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 -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Tuesday, April 27, 2010 9:00 AM To: [email protected] Subject: Biojava-l Digest, Vol 87, Issue 26 Send Biojava-l mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://lists.open-bio.org/mailman/listinfo/biojava-l or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of Biojava-l digest..." 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 <[email protected]> Subject: Re: [Biojava-l] PDBFileParser and Atom element symbol To: Andy Thomas-Cramer <[email protected]> Cc: [email protected] Message-ID: <[email protected]> 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:* [email protected] [mailto:[email protected]] *On > Behalf Of *Andreas Prlic > *Sent:* Friday, April 23, 2010 6:52 PM > *To:* Andy Thomas-Cramer > *Cc:* [email protected] > *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 < > [email protected]> 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 - [email protected] > 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 <[email protected]> Subject: [Biojava-l] Google Summer of Code - accepted students To: [email protected] Message-ID: <[email protected]> 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 <[email protected]> Subject: [Biojava-l] accepted GSoC projects To: Jianjiong Gao <[email protected]>, Mark Chapman <[email protected]>, Biojava <[email protected]>, biojava-dev <[email protected]> Cc: "Rose, Peter" <[email protected]>, Scooter Willis <[email protected]>, Kyle Ellrott <[email protected]> Message-ID: <[email protected]> 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 <[email protected]> Subject: [Biojava-l] Google Summer of Code - accepted students To: BioPerl List <[email protected]>, BioPython List <[email protected]>, BioJava List <[email protected]>, BioRuby List <[email protected]>, BioSQL List <[email protected]>, BioLib List <[email protected]>, Open-Bio List <[email protected]>, BioDAS List <[email protected]> Message-ID: <[email protected]> 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 ------------------------------ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l End of Biojava-l Digest, Vol 87, Issue 26 ***************************************** _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
