Vitrite Database

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2019年9月よりhttps://vitroid.github.ioに移転しました。
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• Vitrite ( Network Motif of Water ) Database
  • URL
  • What is it?
  • How to get a graph in XML.
  • How to get the results by narrowing search in XML.
  • XML
    • A sample code to convert the result XML into a simple table
  • ChangeLog

[web service]
[多面体構造]
[vitrite]
[water]

Vitrite ( Network Motif of Water ) Database

 URL

http://vitrite.chem.okayama-u.ac.jp/cgi-bin/vitrite.cgi

 What is it?

Vitrite ("非晶子" in Chinese and Japanese) is the typical network motif of water at low temperature. It is defined as a graph satisfying the following conditions:

1. Each vertex must be 2- or 3-connected.
2. Each edge must be shared by two rings.
3. Consists of 3- to 8-membered rings.
4. Must satisfy the following Euler's formula for planar graph:

F - E + V = 2
where F, E, V are number of rings, edges, and vertices, respectively.

Note that not all the graphs in this database satisfy these conditions. Volume and topological volume are not shown for the graph not satisfying the conditions.

Almost all the vitrite found in low density amorphous ice is recorded in the database. It is also planned to import new vitrites into the database when it is queried.

 How to get a graph in XML.

Here is a sample URL to get a graph and its topological/geometrical attributes in XML:

• Sample Query

vitrite.cgi?id=39&form=xml&field=ringset,shape

The parameter 'id' specifies the graph ID in the database. You can specify multiple attributes for 'field' parameter in comma-separated format. Currently you can specify the following fields:

• spectrum
• solid
• volume
• ringset
• crystalviewer
• isvitrite
• image
• symmetry
• ringcount
• eulerindex
• topovolume
• shape
• graph
• rd

Note that 'graph' is mandatory.
You can also search by exact graph matching. Graph topology is specified in simple notation. Here is an example query for vitrite #8.

• Sample Query

vitrite.cgi?simple=A-B-C-D-E-F-A,C-G-H-F&form=xml&field=ringset

 How to get the results by narrowing search in XML.

To get a set of graphs satisfying a couple of conditions at a time, a sample URL is following:

• Sample Query

vitrite.cgi?form=xml&field=graph,isvitrite&key1=id&op1=in&val1=3,5,7-9&key2=isvitrite&op2=eq&val2=0

Number of query results can be limited by keywords 'sta'(starts) and 'rec'(records). If you need only the first 50 records out of 1000 query results, add 'sta=0&rec=50' to the URL. if you want the second 50 records, it becomes 'sta=50&rec=50'. If rec is unspecified, number of query results is limited to 1000 for fail-safe. See the following sample queries.

• Sample Query 1 (first 10 matches)

vitrite.cgi?form=xml&field=isvitrite&key1=isvitrite&op1=eq&val1=0&sta=0&rec=10

• Sample Query 2 (second 9 matches)

vitrite.cgi?form=xml&field=isvitrite&key1=isvitrite&op1=eq&val1=0&sta=10&rec=9

A condition is given by parameters key1, op1, and val1, specifying the field name, comparison operator, and the (threshold) value, respectively. Currently you can specify the following fields.

field	explanation
id	Graph ID
volume	Volume*
solid	Total solid angle* of the vertices cropped by the polyhedron in 4 pi steradian. It indicates the actual number of atoms contained in the polyhedron.
isvitrite	Is a vitrite?(0=yes)
symmetry	Symmetry Number
ring3	3-ring
ring4	4-ring
ring5	5-ring
ring6	6-ring
ring7	7-ring
ring8	8-ring
topo0	Euler Index
topo1	Number of Rings
topo2	Number of Edges
topo3	Number of Vertices
topovolume	Topological Volume
rd	Residual Distortion*

Note that '*' indicates the value is not exact (i.e. not a topological index).
Available operators are also listed.

operator	explanation
lt	< value
gt	> value
eq	== value
ne	!= value
in	in ranges

 XML

You can write some convenient tools by yourself to access the vitrite DB.

To get perl library in CPAN

http://www.cpan.org/misc/cpan-faq.html#How_install_Perl_modules

To parse XML by perl

http://search.cpan.org/dist/XML-Parser-EasyTree/EasyTree.pm

To dump the content of perl hash

http://search.cpan.org/~ilyam/Data-Dumper-2.121/Dumper.pm

A sample code to convert the result XML into a simple table

• preparation

# perl -MCPAN -e 'install XML::Parser::EasyTree'
# perl -MCPAN -e 'install Data::Dumper'

• source code in perl

#!/usr/bin/env perl
use strict;
use XML::Parser;
use XML::Parser::EasyTree;
use Data::Dumper;

#initialize XML Parser
$XML::Parser::EasyTree::Noempty=1;
my $p=new XML::Parser(Style=>'EasyTree');

#input the string from STDIN to $xml.
#For example,
#curl 'http://vitrite.chem.okayama-u.ac.jp/cgi-bin/vitrite.cgi?form=xml&field=isvitrite&key1=isvitrite&op1=eq&val1=0&sta=0&rec=10' | dumpvitritedb.pl
my $xml = join("", <STDIN>);
my $tree=$p->parse($xml);

#Peek the contents
print STDERR Dumper($tree);

if ( $tree->[0]{name} eq 'vitrites' ){
    foreach my $element ( @{$tree->[0]{content}} ){
	print table1( $element );
    }
}
elsif ( $tree->[0]{name} eq 'vitrite' ){
    print table1( $tree->[0] );
}



sub table1{
    my ( $element ) = @_;
    my $id = $element->{attrib}{id};
    my $text;
    $text .= "id $id ";
    foreach my $field ( @{$element->{content}} ){
	my $label = $field->{name};
	my $value = $field->{content}[0]{content};
	$text .= "$label $value ";
    }
    $text .= "\n";
    return $text;
}

 ChangeLog

2014-12-25

Moved to a new server.

2008-12-03

"Solid", i.e. solid angle of the vertices is added to the field list. Now you can estimate the number density of one fragment.

2007-11-29

Index was missing to id field of the database, which was the reason why DB access is so slow. Fixed. Simple notation is introduced for topological search query.

2007-11-27

The algorithm of shape module, which estimates the most unstrained geometry, is improved.

[2007年11月27日]

vitrite/ice i (eye)/Ice 0/ice 0?

[2004年10月26日]