Merge pull request #86 from jordansafer/master

Fix header typo for easier parsing
Merge pull request #97 from Discngine/mypocket
2026-06-04 20:04:22 +08:00 · 2023-02-22 04:16:15 -05:00 · 2023-02-22 04:04:43 -05:00 · 2023-02-22 10:01:48 +01:00 · 2023-02-20 14:20:43 +01:00 · 2023-02-20 14:16:06 +01:00
1954 changed files with 468739 additions and 57017 deletions
--- a/.dockerignore
+++ b/.dockerignore
@@ -0,0 +1 @@
+*.o
--- a/.gitattributes
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+*.tcl linguist-detectable=false
+*.c linguist-detectable=true
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
--- a/.github/ISSUE_TEMPLATE/question.md
+++ b/.github/ISSUE_TEMPLATE/question.md
@@ -0,0 +1,10 @@
+---
+name: Question
+about: Custom question
+title: ''
+labels: question
+assignees: ''
+
+---
+
+
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -0,0 +1,28 @@
+name: C/C++ CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build-and-test-linux:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: netcdf
+      run: sudo apt-get install libnetcdf-dev
+    - name: make
+      run: make fpocket
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+    - name: create conda environment
+      run: conda env update -f ./tests/environment.yml   
+    - name : activate
+      run : |
+            eval "$(conda shell.bash hook)"
+            conda activate fpocket_test
+            pytest
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,8 @@
 nbproject
 *.o
-*_out
 .vscode
-src/qhull/bin/
+src/qhull/bin/
+src/qhull/lib/libqhullstatic_r.a
+src/qhull/lib/libqhullstatic.a
+*.pyc
+vmd/plugins
--- a/22
+++ b/22
@@ -0,0 +1,22 @@
+FROM debian:bullseye-slim
+RUN groupadd -r fpocket && useradd --no-log-init -r -g fpocket fpocket
+RUN apt update -y && apt install -y gcc g++ make libnetcdf-dev && rm -rf /var/lib/apt/lists/*
+
+# all of this mess is essentially to have a minimalistic build at the end
+COPY makefile /opt/fpocket/
+COPY src /opt/fpocket/src
+COPY man /opt/fpocket/man
+COPY headers /opt/fpocket/headers
+COPY obj /opt/fpocket/obj
+COPY scripts /opt/fpocket/scripts
+COPY bin /opt/fpocket/bin
+COPY plugins/LINUXAMD64 /opt/fpocket/plugins/LINUXAMD64
+COPY plugins/include /opt/fpocket/plugins/include
+COPY plugins/noarch /opt/fpocket/plugins/noarch
+
+WORKDIR /opt/fpocket
+
+RUN make && make install && make clean
+USER fpocket
+WORKDIR /tmp
+CMD ["fpocket"]
--- a/29
+++ b/29
@@ -0,0 +1,29 @@
+FROM ubuntu:latest
+RUN groupadd -r fpocket && useradd --no-log-init -r -g fpocket fpocket
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PLUGINDIR=compiled
+RUN apt update -y && apt install -y vim gdb gcc g++ make libnetcdf-dev && rm -rf /var/lib/apt/lists/* 
+
+# all of this mess is essentially to have a minimalistic build at the end
+COPY vmd /vmd
+WORKDIR /vmd/plugins
+RUN make LINUXAMD64 && make distrib
+
+COPY makefile /opt/fpocket/
+COPY src /opt/fpocket/src
+COPY data/sample /opt/fpocket/sample
+COPY man /opt/fpocket/man
+COPY headers /opt/fpocket/headers
+COPY obj /opt/fpocket/obj
+COPY scripts /opt/fpocket/scripts
+COPY bin /opt/fpocket/bin
+COPY plugins/LINUXAMD64 /opt/fpocket/plugins/LINUXAMD64
+COPY plugins/include /opt/fpocket/plugins/include
+COPY plugins/noarch /opt/fpocket/plugins/noarch
+
+WORKDIR /opt/fpocket
+RUN cp -r /vmd/plugins/molfile_plugin/compiled/LINUXAMD64/molfile/* plugins/LINUXAMD64/molfile/
+#RUN make && make install && make clean
+USER fpocket
+WORKDIR /tmp
+CMD ["fpocket"]
--- a/README.md
+++ b/README.md
@@ -1,19 +1,31 @@
-# fpocket project
+
+![fpocket logo](doc/images/fpocket_logo.png) 
+
+[![Build Status](https://dev.azure.com/3decision/fpocket/_apis/build/status/Discngine.fpocket?branchName=master)](https://dev.azure.com/3decision/fpocket/_build/latest?definitionId=2&branchName=master)
+[![Join the chat at https://gitter.im/fpocket/community](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/fpocket-official/community?utm_source=badge&utm_medium=badge&utm_content=badge)
+
 The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

+Detailed documentation is available here: [User Manual](doc/MANUAL.md). 
+The documentation below here is just a quick & rough overview.
+
 ## Content
-fpocket: the original pocket prediction on a single protein structure 
-mdpocket: extension of fpocket to analyse conformational ensembles of proteins (MD trajectories for instance)
-dpocket: extract pocket descriptors
-tpocket: test your pocket scoring function
+
+* __fpocket__   : the original pocket prediction on a single protein structure 
+* __mdpocket__  : extension of fpocket to analyse conformational ensembles of proteins (MD trajectories for instance)
+* __dpocket__   : extract pocket descriptors
+* __tpocket__   : test your pocket scoring function

 ## What's new compared to fpocket 2.0 (old sourceforge repo)
-fpocket: 
+__fpocket__: 
+- fpocket now supports mmCIF as input and output format together with the classical PDB format
+- support was added to define / delete and handle protein chains or sets of them to enable characterization of protein protein binding epitopes
 - is now able to consider explicit pockets when you want to calculate properties for a known binding site
 - cli changed a bit
 - pocket flexibility using temperature factors is better considered (less very flexible pockets on very solvent exposed areas)
 - druggability score has been reoptimized vs original paper. Yields now slightly better results than the original implementation.
 - compiler bug on newer compilers fixed
+
 mdpocket: 
 - can now read Gromacs XTC, netcdf and dcd trajectories
 - can also read prmtop topologies
@@ -22,12 +34,11 @@ mdpocket:

 ## Getting Started

-These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
-
-### Prerequisites
+### Prerequisites (if you want to compile it)

 The most recent versions (starting with fpocket 3.0) make use of the molfile plugin from VMD. This plugin is shipped with fpocket. However, now you need to install the netcdf library on your system. This is typically called netcdf-devel or so, depending on you linux distribution.
-fpocket needs to be compiled to run on your machine. For this you'll need the gnu c compiler (or another one, but didn't test with others than GCC).
+fpocket needs to be compiled to run on your machine. For this you'll need the gnu c compiler (or another one).
+
 install netcdf-devel on ubuntu type : 
 ```
 sudo apt-get install libnetcdf-dev
@@ -37,6 +48,44 @@ on a RHEL based distribution something like this should do:
 sudo yum install netcdf-devel.x86_64
 ```

+on OSX:
+
+Install MacPorts https://www.macports.org/ for instance (needed for netcdf install)
+
+```bash
+sudo port install netcdf
+export LIBRARY_PATH=/opt/local/lib
+```
+
+### Docker Image
+
+#### Using the official fpocket docker image
+
+The following command will pull the latest fpocket docker image from the dockerhub. 
+
+```bash
+docker pull fpocket/fpocket
+```
+
+#### Building the docker image
+
+
+You can create a docker image with fpocket using the provided Dockerfile of the repo (obviously you'd need docker to do that): 
+
+```bash
+docker build -t fpocket/fpocket .
+```
+
+#### Using the docker image
+
+This will build fpocket into your local fpocket/fpocket image. You can then run fpocket/mdpocket etc using: 
+
+```bash
+docker run -v `pwd`:/WORKDIR fpocket/fpocket fpocket -f data/sample/1UYD.pdb
+```
+
+Here you mount your current directory with your input files into the preconfigured `/WORKDIR` in the docker container and then run fpocket on a file in that mounted folder.
+
 ### Installing

 Download the sources from github via the website or using git clone and then build and deploy fpocket using the following commands.
@@ -51,93 +100,91 @@ sudo make install
 ```

 #### Compiling on Mac
-Install MacPorts https://www.macports.org/ for instance (needed for netcdf install)
 ```
-sudo port install netcdf
-export LIBRARY_PATH=/opt/local/lib
 git clone https://github.com/Discngine/fpocket.git
 cd fpocket
 make ARCH=MACOSXX86_64
 sudo make install
 ```

+#### Using conda

+There's also a conda package of fpocket available thanks to Simon Bray. You can install fpocket using conda with:
+```
+conda config --add channels conda-forge
+conda install fpocket
+```

-End with an example of getting some data out of the system or using it for a little demo
+#### Testing your installation

-## Running the tests
+In order to test if the compilation went well you can compare results from fpocket sample files to reference results shipped with fpocket. The easiest way to do that is by using pytest. If you do not have pytest yet, you can install the required library using the conda environment file in the tests folder: 

-The source code of fpocket is shipped with samples. They can be found in the data/sample folder. Try to run fpocket against the 1uyd sample to check if it's running OK. 
+```bash
+conda env create -f tests/environment.yml
+conda activate fpocket_test
+```
+
+Once your conda environment activated you can run 

 ```
-cd data/sample
-fpocket -f 1UYD.pdb
-```
-fpocket should state when it's beginning to search pocket and also when it's ending the search. Upon completion the folder should now contain a folder called 1UYD_out. Check whether the folder exists and the pdb files contain data and the pocket info file contains results. 
-
-
-## User Manual
-For now the user manual (still the one from fpocket 2.0) can be found in the doc folder. When I have some time to kill (or if somebody else has) we could add that here somewhere.
-
-## Frequent issues encountered
-### netcdf issues
-```
-cannot find -lnetcdf
-```
-mdpocket supports reading and writing NETCDF formatted files. In order to use this you need to install the netcdf development libraries on your system. 
-In centos this can be achieved like this : 
-```
-yum install -y epel-release #if the epel repo is not yet activated on your system
-yum install -y netcdf-devel
+pytest

 ```

-Run make again after installing this library. Mdpocket should build just fine now. 
+If everything works fine you should get something like this output here:
+```bash
+fpocket_test) Mac-Pro:fpocket peter$ pytest 
+============================================================= test session starts ==============================================================
+platform darwin -- Python 3.7.7, pytest-5.4.2, py-1.8.1, pluggy-0.13.1
+rootdir: /Users/peter/Documents/Work/fpocket_git/fpocket
+collected 4 items                                                                                                                              
+
+tests/test_fpocket.py ....                                                                                                               [100%]
+
+============================================================== 4 passed in 40.92s ==============================================================

-### stdc++ issues
 ```
-cannot find -lstdc++
-```
-You need to install the stc++ static libraries to build fpocket & mdpocket. On centos 7.4 this can be done like this : 
-```
-yum install -y libstc++-static
+If something fails in there you'll have a rather verbose and red output ... trust me you'll notice and panic ;)
+
+
+### Running fpocket
+
+You can run fpocket using the following command line as an example:
+```bash
+fpocket -f 1uyd.pdb
 ```

-### linking to molfile plugin issues
-If you observe an error similar to this one
+fpocket now also eats cif as input, so this would work as well. Make sure to use proper file extensions
+```bash
+fpocket -f 1uyd.cif
 ```
-ld: warning: ignoring file plugins/MACOSXX86/molfile/libmolfile_plugin.a, file was built for archive which is not the architecture being linked (x86_64): plugins/MACOSXX86/molfile/libmolfile_plugin.a
-Undefined symbols for architecture x86_64:
-  "_molfile_parm7plugin_init", referenced from:
-      _read_topology in topology.o
-  "_molfile_parm7plugin_register", referenced from:
-      _read_topology in topology.o
-ld: symbol(s) not found for architecture x86_64
-clang: error: linker command failed with exit code 1 (use -v to see invocation)
-make[1]: *** [bin/fpocket] Error 1
-make: *** [all] Error 2
+
+This will detect all pockets on the input pdb file, named 1uyd.pdb
+If you want to get all command line args for fpocket, simply type `fpocket``
+
+### Running mdpocket
+To detect all pockets and create a pocket frequency grid on a sample input trajectory in an xtc format for instance you can run: 
+
+```bash
+mdpocket --trajectory_file input.xtc --trajectory_format xtc -f topology.pdb
 ```
-then statically built libmolfile_plugin is not compatible with your machine. First check out that the ARCH variable set in the first line of the Makefile of fpocket actually reflects the architecture you want. For now I'm trying to support linux 64 bit systems and OSX 64 (LINUXAMD64) bit systems built with clang (MACOSXX86). So both should work out of the box. If they do not, you might need to build the molfile plugin for your architecture. All available system architectures for the molfile plugin can be found in the plugins folder tree : [plugins directory](https://github.com/Discngine/fpocket/tree/master/plugins). 
-Here you can find more information on how to build the molfile plugin on CentOS 7.4: 
-[compile molfile plugin on centos 7.4 - Discngine blog post](https://www.discngine.com/blog/2019/5/25/building-the-vmd-molfile-plugin-from-source-code)
-Once built, copy the architecture folder into the fpocket/plugins directory and make sure to declare this architecture in the ARCH variable in the Makefile. Finally run make again.
-If you manage to build for other architectures and it works, I'd be happy to accept PR's with the relevant plugin architectures as I cannot build all of them on my own ;).
+
+## Detailed User Manual
+
+You can access the detailed user manual here * [User Manual](doc/MANUAL.md)

 ## Contributing

 Please read [CONTRIBUTING.md](https://gist.github.com/PurpleBooth/b24679402957c63ec426) for details on our code of conduct, and the process for submitting pull requests to us.

-
 ## Authors

 * **Peter Schmidtke** - *Initial work* - [pschmidtke](https://github.com/pschmidtke)
 * **Vincent Le Guilloux** - *Initial work* - [leguilv](https://github.com/leguilv)
+* **Mael Shorkar** - *Chain handling, MMCIF support* - [shorkarmael](https://github.com/shorkarmael)


 ## License

 This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details

-## Acknowledgments
-
-* to be filled
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -0,0 +1,49 @@
+# C/C++ with GCC
+# Build your C/C++ project with GCC using make.
+# Add steps that publish test results, save build artifacts, deploy, and more:
+# https://docs.microsoft.com/azure/devops/pipelines/apps/c-cpp/gcc
+
+trigger: none                       # will disable CI builds entirely i.e. merges, check-ins do not trigger this build
+
+pr:
+  - master                          # trigger on a PR to master
+
+jobs:
+ - job: build_and_test_linux
+   pool:
+      vmImage: 'ubuntu-latest'
+   steps:
+      - script: conda env create --file tests/environment.yml --name fpocket_test
+        displayName: Create Anaconda environment
+      - script: conda env list
+        displayName:  environment installation verification
+      - task: Bash@3
+        inputs:
+          targetType: 'inline'
+          script: |
+            eval "$(conda shell.bash hook)"
+            sudo apt-get install libnetcdf-dev
+            conda activate fpocket_test
+            make
+            pytest
+        displayName: Active
+
+ - job: build_and_test_mac
+   pool:
+      vmImage: 'macOS-10.15'
+   steps:
+      - bash: sudo chown -R $USER $CONDA
+      - script: conda env create --file tests/environment.yml --name fpocket_test
+        displayName: Create Anaconda environment
+      - script: conda env list
+        displayName:  environment installation verification
+      - task: Bash@3
+        inputs:
+          targetType: 'inline'
+          script: |
+            eval "$(conda shell.bash hook)"
+            conda activate fpocket_test
+            make fpocket ARCH=MACOSXX86_64
+            pytest
+        displayName: Active
+
--- a/bugreport.txt
+++ b/bugreport.txt
@@ -1,38 +0,0 @@
-============================================================================
-                             FPOCKET BUG REPORT
-============================================================================
-
-
-Your name		:	
-Your email address	:	
-
-
-System Configuration
- ---------------------
-  Architecture (example: Intel Pentium, AMD Opteron)  	:	
-
-  Operating System (example: openSuse, Mac OS X) 	:
-
-  Fpocket version (example: Fpocket-1.0)  :  
-
-  Compiler used (example:  gcc 2.7.2)		:	
-
-
-Please enter a FULL description of your problem:
- ------------------------------------------------
-
-
-Please describe a way to repeat the problem. Please try to provide a
-concise reproducible example, if at all possible: 
- ----------------------------------------------------------------------
-
-
-If you know how this problem might be fixed, list the solution below:
- ---------------------------------------------------------------------
-
-
-
-=============================================================================
-!!! Please send this bug report to fpocket-support@lists.sourceforge.net  !!!
-!!! The development team will try to fix your problem as soon as possible !!!
-=============================================================================
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,16 +0,0 @@
-
->>>>>>>>>>>>>>> FPocket V1.0 -> V1.1 <<<<<<<<<<<<<<<
-
-
->>>>>>>>>>>>>>> FPocket V1.0 -> V1.0 <<<<<<<<<<<<<<<
-
-***** MAJOR CHANGES
-
-  19-02-2010  (vl) Created (not too soon... ;) )
-
-*****MINOR CHANGES
-
-  19-02-2010  (vl) Created (not too soon... ;) )
-
-
-***** GENERAL COMMENTS
--- a/configure.ac
+++ b/configure.ac
@@ -1,32 +0,0 @@
-#                                               -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-# Need the 2.59 version of autoconf
-AC_PREREQ(2.59)
-
-# Intialize autoconf, specifiting package name, version and authors
-AC_INIT([fpocket], 1.0, [P. Schmidtke <pschmidtke@mmb.pcb.ub.es> and V. Le Guilloux <vincent.le-guilloux@univ-orleans.fr>])
-
-# Check that we run autoconf in the right directory
-AC_CONFIG_SRCDIR([src/fpmain.c])
-
-# Auxiliary scripts such as install-sh and depcomp should be in builx-aux
-# AC_CONFIG_AUX_DIR([build-aux])
-
-# Initialize automake (foreign package for the moment)
-AM_INIT_AUTOMAKE([-Wall -Werror foreign])
-
-# Check for C compiler and make utility
-AC_PROG_CC
-AC_PROG_MAKE_SET
-
-# Declare output header and output files (Makefiles)
-AC_CONFIG_HEADERS([config.h])
-AC_CONFIG_FILES([
-        Makefile
-        man/Makefile
-        bin/Makefile
-        ])
-
-# Launch the tool
-AC_OUTPUT
--- a/data/.gitignore
+++ b/data/.gitignore
@@ -0,0 +1,7 @@
+nbproject
+*.o
+*.out
+.vscode
+src/qhull/bin/
+src/qhull/lib/libqhullstatic_r.a
+src/qhull/lib/libqhullstatic.a
--- a/data/sample/1ATP.pdb
+++ b/data/sample/1ATP.pdb
--- a/data/sample/1QNH.cif
+++ b/data/sample/1QNH.cif
--- a/data/sample/1UYD.cif
+++ b/data/sample/1UYD.cif
--- a/data/sample/1UYD_wrote.cif
+++ b/data/sample/1UYD_wrote.cif
--- a/data/sample/1UYD_wrote.pdb
+++ b/data/sample/1UYD_wrote.pdb
--- a/data/sample/1g50.cif
+++ b/data/sample/1g50.cif
--- a/data/sample/1g50.pdb
+++ b/data/sample/1g50.pdb
--- a/data/sample/1orc.cif
+++ b/data/sample/1orc.cif
--- a/data/sample/1orc.pdb
+++ b/data/sample/1orc.pdb
@@ -0,0 +1,877 @@
+HEADER    GENE REGULATING PROTEIN                 30-OCT-95   1ORC              
+TITLE     CRO REPRESSOR INSERTION MUTANT K56-[DGEVK]                            
+COMPND    MOL_ID: 1;                                                            
+COMPND   2 MOLECULE: CRO REPRESSOR INSERTION MUTANT K56-[DGEVK];                
+COMPND   3 CHAIN: A;                                                            
+COMPND   4 ENGINEERED: YES;                                                     
+COMPND   5 MUTATION: YES;                                                       
+COMPND   6 OTHER_DETAILS: RESULTS IN A 71-RESIDUE STABLE "MONOMER"              
+COMPND   7 MUTANT                                                               
+SOURCE    MOL_ID: 1;                                                            
+SOURCE   2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA;                    
+SOURCE   3 ORGANISM_TAXID: 10710;                                               
+SOURCE   4 GENE: CRO MUTANT K56-[DGEVK];                                        
+SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
+SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        
+SOURCE   7 EXPRESSION_SYSTEM_GENE: CRO MUTANT K56-[DGEVK]                       
+KEYWDS    GENE REGULATING PROTEIN                                               
+EXPDTA    X-RAY DIFFRACTION                                                     
+AUTHOR    R.A.ALBRIGHT,M.C.MOSSING,B.W.MATTHEWS                                 
+REVDAT   2   24-FEB-09 1ORC    1       VERSN                                    
+REVDAT   1   23-DEC-96 1ORC    0                                                
+JRNL        AUTH   R.A.ALBRIGHT,M.C.MOSSING,B.W.MATTHEWS                        
+JRNL        TITL   HIGH-RESOLUTION STRUCTURE OF AN ENGINEERED CRO               
+JRNL        TITL 2 MONOMER SHOWS CHANGES IN CONFORMATION RELATIVE TO            
+JRNL        TITL 3 THE NATIVE DIMER.                                            
+JRNL        REF    BIOCHEMISTRY                  V.  35   735 1996              
+JRNL        REFN                   ISSN 0006-2960                               
+JRNL        PMID   8547253                                                      
+JRNL        DOI    10.1021/BI951958N                                            
+REMARK   1                                                                      
+REMARK   1 REFERENCE 1                                                          
+REMARK   1  AUTH   M.C.MOSSING,R.T.SAUER                                        
+REMARK   1  TITL   STABLE, MONOMERIC VARIANTS OF LAMBDA CRO OBTAINED            
+REMARK   1  TITL 2 BY INSERTION OF A DESIGNED BETA-HAIRPIN SEQUENCE             
+REMARK   1  REF    SCIENCE                       V. 250  1712 1990              
+REMARK   1  REFN                   ISSN 0036-8075                               
+REMARK   2                                                                      
+REMARK   2 RESOLUTION.    1.54 ANGSTROMS.                                       
+REMARK   3                                                                      
+REMARK   3 REFINEMENT.                                                          
+REMARK   3   PROGRAM     : TNT                                                  
+REMARK   3   AUTHORS     : TRONRUD,TEN EYCK,MATTHEWS                            
+REMARK   3                                                                      
+REMARK   3  DATA USED IN REFINEMENT.                                            
+REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54                           
+REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
+REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
+REMARK   3   COMPLETENESS FOR RANGE        (%) : NULL                           
+REMARK   3   NUMBER OF REFLECTIONS             : 9834                           
+REMARK   3                                                                      
+REMARK   3  USING DATA ABOVE SIGMA CUTOFF.                                      
+REMARK   3   CROSS-VALIDATION METHOD          : NULL                            
+REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL                            
+REMARK   3   R VALUE     (WORKING + TEST SET) : NULL                            
+REMARK   3   R VALUE            (WORKING SET) : 0.178                           
+REMARK   3   FREE R VALUE                     : NULL                            
+REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL                            
+REMARK   3   FREE R VALUE TEST SET COUNT      : NULL                            
+REMARK   3                                                                      
+REMARK   3  USING ALL DATA, NO SIGMA CUTOFF.                                    
+REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL                   
+REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.1780                 
+REMARK   3   FREE R VALUE                  (NO CUTOFF) : NULL                   
+REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL                   
+REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL                   
+REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 9834                   
+REMARK   3                                                                      
+REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
+REMARK   3   PROTEIN ATOMS            : 500                                     
+REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
+REMARK   3   HETEROGEN ATOMS          : 0                                       
+REMARK   3   SOLVENT ATOMS            : 59                                      
+REMARK   3                                                                      
+REMARK   3  WILSON B VALUE (FROM FCALC, A**2) : NULL                            
+REMARK   3                                                                      
+REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.    RMS    WEIGHT  COUNT           
+REMARK   3   BOND LENGTHS                 (A) : 0.015 ; NULL  ; NULL            
+REMARK   3   BOND ANGLES            (DEGREES) : 2.300 ; NULL  ; NULL            
+REMARK   3   TORSION ANGLES         (DEGREES) : NULL  ; NULL  ; NULL            
+REMARK   3   PSEUDOROTATION ANGLES  (DEGREES) : NULL  ; NULL  ; NULL            
+REMARK   3   TRIGONAL CARBON PLANES       (A) : NULL  ; NULL  ; NULL            
+REMARK   3   GENERAL PLANES               (A) : NULL  ; NULL  ; NULL            
+REMARK   3   ISOTROPIC THERMAL FACTORS (A**2) : NULL  ; NULL  ; NULL            
+REMARK   3   NON-BONDED CONTACTS          (A) : NULL  ; NULL  ; NULL            
+REMARK   3                                                                      
+REMARK   3  INCORRECT CHIRAL-CENTERS (COUNT) : NULL                             
+REMARK   3                                                                      
+REMARK   3  BULK SOLVENT MODELING.                                              
+REMARK   3   METHOD USED : NULL                                                 
+REMARK   3   KSOL        : NULL                                                 
+REMARK   3   BSOL        : NULL                                                 
+REMARK   3                                                                      
+REMARK   3  RESTRAINT LIBRARIES.                                                
+REMARK   3   STEREOCHEMISTRY : NULL                                             
+REMARK   3   ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL                         
+REMARK   3                                                                      
+REMARK   3  OTHER REFINEMENT REMARKS:  BOTH TERMINI OF CRO K56-[DGEVK]ARE       
+REMARK   3  DISORDERED. RESIDUES 1, 2, 62, 63, 64, 65, AND 66 HAVE NO           
+REMARK   3  INTERPRETABLE DENSITY AND ARE NOT INCLUDED IN THE MODEL.            
+REMARK   3  RESIDUES 3 AND 61 EXTEN AWAY FROM THE GLOBULAR PORTION OF THE       
+REMARK   3  MOLECULE AND ARE MOST PROBABLY IN MULTIPLE CONFORMATIONS. THE       
+REMARK   3  GLOBULAR PORTION OF THE MOLECULE (RESIDUES 4 - 59) IS               
+REMARK   3  EXCEPTIONALLY WELL-DEFINED IN THE DENSITY.                          
+REMARK   4                                                                      
+REMARK   4 1ORC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
+REMARK 100                                                                      
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.                                
+REMARK 200                                                                      
+REMARK 200 EXPERIMENTAL DETAILS                                                 
+REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
+REMARK 200  DATE OF DATA COLLECTION        : 26-SEP-93                          
+REMARK 200  TEMPERATURE           (KELVIN) : NULL                               
+REMARK 200  PH                             : NULL                               
+REMARK 200  NUMBER OF CRYSTALS USED        : NULL                               
+REMARK 200                                                                      
+REMARK 200  SYNCHROTRON              (Y/N) : N                                  
+REMARK 200  RADIATION SOURCE               : NULL                               
+REMARK 200  BEAMLINE                       : NULL                               
+REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
+REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
+REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418                             
+REMARK 200  MONOCHROMATOR                  : NULL                               
+REMARK 200  OPTICS                         : NULL                               
+REMARK 200                                                                      
+REMARK 200  DETECTOR TYPE                  : AREA DETECTOR                      
+REMARK 200  DETECTOR MANUFACTURER          : XUONG-HAMLIN MULTIWIRE             
+REMARK 200  INTENSITY-INTEGRATION SOFTWARE : SDMS                               
+REMARK 200  DATA SCALING SOFTWARE          : NULL                               
+REMARK 200                                                                      
+REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 9834                               
+REMARK 200  RESOLUTION RANGE HIGH      (A) : NULL                               
+REMARK 200  RESOLUTION RANGE LOW       (A) : NULL                               
+REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
+REMARK 200                                                                      
+REMARK 200 OVERALL.                                                             
+REMARK 200  COMPLETENESS FOR RANGE     (%) : 95.8                               
+REMARK 200  DATA REDUNDANCY                : 4.600                              
+REMARK 200  R MERGE                    (I) : 0.02900                            
+REMARK 200  R SYM                      (I) : NULL                               
+REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL                               
+REMARK 200                                                                      
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
+REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL                     
+REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL                     
+REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
+REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
+REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
+REMARK 200  R SYM FOR SHELL            (I) : NULL                               
+REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
+REMARK 200                                                                      
+REMARK 200 DIFFRACTION PROTOCOL: NULL                                           
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL                         
+REMARK 200 SOFTWARE USED: NULL                                                  
+REMARK 200 STARTING MODEL: NULL                                                 
+REMARK 200                                                                      
+REMARK 200 REMARK: NULL                                                         
+REMARK 280                                                                      
+REMARK 280 CRYSTAL                                                              
+REMARK 280 SOLVENT CONTENT, VS   (%): 40.87                                     
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08                     
+REMARK 280                                                                      
+REMARK 280 CRYSTALLIZATION CONDITIONS: NULL                                     
+REMARK 290                                                                      
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
+REMARK 290                                                                      
+REMARK 290      SYMOP   SYMMETRY                                                
+REMARK 290     NNNMMM   OPERATOR                                                
+REMARK 290       1555   X,Y,Z                                                   
+REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
+REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
+REMARK 290       4555   X+1/2,-Y+1/2,-Z                                         
+REMARK 290                                                                      
+REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
+REMARK 290           MMM -> TRANSLATION VECTOR                                  
+REMARK 290                                                                      
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
+REMARK 290 RELATED MOLECULES.                                                   
+REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
+REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
+REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
+REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       17.38500            
+REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
+REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       24.15500            
+REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
+REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       19.58500            
+REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       24.15500            
+REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       17.38500            
+REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       19.58500            
+REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
+REMARK 290                                                                      
+REMARK 290 REMARK: NULL                                                         
+REMARK 300                                                                      
+REMARK 300 BIOMOLECULE: 1                                                       
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
+REMARK 300 BURIED SURFACE AREA.                                                 
+REMARK 350                                                                      
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
+REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
+REMARK 350                                                                      
+REMARK 350 BIOMOLECULE: 1                                                       
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
+REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
+REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
+REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
+REMARK 465                                                                      
+REMARK 465 MISSING RESIDUES                                                     
+REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
+REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
+REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
+REMARK 465                                                                      
+REMARK 465   M RES C SSSEQI                                                     
+REMARK 465     MET A     1                                                      
+REMARK 465     GLU A     2                                                      
+REMARK 465     LYS A    62                                                      
+REMARK 465     LYS A    63                                                      
+REMARK 465     THR A    64                                                      
+REMARK 465     THR A    65                                                      
+REMARK 465     ALA A    66                                                      
+REMARK 470                                                                      
+REMARK 470 MISSING ATOM                                                         
+REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER;            
+REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
+REMARK 470 I=INSERTION CODE):                                                   
+REMARK 470   M RES CSSEQI  ATOMS                                                
+REMARK 470     LYS A  21    CG   CD   CE   NZ                                   
+REMARK 500                                                                      
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
+REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
+REMARK 500                                                                      
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
+REMARK 500                                                                      
+REMARK 500 STANDARD TABLE:                                                      
+REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)               
+REMARK 500                                                                      
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
+REMARK 500                                                                      
+REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION                     
+REMARK 500    GLU A  54   CD    GLU A  54   OE2     0.069                       
+REMARK 500                                                                      
+REMARK 500 REMARK: NULL                                                         
+REMARK 500                                                                      
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
+REMARK 500                                                                      
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
+REMARK 500                                                                      
+REMARK 500 STANDARD TABLE:                                                      
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
+REMARK 500                                                                      
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
+REMARK 500                                                                      
+REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
+REMARK 500    ASP A   9   CB  -  CG  -  OD2 ANGL. DEV. =  -5.6 DEGREES          
+REMARK 500    ASP A  47   CB  -  CG  -  OD1 ANGL. DEV. =   6.5 DEGREES          
+REMARK 500    ASP A  47   CB  -  CG  -  OD2 ANGL. DEV. =  -5.5 DEGREES          
+REMARK 500    ASP A  56A  CB  -  CG  -  OD2 ANGL. DEV. =  -6.3 DEGREES          
+REMARK 500                                                                      
+REMARK 500 REMARK: NULL                                                         
+REMARK 525                                                                      
+REMARK 525 SOLVENT                                                              
+REMARK 525                                                                      
+REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT                    
+REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST                  
+REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT                 
+REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE                       
+REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;                             
+REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE                  
+REMARK 525 NUMBER; I=INSERTION CODE):                                           
+REMARK 525                                                                      
+REMARK 525  M RES CSSEQI                                                        
+REMARK 525    HOH A 148        DISTANCE =  5.42 ANGSTROMS                       
+DBREF  1ORC A    1    66  UNP    P03040   RCRO_LAMBD       1     66             
+SEQADV 1ORC GLU A   54  UNP  P03040              INSERTION                      
+SEQADV 1ORC VAL A   55  UNP  P03040              INSERTION                      
+SEQADV 1ORC LYS A   56  UNP  P03040              INSERTION                      
+SEQADV 1ORC ASP A   56A UNP  P03040              INSERTION                      
+SEQADV 1ORC GLY A   56B UNP  P03040              INSERTION                      
+SEQRES   1 A   71  MET GLU GLN ARG ILE THR LEU LYS ASP TYR ALA MET ARG          
+SEQRES   2 A   71  PHE GLY GLN THR LYS THR ALA LYS ASP LEU GLY VAL TYR          
+SEQRES   3 A   71  GLN SER ALA ILE ASN LYS ALA ILE HIS ALA GLY ARG LYS          
+SEQRES   4 A   71  ILE PHE LEU THR ILE ASN ALA ASP GLY SER VAL TYR ALA          
+SEQRES   5 A   71  GLU GLU VAL LYS ASP GLY GLU VAL LYS PRO PHE PRO SER          
+SEQRES   6 A   71  ASN LYS LYS THR THR ALA                                      
+FORMUL   2  HOH   *57(H2 O)                                                     
+HELIX    1   1 LEU A    7  PHE A   14  1                                   8    
+HELIX    2   2 GLN A   16  LEU A   23  1                                   8    
+HELIX    3   3 GLN A   27  HIS A   35  1                                   9    
+SHEET    1   A 3 LYS A  39  ILE A  44  0                                        
+SHEET    2   A 3 VAL A  50  LYS A  56 -1  N  VAL A  55   O  LYS A  39           
+SHEET    3   A 3 GLU A  56C PRO A  57 -1  N  LYS A  56E  O  GLU A  54           
+CISPEP   1 PHE A   58    PRO A   59          0        -0.65                     
+CRYST1   34.770   39.170   48.310  90.00  90.00  90.00 P 21 21 21    4          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      0.028760  0.000000  0.000000        0.00000                         
+SCALE2      0.000000  0.025530  0.000000        0.00000                         
+SCALE3      0.000000  0.000000  0.020700        0.00000                         
+ATOM      1  N   GLN A   3      12.772  36.309   7.065  1.00100.00           N  
+ATOM      2  CA  GLN A   3      12.632  37.265   8.163  1.00 48.14           C  
+ATOM      3  C   GLN A   3      13.732  37.165   9.263  1.00 52.27           C  
+ATOM      4  O   GLN A   3      14.053  36.101   9.788  1.00 44.13           O  
+ATOM      5  CB  GLN A   3      11.223  37.222   8.746  1.00 74.94           C  
+ATOM      6  CG  GLN A   3      10.520  38.577   8.616  1.00100.00           C  
+ATOM      7  CD  GLN A   3      10.533  39.326   9.931  1.00100.00           C  
+ATOM      8  OE1 GLN A   3       9.824  38.926  10.900  1.00100.00           O  
+ATOM      9  NE2 GLN A   3      11.382  40.376   9.990  1.00 83.72           N  
+ATOM     10  N   ARG A   4      14.321  38.294   9.634  1.00 25.53           N  
+ATOM     11  CA  ARG A   4      15.360  38.275  10.642  1.00 18.68           C  
+ATOM     12  C   ARG A   4      14.763  38.034  12.028  1.00 21.79           C  
+ATOM     13  O   ARG A   4      13.620  38.418  12.306  1.00 21.16           O  
+ATOM     14  CB  ARG A   4      16.095  39.616  10.699  1.00 18.77           C  
+ATOM     15  CG  ARG A   4      16.778  40.003   9.403  1.00 24.51           C  
+ATOM     16  CD  ARG A   4      17.273  41.464   9.421  1.00 32.20           C  
+ATOM     17  NE  ARG A   4      18.202  41.755   8.324  1.00 36.56           N  
+ATOM     18  CZ  ARG A   4      17.806  41.955   7.070  1.00 84.82           C  
+ATOM     19  NH1 ARG A   4      16.515  41.892   6.756  1.00 46.36           N  
+ATOM     20  NH2 ARG A   4      18.690  42.219   6.117  1.00 31.29           N  
+ATOM     21  N   ILE A   5      15.549  37.392  12.890  1.00 17.55           N  
+ATOM     22  CA  ILE A   5      15.183  37.125  14.284  1.00 14.87           C  
+ATOM     23  C   ILE A   5      16.203  37.872  15.172  1.00 16.47           C  
+ATOM     24  O   ILE A   5      17.401  37.815  14.843  1.00 17.02           O  
+ATOM     25  CB  ILE A   5      15.285  35.595  14.525  1.00 15.08           C  
+ATOM     26  CG1 ILE A   5      14.275  34.892  13.658  1.00 40.26           C  
+ATOM     27  CG2 ILE A   5      15.049  35.246  15.983  1.00 14.47           C  
+ATOM     28  CD1 ILE A   5      14.495  33.386  13.673  1.00 45.11           C  
+ATOM     29  N   THR A   6      15.800  38.526  16.285  1.00 13.28           N  
+ATOM     30  CA  THR A   6      16.814  39.214  17.093  1.00 11.96           C  
+ATOM     31  C   THR A   6      17.671  38.212  17.779  1.00 14.04           C  
+ATOM     32  O   THR A   6      17.266  37.055  17.907  1.00 14.20           O  
+ATOM     33  CB  THR A   6      16.173  40.127  18.156  1.00 14.58           C  
+ATOM     34  OG1 THR A   6      15.450  39.272  19.028  1.00 17.32           O  
+ATOM     35  CG2 THR A   6      15.146  41.042  17.451  1.00 14.30           C  
+ATOM     36  N   LEU A   7      18.849  38.618  18.202  1.00 13.73           N  
+ATOM     37  CA  LEU A   7      19.728  37.670  18.894  1.00 13.16           C  
+ATOM     38  C   LEU A   7      19.041  37.135  20.139  1.00 15.87           C  
+ATOM     39  O   LEU A   7      19.090  35.912  20.454  1.00 12.79           O  
+ATOM     40  CB  LEU A   7      21.048  38.383  19.263  1.00 12.68           C  
+ATOM     41  CG  LEU A   7      21.982  37.558  20.140  1.00 17.98           C  
+ATOM     42  CD1 LEU A   7      22.427  36.311  19.389  1.00 20.47           C  
+ATOM     43  CD2 LEU A   7      23.218  38.409  20.407  1.00 18.75           C  
+ATOM     44  N   LYS A   8      18.371  38.033  20.873  1.00 14.10           N  
+ATOM     45  CA  LYS A   8      17.689  37.619  22.103  1.00 14.00           C  
+ATOM     46  C   LYS A   8      16.593  36.611  21.795  1.00 19.65           C  
+ATOM     47  O   LYS A   8      16.429  35.627  22.507  1.00 19.85           O  
+ATOM     48  CB  LYS A   8      17.076  38.822  22.826  1.00 15.93           C  
+ATOM     49  CG  LYS A   8      16.367  38.544  24.133  1.00 20.77           C  
+ATOM     50  CD  LYS A   8      15.511  39.771  24.498  1.00 38.02           C  
+ATOM     51  CE  LYS A   8      15.092  39.901  25.953  1.00 83.24           C  
+ATOM     52  NZ  LYS A   8      14.141  41.009  26.161  1.00 99.56           N  
+ATOM     53  N   ASP A   9      15.797  36.854  20.746  1.00 12.13           N  
+ATOM     54  CA  ASP A   9      14.716  35.901  20.441  1.00 12.04           C  
+ATOM     55  C   ASP A   9      15.261  34.577  19.956  1.00 16.77           C  
+ATOM     56  O   ASP A   9      14.676  33.565  20.239  1.00 17.35           O  
+ATOM     57  CB  ASP A   9      13.754  36.452  19.381  1.00 16.98           C  
+ATOM     58  CG  ASP A   9      12.817  37.489  19.951  1.00 30.47           C  
+ATOM     59  OD1 ASP A   9      12.548  37.571  21.130  1.00 29.85           O  
+ATOM     60  OD2 ASP A   9      12.329  38.272  19.045  1.00 30.89           O  
+ATOM     61  N   TYR A  10      16.369  34.570  19.227  1.00 13.45           N  
+ATOM     62  CA  TYR A  10      16.968  33.316  18.763  1.00 12.08           C  
+ATOM     63  C   TYR A  10      17.425  32.470  19.933  1.00 13.52           C  
+ATOM     64  O   TYR A  10      17.190  31.235  19.970  1.00 14.35           O  
+ATOM     65  CB  TYR A  10      18.152  33.638  17.846  1.00 14.33           C  
+ATOM     66  CG  TYR A  10      18.675  32.467  17.052  1.00 13.99           C  
+ATOM     67  CD1 TYR A  10      19.677  31.649  17.566  1.00 14.46           C  
+ATOM     68  CD2 TYR A  10      18.162  32.193  15.781  1.00 15.06           C  
+ATOM     69  CE1 TYR A  10      20.159  30.568  16.820  1.00 14.84           C  
+ATOM     70  CE2 TYR A  10      18.645  31.118  15.037  1.00 17.89           C  
+ATOM     71  CZ  TYR A  10      19.654  30.307  15.551  1.00 13.52           C  
+ATOM     72  OH  TYR A  10      20.113  29.235  14.810  1.00 18.91           O  
+ATOM     73  N   ALA A  11      18.053  33.115  20.912  1.00 14.43           N  
+ATOM     74  CA  ALA A  11      18.530  32.389  22.104  1.00 17.07           C  
+ATOM     75  C   ALA A  11      17.358  31.828  22.884  1.00 17.90           C  
+ATOM     76  O   ALA A  11      17.431  30.725  23.401  1.00 17.23           O  
+ATOM     77  CB  ALA A  11      19.353  33.293  23.015  1.00 13.38           C  
+ATOM     78  N   MET A  12      16.267  32.569  22.941  1.00 13.72           N  
+ATOM     79  CA  MET A  12      15.110  32.087  23.658  1.00 13.95           C  
+ATOM     80  C   MET A  12      14.489  30.885  22.958  1.00 16.33           C  
+ATOM     81  O   MET A  12      13.821  30.024  23.529  1.00 15.90           O  
+ATOM     82  CB  MET A  12      14.085  33.240  23.737  1.00 16.34           C  
+ATOM     83  CG  MET A  12      14.166  34.057  24.981  1.00 55.28           C  
+ATOM     84  SD  MET A  12      13.007  35.441  24.890  1.00100.00           S  
+ATOM     85  CE  MET A  12      13.748  36.594  26.079  1.00 98.88           C  
+ATOM     86  N   ARG A  13      14.591  30.843  21.623  1.00 14.91           N  
+ATOM     87  CA  ARG A  13      14.011  29.725  20.874  1.00 13.59           C  
+ATOM     88  C   ARG A  13      14.894  28.499  20.818  1.00 14.85           C  
+ATOM     89  O   ARG A  13      14.377  27.403  20.833  1.00 16.17           O  
+ATOM     90  CB  ARG A  13      13.631  30.085  19.422  1.00 13.23           C  
+ATOM     91  CG  ARG A  13      12.343  30.937  19.399  1.00 25.46           C  
+ATOM     92  CD  ARG A  13      12.232  31.960  18.236  1.00 26.76           C  
+ATOM     93  NE  ARG A  13      10.993  32.722  18.331  1.00 32.94           N  
+ATOM     94  CZ  ARG A  13      10.675  33.572  19.327  1.00 49.00           C  
+ATOM     95  NH1 ARG A  13      11.504  33.835  20.326  1.00 49.46           N  
+ATOM     96  NH2 ARG A  13       9.491  34.194  19.329  1.00 62.76           N  
+ATOM     97  N   PHE A  14      16.201  28.679  20.678  1.00 11.35           N  
+ATOM     98  CA  PHE A  14      17.091  27.571  20.478  1.00 12.06           C  
+ATOM     99  C   PHE A  14      18.062  27.296  21.591  1.00 16.73           C  
+ATOM    100  O   PHE A  14      18.752  26.272  21.544  1.00 17.92           O  
+ATOM    101  CB  PHE A  14      17.937  27.839  19.221  1.00 12.10           C  
+ATOM    102  CG  PHE A  14      17.051  27.815  18.032  1.00 21.70           C  
+ATOM    103  CD1 PHE A  14      16.447  26.617  17.644  1.00 20.65           C  
+ATOM    104  CD2 PHE A  14      16.771  28.999  17.344  1.00 23.31           C  
+ATOM    105  CE1 PHE A  14      15.616  26.604  16.530  1.00 30.57           C  
+ATOM    106  CE2 PHE A  14      15.924  29.013  16.241  1.00 24.51           C  
+ATOM    107  CZ  PHE A  14      15.349  27.803  15.854  1.00 29.75           C  
+ATOM    108  N   GLY A  15      18.187  28.213  22.551  1.00 12.81           N  
+ATOM    109  CA  GLY A  15      19.126  28.023  23.641  1.00 16.07           C  
+ATOM    110  C   GLY A  15      20.448  28.715  23.368  1.00 15.58           C  
+ATOM    111  O   GLY A  15      20.833  28.977  22.216  1.00 15.80           O  
+ATOM    112  N   GLN A  16      21.160  29.060  24.429  1.00 19.00           N  
+ATOM    113  CA  GLN A  16      22.448  29.783  24.302  1.00 23.07           C  
+ATOM    114  C   GLN A  16      23.545  28.961  23.693  1.00 19.82           C  
+ATOM    115  O   GLN A  16      24.387  29.465  22.952  1.00 22.09           O  
+ATOM    116  CB  GLN A  16      22.898  30.455  25.608  1.00 31.37           C  
+ATOM    117  CG  GLN A  16      21.973  31.648  25.860  1.00 44.42           C  
+ATOM    118  CD  GLN A  16      22.477  32.563  26.928  1.00 89.98           C  
+ATOM    119  OE1 GLN A  16      21.674  33.132  27.677  1.00100.00           O  
+ATOM    120  NE2 GLN A  16      23.797  32.701  27.003  1.00 83.25           N  
+ATOM    121  N   THR A  17      23.503  27.676  23.943  1.00 14.81           N  
+ATOM    122  CA  THR A  17      24.522  26.836  23.410  1.00 14.49           C  
+ATOM    123  C   THR A  17      24.469  26.755  21.886  1.00 18.16           C  
+ATOM    124  O   THR A  17      25.485  26.941  21.176  1.00 18.87           O  
+ATOM    125  CB  THR A  17      24.387  25.482  24.095  1.00 29.61           C  
+ATOM    126  OG1 THR A  17      24.840  25.669  25.428  1.00 37.58           O  
+ATOM    127  CG2 THR A  17      25.221  24.420  23.405  1.00 37.41           C  
+ATOM    128  N   LYS A  18      23.271  26.451  21.353  1.00 15.02           N  
+ATOM    129  CA  LYS A  18      23.171  26.378  19.902  1.00 14.97           C  
+ATOM    130  C   LYS A  18      23.473  27.761  19.265  1.00 19.02           C  
+ATOM    131  O   LYS A  18      24.128  27.857  18.233  1.00 17.30           O  
+ATOM    132  CB  LYS A  18      21.799  25.902  19.488  1.00 15.62           C  
+ATOM    133  CG  LYS A  18      21.565  26.030  17.979  1.00 17.87           C  
+ATOM    134  CD  LYS A  18      20.302  25.331  17.522  1.00 20.77           C  
+ATOM    135  CE  LYS A  18      19.938  25.641  16.061  1.00 21.05           C  
+ATOM    136  NZ  LYS A  18      21.070  25.348  15.174  1.00 23.25           N  
+ATOM    137  N   THR A  19      22.998  28.826  19.929  1.00 13.94           N  
+ATOM    138  CA  THR A  19      23.232  30.176  19.408  1.00 15.11           C  
+ATOM    139  C   THR A  19      24.728  30.452  19.247  1.00 17.10           C  
+ATOM    140  O   THR A  19      25.195  30.883  18.197  1.00 16.28           O  
+ATOM    141  CB  THR A  19      22.562  31.204  20.345  1.00 14.30           C  
+ATOM    142  OG1 THR A  19      21.163  30.972  20.435  1.00 16.12           O  
+ATOM    143  CG2 THR A  19      22.748  32.585  19.777  1.00 18.66           C  
+ATOM    144  N   ALA A  20      25.504  30.162  20.312  1.00 15.42           N  
+ATOM    145  CA  ALA A  20      26.961  30.386  20.308  1.00 16.54           C  
+ATOM    146  C   ALA A  20      27.601  29.564  19.216  1.00 18.55           C  
+ATOM    147  O   ALA A  20      28.435  30.047  18.448  1.00 16.40           O  
+ATOM    148  CB  ALA A  20      27.581  30.040  21.665  1.00 18.19           C  
+ATOM    149  N   LYS A  21      27.178  28.327  19.124  1.00 15.87           N  
+ATOM    150  CA  LYS A  21      27.755  27.471  18.068  1.00 14.12           C  
+ATOM    151  C   LYS A  21      27.417  27.978  16.665  1.00 23.53           C  
+ATOM    152  O   LYS A  21      28.261  27.983  15.775  1.00 22.00           O  
+ATOM    153  CB  LYS A  21      27.380  25.988  18.165  1.00 19.74           C  
+ATOM    154  N   ASP A  22      26.163  28.359  16.428  1.00 13.98           N  
+ATOM    155  CA  ASP A  22      25.792  28.797  15.096  1.00 13.60           C  
+ATOM    156  C   ASP A  22      26.555  30.021  14.674  1.00 17.42           C  
+ATOM    157  O   ASP A  22      26.763  30.257  13.483  1.00 18.55           O  
+ATOM    158  CB  ASP A  22      24.285  29.133  15.132  1.00 17.16           C  
+ATOM    159  CG  ASP A  22      23.463  27.892  15.121  1.00 21.24           C  
+ATOM    160  OD1 ASP A  22      23.956  26.806  14.917  1.00 21.84           O  
+ATOM    161  OD2 ASP A  22      22.212  28.101  15.342  1.00 21.83           O  
+ATOM    162  N   LEU A  23      26.917  30.836  15.671  1.00 16.70           N  
+ATOM    163  CA  LEU A  23      27.573  32.091  15.415  1.00 17.48           C  
+ATOM    164  C   LEU A  23      29.059  31.985  15.508  1.00 21.83           C  
+ATOM    165  O   LEU A  23      29.783  32.927  15.155  1.00 32.31           O  
+ATOM    166  CB  LEU A  23      27.082  33.234  16.362  1.00 17.26           C  
+ATOM    167  CG  LEU A  23      25.591  33.560  16.187  1.00 21.17           C  
+ATOM    168  CD1 LEU A  23      25.236  34.773  17.030  1.00 23.34           C  
+ATOM    169  CD2 LEU A  23      25.395  33.916  14.721  1.00 27.21           C  
+ATOM    170  N   GLY A  24      29.528  30.890  16.014  1.00 19.23           N  
+ATOM    171  CA  GLY A  24      30.950  30.717  16.194  1.00 19.43           C  
+ATOM    172  C   GLY A  24      31.518  31.656  17.260  1.00 25.53           C  
+ATOM    173  O   GLY A  24      32.607  32.153  17.082  1.00 29.65           O  
+ATOM    174  N   VAL A  25      30.822  31.922  18.393  1.00 18.56           N  
+ATOM    175  CA  VAL A  25      31.348  32.806  19.455  1.00 18.47           C  
+ATOM    176  C   VAL A  25      31.227  31.997  20.731  1.00 29.23           C  
+ATOM    177  O   VAL A  25      30.609  30.971  20.707  1.00 35.08           O  
+ATOM    178  CB  VAL A  25      30.567  34.121  19.584  1.00 20.81           C  
+ATOM    179  CG1 VAL A  25      30.841  34.963  18.347  1.00 28.96           C  
+ATOM    180  CG2 VAL A  25      29.091  33.779  19.602  1.00 30.28           C  
+ATOM    181  N   TYR A  26      31.767  32.399  21.827  1.00 16.42           N  
+ATOM    182  CA  TYR A  26      31.548  31.539  22.976  1.00 16.61           C  
+ATOM    183  C   TYR A  26      30.335  32.063  23.742  1.00 26.02           C  
+ATOM    184  O   TYR A  26      29.975  33.190  23.562  1.00 20.21           O  
+ATOM    185  CB  TYR A  26      32.816  31.460  23.844  1.00 15.69           C  
+ATOM    186  CG  TYR A  26      33.397  32.834  24.133  1.00 15.36           C  
+ATOM    187  CD1 TYR A  26      33.008  33.568  25.261  1.00 19.73           C  
+ATOM    188  CD2 TYR A  26      34.370  33.356  23.286  1.00 20.92           C  
+ATOM    189  CE1 TYR A  26      33.566  34.821  25.529  1.00 22.18           C  
+ATOM    190  CE2 TYR A  26      34.915  34.612  23.529  1.00 20.77           C  
+ATOM    191  CZ  TYR A  26      34.528  35.334  24.653  1.00 23.19           C  
+ATOM    192  OH  TYR A  26      35.125  36.565  24.868  1.00 37.78           O  
+ATOM    193  N   GLN A  27      29.724  31.279  24.636  1.00 15.04           N  
+ATOM    194  CA  GLN A  27      28.470  31.644  25.313  1.00 16.50           C  
+ATOM    195  C   GLN A  27      28.439  32.914  26.073  1.00 18.25           C  
+ATOM    196  O   GLN A  27      27.478  33.680  26.054  1.00 21.76           O  
+ATOM    197  CB  GLN A  27      27.876  30.468  26.136  1.00 20.07           C  
+ATOM    198  CG AGLN A  27      27.570  29.232  25.290  0.50 12.45           C  
+ATOM    199  CG BGLN A  27      26.388  30.644  26.494  0.50 28.90           C  
+ATOM    200  CD AGLN A  27      26.956  28.056  26.052  0.50 20.66           C  
+ATOM    201  CD BGLN A  27      26.083  30.009  27.823  0.50 30.43           C  
+ATOM    202  OE1AGLN A  27      27.168  26.882  25.699  0.50 22.61           O  
+ATOM    203  OE1BGLN A  27      25.473  30.610  28.715  0.50 34.69           O  
+ATOM    204  NE2AGLN A  27      26.206  28.365  27.097  0.50 23.95           N  
+ATOM    205  NE2BGLN A  27      26.508  28.766  27.938  0.50 41.63           N  
+ATOM    206  N   SER A  28      29.464  33.122  26.809  1.00 15.52           N  
+ATOM    207  CA  SER A  28      29.586  34.339  27.606  1.00 16.10           C  
+ATOM    208  C   SER A  28      29.401  35.614  26.777  1.00 21.89           C  
+ATOM    209  O   SER A  28      28.767  36.563  27.222  1.00 20.41           O  
+ATOM    210  CB  SER A  28      30.919  34.313  28.380  1.00 14.82           C  
+ATOM    211  OG  SER A  28      30.982  35.513  29.123  1.00 26.67           O  
+ATOM    212  N   ALA A  29      29.961  35.637  25.564  1.00 17.59           N  
+ATOM    213  CA  ALA A  29      29.883  36.770  24.667  1.00 17.67           C  
+ATOM    214  C   ALA A  29      28.484  37.014  24.183  1.00 27.65           C  
+ATOM    215  O   ALA A  29      28.089  38.132  23.981  1.00 20.63           O  
+ATOM    216  CB  ALA A  29      30.757  36.537  23.465  1.00 21.94           C  
+ATOM    217  N   ILE A  30      27.751  35.952  23.955  1.00 23.64           N  
+ATOM    218  CA  ILE A  30      26.369  36.053  23.551  1.00 36.96           C  
+ATOM    219  C   ILE A  30      25.512  36.766  24.653  1.00 26.56           C  
+ATOM    220  O   ILE A  30      24.675  37.683  24.424  1.00 21.49           O  
+ATOM    221  CB  ILE A  30      25.777  34.653  23.188  1.00 26.00           C  
+ATOM    222  CG1 ILE A  30      26.348  34.051  21.899  1.00 22.78           C  
+ATOM    223  CG2 ILE A  30      24.260  34.754  23.064  1.00 24.42           C  
+ATOM    224  CD1 ILE A  30      26.113  34.938  20.703  1.00 24.43           C  
+ATOM    225  N   ASN A  31      25.684  36.302  25.886  1.00 26.96           N  
+ATOM    226  CA  ASN A  31      24.929  36.844  27.012  1.00 24.13           C  
+ATOM    227  C   ASN A  31      25.256  38.335  27.274  1.00 17.11           C  
+ATOM    228  O   ASN A  31      24.450  39.220  27.547  1.00 18.57           O  
+ATOM    229  CB  ASN A  31      25.209  35.902  28.208  1.00 28.18           C  
+ATOM    230  CG  ASN A  31      24.270  36.176  29.328  1.00100.00           C  
+ATOM    231  OD1 ASN A  31      24.697  36.533  30.445  1.00 89.90           O  
+ATOM    232  ND2 ASN A  31      22.981  36.068  28.999  1.00 64.11           N  
+ATOM    233  N   LYS A  32      26.471  38.639  27.080  1.00 16.17           N  
+ATOM    234  CA  LYS A  32      26.812  40.008  27.294  1.00 17.05           C  
+ATOM    235  C   LYS A  32      26.216  40.905  26.218  1.00 31.66           C  
+ATOM    236  O   LYS A  32      25.732  41.995  26.518  1.00 29.57           O  
+ATOM    237  CB  LYS A  32      28.306  40.081  27.162  1.00 21.07           C  
+ATOM    238  CG  LYS A  32      28.902  41.412  27.606  1.00 52.04           C  
+ATOM    239  CD  LYS A  32      30.396  41.492  27.303  1.00 81.78           C  
+ATOM    240  CE  LYS A  32      31.140  42.468  28.196  1.00100.00           C  
+ATOM    241  NZ  LYS A  32      30.873  43.865  27.856  1.00 43.46           N  
+ATOM    242  N   ALA A  33      26.285  40.437  24.956  1.00 19.80           N  
+ATOM    243  CA  ALA A  33      25.747  41.180  23.787  1.00 21.92           C  
+ATOM    244  C   ALA A  33      24.297  41.500  23.968  1.00 21.92           C  
+ATOM    245  O   ALA A  33      23.806  42.585  23.666  1.00 22.77           O  
+ATOM    246  CB  ALA A  33      25.948  40.430  22.479  1.00 18.69           C  
+ATOM    247  N   ILE A  34      23.591  40.542  24.444  1.00 18.08           N  
+ATOM    248  CA  ILE A  34      22.199  40.740  24.698  1.00 21.87           C  
+ATOM    249  C   ILE A  34      22.059  41.741  25.810  1.00 43.97           C  
+ATOM    250  O   ILE A  34      21.320  42.721  25.716  1.00 33.65           O  
+ATOM    251  CB  ILE A  34      21.594  39.409  25.069  1.00 29.26           C  
+ATOM    252  CG1 ILE A  34      21.436  38.525  23.825  1.00 21.75           C  
+ATOM    253  CG2 ILE A  34      20.239  39.555  25.760  1.00 34.93           C  
+ATOM    254  CD1 ILE A  34      20.948  37.106  24.189  1.00 26.89           C  
+ATOM    255  N   HIS A  35      22.822  41.512  26.856  1.00 29.05           N  
+ATOM    256  CA  HIS A  35      22.815  42.399  28.012  1.00 39.46           C  
+ATOM    257  C   HIS A  35      23.018  43.838  27.625  1.00 23.68           C  
+ATOM    258  O   HIS A  35      22.323  44.672  28.118  1.00 38.17           O  
+ATOM    259  CB  HIS A  35      23.911  42.003  29.015  1.00 30.65           C  
+ATOM    260  CG  HIS A  35      24.280  43.102  29.942  1.00100.00           C  
+ATOM    261  ND1 HIS A  35      25.418  43.879  29.708  1.00 68.44           N  
+ATOM    262  CD2 HIS A  35      23.672  43.529  31.112  1.00 35.25           C  
+ATOM    263  CE1 HIS A  35      25.494  44.750  30.724  1.00100.00           C  
+ATOM    264  NE2 HIS A  35      24.463  44.573  31.588  1.00 46.69           N  
+ATOM    265  N   ALA A  36      23.981  44.104  26.778  1.00 20.84           N  
+ATOM    266  CA  ALA A  36      24.334  45.408  26.286  1.00 24.23           C  
+ATOM    267  C   ALA A  36      23.305  45.982  25.291  1.00 36.12           C  
+ATOM    268  O   ALA A  36      23.444  47.124  24.846  1.00 33.39           O  
+ATOM    269  CB  ALA A  36      25.665  45.379  25.545  1.00 19.30           C  
+ATOM    270  N   GLY A  37      22.302  45.192  24.903  1.00 24.14           N  
+ATOM    271  CA  GLY A  37      21.290  45.659  23.941  1.00 29.84           C  
+ATOM    272  C   GLY A  37      21.854  46.026  22.565  1.00 35.89           C  
+ATOM    273  O   GLY A  37      21.472  46.990  21.917  1.00 30.09           O  
+ATOM    274  N   ARG A  38      22.782  45.260  22.076  1.00 17.99           N  
+ATOM    275  CA  ARG A  38      23.322  45.550  20.761  1.00 19.82           C  
+ATOM    276  C   ARG A  38      22.220  45.138  19.756  1.00 18.28           C  
+ATOM    277  O   ARG A  38      21.405  44.264  20.065  1.00 20.34           O  
+ATOM    278  CB  ARG A  38      24.653  44.808  20.523  1.00 19.50           C  
+ATOM    279  CG  ARG A  38      25.693  45.271  21.551  1.00 25.48           C  
+ATOM    280  CD  ARG A  38      26.965  44.505  21.472  1.00 24.57           C  
+ATOM    281  NE  ARG A  38      27.490  44.392  20.140  1.00 20.97           N  
+ATOM    282  CZ  ARG A  38      28.580  43.686  19.958  1.00 26.05           C  
+ATOM    283  NH1 ARG A  38      29.167  43.092  20.984  1.00 23.69           N  
+ATOM    284  NH2 ARG A  38      29.095  43.570  18.741  1.00 23.73           N  
+ATOM    285  N   LYS A  39      22.188  45.755  18.596  1.00 16.48           N  
+ATOM    286  CA  LYS A  39      21.140  45.482  17.629  1.00 17.09           C  
+ATOM    287  C   LYS A  39      21.666  44.466  16.675  1.00 16.45           C  
+ATOM    288  O   LYS A  39      22.313  44.817  15.683  1.00 18.25           O  
+ATOM    289  CB  LYS A  39      20.764  46.788  16.930  1.00 19.95           C  
+ATOM    290  CG  LYS A  39      20.222  47.767  17.972  1.00 24.06           C  
+ATOM    291  CD  LYS A  39      20.513  49.217  17.614  1.00 32.96           C  
+ATOM    292  CE  LYS A  39      19.981  50.191  18.673  1.00 45.86           C  
+ATOM    293  NZ  LYS A  39      19.454  51.472  18.095  1.00 53.67           N  
+ATOM    294  N   ILE A  40      21.410  43.183  17.021  1.00 13.44           N  
+ATOM    295  CA  ILE A  40      21.938  42.065  16.280  1.00 15.20           C  
+ATOM    296  C   ILE A  40      20.773  41.250  15.766  1.00 13.22           C  
+ATOM    297  O   ILE A  40      19.848  40.929  16.498  1.00 12.59           O  
+ATOM    298  CB  ILE A  40      22.888  41.267  17.200  1.00 10.03           C  
+ATOM    299  CG1 ILE A  40      24.136  42.108  17.439  1.00 12.39           C  
+ATOM    300  CG2 ILE A  40      23.375  40.058  16.441  1.00 12.12           C  
+ATOM    301  CD1 ILE A  40      24.876  41.612  18.651  1.00 16.76           C  
+ATOM    302  N   PHE A  41      20.831  40.957  14.469  1.00 13.05           N  
+ATOM    303  CA  PHE A  41      19.729  40.244  13.782  1.00 13.58           C  
+ATOM    304  C   PHE A  41      20.273  39.045  13.004  1.00 17.16           C  
+ATOM    305  O   PHE A  41      21.284  39.108  12.333  1.00 15.68           O  
+ATOM    306  CB  PHE A  41      18.882  41.229  12.858  1.00 21.85           C  
+ATOM    307  CG  PHE A  41      18.442  42.514  13.603  1.00 18.36           C  
+ATOM    308  CD1 PHE A  41      17.305  42.513  14.419  1.00 24.71           C  
+ATOM    309  CD2 PHE A  41      19.182  43.703  13.501  1.00 20.79           C  
+ATOM    310  CE1 PHE A  41      16.918  43.656  15.133  1.00 21.54           C  
+ATOM    311  CE2 PHE A  41      18.813  44.845  14.214  1.00 17.68           C  
+ATOM    312  CZ  PHE A  41      17.672  44.826  15.021  1.00 18.87           C  
+ATOM    313  N   LEU A  42      19.580  37.919  13.130  1.00 13.76           N  
+ATOM    314  CA  LEU A  42      20.040  36.694  12.507  1.00 13.18           C  
+ATOM    315  C   LEU A  42      19.086  36.217  11.421  1.00 17.74           C  
+ATOM    316  O   LEU A  42      17.873  36.362  11.506  1.00 17.28           O  
+ATOM    317  CB  LEU A  42      19.994  35.580  13.591  1.00 15.42           C  
+ATOM    318  CG  LEU A  42      21.233  35.539  14.492  1.00 18.78           C  
+ATOM    319  CD1 LEU A  42      21.341  36.862  15.260  1.00 23.71           C  
+ATOM    320  CD2 LEU A  42      21.058  34.350  15.470  1.00 25.37           C  
+ATOM    321  N   THR A  43      19.673  35.634  10.383  1.00 16.26           N  
+ATOM    322  CA  THR A  43      18.880  35.050   9.288  1.00 15.99           C  
+ATOM    323  C   THR A  43      19.275  33.561   9.186  1.00 17.09           C  
+ATOM    324  O   THR A  43      20.473  33.256   9.056  1.00 17.62           O  
+ATOM    325  CB  THR A  43      19.298  35.726   7.940  1.00 22.81           C  
+ATOM    326  OG1 THR A  43      18.835  37.049   8.024  1.00 25.25           O  
+ATOM    327  CG2 THR A  43      18.677  35.005   6.742  1.00 31.16           C  
+ATOM    328  N   ILE A  44      18.298  32.679   9.252  1.00 15.60           N  
+ATOM    329  CA  ILE A  44      18.568  31.274   9.131  1.00 20.91           C  
+ATOM    330  C   ILE A  44      18.383  30.861   7.696  1.00 15.87           C  
+ATOM    331  O   ILE A  44      17.359  31.193   7.095  1.00 18.91           O  
+ATOM    332  CB  ILE A  44      17.632  30.429  10.008  1.00 30.28           C  
+ATOM    333  CG1 ILE A  44      17.843  30.827  11.458  1.00 46.11           C  
+ATOM    334  CG2 ILE A  44      17.844  28.902   9.819  1.00 25.10           C  
+ATOM    335  CD1 ILE A  44      16.714  30.328  12.352  1.00 70.44           C  
+ATOM    336  N   ASN A  45      19.384  30.184   7.182  1.00 14.10           N  
+ATOM    337  CA  ASN A  45      19.327  29.689   5.821  1.00 20.16           C  
+ATOM    338  C   ASN A  45      18.803  28.263   5.824  1.00 19.07           C  
+ATOM    339  O   ASN A  45      18.874  27.527   6.819  1.00 17.69           O  
+ATOM    340  CB  ASN A  45      20.686  29.784   5.149  1.00 20.11           C  
+ATOM    341  CG  ASN A  45      21.184  31.231   5.162  1.00 24.66           C  
+ATOM    342  OD1 ASN A  45      20.402  32.125   4.864  1.00 26.94           O  
+ATOM    343  ND2 ASN A  45      22.436  31.444   5.569  1.00 26.52           N  
+ATOM    344  N   ALA A  46      18.251  27.870   4.705  1.00 22.61           N  
+ATOM    345  CA  ALA A  46      17.669  26.544   4.653  1.00 24.21           C  
+ATOM    346  C   ALA A  46      18.690  25.448   4.868  1.00 24.78           C  
+ATOM    347  O   ALA A  46      18.367  24.365   5.260  1.00 22.23           O  
+ATOM    348  CB  ALA A  46      16.890  26.345   3.375  1.00 22.88           C  
+ATOM    349  N   ASP A  47      19.940  25.755   4.671  1.00 21.26           N  
+ATOM    350  CA  ASP A  47      20.948  24.771   4.860  1.00 17.60           C  
+ATOM    351  C   ASP A  47      21.370  24.710   6.266  1.00 20.70           C  
+ATOM    352  O   ASP A  47      22.319  24.028   6.584  1.00 25.05           O  
+ATOM    353  CB  ASP A  47      22.175  25.020   3.980  1.00 23.87           C  
+ATOM    354  CG  ASP A  47      22.912  26.289   4.380  1.00 32.11           C  
+ATOM    355  OD1 ASP A  47      22.589  27.015   5.289  1.00 28.98           O  
+ATOM    356  OD2 ASP A  47      23.950  26.520   3.643  1.00 37.94           O  
+ATOM    357  N   GLY A  48      20.729  25.468   7.113  1.00 19.80           N  
+ATOM    358  CA  GLY A  48      21.127  25.428   8.525  1.00 23.59           C  
+ATOM    359  C   GLY A  48      22.139  26.456   8.966  1.00 24.53           C  
+ATOM    360  O   GLY A  48      22.305  26.655  10.164  1.00 27.05           O  
+ATOM    361  N   SER A  49      22.816  27.109   8.050  1.00 19.46           N  
+ATOM    362  CA  SER A  49      23.797  28.088   8.500  1.00 16.49           C  
+ATOM    363  C   SER A  49      23.061  29.352   8.896  1.00 20.85           C  
+ATOM    364  O   SER A  49      21.918  29.501   8.514  1.00 19.20           O  
+ATOM    365  CB  SER A  49      24.762  28.375   7.397  1.00 16.59           C  
+ATOM    366  OG  SER A  49      24.021  28.847   6.295  1.00 21.47           O  
+ATOM    367  N   VAL A  50      23.714  30.240   9.682  1.00 15.49           N  
+ATOM    368  CA  VAL A  50      23.094  31.441  10.161  1.00 14.53           C  
+ATOM    369  C   VAL A  50      23.925  32.627   9.792  1.00 16.31           C  
+ATOM    370  O   VAL A  50      25.113  32.563   9.905  1.00 20.11           O  
+ATOM    371  CB  VAL A  50      22.977  31.330  11.699  1.00 15.44           C  
+ATOM    372  CG1 VAL A  50      22.459  32.568  12.367  1.00 17.50           C  
+ATOM    373  CG2 VAL A  50      22.009  30.175  11.994  1.00 19.25           C  
+ATOM    374  N   TYR A  51      23.309  33.678   9.343  1.00 16.72           N  
+ATOM    375  CA  TYR A  51      24.067  34.887   9.017  1.00 21.29           C  
+ATOM    376  C   TYR A  51      23.627  35.971  10.032  1.00 20.19           C  
+ATOM    377  O   TYR A  51      22.451  36.117  10.309  1.00 20.05           O  
+ATOM    378  CB  TYR A  51      23.801  35.345   7.558  1.00 21.31           C  
+ATOM    379  CG  TYR A  51      24.146  36.813   7.269  1.00 22.84           C  
+ATOM    380  CD1 TYR A  51      25.466  37.186   7.021  1.00 29.04           C  
+ATOM    381  CD2 TYR A  51      23.158  37.789   7.193  1.00 27.80           C  
+ATOM    382  CE1 TYR A  51      25.841  38.500   6.745  1.00 29.93           C  
+ATOM    383  CE2 TYR A  51      23.506  39.112   6.911  1.00 28.96           C  
+ATOM    384  CZ  TYR A  51      24.837  39.466   6.685  1.00 28.90           C  
+ATOM    385  OH  TYR A  51      25.164  40.777   6.417  1.00 75.56           O  
+ATOM    386  N   ALA A  52      24.576  36.653  10.690  1.00 14.21           N  
+ATOM    387  CA  ALA A  52      24.167  37.639  11.639  1.00 13.99           C  
+ATOM    388  C   ALA A  52      24.736  38.973  11.230  1.00 16.81           C  
+ATOM    389  O   ALA A  52      25.857  39.062  10.734  1.00 17.86           O  
+ATOM    390  CB  ALA A  52      24.691  37.252  13.008  1.00 15.37           C  
+ATOM    391  N   GLU A  53      23.966  40.019  11.468  1.00 16.09           N  
+ATOM    392  CA  GLU A  53      24.423  41.342  11.157  1.00 16.97           C  
+ATOM    393  C   GLU A  53      24.076  42.266  12.282  1.00 15.88           C  
+ATOM    394  O   GLU A  53      23.093  42.080  12.971  1.00 18.62           O  
+ATOM    395  CB  GLU A  53      23.888  41.872   9.817  1.00 19.03           C  
+ATOM    396  CG  GLU A  53      22.411  42.061   9.859  1.00 24.25           C  
+ATOM    397  CD  GLU A  53      21.897  42.057   8.458  1.00 35.71           C  
+ATOM    398  OE1 GLU A  53      22.525  42.491   7.526  1.00 27.95           O  
+ATOM    399  OE2 GLU A  53      20.769  41.448   8.336  1.00 36.91           O  
+ATOM    400  N   GLU A  54      24.926  43.267  12.481  1.00 15.46           N  
+ATOM    401  CA  GLU A  54      24.720  44.221  13.546  1.00 16.14           C  
+ATOM    402  C   GLU A  54      24.543  45.641  12.961  1.00 21.40           C  
+ATOM    403  O   GLU A  54      25.130  46.003  11.948  1.00 25.19           O  
+ATOM    404  CB  GLU A  54      25.935  44.261  14.482  1.00 14.41           C  
+ATOM    405  CG  GLU A  54      25.673  45.177  15.692  1.00 18.40           C  
+ATOM    406  CD  GLU A  54      26.800  45.153  16.699  1.00 26.54           C  
+ATOM    407  OE1 GLU A  54      27.830  44.520  16.500  1.00 30.33           O  
+ATOM    408  OE2 GLU A  54      26.550  45.857  17.788  1.00 25.55           O  
+ATOM    409  N   VAL A  55      23.667  46.370  13.573  1.00 21.13           N  
+ATOM    410  CA  VAL A  55      23.440  47.727  13.144  1.00 27.58           C  
+ATOM    411  C   VAL A  55      24.110  48.583  14.182  1.00 27.92           C  
+ATOM    412  O   VAL A  55      23.780  48.514  15.389  1.00 25.31           O  
+ATOM    413  CB  VAL A  55      21.968  48.051  13.114  1.00 29.65           C  
+ATOM    414  CG1 VAL A  55      21.807  49.529  12.757  1.00 38.38           C  
+ATOM    415  CG2 VAL A  55      21.329  47.161  12.055  1.00 23.49           C  
+ATOM    416  N   LYS A  56      25.062  49.374  13.733  1.00 28.14           N  
+ATOM    417  CA  LYS A  56      25.762  50.207  14.693  1.00 58.37           C  
+ATOM    418  C   LYS A  56      26.180  51.499  14.044  1.00 33.42           C  
+ATOM    419  O   LYS A  56      26.815  51.453  12.959  1.00 31.02           O  
+ATOM    420  CB  LYS A  56      27.010  49.460  15.125  1.00 49.75           C  
+ATOM    421  CG  LYS A  56      27.697  49.942  16.393  1.00 39.95           C  
+ATOM    422  CD  LYS A  56      28.812  48.968  16.750  1.00100.00           C  
+ATOM    423  CE  LYS A  56      29.778  49.430  17.831  1.00100.00           C  
+ATOM    424  NZ  LYS A  56      30.915  48.498  18.004  1.00100.00           N  
+ATOM    425  N   ASP A  56A     25.831  52.621  14.696  1.00 53.90           N  
+ATOM    426  CA  ASP A  56A     26.191  53.931  14.169  1.00 49.50           C  
+ATOM    427  C   ASP A  56A     25.702  54.051  12.772  1.00 54.12           C  
+ATOM    428  O   ASP A  56A     26.476  54.298  11.863  1.00 49.28           O  
+ATOM    429  CB  ASP A  56A     27.710  54.134  14.031  1.00 47.57           C  
+ATOM    430  CG  ASP A  56A     28.484  53.954  15.317  1.00100.00           C  
+ATOM    431  OD1 ASP A  56A     28.021  54.228  16.433  1.00 92.41           O  
+ATOM    432  OD2 ASP A  56A     29.701  53.474  15.101  1.00100.00           O  
+ATOM    433  N   GLY A  56B     24.457  53.821  12.567  1.00 39.18           N  
+ATOM    434  CA  GLY A  56B     24.042  53.992  11.222  1.00 28.07           C  
+ATOM    435  C   GLY A  56B     24.539  52.950  10.315  1.00 36.07           C  
+ATOM    436  O   GLY A  56B     23.996  52.846   9.210  1.00 57.51           O  
+ATOM    437  N   GLU A  56C     25.519  52.134  10.743  1.00 28.59           N  
+ATOM    438  CA  GLU A  56C     25.964  51.070   9.818  1.00 40.34           C  
+ATOM    439  C   GLU A  56C     25.580  49.623  10.131  1.00 27.57           C  
+ATOM    440  O   GLU A  56C     25.320  49.256  11.286  1.00 35.60           O  
+ATOM    441  CB  GLU A  56C     27.401  51.139   9.280  1.00 47.14           C  
+ATOM    442  CG  GLU A  56C     27.803  52.562   8.881  1.00 68.41           C  
+ATOM    443  CD  GLU A  56C     27.611  52.798   7.413  1.00100.00           C  
+ATOM    444  OE1 GLU A  56C     27.850  51.956   6.548  1.00100.00           O  
+ATOM    445  OE2 GLU A  56C     27.166  54.002   7.176  1.00100.00           O  
+ATOM    446  N   VAL A  56D     25.610  48.868   9.016  1.00 30.28           N  
+ATOM    447  CA  VAL A  56D     25.278  47.464   8.936  1.00 30.80           C  
+ATOM    448  C   VAL A  56D     26.504  46.588   8.684  1.00 65.18           C  
+ATOM    449  O   VAL A  56D     27.082  46.538   7.616  1.00 31.22           O  
+ATOM    450  CB  VAL A  56D     24.104  47.217   7.973  1.00 46.38           C  
+ATOM    451  CG1 VAL A  56D     24.562  47.175   6.517  1.00 64.25           C  
+ATOM    452  CG2 VAL A  56D     23.430  45.913   8.324  1.00 41.05           C  
+ATOM    453  N   LYS A  56E     26.927  45.885   9.709  1.00 32.07           N  
+ATOM    454  CA  LYS A  56E     28.089  45.034   9.600  1.00 33.83           C  
+ATOM    455  C   LYS A  56E     27.784  43.617  10.073  1.00 26.57           C  
+ATOM    456  O   LYS A  56E     26.887  43.381  10.856  1.00 23.11           O  
+ATOM    457  CB  LYS A  56E     29.150  45.562  10.580  1.00 24.98           C  
+ATOM    458  CG  LYS A  56E     29.528  47.024  10.411  1.00 56.26           C  
+ATOM    459  CD  LYS A  56E     30.733  47.223   9.465  1.00100.00           C  
+ATOM    460  CE  LYS A  56E     30.415  47.974   8.156  1.00100.00           C  
+ATOM    461  NZ  LYS A  56E     30.878  47.300   6.922  1.00100.00           N  
+ATOM    462  N   PRO A  57      28.618  42.711   9.677  1.00 31.74           N  
+ATOM    463  CA  PRO A  57      28.533  41.324  10.100  1.00 30.22           C  
+ATOM    464  C   PRO A  57      28.844  41.214  11.584  1.00 24.56           C  
+ATOM    465  O   PRO A  57      29.574  42.010  12.109  1.00 22.29           O  
+ATOM    466  CB  PRO A  57      29.695  40.627   9.395  1.00 56.22           C  
+ATOM    467  CG  PRO A  57      30.582  41.730   8.819  1.00100.00           C  
+ATOM    468  CD  PRO A  57      29.703  42.961   8.705  1.00 57.16           C  
+ATOM    469  N   PHE A  58      28.273  40.220  12.248  1.00 17.63           N  
+ATOM    470  CA  PHE A  58      28.556  39.967  13.639  1.00 18.93           C  
+ATOM    471  C   PHE A  58      28.895  38.479  13.733  1.00 25.61           C  
+ATOM    472  O   PHE A  58      28.195  37.659  13.133  1.00 26.61           O  
+ATOM    473  CB  PHE A  58      27.305  40.192  14.482  1.00 17.79           C  
+ATOM    474  CG  PHE A  58      27.530  39.734  15.890  1.00 25.73           C  
+ATOM    475  CD1 PHE A  58      28.200  40.537  16.816  1.00 25.33           C  
+ATOM    476  CD2 PHE A  58      27.080  38.479  16.310  1.00 25.86           C  
+ATOM    477  CE1 PHE A  58      28.407  40.112  18.135  1.00 17.65           C  
+ATOM    478  CE2 PHE A  58      27.279  38.039  17.628  1.00 20.68           C  
+ATOM    479  CZ  PHE A  58      27.961  38.851  18.537  1.00 23.05           C  
+ATOM    480  N   PRO A  59      29.937  38.104  14.484  1.00 25.63           N  
+ATOM    481  CA  PRO A  59      30.784  38.992  15.209  1.00 25.99           C  
+ATOM    482  C   PRO A  59      31.647  39.704  14.228  1.00 49.28           C  
+ATOM    483  O   PRO A  59      31.863  39.264  13.106  1.00 28.39           O  
+ATOM    484  CB  PRO A  59      31.738  38.121  15.985  1.00 25.40           C  
+ATOM    485  CG  PRO A  59      31.704  36.771  15.325  1.00 25.66           C  
+ATOM    486  CD  PRO A  59      30.415  36.709  14.528  1.00 30.42           C  
+ATOM    487  N   SER A  60      32.184  40.798  14.653  1.00 49.75           N  
+ATOM    488  CA  SER A  60      33.009  41.550  13.738  1.00100.00           C  
+ATOM    489  C   SER A  60      34.406  41.011  13.645  1.00100.00           C  
+ATOM    490  O   SER A  60      34.934  40.769  12.543  1.00 95.05           O  
+ATOM    491  CB  SER A  60      33.118  42.996  14.188  1.00100.00           C  
+ATOM    492  OG  SER A  60      34.194  43.115  15.114  1.00100.00           O  
+ATOM    493  N   ASN A  61      34.965  40.865  14.851  1.00100.00           N  
+ATOM    494  CA  ASN A  61      36.322  40.475  15.074  1.00100.00           C  
+ATOM    495  C   ASN A  61      36.615  40.874  16.519  1.00100.00           C  
+ATOM    496  O   ASN A  61      36.488  42.053  16.901  1.00100.00           O  
+ATOM    497  CB  ASN A  61      37.166  41.359  14.114  1.00100.00           C  
+ATOM    498  CG  ASN A  61      38.647  41.049  13.964  1.00100.00           C  
+ATOM    499  OD1 ASN A  61      39.421  41.895  13.468  1.00100.00           O  
+ATOM    500  ND2 ASN A  61      39.046  39.835  14.348  1.00100.00           N  
+TER     501      ASN A  61                                                      
+HETATM  502  O   HOH A 100      16.567  43.265   4.042  1.00 34.53           O  
+HETATM  503  O   HOH A 101      20.456  38.947   9.389  1.00 23.99           O  
+HETATM  504  O   HOH A 102      12.849  38.495  16.591  1.00 22.30           O  
+HETATM  505  O   HOH A 103      13.926  40.856  20.884  1.00 41.05           O  
+HETATM  506  O   HOH A 104      18.819  40.954  20.655  1.00 19.73           O  
+HETATM  507  O   HOH A 105      22.693  27.151  27.634  1.00 70.09           O  
+HETATM  508  O   HOH A 106      21.061  42.196  21.789  1.00 41.39           O  
+HETATM  509  O   HOH A 107      18.782  42.676  18.500  1.00 18.57           O  
+HETATM  510  O   HOH A 108      16.220  42.191  21.534  1.00 50.13           O  
+HETATM  511  O   HOH A 109      17.337  35.292  25.464  1.00 39.26           O  
+HETATM  512  O   HOH A 112      10.684  35.559  22.027  1.00 57.92           O  
+HETATM  513  O   HOH A 113      20.062  26.858  12.663  1.00 44.33           O  
+HETATM  514  O   HOH A 114      21.057  25.359  22.646  1.00 20.07           O  
+HETATM  515  O   HOH A 115      10.987  37.712  13.387  1.00 53.83           O  
+HETATM  516  O   HOH A 116      21.175  25.792  25.461  1.00 45.82           O  
+HETATM  517  O   HOH A 117      26.070  29.114  11.027  1.00 22.17           O  
+HETATM  518  O   HOH A 118      11.734  37.820   3.909  1.00 69.47           O  
+HETATM  519  O   HOH A 119      11.313  40.892  19.018  1.00 47.45           O  
+HETATM  520  O   HOH A 120       9.440  37.991  19.579  1.00 59.14           O  
+HETATM  521  O   HOH A 121      12.308  39.937  22.921  1.00 66.69           O  
+HETATM  522  O   HOH A 123      31.715  37.994  27.757  1.00 35.80           O  
+HETATM  523  O   HOH A 124      33.332  38.551  25.542  1.00 72.97           O  
+HETATM  524  O   HOH A 125      28.935  43.074  23.912  1.00 34.25           O  
+HETATM  525  O   HOH A 126      29.860  40.122  23.720  1.00 32.71           O  
+HETATM  526  O   HOH A 127      15.525  33.748   9.130  1.00 31.50           O  
+HETATM  527  O   HOH A 128      31.988  41.342  17.207  1.00 59.78           O  
+HETATM  528  O   HOH A 129      29.634  43.327  14.724  1.00 33.16           O  
+HETATM  529  O   HOH A 130      22.330  39.552  29.588  1.00 65.61           O  
+HETATM  530  O   HOH A 131      27.765  44.818  28.495  1.00 38.62           O  
+HETATM  531  O   HOH A 133      24.462  47.460  17.919  1.00 23.88           O  
+HETATM  532  O   HOH A 134      24.899  49.304  19.604  1.00 47.82           O  
+HETATM  533  O   HOH A 135      26.021  28.115  30.069  1.00 59.83           O  
+HETATM  534  O   HOH A 136      18.018  27.146  28.371  1.00 70.16           O  
+HETATM  535  O   HOH A 138      16.935  29.765  26.527  1.00 48.67           O  
+HETATM  536  O   HOH A 139      18.048  29.690   2.604  1.00 43.98           O  
+HETATM  537  O   HOH A 141      31.065  26.910  15.705  1.00 64.63           O  
+HETATM  538  O   HOH A 142      30.020  29.019  13.276  1.00 57.01           O  
+HETATM  539  O   HOH A 143      29.845  26.873  22.152  1.00 79.81           O  
+HETATM  540  O   HOH A 146      13.383  39.438   6.579  1.00 63.02           O  
+HETATM  541  O   HOH A 147      20.711  27.622   2.096  1.00 49.53           O  
+HETATM  542  O   HOH A 148      14.196  30.133  28.935  1.00 79.60           O  
+HETATM  543  O   HOH A 150      28.792  35.220  12.803  1.00 70.46           O  
+HETATM  544  O   HOH A 151      27.559  30.392   9.833  1.00 74.79           O  
+HETATM  545  O   HOH A 152      28.329  26.679  12.467  1.00 58.31           O  
+HETATM  546  O   HOH A 154      27.463  36.350  10.486  1.00 61.38           O  
+HETATM  547  O   HOH A 156      18.107  32.722   3.682  1.00 53.96           O  
+HETATM  548  O   HOH A 161      25.605  26.383  11.780  1.00 58.16           O  
+HETATM  549  O   HOH A 162      16.433  43.785  10.736  1.00 59.32           O  
+HETATM  550  O   HOH A 163      10.518  36.164  16.394  1.00 64.24           O  
+HETATM  551  O   HOH A 166      19.795  28.946  27.147  1.00 45.05           O  
+HETATM  552  O   HOH A 171      13.409  41.652  13.265  1.00 61.60           O  
+HETATM  553  O   HOH A 174      27.287  32.431  11.584  1.00 64.21           O  
+HETATM  554  O   HOH A 180      23.741  29.905   2.072  1.00 58.63           O  
+HETATM  555  O   HOH A 181      32.794  51.457  17.245  1.00 65.72           O  
+HETATM  556  O   HOH A 183       9.101  40.801  20.870  1.00 71.78           O  
+HETATM  557  O  AHOH A 301      13.464  41.125   8.469  0.50 20.23           O  
+HETATM  558  O  BHOH A 301      12.554  42.700   8.853  0.50 26.40           O  
+HETATM  559  O  AHOH A 303      22.944  52.797  14.104  0.50 34.59           O  
+HETATM  560  O  BHOH A 303      22.676  52.579  15.869  0.50 32.63           O  
+MASTER      259    0    0    3    3    0    0    6  559    1    0    6          
+END                                                                             
--- a/data/sample/1ttv.cif
+++ b/data/sample/1ttv.cif
--- a/data/sample/1ttv.pdb
+++ b/data/sample/1ttv.pdb
--- a/data/sample/2P0R.cif
+++ b/data/sample/2P0R.cif
--- a/data/sample/2P0R.pdb
+++ b/data/sample/2P0R.pdb
--- a/data/sample/2P0R_mod.cif
+++ b/data/sample/2P0R_mod.cif
--- a/data/sample/2P0R_mod.pdb
+++ b/data/sample/2P0R_mod.pdb
--- a/data/sample/2P0R_wrote.cif
+++ b/data/sample/2P0R_wrote.cif
--- a/data/sample/2P0R_wrote.pdb
+++ b/data/sample/2P0R_wrote.pdb
--- a/data/sample/3LKF.pdb
+++ b/data/sample/3LKF.pdb
--- a/data/sample/3VI4.cif
+++ b/data/sample/3VI4.cif
--- a/data/sample/3vi4.pdb
+++ b/data/sample/3vi4.pdb
--- a/data/sample/4bdf.cif
+++ b/data/sample/4bdf.cif
--- a/data/sample/4bdf.pdb
+++ b/data/sample/4bdf.pdb
--- a/data/sample/5RGF.cif
+++ b/data/sample/5RGF.cif
--- a/data/sample/5rgf.pdb
+++ b/data/sample/5rgf.pdb
--- a/data/sample/6TL9.cif
+++ b/data/sample/6TL9.cif
--- a/data/sample/6X3P.cif
+++ b/data/sample/6X3P.cif
--- a/data/sample/6tl9.pdb
+++ b/data/sample/6tl9.pdb
--- a/data/sample/6x3p.pdb
+++ b/data/sample/6x3p.pdb
--- a/data/sample/7TAA.pdb
+++ b/data/sample/7TAA.pdb
--- a/data/sample/test_dpocket.txt
+++ b/data/sample/test_dpocket.txt
@@ -0,0 +1,3 @@
+data/sample/3LKF.pdb   pc
+data/sample/1ATP.pdb   atp
+data/sample/7TAA.pdb   abc
--- a/descall.sh
+++ b/descall.sh
@@ -1,21 +0,0 @@
-#! /bin/sh
-
-D=1.73
-m=3.0
-M=6.0
-i=36
-n=2
-out="desc_all_D"$D"_m"$m"_M"$M"_i"$i"_n"$n
-
-mkdir $out
-
-echo "== Describing training set"
-./bin/dpocket -f data/train-d.txt -D $D -m $m -M $M -i $i -n $n
-mv dpout_fpocketnp.txt dpout_fpocketnp_train.txt
-mv dpout_fpocketp.txt dpout_fpocketp_train.txt
-mv dpout_fpocket*_train.txt $out
-
-cat $out/dpout_fpocketp_train.txt > $out/all_train.txt
-awk 'NR > 1' $out/dpout_fpocketnp_train.txt >> $out/all_train.txt
-sed 's/[ ]\{1,100\}/;/g' $out/all_train.txt > $out/all_train.csv
-
--- a/doc/GETTINGSTARTED.md
+++ b/doc/GETTINGSTARTED.md
@@ -0,0 +1,985 @@
+# Getting started & Advanced guides
+
+##### fpocket
+
+* [fpocket basics](#fpocket-simple-pocket-detection)
+* [fpocket advanced](#fpocket-advanced)
+
+##### mdpocket
+
+* [mdpocket basics](#mdpocket-pocket-detection-on-md-trajectories)
+* [mdpocket advanced](#mdpocket-advanced)
+
+##### dpocket
+
+* [dpocket basics](#dpocket-descriptor-extraction)
+* [dpocket advanced](#dpocket-advanced)
+
+##### tpocket
+
+* [tpocket basics](#tpocket-scoring-ranging-and-evaluation)
+* [tpocket advanced](#tpocket-advanced)
+
+##### other
+
+* [pocket descriptors](#pocket-descriptors)
+* [cofactor definitions](#Cofactor-definition)
+* [customizing fpocket/mdpocket](#Customizing-fpocket)
+
+
+## fpocket - simple pocket detection
+
+To run the following examples, we use several sample input file `data/sample/` directory). 
+
+### Example
+
+Here you have a very simple and straightforward example of how to run fpocket on a single PDB file downloaded from the RCSB PDB. The following command line will execute fpocket on the 1UYD.pdb file situated in the sample directory.
+
+`fpocket -f sample/1UYD.pdb`
+
+It is also possible to run fpocket on a PDBx/mmcif file type, for example :
+
+`fpocket -f sample/2P0R.cif`
+
+It is mandatory to give a PDB input file using the -f flag in command line. If nothing is given, fpocket prints the fpocket usage/help to the screen. fpocket will use standard parameters for the detection of pockets. Fore more information about these parameters see the [advanced fpocket features](#fpocket-advanced).
+
+If fpocket works properly the output on the screen should look like this :
+```bash
+=========== Pocket hunting begins ==========
+=========== Pocket hunting ends ============
+```
+
+If you have a look now in the sample directory, you will notice that fpocket created a folder named 1UYD_out/. This folder contains all the output from fpocket, so what you are actually interested in. If you just want to see rapidly the results, go to the 1UYD_out directory and launch the 1UYD_VMD.sh script. This script will launch the VMD molecular visualizer and load the protein with binding site information coming from fpocket.
+
+![VMD with fpocket output](images/vmd1.png)
+
+The illustration above is somehow what you will see if you launch the VMD script. VMD is well suited for representing the volume of alpha spheres and their respective centers. Usually the visual volume information is not of primordial importance, as the larger alpha spheres tend to reach far out of the protein and smaller alpha spheres are not visible because they are recovered by larger ones. As it can be seen within the Main VMD window, the visualization script loads 3 structures, all of them are explained in more detail in the output section of this chapter.
+
+If you had a closer look before on the methodological aspects of this algorithm (we invite you to read the paper) a natural question would be how to represent apolar and polar alpha spheres. Currently the color code represents only the residue ID (rank of the cavity). If you want to see characteristics of alpha spheres we invite you to change the representation of alpha spheres. This can be found by clicking Graphics -> Representations. Another window will show up. There you select the first molecule (1UYD_out.pdb), like represented on the figure below.
+
+![VMD representations](images/vmd2.png)
+
+A script for fast visualization using PyMOL is also provided. PyMOL provides nice features browsing and selecting different pockets, using the predefined selection patterns on the right side of the main window. However, PyMOL does not interpret well the pqr file format, so alpha sphere volumes are not accurate and only alpha sphere centers can be shown.
+
+![VMD representations](images/pymol1.png)
+
+### Basic input
+
+#### Mandatory (1 OR 2):
+
+	1: flag -f :    one standard PDB or PDBx/mmcif file name.
+	2: flag -F :    one text file containing a simple list of pdb path
+
+#### Optional:
+For more details on optional fpocket arguments see [advanced fpocket features](#fpocket-advanced).
+
+
+### Output
+Fpocket output is made of many files. To have a detailed overview of those files, see [advanced fpocket features](#fpocket-advanced).
+
+Is there something else? No, you are done. Congratulations, you have successfully performed your first pocket prediction with fpocket...without any accidents we hope. As you might have seen, usage of fpocket is rather simple, although it is command line based software. Furthermore you should have seen that fpocket is very fast, well, lets say if you do not run it on a P1 100Mhz.
+As mentioned before, fpocket provides much more possibilities especially for filtering out unwanted pockets, clustering of alpha spheres. For all these issues and usage of these more advanced features, refer to [advanced fpocket features](#fpocket-advanced)
+
+
+
+## mdpocket pocket detection on MD trajectories
+
+The fpocket developer team is proud to present a very new feature as part of the fpocket software package. As programmers are very creative people, as you might know, we called this program mdpocket, as acronym of Molecular Dynamics pocket (very original isn't it?). In the next paragraphs we will refer to Molecular Dynamics as MD.
+
+Well, mdpocket is a freely available software that allows you to do the following very nice things in a quite fast way :
+
+* pocket detection on MD trajectories (I already said this one)
+* visualization of transient pockets (oh, will we have all the Pharma people on our back?)
+* extraction of pocket descriptors during the MD trajectory (like pocket volume for example)
+* get a static image of pocket occurrences during the MD trajectory (this you do not necessarily see the usefulness, but this will become clearer later)
+* perform on the fly energy calculations within a detected pocket
+
+If you are already used to run and analyze MD trajectories you know that there is a bunch of different software available to perform calculation and analysis of MD trajectories. Mdpocket is able to read plain PDB files describing the conformations of a protein, but now you can also read Amber crd files, gromacs xtc, netcdf and charmm and Namd dcd files (that was a nightmare to integrate and compile, so please make use of it).
+
+### Example
+It is VERY IMPORTANT to first align (superimpose) all snapshots onto each other. Why? Well, you have to do this due to the methodology used behind mdpocket. For more information on how mdpocket works feel free to read the mdpocket paper:
+(http://bioinformatics.oxfordjournals.org/content/27/23/3276.long)
+
+Below is an example for Amber for instance, but you can do the same with gromacs tools, mdtraj in python or in VMD analyzing NAMD trajectories for instance:
+
+ With Amber you can do the structural alignment and transformation using the freely available ptraj or cpptraj program and the following steps:
+
+- 1: create a ptraj input file with the following content :
+
+        trajin ../md_1.x.gz 1 250 10
+        trajin ../md_2.x.gz 1 250 10
+        trajin ../md_3.x.gz 1 250 10
+        reference ../reference.pdb
+        strip !:1-208
+        rms reference :25-88,120-196@CA,C,N,O
+        trajout trajectory_superimposed.dcd charmm
+        go
+- 2: 	Run ptraj using the following command:
+`ptraj your_topology.top < ptraj_input_file.ptr`
+
+A few words about what we are doing here. First, the ptraj input reads trajectory files. In this example, the trajectory is split up in 3 files. Each file has 250 snapshots. Here we only read every tenth snapshot of the 250. We set a reference PDB structure for the alignment.
+
+The strip command allows you to drop residues, here everything other than the protein (solvent, counter ions etc...).
+
+Next, we align each snapshot on the reference structure, using only the heavy atoms of residues 25-88 and 120 to 196.
+
+The output is written to trajectory_superimposed.dcd. Here we write a dcd file just for demonstration purposes, you can write mdcrd or netcdf files as well with ptraj.
+
+Now, here we are, we can run mdpocket (finally...):
+
+`mdpocket --trajectory_file trajectory_superimposed.dcd --trajectory_format dcd -f reference.pdb`
+
+NB: you still have to provide a pdb file containing the actual topology of the structure as most of the supported MD formats only store coordinates, but no information on the actual atom & residue types of the structure.
+
+The following part will take a while, depending on the number of atoms in your system and the number of snapshots you analyze. In average on a sample MD of 4000 snapshots (3258 atoms) 0.4 seconds of calculation time were necessary for analysis of 1 snapshot on one core of a 2.66Ghz Intel Quad with 4Gb of RAM.  
+
+Mdpocket will print out some things and the actual status of advance of the calculation. Once finished you will be able to find the following output files in your current folder :
+
+* `mdpout_freq_grid.dx`: This is an output grid file. The grid contains only a measure of frequency of how many times the pocket was open during a MD trajectory. This, averaged by the number of snapshots, gives a range of possible iso-values between 0 and 1. Currently we provide both types of grid files (frequency & density, as both have proven their usefulness during in-house studies. However, the frequency grid file is usually much easier to interpret.
+This representation gives you already a lot of information especially about existing paths during a MD. For mechanistic studies this can often be enough, However, if you want to do measurements of the volume (for example) of a certain pocket you have to select this region first. As VMD and the grid file are not really suitable for selection, mdpocket provides two last output files called :
+
+* `mdpout_dens_grid.dx`: This is one of the two grid output files coming from mdpocket. Briefly, a grid is superposed to all alpha spheres of all snapshots and the number of alpha spheres around each grid point is counted. This output is very useful as working file for a first crude visualization using PyMOL or VMD. In the following example we will show VMD as the visualization of grids is easier and less heavy with it. Open VMD and load the DX file. You should have something like this (colors are different) :
+
+![VMD with mdpocket output](images/vmd3.png)
+
+Well, this is nice, but you can hardly see anything interpretable in there. In order to see more clearly we recommend to change the representation by going to Graphics -> Representations as shown in the following illustration:
+
+![VMD with mdpocket output](images/vmd4.png)
+
+Now you basically can play with the Isovalue slider to get more or less conserved cavities during the MD trajectory. The unit of this isovalue can be expressed as number of Voronoi Vertices (alpha sphere centers) in a 8Å3 cube around each grid point per snapshot. The more a cavity is conserved (or dense) the higher this value. Thus, you will usually get internal pockets and protein internal channels. If you are interested in very superficial or transient binding sites you should decrease the isovalue until you see it.
+
+* `mdpout_dens_iso_8.pdb`: This file contains all grid points having 3 or more Voronoi Vertices in the 8A3 volume around the grid point for each snapshot. Using PyMOL you can now select and save only the grid points of the pocket you are interested in. Save these points to another pdb file. Let us call this file my_pocket.pdb. The choice of the correct grid points for your pocket definition depends completely on you. As rule of a thumb we would recommend to use a high (like 5) isovalue if you want to show open channels in a protein or protein internal binding pockets. You should lower this isovalue (maybe to 2 or 3) if you are interested in transient phenomena (opening, closing of paths, transient pockets etc...). Refer to advanced features to know how to extract these pdb files with other iso values.
+
+* `mdpout_freq_iso_0_5.pdb`: This is similar to the previous pdb file, just being produced on the frequency grid with a cut-off of 0.5.
+
+In order to measure the pocket around your previously defined pocket during the MD trajectory you have to rerun mdpocket in a slightly different way:
+
+`mdpocket --trajectory_file trajectory_superimposed.dcd --trajectory_format dcd -f reference.pdb --selected_pocket my_pocket.pdb`
+
+As you can see, now you have to pass your pocket definition using the --selected_pocket flag of mdpocket. To see how to define your pocket, see the section [Pocket Selection](#pocket-selection). The -v flag is optional, it is just to provide reasonably good volume calculations in a reasonably good execution time. As during the first mdpocket run you should see some output first and the advancement of mdpocket through all you snapshots. Once finished you will find some other output files in your folder:
+
+* `mdpout_mdpocket.pdb`: This is a pdb file that contains all Voronoi vertices in the selected pocket zone for each snapshot. Each snapshot is handled as separated model (like a NMR structure) and can thus be viewed as MD using PyMOL. Show the surface of the vertices and you can visualize the movement of your pocket. Be careful, VMD does not read this file, as from one snapshot to the other a different number and type of Voronoi vertices can be part of the model.
+
+* `mdpout_mdpocket_atoms.pdb`: This is a pdb file similar to the previous output, but this time containing all receptor atoms defining the binding pocket.
+
+* `mdpout_descritpors.txt`: Last but not least, maybe the most important file containing the pocket descriptors. You will find for each snapshot the pocket volume, the number of alpha spheres and all other default fpocket descriptors:
+
+        snapshot 	pock_volume 	nb_AS 	mean_as_ray ...
+        1 		793.47 		183 		3.76
+        2 		726.95 		158 		3.86
+        3 		711.87 		213 		3.59
+        4 		700.82 		172 		3.61
+        5 		762.24 		196 		3.85
+        6 		618.31 		193 		3.77
+
+This output file can be easily analyzed using R, gnuplot or other suitable software. An example R output for the pocket volume would be:
+
+![Pocket volume plot](images/volume.png)
+
+If you want to reproduce this, simply launch R and type:
+
+```R
+r=read.table("mdpout_descriptors.txt",h=T)
+ylim=c(400,1200)
+plot(r[,"pock_volume"],ty='l',ylim=ylim,main="",xlab="",ylab="")
+par(new=T)
+plot(smooth.spline(r[,"pock_volume"],df=40),col="red",lwd=3,ylim=ylim,ty="l",xlab="snapshot",ylab="volume")
+```
+
+On this figure you can see a clear volume increase of the pocket in the beginning of the trajectory. Now you can check to what phenomena this increase is due to by analyzing the mdpout_mdpocket.pdb output  in PyMOL. Not shown in this example, mdpocket now provides also measurements of the polar and apolar surface area (van der Waals + 1.4Å probe) of the pocket.
+
+### Pocket Selection
+In order to be able to track some nifty properties of your cavities, like the solvent accessible surface area, the volume or other fpocket descriptors, you have to select the zone you are interested in. This process is crucial and can depply influence sub-sequent results.
+
+But first of all, what is a selected pocket here? Here, this means a PDB file containing dummy atoms at the positions of grid points that overlap with grid points in the pocket grid you calculated in the first run (frequency or density grid). How can you obtain these dummy atoms? This can be done in two different ways.
+
+__The fast way:__ The first, easy and not very accurate way is to use the defaut pdb files coming from the first run of mdpocket to detect the pocket grids. If you read this manual with a huge attention and did not fall asleep in between, then you remember that mdpocket provides two files called `mdpout_freq_iso_0_5.pdb` and `mdpout_dens_8.pdb`. These files contain dummy atoms at grid point positions that were extracted at grid points having a given value or higher (iso-value of 0.5 and 8 respectively). Now you can use one of these files (depending on if you are more comfortable with one or the other grid, and open them in a molecular viewer that is able to edit structures. PyMOL is an excellent choice to perform this task. Simply select all dummy atoms in the zone of interest (your pocket you want to track) and then create an object with this selection. In the end, the result should look somehow like this:
+
+![pocket selection](images/pymol2.png)
+
+Here the red cloud corresponds to the grid points I have selected by hand. You can now save the grid points that you selected as a PDB file and use this as an input for tracking the properties of the cavity.
+
+__The better way:__ In order to get a good estimate of the volume and extent of the pocket you will notice that the default output pdb files for the two grids are not always sufficient, because of their predefined iso-values. This why you should extract the grid points as a PDB file using your own choice of iso-values. As a general rule, take the iso-values as low as possible. You should still be able to distinguish the different pockets in the density grid, but it's volume should not be very tiny!
+
+You can extract these grid points using a python script that is available in the scripts directory of the fpocket distribution, called `extractIso.py`. Simply execute it with `python extractIso.py` to see how to use it.
+
+### Basic Input
+#### Mandatory (running mode 1 - detecting pockets):
+##### either: 
+    --trajectory_file   : input trajectory file in one of the supported formats
+    --trajectory_format : (dcd,xtc,netcdf,crd,crdbox,dtr,trr)
+    -f                  : topology of the structure as input PDB file
+
+##### or : 
+	-L: a mdpocket input file, this file has to contain the paths to the PDB files of all snapshots (one path per line)
+
+#### Mandatory (running mode 2 - calculating descriptors):
+##### either: 
+
+    --trajectory_file   : input trajectory file in one of the supported formats
+    --trajectory_format : (dcd,xtc,netcdf,crd,crdbox,dtr,trr)
+    -f                  : topology of the structure as input PDB file
+    --selected_pocket   : a PDB file containing the sitepoints in the pocket to be selected
+
+##### or : 
+
+	-L: a mdpocket input file, this file has to contain the paths to the PDB files of all snapshots (one path per line)
+	--selected_pocket   : a PDB file containing the sitepoints in the pocket to be selected
+
+#### Optional:
+
+	-o : the prefix you want to give to mdpocket output files
+
+Note that mdpocket determines its running mode by the input given by the user. Thus if you do not provide a wanted pocket using the --selected_pocket flag, mdpocket will automatically only perform cavity detection. mdpocket offers much more optional parameters in order to guide the pocket detection. All fpocket parameters for pocket clustering and filtering are also available in mdpocket. For this see [advanced mdpocket features](#mdpocket-advanced).
+
+### Output (running mode 1 - pocket detection)
+
+* `mdpout_dens_grid.dx`: A dx formatted grid output. This grid contains the number of Voronoi vertices seen per snapshot nearby the grid point. It can be easily visualized using VMD.
+* `mdpout_freq_grid.dx`: Similar to the prevous file, this grid file contains the frequency of opening of a pocket at each grid point. It can be visualized using VMD.
+* `mdpout_dens_iso_8.pdb`: A pdb file of all grid point positions corresponding to grid points having 8 or more Voronoi vertices nearby per snapshot. This file is provided in order to be able to edit the grid points using PyMOL and select only the points defining the pocket of interest. This pocket of interest should be used as input of mdpocket in the 2nd running mode. If you want to extract gridpoints with other isovalues, use the provided `extractISO.py` file in the scripts directory.
+* `mdpout_freq_iso_0_5.pdb`: A pdb file of all grid point positions corresponding to grid points that are 50% of the trajectory overlapping with a pocket. This file is provided in order to be able to edit the grid points using PyMOL and select only the points defining the pocket of interest. This pocket of interest should be used as input of mdpocket in the 2nd running mode. If you want to extract gridpoints with other isovalues, use the provided `extractISO.py` file in the scripts directory.
+
+### Output (running mode 2 - pocket characterization)
+
+* `mdpout_mdpocket.pdb`: A pdb file containing all Voronoi vertices within the selected pocket region for all snapshots. This file is an NMR like file, containing each snapshot as 
+separated model. This file is best viewed using PyMOL and can be used to create pocket motion movies.
+
+* `mdpout_mdpocket_atoms.pdb`: A pdb file containing all receptor atoms surrounding the selected pocket region. Like the previous output file, this is a NMR like file, containing each snapshot as separated model. This file can be viewed with VMD and PyMOL.
+
+* `mdpout_descriptors.txt`: A text file containing the fpocket pocket descriptors of the selected pocket region for each snapshot. This file can be easily analyzed using standard statistical software like R.
+
+## dpocket descriptor extraction
+
+Until now you have seen what the majority of cavity detection algorithms can do. So a part from speed and hopefully prediction results, nothing distinguishes fpocket from other algorithms like ligsite, sitemap, sitefinder, pocketpicker, pass ...
+This is just partially true, because the fpocket package contains dpocket. D is an acronym for describing. One purpose a cavity detection algorithm can be used for is the extraction of descriptors of the physico-chemical environment of the cavity. dpocket allows to do this in a very simple and straightforward way. As extracting binding pocket descriptors on only one protein would be somehow meaningless for studying pocket characteristics, dpocket enables analysis of multiple structures. So now, no longer scripting and automation is necessary to do these kind of things. But lets have a closer look using again a very simple example you can try on your workstation.
+
+### Example 
+
+Here we go. dpocket requires one single input file. This input file must be a text file containing the following information: 
+- 1: the PDB file of the protein you want to analyze and 
+- 2: the ID of the ligand you would like to have as reference in order to define an explicitly defined binding pocket. The file used in this example (data/sample/test_dpocket.txt) looks like this :
+
+```
+data/sample/3LKF.pdb   pc1	
+data/sample/1ATP.pdb   atp
+data/sample/7TAA.pdb   abc
+```
+
+Here we analyze three pdb files. Note that the ligand name should be separated by a tabulation from the pdb file name. You can launch dpocket on this sample file using the following command:
+
+`dpocket -f sample/test_dpocket.txt`
+
+dpocket will yield 3 results files in the current directory. These files will be by default :
+
+    - dpout_explicitp.txt
+    - dpout_fpocketnp.txt
+    - dpout_fpocketp.txt
+
+If you want to change naming of these files, use the `-o` flag in command line to define a new prefix for the fpocket output files, for example `my_test` as prefix would yield `my_test_explicitp.txt`. The three output files contain the in fpocket implemented pocket descriptors for each binding pocket found by fpocket :
+
+- __fpocketp.txt__:  describes all binding pockets found by fpocket that match one of the detection criteria. In other word, fpocket found several pocket in the protein, and this file will contain descriptors of pocket that are considered to be the binding pocket using some detection criteria.
+- __fpocketnp.txt__: describes on the contrary all pockets found by fpocket that are not found to be the actual pocket using the detection criteria.
+- __explicitp.txt__: describes the pockets explicitely defined. By explicitely defined here, we mean that the pocket will be defined as all vertices/atoms situated at a given distance of the ligand (4A by default), regardless of what fpocket found during the algorithm.
+
+
+The ouput files are tab separated ASCII text files that are easy to parse using statistical software such as R. Thus statistical analysis of pocket descriptors becomes a very straightforward and easy process. Basically, the two first files might be used to establish a new scoring function as they describe what fpocket finds, while the last file could be used for a more detailed and accurate analysis of the exact part of the protein that interact with the ligand.
+For more details of the output refer to the output section below, or to [advanced dpocket features](#dpocket-advanced).
+
+
+### Basic input
+
+#### Mandatory:
+
+	flag -f : a dpocket input file, this file  has to contain the path to the PDB file, as well as the residuename of the reference ligand, separated by tabulation.
+
+#### Optional:
+
+	flag -o : the prefix you want to give to dpocket output files
+dpocket offers much more optional parameters in order to guide the pocket detection. For this see Advanced features chapter – [advanced dpocket features](#dpocket-advanced).
+
+### Output
+
+Refer to [advanced dpocket features](#dpocket-advanced) for a detailed description of the dpocket output files. 
+
+In conclusion of this first very easy dpocket run, you can see that you have a very fast and reliable tool to extract pocket descriptors, of binding pockets and “non binding pockets” on a large scale level. These descriptor files provide an excellent tool for further statistical analysis and model building, which leads immediately to your wish to write a new scoring function for ranking pockets using the different descriptors. Well, fpocket, dpocket and tpocket are very useful tools to do exactly this! So go ahead. Lets suppose you have passed several thousands of PDB files and analyzed statistically the significance of all descriptors. You have set up a new scoring function. Now you have an external test set of PDB files you haven't tested. How can you evaluate your scoring function? This is actually also a very easy task, using tpocket.
+
+
+## tpocket scoring ranging and evaluation
+
+As already mentioned in the previous paragraph, tpocket can be used in order to evaluate rapidly cavity scoring functions. If you are for example in the pharmaceutical industry and you want to set up the ultimate drugability prediction score, you might be able to do this with fpocket and dpocket. Afterwards you can actually test your method using tpocket. T is an acronym for testing, here. 
+
+Something fancy we did not tell you about before is that you can also test your scoring function on apo structures using tpocket. The only requirement is the need to align holo and apo structure to obtain superposed apo and holo pockets. But lets explain this with an example. Of course, testing a holo dataset is even more easy, you just need to provide the resname of the ligand and tpocket will do the rest.
+
+### Example – tpocket on apo structures
+
+If you had a look to the fpocket paper, you might have seen that the algorithm was validated on a dataset of 48 proteins previously used to evaluate several pocket detection algorithms. As fpocket programmers are, by definition, very nice people, they have included this data set (holo and aligned apo structures) in the distribution of fpocket, released as `fpocket-1.0-data` with the original fpocket 1 release. [The tar.gz is available on sourceforge](https://sourceforge.net/projects/fpocket/files/fpocket-1.0/fpocket-src-1.0/fpocket-data-1.0.tgz/download)
+
+So let us use this set as example here. When you extract the dataset in your folder you should have a data folder containing among others two files, `pp_apo-t.txt` and `pp_cplx-t.txt`. The first file is a tpocket input file in order to assess the capacity of the scoring function to rank correctly known binding sites on apo structures. The second file is also a tpocket inputfile, but this time for known binding sites on holo structures. Here is a part of `pp_apo-t.txt`:
+
+    data/pp_data/unbound/1QIF-1ACJ.pdb      data/pp_data/complex/1ACJ.pdb   tha
+    data/pp_data/unbound/3APP-1APU.pdb      data/pp_data/complex/1APU.pdb   iva
+    data/pp_data/unbound/1HSI-1IDA.pdb      data/pp_data/complex/1IDA.pdb   qnd
+    data/pp_data/unbound/1PSN-1PSO.pdb      data/pp_data/complex/1PSO.pdb   iva
+    data/pp_data/unbound/1L3F-2TMN.pdb      data/pp_data/complex/2TMN.pdb   po3
+    data/pp_data/unbound/3TMS-1BID.pdb      data/pp_data/complex/1BID.pdb   UMP
+    data/pp_data/unbound/8ADH-1CDO.pdb      data/pp_data/complex/1CDO.pdb   NAD
+    data/pp_data/unbound/1HXF-1DWD.pdb      data/pp_data/complex/1DWD.pdb   MID
+
+Here the first column contains the path to the apo structure, aligned to the holo structure, which is given in the second column. Using a holo dataset, the first and the second column would be the same. The third column indicates the PDB HETATM code of the ligand in the holo structure that is situated in the binding site.
+
+You can use this file to run tpocket using the following command line :
+
+`tpocket -L data/pp_apo-t.txt`
+
+Let us continue with the more interesting case, the first example, with a lot of structures. After some time of calculation, tpocket will provide two standard output files. The moment has come, you will finally know if you discovered the ultimate method of drugability prediction, or sugar binding site prediction or whatever. The first file is called by default `stats_g.txt`. It contains global statistics about the prediction using all evaluation criterias available in tpocket, so for example how many binding sites you found among the 3 first ranked cavities. For representational purposes only the first of the six tables available in this file is depicted hereafter:
+
+    Ratio of good predictions (dist = 4A)
+    -------------------------------------
+    Rank <=  1  :		  0.69
+    Rank <=  2  :		  0.83
+    Rank <=  3  :		  0.94
+    Rank <=  4  :		  0.94
+    Rank <=  5  :		  0.94
+    Rank <=  6  :		  0.94
+    Rank <=  7  :		  0.94
+    Rank <=  8  :		  0.94
+    Rank <=  9  :		  0.94
+    Rank <= 10  :		  0.94
+    -------------------------------------
+    Mean distance          : 2.924573
+    Mean relative overlap  : 39.373226
+
+This table schedules the capacity of your scoring function to identify the binding sites of the 48 apo structures using the criteria published within the original pocket picker paper. Not represented here, tpocket provides two other, maybe more accurate, measures for a correctly identified binding site. These measures are explained in more detail in the [advanced tpocket features section](#tpocket-advanced), as they can be a bit more tricky.
+
+The second output file provides more accurate statistics about each structure analyzed. This file, called `stats_p.txt` enables the user to analyze more closely why scoring might not work well on a specific structure. Here is an extract of the first columns and lines of this file:
+
+    LIG | COMPLEXE | APO | NB_PCK | OVLP1 | OVLP2 | DIST_CM | POS1 | POS2 | POS3
+    THA 1ACJ.pdb 1QIF-1ACJ.pdb    22   79.31   78.33    0.00    1    1    0
+    IVA 1APU.pdb 3APP-1APU.pdb     4    0.00    0.00    3.43    0    0    1
+    QND 1IDA.pdb 1HSI-1IDA.pdb     4   82.69   81.65    3.19    1    1    1
+    IVA 1PSO.pdb 1PSN-1PSO.pdb     9   80.00   51.38    3.49    1    1    1
+    PO3 2TMN.pdb 1L3F-2TMN.pdb    10   58.33   72.00    2.69    1    1    1
+    UMP 1BID.pdb 3TMS-1BID.pdb    15   63.64   60.78    3.52    1    1    1
+    NAD 1CDO.pdb 8ADH-1CDO.pdb    18    0.00    0.00    3.41    0    0    1
+    MID 1DWD.pdb 1HXF-1DWD.pdb    10   93.48   81.37    3.86    1    1    1
+
+Using this output you have a detailed view of what worked and what did not worked for all criteria. For instance, in this example, fpocket detects well all apo binding sites a part from the first one using the PocketPicker criterion for binding site identification (DIST_CM). POS3 corresponds to the rank  of the cavity using the scoring function of fpocket. You have further information about the number of pockets per protein and the exact overlap with the actual pocket.
+
+Now if you want to assess your scoring function on holo structures, you also can use tpocket. This time you only have to provide the `pp_cplx.txt`, also provided within the sample tar.gz file. As you can see, this file is very similar to `pp_apo.txt`. Only the first column repeats the path to the complex structure like this:
+
+    data/pp_data/complex/1acj.pdb   data/pp_data/complex/1acj.pdb   tha
+    data/pp_data/complex/1apu.pdb   data/pp_data/complex/1apu.pdb   iva
+    data/pp_data/complex/1ida.pdb   data/pp_data/complex/1ida.pdb   qnd
+    data/pp_data/complex/1pso.pdb   data/pp_data/complex/1pso.pdb   iva
+    data/pp_data/complex/2tmn.pdb   data/pp_data/complex/2tmn.pdb   po3
+    data/pp_data/complex/1bid.pdb   data/pp_data/complex/1bid.pdb   ump
+    data/pp_data/complex/1cdo.pdb   data/pp_data/complex/1cdo.pdb   nad
+
+### Basic Input
+
+#### Mandatory:
+
+	flag -L : a tpocket input file, this file  has to contain the paths to the PDB files (apo, holo or holo,holo if you want to test fpocket only on holo structures), as well as the residuename of the reference ligand, separated by tabulation.
+
+#### Optional:
+	flag -o : the prefix you want to give to tpocket detailed statistics
+	flag -e : the prefix you want to give to tpocket general statistics
+
+tpocket offers much more optional parameters in order to guide the pocket detection. For this see the [advanced tpocket features section](#tpocket-advanced).
+
+### Output
+Using standard parameters on the example tpocket list given in the example paragraph above, tpocket returns two output files:
+
+* `stats_p.txt`: This file contains the detailed statistics of tpocket. The name and the ligand of the analyzed PDB structure are repeated, as well as the exact overlap of the fpocket identified binding pocket with the actual binding pocket (identified with the help of the ligand, called OVLP here). You will see two different overlaps in the output. For further informations refer to the  [advanced tpocket features section](#tpocket-advanced). Furthermore, the distance criterion used in the Chemistry Central Journal paper for publication of PocketPicker was used (DIST_CM). Next, you can also have exact information about the rank of the cavity using the fpocket scoring function.
+* `sats_g.txt`: Second, tpocket provides more general statistics about pocket identification on the dataset provided. For both overlap criterions the ranking performance (the capacity of the fpocket scoring to rank correctly a binding site having a certain minimum overlap with the actual binding site) is printed into this file. Thus, statistics in this file gives you a rapid overview over the global performance of your method.
+
+Summarizing features of tpocket, one could retain, that tpocket is a very fast way to test fpockets performance on your own dataset and test your own scoring functions for ranking purposes of identified binding sites.
+
+You have finished the Getting started section. We hope that you notice the usefulness (hopefully;) of this package of programs for the research of new features, descriptors and scoring functions in the binding site identification field. Well, this was only a very fast overview over the very basic features of fpocket, dpocket and tpocket. If you want to dive into development of your own pocket descriptors and scoring functions, or if you want to change the pocket detection parameters for your purposes, continue with the Advanced features section, next.
+
+
+# Advanced Features
+
+You want to know more about fpocket? This is the section for you, here we tried to compile in a (we hope) comprehensive manner the most important details of fpocket, dpocket and tpocket, to which you have access by command line. It is primordial to know, that fpockets performance was assessed and scoring function was established for standard parameters. The performance of pocket detection and scoring is highly dependent on these parameters, so keep in mind that you might have to adapt scoring to your specific problem.
+Note that this section does not provide too much information about the theoretical background of the way fpocket works. In order to learn more about this read the Materials & Methods of the [freely available paper on the BMC Bioinformatics](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-168) website. Nevertheless, we tried to keep it as clear as possible, using some application examples.
+
+## fpocket advanced
+
+### Input command line arguments
+
+#### Mandatory:
+The simplest way to run fpocket is either by providing a single pdb file, or by providing a list of pdb file, stored in a simple text file. You will need one of these two input to run fpocket:
+
+    -f string : one standard PDB filename that you want to analyze with fpocket
+##### or:
+    -F string : filename of a simple list of pdb files.
+
+
+#### Optional:
+
+    -m float: (default 3.4Å) This flag enables the user to modify the minimum radius an alpha sphere might have in a binding pocket. An alpha sphere is a contact sphere, that touches 4 atoms in 3D space without having any internal atoms. Here 3Å allow filtering of too small (protein internal) alpha spheres. If you want to analyze internal interstices, lower this parameter. In the contrary, if you want to analyze more solvent exposed cavities, you can raise this parameter in order to filter out too buried cavities.
+    
+    -M float: (default 6.2Å) Here you can modify the maximum radius of alpha spheres in a pocket. An alpha sphere is a contact sphere, that touches 4 atoms in 3D space without having any internal atoms. Here 7Å allow to filter out too large contact spheres, that are lying on the protein surface. If you want to analyze very flat and solvent exposed surface depressions, raise this parameter. For analysis of buried parts of the protein you can lower this parameter. Higher radii might be more interesting for identification of protein protein binding sites or polysaccharide binding sites. Smaller radii enable detection of buried cavities for small organic molecules (drugs, for instance).
+    
+    -l int: (None) If you have an input PDB file of an NMR structure or one with multiple models you can specify which model (conformation) you'd like to analyse
+    
+    -C char: (default s) The clustering method to be used here. By default a pairwise single linkage clustering is used here. 
+        's': pairwise single linkage clustering,
+        'm': pairwise maximum- (or complete-) linkage clustering, 
+        'a': pairwise average-linkage clustering, 
+        'c': pairwise centroid-linkage clustering
+    
+    -e char: (default e) The distance measure used for the clustering algorithm. 
+        'e': Euclidean distance
+        'b': City-block distance
+        'c': correlation
+        'a': absolute value of the correlation
+        'u': uncentered correlation
+        'x': absolute uncentered correlation
+        's': Spearman's rank correlation
+        'k': Kendall's tau
+    
+    -i int: (default 15) This flag indicates how many alpha spheres a pocket must contain at least in order to figure in the results provided by fpocket. This parameter enables filtering of too small cavities. Thus, if you want to analyze smaller cavities also, lower this parameter, if you are only interested in huge cavities, like NADP binding sites, you can raise it in order to retain only very few pockets in the end. To give you an idea, a rather big cavity, like a NADP binding site, can have hundreds of alpha spheres. Thus, 30 as standard parameter enables also to keep smaller binding sites.
+    
+    -A int: (default 3) Fpocket distinguishes between two types of alpha spheres. Polar alpha spheres and apolar alpha spheres. This flag ranges from 0 to 4 and modifies the definition of the alpha sphere type. By default, an alpha sphere contacting at least 3 apolar atoms (having an electronegativity below 2.8) is considered as apolar. If this is not the case it is considered as polar.
+    
+    -D float: (default 2.4Å) this parameter changed compared to the previous versions of fpocket as we completely replaced the clustering algorithms entirely. This measure is now used to analyze a hierarchical distance and cut sub-trees at the desired distance. The bigger the distance, the larger the clusters you'll get. 
+    
+    -p float: (default 0.0) This is another parameter for filtering unwanted pockets. It defines the maximum ratio of apolar alpha spheres and the number of alpha spheres in a pocket in order to keep the pocket in the results list. That is to say, by default every pocket is kept (0.0). Now, if you would like to filter rather hydrophobic pockets, raise this parameter and very polar cavities will be filtered out. This parameter is a ratio, not a percentage, thus it ranges from 0 to 1.
+    
+    -v int: (default 2500) By default, pockets volume are calculated using a monte-carlo algorithm. Basically, the algorithm picks a random point in the space and check if it is included in any alpha sphere, and stores this status. This is repeated N times, and we estimate the volume of the pocket using ratio between the number of hit and the number of iteration, scaled by the size of the box. This parameter defines the number of iteration to perform. Of course, the higher the value is, the greater the accuracy will be, but the performance will be slowed down.
+    
+    -b (none): (NOT USED BY DEFAULT) This option allows the user to choose a discrete algorithm  to calculate  the  volume of each pocket instead of the Monte Carlo method. This algorithm puts each pocket into a grid of dimension (1/N*X  ;  1/N*Y  ;  1/N*Z),  N being the value given using this option, and X, Y and Z being the box dimensions,  determined using coordinates of vertices. Then, a triple iteration on each dimensions is used to estimate the volume, checking if each points  given  by the iteration is in one of the pocket’s vertices. This parameter defines the grid discretization. If this parameter is used, this algorithm will be used instead of the Monte Carlo algorithm. 
+    Warning: Although this algorithm could be more accurate, a high value might dramatically slow down the program, as this algorithm has a maximum complexity of N*N*N*nb_vertices, and a minimum of N*N*N !!!
+
+    -d (none): Option allowing you to output pockets and properties in a condensed format. This will put to the stdout pocket properties in a tab separated string and write pocket files in a subfolder
+    
+    -r string: (None) This parameter allows you to run fpocket in a restricted mode. Let's suppose you have a very shallow or large pocket with a ligand inside and the automatic pocket prediction always splits up you pocket or you have only a part of the pocket found. Specifying your ligand residue with -r allows you to detect and characterize you ligand binding site explicitly. For instance for `1UYD.pdb` you can specify `-r 1224:PU8:A` (residue number of the ligand: residue name of the ligand: chain of the ligand)
+
+    -P string: (None) Binding site delimited by the user through the input. You can inidcate which amino-acids are part of the binding site you'd like to "identify" and calculate descriptors for. fpocket will run its usual alpha-sphere detection and clustering will be guided to collect all alpha spheres in contact with residues of interest. You should enter a string of residues with residue numbers, insertion codes & chain codes: 'residuenumber1:insertioncode1:chaincode1.residuenumber2:insertioncode2:chaincode2.residuenumber3:insertioncode3:chaincode3'. Insertion codes can be empty. `-P 107::A.138::A.51::A.98::A.55::A.93::A` for instance for part of the HSP90 binding site of 4cwr. NB: If you use an mmcif file as input, you need to use the automatically assigned residue number instead of author defined number for this to work.
+    
+    -y string: (filename) EXPERIMENTAL: here you can specify a topology filename in the Amber prmtop format. This can then be used by fpocket & mdpocket to calculate energy grids for your pockets. NB: you have to specify the -x flag to run energy calculations
+    
+    -x None: (None) EXPERIMENTAL: specify this flag if you want to run energy calculations on calculated pockets. That's not fully functional and only one or two probes are currently generated and output density grids written. Use with caution
+    
+    -c char : (Default is none): Use this flag to choose which chains you want to delete before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-c B,D' or '-c B:D'. You can delete up to 20 different chains.
+    
+    -k char : (Default is none): Use this flag to choose which chains you want to keep before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-k A,B,E' or '-k A:B:E'. You can keep up to 20 different chains.
+    
+    -a char : (Default is none): With this flag you can select a chain you want to be considered as a ligand. Works the same way as the "-r" flag but with a whole chain. Only a single chain can be chosen, for example '-a D'.
+    
+    -w char : (Default is 'd') : With this flag you are able to choose what kind of writing file output you want, 'd' -> default (same format outpout as input)| 'b' or "both"-> both pdb and mmcif | 'p' or "pdb"-> pdb | 'm' or "cif" or "mmcif" -> mmcif, for example "-w cif" or "-w p"
+
+
+###  Output files description
+
+fpocket yields output directly in the directory of the data file, creating a directory using the name of the PDB file followed bu the _out extension. Here, the command ll sample/3LKF_out of the current sample run would look something like this:
+
+        total 332
+        -rw-r--r-- 1 peter users    769 Nov 29 00:14 3LKF.pml
+        -rw-r--r-- 1 peter users    698 Nov 29 00:14 3LKF.tcl
+        -rwxr-xr-x 1 peter users     30 Nov 29 00:14 3LKF_PYMOL.sh
+        -rwxr-xr-x 1 peter users     41 Nov 29 00:14 3LKF_VMD.sh
+        -rw-r--r-- 1 peter users 245835 Nov 29 00:14 3LKF_out.pdb
+        -rw-r--r-- 1 peter users   6725 Nov 29 00:14 3LKF_pockets.info
+        -rw-r--r-- 1 peter users  49355 Nov 29 00:14 3LKF_pockets.pqr
+        -rw-r--r-- 1 peter users   4073 Nov 29 00:14 3LKF_info.txt
+        drwxr-xr-x 2 peter users   4096 Nov 29 00:14 pockets
+
+As you can see, fpocket provides a lot of files and another subdirectory. However, majority of these files are necessary for easy visualization of binding pockets. Lets explain the content and utility of each file:
+
+* `3LKF_info.txt`: this file contains human readable information (descriptors) about the pockets found on the protein. Notably this file contains a pocket score (likeliness this is a small molecule binding site) and a druggability score (how druggable the binding site is) Here an extract:
+    Pocket 1 :
+            Score :         0.490
+            Druggability Score :    0.019
+            Number of Alpha Spheres :       21
+            Total SASA :    19.687
+            Polar SASA :    7.611
+            Apolar SASA :   12.076
+            Volume :        270.934
+            Mean local hydrophobic density :        3.000
+            Mean alpha sphere radius :      3.816
+            Mean alp. sph. solvent access :         0.519
+            Apolar alpha sphere proportion :        0.190
+            Hydrophobicity score:   23.889
+            ...
+
+* `3LKF.pml`: this is a PyMOL script for visualization of binding pockets using PyMOL
+* `3LKF.tcl`: this a tcl script for visualization of binding pockets using VMD
+* `3LKF_PYMOL.sh`: this is the executable script to launch fast visualization using PYMOL
+* `3LKF_VMD.sh`: this is the executable script to launch fast visualization using VMD
+* `3LKF_out.pdb`: this is the most important file, it contains the initial PDB structure given as input. Non cofactor HETATM occurrences will be stripped off in this file compared to the original PDB input file. The PDB file contains centers of alpha spheres using the HETATM definition as dummy atoms. These alpha sphere centers are attached in the end of the PDB file, using the STP residue name (for site point). Apolar alpha spheres carry the atom name APOL, polar alpha spheres the atom name POL. Pockets are sets of alpha spheres. They can be distinguished by residue number. Thus residue STP 1 would be the first binding pocket according to fpocket. To show this more clearly here is an extract of the `3LKF_out.pdb`:
+        
+        ATOM   2349   CD LYS A 299       9.679  16.827 105.636  0.00  0.00           C 0
+        ATOM   2350   CE LYS A 299      10.371  16.314 104.370  0.00  0.00           C 0
+        ATOM   2351   NZ LYS A 299      11.749  15.794 104.597  0.00  0.00           N 0
+        ATOM   2352  OXT LYS A 299       5.240  20.009 107.670  0.58  9.64           O 0
+        HETATM    1 APOL STP C   1      27.849  33.435 123.906  0.00  0.00          Ve  
+        HETATM    2 APOL STP C   1      29.108  33.195 122.206  0.00  0.00          Ve  
+        HETATM    3 APOL STP C   1      28.611  33.141 119.797  0.00  0.00          Ve  
+        HETATM    4 APOL STP C   1      26.830  32.143 118.779  0.00  0.00          Ve  
+
+* `3LKF_pockets.pqr`: This file contains all alpha sphere centers, as the 3LKF_out.pdb file, but contains no information about the protein structure. Furthermore using the pqr format enables writing of the van der Waals radius of atoms explicitely in this file. Here this possibility was used to output the radii of alpha spheres of a pocket. Charging this pqr file, one can analyze more precisely the volume recognized by fpocket. Note that, currently only VMD supports reading this format correctly. PyMOL is able to read pqr file, but does not interpret van der Waals radii.    
+
+* `pockets/`: Well, again a subdirectory. But I promise, it's the last one. For development purposes or easy analysis, fpocket proposes this directory which contains according to the current example:
+
+        pocket0_atm.pdb   pocket2_vert.pqr  pocket5_atm.pdb   pocket7_vert.pqr
+        pocket0_vert.pqr  pocket3_atm.pdb   pocket5_vert.pqr  pocket8_atm.pdb
+        pocket1_atm.pdb   pocket3_vert.pqr  pocket6_atm.pdb   pocket8_vert.pqr
+        pocket1_vert.pqr  pocket4_atm.pdb   pocket6_vert.pqr  pocket9_atm.pdb
+        pocket2_atm.pdb   pocket4_vert.pqr  pocket7_atm.pdb   pocket9_vert.pqr
+
+* `*_atm.pdb`: These files contain only the atoms contacted by alpha spheres in the given pocket. Complementary to this information, `*_vert.pqr` files contain only the centers and radii of alpha spheres within the respective pocket. As extensions mention, atoms are output in the PDB file format and alpha sphere centers in the PQR file format.
+
+### A word on druggability
+
+With the [Understanding Druggability paper](https://pubs.acs.org/doi/abs/10.1021/jm100574m) we introduced an alternative scoring function in fpocket allowing you to assess the likelihood of a binding site to bind small druglike molecules. Since the publication the score has been retrained and performance improved (no paper for that work out). Roughly, if you get a druggability score of 0 or close to 0 it's predicted no-druggable with drug like molecules. If the score is above 0.5 there might be a chance to find drug-like molecules.
+The druggability assessment is done using some of the pocket descriptors extracted by fpocket. IT DOES BY NO MEANS indicate that no molecule binds to a pocket. I.E. a peptide binding site will bind peptides, but peptides won't necessarily be considered as drug-like molecules. 
+
+## mdpocket advanced
+
+A lot of the functionality of mdpocket has already been covered in the Getting started section. However, there is at least one little functionality that you can access via mdpocket that you don't know about yet.
+
+### Detect transient druggable binding pockets
+
+The current version of fpocket contains two scoring methods to score the pockets. The first one is the original fpocket score, published in the first release and the scientific paper. Later, a second pocket score was added. This score, called druggability score intends to assess at what point the identified pocket is likely to bind drug like molecules. This drug score is a value between 0 and 1, 0 signifying that the pocket is likely to not bind a drug like molecule and 1, that it is very likely to bind the latter. In combination with mdpocket the drug score can be of use when someone wants to assess if during a MD trajectory somewhere “druggable” pockets appear. You can do this during the first explorative mdpocket run (without studying a particular pocket), by specifying the `-S` flag in command line when calling mdpocket. This flag will yield mdpocket not to do the following thing: For each snapshot fpocket is run normally and a druggability score is associated to each pocket. Voronoi vertices near to grid points are used to map the drug score to each grid point (instead of counting them, we increment by the drug score of the pocket). We thus recommend to analyze the frequency grid when running mdpocket with `-S`. You will immediately notice that much less pockets are found in the grid at higher iso-values. This can also help to focus initially on your drug binding site (if you are coming from big pharma), especially for the tedious pocket selection by hand, this is very handy.
+
+If you want to draw conclusions about the “mean druggability” of some pockets using the frequency grid you should beware of the fact, that the mean drug score that you see there (the iso-value) is very underestimated compared to values you obtain on crystal structures.
+
+Last, but very important : if you plan to run a mdpocket calculation using `-S`, you should use the fpocket default pocket detection parameters. Using different parameters, like for channels etc makes strictly no sense as the druggability score was trained using the default fpocket parameters.
+
+### Detect different types of pockets
+
+Fpocket was initially created to detect small molecule binding sites on proteins. That is what most people are interested in (a big assumption, we know). But as we want to please a maximum number of you, distinguished fpocket users, we try to keep fpocket as flexible as possible via these various (probably a bit opaque) command line arguments. These arguments become very interesting when one is interested in a different type of pocket detection. For instance, detecting channels and gaz pathways in a protein is a completely different topic compared to finding drug binding sites.
+
+If one wants to identify transient internal pockets and channels one could modify the pocket detection parameters for fpocket / mdpocket. Here we give examples of typical parameters and what type of pockets you are likely to get back from fpocket / mdpocket :
+
+__Detect small molecule binding sites__ : Use the default parameters (don't specify anything)
+
+__Detect putative channels and small cavities__ : -m 2.8 -M 5.5 -i 3 
+
+__Detect pockets where sterically water binding is possible__ : -m 3.5 -M 5.5 -i 3 
+
+__Detect rather big, external pockets__ : -m 3.5 -M 10.0 -i 3
+
+### Additional scripts
+
+In order to facilitate some simple tasks for conversion, extraction and creation of input files the fpocket distribution contains some additional python scripts that can be of use for some specific tasks but do not have anything to do in a concrete way with the pocket detection itself. This is why they are not included as standalone program here.
+
+* `createMDPocketInputFile.py`: This is a standard python script (that should work out of the box on all machines having python installed on it) that takes the path of all the snapshot PDB files of a MD trajectory as input and creates a valid mdpocket input file (alpha numerically sorted list of paths). We recommend you to use this script if you need a valid mdpocket input file without worrying about how to order in a alphanumeric way your file names to form a valid list.
+
+* `extractISO.py`: This is a python script that makes use of the numpy library. If you do not have numpy installed this will not work. However installing numpy is a rather good idea as this is a very nice library ;). The script takes as input a mdpocket dx grid file, a filename (the one you want for the output) and a wanted isvalue. The script will write all grid point coordinates from the dx file having a grid value higher or equal than the wanted isovalue to the output file.
+
+
+## dpocket advanced
+
+Input command line arguments
+
+### Mandatory:
+
+    -f : a dpocket input file, this file has to contain the path to the PDB file, as well as the residuename (PDB HET residue tag, like “hem”, for heme) of the reference ligand, separated by a tabulation. 
+
+See the [Getting started section of dpocket](#dpocket-descriptor-extraction) for an example of such a file.
+
+### Optional:
+
+    -o : (default dpout) the prefix you want to give to dpocket output files. The standard will produce three output files named dpout_fpocketnp.txt, dpout_fpocketp.txt, dpout_explicitp.txt.
+    
+    -e : Use the first explicit interface definition (default): we define  the explicit pocket  as  being  all  atoms  contacted  by  alpha spheres situated at a distance of d A° from any ligand atom.
+    
+    -E : Use  the  second  explicit  interface  definition: we define the explicit pocket as being all atoms situated at a distance  of  d A° from any ligand atom.
+    
+    -d : The distance criteria used for the explicit pocket definition.
+    Last, all optional parameters used by fpocket are also accessible on command line through dpocket. Refer to the preceding paragraph to see details about fpocket parameters.
+
+### Output files description
+
+As shown in the example, dpocket creates 3 output files. Lets describe them a bit more in detail here:
+
+* `dpout_explicitp.txt`: This file contains all pocket descriptors implemented in fpocket of the explicitly defined binding pocket. What does this mean, explicitly? In the input you have associated a ligand identification to each PDB file. This ligand is used by fpocket in order to identify the actual binding pocket. 
+
+        pdb ligand overlap lig_vol pocket_vol nb_alpha_spheres mean_asph_ray
+        data/3LKF.pdb PC 100.00   132.90  1678.64    29  3.94
+        data/1ATP.pdb ATP 100.00   322.62  2127.53    65  3.59
+        data/7TAA.pdb ABC 100.00   608.66  4977.48    97  4.20
+
+Note that this is only an extract of this file. It contains a lot of columns (descriptors) that are not represented here. The first line describes the nature of the entry. The next line recapitulates the pdb structure analyzed (`data/sample/3LKF.pdb`), the ligand used as reference (PC). Next the overlap between the actual and found binding pocket is shown, here 100% as this is an explicitly defined binding pocket. The next entries can be used as descriptors, like the ligand volume, the pocket volume, the number of alpha spheres in the binding pocket, the mean alpha sphere radius ... For a complete list of all implemented descriptors in fpocket, refer to the Advanced features – [Pocket descriptors section](#pocket-descriptors).
+
+The volumes calculated here are not accurate at all. If you want to calculate accurate volumes you have to change parameters for volume calculation. As volume calculations are generally over-estimated using alpha sphere approaches, especially for open binding pockets, this calculation is made available, but uses the minimum sampling for the calculation. For more accurate calculation significantly more calculation time would be necessary. You can provide a higher sampling via the `-v` flag in the command line.
+
+* `dpout_fpocketnp.txt`: This file contains the same kind of descriptors as the preceding one, but this time for pockets identified by fpocket, that are “non binding pockets”. Non binding pockets means here, that the pockets do not correspond to the pocket where the reference ligand binds. Be careful, this does not necessarily mean that other pockets do not bind anything.
+
+* `dpout_fpocketp.txt`: The last file is also formated the same way as the preceding both. This file contains the binding pocket, this time identified by fpocket and not explicitly by the ligand.
+
+## tpocket advanced
+
+This program of the fpocket package is certainly very useful for testing new scoring methods rapidly on a large dataset of protein ligand complexes. However one might encounter difficulties to understand results, interest, advantages and drawbacks of this methodology. In order to facilitate your understanding of this package we provide some more fundamental information first, before treating more practical questions about tpocket.
+
+### Input command line arguments
+
+#### Mandatory:
+
+    -L : a tpocket input file. This file has to contain the paths to the PDB files (apo, holo or holo,holo if you want to test fpocket only on holo structures), as well as the residuename (PDB HET residue tag, like “hem” for heme) of the reference ligand, separated by tabulations.
+
+#### Optional:
+	-o : (default ./stats_p.txt) The filename you want to give to tpocket detailed statistics.
+	-e : (default ./stats_g.txt) The filename you want to give to tpocket global statistics.
+	-d : Distance  criteria used for one of the 3 definition of a pocket: All atoms situated at a distance lower of equal that d will be  considered as part of the actual pocket.
+	-k : Keep fpocket output for each pdb test.
+
+Last, all optional parameters used by fpocket are also accessible on command line through tpocket. Refer to [fpocket advanced](#fpocket-advanced) for fpocket parameters.
+
+### Actual pocket definition for evaluation of fpocket
+
+Delimiting, and more generally defining what is the exact binding pocket of a protein in an automated way is not that easy. Finding a criteria that evaluate correctly the ability of fpocket to detect the actual binding site of a protein is consequently even more difficult.  
+
+Tpocket makes use of 6 different ways to determine if a pocket found by fpocket could be considered as the actual binding pocket, with respect to a given ligand:
+
+*	1 – The actual binding site is reduced to a single point, the barycenter of the pocket (calculated using alpha spheres). The binding pocket is defined as the pocket which barycenter is situated at a distance of 4A of any ligand atom. It corresponds to the Ppc discussed in the paper.
+
+*	2 – The actual binding pocket is defined by the set of atoms that are in contact with alpha sphere that are nearby (< 3A) the actual ligand. This set of atoms is then compared to all atoms contacted by all voronoi vertices included in each pocket found by fpocket. WARNING: this is currently not safely usable for an holo/apo dataset.
+
+*	3 – The actual binding pocket is defined by the set of atoms that are nearby (4A) the actual ligand. The same procedure as for the first definition is then applied to say whether a pocket can be considered as the actual pocket or not. WARNING: this is currently not safely usable for an holo/apo dataset.
+
+*	4 – The actual binding pocket is defined by the set of alpha sphere nearby (< 3A) the actual ligand. Then, for a given pocket, we calculate the correspondence between alpha sphere in the pocket, and alpha sphere in the actual binding pocket. If this ratio exceed a certain value (25%), we consider this pocket as being the actual pocket.
+
+*	5 – For a given pocket, we calculate the proportion of ligand atom that are nearby (< 3A) at least one alpha sphere of pocket. If this proportion exceed a certain value (50%), we consider this pocket as being the actual pocket.
+
+*	6 – A combination of both 5th and 6th criteria described above. If both 4th and 5th criterion are satisfied, then this criteria is. This corresponds to the MOc (Mutual Overlap criterion) discussed in the paper.
+
+The reason why we choose 3A for the criteria 2, 4 and 5 is quite simple: as in the current algorithm, the minimum radius of an alpha sphere is 3A, a ligand atom situated at a distance lower or equal than this value can be considered as included in this alpha sphere, and therefore detected. Of course, this applies to alpha sphere with higher radius too.
+
+All of these criteria have their strengths and witnesses, that's why we choose to implement all of them.
+
+
+
+## Pocket descriptors
+
+In order to discriminate an interesting pocket from a lot of uninteresting ones, fpocket uses descriptors for each pocket. A scoring function, using these descriptors, was trained to well identify what we generally call “binding site”. Here are set together all descriptors implemented in fpocket. The ones that are currently used for scoring are marked with a *, and the one having the tag normalized associated with have a normalized (ie. scaled to a [0, 1] range, the highest (resp the lowest) value of a given descriptor being set to 1 (resp 0))  equivalent descriptor.
+
+### Number of alpha spheres (normalized)
+
+As the title says, this is surely the most simple descriptor. The number of alpha spheres reflects generally more or less proportionally the size of the cavity.
+
+### Density of the cavity (normalized)
+
+This descriptor tends to measure the density and “buriedness” of a pocket. It is nothing else than the mean value of all alpha sphere pair to pair distances in the binding pocket. Thus, a small value indicates a rather big compactness of the binding pocket and thus a rather burried pocket. Larger values give indication about more extended and exposed cavities.
+
+### Polarity Score (normalized)
+
+In the contrary to hydrophobicity this descriptor tries to measure the hydrophilicity character of a binding pocket. To each residue of the binding pocket a polarity score is assigned (as published on http://www.info.univ-angers.fr/~gh/Idas/proprietes.htm). The final polarity score is the mean of all polarity scores of all residues in the binding pocket. This is extremely approximative, so should not be overestimated. Each residue is evaluated only once.
+
+### Mean local hydrophobic density (normalized)
+
+This descriptor tries to identify if the binding pocket contains local parts that are rather hydrophobic. For each apolar alpha sphere the number of apolar alpha sphere neighbors is detected by seeking for overlapping apolar alpha spheres. The sum of all apolar alpha sphere neighbors is divided by the total number of apolar alpha spheres in the pocket. Last this score is normalized compared to other binding pockets.
+
+### Proportion of apolar alpha spheres (normalized)
+
+This descriptor, returned as percentage, reflects the proportion of apolar alpha spheres among all alpha spheres of one pocket identified by fpocket. This can reflect somehow the hydrophobic/-philic character of a binding pocket.
+
+### Druggability Score
+
+The druggability score is a numerical value between 0 and 1 associated to each pocket using a logistic function. This scores intends to assess the likeliness of the pocket to bind a small drug like molecule. A low score indicates that drug like molecules are likely to not bind to this pocket. A druggability score at 0.5 (the threshold) indicates that binding of prodrugs or druglike molecules can be possible. 1 indicates that binding of druglike molecules is very likely. The theoretical basis of the score is currently in the lengthy process of scientific publication.
+
+### Maximum distance between two alpha sphere (normalized)
+
+This descriptor store the maximum distance found between two alpha sphere in a given pocket.
+
+### Hydrophobicity Score
+
+This descriptor is based on a residue based hydrophobicity scale published by Monera & al. in the Journal of Protein Science 1, 319-329 (1995). For all residues implicated in the binding site the mean hydrophobicity score is calculated and is used as descriptor for the whole pocket. Each residue is evaluated only once.
+
+### Charge Score
+
+According to (http://www.info.univ-angers.fr/~gh/Idas/proprietes.htm) the charge of each amino acid in the binding site is tracked. The mean charge for all amino acids in contact with at least one alpha sphere of the pocket is calculated to form this charge score. Each residue is evaluated only once.
+
+### Volume Score
+
+Similarly to other descriptors, this one is based on data published on (http://www.info.univ-angers.fr/~gh/Idas/proprietes.htm). This data resumes relative volume of different amino acids. In order to calculate this descriptor the mean volume score of all amino acids in contact with at least one alpha sphere of the pocket is calculated. Each residue is evaluated only once.
+
+### Composition of amino acids
+
+As the name indicates, fpocket tracks the composition in amino acids of binding pockets. If at least one atom of a residue is in contact with at least one alpha sphere of a binding pocket it is accounted to be part of the binding site. This descriptor is returned as cumulative list, for instance you can find 2 valines, 3 glutamates etc... in the binding site.
+Occurences of amino acids in different descriptor outputs are given in the following order : Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, Tyr.
+
+### Pocket volume
+
+As indicated by the name, this descriptor tries to evaluate the volume of a binding pocket using a Monte-Carlo algorithm that calculates full volume occupied by all alpha sphere in a given pocket. The number of iteration of this algorithm can be controlled using fpocket input parameters.
+
+### Polar Surface Area
+
+This descriptor provides an estimation of the polar surface area of the pocket based on information of the receptor atoms. The method used to calculate the area only provides an approximation, but should be good enough to get some rather relevant estimates.
+
+### Apolar Surface Area
+
+See polar surface area in the previous point, only for apolar atoms.
+
+### Total Surface Area
+
+The sum of the polar and apolar surface area of the pocket, that is to say the receptor side surface area of the pocket.
+
+### B-factor score (normalized)
+
+Please handle with a lot of care this score with native crystal structures. This score is based on the mean B-factor of all atoms of the binding pocket (atoms that are contacted by at least one alpha sphere). As the B factor does not necessarily reflect flexibility in crystal structures, this score is somehow abusive. However, one could imagine performing molecular dynamics or other in order to determine relative flexibility of atoms and store this information in the B-factor column of the PDB file format.
+
+This descriptor is normalized with other pockets of the same protein.
+
+### List of abbreviations used in dpocket & mdpocket output
+
+- pdb : pdb file name
+- lig : ligand HET ID
+- overlap : overlap of atoms in the actual pocket versus atoms in the pocket identified with fpocket
+- PP-crit : binary PocketPicker criterion (1 if the ligand is < 4A from the center of mass of the alpha spheres, 0 else)
+- PP-dst : the minimum distance between the center of mass of the pocket and the ligand
+- crit4 : proportion of ligand atoms that have at least one vertice that lies within 3 A
+- crit5 : proportion of alpha spheres that lie within 3A from any ligand atom
+- crit6 : binary criterion that is 1 if crit4 >=0.5 and crit5>=0.2, 0 else
+- crit6_continue : a continuous measure of crit6, but this is experimental and we currently don't use it...
+- lig_vol : volume of the ligand
+- pock_vol : volume of the pocket
+- nb_AS : number of alpha spheres
+- nb_AS_norm : number of alpha spheres normalized by all pockets on the protein
+- mean_as_ray : mean alpha sphere radius
+- mean_as_solv_acc : mean alpha sphere solvent accessibility
+- apol_as_prop : proportion of apolar alpha spheres in the pocket
+- apol_as_prop_norm : normalized proportion of apolar alpha spheres
+- mean_loc_hyd_dens : mean local hydrophobic density
+- mean_loc_hyd_dens_norm : normalized mean local hydrophobic density
+- polarity_score_norm : normalized polarity score
+- flex : measure of the flexibility of the pocket (B-factor based)
+- prop_polar_atm : proportion of polar atoms
+- as_density : alpha sphere density
+- as_density_norm : normalized alpha sphere density
+- as_max_dst : maximum distance between the center of mass and all alpha spheres
+- as_max_dst_norm : normalized as_max_dst
+- drug_score : druggability score
+- pock_asa : solvent accessible surface area of the pocket
+- pock_pol_asa : polar solvent accessible surface area of the pocket
+- pock_apol_asa : apolar solvent accessible surface area of the pocket
+- pock_asa22 : accessible surface area using a probe of 2.2 A instead of 1.4
+- pock_pol_asa22 : see pock_pol_asa and pock_asa22
+- pock_apol_asa22 : see pocket_apol_asa and pock_asa22
+
+## Cofactor definition
+
+fpocket, dpocket and tpocket contain in the current release a fixed set of cofactors. So far so good, but what for? Cofactors are often structurally necessary or must be present in the protein structure for ligand binding. The PDB nomenclature, however, treats them as usual hetero atoms, using the HETATM tag. This is the tag that fpocket uses to identify and eliminate crystallographic waters and possible ligands of holo protein structures. In order to force fpocket to keep the cofactor you are interested in, that is to say, to consider it as entire part of the protein structure for binding pocket detection, a list list of HETATM names is defined in the beginning of the `rpdb.c` file under (https://github.com/Discngine/fpocket/blob/master/src/rpdb.c#L39) the name `static const char *ST_keep_hetatm[]`. The next line of code defines the number of cofactors defined in this list :  `static const int ST_nb_keep_hetatm = 111` ;
+
+If you would like to add a new cofactor, you have to modifiy this code. First you add the whished HETATM tag to `ST_keep_hetatm` in the end of the list. Thus for example, `“MSE”` will become `“MSE”,”PTE”` if your  cofactor has the HETATM tag PTE. Do not forget to increment the `ST_nb_keep_hetatm` variable to `112`, else this cofactor will not be taken into account.
+
+Next you have to recompile the program, before being able to use this new definition.
+In future releases this cofactor definition will be done dynamically with an external list.
+
+The following list resumes the cofactors fpocket considers as recurrent in the PDB and useful to keep in protein structures in a systematic manner.
+
+## Customizing fpocket
+
+This section will introduce several ways of customizing fpocket by modifying the source code. We will first gives all instructions needed to recompile and rebuild the full package when any modification of the source code has to be taken into account. Then, we will describe how to write a new scoring function, and how to write your own descriptors and include it to dpocket output. We will not show the full content of the function to modify as we want to stay as concise as possible. The newly added code for these examples will be highlighted in blue.
+
+### How to rebuild the package
+
+After any modification to the fpocket source code, you will logically need to rebuild the package so the modification could be taken into account. Here is the current procedure to do so:
+
+Go to your fpocket codebase: 
+
+```bash
+make uninstall
+make clean
+```
+
+Then, you will have to perform the installation process again to rebuild the package.
+
+### Writing your own scoring function
+
+Writing your own scoring function using currently implemented descriptors is a simple task, provided that you are not afraid to write one line of C code. Currently, the fpocket algorithm sort pockets using each pocket score. Each score is calculated by a single function. The source file src/pscoring.c contains the definition of this function that have the following prototype:
+```C
+float score_pocket(s_desc *pdesc) ;
+```
+
+The function takes as argument a pointer to a structure that contains all descriptors currently available in fpocket, and is called for each pocket to be scored. All descriptors available have been described previously, and you can check the exact name given to each of them in the source file headers/descriptors.h that defines the s_desc structure shown here.
+
+Lets say that you just want to score pockets according to the number of alpha sphere of each pocket. To do so, you just have to change the content of score_pocket function and return the right value:
+
+```C
+float score_pocket(s_desc *pdesc)
+	{
+		float score = (float) pdesc->nb_asph ;
+		return score ;
+	}
+```
+
+Although this example is really simple, you may now understand that you can write any kind of scoring function, like a linear or non-linear combination of descriptors derived from a regression model or any other method. The only limitation is the use of available descriptors implemented in fpocket.
+
+Of course, although the current scoring function has very satisfying performances using only 4 of the available descriptors, you may want to implement your own set. The next section will give you the basics to do so.
+
+### Writing your own descriptor
+
+So what if you want to write your own descriptors? Well this will be a little more difficult than writing your own scoring function, but nothing is impossible!
+
+Suppose that we want to add a new (and very simple) descriptor: the maximum alpha sphere radius in a given pocket.
+
+First of all, you have to add the variable that will store your descriptor to the structure containing all descriptors.  This has to be done in the descriptor.h source file, in the definition of the structure `s_desc`. We will add the following line:
+
+```C
+typedef struct s_desc
+	{	...
+		float as_max_r ;
+	} s_desc ;
+
+```
+
+After adding our variable, we need to give a default value when no calculation have been performed, lets say -1. This is done in the function reset_desc located in the same file:
+
+```C
+void reset_desc(s_desc *desc)
+	{	...
+		desc->as_max_r = -1.0 ;
+	}
+
+```
+
+Let's now implement our descriptor. Go to the `src/descriptor.c` source file. In this file, you fill find the main function that calculate descriptors based on a list of atoms and a list of alpha sphere. Here is the prototype of this function:
+
+```C
+void set_descriptors( s_atm **tatoms, int natoms,
+			    	  s_vvertice **tvert, int nvert,
+			    	  s_desc *desc) ;
+```
+
+As you can see, the function takes in argument a list of atoms, a list of vertices, and an input/output descriptor structure that will actually store all descriptors calculated. When descriptors has to be calculated on a given pocket, we first get all atoms and vertices of the pocket, and we call this function using those atoms and vertices as arguments. The calculation then use information on atoms and vertices to calculate descriptors.
+
+Based on those parameters, you will have to write your own code in this function, and update in consequent the desc variable given in argument so the descriptor value could be stored. Lets do this. You will probably notice that the current code is not fully modular. This is because of computational optimization: a fully modular code sometimes requires additional loop and treatment compared to an optimized code. Anyway, the task is still very simple. Lets go into the part of the code that will do the job.
+
+```C
+	void set_descriptors( s_atm **tatoms, int natoms,
+			    	  s_vvertice **tvert, int nvert,
+			    	  s_desc *desc)
+	{	...
+		float as_max_r = -1.0 ; /* Declare and initialize the descriptor */
+		...
+
+		for(i = 0 ; i < nvert ; i++) {
+			/* Loop through all vertices and update descriptors */
+			vcur = tvert[i] ;
+			if(vcur->ray > as_max_r) as_max_r = vcur->ray ;
+			...
+		}
+		...
+		desc->as_max_r = as_max_r ; 	/* Store the descriptor */
+	}
+```
+
+That's it, your descriptor is implemented, as each pocket descriptors is automatically calculated using this function at the end of the fpocket algorithm. Thus, it can now be used in the scoring function described previously, after rebuilding the package of course.
+
+### Normalizing your descriptors
+
+An advantage of normalization is that two descriptors generated from pockets of two different proteins can be compared to each other at a certain degree, depending on the normalization process. For example, if we normalize the number of alpha sphere between 0 and 1 (well here it's more a scaling than a normalization), the largest pocket of any protein will always have 1 as value for the normalized descriptor.
+
+To do so, we can't use the exact same process as adding a given descriptor, because all descriptors of all pockets  need to be calculated before the normalization step. Consequently, the calculation of all normalized descriptors is currently performed in the `src/pocket.c` source file. In this file, the function `set_normalized_descriptors` does the job, and have the following prototype:
+
+```C
+void set_normalized_descriptors(c_lst_pockets *pockets)
+```
+
+As you can see, it simply takes in argument a list of pockets, in fact a simple chained list, e.g. all pockets found in a given protein. Of course each pocket contained in this structure have a descriptor structure associated with.
+
+Lets now enter more deeply into the code, and implement a normalized version of the new descriptors so it ranges between 0 and 1. The first step is similar to the first step needed to implement a new descriptors: you need to add a variable that will store this normalized descriptor in the structures pdesc:
+
+```C
+typedef struct s_desc
+	{	...
+		float as_max_r ;
+		float as_max_r_norm ;
+	} s_desc ;
+```
+
+You can now add the default initialization of this descriptor:
+
+```C
+void reset_desc(s_desc *desc)
+	{	...
+		desc->as_max_r = -1.0 ;
+		desc->as_max_r_norm = -1.0 ;
+	}
+```
+
+Lets implement the descriptor now. Go to the `src/pocket.c` source file, set_normalized_descriptor function. To calculate the normalized descriptor, we need the min and max value of the non-normalized descriptors. Next, we have to loop on the pocket list, update the min and max if necessary, and perform the normalization at the end of the loop. So easy:
+
+```C
+void set_normalized_descriptors(c_lst_pockets *pockets)
+	{	...
+		/* Declare min and max */
+		float 	as_max_r_m = 1000,  	/* Initialize to a large value*/
+			as_max_r_M = -1.0 ;		/* Initialize to a small value */
+		...
+		cur = pockets->first ;
+		/* Perform a first processing step, e.g. to set min and max */
+		while(cur) {
+			dcur = pcur->pdesc ;
+            if(cur == pockets->first) {
+				...
+				/* If it is the first pocket, min = max = pocket */
+				as_max_r_m =  as_max_r_M = dcur->as_max_r ;
+			}
+			else {
+				...
+				/* If it is the Nth != 1 pocket, check and update
+				   min and max if necessary*/
+				if(dcur->as_max_r > as_max_r_M)
+					as_max_r_M = dcur-> as_max_r ;
+				else if(dcur->as_max_r < as_max_m)
+					as_max_r_m = dcur->as_max_r ;
+			}
+			cur = cur->next ;
+		}
+		
+		/* Perform a second loop to do the actual normalisation */
+		cur = pockets->first ;
+		while(cur) {
+			dcur = cur->pocket->pdesc ;
+			...
+			dcur->as_max_r_norm = (dcur->as_max_r - as_max_r_m)
+						   / (as_max_r_M - as_max_r_m) ;
+		}
+	}
+
+```
+
+And that's it. There is a little bit more effort to provide here to normalize the descriptor, but we believe it's not that much to do.
+
+Unfortunately, we haven't taken the time to automatically add any new descriptor to the dpocket input. So basically here, your descriptors is implemented and can be used by a scoring function, but is not written to the dpocket output. The next paragraph will learn you how to so, it's very easy.
+
+### Including your descriptor in dpocket
+
+Although it would be possible, we haven't taken the time to construct a system that would detect and add automatically any new descriptor to the dpocket output.
+
+So let's do this manually. The dpocket output format is defined by 3 macros in the dpocket.h header file:
+
+```C
+#define M_DP_OUTP_HEADER "pdb lig ...”
+#define M_DP_OUTP_FORMAT "%s %s ...”
+#define M_DP_OUTP_VAR (fc, l, ovlp, status, dst, lv, d) fc, l, ...
+```
+
+The first macro defines the header of the output file. The second macro corresponds to the format of each value to output given to the fprintf function. Finally, the last macro is the list of variables, with d being the pointer to the descriptor structure defined previously. Basically, writing the dpocket output for each pocket requires two main processes: write the header, and loop to write each pocket descriptor.
+
+To include our descriptor into the dpocket output, we just need to add the header label of the descriptor, add the output format of the descriptor, and add the descriptor itself. Those three steps will modify the first, the second, and the third macro defined previously, respectively. The only difficulty is to keep the correspondence between of all 3 positions (header, format and variable) in the line: column number (position) of the header corresponding to the number of alpha sphere must correspond the that of the format and variable. For example, if we want to add our normalized variable at the first position of dpocket output, it would give:
+
+```C
+#define M_DP_OUTP_HEADER "as_max_r pdb lig ...”
+#define M_DP_OUTP_FORMAT "%3.5f %s %s ...”
+#define M_DP_OUTP_VAR (fc, l, ovlp, status, dst, lv, d) d->as_max_r, 										    fc, l, ovlp, ...
+```
+
+That's all. Remember to be careful on this step: adding a new descriptor to dpocket is really easy in theory, but losing the correspondence between header, format and variable position columns is easy too, in which case interpretation, visualization and analysis of dpocket output can become somehow difficult or even meaningless.
+
+### Including your descriptor in mdpocket
+
+Adding a descriptor to mdpocket works pretty much the same way than in dpocket. So write your own descriptor like described previously for dpocket. The only difference is the last step, instead of modifying the dpocket.h macros you should modify the macros of mdpocket.h. They are constructed exactly the same way and are even somehow easier because smaller:
+
+```C
+#define M_MDP_OUTP_HEADER "snapshot pock_volume nb_AS...”
+#define M_MDP_OUTP_FORMAT "%d %4.2f %d %4.2f %4.2f %4.2f..."
+#define M_MDP_OUTP_VAR(i, d) i, d->volume ...
+```
+
+Simply add the header of your descriptor the output header macro, the output format to the format macro and the variable to the variable macro, exactly like in the previously described dpocket.h file.
--- a/doc/INSTALLATION.md
+++ b/doc/INSTALLATION.md
@@ -0,0 +1,152 @@
+# Installation
+
+## Prerequisites
+Currently fpocket proposes two different ways for visualization of binding pockets. Both are based on commonly used molecular visualization tools : VMD and PyMol. In order to use visualization you need to install at least one of both softwares, or any other valid tool able to read standard PDB files (Chimera, MOE, Maestro etc). 
+
+Currently, visualization using VMD has better rendering and performances and visualization using PyMol better handling of binding pockets. You can download VMD for free from http://www.ks.uiuc.edu/Research/vmd/. PyMol can be freely downloaded from https://pymol.org/2/.
+
+
+## Dependencies
+
+fpocket relies on Qhull. In the officially released version fpocket ships Qhull with it and Qhull compilation is automatically done when compiling and installing fpocket. Since the 3.0 release of fpocket 
+
+- libnetcdf and 
+- libstdc++ 
+
+are required to compile fpocket.
+
+## System Requirements
+
+fpocket is available for Linux/Unix type OS's, and also MacOSX (so basically all OS's that don't completely suck).
+In order to run fpocket, you should have at minimum a Pentium III 500 Mhz (does that still exist?) with 128Mb of RAM (lol). This program was co-developed and tested under the following Linux distributions : openSuse 10.3 (and newer), Centos 5.2, Fedora Core 7, Ubuntu 8.10 as well as Mac OS X (10.5, 10.6, 10.14.6). You need a valid C compiler like gcc or clang (for mac).
+
+## Getting Started
+
+These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
+
+### Prerequisites
+
+The most recent versions (starting with fpocket 3.0) make use of the molfile plugin from VMD. This plugin is shipped with fpocket. However, now you need to install the netcdf library on your system. This is typically called netcdf-devel or so, depending on you linux distribution.
+fpocket needs to be compiled to run on your machine. For this you'll need the gnu c compiler (or another one, but didn't test with others than GCC).
+install netcdf-devel on ubuntu type : 
+```
+sudo apt-get install libnetcdf-dev
+```
+on a RHEL based distribution something like this should do:
+```
+sudo yum install netcdf-devel.x86_64
+```
+
+### Installing
+
+Download the sources from github via the website or using git clone and then build and deploy fpocket using the following commands.
+
+#### Compiling on Linux
+
+```bash
+git clone https://github.com/Discngine/fpocket.git
+cd fpocket
+make 
+sudo make install
+```
+
+#### Compiling on OSX
+Install MacPorts https://www.macports.org/ for instance (needed for netcdf install)
+```bash
+sudo port install netcdf
+export LIBRARY_PATH=/opt/local/lib
+git clone https://github.com/Discngine/fpocket.git
+cd fpocket
+make ARCH=MACOSXX86_64
+sudo make install
+```
+
+
+
+End with an example of getting some data out of the system or using it for a little demo
+
+## Running the tests
+
+The source code of fpocket is shipped with samples. They can be found in the data/sample folder. Try to run fpocket against the 1uyd sample to check if it's running OK. 
+
+```
+cd data/sample
+fpocket -f 1UYD.pdb
+```
+fpocket should state when it's beginning to search pocket and also when it's ending the search. Upon completion the folder should now contain a folder called 1UYD_out. Check whether the folder exists and the pdb files contain data and the pocket info file contains results. 
+
+
+## Frequent issues encountered
+### netcdf issues
+```
+cannot find -lnetcdf
+```
+mdpocket supports reading and writing NETCDF formatted files. In order to use this you need to install the netcdf development libraries on your system. 
+
+#### Centos: 
+This can be achieved like this : 
+```
+yum install -y epel-release #if the epel repo is not yet activated on your system
+yum install -y netcdf-devel
+```
+
+#### Ubuntu: 
+```
+sudo apt-get install libnetcdf-dev
+```
+
+#### OSX:
+
+Install MacPorts https://www.macports.org/ for instance (needed for netcdf install)
+
+```
+sudo port install netcdf
+export LIBRARY_PATH=/opt/local/lib
+```
+
+Run make again after installing this library. Mdpocket / fpocket should build just fine now. 
+
+### stdc++ issues
+```
+cannot find -lstdc++
+```
+You need to install the stc++ static libraries to build fpocket & mdpocket. 
+
+#### Centos:
+
+On centos 7.4 this can be done like this : 
+```
+yum install -y libstc++-static
+```
+
+#### Ubuntu: 
+```
+sudo apt-get install libstdc++6
+```
+
+
+### Linking to molfile plugin issues
+If you observe an error similar to this one
+```
+ld: warning: ignoring file plugins/MACOSXX86/molfile/libmolfile_plugin.a, file was built for archive which is not the architecture being linked (x86_64): plugins/MACOSXX86/molfile/libmolfile_plugin.a
+Undefined symbols for architecture x86_64:
+  "_molfile_parm7plugin_init", referenced from:
+      _read_topology in topology.o
+  "_molfile_parm7plugin_register", referenced from:
+      _read_topology in topology.o
+ld: symbol(s) not found for architecture x86_64
+clang: error: linker command failed with exit code 1 (use -v to see invocation)
+make[1]: *** [bin/fpocket] Error 1
+make: *** [all] Error 2
+```
+then statically built libmolfile_plugin is not compatible with your machine. First check out that the ARCH variable set in the first line of the Makefile of fpocket actually reflects the architecture you want. For now I'm trying to support linux 64 bit systems and OSX 64 (LINUXAMD64) bit systems built with clang 32 and 64 bit (MACOSXX86 MACOSXX86_64). So all should work out of the box. If they do not, you might need to build the molfile plugin for your architecture. All available system architectures for the molfile plugin can be found in the plugins folder tree : [plugins directory](https://github.com/Discngine/fpocket/tree/master/plugins). 
+Here you can find more information on how to build the molfile plugin on CentOS 7.4: 
+[compile molfile plugin on centos 7.4 - Discngine blog post](https://www.discngine.com/blog/2019/5/25/building-the-vmd-molfile-plugin-from-source-code)
+Once built, copy the architecture folder into the fpocket/plugins directory and make sure to declare this architecture in the ARCH variable in the Makefile. Finally run make again.
+If you manage to build for other architectures and it works, I'd be happy to accept PR's with the relevant plugin architectures as I cannot build all of them on my own ;).
+
+
+## Read next
+
+* [Getting Started & Advanced Features](GETTINGSTARTED.md)
+
--- a/doc/INTRODUCTION.md
+++ b/doc/INTRODUCTION.md
@@ -0,0 +1,43 @@
+
+
+# Introduction
+
+Thanks for taking the time to read this official userguide of fpocket. In this guide are presented general functionalities of the fpocket program and its derivatives, dpocket, tpocket and mdpocket. Yes, indeed fpocket is a package of four distinct programs, mentioned here before. fpocket is an acronym for “finding” pocket; dpocket is an acronym for “describing” pockets as it is for extraction of physico-chemical descriptors of pockets; tpocket is an acronym for “testing” pockets, as it is used for testing on a large scale scoring function for ranking protein cavities developed with fpocket, among each other. mdpocket was named after pocket detection on molecular dynamics (MD) trajectories.
+
+This is not a usual guide. You can find here elements you can find in usual user guides, but we included several examples in the getting started section, which should enhance fast understanding of how to work with fpocket. The getting started guide can be understood like a mini tutorial of basic functionality of this software.
+
+Furthermore, we don't take ourselves too seriously, so the way this manual is written might not correspond to the industry standard ;)
+
+## License & Copyright
+
+This program is published under the MIT Licence. Basically do whatever you want with it. 
+Vincent Le Guilloux, Peter Schmidtke are authors of fpocket, dpocket, tpocket (which perform protein cavity detection, cavity descriptor extraction, large scale cavity prediction evaluations) Peter Schmidtke is the author of mdpocket which performs pocket detection and descriptor extraction on MD trajectories).
+Contributions
+The initial fpocket software was developed, validated, documented and distributed by Vincent Le Guilloux & Peter Schmidtke. Both, contributed equally to this project. The initial work on fpocket was initiated and supervised by Pierre Tufféry.
+Latest extensions were developed, validated, documented and distributed by Peter Schmidtke (mdpocket, druggability score, energy calculations) supervised by Xavier Barril.
+
+
+## Publication & Citation
+
+The methods paper about this software was published in BMC Bioinformatics. In order to cite fpocket in the future, please cite this paper :
+
+- Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, “Fpocket: An open source platform for ligand pocket detection”, BMC Bioinformatics 2009, 10:168
+
+If you use the druggability score of fpocket, please cite :
+
+- Peter Schmidtke & Xavier Barril “Understanding and predicting druggability. A high-throughput method for detection of drug binding sites.”, J Med Chem, 2010, 53(15):5858-67
+
+Last, the mdpocket paper has been published too and can be cited using:
+
+- Peter Schmldtke, Axel Bidon-Chanal, Javier Luque, Xavier Barril, “MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories.”, Bioinformatics. 2011 Dec 1;27(23):3276-85
+
+Contact
+If you want to contact the fpocket developers please create a github issue here: https://github.com/Discngine/fpocket/issues
+
+We are happy about positive, negative, in any way constructive feedback.
+
+## Read next
+
+* [Installation](INSTALLATION.md)
+
+* [Getting Started](GETTINGSTARTED.md)
--- a/doc/MANUAL.md
+++ b/doc/MANUAL.md
@@ -0,0 +1,15 @@
+# fpocket User Manual
+fpocket is a protein pocket prediction algorithm. Given a PDB protein structure it enables the user to identify potent binding sites. Based on Voronoi tessellation, this algorithm is very fast and particularly well suited for large scale protein binding pocket screenings and development of scoring functions for binding pocket characterization. Now, fpocket also allows pocket detection on MD trajectories and assessment of the volume & the druggability of a binding site. Last, also interaction energy calculations are now possible using fpocket & mdpocket.
+
+## Notes
+1.	This program uses output coming from Qhull. Qhull is integrated within fpocket. More information about Qhull can be found in the paper : Barber, C.B., Dobkin, D.P., and Huhdanpaa, H.T., "The Quickhull algorithm for convex hulls," ACM Trans. on Mathematical Software, 22(4):469-483, Dec 1996, http://www.qhull.org
+2.	Part of this software includes code based on external code developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. The PDB parser of the Molfile Plugin of VMD were modified for the purposes of fpocket's PDB parsing. Furthermore, the molfile plugin allows now mdpocket to analyse various MD trajectory formats.
+3.	Within the whole documentation code and output from computer programs are represented and formatted in the following way : `ls -1 > out.txt`
+4.	This documentation, as well as the software itself, is under steady change. The fpocket developer team tries to provide a useful and easy to understand documentation, a thing that completely lacks in most of scientific open source softwares nowadays. In our opinion an open source software is useless without documentation of the source code on one side and documentation of the software on the other. Thus, we welcome every suggestion to improve this documentation in terms of accuracy, clarity and completeness.
+
+## Contents
+* [Introduction](INTRODUCTION.md)
+
+* [Installation](INSTALLATION.md)
+
+* [Getting Started & Advanced Features](GETTINGSTARTED.md)
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Author	SHA1	Message	Date
Peter Schmidtke	9c7be61644	Merge pull request #86 from jordansafer/master Fix header typo for easier parsing	2023-02-22 04:16:15 -05:00
Peter Schmidtke	f05cdb7cdd	Merge pull request #97 from Discngine/mypocket Adding support for definition of explicit pockets	2023-02-22 04:04:43 -05:00
pschmidtke	115128de62	fix for mmcif structures & explicit pockets	2023-02-22 10:01:48 +01:00
pschmidtke	ee1cc7373f	missing voronoi.c	2023-02-20 14:20:43 +01:00
pschmidtke	ac18b146ff	functional in PDB format	2023-02-20 14:16:06 +01:00
pschmidtke	9c2cbca91a	parameter parsing finished	2023-02-20 08:00:22 +01:00
pschmidtke	c00ab205b6	backup	2023-02-18 22:39:41 +01:00
pschmidtke	86a4a97ac7	first steps in fparams	2023-02-16 07:23:36 +01:00
pschmidtke	ce4997d6e6	introducing P parameter (WIP)	2023-02-13 09:27:34 +01:00
pschmidtke	a0bbee64f8	Explicit pockets with various alternates handling	2023-02-02 11:43:24 +01:00
Peter Schmidtke	d82104b99a	Dropping for security reasons	2022-10-24 13:47:59 +02:00
Jordan Safer	5ef19079e9	Fix header typo for easier parsing	2022-10-11 12:18:32 -04:00
pschmidtke	cd00b961e6	adding linux built molfileplugin	2022-05-10 11:13:07 +02:00
pschmidtke	84967334d8	fixes on alternate locations in cif & output as cif	2022-05-10 10:58:46 +02:00
pschmidtke	9906237e6d	dropping dependency on /tmp	2021-11-17 21:37:18 +01:00
pschmidtke	71637e923f	update for osx	2021-11-17 16:21:03 +01:00
pschmidtke	127c60a49b	last fixes for cif support for models	2021-11-16 21:47:15 +01:00
pschmidtke	3a60a4c86e	adding mac	2021-11-16 21:41:09 +01:00
pschmidtke	91e3d2dbbe	debug env with molfileplugin for linux	2021-11-16 21:40:22 +01:00
pschmidtke	f99a6ed96d	pdbxpluging update	2021-11-15 21:46:24 +01:00
pschmidtke	855bad8cce	update molfilepluging linux & osx	2021-11-10 15:16:39 +01:00
pschmidtke	5408f01005	support for model flag even no model is available	2021-11-09 22:02:24 +01:00
pschmidtke	2acab799f4	adding sample NMR structure	2021-11-09 22:01:36 +01:00
pschmidtke	edfd87c188	support for OSX & residue selection on mmcif	2021-11-09 21:10:03 +01:00
pschmidtke	5e3b4f31dc	adding new dockerfile	2021-11-04 07:47:56 +01:00
pschmidtke	8bcf81635e	adding dockerfile for debian-slim distrib	2021-11-03 18:31:49 +01:00
Peter Schmidtke	38a1c49440	Update README.md	2021-02-02 21:47:44 +01:00
Peter Schmidtke	efd7b0ebb7	Update README.md	2021-02-02 21:46:03 +01:00
Peter Schmidtke	0a84309db4	Merge pull request #59 from Discngine/mmcif Documentation stuff missing	2021-02-02 21:44:54 +01:00
pschmidtke	6e80f9203c	Merge branch 'master' into mmcif	2021-02-02 21:43:55 +01:00
pschmidtke	e22d38054a	adding missing doc in fparams	2021-02-02 21:42:35 +01:00
Peter Schmidtke	439da234a3	Merge pull request #55 from HTian1997/master Update GETTINGSTARTED.md	2021-02-02 21:14:01 +01:00
Peter Schmidtke	b68d547fd5	Merge pull request #53 from Discngine/mmcif Enabling Mmcif support in fpocket	2021-02-02 21:11:49 +01:00
pschmidtke	e57afc2bad	working now?	2021-02-02 21:07:36 +01:00
pschmidtke	9617bda214	missing asa header in descriptors	2021-02-02 20:59:37 +01:00
pschmidtke	8e81c0c807	minor ui adjustments	2021-02-02 20:52:24 +01:00
Hao Tian	7b500b4dd6	Update GETTINGSTARTED.md	2020-08-27 12:40:59 -05:00
ShorkarMael	209f93aa69	Update c-cpp.yml working version for pytest	2020-07-31 09:13:18 +02:00
ShorkarMael	c50e921077	Update c-cpp.yml test	2020-07-31 09:11:00 +02:00
ShorkarMael	a2c1745242	Update c-cpp.yml test	2020-07-31 09:00:40 +02:00
ShorkarMael	877014bd60	Update c-cpp.yml	2020-07-31 08:54:03 +02:00
ShorkarMael	9d11cbb2fb	Update c-cpp.yml test	2020-07-31 08:42:50 +02:00
ShorkarMael	296fb4789c	Update c-cpp.yml test	2020-07-31 00:35:03 +02:00
ShorkarMael	e89a312df2	Update c-cpp.yml python version	2020-07-31 00:28:00 +02:00
ShorkarMael	0d1a74253c	Update c-cpp.yml test	2020-07-31 00:21:43 +02:00
ShorkarMael	f4208748ed	Update c-cpp.yml test	2020-07-31 00:19:04 +02:00
ShorkarMael	b91c92d5b4	Update c-cpp.yml test	2020-07-31 00:11:04 +02:00
ShorkarMael	e191b547dc	Update c-cpp.yml test	2020-07-31 00:05:44 +02:00
ShorkarMael	73ce917ea0	Update c-cpp.yml test	2020-07-30 23:57:19 +02:00
ShorkarMael	10fd5e5cef	Update c-cpp.yml v2	2020-07-30 23:52:22 +02:00
ShorkarMael	b715bec165	Update c-cpp.yml test	2020-07-30 23:51:17 +02:00
ShorkarMael	2a1702fceb	Update c-cpp.yml test	2020-07-30 22:20:37 +02:00
ShorkarMael	28031f4cf8	Update c-cpp.yml 1	2020-07-30 21:11:20 +02:00
ShorkarMael	84af7678e1	Update c-cpp.yml pytest	2020-07-30 21:02:10 +02:00
ShorkarMael	f58b5ffa43	Update c-cpp.yml test	2020-07-30 20:53:11 +02:00
ShorkarMael	1f01eefe25	Update c-cpp.yml test	2020-07-30 20:49:07 +02:00
ShorkarMael	17d63260d5	Update c-cpp.yml Rmv init	2020-07-30 20:02:26 +02:00
ShorkarMael	1572782a39	Update c-cpp.yml source	2020-07-30 19:51:30 +02:00
ShorkarMael	888a6eee19	Update c-cpp.yml test	2020-07-30 19:46:35 +02:00
ShorkarMael	76d21c256b	Update c-cpp.yml init	2020-07-30 19:40:31 +02:00
ShorkarMael	fad1337ad5	Update c-cpp.yml init	2020-07-30 19:37:20 +02:00
ShorkarMael	fce9c66825	Update c-cpp.yml source	2020-07-30 19:31:32 +02:00
ShorkarMael	cffeb8f14d	Update c-cpp.yml conda setup	2020-07-30 19:26:34 +02:00
ShorkarMael	3363536b08	Update c-cpp.yml test	2020-07-30 19:23:28 +02:00
ShorkarMael	267e63050c	Update c-cpp.yml test	2020-07-30 19:18:41 +02:00
ShorkarMael	620f3431c6	Update c-cpp.yml test	2020-07-30 19:09:35 +02:00
ShorkarMael	74471a1123	Update c-cpp.yml conda changes	2020-07-30 19:03:18 +02:00
ShorkarMael	927c988b09	Merge branch 'mmcif' of https://github.com/Discngine/fpocket into mmcif	2020-07-30 08:36:22 -07:00
ShorkarMael	0a92618189	bug fixes for writing	2020-07-30 08:36:06 -07:00
pschmidtke	06e8ee4ab0	update osx version	2020-07-30 11:37:08 +02:00
pschmidtke	9a7a1d321c	shared library update OSX86_64	2020-07-30 11:34:06 +02:00
pschmidtke	f31205a0b8	correct corrupted makefile	2020-07-30 11:29:25 +02:00
Peter Schmidtke	ff35953eb5	Update makefile enabling proper make fpocket	2020-07-30 11:24:05 +02:00
ShorkarMael	1565cc0701	Merge branch 'mmcif' of https://github.com/Discngine/fpocket into mmcif	2020-07-30 02:15:36 -07:00
ShorkarMael	653472798e	writepocket.h upadate	2020-07-30 02:15:31 -07:00
ShorkarMael	bbb138378e	Merge branch 'master' into mmcif	2020-07-29 23:16:44 +02:00
ShorkarMael	0e15bc672d	added a test for multiple chains as ligand	2020-07-29 13:43:09 -07:00
ShorkarMael	521f6a2701	added mmcif doc and multiple chains as ligand	2020-07-29 10:15:23 -07:00
ShorkarMael	faf35bb9c0	added long chain args and update log	2020-07-23 17:18:41 -07:00
ShorkarMael	98fdedb1c5	tests for mmcif added	2020-07-23 09:14:33 -07:00
ShorkarMael	e635a3e359	PYMOL and VMD reading special	2020-07-23 02:07:48 -07:00
ShorkarMael	70917d144b	documentation on writing params	2020-07-22 09:25:31 -07:00
ShorkarMael	5b177bc7bd	write mode selection	2020-07-22 09:14:26 -07:00
ShorkarMael	01b2099469	writing mmcif fonctionnal and separate pockets	2020-07-22 05:16:21 -07:00
ShorkarMael	ae1f26089c	insertion code reading	2020-07-17 05:01:36 -07:00
ShorkarMael	fca9e379c5	longer chain names	2020-07-17 01:18:55 -07:00
ShorkarMael	3ef844937b	take into account 2 letters chain names	2020-07-16 11:31:45 -07:00
ShorkarMael	6b87b664ab	show info	2020-07-16 02:28:30 -07:00
ShorkarMael	81618554df	updated pdbxplugin	2020-07-16 02:12:02 -07:00
ShorkarMael	78a6e541fb	added missing sample	2020-07-15 06:42:38 -07:00
ShorkarMael	4287ca1a27	added file format detection in main	2020-07-15 06:36:21 -07:00
ShorkarMael	d0e25956ab	fatal error fixed	2020-07-13 09:01:34 -07:00
ShorkarMael	62d1a12438	mmcif_reading works but outputs fatal error	2020-07-13 07:58:46 -07:00
ShorkarMael	e82a452044	molfile_plugin src modif	2020-07-08 15:46:15 -07:00
Peter Schmidtke	de94aada19	Merge pull request #51 from Discngine/explicit-pocket Explicit pocket and keep chains	2020-07-08 11:28:54 +02:00
ShorkarMael	858073a4e1	fixed typo and deleted mod 2POR	2020-07-05 11:53:26 -07:00
ShorkarMael	93772970c9	deleted the prints	2020-07-03 17:44:01 -07:00
ShorkarMael	f0e7efa86d	small changes	2020-07-03 17:03:16 -07:00
ShorkarMael	642bc8f12b	reading mmcif with read_mmcif.c	2020-07-03 02:47:32 -07:00
ShorkarMael	e5b2d2d9af	deleted useless print	2020-06-25 09:27:06 -07:00
ShorkarMael	294b1a6e07	added doc ,tests and keep chains	2020-06-25 09:21:45 -07:00
ShorkarMael	70de53b855	params added to desciption	2020-06-25 01:38:16 -07:00
ShorkarMael	df613de93a	chain as a ligand working (pytest included)	2020-06-24 09:54:54 -07:00
ShorkarMael	7f0b864de2	del the chain chose as ligand	2020-06-22 01:48:45 -07:00
ShorkarMael	370a8aa016	first release explicit chain as ligand	2020-06-18 11:57:03 -07:00
Peter Schmidtke	a0eaccea0a	Update c-cpp.yml	2020-06-16 00:00:32 +02:00
Peter Schmidtke	3e96d21c37	Update c-cpp.yml	2020-06-15 23:58:37 +02:00
Peter Schmidtke	e4c728043d	Update c-cpp.yml	2020-06-15 23:56:03 +02:00
Peter Schmidtke	fe4dd1c68f	Update c-cpp.yml	2020-06-15 23:50:03 +02:00
Peter Schmidtke	846465d8c3	adding pytest to github actions lilely not working	2020-06-15 23:48:38 +02:00
Peter Schmidtke	a5c7a69125	Update c-cpp.yml	2020-06-15 23:45:08 +02:00
Peter Schmidtke	6e0d0330f3	install netcdf	2020-06-15 23:43:38 +02:00
Peter Schmidtke	0f3bf034ff	making only fpocket	2020-06-15 23:37:15 +02:00
Peter Schmidtke	32aaabe217	integration of github actions linux and mac builds - without netcdf support for now	2020-06-15 23:34:39 +02:00
pschmidtke	5ae071daf4	adding git attributes	2020-06-15 23:27:22 +02:00
Peter Schmidtke	2bfc2a15a6	Merge pull request #46 from Discngine/testToDelete Test to delete	2020-06-15 23:20:50 +02:00
Peter Schmidtke	2b97e041f7	gitter badge update	2020-06-15 15:49:32 +02:00
ShorkarMael	7766583153	Merge branch 'master' into testToDelete	2020-06-15 02:54:35 -07:00
ShorkarMael	ebcca8a0aa	test in the same function	2020-06-15 02:51:09 -07:00
ShorkarMael	7a334f524a	added a test for long parameter drop chains	2020-06-15 02:26:09 -07:00
ShorkarMael	546c99a41b	fixed the long option for drop chains	2020-06-15 02:12:51 -07:00
ShorkarMael	180e480a4b	fixed the 0 pocket issue	2020-06-14 14:13:44 -07:00
pschmidtke	e22d9ae636	dropping deprecated maintainer from dockerfile	2020-06-14 13:28:54 +02:00
Peter Schmidtke	e2f4513ec8	Merge pull request #49 from Discngine/docker docker file and documentation update	2020-06-13 23:41:11 +02:00
pschmidtke	ed7ff872e4	docker file and documentation update	2020-06-13 23:40:21 +02:00
Peter Schmidtke	db835c175b	trigger build only on PR's on master	2020-06-13 19:45:57 +02:00
Peter Schmidtke	64f94d710a	correction on gitter badge placement	2020-06-13 18:53:43 +02:00
Peter Schmidtke	2d4c972862	adding gitter badge	2020-06-13 18:51:16 +02:00
pschmidtke	bd700f5c2c	adding explicit pocket to test cases	2020-06-13 18:27:10 +02:00
Peter Schmidtke	9b973a7470	Adding build status badges	2020-06-13 18:11:50 +02:00
Peter Schmidtke	933f62c93d	Update azure-pipelines.yml for Azure Pipelines	2020-06-13 18:09:09 +02:00
Peter Schmidtke	fcbad192f1	Update azure-pipelines.yml for Azure Pipelines	2020-06-13 18:06:03 +02:00
Peter Schmidtke	ca599f8be0	Update azure-pipelines.yml for Azure Pipelines	2020-06-13 18:02:43 +02:00
Peter Schmidtke	3f9d19f2dd	Update azure-pipelines.yml for Azure Pipelines	2020-06-13 17:59:08 +02:00
Peter Schmidtke	18b6dd8144	Update azure-pipelines.yml for Azure Pipelines	2020-06-13 17:53:56 +02:00
Peter Schmidtke	2531c98bb4	Update azure-pipelines.yml for Azure Pipelines	2020-06-13 17:48:11 +02:00
Peter Schmidtke	65380b5ecd	Update azure-pipelines.yml for Azure Pipelines	2020-06-13 17:45:51 +02:00
Peter Schmidtke	246181b712	adding conda pytest to Pipeline	2020-06-13 17:34:31 +02:00
Peter Schmidtke	e1ad76a8a7	installing netcdf dependency	2020-06-13 17:30:59 +02:00
Peter Schmidtke	e99e1574ea	Set up CI with Azure Pipelines [skip ci]	2020-06-13 17:24:06 +02:00
ShorkarMael	23ff71386e	documentation update with delete chains	2020-06-12 08:21:13 -07:00
Peter Schmidtke	dbe7470906	Update issue templates	2020-06-12 11:33:44 +02:00
ShorkarMael	ea2dfc4960	test 2P0R	2020-06-11 06:16:47 -07:00
ShorkarMael	cd84135740	Merge branch 'master' into testToDelete	2020-06-11 05:32:46 -07:00
ShorkarMael	110f92f8b5	droping multiple chains	2020-06-11 05:09:34 -07:00
Peter Schmidtke	587003c60a	Merge pull request #45 from Discngine/testing Testing	2020-06-09 23:00:38 +02:00
pschmidtke	a32bd136bc	adding reference results to repo	2020-06-09 22:59:09 +02:00
pschmidtke	9687d920f1	test cases added	2020-06-09 22:58:46 +02:00
pschmidtke	ada630181b	readme update for testing	2020-06-09 22:58:36 +02:00
ShorkarMael	fe804441c9	deletes one chain and find pockets works	2020-06-09 07:28:09 -07:00
ShorkarMael	8b1e011254	delete 1 selected chain still has bugs	2020-06-08 16:51:26 -07:00
ShorkarMael	35d3f17520	Merge branch 'testToDelete' of https://github.com/Discngine/fpocket into testToDelete	2020-06-07 07:37:04 -07:00
ShorkarMael	39a447bac6	test1	2020-06-07 07:36:58 -07:00
pschmidtke	cc5ca7595d	simple test case	2020-06-06 21:56:58 +02:00
pschmidtke	56e9ea2735	reference output 1uyd	2020-06-06 21:56:29 +02:00
pschmidtke	0bd608de42	adding conda environment for testing	2020-06-06 19:22:26 +02:00
pschmidtke	43acf4898e	putting back the readme	2020-06-06 19:22:16 +02:00
pschmidtke	c75129ebcc	cleaning up	2020-06-06 19:12:44 +02:00
Peter Schmidtke	bfeeb399a9	Merge pull request #43 from Discngine/documentation adding conda install instructions	2020-06-06 16:14:40 +02:00
pschmidtke	e274275fd8	adding conda install instructions	2020-06-06 16:13:54 +02:00
Peter Schmidtke	39f2df9ba9	Merge pull request #42 from Discngine/documentation Documentation	2020-06-06 16:07:31 +02:00
pschmidtke	16ed338bc1	moving old documentation to deprecated	2020-06-06 16:04:20 +02:00
pschmidtke	fdb4de240a	documentation test	2020-06-06 16:00:27 +02:00
pschmidtke	e30a9f3641	fpocket advanced doc	2020-06-06 14:24:58 +02:00
pschmidtke	9f10e283c5	mdpocket basic features	2020-06-05 23:43:38 +02:00
pschmidtke	6e7e62d0f6	documentation update	2020-06-05 22:46:51 +02:00
pschmidtke	8f72305ee4	adding dpocket sample files & images	2020-06-05 21:47:06 +02:00
pschmidtke	707de5ad96	update main readme	2020-06-05 20:49:13 +02:00
pschmidtke	f91bd7a1fc	documentation revamp 1	2020-06-05 20:34:34 +02:00
ShorkarMael	6a54364b67	test	2020-06-02 09:26:03 -07:00
pschmidtke	65c809d04b	explaining explicit pocket detection params	2020-06-02 17:36:07 +02:00