[Biojava-l] PDBFileParser and Atom element symbol
Peter Rose
pwrose at ucsd.edu
Thu Apr 29 19:53:33 UTC 2010
Since there was a request to be able to access element information, I've
added an Element enum to the org.biojava.bio.structure package that I had
developed for another application.
Each element has a number of properties such as atomic number, mass, min and
max valence, electronegativity, etc. that should be useful.
The AtomImpl class now has a getter and setter for Element.
Also, the PDB parser now populates the Element in the Atom class. By default
the PDB parser tries to parse the element from columns 77-78. As a fallback
for mis-formatted PDB files that don't contain an element column, the
element is parsed from the atom name.
We'll also add element support for the cif parser soon.
-Peter
________________________________________________
Peter Rose, Ph.D.
Scientific Lead
RCSB Protein Data Bank (www.pdb.org)
San Diego Supercomputer Center (SDSC) and
Skaggs School of Pharmacy and Pharmaceutical Sciences
Pharmaceutical Sciences Building
University of California San Diego
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Today's Topics:
1. Re: PDBFileParser and Atom element symbol (Andreas Prlic)
2. Google Summer of Code - accepted students (Robert Buels)
3. accepted GSoC projects (Andreas Prlic)
4. Google Summer of Code - accepted students (Robert Buels)
----------------------------------------------------------------------
Message: 1
Date: Mon, 26 Apr 2010 18:07:53 -0700
From: Andreas Prlic <andreas at sdsc.edu>
Subject: Re: [Biojava-l] PDBFileParser and Atom element symbol
To: Andy Thomas-Cramer <thomascramera at dnastar.com>
Cc: biojava-l at lists.open-bio.org
Message-ID:
<m2v59a41c431004261807h4440eac5t31871134c0a5d02f at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Andy
Questions:
> * Is this pattern documented in the PDB specification?
>
see here:
http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
> * If this pattern can be relied on, why are columns 77-78 also dedicated
to
> the element symbol?
>
That is the atom's element symbol (as given in the periodic table), in
contrast to the first name, which contains numbering information.
* Should reliance on the pattern be hidden behind a BioJava method?
>
If you think that is important we could probably provide an enum for all
atom types. There are two categories though: the periodic table symbol and
the one that is related to the position in an amino acid....
Andreas
>
>
>
> ------------------------------
>
> *From:* andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] *On
> Behalf Of *Andreas Prlic
> *Sent:* Friday, April 23, 2010 6:52 PM
> *To:* Andy Thomas-Cramer
> *Cc:* biojava-l at lists.open-bio.org
> *Subject:* Re: [Biojava-l] PDBFileParser and Atom element symbol
>
>
>
> Hi Andy,
>
> you could check with Atom.getFullname(), which contains the space
> characters from the PDB file:
> e.g Calpha: " CA ", Calcium "CA "
>
> in addition the parent group of a Calpha atom is usually an AminoAcid and
> for Calciums it is a Hetatom group...
>
> Andreas
>
> On Fri, Apr 23, 2010 at 3:58 PM, Andy Thomas-Cramer <
> thomascramera at dnastar.com> wrote:
>
>
>
> Is there an easy way to identify the type of atom referenced by an Atom
> object?
>
> For example, if Atom.getName() is "CA", is the element calcium or the
> atom carbon alpha?
>
> If not, would it be feasible to add a method providing this in Atom,
> AtomImpl, and parsing it in PDBFileParser, using the columns defined at
> http://www.wwpdb.org/documentation/format32/sect9.html#ATOM?
>
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>
--
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------
------------------------------
Message: 2
Date: Mon, 26 Apr 2010 15:02:11 -0700
From: Robert Buels <rmb32 at cornell.edu>
Subject: [Biojava-l] Google Summer of Code - accepted students
To: rmb32 at cornell.edu
Message-ID: <4BD60D63.1040400 at cornell.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi all,
I'm pleased to announce the acceptance of OBF's 2010 Google Summer of
Code students, listed in alphabetical order with their project titles
and primary mentors:
Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including
Implementation of Multiple Sequence Alignment Algorithms
Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification,
Classification, and Visualization of Posttranslational Modification of
Proteins
Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby
Sara Rayburn (PM Christian Zmasek) - Implementing Speciation &
Duplication Inference Algorithm for Binary and Non-binary Species Tree
Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending
Bio.PDB: broadening the usefulness of BioPython's Structural Biology module
Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring
Congratulations to our accepted students!
All told, we had 52 applications submitted for the 6 slots (5 originally
assigned, plus 1 extra) allotted to us by Google. Proposals were
extremely competitive: 6 out of 52 translates to an 11.5% acceptance
rate. We received a lot of really excellent proposals, the decisions
were not easy.
Thanks very much to all the students who applied, we very much
appreciate your hard work.
Here's to a great 2010 Summer of Code, I'm sure these students will do
some wonderful work.
Rob Buels
OBF GSoC 2010 Administrator
------------------------------
Message: 3
Date: Mon, 26 Apr 2010 22:33:51 -0700
From: Andreas Prlic <andreas at sdsc.edu>
Subject: [Biojava-l] accepted GSoC projects
To: Jianjiong Gao <jianjong.gao at gmail.com>, Mark Chapman
<chapman at cs.wisc.edu>, Biojava <biojava-l at lists.open-bio.org>,
biojava-dev <biojava-dev at lists.open-bio.org>
Cc: "Rose, Peter" <pwrose at ucsd.edu>, Scooter Willis
<HWillis at scripps.edu>, Kyle Ellrott <kellrott at ucsd.edu>
Message-ID:
<u2w59a41c431004262233xe5553c17je23c2b42a3aae81d at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear all,
Google has released the results for GSoC: Congratulations to Mark Chapman
and Jianjiong Gao for having been accepted to work on the MSA and PTM
projects for BioJava! Let's start the "community bonding" process (
http://en.flossmanuals.net/GSoCMentoring/MindtheGap ) and we all are
looking forward to work with you on this during the summer. The Mentors and
co-mentors will be Peter Rose for the PTM and Scooter Willis and Kyle
Ellrott for the MSA project (and me).
I want to thank all of of you who submitted proposals or showed interest in
other ways for the Google Summer of Code. We hope you are not too
disappointed if your application did not get accepted this time. We had a
large number (52) applications and the the overall quality of the
submissions was very high. We would like to stay in touch with you and we
hope that you are interested in BioJava also beyond the scope of GSoC. There
are a number of different ways how to contribute: We are always looking for
people who provide code and patches to further improve our library, help out
with the documentation on the Wiki page, or answer questions on the mailing
lists.
Let's all give Mark and Jianjiong a warm welcome to the BioJava community.
For those of you who are interested in following the progress of the
projects, as usually, the development related discussions are going to be on
the biojava-dev list.
Happy coding!
Andreas
------------------------------
Message: 4
Date: Mon, 26 Apr 2010 22:52:57 -0700
From: Robert Buels <rmb32 at cornell.edu>
Subject: [Biojava-l] Google Summer of Code - accepted students
To: BioPerl List <bioperl-l at lists.open-bio.org>, BioPython List
<biopython at lists.open-bio.org>, BioJava List
<biojava-l at lists.open-bio.org>, BioRuby List
<bioruby at lists.open-bio.org>, BioSQL List
<biosql-l at lists.open-bio.org>, BioLib List
<biolib-dev at lists.open-bio.org>, Open-Bio List
<open-bio-l at lists.open-bio.org>, BioDAS List
<das at lists.open-bio.org>
Message-ID: <4BD67BB9.3000804 at cornell.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi all,
I'm pleased to announce the acceptance of OBF's 2010 Google Summer of
Code students, listed in alphabetical order with their project titles
and primary mentors:
Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including
Implementation of Multiple Sequence Alignment Algorithms
Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification,
Classification, and Visualization of Posttranslational Modification of
Proteins
Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby
Sara Rayburn (PM Christian Zmasek) - Implementing Speciation &
Duplication Inference Algorithm for Binary and Non-binary Species Tree
Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending
Bio.PDB: broadening the usefulness of BioPython's Structural Biology module
Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring
Congratulations to our accepted students!
All told, we had 52 applications submitted for the 6 slots (5 originally
assigned, plus 1 extra) allotted to us by Google. Proposals were
extremely competitive: 6 out of 52 translates to an 11.5% acceptance
rate. We received a lot of really excellent proposals, the decisions
were not easy.
Thanks very much to all the students who applied, we very much
appreciate your hard work.
Here's to a great 2010 Summer of Code, I'm sure these students will do
some wonderful work.
Rob Buels
OBF GSoC 2010 Administrator
------------------------------
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