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commit 7490633022c471dc0cbef357d7d6fd27d84c43c4 1 parent 7514fe6
@georgeG authored
Showing with 12 additions and 18 deletions.
  1. +12 −18 README.rdoc
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30 README.rdoc
@@ -2,17 +2,15 @@
The isoelectric point (pI), sometimes abbreviated to iep, is the pH at which a particular molecule or surface carries no net electrical charge.
-This library is a ruby implementation for estimating the isoelectric point of a protein, based on the bioperl’s approach. It can be installed as a bioruby-plugin.
-
-Support for the following Pka sets is available
+This library is a Ruby implementation for estimating the isoelectric point of a protein.
+The following Pka sets are supported
* dtaselect
* emboss
* rodwell
* wikipedia
* sillero
-
-You can also create a custom Pka set as shown in the example
+Custom Pka sets are also supported
== Installation
@@ -23,18 +21,17 @@ You can also create a custom Pka set as shown in the example
gem uninstall bio-isoelectric_point
== Usage
+ require 'bio-isoelectric_point'
- require 'bio-isoelectric_point'
+ protein_seq = Bio::Sequence::AA.new("KKGFTCGELA")
- protein_seq = Bio::Sequence::AA.new("KKGFTCGELA")
+ #what is the protein charge at ph 14?
+ charge = protein_seq.charge_at(14) #=>-2.999795857467562
- #what is the protein charge at ph 14?
- charge = protein_seq.charge_at(14) #=>-2.999795857467562
+ #calculate the pH using dtaselect pka set and round off to 3 decimal places
+ isoelectric_point = protein_seq.isoelectric_point('dtaselect', 3) #=>8.219
- #calculate the pH using dtaselect pka set and round off to 3 decimal places
- isoelectric_point = protein_seq.isoelectric_point('dtaselect', 3) #=>8.219
-
- # calculate the iep ph with a custom set
+ #calculate the iep ph with a custom set
custom_pka_set = { "N_TERMINUS" => 8.1,
"K" => 10.1,
"R" => 12.1,
@@ -46,20 +43,17 @@ You can also create a custom Pka set as shown in the example
"Y" => 9.5
}
iep_ph = protein_seq.isoelectric_point(custom_pka_set, 3) #=> 8.193
-
== Contributing to bio-isoelectric_point
* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
-* Fork the project
* Start a feature/bugfix branch
* Commit and push until you are happy
* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
== Copyright
-
-Copyright (c)2011 George Githinji. See LICENSE.txt for
-further details.
+Copyright (c)2011 George Githinji.
+See LICENSE.txt for more details.
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