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View Code? Open in Web Editor NEWSMILES Depiction Generator
License: GNU Lesser General Public License v2.1
SMILES Depiction Generator
License: GNU Lesser General Public License v2.1
Aesthetics more than anything else: The more recent versions show a title by default (black), but then let you display the title as an extra as well (red) - which kind of looks strange on the main page. However just deactivating the title option means we don't get titles in the individual URLs...
via direct hyperlink it looks nice:
This feature request seeks to disable the Thiele ring depicting aromaticity, either a) as an option to toggle-on/off (similar to the CIP labels), or b) to disable this feature for good.
I just submitted the two SMILES strings to CDKDepict's input mask
[S@@](O)(=O)(=O)CC(=O)OC(=O)c1c2[n](C)c3[n]1CC(=O)OC(=O)c4ccccc4.C3OC.C2O
CN1[C]2N3C4=C1CO.C3C(=O)OC(=O)c5ccccc5.C2OC.C4(=O)OC(=O)C[S@](=O)(=O)O
which yields two (first structure, vide infra) or one (second structure) dots like for radical compounds in the structure formulae in simultaneous presence of the Thiele ring. Often the Thiele ring has been used to symbolize aromaticity, in case of mononucleous aromatic compounds like benzene, cyclopentadiene, etc. the presence of six \pi electrons. Despite the N-alkylation, however, it would be misleading to assume that there are six \pi electrons plus one (or even two) radical electrons for a total of seven or eight. In addition to offer an easier easier count on electrons, it would yield more consistency in the representation of structure formulae (e.g., the first/left structure used the Thiele ring on the phenyl moiety, the second/right structure does not).
Hey,
I was wondering if it was possible to download the 2D depictions as .png in batch instead of going through them one by one?
Also is there any possibility to standardize the depictions, for example, I want my double bond to be of the same in pictures instead of it zooming out to fit it (i.e. making the double bond shorter in larger compounds).
Regards :)
Reproduce: sudo docker run -p 9081:8080 simolecule/cdkdepict:1.9.2
Expected: Depict website
Got:
org.springframework.web.util.NestedServletException: Handler dispatch failed; nested exception is java.lang.NoSuchMethodError: javax.servlet.http.HttpServletResponse.setContentLengthLong(J)V
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1082)
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:963)
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898)
javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883)
javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
org.apache.catalina.filters.ExpiresFilter.doFilter(ExpiresFilter.java:1179)
Works fine with version 1.8
I thought we'd discussed this but can't find the trace ... would it be possible to accept multiple SMARTS to highlight? I have a functional group of varying length (repeater unit) that I'd like to highlight, see e.g.:
can't capture the entire CF2 chain
vs
can capture the CF2 but not the SO2 vs
only the SO2 ... if I could enter:
S(=O)(=O)C(F)(F),C(F)(F)C(F)(F)
I would be able to highlight the entire chain plus the SO2s that are only connected to CF2s, which is what I am after.
Some URLs:
http://simolecule.com/cdkdepict/depict/cow/svg?smi=OCCNS(%3DO)(%3DO)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F%09FBSE&abbr=off&hdisp=bridgehead&showtitle=false&sma=S(%3DO)(%3DO)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F&zoom=1.6&annotate=none
http://simolecule.com/cdkdepict/depict/cow/svg?smi=OCCNS(%3DO)(%3DO)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F%09FBSE&abbr=off&hdisp=bridgehead&showtitle=false&sma=S(%3DO)(%3DO)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F&zoom=1.6&annotate=none
and smiles:
OCCNS(=O)(=O)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F FBSE
CCNS(=O)(=O)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)F EtFOSE
Other ideas also welcome, this is just one example, thanks!
Benzene-D6: [2H]C1=C([2H])C([2H])=C([2H])C([2H])=C1[2H]
From https://comptox.epa.gov/dashboard/dsstoxdb/results?search=DTXSID7037769
fails:
http://simolecule.com/cdkdepict/depict/bow/svg?smi=[2H]C1=C([2H])C([2H])=C([2H])C([2H])=C1[2H]&abbr=off&hdisp=bridgehead&showtitle=true&zoom=1.3&annotate=none
Workaround with "D" displays:
http://simolecule.com/cdkdepict/depict/bow/svg?smi=[D]C1=C([D])C([D])=C([D])C([D])=C1[D]&abbr=off&hdisp=bridgehead&showtitle=true&zoom=1.3&annotate=none
But I haven't found a nice display workaround for 13C yet - any suggestions?
C1=CC=[13CH]C=C1
Source: https://comptox.epa.gov/dashboard/dsstoxdb/results?search=DTXSID60480506
[13CH]1=[13CH][13CH]=[13CH][13CH]=[13CH]1
Source: https://pubchem.ncbi.nlm.nih.gov/compound/11309472#section=Isomeric-SMILES
Highlighting via SMARTS is possible, but having an extra checkbox to say "align" would be great. I've missed this multiple times. Not sure how much work this would be for you, but just flagging it up.
*c1ncc(c2c1cc(c(c2)OC)OC)C(=O)OCC |$_AP1$|
When the UI flip option is ticked it should also flipped and wedges.
Great work! it's very useful for numbering of molecules.
Recently I referred to CDK API mannual. One of CDKContants is ACDLABS_LABEL。So how
to use it in terms of numbering molecules. Is it be possibble to depict a labeled/numbering molucule follows as the numbering rule of ACDLab ChemSketch? if so, how to configure this contant?
the attachment labeled molecule(top right) drawed in ChemSketch.
Molecules over 40 atoms can not be generated using the mol text in the parameter.
It might be due to a limitation in characters of the URL.
For example:
CC(C)CC(C=C1)=CC=C1C2=CC3=CC=CC(C4=CC5=C(C=C(C6=CC=CC7=C6C=CC=C7)C=C5)C=C4)=C3C=C2
smiles works fine
mol text fails
the same with one carbon less
CCCC(C=C1)=CC=C1C2=CC3=CC=CC(C4=CC5=C(C=C(C6=CC=CC7=C6C=CC=C7)C=C5)C=C4)=C3C=C2
both work fine.
Hi,
I just realized that http://www.simolecule.com/ does not work anymore. Are you decommissioning it?
Not sure if this is feasible ... but wanted to ask ;-)
The reaction SMILES functionality is awesome ... any chance we can deal with more steps?
The top three of these work ... the bottom one is invalid ... but would represent the flow of the top three.
Top two: individual steps. Third: a "two step" reaction that works ... Fourth: nice to have but invalid.
If it's already possible and I just got the syntax wrong, I'm all ears!
C(=O)(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)O PFHpA to PFHxA
C(=O)(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)O PFHxA to PFPeA
C(=O)(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss (x2)]>C(=O)(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)O PFHpA to PFPeA
C(=O)(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)O PFHpA to PFHxA to PFPeA
Am trying to highlight an imidazole fragment on a parent compound. Tried a number of variations on the
imidazole SMILES without success. Past github requests of this issue have disappeared??
Following code will not highlight imidazole? Can anyone help??
tmp_smi
[1] "CC(n1c(C)ncc1c1ccnc(n1)Nc1ccc(cc1)S(=O)(=O)C)C"
tmp_label
[1] "CMGC:CDC2:6gu3:A:FB8"
pen <- parse_smiles(paste(tmp_smi, tmp_label,sep=" "))
atms <- pen$atoms()
bnds <- pen$bonds()
tmp_frag <- 'c1cnc[nH]1' #1H-imidazole
cav <- parse.smiles(tmp_frag)
lactam <- match_smarts(tmp_frag, pen)
depiction() %>%
highlight_atoms(atms, color$LIGHT_GRAY) %>%
highlight_atoms(bnds, color$LIGHT_GRAY) %>%
highlight_atoms(lactam, color$GREEN) %>%
set_size(1400, 1400) %>%
set_zoom(4) %>%
outerglow() %>%
depict(pen) %>%
get_image() %>%
grid::grid.raster()
Would it be possible to have API documentation? In particular, I'm wondering how to depict MOL files which someone in a pub told me was possible.
Sometimes, it is hard to spot missing stereo on structures, having a way to mark them would be helpful to many of us, I guess!
Please tell me if further development is needed! 😊
The on-line version at http://www.simolecule.com/cdkdepict/depict.html displays nicely the non-kekulisable SMILES like 'n1cccc1', but fails to produce an image when "Highlight" is requested:
Error (exception) message, available at the "broken image" link, was: 'org.springframework.web.util.NestedServletException: Request processing failed; nested exception is java.lang.NullPointerException: Bond order was not set.'.
The issue is not reproducible locally, as the downloaded or checked-out and compiled cdkdepict 0.{1,2,3} releases do not parse the 'n1cccc1' on the local machines (see issue #8 ).
Hello, there is a question recently that is very troublesome. Is it possible to set the font of the substituent separately, because the default substituent is italic, and the substituent I want to generate is a normal font. In addition, can the number in the upper right corner of the substituent be placed in the lower right corner? I don’t know where to set it. thank you very much
Would it be possible to display atom mapping and colour map at the same time? I have had a few tries but haven't found a workaround yet, I would like to combine e.g.:
http://simolecule.com/cdkdepict/depict/cow/svg?smi=[CH3%3A9][CH%3A8]([CH3%3A10])[c%3A7]1[cH%3A11][cH%3A12][cH%3A13][cH%3A14][cH%3A15]1.[CH2%3A3]([CH2%3A4][C%3A5](=[O%3A6])Cl)[CH2%3A2][Cl%3A1]%3E[Al%2B3].[Cl-].[Cl-].[Cl-].C(Cl)Cl%3E[CH3%3A9][CH%3A8]([CH3%3A10])[c%3A7]1[cH%3A11][cH%3A12][c%3A13]([cH%3A14][cH%3A15]1)[C%3A5](=[O%3A6])[CH2%3A4][CH2%3A3][CH2%3A2][Cl%3A1]%20%7Cf%3A2.3.4.5%7C%20Friedel-Crafts%20acylation%20[3.10.1]&abbr=off&hdisp=bridgehead&showtitle=false&zoom=1.3&annotate=mapidx
and
http://simolecule.com/cdkdepict/depict/cow/svg?smi=[CH3%3A9][CH%3A8]([CH3%3A10])[c%3A7]1[cH%3A11][cH%3A12][cH%3A13][cH%3A14][cH%3A15]1.[CH2%3A3]([CH2%3A4][C%3A5](=[O%3A6])Cl)[CH2%3A2][Cl%3A1]%3E[Al%2B3].[Cl-].[Cl-].[Cl-].C(Cl)Cl%3E[CH3%3A9][CH%3A8]([CH3%3A10])[c%3A7]1[cH%3A11][cH%3A12][c%3A13]([cH%3A14][cH%3A15]1)[C%3A5](=[O%3A6])[CH2%3A4][CH2%3A3][CH2%3A2][Cl%3A1]%20%7Cf%3A2.3.4.5%7C%20Friedel-Crafts%20acylation%20[3.10.1]&abbr=off&hdisp=bridgehead&showtitle=false&zoom=1.3&annotate=colmap
We have some great use cases. Thanks!
The SMILES string [N+](=O)([O-])[O-]
is incorrectly depicted. There should be an O-
in the depiction. (Not a fan of the coordinate bond, BTW - doesn't make sense to me in this context.)
The highlighted parts are not symmetrical in nature- is this expected?
Case1:
[O:1]=[C:2]([NH2:3])[CH2:4][CH2:5][CH2:6][CH3:7]>[NH4+:3]>[NH3:3]
Case:2
[NH3:3]>[NH4+:3]>[O:1]=[C:2]([NH2:3])[CH2:4][CH2:5][CH2:6][CH3:7]
Cheers,
-Asad
The charges go missing, could make the arrow bond optional
[B-](C)1=[N+](C)C=CC=C1
Nice app! But what are the query parameters that the endpoint accepts? I'm wanting to make use of the SVG generation by calling the API.
Hi,
I'm trying to reproduce the http://www.simolecule.com/cdkdepict/depict.html server action locally on my host, but the local version, both from pre-compiled jars and compiled from sources, fails to parse non-kekulisable SMILES, such as 'n1cccc1' or '[Cu]12(Oc3c(C(=[N]2N=C(O1)c1ccc(O)cc1)C)cc(Br)cc3)[n]1ccccc1' ;). My locally installed version fails "... with root cause
org.openscience.cdk.exception.InvalidSmilesException: could not parse 'n1cccc1', a valid kekulé structure could not be assigned". Compiling CDK and/or Depict from sources works exactly the same (i.e. raises exception), as does a command-line wrapper around CDK 2.1 or 2.2.
While this behaviour apparently stems from the underlying CDK SmilesParser, and seems to be a feature, not a bug, the on-line 'cdkdepict' version mentioned above does parse these SMILES and depicts them nicely ;) (see the attached screen-shot):
Does this mean that the server uses different/newer CDK libraries? If so, would it be possible to have them pushed into the GitHub repo (maybe as an experimental branch)?
Exception messages would also be helpful to debug the case, if presented next to the broken image icon.
The platform for running the 'cdkdepict' 0.3 was:
saulius@koala depict-0.3/ $ java -version
openjdk version "1.8.0_151"
OpenJDK Runtime Environment (build 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12)
OpenJDK 64-Bit Server VM (build 25.151-b12, mixed mode)
saulius@koala depict-0.3/ $ uname -a
Linux koala 4.13.0-32-generic #35~16.04.1-Ubuntu SMP Thu Jan 25 10:13:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
saulius@koala depict-0.3/ $ osname
Ubuntu-16.04
Sincerely,
Saulius (join("@", ( "grazulis", join(".", ("ibt","lt")))) to mail me directly ;)
The build seems broken at the moment (both on master and the 0.3 tag).
It's failing because if can't find com.simolecule:centres-cdk:jar in the maven repo, and indeed that artifact does not seem to be in the OSSRH or Maven Central repos.
[ERROR] Failed to execute goal on project cdkdepict: Could not resolve dependencies for project org.openscience.cdk:cdkdepict:war:0.3: Could not find artifact com.simolecule:centres-cdk:jar:0.1-SNAPSHOT in OSSRH (https://oss.sonatype.org/content/repositories/snapshots) -> [Help 1]
Hi cdk-depict dev team,
a trivy scan found two critical security issues on cdk-depict.. Do you know if the vulnerabilities are accessible via user input? (SMILS, SMARTS,..)
org.springframework:spring-core | CVE-2018-1270 | CRITICAL | 4.2.6.RELEASE | 4.3.16, 5.0.5 | spring-framework: Possible RCE via spring messaging -->avd.aquasec.com/nvd/cve-2018-1270 |
CVE-2018-1275 | 5.0.5, 4.3.16 | spring-framework: Address partial fix for CVE-2018-1270 -->avd.aquasec.com/nvd/cve-2018-1275 | |||
org.springframework:spring-core | CVE-2018-1270 | CRITICAL | 4.2.6.RELEASE | 4.3.16, 5.0.5 | spring-framework: Possible RCE via spring messaging -->avd.aquasec.com/nvd/cve-2018-1270 |
CVE-2018-1275 | 5.0.5, 4.3.16 | spring-framework: Address partial fix for CVE-2018-1270 -->avd.aquasec.com/nvd/cve-2018-1275 |
When using CXSMILES with coordinates to depict an image the stereochemistry is ignored. But if I try to generate an absolute SMILES back from the parsed SMILES I could see that the stereochemistry is still preserved.
C[C@@H](C1=CC=CC=C1)NC(=O)[C@H](C2=CC=CC=C2)NC(=S)NC3=CC=CC=C3 |(-0.5,2.0,;-2.0,1.9,;-2.7,0.6,;-4.2,0.6,;-4.9,-0.8,;-4.1,-2.0,;-2.6,-2.0,;-1.9,-0.7,;-2.8,3.2,;-2.1,4.5,;-0.6,4.6,;-2.9,5.8,;-4.4,5.8,;-5.2,7.0,;-6.7,7.0,;-7.4,5.7,;-6.6,4.4,;-5.1,4.4,;-2.2,7.1,;-3.0,8.4,;-4.5,8.4,;-2.3,9.7,;-3.1,11.0,;-4.6,10.9,;-5.4,12.2,;-4.7,13.5,;-3.2,13.6,;-2.4,12.3,)|
Hi John. Would it be possible to add an option (or make it the default) to use the coordinates as provided if a Molfile is passed in? As far as I can tell, the sdg is always called, but preserving the coords is pretty much the use-case for sending in a Molfile - the med chemists within a project standardise on certain orientations and preserving this helps them.
Hello author, I encountered the following 4 questions in the use of CDK to generate molecular pictures, I hope to get your answer, thank you.
I want to know how to generate a wavy line pattern as shown in the right half of the figure above when there are 3 C atoms connected to the ring structure.
In addition, regarding the molecular short form, there are no pictures in StandardAtomGenerator.generatePseudoSymbol() that can generate images similar to CH, CH2, CH3, etc.
For those that contain * in smiles, the CDK is generated according to the surface meaning. In fact, some refer to A, W, X, H, etc. I want to know how to set up to generate a molecular diagram like the right half of the above picture.
Finally abrv.setEnabled("Me", false);//Maybe we don't want'Me' in the depiction but the generated picture still contains "Me". why
It would be nice to be able to see the isotope designation on an asterisk, which is one way to label R groups. Consider "[15*][15C]", where only the C has the 15 depicted.
I would welcome an option to number the atoms according to the numbering in the InChI. Can I request that, please?
I have tried: mvn clean install
, but I get:
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 3.708 s
[INFO] Finished at: 2017-08-08T09:37:32+02:00
[INFO] Final Memory: 10M/206M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project cdkdepict: Could not resolve dependencies for project com.nextmovesoftware:cdkdepict:war:0.2: The following artifacts could not be resolved: org.openscience.cdk:cdk-depict:jar:2.0-SNAPSHOT, org.openscience.cdk:cdk-forcefield:jar:2.0-SNAPSHOT, uk.ac.ebi.beam:beam-core:jar:0.9.3: Could not find artifact org.openscience.cdk:cdk-depict:jar:2.0-SNAPSHOT -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
We're trying to get our CxSMILES compatible between ChemAxon and CDK, testing visually with CDK Depict. We've run into this - the top example works, but no others (of 27 we've tried) do. Below a selection of the smallest. All 26 SMILES that fail have this "lp" field in the extended SMILES bit, the one that works doesn't. If I select "title" the extended part is just printed out as the title, i.e. it's not recognising it somehow.
C*.CC1=CC=CC=C1 |c:4,6,t:2,m:1:4.5.6|
C*.S=C1NC2=CC=CC=C2N1 |c:6,8,t:4,lp:2:2,4:1,11:1,m:1:8.9|
CCC1=CC=CC=C1.Br*.Br* |c:4,6,t:2,lp:8:3,10:3,m:9:3.4,11:4.5.6.7|
Cl*.Cl*.ClCC1=CC=CC=C1 |c:6,8,t:4,lp:0:3,2:3,4:3,m:1:7.8,3:8.9.10.11|
*C=O.C1CC2C3CCC(C3)C2C1 |lp:2:2,m:0:3.4.5.6.7.8.9.10.11.12|
Are there any plans to add functionality to control rotation/orientation of depictions?
E.g. could I get this:
C[N+]1=CC=C(C=C1)C1=CC=CC=C1
http://simolecule.com/cdkdepict/depict/cot/svg?smi=C[N%2B]1=CC=C(C=C1)C1=CC=CC=C1&abbr=off&hdisp=bridgehead&showtitle=false&zoom=1.6&annotate=none
to lie horizontal instead of vertical, as just a simple example?
This is really useful to help demonstrate structural similarity/differences, where it would be great to keep the orientation of the "base structure" consistent so that one can see/highlight the structural changes. I always ask for this as a reviewer, but can't do it myself yet automatically and I would love to be able to control this ... (or have I missed the option?). Sometimes a slight change in a substituent changes the entire orientation ..
Example (from ChemSketch, just to demonstrate):
I'd add an "enhancement" label if I could ... it's just a suggestion but would be great.
Please correct me if I'm wrong, but in:
C[C@@]1(C)CC/C=C/(C)C1/C=C/C(C)=C/C=C/C(C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C2C/(C)=C/CC[C@]2(C)C
All double-bonds have their configurations defined, including the two that form part of six membered rings.
The last double bond in the SMILES however is depicted as being a crossed bond, despite both being defined and in the same environment (constrained by being in a 6-membered ring) as the first double bond in the SMILES.
http://www.simolecule.com/cdkdepict/depict/bow/svg?smi=C[C@@]1(C)CC%2FC=C%2F(C)C1%2FC=C%2FC(C)=C%2FC=C%2FC(C)=C%2FC=C%2FC=C(C)%2FC=C%2FC=C(C)%2FC=C%2FC2C%2F(C)=C%2FCC[C@]2(C)C&w=80&h=50&abbr=on&hdisp=bridgehead&showtitle=true&zoom=5&annotate=none
The molecule in question is epsilon,epsilon-carotene
The images with transparent background seem to have a minor bug in the display of labeled groups, e.g.
Colour on transparent:
http://www.simolecule.com/cdkdepict/depict/cot/svg?smi=CC(C)[C@H](N*)C(*)=O%20%7C%24%3B%3B%3B%3B%3B_AP1%3B%3B_AP2%3B%24%7C%20valine%20monomer&abbr=off&hdisp=bridgehead&showtitle=false&sma=a1aaaaa1%20&zoom=1.9&annotate=none
But on black or white background you see the 1 and 2, not just black dots.
I can't seem to access the website at the moment (has otherwise been working fine the last few days and as always been super useful!):
https://www.simolecule.com/cdkdepict/depict.html
Any ideas? Thanks in advance (and once again for keeping this up, it is so helpful...)
Hi,
by using the depict webapp client , a saved png file has no backgound (backgound is transparent,see attach.). but i cannot reproduce this operation on server side. That is to say, on the server side , exporting a png image will produce backgound. so how to save a png image without backgroud on server side? here are my codes:
DepictionGenerator dg = new DepictionGenerator();
IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
SmilesParser smipar = new SmilesParser(bldr);
IAtomContainer mol = smipar.parseSmiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C");
dg.withSize(256, 256)
.withMargin(10)
.withAtomNumbers()
.depict(mol)
.writeTo(Depiction.PNG_FMT,"C:\Users\Alan\Desktop\cdk-mol.png");
I prefer to have ketene spelled out as C=C=O rather than C=CO
as in acetyl ketene
@johnmay we can't seem to access the website - first observed by Emma P (@Emma-Palm) yesterday - I also can't access it right now either. We're in withdrawal already ... ;-)
(thanks again for keeping this up, it's so useful!)
This spurs off of a discussion here and a contribution by @Adafede about atom numbering. At present, the program allows input as SMILES, or copy-paste of .sdf. If present and requested, it can can assign and label stereochemistry, too.
Venturing out a couple of variations about and around tartaric acid sketched in DataWarrior (repository on GitHub), I noticed CDKdepict does not process DataWarrior's structures exported in the more recent V3000 dialect of .sdf. Extending the more senior format, this allows to store and process extended stereochemistry as in &
and or
for a stereogenic centre:
Do you think the additional file format and its extended functionality would be worth the effort to be implemented into future versions of CDKDepict?
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