Re: [Cdk-user] CDK v2.2

[Syed Asad Rahman]

I agree that a customised constructor is good and efficient though sometimes 
there is an overhead in doing so. It’s a choice between driving ones car or 
taking a public transport to work 

From: John Mayfield 
Date: Tuesday, 30 October 2018 at 17:00
To: Christoph Steinbeck 
Cc: Syed Asad Rahman , cdkuser 

Subject: Re: [Cdk-user] CDK v2.2

It's more that clone() is an indication of bad style. Unfortunately a lot of 
the CDK (particularly the QSAR code) is built on the premise this is easy and 
cheap. Also all out clone() implementations throw CloneNotSupported when they 
shouldn't this leads to ugly try/catch down stream.

It is true there isn't a viable alternative for a deep copy and having a 
AtomContainerManipulator.copy() for example would help, ideally the copy 
constructor should have been a deep copy (it's currently a shallow).

John


On Tue, 30 Oct 2018 at 16:50, Christoph Steinbeck 
mailto:christoph.steinb...@uni-jena.de>> wrote:

> On 30. Oct 2018, at 17:15, John Mayfield 
> mailto:john.wilkinson...@gmail.com>> wrote:
>
> 2) Looks like a bug, but you really really really should not be using clone.

You also say that in https://github.com/cdk/cdk/wiki/AtomContainer2, which is a 
great guidance, apart from indicating alternatives cloning for the less 
enlightened :)

The only alternative to cloning is to write code which comes down to a custom 
clone method, or not? i.e. you create a new AtomContainer and copy over the 
objects that you need for your algorithm, by, say, instantiating new atoms with 
identical properties, and adding them to the AC.

Is your argument that clone does a lot more work than one might need in one's 
specific case?

Kind regards,

Chris

—
Prof. Dr. Christoph Steinbeck
Analytical Chemistry - Cheminformatics and Chemometrics
Friedrich-Schiller-University Jena, Germany
Phone Secretariat: +49-3641-948171
http://cheminf.uni-jena.de
http://orcid.org/-0001-6966-0814

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
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Re: [Cdk-user] CDK v2.2

[John Mayfield]

On (2) you can also just remove all the Sgroup info, likely you're not even
using it.

mol.setProperty(CDKConstants.CTAB_SGROUPS, null);
>

On Tue, 30 Oct 2018 at 16:15, John Mayfield 
wrote:

> 1) You can just include cdk-legacy and use the existing, but the
> functionality was just a connivence the same as getMinMax(container) but
> without the Java AWT dependency which caused problems for Andriod/SWT. IIRC
> this was the only place AWT was use in the core package. If you just want
> the width/height use: get2DDimension. Note this was 4+ years ago :-)
> https://github.com/cdk/cdk/commit/214785ce18e2d06f1ba7d9fddc82c0ea9753a385#diff-9a119f1ec045c70b21aa694d01bbc773
> 2) Looks like a bug, but you really really really should not be using
> clone.
>
> On Tue, 30 Oct 2018 at 15:51, Syed Asad Rahman  wrote:
>
>> Thanks.
>>
>>
>>
>> I have started to play with the new release.
>>
>> Got few regression which is fine with API changes.
>>
>>
>>
>> Any pointer please?
>>
>>
>>
>> Q1) What is the equivalent of GeometryTools.getRectangle2D in the new
>> GeometryUtil?
>>
>> import static org.openscience.cdk.geometry.GeometryTools.getRectangle2D;
>>
>> Q2)
>>
>> IAtomContainer clone = org.clone();
>>
>>
>>
>> Throws java.lang.ClassCastException: java.util.ArrayList cannot be cast
>> to org.openscience.cdk.sgroup.SgroupBracket
>>
>> java.lang.ClassCastException: java.util.ArrayList cannot be cast to
>> org.openscience.cdk.sgroup.SgroupBracket
>>
>> at
>> org.openscience.cdk.tools.manipulator.SgroupManipulator.copy(SgroupManipulator.java:108)
>>
>> at
>> org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1408)
>>
>>
>>
>> *From: *John Mayfield 
>> *Date: *Tuesday, 30 October 2018 at 15:39
>> *To: *Syed Asad Rahman 
>> *Cc: *cdkuser 
>> *Subject: *Re: [Cdk-user] CDK v2.2
>>
>>
>>
>> Yes, but there has been no changes to SilentChemObjectBuilder...?
>>
>>
>>
>> - I did try testing RDT with the new AtomContainer APIs but your tests
>> took too long to run and I have stuff to do :-).
>>
>> - Likewise I did the same with Ambit but there are integration tests with
>> dependencies on DBs etc so difficult to see if there is actually anything
>> wrong. Bigger problem in Ambit is extended type (e.g. SuppleAtomContainer)
>> which needs to implement some new methods. Often trivial stuff convenience
>> stuff that could be resolved with Java 8 and default method implementations
>> on interfaces, but we're currently on Java 7 so not an option.
>>
>>
>>
>> John
>>
>>
>>
>> On Tue, 30 Oct 2018 at 14:47, Syed Asad Rahman  wrote:
>>
>> Thank you John and Developers!
>>
>>
>>
>> This is a fantastic news!
>>
>> One quick question before I pull it into SMSD and RDT - Is 
>> SilentChemObjectBuilder thread safe?
>>
>> Best wishes,
>>
>> -Asad
>>
>>
>>
>> *From: *John Mayfield 
>> *Date: *Tuesday, 30 October 2018 at 12:01
>> *To: *cdkuser 
>> *Subject: *[Cdk-user] CDK v2.2
>>
>>
>>
>> Dear CDK users,
>>
>>
>>
>> CDK 2.2 is now released and can be obtained from Maven central or the
>> GitHub <https://github.com/cdk/cdk/releases/tag/cdk-2.2> site. The full 
>> release
>> notes <https://github.com/cdk/cdk/wiki/2.2-Release-Notes> provide
>> details on the new features and changes.
>>
>>
>>
>> As noted in v2.1/v2.1.1 the AtomContainer2
>> <https://github.com/cdk/cdk/wiki/AtomContainer2> is now the default so
>> if you didn't try running v2.1/v2.1.1 with the flag
>> CdkUseLegacyAtomContainer=false you may some breakages. As highlighted on
>> the wiki page <https://github.com/cdk/cdk/wiki/AtomContainer2> this
>> normally just requires addAtom/Bond statements be reordered and using
>> ``Objects.equals(container1, container2)`` instead of reference comparison
>> (container1 == container2).
>>
>>
>>
>> - John
>>
>>
>>
>>
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Re: [Cdk-user] CDK v2.2

[John Mayfield]

It's more that clone() is an indication of bad style. Unfortunately a lot
of the CDK (particularly the QSAR code) is built on the premise this is
easy and cheap. Also all out *clone()* implementations throw
*CloneNotSupported* when they shouldn't this leads to ugly try/catch down
stream.

It is true there isn't a viable alternative for a deep copy and having a
*AtomContainerManipulator.copy()* for example would help, ideally the copy
constructor should have been a deep copy (it's currently a shallow).

John


On Tue, 30 Oct 2018 at 16:50, Christoph Steinbeck <
christoph.steinb...@uni-jena.de> wrote:

>
> > On 30. Oct 2018, at 17:15, John Mayfield 
> wrote:
> >
> > 2) Looks like a bug, but you really really really should not be using
> clone.
>
> You also say that in https://github.com/cdk/cdk/wiki/AtomContainer2,
> which is a great guidance, apart from indicating alternatives cloning for
> the less enlightened :)
>
> The only alternative to cloning is to write code which comes down to a
> custom clone method, or not? i.e. you create a new AtomContainer and copy
> over the objects that you need for your algorithm, by, say, instantiating
> new atoms with identical properties, and adding them to the AC.
>
> Is your argument that clone does a lot more work than one might need in
> one's specific case?
>
> Kind regards,
>
> Chris
>
> —
> Prof. Dr. Christoph Steinbeck
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> Phone Secretariat: +49-3641-948171
> http://cheminf.uni-jena.de
> http://orcid.org/-0001-6966-0814
>
> What is man but that lofty spirit - that sense of enterprise.
> ... Kirk, "I, Mudd," stardate 4513.3..
>
>
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Re: [Cdk-user] CDK v2.2

[Christoph Steinbeck]

> On 30. Oct 2018, at 17:15, John Mayfield  wrote:
> 
> 2) Looks like a bug, but you really really really should not be using clone. 

You also say that in https://github.com/cdk/cdk/wiki/AtomContainer2, which is a 
great guidance, apart from indicating alternatives cloning for the less 
enlightened :)

The only alternative to cloning is to write code which comes down to a custom 
clone method, or not? i.e. you create a new AtomContainer and copy over the 
objects that you need for your algorithm, by, say, instantiating new atoms with 
identical properties, and adding them to the AC. 

Is your argument that clone does a lot more work than one might need in one's 
specific case?

Kind regards, 

Chris

— 
Prof. Dr. Christoph Steinbeck
Analytical Chemistry - Cheminformatics and Chemometrics
Friedrich-Schiller-University Jena, Germany
Phone Secretariat: +49-3641-948171
http://cheminf.uni-jena.de
http://orcid.org/-0001-6966-0814

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..



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Re: [Cdk-user] CDK v2.2

[Syed Asad Rahman]

Thanks!

  1.  Great- perhaps I was out of touch 
  2.  As of now, I will perhaps remove the S-groups flag. What would be a 
preferred way to circumvent clone?
-Asad

From: John Mayfield 
Date: Tuesday, 30 October 2018 at 16:15
To: Syed Asad Rahman 
Cc: cdkuser 
Subject: Re: [Cdk-user] CDK v2.2

1) You can just include cdk-legacy and use the existing, but the functionality 
was just a connivence the same as getMinMax(container) but without the Java AWT 
dependency which caused problems for Andriod/SWT. IIRC this was the only place 
AWT was use in the core package. If you just want the width/height use: 
get2DDimension. Note this was 4+ years ago :-) 
https://github.com/cdk/cdk/commit/214785ce18e2d06f1ba7d9fddc82c0ea9753a385#diff-9a119f1ec045c70b21aa694d01bbc773
2) Looks like a bug, but you really really really should not be using clone.

On Tue, 30 Oct 2018 at 15:51, Syed Asad Rahman 
mailto:s9a...@gmail.com>> wrote:
Thanks.

I have started to play with the new release.
Got few regression which is fine with API changes.

Any pointer please?

Q1) What is the equivalent of GeometryTools.getRectangle2D in the new 
GeometryUtil?
import static org.openscience.cdk.geometry.GeometryTools.getRectangle2D;
Q2)
IAtomContainer clone = org.clone();

Throws java.lang.ClassCastException: java.util.ArrayList cannot be cast to 
org.openscience.cdk.sgroup.SgroupBracket
java.lang.ClassCastException: java.util.ArrayList cannot be cast to 
org.openscience.cdk.sgroup.SgroupBracket
at 
org.openscience.cdk.tools.manipulator.SgroupManipulator.copy(SgroupManipulator.java:108)
at 
org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1408)

From: John Mayfield 
mailto:john.wilkinson...@gmail.com>>
Date: Tuesday, 30 October 2018 at 15:39
To: Syed Asad Rahman mailto:s9a...@gmail.com>>
Cc: cdkuser 
mailto:cdk-user@lists.sourceforge.net>>
Subject: Re: [Cdk-user] CDK v2.2

Yes, but there has been no changes to SilentChemObjectBuilder...?

- I did try testing RDT with the new AtomContainer APIs but your tests took too 
long to run and I have stuff to do :-).
- Likewise I did the same with Ambit but there are integration tests with 
dependencies on DBs etc so difficult to see if there is actually anything 
wrong. Bigger problem in Ambit is extended type (e.g. SuppleAtomContainer) 
which needs to implement some new methods. Often trivial stuff convenience 
stuff that could be resolved with Java 8 and default method implementations on 
interfaces, but we're currently on Java 7 so not an option.

John

On Tue, 30 Oct 2018 at 14:47, Syed Asad Rahman 
mailto:s9a...@gmail.com>> wrote:
Thank you John and Developers!


This is a fantastic news!

One quick question before I pull it into SMSD and RDT - Is 
SilentChemObjectBuilder thread safe?
Best wishes,
-Asad

From: John Mayfield 
mailto:john.wilkinson...@gmail.com>>
Date: Tuesday, 30 October 2018 at 12:01
To: cdkuser 
mailto:cdk-user@lists.sourceforge.net>>
Subject: [Cdk-user] CDK v2.2

Dear CDK users,

CDK 2.2 is now released and can be obtained from Maven central or the 
GitHub<https://github.com/cdk/cdk/releases/tag/cdk-2.2> site. The full release 
notes<https://github.com/cdk/cdk/wiki/2.2-Release-Notes> provide details on the 
new features and changes.

As noted in v2.1/v2.1.1 the 
AtomContainer2<https://github.com/cdk/cdk/wiki/AtomContainer2> is now the 
default so if you didn't try running v2.1/v2.1.1 with the flag 
CdkUseLegacyAtomContainer=false you may some breakages. As highlighted on the 
wiki page<https://github.com/cdk/cdk/wiki/AtomContainer2> this normally just 
requires addAtom/Bond statements be reordered and using 
``Objects.equals(container1, container2)`` instead of reference comparison 
(container1 == container2).

- John

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Re: [Cdk-user] CDK v2.2

[John Mayfield]

1) You can just include cdk-legacy and use the existing, but the
functionality was just a connivence the same as getMinMax(container) but
without the Java AWT dependency which caused problems for Andriod/SWT. IIRC
this was the only place AWT was use in the core package. If you just want
the width/height use: get2DDimension. Note this was 4+ years ago :-)
https://github.com/cdk/cdk/commit/214785ce18e2d06f1ba7d9fddc82c0ea9753a385#diff-9a119f1ec045c70b21aa694d01bbc773
2) Looks like a bug, but you really really really should not be using
clone.

On Tue, 30 Oct 2018 at 15:51, Syed Asad Rahman  wrote:

> Thanks.
>
>
>
> I have started to play with the new release.
>
> Got few regression which is fine with API changes.
>
>
>
> Any pointer please?
>
>
>
> Q1) What is the equivalent of GeometryTools.getRectangle2D in the new
> GeometryUtil?
>
> import static org.openscience.cdk.geometry.GeometryTools.getRectangle2D;
>
> Q2)
>
> IAtomContainer clone = org.clone();
>
>
>
> Throws java.lang.ClassCastException: java.util.ArrayList cannot be cast to
> org.openscience.cdk.sgroup.SgroupBracket
>
> java.lang.ClassCastException: java.util.ArrayList cannot be cast to
> org.openscience.cdk.sgroup.SgroupBracket
>
> at
> org.openscience.cdk.tools.manipulator.SgroupManipulator.copy(SgroupManipulator.java:108)
>
> at
> org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1408)
>
>
>
> *From: *John Mayfield 
> *Date: *Tuesday, 30 October 2018 at 15:39
> *To: *Syed Asad Rahman 
> *Cc: *cdkuser 
> *Subject: *Re: [Cdk-user] CDK v2.2
>
>
>
> Yes, but there has been no changes to SilentChemObjectBuilder...?
>
>
>
> - I did try testing RDT with the new AtomContainer APIs but your tests
> took too long to run and I have stuff to do :-).
>
> - Likewise I did the same with Ambit but there are integration tests with
> dependencies on DBs etc so difficult to see if there is actually anything
> wrong. Bigger problem in Ambit is extended type (e.g. SuppleAtomContainer)
> which needs to implement some new methods. Often trivial stuff convenience
> stuff that could be resolved with Java 8 and default method implementations
> on interfaces, but we're currently on Java 7 so not an option.
>
>
>
> John
>
>
>
> On Tue, 30 Oct 2018 at 14:47, Syed Asad Rahman  wrote:
>
> Thank you John and Developers!
>
>
>
> This is a fantastic news!
>
> One quick question before I pull it into SMSD and RDT - Is 
> SilentChemObjectBuilder thread safe?
>
> Best wishes,
>
> -Asad
>
>
>
> *From: *John Mayfield 
> *Date: *Tuesday, 30 October 2018 at 12:01
> *To: *cdkuser 
> *Subject: *[Cdk-user] CDK v2.2
>
>
>
> Dear CDK users,
>
>
>
> CDK 2.2 is now released and can be obtained from Maven central or the
> GitHub <https://github.com/cdk/cdk/releases/tag/cdk-2.2> site. The full 
> release
> notes <https://github.com/cdk/cdk/wiki/2.2-Release-Notes> provide details
> on the new features and changes.
>
>
>
> As noted in v2.1/v2.1.1 the AtomContainer2
> <https://github.com/cdk/cdk/wiki/AtomContainer2> is now the default so if
> you didn't try running v2.1/v2.1.1 with the flag
> CdkUseLegacyAtomContainer=false you may some breakages. As highlighted on
> the wiki page <https://github.com/cdk/cdk/wiki/AtomContainer2> this
> normally just requires addAtom/Bond statements be reordered and using
> ``Objects.equals(container1, container2)`` instead of reference comparison
> (container1 == container2).
>
>
>
> - John
>
>
>
>
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Re: [Cdk-user] CDK v2.2

[Syed Asad Rahman]

Thanks.

I have started to play with the new release.
Got few regression which is fine with API changes.

Any pointer please?

Q1) What is the equivalent of GeometryTools.getRectangle2D in the new 
GeometryUtil?
import static org.openscience.cdk.geometry.GeometryTools.getRectangle2D;
Q2)
IAtomContainer clone = org.clone();

Throws java.lang.ClassCastException: java.util.ArrayList cannot be cast to 
org.openscience.cdk.sgroup.SgroupBracket
java.lang.ClassCastException: java.util.ArrayList cannot be cast to 
org.openscience.cdk.sgroup.SgroupBracket
at 
org.openscience.cdk.tools.manipulator.SgroupManipulator.copy(SgroupManipulator.java:108)
at 
org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1408)

From: John Mayfield 
Date: Tuesday, 30 October 2018 at 15:39
To: Syed Asad Rahman 
Cc: cdkuser 
Subject: Re: [Cdk-user] CDK v2.2

Yes, but there has been no changes to SilentChemObjectBuilder...?

- I did try testing RDT with the new AtomContainer APIs but your tests took too 
long to run and I have stuff to do :-).
- Likewise I did the same with Ambit but there are integration tests with 
dependencies on DBs etc so difficult to see if there is actually anything 
wrong. Bigger problem in Ambit is extended type (e.g. SuppleAtomContainer) 
which needs to implement some new methods. Often trivial stuff convenience 
stuff that could be resolved with Java 8 and default method implementations on 
interfaces, but we're currently on Java 7 so not an option.

John

On Tue, 30 Oct 2018 at 14:47, Syed Asad Rahman 
mailto:s9a...@gmail.com>> wrote:
Thank you John and Developers!


This is a fantastic news!

One quick question before I pull it into SMSD and RDT - Is 
SilentChemObjectBuilder thread safe?
Best wishes,
-Asad

From: John Mayfield 
mailto:john.wilkinson...@gmail.com>>
Date: Tuesday, 30 October 2018 at 12:01
To: cdkuser 
mailto:cdk-user@lists.sourceforge.net>>
Subject: [Cdk-user] CDK v2.2

Dear CDK users,

CDK 2.2 is now released and can be obtained from Maven central or the 
GitHub<https://github.com/cdk/cdk/releases/tag/cdk-2.2> site. The full release 
notes<https://github.com/cdk/cdk/wiki/2.2-Release-Notes> provide details on the 
new features and changes.

As noted in v2.1/v2.1.1 the 
AtomContainer2<https://github.com/cdk/cdk/wiki/AtomContainer2> is now the 
default so if you didn't try running v2.1/v2.1.1 with the flag 
CdkUseLegacyAtomContainer=false you may some breakages. As highlighted on the 
wiki page<https://github.com/cdk/cdk/wiki/AtomContainer2> this normally just 
requires addAtom/Bond statements be reordered and using 
``Objects.equals(container1, container2)`` instead of reference comparison 
(container1 == container2).

- John

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Re: [Cdk-user] CDK v2.2

[John Mayfield]

Yes, but there has been no changes to SilentChemObjectBuilder...?

- I did try testing RDT with the new AtomContainer APIs but your tests took
too long to run and I have stuff to do :-).
- Likewise I did the same with Ambit but there are integration tests with
dependencies on DBs etc so difficult to see if there is actually anything
wrong. Bigger problem in Ambit is extended type (e.g. SuppleAtomContainer)
which needs to implement some new methods. Often trivial stuff convenience
stuff that could be resolved with Java 8 and default method implementations
on interfaces, but we're currently on Java 7 so not an option.

John

On Tue, 30 Oct 2018 at 14:47, Syed Asad Rahman  wrote:

> Thank you John and Developers!
>
>
>
> This is a fantastic news!
>
> One quick question before I pull it into SMSD and RDT - Is 
> SilentChemObjectBuilder thread safe?
>
> Best wishes,
>
> -Asad
>
>
>
> *From: *John Mayfield 
> *Date: *Tuesday, 30 October 2018 at 12:01
> *To: *cdkuser 
> *Subject: *[Cdk-user] CDK v2.2
>
>
>
> Dear CDK users,
>
>
>
> CDK 2.2 is now released and can be obtained from Maven central or the
> GitHub <https://github.com/cdk/cdk/releases/tag/cdk-2.2> site. The full 
> release
> notes <https://github.com/cdk/cdk/wiki/2.2-Release-Notes> provide details
> on the new features and changes.
>
>
>
> As noted in v2.1/v2.1.1 the AtomContainer2
> <https://github.com/cdk/cdk/wiki/AtomContainer2> is now the default so if
> you didn't try running v2.1/v2.1.1 with the flag
> CdkUseLegacyAtomContainer=false you may some breakages. As highlighted on
> the wiki page <https://github.com/cdk/cdk/wiki/AtomContainer2> this
> normally just requires addAtom/Bond statements be reordered and using
> ``Objects.equals(container1, container2)`` instead of reference comparison
> (container1 == container2).
>
>
>
> - John
>
>
>
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Re: [Cdk-user] CDK v2.2

[Syed Asad Rahman]

Thank you John and Developers!


This is a fantastic news!

One quick question before I pull it into SMSD and RDT - Is 
SilentChemObjectBuilder thread safe?
Best wishes,
-Asad

From: John Mayfield 
Date: Tuesday, 30 October 2018 at 12:01
To: cdkuser 
Subject: [Cdk-user] CDK v2.2

Dear CDK users,

CDK 2.2 is now released and can be obtained from Maven central or the 
GitHub<https://github.com/cdk/cdk/releases/tag/cdk-2.2> site. The full release 
notes<https://github.com/cdk/cdk/wiki/2.2-Release-Notes> provide details on the 
new features and changes.

As noted in v2.1/v2.1.1 the 
AtomContainer2<https://github.com/cdk/cdk/wiki/AtomContainer2> is now the 
default so if you didn't try running v2.1/v2.1.1 with the flag 
CdkUseLegacyAtomContainer=false you may some breakages. As highlighted on the 
wiki page<https://github.com/cdk/cdk/wiki/AtomContainer2> this normally just 
requires addAtom/Bond statements be reordered and using 
``Objects.equals(container1, container2)`` instead of reference comparison 
(container1 == container2).

- John

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[Cdk-user] CDK v2.2

[John Mayfield]

Dear CDK users,

CDK 2.2 is now released and can be obtained from Maven central or the GitHub
 site. The full release
notes  provide details
on the new features and changes.

As noted in v2.1/v2.1.1 the AtomContainer2
 is now the default so if
you didn't try running v2.1/v2.1.1 with the flag
CdkUseLegacyAtomContainer=false you may some breakages. As highlighted on
the wiki page  this
normally just requires addAtom/Bond statements be reordered and using
``Objects.equals(container1, container2)`` instead of reference comparison
(container1 == container2).

- John
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