary ... no

On startup, GChemPaint will also check the $HOME/.chempaint/mime-types file and test if mime types listed there (one per line) are supported, so that a user might add some other types. I'll try to write a user interface to populate this file from GChemPaint.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 31 Dec 2006 10:06:12 AM UTC, comment #4:

Tiff, png, jpeg and eps are already supported (may be not tiff in 0.6.6). gif will be when gdk-pixbuf supports it.

AFAIK, OpenBabel supports .ct files.

PubChem files are not that easy to support. Mainly because they have no mime type, AFAIK. But it should be possible anyway.

Best wishes for 2007.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 31 Dec 2006 09:14:35 AM UTC, comment #3:

OK, it worked.

I add now that an important feature of openbabel (import of PubChem *.ps files) could allow accessing tough gchempaint a FREE large database of structures, not so large as Chemical Abstract though large enough to be of practical use in science. It is 2D. I add that 3D is not necesary for presentations (thus for gchempaint). The rare instances of 3D need for publications are best accomplished with a unix-native molecular mechanics package in OpenGL and with PovRay rendering (that is my way of publishing).

Perhaps it is useful to remember the graphical requests by two major editor, in regard to planning the future of gchempaint, as follows.

RSC (Royal Society of Chemstry). For general graphics TIFF EPS/POSTSCIPT GIF/JPEG. For chem drawing: the outputs of ChemDraw ChemWindows IsisDraw.

ACS (American Chemical Society) musch as RSC, insisting on ChemDraw, specifying settings for it (see ACS on Internet).

I lack expertise in programming, though I offer all the time I can for what I can. I'll submit requests to openbabel once the *.ct format of ChemDraw is creal to me.

Cheers and best wishes for nex year from
francesco pietra

Francesco Pietra <chiendarret>
Sun 31 Dec 2006 09:02:38 AM UTC, comment #2:

I posted a detailed comment, though it was not forwarded. Attached is aconinate.wmf (Window Mefile to be opened with OpenOffice Impress) which shows needed feature (non-wedged bonds, crossed bonds, atom numbering, variable line with, variable bond length and so on, requested by editors).

Once this reply works, I can be more detailed
cheers
francesco pietra

(file #11655)

Francesco Pietra <chiendarret>
Sat 30 Dec 2006 09:50:50 PM UTC, comment #1:

The currently supported formats are: mol, pdb and cml. Export format is choosen according to the file name extension (this will change in next major release).

About numbering, I don't understand what you would like to have.

The other file you atached (.chm, .skc and .cdx) are not supported by openbabel. So you might open a file format request there (if chemdraw files were easy to support, they would have been for long). You'll find supported file formats at http://openbabel.sourceforge.net/wiki/Category:Formats
If some are 2D formats, it would be easy to add them in GChemPaint.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sat 30 Dec 2006 09:11:53 PM UTC, original submission:

On brief examination, I found gchempaint 0.6.6 (on debian i386 etch kernel 2.6.-18.3-k7, GNOME 2.14.3) a very attractive tool that merits full development for scientific use.

Before suggesting additions/changes - which requires a long use of the software - I am concerned about file import / export, a unavoidable task. In principle, gchempaint should automatically export/import according to the capability of opebabel 2.0.2-1 installed on my system. It does not, and I wonder whether there is any support lacking on my system. The only file type I was able to import was *.mol (MDL).

Should the above problem be resolved, I do not understand how file export succeeds because I was unable to see any file setting.

I am attaching a few files, among which only *.mol was imported (quite correctly imported, except for lacking numbering, as it occurs with aconitane.mol). Most other file types are not even detected.

I was able to export *.jpg format, feeding it to OpenOffice and other software.

Thanks for your attention

francesco pietra

Francesco Pietra <chiendarret>

 

Attached Files
file #11655:  aconitane.wmf added by chiendarret (3KiB - application/octet-stream)
file #11634:  aconitane.mol added by chiendarret (2KiB - chemical/x-mdl-molfile - Could submit separately many more files, if needed.)
file #11635:  aconitane.skc added by chiendarret (2KiB - application/octet-stream - Could submit separately many more files, if needed.)
file #11636:  aconitane.chm added by chiendarret (1KiB - application/octet-stream - Could submit separately many more files, if needed.)
file #11637:  6 Glucosylceramid.CDX added by chiendarret (7KiB - chemical/x-cdx - Could submit separately many more files, if needed.)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by jean_brefort (Posted a comment)
  • -unavailable- added by chiendarret (Submitted the item)
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    Follow 11 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon 28 May 2007 04:17:45 PM UTCjean_brefortOpen/ClosedOpen=>Closed
    Wed 03 Jan 2007 09:26:58 PM UTCjean_brefortStatusConfirmed=>Fixed
    Sun 31 Dec 2006 09:02:38 AM UTCchiendarretAttached File-=>Added aconitane.wmf, #11655
    Sat 30 Dec 2006 09:50:50 PM UTCjean_brefortSeverity3 - Normal=>1 - Wish
      StatusNone=>Confirmed
      Assigned toNone=>jean_brefort
    Sat 30 Dec 2006 09:11:53 PM UTCchiendarretAttached File-=>Added aconitane.mol, #11634
      Attached File-=>Added aconitane.skc, #11635
      Attached File-=>Added aconitane.chm, #11636
      Attached File-=>Added 6 Glucosylceramid.CDX, #11637
      Carbon-Copy-=>Added -unavailable-

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