README

=================
PDB_Tool (v4.80)
date: 2018.05.20
=================

Title:
PDB_Tool: a versatile tool to process PDB file

Author: 
Sheng Wang 

Contact email: 
realbigws@gmail.com 

--------------------------------------------------------



=========
Abstract:
=========

1. Convert official PDB to compact form which only contains the necessary ATOM co-ordinate information.
   e.g.,  ./PDB_Tool -i examples/1paz.pdb -r A -o 1pazA.pdb

2. Extract structural features from input PDB file by '-F' option.
   e.g.,  ./PDB_Tool -i examples/1paz.pdb -r A -o 1pazA.pdb -F 3

3. Specify residue range by '-r' option, which could be applied to process SCOP domain.
   e.g.,  ./PDB_Tool -i examples/2c2l.pdb -r A:24-224 -o d2c2la1.pdb

4. Fix the missing main-chain and/or side-chain atoms by '-R 1' option.
   e.g.,  ./PDB_Tool -i examples/1paz_caonly.pdb -R 1 -o 1pazA_fix.pdb 


========
Install:
========

1. download the package

git clone https://github.com/realbigws/PDB_Tool
cd PDB_Tool/

--------------

2. compile

cd source_code/
	make
cd ../

--------------

3. update the package

git pull



======
Usage:
======

========================================================|
PDB_Tool  (version 4.80) [2018.05.20]                   |
          a versatile tool to process PDB file          |
Usage:   ./PDB_Tool <-i input> <-r range> <-o output>   |
Or,      ./PDB_Tool <-i inroot> <-L list> <-o outroot>  |
--------------------------------------------------------|
For <-i input> input type,                              |
-i input  : input original PDB file, e.g., 1col.pdb     |
-r range  : input residue range, e.g., A:1-51           |
-o output : output PDB file, e.g., 1colA.pdb            |
--------------------------------------------------------|
For <-L list> input type,                               |
-i inroot  : input directory of original PDBs           |
-o outroot : output directory for generated PDBs        |
The rows in <list> indicate [input range output]        |
          e.g.,  1col.pdb A:1-51 1colA.pdb              |
========================================================|
                Primary options                         |
--------------------------------------------------------|
-M mode : Specify the atoms for output.                 |
          -2,  output CA+CB                             |
          -1,  output CA                                |
           0,  output backbone+CB                       |
          [1], output full atoms (Set as default)       |
--------------------------------------------------------|
-N num  : Specify the numbering type for output.        |
          -1,  full sequential, for atom and residue    |
           0,  part sequential, for atom only           |
          [1], PDB numbering (Set as default)           |
--------------------------------------------------------|
                Additional options                      |
--------------------------------------------------------|
The following arguments for both input types            |
        -C 1 to consider non-CA atoms                   |
        -R 1 to reconstruct missing CB and backbone     |
        -F 1 for AMI,CLE,SSE; 2 for ACC; 4 for FEAT     |
           these output files could be combined         |
           8 for output phi/psi/omega and theta/thor    |
           9 for output Ca-Ca, Cb-Cb, and N-O distance  |
The following arguments only for <-L list> input type   |
        -G 1 to output three log files                  |
========================================================|




================
Running example:
================

./PDB_Tool -i examples/1paz.pdb -r A -o 1pazA.pdb




=================
PDB_Tool options:
=================

---------------------------------------
structural features output by -F option
---------------------------------------

(1) AMI (amino acid sequence)
(2) CLE (conformational letter sequence in 17-state, defined according to [Wang & Zheng] )
(3) SSE (secondary structure element sequence in 8-state, defined according to [Kabsch & Sander] )
(4) ACC (relative solvent accessbility value calculated by [Kabsch & Sander], as well as the 3-state defined as [Ma & Wang] )
(5) FEAT (structural features containing AMI,CLE,SSE,ACC,rACC; contact number with CA and CB; and co-ordinate of CA and CB )


feature file example
--------------------
-F 1 to output AMI,CLE,SSE
-F 2 to output ACC and rACC
-F 4 to output FEAT     
           
Note that these output files could be combined, such as 
-F 3 to output AMI,CLE,SSE, and ACC,rACC files
-F 5 to output AMI,CLE,SSE, and FEAT files



----------------------------------
specify residue range by -r option
----------------------------------

symbol explanation:
-------------------
':' for PDB numbering, that the range is selected according to the residue number in the PDB file.
'.' for SEQUENCE numbering, that the range is selected according to sequential order, starting from 1.
'-' to indicate a certain beginning till the end.
'+' to indicate a certain beginning followed by the length range.
'@' to indicate the beginning or the ending of a certain chain.
',' to seperate between two PDB chains.
'!' to select all chains in the structure.
'_' to use the first chain in the structure.


example:   
--------
A:21-179,B.45-@


description:
------------
Two segments from the input structure are selected.                             
For chain A we select from residue 21 to residue 179 according to PDB numbering,
whereas for chain B we select from position 45 to the end in sequential order.  
--------------------------------------------------------------------------------

Note that the range symbol definition above is compatible with SCOP. 
    Then PDB_Tool could be applied to process SCOP domain defined as [Brenner et.al], for instance,

SCOP domain:
    d2c2la1 a.118.8.1 (A:24-224)
range process:
    ./PDB_Tool -i 2c2l.pdb -r A:24-224 -o d2c2la1.pdb





===========
References:
===========

[Wang & Zheng]: CLePAPS: fast pair alignment of protein structures based on conformational letters
      Sheng Wang and Wei-mou Zheng
      J Bioinform Comput Biol. 2008 Apr;6(2):347-66.
      http://www.ncbi.nlm.nih.gov/pubmed/18464327

[Kabsch & Sander]: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
      Kabsch W, Sander C.
      Biopolymers. 1983 Dec;22(12):2577-637.
      http://onlinelibrary.wiley.com/doi/10.1002/bip.360221211/abstract

[Ma & Wang]: AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multitask Learning Framework under the Conditional Neural Fields Model
      Jianzhu Ma and Sheng Wang
      BioMed Research International. 2015 
      http://www.hindawi.com/journals/bmri/aa/678764/

[Brenner et.al]: The ASTRAL compendium for protein structure and sequence analysis
      Steven E. Brenner,a Patrice Koehl, and Michael Levitt
      Nucleic Acids Res. 2000 Jan 1; 28(1): 254-256.
      http://nar.oxfordjournals.org/content/28/1/254.abstract