FastHinge 1.0   (c) Tetsuo Shibuya

1. Introduction
The FastHinge 1.0 is a very fast hinge prediction program that predicts 
hinge positions by comparing already-aligned two flexible structures [1]. 
DO NOT use this software if you do not agree with the followings: 

 1-1. If the software is contributed to your scientific publication, e.g., 
in a journal, conference paper, a book chapter, or any web pages, the author(s) 
must cite the relevant publication (that is [1].)

 1-2. You can use this software both for academic research and for commercial research. 
But you must not include this software in any commercial products without obtaining 
my permission. Please contact me if you want to do so. 

 1-3. You can redistribute this package to anyone, with this document. 

 1.4. You can decompile this package. You can change this program as you like, 
but when you redistribute the modified package, you must include this original 
package in your new package. 

 1-5. This package is just a program in the development stage. 

 1-6. I shall not be liable for any damage, claim, demand, cost or expense resulting 
from this software package. 


2. Files
This package contains the following 5 files. 

hinge.exe	- Windows execution file (compiled on Cygwin platform on Windows XP)
hinge.sunOS	- Solaris execution file (compiled on SunOS 5.8)
LB1.pdb		- Test file
LB2.pdb		- Test file
README.txt	- This file


3. Usage

Before using this program, you must prepare two PDB files to compare. 
Each PDB file must contain only 1 structure (with only 1 data, 1 model, and 1 chain in it). 
Moreover, you should remove non-backbone atoms from the data as in the 
PDB files (LB1.pdb/LB2.pdb) contained in this package. 
The data in LB1.pdb and LB2.pdb consists of only C alpha atoms. 

Let the two prepared files be PDB_file1 and PDB_file2, and 
set the number of hinges by using the -k option as follows: 

[On SunOS]
 % ./hinge.SunOS PDB_file1 PDB_file2 -k number_of_hinges
[Cygwin on Windows XP]
./hinge.exe PDB_file1 PDB_file2 -k number_of_hinges

For example: 
[On SunOS]
 % ./hinge.SunOS LB1.pdb LB2.pdb -k 2
[Cygwin on Windows XP]
 % ./hinge.exe LB1.pdb LB2.pdb -k 2

Then the result will be like this: 
===========================================
length = 238, max_n_hinges = 2
RMSD = 4.698512
RMSDh = 3.126366, hinge_position = 91/92
Computed RMSDh DP table in 0.3440000000 sec (system time: 0.0000000000 sec)
Traversed RMSDh DP table in 0.0000000000 sec (system time: 0.0000000000 sec)
- RMSDh values -
 RMSDh(0) = 4.698512
 RMSDh(1) = 3.126366
 RMSDh(2) = 0.473428
- Rigid Regions and Their RMSDs -
 RMSD[1..90] = 0.323389
 RMSD[91..191] = 0.625038
 RMSD[192..238] = 0.308524
===========================================

The 'RMSDh values - shows the RMSDh(k) values' (see [1] for details) for 
each k that is at most number_of_hinges you specified by the -k option.

The hinge_position showed in the third line is not the result.
(It is the hinge position obtained by setting k=1, regardless of 
what number you set for number_of_hinges.)
To know the predicted hinge positions, you should see the 
'Rigid Regions and Their RMSDs' part.
In the part, the line 
 "RMSD[1..90] = 0.323389"
means the first rigid fragment ends at the 90th atom, and 
the RMSD between two fragments (i.e. [1..90] of the two structures)
is 0.323389. 


5. Reference

[1] Tetsuo Shibuya, Fast Hinge Detection Algorithms for Flexible Protein Structures, 
IEEE/ACM Transactions on Computational Biology and Bioinformatics, to appear. 
