Structure File questions

Jalview Developers
#1

I’m looking at my FileFormatI branch and wanting to minimise, and ideally remove, ‘special case’ treatment of structure files (PDB/mmCIF) as a format.

Questions arising:

  • enum StructureFileType doesn’t seem to get used - can it be removed?

    • corollary: we don’t do anything with MMTF format?

  • StructureFile.dbRefType doesn’t seem to get used - can it be removed?

  • StructureFile.structureFileType (this is PDB or mmCIF)

    • looks like it could be passed as a method parameter (to postProcessChain()) rather than saved in a field
    • the value gets copied to PDBEntry.type - which is therefore PDB or mmCIF after parsing a structure file
    • however a Uniprot fetch (uniprot_mapping.xml) binds ‘dbReference’ to PDBEntry
    • so in this context, PDBEntry.type is “PDB” or “EMBL” or “Ensembl” etc (see Uniprot.uniprotEntryToSequenceI())1. would it make more sense to bind Uniprot dbrefs to DBRefEntry instead?
    1. should PDBEntry.type get set to PDB (as the database source) also for mmCIF format?

  • is the MCView parser now obsolete? in which case can we get rid of it?

    • perhaps move remaining datamodel classes used in the package to a datamodel.structure package?
    • with a suitable ceremony (MC is Michelle Clamp?)

thanks,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

#2

Ahhh, MCView… This was the prototype Jalview started in 1996 in Oxford (yes, MC is Michele Clamp (note one ‘l’)). It had been renamed Jalview by 1998 but neither Michele nor I can remember exactly when the change happened.

G.

I’m looking at my FileFormatI branch and wanting to minimise, and ideally remove, ‘special case’ treatment of structure files (PDB/mmCIF) as a format.

Questions arising:

  • enum StructureFileType doesn’t seem to get used - can it be removed?

    • corollary: we don’t do anything with MMTF format?

  • StructureFile.dbRefType doesn’t seem to get used - can it be removed?

  • StructureFile.structureFileType (this is PDB or mmCIF)

    • looks like it could be passed as a method parameter (to postProcessChain()) rather than saved in a field
    • the value gets copied to PDBEntry.type - which is therefore PDB or mmCIF after parsing a structure file
    • however a Uniprot fetch (uniprot_mapping.xml) binds ‘dbReference’ to PDBEntry
    • so in this context, PDBEntry.type is “PDB” or “EMBL” or “Ensembl” etc (see Uniprot.uniprotEntryToSequenceI())1. would it make more sense to bind Uniprot dbrefs to DBRefEntry instead?
    1. should PDBEntry.type get set to PDB (as the database source) also for mmCIF format?

  • is the MCView parser now obsolete? in which case can we get rid of it?

    • perhaps move remaining datamodel classes used in the package to a datamodel.structure package?
    • with a suitable ceremony (MC is Michelle Clamp?)

thanks,

Mungo

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

The University of Dundee is a registered Scottish Charity, No: SC015096

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[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
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The University of Dundee is a registered Scottish Charity, No: SC015096

···

On 28/11/2016 09:37, Mungo Carstairs (Staff) wrote:

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

The University of Dundee is registered Scottish charity: No.SC015096
#3

The StructureFileType enum is used by the method StructureFile.isStructureFile(fileType) to determine if a given file format is a structure file or not. It was introduced after 2.10.0 to replace explicit checks for ‘PDB’, ‘mmCIF’, or other structure file formats is some parts of the src code. See JAL-2280 for more history on this.

I can confirm that StructureFile.dbRefType is currently not used - that shouldn’t be the case though. I’d have to check the commit history to figure out what has gone wrong.

We currently don’t utilise the MMTF format. However, the StructureFileType enum should Ideally contain structure file formats that is/could be supported by Jalview.

The MCView parser is now kind of obsolete, however it was left for legacy purposes (i.e. importing older project files). IMHO, I think we could move the data model classes as suggested, but hold-up getting rid of the old parser for now.

Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

#4

The StructureFileType enum is used by the method StructureFile.isStructureFile(fileType)

…but as far as I can see isStructureFile() is not used?

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Charles Ofoegbu (Staff) t.c.n.ofoegbu@dundee.ac.uk
Sent: 28 November 2016 15:04:56
To: Jalview Development List
Subject: Re: [Jalview-dev] Structure File questions

The StructureFileType enum is used by the method StructureFile.isStructureFile(fileType) to determine if a given file format is a structure file or not. It was introduced after 2.10.0 to replace explicit checks for ‘PDB’, ‘mmCIF’, or other structure file formats is some parts of the src code. See JAL-2280 for more history on this.

I can confirm that StructureFile.dbRefType is currently not used - that shouldn’t be the case though. I’d have to check the commit history to figure out what has gone wrong.

We currently don’t utilise the MMTF format. However, the StructureFileType enum should Ideally contain structure file formats that is/could be supported by Jalview.

The MCView parser is now kind of obsolete, however it was left for legacy purposes (i.e. importing older project files). IMHO, I think we could move the data model classes as suggested, but hold-up getting rid of the old parser for now.

Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

On 28 Nov 2016, at 09:37, Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

I’m looking at my FileFormatI branch and wanting to minimise, and ideally remove, ‘special case’ treatment of structure files (PDB/mmCIF) as a format.

Questions arising:

  • enum StructureFileType doesn’t seem to get used - can it be removed?

    • corollary: we don’t do anything with MMTF format?

  • StructureFile.dbRefType doesn’t seem to get used - can it be removed?

  • StructureFile.structureFileType (this is PDB or mmCIF)

    • looks like it could be passed as a method parameter (to postProcessChain()) rather than saved in a field
    • the value gets copied to PDBEntry.type - which is therefore PDB or mmCIF after parsing a structure file
    • however a Uniprot fetch (uniprot_mapping.xml) binds ‘dbReference’ to PDBEntry
    • so in this context, PDBEntry.type is “PDB” or “EMBL” or “Ensembl” etc (see Uniprot.uniprotEntryToSequenceI())1. would it make more sense to bind Uniprot dbrefs to DBRefEntry instead?
    1. should PDBEntry.type get set to PDB (as the database source) also for mmCIF format?

  • is the MCView parser now obsolete? in which case can we get rid of it?

    • perhaps move remaining datamodel classes used in the package to a datamodel.structure package?
    • with a suitable ceremony (MC is Michelle Clamp?)

thanks,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

#5

isStructureFile() method is called from drop(…) method in AlignFrame class (line 4899). The changes are about 4 weeks old now. Which branch are you on and when last did you pull from develop? maybe your branch needs updating??

Charles.

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

From: jalview-dev-bounces@jalview.org <jalview-dev-bounces@jalview.org> on behalf of Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk>
Sent: 28 November 2016 15:04:56
To: Jalview Development List
Subject: Re: [Jalview-dev] Structure File questions

The StructureFileType enum is used by the method StructureFile.isStructureFile(fileType) to determine if a given file format is a structure file or not. It was introduced after 2.10.0 to replace explicit checks for ‘PDB’, ‘mmCIF’, or other structure file formats is some parts of the src code. See JAL-2280 for more history on this.

I can confirm that StructureFile.dbRefType is currently not used - that shouldn’t be the case though. I’d have to check the commit history to figure out what has gone wrong.

We currently don’t utilise the MMTF format. However, the StructureFileType enum should Ideally contain structure file formats that is/could be supported by Jalview.

The MCView parser is now kind of obsolete, however it was left for legacy purposes (i.e. importing older project files). IMHO, I think we could move the data model classes as suggested, but hold-up getting rid of the old parser for now.

Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

On 28 Nov 2016, at 09:37, Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

I’m looking at my FileFormatI branch and wanting to minimise, and ideally remove, ‘special case’ treatment of structure files (PDB/mmCIF) as a format.

Questions arising:

  • enum StructureFileType doesn’t seem to get used - can it be removed?

    • corollary: we don’t do anything with MMTF format?

  • StructureFile.dbRefType doesn’t seem to get used - can it be removed?

  • StructureFile.structureFileType (this is PDB or mmCIF)

    • looks like it could be passed as a method parameter (to postProcessChain()) rather than saved in a field
    • the value gets copied to PDBEntry.type - which is therefore PDB or mmCIF after parsing a structure file
    • however a Uniprot fetch (uniprot_mapping.xml) binds ‘dbReference’ to PDBEntry
    • so in this context, PDBEntry.type is “PDB” or “EMBL” or “Ensembl” etc (see Uniprot.uniprotEntryToSequenceI())1. would it make more sense to bind Uniprot dbrefs to DBRefEntry instead?
    1. should PDBEntry.type get set to PDB (as the database source) also for mmCIF format?

  • is the MCView parser now obsolete? in which case can we get rid of it?

    • perhaps move remaining datamodel classes used in the package to a datamodel.structure package?
    • with a suitable ceremony (MC is Michelle Clamp?)

thanks,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

The University of Dundee is a registered Scottish Charity, No: SC015096

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

The University of Dundee is a registered Scottish Charity, No: SC015096_______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev