Re: SMSD Sync with CDK

[Egon Willighagen-5]

Hi Syed,

do you have experience with 'git' already? BTW, feel free to drop in
on IRC, #cdk at the irc.freenode.net network..

On Mon, Oct 26, 2009 at 3:21 PM, Syed Asad Rahman <asad@...> wrote:
>> Where: a git branch, and we'll put the code in a new, so-called, CDK
>> module 'smsd'...
>
> Send the the commands/protocol and I will synchronize the code by today.

I suggest to get a GitHub account, www.github.com, and clone the cdk
repository I have there for CDK master:

http://github.com/egonw/cdk

(once you have an account, the above link should have an fork button)

Then you can check out that code locally, and I'll explain that when
you have an account and made the fork... (because I need your account
name (not pwd, of course :) to give the exact commands)... Do you have
a public SSH key? You'll need that for uploading patches to your
GitHub git repository...

Alternatively, you can set up a git repostory on your EBI webpage,
just like Stefan did for their JChemPaint patches:

http://www.ebi.ac.uk/steinbeck-srv/git/jchempaint-primary-public/

(But I think GitHub is easier...)

Egon

--
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[Egon Willighagen-5]

On Mon, Oct 26, 2009 at 3:48 PM, Syed Asad Rahman <asad@...> wrote:
>> Then you can check out that code locally, and I'll explain that when
>> you have an account and made the fork... (because I need your account
>> name (not pwd, of course :) to give the exact commands)... Do you have
>> a public SSH key? You'll need that for uploading patches to your
>> GitHub git repository...
>
> I think I have a public key ..will this help?

Add the public key via: https://github.com/account

> I did fork the link and my account link is http://github.com/asad/cdk

Excellent.

make a check out with:

  git clone git@...:asad/cdk.git
  cd cdk

Configure git to match your personal info, using 'git config'. Something like:

git config —global user.name “David Beckwith”
git config —global user.email “dbitsolutions@...”

This ensures that the patches have your name and email, needed for
copyright reasons. Feel free to use whatever email address you prefer.

Then make a branch:

  git checkout -b smsd master

then add your code, and use 'git add' and a 'git commit' to create
patches (see for example [0]). (Are you running Linux, or something
unix alike?)

  git add src/main/org/openscience/cdk/smds/SomeClass.java
  git commit -m "Added main SMSD tool"

(you can 'git add' more than one file, of course)

Then you can 'push' this your new branch to GitHub with:

  git push github smsd

(You can do this actually directly after you branched with 'git
checkout -b' too)

Egon

--
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[Egon Willighagen-5]

On Mon, Oct 26, 2009 at 4:05 PM, Egon Willighagen
<egon.willighagen@...> wrote:
> then add your code, and use 'git add' and a 'git commit' to create
> patches (see for example [0]). (Are you running Linux, or something
> unix alike?)

0. http://github.com/guides/git-cheat-sheet

But there are many more git tutorials on the net...

Egon

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[Egon Willighagen-5]

On Mon, Oct 26, 2009 at 3:48 PM, Syed Asad Rahman <asad@...> wrote:
> I did fork the link and my account link is http://github.com/asad/cdk

Oh, I just noted that it 'forked' all my branches too (cdk-1.2.x,
73-rdf, 81-ojdcheck), which is not really needed... you can remove
them from your fork on GitHub with these commands (note the ':' in
front of the branch name, which means 'delete'):

  git push origin :73-rdf
  git push origin :81-ojdcheck
  git push origin :cdk-1.2.x

BTW, I just realized that the push I mentioned to get your smsd branch
on GitHub had 'github' instead of 'origin'... the third param in the
'git push' command is the alias for the remote service... with a
normal 'git clone' this will be 'origin', not 'github'... you can see
what aliases you have defined for remote repositories with:

  git remote -v

Egon

--
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[Syed Asad Rahman-2]

SMSD branch is now on Github

Hope this helps :-)

Thanks for the help Egon!

--

****************************************************************

Dr. Syed Asad Rahman (B.Engg, PhD)
Research Scientist

EMBL-EBI                       Phone: [phone]
Wellcome Trust Genome Campus   Fax: [phone]
Hinxton CB10 1SD               E-mail: asad@...
Cambridge, UK                  Home Page: www.ebi.ac.uk/~asad

*****************************************************************




Egon Willighagen wrote:

> On Mon, Oct 26, 2009 at 3:48 PM, Syed Asad Rahman <asad@...> wrote:
>  
>> I did fork the link and my account link is http://github.com/asad/cdk
>>    
>
> Oh, I just noted that it 'forked' all my branches too (cdk-1.2.x,
> 73-rdf, 81-ojdcheck), which is not really needed... you can remove
> them from your fork on GitHub with these commands (note the ':' in
> front of the branch name, which means 'delete'):
>
>   git push origin :73-rdf
>   git push origin :81-ojdcheck
>   git push origin :cdk-1.2.x
>
> BTW, I just realized that the push I mentioned to get your smsd branch
> on GitHub had 'github' instead of 'origin'... the third param in the
> 'git push' command is the alias for the remote service... with a
> normal 'git clone' this will be 'origin', not 'github'... you can see
> what aliases you have defined for remote repositories with:
>
>   git remote -v
>
> Egon
>
>  

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[Egon Willighagen-5]

On Mon, Oct 26, 2009 at 6:36 PM, Syed Asad Rahman <asad@...> wrote:
> SMSD branch is now on Github

Indeed! This is the whole lot?

> Hope this helps :-) Thanks for the help Egon!

I will set up a Nightly for your branch as soon as possible. For this I will:

* fork your branch
* add @cdk.module bits

I'll try to do this this week.

I had a quick glance at the code, and there is quite some work to do
to make it 'CDK clean'... getting unit tests added, is a rather
important step...

BTW, I also noted Vector<Foo>... better the use List<Foo> there. List
is the interface behind Vector, and that allows you to use ArrayList
at places if the List is then not access in a parallel nature... that
will speed up the performance of the code, and using interfaces in the
API is generally more clean anyway...

But before I give more comments, I'll first set up Nightly :)

BTW, to *all*, everyone is free to join in making this code CDK stable
(that applies to any patch set, of course). To more people help, to
sooner it can enter the main CDK tree.

Egon

--
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Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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[Mark Rijnbeek]

Egon Willighagen wrote:
> On Mon, Oct 26, 2009 at 6:36 PM, Syed Asad Rahman <asad@...> wrote:
>> SMSD branch is now on Github
>

I wanted to have a look, but I can't get my hands on the code..

bash-3.00$ git clone git://github.com/asad/cdk.git

Initialized empty Git repository in /home/markr/git/asad/cdk/.git/
fatal: The remote end hung up unexpectedly

Seems this happens more often:
http://support.github.com/discussions/repos/1680-cannot-clone-gitgithubcominsider42mangosgit
I'll try again later..


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[Egon Willighagen-5]

On Mon, Oct 26, 2009 at 7:28 PM, Mark Rijnbeek <markr@...> wrote:

> Egon Willighagen wrote:
>> On Mon, Oct 26, 2009 at 6:36 PM, Syed Asad Rahman <asad@...> wrote:
>>> SMSD branch is now on Github
>
> I wanted to have a look, but I can't get my hands on the code..
>
> bash-3.00$ git clone git://github.com/asad/cdk.git
>
> Initialized empty Git repository in /home/markr/git/asad/cdk/.git/
> fatal: The remote end hung up unexpectedly

Same problem here.

Egon

--
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Homepage: http://egonw.github.com/
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[Egon Willighagen-5]

Hi all,

On Mon, Oct 26, 2009 at 8:44 PM, Egon Willighagen
<egon.willighagen@...> wrote:
> On Mon, Oct 26, 2009 at 7:28 PM, Mark Rijnbeek <markr@...> wrote:
>> I wanted to have a look, but I can't get my hands on the code..
>>
>> bash-3.00$ git clone git://github.com/asad/cdk.git
>>
>> Initialized empty Git repository in /home/markr/git/asad/cdk/.git/
>> fatal: The remote end hung up unexpectedly
>
> Same problem here.

Filed the problem here:

http://github.com/defunkt/github-issues/issues/#issue/167

I am sure it helps if you vote there, or add your copy of what happens.

Egon

--
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[Syed Asad Rahman-2]

Hi All,

I have used List<foo> instead of vector<foo> where possible.

I am just wondering if the cdk-smsd git clone is working?

I would really appreciate if CDK developers can use the SMSD code and
send me their feedbacks.

Best wishes,

Asad

--

****************************************************************

Dr. Syed Asad Rahman (B.Engg, PhD)
Research Scientist

EMBL-EBI                       Phone: [phone]
Wellcome Trust Genome Campus   Fax: [phone]
Hinxton CB10 1SD               E-mail: asad@...
Cambridge, UK                  Home Page: www.ebi.ac.uk/~asad

*****************************************************************




Egon Willighagen wrote:

> On Mon, Oct 26, 2009 at 6:36 PM, Syed Asad Rahman <asad@...> wrote:
>  
>> SMSD branch is now on Github
>>    
>
> Indeed! This is the whole lot?
>
>  
>> Hope this helps :-) Thanks for the help Egon!
>>    
>
> I will set up a Nightly for your branch as soon as possible. For this I will:
>
> * fork your branch
> * add @cdk.module bits
>
> I'll try to do this this week.
>
> I had a quick glance at the code, and there is quite some work to do
> to make it 'CDK clean'... getting unit tests added, is a rather
> important step...
>
> BTW, I also noted Vector<Foo>... better the use List<Foo> there. List
> is the interface behind Vector, and that allows you to use ArrayList
> at places if the List is then not access in a parallel nature... that
> will speed up the performance of the code, and using interfaces in the
> API is generally more clean anyway...
>
> But before I give more comments, I'll first set up Nightly :)
>
> BTW, to *all*, everyone is free to join in making this code CDK stable
> (that applies to any patch set, of course). To more people help, to
> sooner it can enter the main CDK tree.
>
> Egon
>
>  

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[Egon Willighagen-5]

On Tue, Oct 27, 2009 at 10:18 PM, Syed Asad Rahman <asad@...> wrote:
> I have used List<foo> instead of vector<foo> where possible.

Great.

> I am just wondering if the cdk-smsd git clone is working?

Not for met yet.

The bug report I filed on GitHub was apparently at the wrong place,
but will shortly file it in the correct tracker.

Do you have test cases for your code which we could use for unit testing?

Egon

--
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[Egon Willighagen-5]

Hi all,

On Wed, Oct 28, 2009 at 3:41 PM, Egon Willighagen
<egon.willighagen@...> wrote:
> The bug report I filed on GitHub was apparently at the wrong place,
> but will shortly file it in the correct tracker.

GitHub has fixed the problem. For one reason or another, the fork was
not set for public clone... (I asked what that actually means...)

You should be able to clone now.

Egon

--
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[Syed Asad Rahman-2]

Dear Developers,

As requested by Egon, I am posting the terms and condition for using SMSD.


a) Please cite our paper when you use SMSD in any form.

Publication : S. Asad Rahman, M. Bashton, G. L. Holliday, R. Schrader
and J. M. Thornton: Small Molecule Subgraph Detector (SMSD) Toolkit,
Journal of Cheminformatics 2009, 1:12 doi:10.1186/1758-2946-1-12


Generic license for the SMSD

/**
*
* Copyright (C) 2006-2009 Syed Asad Rahman {asad@...}
*
* Contact: cdk-devel@...
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the
beginning
* of your source code files, and to any copyright notice that you may
distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*
**/


Overview of the SMSD license:

SMSD consists of several modules, many of them are well established
algorithms.

   1. VF lib implemented for substructure search in SMSD was taken from
      MX lib. This was further extended to report MCS between molecules.
      Hence this will carry original MX license as well as our present
      license.
   2. MCSPlus was is an improved version of the algorithm proposed by
      Leber M: Kodierung enzymatischer Reaktionen.  University of
      Cologne; 2008. The McGregor implementation was developed by
      referring the original code as proposed by Leber et.al and then it
      was modified to be coherent with the SMSD. Since original
      algorithms have already been published the improvements made on
      these algorithms in the SMSD will hold good for our present license.
   3. CDKMCS was taken from CDK and then it was improved to adapt the
      SMSD protocol. This will carry original CDK license and our
      present license.
   4. Chemical filters is a novel concept developed in house and this
      rely mostly on CDK modules. This will carry our present license.
   5. Apart from the above mentioned clauses rest of the code in the
      SMSD will hold good for our present license.


Hope this is helpful.

Best regards,

Asad

--

****************************************************************

Dr. Syed Asad Rahman (B.Engg, PhD)
Research Scientist

EMBL-EBI                       Phone: [phone]
Wellcome Trust Genome Campus   Fax: [phone]
Hinxton CB10 1SD               E-mail: asad@...
Cambridge, UK                  Home Page: www.ebi.ac.uk/~asad

*****************************************************************




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[Egon Willighagen-5]

Hi Asad,

On Tue, Nov 3, 2009 at 11:51 AM, Syed Asad Rahman <asad@...> wrote:
> a) Please cite our paper when you use SMSD in any form.
>
> Publication : S. Asad Rahman, M. Bashton, G. L. Holliday, R. Schrader and J.
> M. Thornton: Small Molecule Subgraph Detector (SMSD) Toolkit, Journal of
> Cheminformatics 2009, 1:12 doi:10.1186/1758-2946-1-12

In all classes where you expect users to end up, you can add this
reference to the JavaDoc as you would do in a paper...

/**
 * This classes does foo and bar. The method is described in detail in
{@cdk.cite HASH}.
 */

The HASH should match an entry in cdk/doc/refs/cheminf.bibx

And then the full reference will show up in the JavaDoc, as in:

http://pele.farmbio.uu.se/nightly-1.2.x/cdk-javadoc-1.2.3.git/org/openscience/cdk/io/CMLReader.html

(See the CMLReader.java for the matching JavaDoc source...)

Egon

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