Gnome Chemistry Utils - Support: sr #108952, GChemPaint: input and output of...
You are not allowed to post comments on this tracker with your current authentication level.
sr #108952: GChemPaint: input and output of ChemDraw files
Submitter: | Bernd Speiser <berndspeiser> | ||
Submitted: | Sun 10 Jan 2016 01:14:25 PM UTC | ||
Category: | None | Priority: | 5 - Normal |
Severity: | 3 - Normal | Status: | Done |
Privacy: | Public | Assigned to: | jean_brefort |
Open/Closed: | Closed | Operating System: | GNU/Linux |
Jump to the original submission
Tue 29 Mar 2016 06:59:58 AM UTC, comment #43: |
Jean Bréfort <jean_brefort> |
Thu 24 Mar 2016 05:22:04 PM UTC, comment #42: Sure, I need to polish some details and release, hopefully next week.
|
Jean Bréfort <jean_brefort> |
Thu 24 Mar 2016 04:55:31 PM UTC, comment #41: yes, nice indeed! So, we will only need a new version now to have this all together. Thanks a lot for these advances. We should now be able to round-trip between GChemPaint and ChemDraw easily.
|
Bernd Speiser <berndspeiser> |
Wed 23 Mar 2016 12:47:33 PM UTC, comment #40: Nice, just what I expected. |
Jean Bréfort <jean_brefort> |
Wed 23 Mar 2016 12:39:55 PM UTC, comment #39: I had no problems with opening the file. |
Georg Zitzer <zit112> |
Wed 23 Mar 2016 12:31:57 PM UTC, comment #38: I'd like to know how this file looks like when loaded in ChemDraw and what it gives when saved back to CDXML. This is probably the last sample I need for this issue (unless ChemDraw is unable to load it). Thanks for all. |
Jean Bréfort <jean_brefort> |
Fri 18 Mar 2016 11:03:30 AM UTC, comment #37: The new CDXML-file looks just like the firt ChemDraw-sample. Could´t find any differences or mistakes. |
Georg Zitzer <zit112> |
Thu 17 Mar 2016 04:32:48 PM UTC, comment #36: The CDXML support is now at least as good than the CDX support, at least hopefully. I still need to enhance a fexw details, but the original sample is now correctly imported and exported by GChemPaint (svn code only for now). |
Jean Bréfort <jean_brefort> |
Thu 17 Mar 2016 01:10:02 PM UTC, comment #35: Thanks. The variable case looks really weird. I'll make all thses persistent. |
Jean Bréfort <jean_brefort> |
Thu 17 Mar 2016 12:48:31 PM UTC, comment #34: The index has the same font size as the text.
|
Georg Zitzer <zit112> |
Thu 17 Mar 2016 11:42:34 AM UTC, comment #33: The index font size should be fixed. I tried another solution for the interline, but I'm not really happy with it. I'd need for another sample with mulitiline texts. The documentation says that the line height set to three different values: auto, variable and some fixed value. As there is nothing in the doc about how this is saved to cdxml, I'd need the cdxml (and the pdf screenshot). The cdx file would not be really useful. |
Jean Bréfort <jean_brefort> |
Tue 15 Mar 2016 11:19:45 AM UTC, comment #32: The issue with the double bond seems to be fixed, but I´ve uploaded the sample with 2-Butene.
|
Georg Zitzer <zit112> |
Fri 11 Mar 2016 04:47:35 PM UTC, comment #31: I tried to fix all previous issues in Sample.cdx. Please tell me if some are still there. The double bond issue should be fixed even if they still don't appear on the same side in GChemPaint. The automatic side is not the same in both programs and GChemPaint does no support manual setting for double bonds for now. I am not sure to understand the CDX documentation since the manually positioned double bond in Sample.cdx is said to be "Left", but I see it at right in the pdf. I'd like a sample with trans-2-butene and a maually positiond double bond (either left or right). |
Jean Bréfort <jean_brefort> |
Thu 03 Mar 2016 03:04:49 PM UTC, comment #30: Confirmed - after installing the patch, the file 0.14.11_test.cdx can be read correctly |
Bernd Speiser <berndspeiser> |
Thu 03 Mar 2016 09:45:04 AM UTC, comment #29: This patch applies to 0.14.11.
|
Jean Bréfort <jean_brefort> |
Thu 03 Mar 2016 09:25:06 AM UTC, comment #28: We have checked again, and indeed, 0.14.11_test.cdx is correctly read by ChemDraw. |
Bernd Speiser <berndspeiser> |
Thu 03 Mar 2016 09:13:36 AM UTC, comment #27: I was bad, the file is correct (but with an empty text run). I'll commit a patch to both branches (avoiding empty runs when saving and supporting them on loading). |
Jean Bréfort <jean_brefort> |
Wed 02 Mar 2016 09:13:10 PM UTC, comment #26: 0.14.11_test.cdx is invalid, or at least looks invalid to me, strange that ChemDraw reads it. |
Jean Bréfort <jean_brefort> |
Wed 02 Mar 2016 01:26:47 PM UTC, comment #25: Thanks for putting this into a new version.
|
Bernd Speiser <berndspeiser> |
Tue 01 Mar 2016 02:04:56 PM UTC, comment #24: The fonts.* samples can't be loaded in GChemPaint, unfortunately, because "Arial" and "Times New Roman" can't be interpreted as chemical symbols. Anyway, I think I know the solution to this issue. I supposed that when the font field was missing ChemDraw would use the default font for the file, but it seems that it uses Arial instead. I'll add the missing string. |
Jean Bréfort <jean_brefort> |
Mon 29 Feb 2016 05:00:37 PM UTC, comment #23: The font change is not related to encoding. I suppose it is an export issue, probably a field that gchempaint skips because it does not use it.
|
Jean Bréfort <jean_brefort> |
Mon 29 Feb 2016 04:32:13 PM UTC, comment #22: The file "fonts" contains two text-objects and two molecules with text, each in "Times New Roman" and "Arial" (Size 12) with subscrepted text. Is it possible that encoding with iso-8859-1, leads to changes of fonts? |
Georg Zitzer <zit112> |
Mon 29 Feb 2016 04:22:22 PM UTC, comment #21: We have compared the original ChemDraw-file and the one after encoding and there are some more changes:
|
Georg Zitzer <zit112> |
Sun 28 Feb 2016 08:22:44 AM UTC, comment #20: I also noticed that one of the C=N bonds has changed. |
Jean Bréfort <jean_brefort> |
Fri 26 Feb 2016 01:01:05 PM UTC, comment #19: The '+' sign appears a bit high, I'll try to enhance that, but it is not that easy to interpret the saved bounding box (which is not a bounding box, both x values are the same). Thanks for the feedback. |
Jean Bréfort <jean_brefort> |
Fri 26 Feb 2016 12:25:25 PM UTC, comment #18: Seems to be the way it schould be (I use ChemDraw Professional V. 15.0.0.106). |
Georg Zitzer <zit112> |
Sun 21 Feb 2016 04:26:45 PM UTC, comment #17: Looks like simple files like Sample.cdx can now be loaded and saved in GChemPaint. The '+' sign will probably be slightly moved unless ChemDraw aligns it automatically.
|
Jean Bréfort <jean_brefort> |
Mon 15 Feb 2016 07:36:56 PM UTC, comment #16: I'll use iso-8859-1 as encoding for Arial and Times New Roman then, and unicode for other fonts until somebody tells me how it is possible to know the encoding used by ChemDraw for each font. GChemPaint always use utf-8 whatever the fonts it uses. |
Jean Bréfort <jean_brefort> |
Mon 15 Feb 2016 02:23:39 PM UTC, comment #15: But it worked. The text-objekt behaves like an usual ChemDraw-text. Now I can edit and save it. |
Georg Zitzer <zit112> |
Mon 15 Feb 2016 12:26:52 PM UTC, comment #14: Not so nice then. I attach the same sample but with iso-8859-1 encoding to be sure that the issue is not related, but I'm pretty sure that it comes from some mandatory missing field(s). |
Jean Bréfort <jean_brefort> |
Mon 15 Feb 2016 10:23:23 AM UTC, comment #13: The sample can be loaded. The text-object can also be moved but editing leads to erasing of the text and it´s not possibe to undo the last step. |
Georg Zitzer <zit112> |
Fri 12 Feb 2016 05:34:41 PM UTC, comment #12: I'd like to know if this new sample is correctly loaded by ChemDraw. I used unicode encoding, not sure it's a good idea but the proper encoding is not so easy to dtermine. |
Jean Bréfort <jean_brefort> |
Wed 10 Feb 2016 01:20:17 PM UTC, comment #11: Yes, I mean that the differences are due to different default behaviors between the two programs, so reimporting into ChemDraw should drop the differences (hopefully, but it needs to be checked).
|
Jean Bréfort <jean_brefort> |
Wed 10 Feb 2016 01:06:51 PM UTC, comment #10: Sorry, I overlooked the different atom order in "OH". Again, in the sample case it is not important.
|
Bernd Speiser <berndspeiser> |
Tue 09 Feb 2016 04:52:58 PM UTC, comment #9: There are some other differences :
|
Jean Bréfort <jean_brefort> |
Tue 09 Feb 2016 03:00:42 PM UTC, comment #8: Thanks for your recent efforts.
|
Bernd Speiser <berndspeiser> |
Sat 06 Feb 2016 10:16:54 AM UTC, comment #7: CDX import of reactions now seems to work in the development branch, just the '+' sign is not properly aligned, but this is almost impossible to fix). For stable branch, things work too, but not fully, reaction conditions are not linked to the arrow because this would need too invasive changes. There are several options:
|
Jean Bréfort <jean_brefort> |
Wed 20 Jan 2016 09:58:56 AM UTC, comment #6: Herewith I attach files representing two mesomeric structures of benzene in cdx, cdxml and pdf format for further testing.
|
Bernd Speiser <berndspeiser> |
Sun 17 Jan 2016 03:20:40 PM UTC, comment #5: Made some progress in CDX import. The style is imported so that now things look more the same in GChemPaint and ChemDraw, see attached GChemPaint printed output.
|
Jean Bréfort <jean_brefort> |
Fri 15 Jan 2016 10:17:12 AM UTC, comment #4: I fixed most of the broken issue, but found another one when testing all the chemdraw files around. I'm a bit sick at the moment so not very productive. The plan is to first import your samples with no loss, then play with export. I don't need other samples for now.
|
Jean Bréfort <jean_brefort> |
Fri 15 Jan 2016 10:02:21 AM UTC, comment #3: Sounds bad and I conclude that first of all the import functionality should be fixed.
|
Bernd Speiser <berndspeiser> |
Mon 11 Jan 2016 06:50:34 AM UTC, comment #2: It will not be easy to fix. Issues are:
|
Jean Bréfort <jean_brefort> |
Sun 10 Jan 2016 08:02:45 PM UTC, comment #1: Hmm, looks like the cdxml importer is badly broken. |
Jean Bréfort <jean_brefort> |
Sun 10 Jan 2016 01:14:25 PM UTC, original submission:
A problem to read and write files from ChemDraw software (either in the cdx or the cdxml format) is found.
|
Bernd Speiser <berndspeiser> |
Depends on the following items: None found
Items that depend on this one: None found
There are 0 votes so far. Votes easily highlight which items people would like to see resolved in priority, independently of the priority of the item set by tracker managers.
Follow 25 latest changes.
Date | Changed by | Updated Field | Previous Value | => | Replaced by |
---|---|---|---|---|---|
2016-03-29 | jean_brefort | Status | In Progress | Done | |
Open/Closed | Open | Closed | |||
2016-03-24 | berndspeiser | Attached File | - | Added GChemPaint-LibreOffice.odt, #36750 | |
Attached File | - | Added GChemPaint-LibreOffice.pdf, #36751 | |||
2016-03-23 | zit112 | Attached File | - | Added anisole.pdf, #36734 | |
Attached File | - | Added anisole.cdxml, #36735 | |||
Attached File | - | Added anisole.cdx, #36736 | |||
2016-03-23 | jean_brefort | Attached File | - | Added anisole.cdxml, #36733 | |
2016-03-18 | zit112 | Attached File | - | Added Sample-gcp.pdf, #36684 | |
2016-03-17 | jean_brefort | Status | None | In Progress | |
Assigned to | None | jean_brefort | |||
2016-03-17 | jean_brefort | Attached File | - | Added Sample-gcp.cdxml, #36672 | |
2016-03-17 | zit112 | Attached File | - | Added Line spacing.cdx, #36669 | |
Attached File | - | Added Line spacing.pdf, #36670 | |||
Attached File | - | Added Line spacing.cdxml, #36671 | |||
2016-03-17 | jean_brefort | Attached File | - | Added Sample-gcp3.cdx, #36668 | |
2016-03-15 | zit112 | Attached File | - | Added 2-Butene.cdx, #36648 | |
Attached File | - | Added 2-Butene.pdf, #36649 | |||
2016-03-11 | jean_brefort | Attached File | - | Added Sample-gcp2.cdx, #36603 | |
2016-03-03 | jean_brefort | Attached File | - | Added empty_runs.patch, #36534 | |
2016-03-02 | berndspeiser | Attached File | - | Added 0.14.11_test.tar, #36527 | |
2016-02-29 | zit112 | Attached File | - | Added fonts.pdf, #36507 | |
Attached File | - | Added fonts.cdxml, #36508 | |||
Attached File | - | Added fonts.cdx, #36509 | |||
2016-02-29 | zit112 | Attached File | - | Added Sample-gcp (4).cdx _.pdf, #36506 |
Powered by Savane 3.13-d3ae.
Corresponding source code
0.14.12 released.
Feel free to open as many bug reports as needed (one per issue, please).