cdk-devel — Developers forum for discussion on the Chemistry Development Kit

[Cdk-devel] Compiling a List of Seminal Papers in Cheminformatics

[Christoph S. <chr...@un...>]

Dear all, 

for teaching and documentation purposes, I would like to compile, with your help, a list of seminal papers in cheminformatics. 
It could be hosted on BlueOblisk.org and be a guidance for teaching and learning. 

It would be great if you could contribute. Please add your favorite paper as a citation to the following spreadsheet, ideally also adding the DOI for de-duplication:
https://docs.google.com/spreadsheets/d/1erXgdfpqOegSWbdevLsYwKU5feQLa0OGA4Rvf7MhV_U/edit?usp=sharing
After a collection phase of 14  days, I would then have a voting phase and eventually publish the ranked list on the Blue Obelisk page. Could be added to the Wikipedia page of Cheminformatics too. 
This poll could be later be compared with a bibliometric analysis. 

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/0000-0001-6966-0814

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

[Cdk-devel] CDK 20y anniversary symposium - Registration now open

[Christoph S. <chr...@un...>]

Dear all, 

following our poll in May this year, a good number people indicated interest in participating in celebrating the 20th anniversary of the Chemistry Development Kit (CDK) next year in a symposium. 
The symposium will be from 11. - 15. May 2020 at Schloss Korb in the Tyrolean mountains close to Bolzano. 

I am now delighted to inform you that the negotiations with Hotel Schloss Korb are finalised and that the registration is open at http://cdk20y.org.
Please read the registration page carefully - it is a 2-step process involving an immediate registration at the Eventbrite site and then you must book your own room with the hotel. The hotel rooms are only held for us until end of October 2019! 
Due to the particularity of the remote location, a stay at another hotel is not foreseen. 

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/0000-0001-6966-0814

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

> On 23. May 2019, at 12:10, Christoph Steinbeck <chr...@un...> wrote:
> 
> Dear all, 
> 
> we are planning to have a symposium to celebrate the 20th anniversary of the Chemistry Development Kit (CDK). 
> It will be from 11. - 15. May 2020 at Schloss Korb in the Tyrolean mountains close to Bolzano. 
> We would be delighted to celebrate this occasion also with friends and colleagues from other open source projects in cheminformatics.
> 
> To help us plan the size of the events and to ask the hotel to block an appropriate amount of rooms, we would like to poll your interest to participate. 
> Indicating your interest does not constitute a booking or a later obligation to participate. We will open a registration page later this years. 
> More information is also included in the following poll. 
> You can always revisit this poll in the future and change your choice. 
> 
> https://doodle.com/poll/cy66agk2kzqby6eq
> 
> Please do also forward the link to interested other parties. 
> 
> 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/0000-0001-6966-0814
> 
> What is man but that lofty spirit - that sense of enterprise.
> ... Kirk, "I, Mudd," stardate 4513.3..
> 
> 
> 
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel

[Cdk-devel] CDK 20y anniversary symposium - poll for interest

[Christoph S. <chr...@un...>]

Dear all, 

we are planning to have a symposium to celebrate the 20th anniversary of the Chemistry Development Kit (CDK). 
It will be from 11. - 15. May 2020 at Schloss Korb in the Tyrolean mountains close to Bolzano. 
We would be delighted to celebrate this occasion also with friends and colleagues from other open source projects in cheminformatics.

To help us plan the size of the events and to ask the hotel to block an appropriate amount of rooms, we would like to poll your interest to participate. 
Indicating your interest does not constitute a booking or a later obligation to participate. We will open a registration page later this years. 
More information is also included in the following poll. 
You can always revisit this poll in the future and change your choice. 

https://doodle.com/poll/cy66agk2kzqby6eq

Please do also forward the link to interested other parties. 

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/0000-0001-6966-0814

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

Re: [Cdk-devel] Set bond length in depiction generator

[Kohulan R. <koh...@gm...>]

Dear John,

Thank you for the explanation. Post layout rescaling is more than enough
for my problem and it works well for me.

Kind regards,
Kohulan.R



“It is our choices that show what we truly are, far more than our
abilities.” - Albus Dumbledore

On Mon, Apr 29, 2019, 5:30 PM John Mayfield <joh...@gm...>
wrote:

> Urgh, typing busy day. Basically the default should do what you want, if
> you set changes parameters it will sometimes make things bigger or smaller
> because it has to.
>
> On Mon, 29 Apr 2019 at 16:27, John Mayfield <joh...@gm...>
> wrote:
>
>> Again, this should be the default. Do you have an example of your code I
>> think you're setting something you shouldn't or misreading one of the
>> parameters?
>>
>> For vector graphics it will render bond lengths as ACS 1996 style
>> guidelines, the values is in Pt.
>> For Raster graphics it will rendering everything as 40px bond length.
>>
>> If the diagraph is too big for the specified size it will shrink it,
>> because it can't do anything else. If you don't specify a size it will just
>> make it as big as it wants with fixed bond lengths. It will only big a
>> depiction bigger if "zoom to fit" is set to true, default is false.
>>
>> On Mon, 29 Apr 2019 at 10:58, Kohulan Rajan <koh...@gm...> wrote:
>>
>>> Dear John,
>>>
>>> Thanks for the reply. I have already done the post layout rescaling.
>>>
>>> Without setting a fixed size to the molecules the bigger molecules try
>>> to shrink to fit the canvas size, which we don't want. we need to depict
>>> all the molecules in our dataset with the same bond length in fixed canvas
>>> size, so the molecules will have the same size irrespective of the canvas.
>>>
>>> Kind regards,
>>> Kohulan
>>>
>>> “It is our choices that show what we truly are, far more than our
>>> abilities.” - Albus Dumbledore
>>>
>>>
>>>
>>> On Sun, Apr 28, 2019 at 10:24 PM John Mayfield <
>>> joh...@gm...> wrote:
>>>
>>>>
>>>> http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/layout/StructureDiagramGenerator.html#setBondLength-double-
>>>>
>>>> But as it says you're better off doing a post layout re-scale, the bond
>>>> length is only a hint as some bonds will be stretch/shrunk to fit. Do you
>>>> have an particular example of why you want to change it?
>>>>
>>>> On Sun, 28 Apr 2019 at 09:48, Kohulan Rajan <koh...@gm...>
>>>> wrote:
>>>>
>>>>> Dear CDK Developers,
>>>>>
>>>>> Is there a way to set the bond length of the molecules in Depiction
>>>>> generator in order to depict all molecules with same bond lengths?
>>>>>
>>>>> Kind regards,
>>>>> Kohulan
>>>>>
>>>>> _______________________________________________
>>>>> Cdk-devel mailing list
>>>>> Cdk...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>>>
>>>> _______________________________________________
>>>> Cdk-devel mailing list
>>>> Cdk...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>>
>>> _______________________________________________
>>> Cdk-devel mailing list
>>> Cdk...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>
>> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>

Re: [Cdk-devel] Set bond length in depiction generator

[John M. <joh...@gm...>]

Urgh, typing busy day. Basically the default should do what you want, if
you set changes parameters it will sometimes make things bigger or smaller
because it has to.

On Mon, 29 Apr 2019 at 16:27, John Mayfield <joh...@gm...>
wrote:

> Again, this should be the default. Do you have an example of your code I
> think you're setting something you shouldn't or misreading one of the
> parameters?
>
> For vector graphics it will render bond lengths as ACS 1996 style
> guidelines, the values is in Pt.
> For Raster graphics it will rendering everything as 40px bond length.
>
> If the diagraph is too big for the specified size it will shrink it,
> because it can't do anything else. If you don't specify a size it will just
> make it as big as it wants with fixed bond lengths. It will only big a
> depiction bigger if "zoom to fit" is set to true, default is false.
>
> On Mon, 29 Apr 2019 at 10:58, Kohulan Rajan <koh...@gm...> wrote:
>
>> Dear John,
>>
>> Thanks for the reply. I have already done the post layout rescaling.
>>
>> Without setting a fixed size to the molecules the bigger molecules try to
>> shrink to fit the canvas size, which we don't want. we need to depict all
>> the molecules in our dataset with the same bond length in fixed canvas
>> size, so the molecules will have the same size irrespective of the canvas.
>>
>> Kind regards,
>> Kohulan
>>
>> “It is our choices that show what we truly are, far more than our
>> abilities.” - Albus Dumbledore
>>
>>
>>
>> On Sun, Apr 28, 2019 at 10:24 PM John Mayfield <
>> joh...@gm...> wrote:
>>
>>>
>>> http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/layout/StructureDiagramGenerator.html#setBondLength-double-
>>>
>>> But as it says you're better off doing a post layout re-scale, the bond
>>> length is only a hint as some bonds will be stretch/shrunk to fit. Do you
>>> have an particular example of why you want to change it?
>>>
>>> On Sun, 28 Apr 2019 at 09:48, Kohulan Rajan <koh...@gm...> wrote:
>>>
>>>> Dear CDK Developers,
>>>>
>>>> Is there a way to set the bond length of the molecules in Depiction
>>>> generator in order to depict all molecules with same bond lengths?
>>>>
>>>> Kind regards,
>>>> Kohulan
>>>>
>>>> _______________________________________________
>>>> Cdk-devel mailing list
>>>> Cdk...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>>
>>> _______________________________________________
>>> Cdk-devel mailing list
>>> Cdk...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>
>> _______________________________________________
>> Cdk-devel mailing list
>> Cdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>
>

Re: [Cdk-devel] Set bond length in depiction generator

[John M. <joh...@gm...>]

Again, this should be the default. Do you have an example of your code I
think you're setting something you shouldn't or misreading one of the
parameters?

For vector graphics it will render bond lengths as ACS 1996 style
guidelines, the values is in Pt.
For Raster graphics it will rendering everything as 40px bond length.

If the diagraph is too big for the specified size it will shrink it,
because it can't do anything else. If you don't specify a size it will just
make it as big as it wants with fixed bond lengths. It will only big a
depiction bigger if "zoom to fit" is set to true, default is false.

On Mon, 29 Apr 2019 at 10:58, Kohulan Rajan <koh...@gm...> wrote:

> Dear John,
>
> Thanks for the reply. I have already done the post layout rescaling.
>
> Without setting a fixed size to the molecules the bigger molecules try to
> shrink to fit the canvas size, which we don't want. we need to depict all
> the molecules in our dataset with the same bond length in fixed canvas
> size, so the molecules will have the same size irrespective of the canvas.
>
> Kind regards,
> Kohulan
>
> “It is our choices that show what we truly are, far more than our
> abilities.” - Albus Dumbledore
>
>
>
> On Sun, Apr 28, 2019 at 10:24 PM John Mayfield <
> joh...@gm...> wrote:
>
>>
>> http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/layout/StructureDiagramGenerator.html#setBondLength-double-
>>
>> But as it says you're better off doing a post layout re-scale, the bond
>> length is only a hint as some bonds will be stretch/shrunk to fit. Do you
>> have an particular example of why you want to change it?
>>
>> On Sun, 28 Apr 2019 at 09:48, Kohulan Rajan <koh...@gm...> wrote:
>>
>>> Dear CDK Developers,
>>>
>>> Is there a way to set the bond length of the molecules in Depiction
>>> generator in order to depict all molecules with same bond lengths?
>>>
>>> Kind regards,
>>> Kohulan
>>>
>>> _______________________________________________
>>> Cdk-devel mailing list
>>> Cdk...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>
>> _______________________________________________
>> Cdk-devel mailing list
>> Cdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>

Re: [Cdk-devel] Set bond length in depiction generator

[Kohulan R. <koh...@gm...>]

Dear John,

Thanks for the reply. I have already done the post layout rescaling.

Without setting a fixed size to the molecules the bigger molecules try to
shrink to fit the canvas size, which we don't want. we need to depict all
the molecules in our dataset with the same bond length in fixed canvas
size, so the molecules will have the same size irrespective of the canvas.

Kind regards,
Kohulan

“It is our choices that show what we truly are, far more than our
abilities.” - Albus Dumbledore



On Sun, Apr 28, 2019 at 10:24 PM John Mayfield <joh...@gm...>
wrote:

>
> http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/layout/StructureDiagramGenerator.html#setBondLength-double-
>
> But as it says you're better off doing a post layout re-scale, the bond
> length is only a hint as some bonds will be stretch/shrunk to fit. Do you
> have an particular example of why you want to change it?
>
> On Sun, 28 Apr 2019 at 09:48, Kohulan Rajan <koh...@gm...> wrote:
>
>> Dear CDK Developers,
>>
>> Is there a way to set the bond length of the molecules in Depiction
>> generator in order to depict all molecules with same bond lengths?
>>
>> Kind regards,
>> Kohulan
>>
>> _______________________________________________
>> Cdk-devel mailing list
>> Cdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>

Re: [Cdk-devel] Set bond length in depiction generator

[John M. <joh...@gm...>]

http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/layout/StructureDiagramGenerator.html#setBondLength-double-

But as it says you're better off doing a post layout re-scale, the bond
length is only a hint as some bonds will be stretch/shrunk to fit. Do you
have an particular example of why you want to change it?

On Sun, 28 Apr 2019 at 09:48, Kohulan Rajan <koh...@gm...> wrote:

> Dear CDK Developers,
>
> Is there a way to set the bond length of the molecules in Depiction
> generator in order to depict all molecules with same bond lengths?
>
> Kind regards,
> Kohulan
>
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>

[Cdk-devel] Set bond length in depiction generator

[Kohulan R. <koh...@gm...>]

Dear CDK Developers,

Is there a way to set the bond length of the molecules in Depiction
generator in order to depict all molecules with same bond lengths?

Kind regards,
Kohulan

Re: [Cdk-devel] How to disable the warning and keyerror from CDK

[Xuan C. <dan...@ho...>]

Hi John,

Thank you for the suggestion!

I was trying to convert 2D molecule to 3D molecule. I guess I should just generate 3D coordinate directly.

Thank you!
Xuan
________________________________
From: John Mayfield <joh...@gm...>
Sent: February 23, 2019 1:29
To: Developers forum for discussion about the Chemistry Development Kit (CDK)
Subject: Re: [Cdk-devel] How to disable the warning and keyerror from CDK

You can disable both of these by adjusting the Logger's output level to INFO.
However warnings are warnings for a reason!

In general the 3D generation in CDK is poor, in this case it's literally telling
you it can't find any pre-generated 3D coordinates for your ring system (aka.
"not good"). Likewise it doesn't know any bond length for C-NPYl again not great.

There are some other odd things about your code examples, so I'm wondering
what you're trying to do? Why do you generate both 2D and 3D? Also what do
you think this is doing, why did you add it?

AtomContainerManipulator.suppressHydrogens(atom_container);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(atom_container);

It's cheminformatics equivalent of:

int res = 4 - 1 + 1;

Re: [Cdk-devel] How to disable the warning and keyerror from CDK

[John M. <joh...@gm...>]

>
> You can disable both of these by adjusting the Logger's output level to
INFO.

> However warnings are warnings for a reason!

>
In general the 3D generation in CDK is poor, in this case it's literally
telling

> you it can't find any pre-generated 3D coordinates for your ring system
(aka.

> "not good"). Likewise it doesn't know any bond length for C-NPYl again not
great.

>
There are some other odd things about your code examples, so I'm wondering
what you're trying to do? Why do you generate both 2D and 3D? Also what do
you think this is doing, why did you add it?

>
AtomContainerManipulator.suppressHydrogens(atom_container);

>
AtomContainerManipulator.convertImplicitToExplicitHydrogens(atom_container);

>
It's cheminformatics equivalent of:

>
int res = 4 - 1 + 1;
>
>

[Cdk-devel] How to disable the warning and keyerror from CDK

[Xuan C. <Dan...@ho...>]

Hi All,

When I try to get 3d coordinate by using CDK, I got the warning and KeyError like these:


WARNING: Maybe RingTemplateError!

KEYError: Unknown distance key in pSet: C;NPYL take default bond length: 1.5

KEYError: Unknown distance key in pSet: NPYL;C take default bond length: 1.5

How to disable these warning? Or should I add something to resolve the warning?

Here is my code:


IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();

IAtomContainer mole = builder.newInstance(IAtomContainer.class);

SmilesParser temp_smiles = new SmilesParser(builder);

IAtomContainer atom_container = temp_smiles.parseSmiles(smiles);

AtomContainerManipulator.suppressHydrogens(atom_container);

AtomContainerManipulator.convertImplicitToExplicitHydrogens(atom_container);

StructureDiagramGenerator sdg = new StructureDiagramGenerator();

sdg.setMolecule(atom_container);

sdg.generateCoordinates();

mole = sdg.getMolecule();

ModelBuilder3D mb3d = ModelBuilder3D.getInstance(builder);

IAtomContainer molecule_3D = mb3d.generate3DCoordinates(mole, false);

Thank you so much for your help!
Xuan

Re: [Cdk-devel] Combine two IAtomContainer based on the atom index

[Xuan C. <dan...@ho...>]

Thank you!
________________________________
From: John Mayfield <joh...@gm...>
Sent: January 30, 2019 10:12
To: Developers forum for discussion about the Chemistry Development Kit (CDK)
Subject: Re: [Cdk-devel] Combine two IAtomContainer based on the atom index

It's a constant so you just use it as 'IBond.Order.SINGLE':

IAtom a1;
IAtom a2; // make sure atoms are in the molecule first of all!
mol.addBond(a1, a2, IBond.Order.SINGLE);

On Wed, 30 Jan 2019 at 15:50, Xuan Cao <dan...@ho...<mailto:dan...@ho...>> wrote:
Hi,

Thanks for the suggestion.

I looked at setAtom(), but I think setAtom can only change the atom on specific atom index of atomcontainer (correct me if I am wrong).

I also found the IAtomContainer.add(IAtomContainer), and it is something I want. Thank you!

Another question is that when I try to call IAtomContainer.addBond(IAtom, IAtom, IBond.Order), what is  the right way to initialize IBond.Order? I tried public static final IBond.order single = IBond.order.SINGLE; but it doesn't work.

Thank you!
Xuan

________________________________
From: Egon Willighagen <ego...@gm...<mailto:ego...@gm...>>
Sent: January 29, 2019 23:39
To: Developers forum for discussion about the Chemistry Development Kit (CDK)
Subject: Re: [Cdk-devel] Combine two IAtomContainer based on the atom index



On Tue, Jan 29, 2019 at 11:15 PM Xuan Cao <Dan...@ho...<mailto:Dan...@ho...>> wrote:
I am wondering is there any function that I can combine two atomcontainers based on the atom index from the atomcontainer?

Can you elaborate a bit more? Normally, the indices start at 0 or 1 for both of them. How do you want to combine them?

Or do I have to do the addAtom() and addBond() manually to achieve this goal?

Have you seen setAtom()? See http://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/interfaces/IAtomContainer.html#setAtom-int-org.openscience.cdk.interfaces.IAtom-

Egon

--
Hi, do you like citation networks? Already 51% of all citations are available<https://i4oc.org/> available for innovative new uses<https://twitter.com/hashtag/acs2ioc>. Join me in asking the American Chemical Society to join the Initiative for Open Citations too<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature, the RSC and many others already did<https://i4oc.org/#publishers>.

-----
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286<http://orcid.org/0000-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen
_______________________________________________
Cdk-devel mailing list
Cdk...@li...<mailto:Cdk...@li...>
https://lists.sourceforge.net/lists/listinfo/cdk-devel

Re: [Cdk-devel] Combine two IAtomContainer based on the atom index

[John M. <joh...@gm...>]

It's a constant so you just use it as 'IBond.Order.SINGLE':

IAtom a1;
> IAtom a2; // make sure atoms are in the molecule first of all!
> mol.addBond(a1, a2, IBond.Order.SINGLE);


On Wed, 30 Jan 2019 at 15:50, Xuan Cao <dan...@ho...> wrote:

> Hi,
>
> Thanks for the suggestion.
>
> I looked at setAtom(), but I think setAtom can only change the atom on
> specific atom index of atomcontainer (correct me if I am wrong).
>
> I also found the IAtomContainer.add(IAtomContainer), and it is something I
> want. Thank you!
>
> Another question is that when I try to call IAtomContainer.addBond(IAtom,
> IAtom, IBond.Order), what is  the right way to initialize IBond.Order? I
> tried public static final IBond.order single = IBond.order.SINGLE; but it
> doesn't work.
>
> Thank you!
> Xuan
>
> ------------------------------
> *From:* Egon Willighagen <ego...@gm...>
> *Sent:* January 29, 2019 23:39
> *To:* Developers forum for discussion about the Chemistry Development Kit
> (CDK)
> *Subject:* Re: [Cdk-devel] Combine two IAtomContainer based on the atom
> index
>
>
>
> On Tue, Jan 29, 2019 at 11:15 PM Xuan Cao <Dan...@ho...> wrote:
>
> I am wondering is there any function that I can combine two atomcontainers
> based on the atom index from the atomcontainer?
>
>
> Can you elaborate a bit more? Normally, the indices start at 0 or 1 for
> both of them. How do you want to combine them?
>
>
> Or do I have to do the addAtom() and addBond() manually to achieve this
> goal?
>
>
> Have you seen setAtom()? See
> http://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/interfaces/IAtomContainer.html#setAtom-int-org.openscience.cdk.interfaces.IAtom-
>
> Egon
>
> --
> Hi, do you like citation networks? Already 51% of all citations are
> available <https://i4oc.org/> available for innovative new uses
> <https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
> Chemical Society to join the Initiative for Open Citations too
> <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature,
> the RSC and many others already did <https://i4oc.org/#publishers>.
>
> -----
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
> ImpactStory: https://impactstory.org/u/egonwillighagen
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>

Re: [Cdk-devel] Combine two IAtomContainer based on the atom index

[Xuan C. <dan...@ho...>]

Hi,

Thanks for the suggestion.

I looked at setAtom(), but I think setAtom can only change the atom on specific atom index of atomcontainer (correct me if I am wrong).

I also found the IAtomContainer.add(IAtomContainer), and it is something I want. Thank you!

Another question is that when I try to call IAtomContainer.addBond(IAtom, IAtom, IBond.Order), what is  the right way to initialize IBond.Order? I tried public static final IBond.order single = IBond.order.SINGLE; but it doesn't work.

Thank you!
Xuan

________________________________
From: Egon Willighagen <ego...@gm...>
Sent: January 29, 2019 23:39
To: Developers forum for discussion about the Chemistry Development Kit (CDK)
Subject: Re: [Cdk-devel] Combine two IAtomContainer based on the atom index



On Tue, Jan 29, 2019 at 11:15 PM Xuan Cao <Dan...@ho...<mailto:Dan...@ho...>> wrote:
I am wondering is there any function that I can combine two atomcontainers based on the atom index from the atomcontainer?

Can you elaborate a bit more? Normally, the indices start at 0 or 1 for both of them. How do you want to combine them?

Or do I have to do the addAtom() and addBond() manually to achieve this goal?

Have you seen setAtom()? See http://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/interfaces/IAtomContainer.html#setAtom-int-org.openscience.cdk.interfaces.IAtom-

Egon

--
Hi, do you like citation networks? Already 51% of all citations are available<https://i4oc.org/> available for innovative new uses<https://twitter.com/hashtag/acs2ioc>. Join me in asking the American Chemical Society to join the Initiative for Open Citations too<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature, the RSC and many others already did<https://i4oc.org/#publishers>.

-----
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286<http://orcid.org/0000-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen

Re: [Cdk-devel] Combine two IAtomContainer based on the atom index

[John M. <joh...@gm...>]

IAtomContainer mol1;
IAtomContainer mol2;
mol1.add(mol2);

should work unless you have some other specialised requirements.

On Wed, 30 Jan 2019 at 06:39, Egon Willighagen <ego...@gm...>
wrote:

>
>
> On Tue, Jan 29, 2019 at 11:15 PM Xuan Cao <Dan...@ho...> wrote:
>
>> I am wondering is there any function that I can combine two
>> atomcontainers based on the atom index from the atomcontainer?
>>
>
> Can you elaborate a bit more? Normally, the indices start at 0 or 1 for
> both of them. How do you want to combine them?
>
>
>> Or do I have to do the addAtom() and addBond() manually to achieve this
>> goal?
>>
>
> Have you seen setAtom()? See
> http://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/interfaces/IAtomContainer.html#setAtom-int-org.openscience.cdk.interfaces.IAtom-
>
> Egon
>
> --
> Hi, do you like citation networks? Already 51% of all citations are
> available <https://i4oc.org/> available for innovative new uses
> <https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
> Chemical Society to join the Initiative for Open Citations too
> <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature,
> the RSC and many others already did <https://i4oc.org/#publishers>.
>
> -----
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
> ImpactStory: https://impactstory.org/u/egonwillighagen
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>

Re: [Cdk-devel] Combine two IAtomContainer based on the atom index

[Egon W. <ego...@gm...>]

On Tue, Jan 29, 2019 at 11:15 PM Xuan Cao <Dan...@ho...> wrote:

> I am wondering is there any function that I can combine two atomcontainers
> based on the atom index from the atomcontainer?
>

Can you elaborate a bit more? Normally, the indices start at 0 or 1 for
both of them. How do you want to combine them?


> Or do I have to do the addAtom() and addBond() manually to achieve this
> goal?
>

Have you seen setAtom()? See
http://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/interfaces/IAtomContainer.html#setAtom-int-org.openscience.cdk.interfaces.IAtom-

Egon

-- 
Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.

-----
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen

[Cdk-devel] Combine two IAtomContainer based on the atom index

[Xuan C. <Dan...@ho...>]

Hi,

I am wondering is there any function that I can combine two atomcontainers based on the atom index from the atomcontainer?

Or do I have to do the addAtom() and addBond() manually to achieve this goal?

Thank you!
Xuan

Re: [Cdk-devel] SMARTS legacy parser code not generated with Maven from command line?

[Egon W. <ego...@gm...>]

Umm... really weird. It works now. I regularly do a 'clean install', but
something seems to have gone wrong at some point.

OK, consider the case closed.

Egon


On Mon, Jan 7, 2019 at 12:37 PM John Mayfield <joh...@gm...>
wrote:

> What happens if you run:
>
> mvn clean javacc:javacc javacc:jjtree-javacc
>
> On Mon, 7 Jan 2019 at 11:35, John Mayfield <joh...@gm...>
> wrote:
>
>> Also which Java Version (use 8)
>>
>> On Mon, 7 Jan 2019 at 11:34, John Mayfield <joh...@gm...>
>> wrote:
>>
>>> mvn clean install?
>>>
>>> On Mon, 7 Jan 2019 at 10:32, Egon Willighagen <
>>> ego...@gm...> wrote:
>>>
>>>>
>>>> From the command line:
>>>>
>>>> $ cd cdk/
>>>> $ mvn install
>>>>
>>>> And same problem from the legacy/ folder:
>>>>
>>>> $ cd cdk/legacy
>>>> $ mvn install
>>>>
>>>> Egon
>>>>
>>>>
>>>>
>>>> On Mon, Jan 7, 2019 at 11:16 AM John Mayfield <
>>>> joh...@gm...> wrote:
>>>>
>>>>> How are you compiling, and from which directory?
>>>>>
>>>>> Working on Travis so pretty sure it's fine, no doubt eclipse is being
>>>>> eclipse though :-).
>>>>> _______________________________________________
>>>>> Cdk-devel mailing list
>>>>> Cdk...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>>>
>>>>
>>>>
>>>> --
>>>> Hi, do you like citation networks? Already 51% of all citations are
>>>> available <https://i4oc.org/> available for innovative new uses
>>>> <https://twitter.com/hashtag/acs2ioc>. Join my in asking the American
>>>> Chemical Society to join the Initiative for Open Citations too
>>>> <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature,
>>>> the RSC and many others already did <https://i4oc.org/#publishers>.
>>>>
>>>> -----
>>>> E.L. Willighagen
>>>> Department of Bioinformatics - BiGCaT
>>>> Maastricht University (http://www.bigcat.unimaas.nl/)
>>>> Homepage: http://egonw.github.com/
>>>> Blog: http://chem-bla-ics.blogspot.com/
>>>> PubList: https://www.zotero.org/egonw
>>>> ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
>>>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>>> _______________________________________________
>>>> Cdk-devel mailing list
>>>> Cdk...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>>
>>> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>


-- 
Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join my in asking the American
Chemical Society to join the Initiative for Open Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.

-----
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen

Re: [Cdk-devel] SMARTS legacy parser code not generated with Maven from command line?

[John M. <joh...@gm...>]

What happens if you run:

mvn clean javacc:javacc javacc:jjtree-javacc

On Mon, 7 Jan 2019 at 11:35, John Mayfield <joh...@gm...>
wrote:

> Also which Java Version (use 8)
>
> On Mon, 7 Jan 2019 at 11:34, John Mayfield <joh...@gm...>
> wrote:
>
>> mvn clean install?
>>
>> On Mon, 7 Jan 2019 at 10:32, Egon Willighagen <ego...@gm...>
>> wrote:
>>
>>>
>>> From the command line:
>>>
>>> $ cd cdk/
>>> $ mvn install
>>>
>>> And same problem from the legacy/ folder:
>>>
>>> $ cd cdk/legacy
>>> $ mvn install
>>>
>>> Egon
>>>
>>>
>>>
>>> On Mon, Jan 7, 2019 at 11:16 AM John Mayfield <
>>> joh...@gm...> wrote:
>>>
>>>> How are you compiling, and from which directory?
>>>>
>>>> Working on Travis so pretty sure it's fine, no doubt eclipse is being
>>>> eclipse though :-).
>>>> _______________________________________________
>>>> Cdk-devel mailing list
>>>> Cdk...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>>
>>>
>>>
>>> --
>>> Hi, do you like citation networks? Already 51% of all citations are
>>> available <https://i4oc.org/> available for innovative new uses
>>> <https://twitter.com/hashtag/acs2ioc>. Join my in asking the American
>>> Chemical Society to join the Initiative for Open Citations too
>>> <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature,
>>> the RSC and many others already did <https://i4oc.org/#publishers>.
>>>
>>> -----
>>> E.L. Willighagen
>>> Department of Bioinformatics - BiGCaT
>>> Maastricht University (http://www.bigcat.unimaas.nl/)
>>> Homepage: http://egonw.github.com/
>>> Blog: http://chem-bla-ics.blogspot.com/
>>> PubList: https://www.zotero.org/egonw
>>> ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
>>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>> _______________________________________________
>>> Cdk-devel mailing list
>>> Cdk...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>
>>

Re: [Cdk-devel] SMARTS legacy parser code not generated with Maven from command line?

[John M. <joh...@gm...>]

Also which Java Version (use 8)

On Mon, 7 Jan 2019 at 11:34, John Mayfield <joh...@gm...>
wrote:

> mvn clean install?
>
> On Mon, 7 Jan 2019 at 10:32, Egon Willighagen <ego...@gm...>
> wrote:
>
>>
>> From the command line:
>>
>> $ cd cdk/
>> $ mvn install
>>
>> And same problem from the legacy/ folder:
>>
>> $ cd cdk/legacy
>> $ mvn install
>>
>> Egon
>>
>>
>>
>> On Mon, Jan 7, 2019 at 11:16 AM John Mayfield <
>> joh...@gm...> wrote:
>>
>>> How are you compiling, and from which directory?
>>>
>>> Working on Travis so pretty sure it's fine, no doubt eclipse is being
>>> eclipse though :-).
>>> _______________________________________________
>>> Cdk-devel mailing list
>>> Cdk...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>>
>>
>>
>> --
>> Hi, do you like citation networks? Already 51% of all citations are
>> available <https://i4oc.org/> available for innovative new uses
>> <https://twitter.com/hashtag/acs2ioc>. Join my in asking the American
>> Chemical Society to join the Initiative for Open Citations too
>> <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature,
>> the RSC and many others already did <https://i4oc.org/#publishers>.
>>
>> -----
>> E.L. Willighagen
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Homepage: http://egonw.github.com/
>> Blog: http://chem-bla-ics.blogspot.com/
>> PubList: https://www.zotero.org/egonw
>> ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
>> ImpactStory: https://impactstory.org/u/egonwillighagen
>> _______________________________________________
>> Cdk-devel mailing list
>> Cdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>
>

Re: [Cdk-devel] SMARTS legacy parser code not generated with Maven from command line?

[John M. <joh...@gm...>]

mvn clean install?

On Mon, 7 Jan 2019 at 10:32, Egon Willighagen <ego...@gm...>
wrote:

>
> From the command line:
>
> $ cd cdk/
> $ mvn install
>
> And same problem from the legacy/ folder:
>
> $ cd cdk/legacy
> $ mvn install
>
> Egon
>
>
>
> On Mon, Jan 7, 2019 at 11:16 AM John Mayfield <joh...@gm...>
> wrote:
>
>> How are you compiling, and from which directory?
>>
>> Working on Travis so pretty sure it's fine, no doubt eclipse is being
>> eclipse though :-).
>> _______________________________________________
>> Cdk-devel mailing list
>> Cdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>>
>
>
> --
> Hi, do you like citation networks? Already 51% of all citations are
> available <https://i4oc.org/> available for innovative new uses
> <https://twitter.com/hashtag/acs2ioc>. Join my in asking the American
> Chemical Society to join the Initiative for Open Citations too
> <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature,
> the RSC and many others already did <https://i4oc.org/#publishers>.
>
> -----
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
> ImpactStory: https://impactstory.org/u/egonwillighagen
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>

Re: [Cdk-devel] SMARTS legacy parser code not generated with Maven from command line?

[Egon W. <ego...@gm...>]

>From the command line:

$ cd cdk/
$ mvn install

And same problem from the legacy/ folder:

$ cd cdk/legacy
$ mvn install

Egon



On Mon, Jan 7, 2019 at 11:16 AM John Mayfield <joh...@gm...>
wrote:

> How are you compiling, and from which directory?
>
> Working on Travis so pretty sure it's fine, no doubt eclipse is being
> eclipse though :-).
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>


-- 
Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join my in asking the American
Chemical Society to join the Initiative for Open Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.

-----
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen

Re: [Cdk-devel] SMARTS legacy parser code not generated with Maven from command line?

[John M. <joh...@gm...>]

How are you compiling, and from which directory?

Working on Travis so pretty sure it's fine, no doubt eclipse is being
eclipse though :-).

[Cdk-devel] SMARTS legacy parser code not generated with Maven from command line?

[Egon W. <ego...@gm...>]

Hi all,

when I try to compile the CDK from master on my Debian GNU/Linux system
with Java8 the legacy module fails to compile because the SMARTS compiler
does not get created:

[INFO] Running org.openscience.cdk.smiles.smarts.SMARTSTest
[ERROR] Tests run: 7, Failures: 0, Errors: 1, Skipped: 0, Time elapsed:
0.004 s <<< FAILURE! - in org.openscience.cdk.smiles.smarts.SMARTSTest
[ERROR]
testUnspecifiedIsotope(org.openscience.cdk.smiles.smarts.SMARTSTest)  Time
elapsed: 0.004 s  <<< ERROR!
java.lang.Error:
Unresolved compilation problem:
       The method jjtAccept(SMARTSParserVisitor, Object) from the type
ASTStart refers to the missing type SMARTSParserVisitor

       at
org.openscience.cdk.smiles.smarts.SMARTSTest.testUnspecifiedIsotope(SMARTSTest.java:172)


I actually have the problem in Eclipse too... I'll try to figure it out,
but ideas meanwhile welcome...

Egon

-- 
Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join my in asking the American
Chemical Society to join the Initiative for Open Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.

-----
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen