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SMILES Depiction Generator

License: GNU Lesser General Public License v2.1

Java 75.08% CSS 5.89% HTML 10.17% JavaScript 7.70% Dockerfile 1.15%

depict's Introduction

The Chemistry Development Kit (CDK)

License: LGPL v2, see LICENSE.txt

Home Page | JavaDoc | Wiki | Issues | Mailing List

Introduction

The CDK is an open-source Java library for cheminformatics and bioinformatics.

Key Features:

Molecule and reaction valence bond representation.
Read and write file formats: SMILES, SDF, InChI, Mol2, CML, and others.
Efficient molecule processing algorithms: Ring Finding, Kekulisation, Aromaticity.
Coordinate generation and rendering.
Canonical identifiers for fast exact searching.
Substructure and SMARTS pattern searching.
ECFP, Daylight, MACCS, and other fingerprint methods for similarity searching.
QSAR descriptor calculations

Install

The CDK is a class library intended to be used by other programs, it will not run as a stand-alone program.

The library is built with Apache Maven and currently requires Java 1.7 or later. From the root of the project run to build the JAR files for each module. The bundle/target/ directory contains the main JAR with all dependencies included:

$ mvn install

You can also download a pre-built library JAR from releases.

Include the main JAR on the Java classpath when compiling and running your code:

$ javac -cp cdk-2.9.jar MyClass.java
$ java -cp cdk-2.9.jar:. MyClass

If you are using Maven, you can use the uber cdk-bundle to grab everything, note it is much more efficient to use include the modules you need:

<dependency>
  <artifactId>cdk-bundle</artifactId>
  <groupId>org.openscience.cdk</groupId>
  <version>2.9</version>
</dependency>

If you are a Python user, the Cinfony project provides access via Jython. Noel O'Boyle's Cinfony provides a wrapper around the CDK and over toolkits exposing core functionality as a consistent API. ScyJava can also be used, as explain in ChemPyFormatics.

Further details on building the project in integrated development environments (IDEs) are available on the wiki:

Getting Help

The Toolkit-Rosetta Wiki Page provides some examples for common tasks. If you need help using the CDK and have questions please use the user mailing list, [email protected] (you must subscribe here first to post).

Acknowledgments

The CDK developers use YourKit to profile and optimise code.

YourKit supports open source projects with its full-featured Java Profiler. YourKit, LLC is the creator of YourKit Java Profiler and YourKit .NET Profiler, innovative and intelligent tools for profiling Java and .NET applications.

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depict's Issues

Isotope support?

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

Abbreviation of ketene

I prefer to have ketene spelled out as C=C=O rather than C=CO
as in acetyl ketene

symmetric mapping colour

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

www.simolecule.com does not work anymore

Hi,
I just realized that http://www.simolecule.com/ does not work anymore. Are you decommissioning it?

Multiple SMARTS highlighting?

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!

Fix variable attach in brackets (CXSMILES_

[H]OCCO.C* |lp:1:2,4:2,m:6:3.2,Sg:n:5,1,2,3::ht|

Missing charges

The charges go missing, could make the arrow bond optional

[B-](C)1=[N+](C)C=CC=C1

Inconsistent application of crossed bond

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

depict 1H-imidazole

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() %>%

add_title() %>%

         depict(pen) %>%
         get_image() %>%
         grid::grid.raster()

I encountered the following 4 questions in the use of CDK to generate molecular pictures

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

relabelling of atoms is possible?

I'm not familiar with cdk depict module and can't find a way to relabel atoms for IUPAC atoms labeling order.
so, is it possible to relabel atoms for a molecule?
e.g.: make changes as this way: atom9 relabelled to 1, atom12 to 3, atom2 to 7.....

The on-line version fails when highlighting is requested on no-kekulisable smiles

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 ).

latest Docker fails with exception

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

Smiles aren't aligned properly

*c1ncc(c2c1cc(c(c2)OC)OC)C(=O)OCC |$_AP1$|

@johnmay

feature request: generating multiple molecue structures within one image

Hi,John,
based on multiple extended smiles like: "CN1C=NC2=C1C(=O)N(C(=O)N2C)C caffeine.CN1C=NC2=C1C(=O)N(C(=O)N2C)C caffeine.CN1C=NC2=C1C(=O)N(C(=O)N2C)C caffeine" to generate multiple structures in one image , which contain title informations look like followiing. is it applicabale?

Duplicate Titles

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:

Option to depict Molfile-provided coordinates

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.

API documentation

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.

Fail to build

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

What are the query params?

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.

fork me icon broken?

If I open the image in a separate window, I get:

Downloaded cdkdepict 0.3 works differently than on the server

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 ;)

how to save a png file without background on server side?

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");

vulnerability in trivy scan

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

Salt overlapping bond

Salt placement is usually great but I came across the following where the Br- overlaps a bond.

C=C(C[N+](C)(C)C)OC(=O).[Br-]

Depiction of C/N=C/C not as nice as C/C=C/C

C/N=C/Cis depicted as follows where the connection to the double bond from the carbon could be improved:

In contrast, C/C=C/C looks great:

Negative charge missing

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.)

How to disable the Thiele ring?

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).

CDK Depict website down?

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...)

Flip should flip stereobond

When the UI flip option is ticked it should also flipped and wedges.

Atom Mapping and Colour Map at the same time?

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!

Bug in depicting CXSMILES with Stereochemistry

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,)|

numbering follows rule of ACDLab ChemSketch

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.

CxSMILES compatibility

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|

Long Mol Text Fail

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.

thoughts about input of .sdf (version 3000) / extended stereochemistry

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?

2022-10-26_stereochemistry_variations.zip

Batch download as PNG and standardizing the image size?

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 :)

Aromatic display

Dear all,
is aromatic display (like DepictionGenerator.withAromaticDisplay()) available in the CDK Depict web app? By default, it seems to be turned off (see below) and I could not find a setting to turn it on.

Transparent background bug in labeled group display

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

Black on Transparent:

But on black or white background you see the 1 and 2, not just black dots.

Rotatable depiction possible?

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.

Is it possible to set the font of the substituent independently

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

atom numbering based on the InChI

I would welcome an option to number the atoms according to the numbering in the InChI. Can I request that, please?

missing stereo in CXSMILES depiction

Given two (CX)SMILES:

[*]C(=O)[C@@H](N)CCCCN[*] |Sg:n:1,2,3,4,5,6,7,8,9::ht|
C(=O)[C@@H](N)CCCCN

and CIP Stereo Labeling turned on, only the SMILES and not the CXSMILES shows the CIP label:

Build broken - centres-cdk not in maven repo?

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]

Multi-step reaction SMILES?

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