Merge pull request #45 from Discngine/testing

Testing
adding reference results to repo
2026-06-04 20:04:22 +08:00 · 2020-06-09 23:00:38 +02:00 · 2020-06-09 22:59:09 +02:00 · 2020-06-09 22:58:46 +02:00 · 2020-06-09 22:58:36 +02:00 · 2020-06-06 21:56:58 +02:00
251 changed files with 34309 additions and 257 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,7 @@
 nbproject
 *.o
-*_out
 .vscode
-src/qhull/bin/
+src/qhull/bin/
+src/qhull/lib/libqhullstatic_r.a
+src/qhull/lib/libqhullstatic.a
+*.pyc
--- a/README.md
+++ b/README.md
@@ -8,13 +8,13 @@ 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__: 
 - 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)
@@ -32,7 +32,8 @@ mdpocket:
 ### 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).
+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
@@ -42,6 +43,15 @@ 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
+```
+
 ### Installing

 Download the sources from github via the website or using git clone and then build and deploy fpocket using the following commands.
@@ -56,16 +66,53 @@ sudo make install
 ```

 #### Compiling on Mac
-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
 ```

+#### 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
+```
+
+#### Testing your installation
+
+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: 
+
+```bash
+conda env create -f tests/environment.yml
+conda activate fpocket_test
+```
+
+Once your conda environment activated you can run 
+
+```
+pytest
+
+```
+
+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 ==============================================================
+
+```
+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:
--- 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/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 > $out/all_train.csv
-
--- a/newFeatures.txt
+++ b/newFeatures.txt
@@ -1,26 +0,0 @@
- fixed issues with ugly pdbs and weird coordinates in infinite space
-
-new Features since last release :
- new clustering approach based on clusterlib, allowing to use typical hierarchical clustering of alpha spheres
- possibility of denoising pocket detection by replicating Voronoi vertice detection on slightly shifted coordinates
- the user can now specify its own grid and its own grid dimensions for mdpocket calculations directly in the mdpocket input file
- we start to introduce some energy calculation functionalities into the code, so atom typing and charge assignment for protein atoms with the aim to calculate pocket energy maps
- the molfile plugin of VMD is now integrated allowing to analyse easily a large variety of molecular formats (especially useful for MD trajectories here)
- new look of fpocket input
- dpocket can now be run on cases where the ligand is designated as a chain, particularly useful for polysaccharide and peptide binding site characterization
- new pocket descriptors : 
-	- number of abpas
-	- apolar & polar vdw surface areas at 1.4 - 2.2 A probe radii
-	- convex hull volume
- pocket energy grid calculations using topologies
-
-corrected bugs and code improvements : 
- memory accumulating in mdpocket, dpocket and tpocket and fpocket -L now cleaned up
- compiling issues on newer GCC's on Ubuntu have been solved
- code clean up from things not used anymore
- errors in descriptor output for amino acid based descriptors have been corrected
-
-
-new dependencies :
- libnetcdf,libstdc++
-
--- a/rebuild.sh
+++ b/rebuild.sh
@@ -1,7 +0,0 @@
-#! /bin/sh
-
-aclocal \
-&& autoheader \
-&& automake --gnu --add-missing \
-&& autoconf
-
--- a/testall.sh
+++ b/testall.sh
@@ -1,55 +0,0 @@
-#! /bin/sh
-
-D=1.73
-m=3.0
-M=6.0
-i=36
-n=2
-v=1000
-
-out="perf_all_D"$D"_m"$m"_M"$M"_i"$i"_n"$n
-
-mkdir $out
-echo "== Testing Pocketpicker HOLO"
-
-./bin/tpocket -L ../data/pp-cplx-t.txt -D $D -m $m -M $M -i $i -n $n -v $v #-k
-mv stats_g.txt stats_g_pph.txt
-mv stats_p.txt stats_p_pph.txt
-mv stats_g_pph.txt $out
-mv stats_p_pph.txt $out
-
-echo "== Testing Pocketpicker APO"
-./bin/tpocket -L ../data/pp-apo-t.txt -D $D -m $m -M $M -i $i -n $n -v $v #-k
-mv stats_g.txt stats_g_ppa.txt
-mv stats_p.txt stats_p_ppa.txt
-mv stats_g_ppa.txt $out
-mv stats_p_ppa.txt $out
-
-echo "== Testing cheng set"
-./bin/tpocket -L ../data/cheng-t.txt -D $D -m $m -M $M -i $i -n $n -v $v #-k
-mv stats_g.txt stats_g_ch.txt
-mv stats_p.txt stats_p_ch.txt
-mv stats_g_ch.txt $out
-mv stats_p_ch.txt $out
-
-echo "== Testing astex diverse set"
-./bin/tpocket -L ../data/astex-diverse-t.txt -D $D -m $m -M $M -i $i -n $n -v $v #-k
-mv stats_g.txt stats_g_astex_diverse.txt
-mv stats_p.txt stats_p_astex_diverse.txt
-mv stats_g_astex_diverse.txt $out
-mv stats_p_astex_diverse.txt $out
-
-echo "== Testing training set"
-./bin/tpocket -L ../data/train-t.txt -D $D -m $m -M $M -i $i -n $n -v $v #-k
-mv stats_g.txt stats_g_train.txt
-mv stats_p.txt stats_p_train.txt
-mv stats_g_train.txt $out
-mv stats_p_train.txt $out
-
-echo "== Testing ccdc-clean set"
-./bin/tpocket -L ../data/ccdc-clean-t.txt -D $D -m $m -M $M -i $i -n $n -v $v #-k
-mv stats_g.txt stats_g_ccdc-clean.txt
-mv stats_p.txt stats_p_ccdc-clean.txt
-mv stats_g_ccdc-clean.txt $out
-mv stats_p_ccdc-clean.txt $out
-
--- a/tests/environment.yml
+++ b/tests/environment.yml
@@ -0,0 +1,6 @@
+name: fpocket_test
+channels:
+  - defaults
+dependencies:
+  - python=3.7
+  - pytest
--- a/tests/reference_output/1ATP_out/1ATP.pml
+++ b/tests/reference_output/1ATP_out/1ATP.pml
@@ -0,0 +1,15 @@
+from pymol import cmd,stored
+load 1ATP_out.pdb
+#select pockets, resn STP
+stored.list=[]
+cmd.iterate("(resn STP)","stored.list.append(resi)")	#read info about residues STP
+#print stored.list
+lastSTP=stored.list[-1]	#get the index of the last residu
+hide lines, resn STP
+
+#show spheres, resn STP
+for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
+for my_index in range(2,int(lastSTP)+2): cmd.color(my_index,"pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.3","pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
--- a/tests/reference_output/1ATP_out/1ATP.tcl
+++ b/tests/reference_output/1ATP_out/1ATP.tcl
@@ -0,0 +1,24 @@
+proc highlighting { colorId representation id selection } {
+   puts "highlighting $id"
+   mol representation $representation
+   mol material "Diffuse" 
+    mol color $colorId
+   mol selection $selection
+   mol addrep $id
+}
+
+set id [mol new 1ATP_out.pdb type pdb]
+mol delrep top $id
+highlighting Name "Lines" $id "protein"
+highlighting Name "Licorice" $id "not protein and not resname STP"
+highlighting Element "NewCartoon" $id "protein"
+highlighting "ColorID 7" "VdW 0.4" $id "protein and occupancy>0.95"
+set id [mol new 1ATP_pockets.pqr type pqr]
+                        mol selection "all" 
+                         mol material "Glass3" 
+                         mol delrep top $id 
+                         mol representation "QuickSurf 0.3" 
+                         mol color ResId $id 
+                         mol addrep $id 
+highlighting Index "Points 1" $id "resname STP"
+display rendermode GLSL
--- a/tests/reference_output/1ATP_out/1ATP_PYMOL.sh
+++ b/tests/reference_output/1ATP_out/1ATP_PYMOL.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+pymol 1ATP.pml
--- a/tests/reference_output/1ATP_out/1ATP_VMD.sh
+++ b/tests/reference_output/1ATP_out/1ATP_VMD.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+vmd 1ATP_out.pdb -e 1ATP.tcl
--- a/tests/reference_output/1ATP_out/1ATP_info.txt
+++ b/tests/reference_output/1ATP_out/1ATP_info.txt
@@ -0,0 +1,399 @@
+Pocket 1 :
+	Score : 	0.977
+	Druggability Score : 	0.959
+	Number of Alpha Spheres : 	106
+	Total SASA : 	8.888
+	Polar SASA : 	6.473
+	Apolar SASA : 	2.415
+	Volume : 	585.250
+	Mean local hydrophobic density : 	38.950
+	Mean alpha sphere radius :	3.904
+	Mean alp. sph. solvent access : 	0.457
+	Apolar alpha sphere proportion : 	0.377
+	Hydrophobicity score:	21.630
+	Volume score: 	 4.000
+	Polarity score:	 14
+	Charge score :	 0
+	Proportion of polar atoms: 	43.636
+	Alpha sphere density : 	5.607
+	Cent. of mass - Alpha Sphere max dist: 	14.180
+	Flexibility : 	0.206
+
+Pocket 2 :
+	Score : 	0.140
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	19
+	Total SASA : 	55.125
+	Polar SASA : 	23.727
+	Apolar SASA : 	31.398
+	Volume : 	262.323
+	Mean local hydrophobic density : 	4.000
+	Mean alpha sphere radius :	3.971
+	Mean alp. sph. solvent access : 	0.614
+	Apolar alpha sphere proportion : 	0.263
+	Hydrophobicity score:	12.167
+	Volume score: 	 4.250
+	Polarity score:	 7
+	Charge score :	 1
+	Proportion of polar atoms: 	56.522
+	Alpha sphere density : 	3.460
+	Cent. of mass - Alpha Sphere max dist: 	9.040
+	Flexibility : 	0.893
+
+Pocket 3 :
+	Score : 	0.127
+	Druggability Score : 	0.006
+	Number of Alpha Spheres : 	18
+	Total SASA : 	13.148
+	Polar SASA : 	1.071
+	Apolar SASA : 	12.076
+	Volume : 	77.200
+	Mean local hydrophobic density : 	17.000
+	Mean alpha sphere radius :	3.543
+	Mean alp. sph. solvent access : 	0.402
+	Apolar alpha sphere proportion : 	1.000
+	Hydrophobicity score:	68.875
+	Volume score: 	 5.250
+	Polarity score:	 3
+	Charge score :	 2
+	Proportion of polar atoms: 	7.143
+	Alpha sphere density : 	1.532
+	Cent. of mass - Alpha Sphere max dist: 	3.109
+	Flexibility : 	0.632
+
+Pocket 4 :
+	Score : 	0.120
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	37
+	Total SASA : 	72.975
+	Polar SASA : 	34.331
+	Apolar SASA : 	38.644
+	Volume : 	253.085
+	Mean local hydrophobic density : 	7.000
+	Mean alpha sphere radius :	3.703
+	Mean alp. sph. solvent access : 	0.441
+	Apolar alpha sphere proportion : 	0.216
+	Hydrophobicity score:	21.300
+	Volume score: 	 5.000
+	Polarity score:	 7
+	Charge score :	 0
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	3.103
+	Cent. of mass - Alpha Sphere max dist: 	8.153
+	Flexibility : 	0.345
+
+Pocket 5 :
+	Score : 	0.099
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	22
+	Total SASA : 	49.935
+	Polar SASA : 	36.651
+	Apolar SASA : 	13.284
+	Volume : 	192.686
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.800
+	Mean alp. sph. solvent access : 	0.414
+	Apolar alpha sphere proportion : 	0.045
+	Hydrophobicity score:	53.556
+	Volume score: 	 4.667
+	Polarity score:	 3
+	Charge score :	 1
+	Proportion of polar atoms: 	66.667
+	Alpha sphere density : 	2.630
+	Cent. of mass - Alpha Sphere max dist: 	5.374
+	Flexibility : 	0.461
+
+Pocket 6 :
+	Score : 	0.082
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	17
+	Total SASA : 	33.550
+	Polar SASA : 	21.473
+	Apolar SASA : 	12.076
+	Volume : 	117.318
+	Mean local hydrophobic density : 	4.000
+	Mean alpha sphere radius :	3.603
+	Mean alp. sph. solvent access : 	0.400
+	Apolar alpha sphere proportion : 	0.294
+	Hydrophobicity score:	42.364
+	Volume score: 	 4.091
+	Polarity score:	 4
+	Charge score :	 0
+	Proportion of polar atoms: 	43.750
+	Alpha sphere density : 	1.980
+	Cent. of mass - Alpha Sphere max dist: 	3.596
+	Flexibility : 	0.000
+
+Pocket 7 :
+	Score : 	0.082
+	Druggability Score : 	0.005
+	Number of Alpha Spheres : 	31
+	Total SASA : 	82.474
+	Polar SASA : 	25.715
+	Apolar SASA : 	56.759
+	Volume : 	340.515
+	Mean local hydrophobic density : 	14.750
+	Mean alpha sphere radius :	4.083
+	Mean alp. sph. solvent access : 	0.590
+	Apolar alpha sphere proportion : 	0.516
+	Hydrophobicity score:	15.727
+	Volume score: 	 4.182
+	Polarity score:	 6
+	Charge score :	 0
+	Proportion of polar atoms: 	44.444
+	Alpha sphere density : 	3.292
+	Cent. of mass - Alpha Sphere max dist: 	8.916
+	Flexibility : 	0.730
+
+Pocket 8 :
+	Score : 	0.080
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	15
+	Total SASA : 	24.543
+	Polar SASA : 	6.429
+	Apolar SASA : 	18.114
+	Volume : 	110.939
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	3.630
+	Mean alp. sph. solvent access : 	0.358
+	Apolar alpha sphere proportion : 	0.133
+	Hydrophobicity score:	19.900
+	Volume score: 	 4.200
+	Polarity score:	 6
+	Charge score :	 0
+	Proportion of polar atoms: 	42.857
+	Alpha sphere density : 	1.666
+	Cent. of mass - Alpha Sphere max dist: 	3.746
+	Flexibility : 	0.068
+
+Pocket 9 :
+	Score : 	0.043
+	Druggability Score : 	0.009
+	Number of Alpha Spheres : 	22
+	Total SASA : 	81.162
+	Polar SASA : 	10.803
+	Apolar SASA : 	70.359
+	Volume : 	257.653
+	Mean local hydrophobic density : 	15.000
+	Mean alpha sphere radius :	3.719
+	Mean alp. sph. solvent access : 	0.435
+	Apolar alpha sphere proportion : 	0.727
+	Hydrophobicity score:	61.300
+	Volume score: 	 5.200
+	Polarity score:	 3
+	Charge score :	 0
+	Proportion of polar atoms: 	26.316
+	Alpha sphere density : 	3.360
+	Cent. of mass - Alpha Sphere max dist: 	6.916
+	Flexibility : 	0.655
+
+Pocket 10 :
+	Score : 	0.040
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	16
+	Total SASA : 	74.931
+	Polar SASA : 	39.910
+	Apolar SASA : 	35.021
+	Volume : 	253.870
+	Mean local hydrophobic density : 	6.000
+	Mean alpha sphere radius :	3.866
+	Mean alp. sph. solvent access : 	0.612
+	Apolar alpha sphere proportion : 	0.438
+	Hydrophobicity score:	9.700
+	Volume score: 	 3.500
+	Polarity score:	 5
+	Charge score :	 0
+	Proportion of polar atoms: 	42.105
+	Alpha sphere density : 	3.366
+	Cent. of mass - Alpha Sphere max dist: 	6.920
+	Flexibility : 	0.769
+
+Pocket 11 :
+	Score : 	0.033
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	16
+	Total SASA : 	59.946
+	Polar SASA : 	41.831
+	Apolar SASA : 	18.114
+	Volume : 	189.370
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.746
+	Mean alp. sph. solvent access : 	0.505
+	Apolar alpha sphere proportion : 	0.062
+	Hydrophobicity score:	-5.143
+	Volume score: 	 4.000
+	Polarity score:	 6
+	Charge score :	 1
+	Proportion of polar atoms: 	60.000
+	Alpha sphere density : 	2.650
+	Cent. of mass - Alpha Sphere max dist: 	6.451
+	Flexibility : 	0.948
+
+Pocket 12 :
+	Score : 	0.033
+	Druggability Score : 	0.295
+	Number of Alpha Spheres : 	35
+	Total SASA : 	99.895
+	Polar SASA : 	12.946
+	Apolar SASA : 	86.949
+	Volume : 	306.298
+	Mean local hydrophobic density : 	32.941
+	Mean alpha sphere radius :	3.827
+	Mean alp. sph. solvent access : 	0.450
+	Apolar alpha sphere proportion : 	0.971
+	Hydrophobicity score:	67.091
+	Volume score: 	 5.727
+	Polarity score:	 5
+	Charge score :	 0
+	Proportion of polar atoms: 	19.231
+	Alpha sphere density : 	3.327
+	Cent. of mass - Alpha Sphere max dist: 	6.862
+	Flexibility : 	0.625
+
+Pocket 13 :
+	Score : 	0.023
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	25
+	Total SASA : 	95.745
+	Polar SASA : 	55.893
+	Apolar SASA : 	39.852
+	Volume : 	418.062
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	4.066
+	Mean alp. sph. solvent access : 	0.569
+	Apolar alpha sphere proportion : 	0.080
+	Hydrophobicity score:	3.200
+	Volume score: 	 4.200
+	Polarity score:	 7
+	Charge score :	 2
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	3.596
+	Cent. of mass - Alpha Sphere max dist: 	9.100
+	Flexibility : 	0.563
+
+Pocket 14 :
+	Score : 	0.014
+	Druggability Score : 	0.006
+	Number of Alpha Spheres : 	25
+	Total SASA : 	93.954
+	Polar SASA : 	32.365
+	Apolar SASA : 	61.589
+	Volume : 	370.607
+	Mean local hydrophobic density : 	11.000
+	Mean alpha sphere radius :	4.069
+	Mean alp. sph. solvent access : 	0.617
+	Apolar alpha sphere proportion : 	0.480
+	Hydrophobicity score:	19.000
+	Volume score: 	 4.091
+	Polarity score:	 7
+	Charge score :	 2
+	Proportion of polar atoms: 	41.667
+	Alpha sphere density : 	3.378
+	Cent. of mass - Alpha Sphere max dist: 	9.735
+	Flexibility : 	0.574
+
+Pocket 15 :
+	Score : 	0.006
+	Druggability Score : 	0.009
+	Number of Alpha Spheres : 	29
+	Total SASA : 	113.512
+	Polar SASA : 	38.639
+	Apolar SASA : 	74.873
+	Volume : 	421.636
+	Mean local hydrophobic density : 	15.000
+	Mean alpha sphere radius :	4.236
+	Mean alp. sph. solvent access : 	0.683
+	Apolar alpha sphere proportion : 	0.552
+	Hydrophobicity score:	21.364
+	Volume score: 	 4.000
+	Polarity score:	 7
+	Charge score :	 2
+	Proportion of polar atoms: 	37.037
+	Alpha sphere density : 	4.007
+	Cent. of mass - Alpha Sphere max dist: 	10.728
+	Flexibility : 	0.608
+
+Pocket 16 :
+	Score : 	-0.011
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	17
+	Total SASA : 	78.643
+	Polar SASA : 	50.868
+	Apolar SASA : 	27.775
+	Volume : 	269.811
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.747
+	Mean alp. sph. solvent access : 	0.563
+	Apolar alpha sphere proportion : 	0.059
+	Hydrophobicity score:	-8.143
+	Volume score: 	 4.143
+	Polarity score:	 5
+	Charge score :	 3
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	2.899
+	Cent. of mass - Alpha Sphere max dist: 	7.698
+	Flexibility : 	0.313
+
+Pocket 17 :
+	Score : 	-0.021
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	17
+	Total SASA : 	55.726
+	Polar SASA : 	37.612
+	Apolar SASA : 	18.114
+	Volume : 	169.833
+	Mean local hydrophobic density : 	10.000
+	Mean alpha sphere radius :	3.984
+	Mean alp. sph. solvent access : 	0.501
+	Apolar alpha sphere proportion : 	0.647
+	Hydrophobicity score:	59.333
+	Volume score: 	 4.667
+	Polarity score:	 1
+	Charge score :	 1
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	1.832
+	Cent. of mass - Alpha Sphere max dist: 	3.476
+	Flexibility : 	0.595
+
+Pocket 18 :
+	Score : 	-0.086
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	18
+	Total SASA : 	90.467
+	Polar SASA : 	32.343
+	Apolar SASA : 	58.124
+	Volume : 	257.485
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	4.040
+	Mean alp. sph. solvent access : 	0.490
+	Apolar alpha sphere proportion : 	0.056
+	Hydrophobicity score:	33.300
+	Volume score: 	 4.600
+	Polarity score:	 6
+	Charge score :	 2
+	Proportion of polar atoms: 	47.368
+	Alpha sphere density : 	2.586
+	Cent. of mass - Alpha Sphere max dist: 	5.626
+	Flexibility : 	0.768
+
+Pocket 19 :
+	Score : 	-0.086
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	21
+	Total SASA : 	91.415
+	Polar SASA : 	51.563
+	Apolar SASA : 	39.852
+	Volume : 	201.650
+	Mean local hydrophobic density : 	2.000
+	Mean alpha sphere radius :	3.840
+	Mean alp. sph. solvent access : 	0.453
+	Apolar alpha sphere proportion : 	0.143
+	Hydrophobicity score:	29.125
+	Volume score: 	 5.250
+	Polarity score:	 4
+	Charge score :	 1
+	Proportion of polar atoms: 	53.333
+	Alpha sphere density : 	2.483
+	Cent. of mass - Alpha Sphere max dist: 	6.556
+	Flexibility : 	0.556
+
--- a/tests/reference_output/1ATP_out/1ATP_out.pdb
+++ b/tests/reference_output/1ATP_out/1ATP_out.pdb
--- a/tests/reference_output/1ATP_out/1ATP_pockets.pqr
+++ b/tests/reference_output/1ATP_out/1ATP_pockets.pqr
@@ -0,0 +1,511 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It contains all the pocket vertices found by fpocket.                    
+ATOM      1    O STP     1      12.696  10.125   0.572    0.00     4.14
+ATOM      2    O STP     1      12.658  10.336   0.615    0.00     4.11
+ATOM      3    O STP     1      15.748   7.295   2.281    0.00     3.68
+ATOM      4    O STP     1      15.893   7.629   1.836    0.00     3.66
+ATOM      5    O STP     1      15.737   7.221   2.651    0.00     3.60
+ATOM      6    O STP     1      15.587   7.185   2.383    0.00     3.71
+ATOM      7    O STP     1      15.560   7.162   2.428    0.00     3.71
+ATOM      8    O STP     1      15.411   6.698   2.817    0.00     3.53
+ATOM      9    O STP     1      16.502   8.143  -0.698    0.00     3.61
+ATOM     10    O STP     1      16.245   8.195  -0.256    0.00     3.63
+ATOM     11    O STP     1      16.747   8.027   0.402    0.00     3.47
+ATOM     12    C STP     1       8.391   9.917   4.429    0.00     4.28
+ATOM     13    C STP     1       4.608   9.454   4.528    0.00     3.57
+ATOM     14    O STP     1      12.160   9.989   0.796    0.00     4.32
+ATOM     15    C STP     1       8.419   9.736   3.826    0.00     4.26
+ATOM     16    O STP     1      11.311   9.970   2.834    0.00     3.98
+ATOM     17    O STP     1      10.943   9.949   3.228    0.00     3.99
+ATOM     18    O STP     1       3.964  10.063   4.903    0.00     3.40
+ATOM     19    O STP     1       4.493   9.803   4.348    0.00     3.80
+ATOM     20    O STP     1       8.901   9.248   5.088    0.00     4.03
+ATOM     21    C STP     1       7.945   9.977   4.425    0.00     4.13
+ATOM     22    C STP     1       5.641  10.208   4.133    0.00     4.05
+ATOM     23    C STP     1       5.137   9.948   4.335    0.00     3.86
+ATOM     24    C STP     1       5.973  10.461   4.440    0.00     3.84
+ATOM     25    C STP     1       5.539  10.237   4.137    0.00     4.07
+ATOM     26    C STP     1       5.166  10.162   4.234    0.00     4.02
+ATOM     27    C STP     1       4.419  10.241   4.427    0.00     3.84
+ATOM     28    C STP     1       4.642  10.149   4.193    0.00     4.03
+ATOM     29    O STP     1      15.028  10.431  -1.579    0.00     3.70
+ATOM     30    O STP     1      15.448   9.997  -1.468    0.00     3.58
+ATOM     31    O STP     1      11.920  10.913   2.425    0.00     3.54
+ATOM     32    O STP     1      12.555  10.431   0.673    0.00     4.12
+ATOM     33    O STP     1      12.398  10.456   0.747    0.00     4.16
+ATOM     34    O STP     1      12.462  10.651   0.708    0.00     4.10
+ATOM     35    O STP     1      13.408  11.474  -0.038    0.00     3.58
+ATOM     36    O STP     1      12.575  11.875   1.278    0.00     3.48
+ATOM     37    O STP     1      12.622  11.440   0.498    0.00     3.84
+ATOM     38    O STP     1      12.543  11.701   0.360    0.00     3.70
+ATOM     39    O STP     1      10.964   9.954   3.310    0.00     3.93
+ATOM     40    O STP     1      10.084   9.342   3.463    0.00     4.37
+ATOM     41    C STP     1      10.913   9.938   3.249    0.00     3.99
+ATOM     42    C STP     1       8.417   9.911   4.438    0.00     4.29
+ATOM     43    O STP     1       8.933   9.304   4.971    0.00     4.09
+ATOM     44    C STP     1       9.300   9.308   3.778    0.00     4.49
+ATOM     45    C STP     1       8.797   9.677   4.062    0.00     4.37
+ATOM     46    C STP     1       8.647   9.616   4.763    0.00     4.15
+ATOM     47    C STP     1       8.438   9.899   4.628    0.00     4.19
+ATOM     48    C STP     1       8.422   9.882   4.527    0.00     4.26
+ATOM     49    C STP     1       8.477  10.165   4.509    0.00     4.09
+ATOM     50    O STP     1       8.499  10.142   4.794    0.00     3.94
+ATOM     51    O STP     1       8.496  10.107   4.758    0.00     3.98
+ATOM     52    O STP     1      16.898   7.905   0.868    0.00     3.45
+ATOM     53    O STP     1      16.869   7.884   0.943    0.00     3.45
+ATOM     54    C STP     1       4.361  10.400   4.200    0.00     3.83
+ATOM     55    O STP     1       3.879   9.828   2.663    0.00     3.61
+ATOM     56    C STP     1       5.222  10.328   3.927    0.00     4.06
+ATOM     57    C STP     1       4.638  10.187   4.121    0.00     4.04
+ATOM     58    O STP     1      16.512   8.151  -0.730    0.00     3.61
+ATOM     59    O STP     1      16.501   8.709  -1.584    0.00     3.53
+ATOM     60    O STP     1      16.508   8.126  -0.728    0.00     3.60
+ATOM     61    C STP     1       7.098  10.540   1.083    0.00     3.54
+ATOM     62    C STP     1       5.770  10.197   1.723    0.00     3.89
+ATOM     63    C STP     1       5.664  10.226   1.757    0.00     3.89
+ATOM     64    C STP     1       4.772   9.928   1.248    0.00     3.76
+ATOM     65    O STP     1      11.132   9.536   0.429    0.00     4.22
+ATOM     66    O STP     1      10.011   9.555  -0.632    0.00     3.74
+ATOM     67    O STP     1      11.311   9.372  -0.515    0.00     3.48
+ATOM     68    O STP     1      14.016  11.694  -0.593    0.00     3.44
+ATOM     69    O STP     1       9.627  10.169  -0.589    0.00     3.72
+ATOM     70    C STP     1       8.473  10.880  -0.785    0.00     3.42
+ATOM     71    C STP     1       4.769   9.927   1.247    0.00     3.76
+ATOM     72    C STP     1       4.412   9.621   0.996    0.00     3.65
+ATOM     73    C STP     1       4.769   9.927   1.247    0.00     3.76
+ATOM     74    C STP     1       4.289   9.742   1.121    0.00     3.73
+ATOM     75    C STP     1       4.327   9.797   1.169    0.00     3.75
+ATOM     76    O STP     1      15.472  10.546  -1.499    0.00     3.45
+ATOM     77    O STP     1      15.057  10.749  -1.594    0.00     3.65
+ATOM     78    O STP     1      14.976  11.017  -1.509    0.00     3.58
+ATOM     79    O STP     1      15.047  11.161  -1.927    0.00     3.45
+ATOM     80    O STP     1       9.031   8.924   6.153    0.00     3.46
+ATOM     81    O STP     1      14.459   6.786   2.374    0.00     3.55
+ATOM     82    O STP     1      14.767   7.308   1.990    0.00     3.77
+ATOM     83    O STP     1      11.581   9.247   1.361    0.00     4.54
+ATOM     84    O STP     1      11.373   9.098   1.697    0.00     4.57
+ATOM     85    O STP     1      14.886   7.436   1.738    0.00     3.79
+ATOM     86    O STP     1      14.831   7.840   1.220    0.00     3.82
+ATOM     87    O STP     1      14.929   7.783   1.201    0.00     3.83
+ATOM     88    O STP     1      14.927   7.767   1.259    0.00     3.84
+ATOM     89    C STP     1       8.772   8.499   5.722    0.00     3.51
+ATOM     90    O STP     1      10.096   9.193   3.267    0.00     4.42
+ATOM     91    O STP     1      11.325   9.075   1.723    0.00     4.57
+ATOM     92    O STP     1      11.202   9.037   1.672    0.00     4.55
+ATOM     93    C STP     1      11.147   9.165   1.033    0.00     4.44
+ATOM     94    O STP     1      11.183   9.143   1.108    0.00     4.47
+ATOM     95    O STP     1      11.164   9.093   1.052    0.00     4.42
+ATOM     96    O STP     1      10.152   9.628  -0.115    0.00     4.02
+ATOM     97    O STP     1      10.159   9.604  -0.140    0.00     4.01
+ATOM     98    C STP     1      10.214   9.605  -0.074    0.00     4.04
+ATOM     99    O STP     1       9.953   9.182  -0.393    0.00     3.60
+ATOM    100    C STP     1       6.802   9.905   1.993    0.00     3.86
+ATOM    101    C STP     1       7.362  10.012   1.775    0.00     3.78
+ATOM    102    C STP     1       7.845   9.601   3.100    0.00     4.13
+ATOM    103    C STP     1       8.025   9.593   3.157    0.00     4.18
+ATOM    104    C STP     1       9.377   9.170   3.567    0.00     4.51
+ATOM    105    O STP     1       9.399   8.934   3.561    0.00     4.38
+ATOM    106    O STP     1       9.649   9.131   3.392    0.00     4.48
+ATOM    107    O STP     2      17.904  16.846   2.034    0.00     4.00
+ATOM    108    C STP     2      13.212  24.010  -0.223    0.00     3.56
+ATOM    109    O STP     2      13.590  24.333  -0.124    0.00     3.66
+ATOM    110    C STP     2      16.767  18.684   1.078    0.00     4.22
+ATOM    111    C STP     2      16.715  18.704   1.057    0.00     4.20
+ATOM    112    O STP     2      17.342  17.855   1.830    0.00     4.24
+ATOM    113    O STP     2      17.041  17.846   1.980    0.00     4.08
+ATOM    114    O STP     2      16.580  19.060   0.747    0.00     4.27
+ATOM    115    O STP     2      17.635  17.024   1.403    0.00     3.80
+ATOM    116    O STP     2      17.395  17.419   1.401    0.00     3.89
+ATOM    117    C STP     2      16.900  18.376   1.091    0.00     4.07
+ATOM    118    O STP     2      17.782  16.444   1.256    0.00     3.57
+ATOM    119    O STP     2      14.632  22.244  -1.461    0.00     3.60
+ATOM    120    O STP     2      14.379  23.675  -0.187    0.00     4.18
+ATOM    121    O STP     2      14.950  20.959  -0.498    0.00     4.03
+ATOM    122    O STP     2      16.062  19.544  -0.072    0.00     4.25
+ATOM    123    O STP     2      16.188  19.842  -0.177    0.00     4.42
+ATOM    124    C STP     2      16.044  18.633   0.739    0.00     3.73
+ATOM    125    O STP     2      15.502  19.054  -0.011    0.00     3.68
+ATOM    126    C STP     3       5.666  -2.347   9.650    0.00     3.64
+ATOM    127    C STP     3       5.663  -2.342   9.659    0.00     3.64
+ATOM    128    C STP     3       4.857  -3.237  11.687    0.00     3.51
+ATOM    129    C STP     3       4.909  -3.421  12.179    0.00     3.52
+ATOM    130    C STP     3       4.463  -1.923  10.602    0.00     3.52
+ATOM    131    C STP     3       4.751  -3.640  11.929    0.00     3.49
+ATOM    132    C STP     3       4.816  -3.657  12.202    0.00     3.51
+ATOM    133    C STP     3       5.643  -2.334   9.598    0.00     3.62
+ATOM    134    C STP     3       5.573  -2.273   9.693    0.00     3.63
+ATOM    135    C STP     3       5.625  -2.300   9.658    0.00     3.64
+ATOM    136    C STP     3       5.618  -2.250   9.664    0.00     3.62
+ATOM    137    C STP     3       4.669  -1.977  10.488    0.00     3.53
+ATOM    138    C STP     3       4.819  -1.860  10.403    0.00     3.43
+ATOM    139    C STP     3       4.472  -1.924  10.605    0.00     3.53
+ATOM    140    C STP     3       4.423  -1.750  10.637    0.00     3.43
+ATOM    141    C STP     3       4.474  -1.928  10.609    0.00     3.53
+ATOM    142    C STP     3       4.552  -2.069  10.740    0.00     3.51
+ATOM    143    C STP     3       4.780  -3.687  12.261    0.00     3.48
+ATOM    144    O STP     4      10.707   8.465   9.562    0.00     3.56
+ATOM    145    O STP     4      11.897   7.600  10.387    0.00     3.53
+ATOM    146    O STP     4      11.713   7.651  10.429    0.00     3.61
+ATOM    147    O STP     4      11.722   7.673  10.440    0.00     3.59
+ATOM    148    O STP     4      11.706   7.635  10.442    0.00     3.60
+ATOM    149    O STP     4      13.057   5.577  11.209    0.00     3.45
+ATOM    150    C STP     4      13.599   4.782  12.622    0.00     3.56
+ATOM    151    O STP     4      12.926   5.521  11.298    0.00     3.49
+ATOM    152    O STP     4      11.593   6.620  11.138    0.00     3.56
+ATOM    153    O STP     4      11.150   6.837  11.229    0.00     3.58
+ATOM    154    O STP     4      11.203   6.847  11.061    0.00     3.66
+ATOM    155    O STP     4      10.100   6.854  10.639    0.00     3.72
+ATOM    156    O STP     4      10.043   6.829  10.609    0.00     3.72
+ATOM    157    O STP     4      10.008   6.832  11.002    0.00     3.55
+ATOM    158    O STP     4       9.996   6.814  10.721    0.00     3.65
+ATOM    159    O STP     4      14.136   3.921  15.176    0.00     4.64
+ATOM    160    O STP     4      13.450   4.065  15.198    0.00     4.27
+ATOM    161    O STP     4      14.349   4.009  14.805    0.00     4.61
+ATOM    162    O STP     4      13.844   4.358  14.153    0.00     4.07
+ATOM    163    C STP     4      14.400   4.002  14.664    0.00     4.57
+ATOM    164    C STP     4      13.873   4.433  13.491    0.00     3.88
+ATOM    165    C STP     4      13.578   4.355  12.749    0.00     3.43
+ATOM    166    O STP     4       9.524   6.563  10.325    0.00     3.47
+ATOM    167    C STP     4       9.327   7.050  10.077    0.00     3.46
+ATOM    168    O STP     4      10.903   8.245   9.723    0.00     3.55
+ATOM    169    O STP     4      11.424   7.798  10.169    0.00     3.58
+ATOM    170    O STP     4      10.102   6.908  10.584    0.00     3.71
+ATOM    171    O STP     4      10.425   8.337   9.557    0.00     3.58
+ATOM    172    O STP     4      10.324   8.322   9.469    0.00     3.54
+ATOM    173    O STP     4      10.351   8.314   9.560    0.00     3.59
+ATOM    174    C STP     4      10.082   7.855   9.856    0.00     3.56
+ATOM    175    C STP     4       9.763   7.428   9.952    0.00     3.52
+ATOM    176    C STP     4       9.808   6.869  10.405    0.00     3.64
+ATOM    177    O STP     4      10.016   6.824  10.586    0.00     3.71
+ATOM    178    O STP     4       9.960   6.815  10.553    0.00     3.70
+ATOM    179    O STP     4       9.895   6.462  10.350    0.00     3.45
+ATOM    180    O STP     4       9.826   6.743  10.451    0.00     3.64
+ATOM    181    O STP     5      -3.903   9.091  -8.804    0.00     4.57
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+ATOM    183    O STP     5      -2.044   6.009  -7.092    0.00     3.61
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+ATOM    187    O STP     5      -3.701   8.983  -8.573    0.00     4.49
+ATOM    188    O STP     5      -3.246   8.932  -8.467    0.00     4.30
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+ATOM    191    O STP     5      -1.924   8.885  -8.753    0.00     3.78
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+ATOM    193    O STP     5      -1.773   5.141  -7.052    0.00     3.64
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+ATOM    195    O STP     5      -1.491   5.021  -7.121    0.00     3.59
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+ATOM    201    O STP     5      -1.038   7.720  -7.892    0.00     3.49
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+ATOM    204    C STP     6      17.140  -3.037  -7.495    0.00     3.70
+ATOM    205    C STP     6      17.287  -2.942  -7.558    0.00     3.71
+ATOM    206    O STP     6      15.862  -3.114  -6.582    0.00     3.49
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+ATOM    210    O STP     6      18.178  -1.260  -4.556    0.00     3.40
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+ATOM    226    C STP     7      -3.506 -14.247   3.643    0.00     3.79
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+ATOM    247    C STP     7      -1.682 -14.732   5.030    0.00     4.49
+ATOM    248    C STP     7      -1.616 -13.199   5.185    0.00     4.27
+ATOM    249    C STP     7      -1.612 -13.209   5.227    0.00     4.28
+ATOM    250    C STP     7      -1.726 -13.041   5.798    0.00     4.17
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+ATOM    255    O STP     8      14.467  10.370  -5.296    0.00     3.44
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+ATOM    258    O STP     8      15.660  11.576  -7.445    0.00     3.87
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+ATOM    263    O STP     8      15.544  11.122  -7.297    0.00     3.82
+ATOM    264    O STP     8      15.979  10.444  -7.233    0.00     3.55
+ATOM    265    C STP     8      15.792  10.270  -7.031    0.00     3.50
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+ATOM    268    C STP     9       4.374  24.558   2.469    0.00     3.55
+ATOM    269    C STP     9       6.248  22.839   2.662    0.00     3.65
+ATOM    270    C STP     9       6.687  23.325   2.417    0.00     3.80
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+ATOM    274    C STP     9       6.777  25.942   2.510    0.00     3.88
+ATOM    275    O STP     9       3.851  24.675   2.332    0.00     3.51
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+ATOM    283    C STP     9       7.637  23.976   0.562    0.00     3.48
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+ATOM    409    C STP    15      18.817 -14.364  15.540    0.00     4.62
+ATOM    410    C STP    15      15.023 -10.073  17.441    0.00     4.26
+ATOM    411    C STP    15      15.741 -10.998  17.957    0.00     4.63
+ATOM    412    O STP    15      20.585 -16.489  14.223    0.00     4.09
+ATOM    413    O STP    15      19.415 -15.607  15.364    0.00     4.66
+ATOM    414    C STP    15      15.015 -10.071  17.451    0.00     4.26
+ATOM    415    C STP    15      14.777 -10.089  16.406    0.00     3.47
+ATOM    416    C STP    15      14.855 -10.051  17.251    0.00     4.06
+ATOM    417    O STP    15      13.277  -9.665  17.514    0.00     3.56
+ATOM    418    C STP    15      14.805 -10.108  17.922    0.00     4.49
+ATOM    419    O STP    15      18.495 -14.244  14.923    0.00     4.22
+ATOM    420    O STP    15      18.480 -14.689  14.307    0.00     3.84
+ATOM    421    C STP    15      18.270 -13.858  15.512    0.00     4.47
+ATOM    422    C STP    15      15.741 -10.998  17.957    0.00     4.63
+ATOM    423    C STP    15      15.742 -10.997  17.953    0.00     4.62
+ATOM    424    C STP    15      15.760 -10.982  17.951    0.00     4.60
+ATOM    425    C STP    15      16.138 -10.636  17.830    0.00     4.10
+ATOM    426    C STP    15      16.014 -10.748  17.869    0.00     4.26
+ATOM    427    O STP    15      17.979 -13.868  13.441    0.00     3.43
+ATOM    428    O STP    15      18.105 -13.657  15.491    0.00     4.41
+ATOM    429    O STP    15      17.165 -13.262  16.453    0.00     4.67
+ATOM    430    O STP    15      15.637 -10.294  15.930    0.00     3.65
+ATOM    431    C STP    15      16.936 -12.523  16.560    0.00     4.44
+ATOM    432    C STP    15      17.083 -12.356  16.365    0.00     4.23
+ATOM    433    C STP    15      16.850 -12.331  16.545    0.00     4.35
+ATOM    434    O STP    16      21.605   9.274   6.445    0.00     3.95
+ATOM    435    O STP    16      23.052   4.027   8.218    0.00     3.68
+ATOM    436    O STP    16      20.037  10.202   7.733    0.00     4.60
+ATOM    437    O STP    16      22.942   3.882   8.664    0.00     3.49
+ATOM    438    O STP    16      22.985   4.910   9.082    0.00     3.75
+ATOM    439    O STP    16      22.778   4.706   8.980    0.00     3.57
+ATOM    440    O STP    16      22.932   4.338   8.689    0.00     3.66
+ATOM    441    O STP    16      22.819   4.391   8.749    0.00     3.58
+ATOM    442    O STP    16      22.943   3.580   7.482    0.00     3.63
+ATOM    443    O STP    16      22.800   7.841   5.222    0.00     3.89
+ATOM    444    C STP    16      23.308   3.741   7.149    0.00     3.81
+ATOM    445    O STP    16      23.140   5.515   5.119    0.00     3.59
+ATOM    446    O STP    16      22.972   4.082   6.110    0.00     3.44
+ATOM    447    O STP    16      23.254   3.825   6.901    0.00     3.72
+ATOM    448    O STP    16      23.595   4.080   7.336    0.00     3.93
+ATOM    449    O STP    16      24.143   3.706   7.296    0.00     3.56
+ATOM    450    O STP    16      23.426   3.868   7.200    0.00     3.86
+ATOM    451    C STP    17      20.079 -17.759  -0.802    0.00     3.67
+ATOM    452    O STP    17      21.058 -19.186  -2.154    0.00     3.88
+ATOM    453    O STP    17      22.470 -19.926  -1.235    0.00     4.53
+ATOM    454    O STP    17      22.448 -20.166  -0.692    0.00     4.42
+ATOM    455    C STP    17      21.929 -20.012  -0.119    0.00     4.06
+ATOM    456    O STP    17      21.994 -20.327   0.005    0.00     4.04
+ATOM    457    C STP    17      22.152 -19.454  -1.681    0.00     4.50
+ATOM    458    O STP    17      22.110 -19.403  -1.774    0.00     4.50
+ATOM    459    C STP    17      20.135 -17.782  -0.862    0.00     3.68
+ATOM    460    C STP    17      20.333 -17.868  -1.159    0.00     3.71
+ATOM    461    O STP    17      22.730 -19.052  -1.278    0.00     3.92
+ATOM    462    C STP    17      21.017 -18.682  -1.343    0.00     4.01
+ATOM    463    C STP    17      21.042 -18.693  -1.380    0.00     4.03
+ATOM    464    C STP    17      20.540 -18.564  -0.766    0.00     3.77
+ATOM    465    C STP    17      21.084 -19.267  -0.227    0.00     3.70
+ATOM    466    C STP    17      20.059 -17.765  -0.768    0.00     3.67
+ATOM    467    C STP    17      20.019 -17.679  -0.714    0.00     3.63
+ATOM    468    O STP    18      23.290   7.625 -10.006    0.00     3.65
+ATOM    469    O STP    18      21.998   7.158  -8.997    0.00     3.42
+ATOM    470    O STP    18      21.767   7.080  -9.018    0.00     3.44
+ATOM    471    O STP    18      24.354   9.432 -11.111    0.00     3.89
+ATOM    472    O STP    18      24.924  10.086 -10.852    0.00     3.50
+ATOM    473    O STP    18      24.124   8.241 -11.073    0.00     4.17
+ATOM    474    O STP    18      23.599   7.744 -10.504    0.00     3.89
+ATOM    475    O STP    18      25.034   7.815 -11.334    0.00     4.30
+ATOM    476    O STP    18      24.595   7.493 -10.910    0.00     4.00
+ATOM    477    O STP    18      24.583   8.688 -11.745    0.00     4.51
+ATOM    478    O STP    18      24.433   8.715 -11.668    0.00     4.47
+ATOM    479    O STP    18      24.019   8.832 -11.950    0.00     4.30
+ATOM    480    O STP    18      22.801   8.729 -12.139    0.00     3.77
+ATOM    481    O STP    18      22.207   7.260 -10.194    0.00     3.50
+ATOM    482    C STP    18      24.752   8.793 -13.468    0.00     4.56
+ATOM    483    O STP    18      26.139   6.551 -11.712    0.00     4.46
+ATOM    484    O STP    18      26.177   6.535 -11.779    0.00     4.47
+ATOM    485    O STP    18      26.104   6.506 -11.714    0.00     4.41
+ATOM    486    O STP    19      23.996 -17.991  11.091    0.00     4.35
+ATOM    487    C STP    19      24.960 -14.038   8.738    0.00     3.95
+ATOM    488    O STP    19      22.931 -16.813  10.494    0.00     3.98
+ATOM    489    O STP    19      23.730 -14.416   9.050    0.00     3.79
+ATOM    490    O STP    19      23.534 -14.640   9.195    0.00     3.74
+ATOM    491    O STP    19      23.541 -14.438   9.194    0.00     3.71
+ATOM    492    O STP    19      23.319 -13.996   9.166    0.00     3.47
+ATOM    493    O STP    19      23.506 -14.658   9.215    0.00     3.73
+ATOM    494    O STP    19      22.772 -16.806  10.680    0.00     3.95
+ATOM    495    O STP    19      23.478 -14.756   9.266    0.00     3.71
+ATOM    496    O STP    19      22.867 -16.689  10.427    0.00     3.96
+ATOM    497    O STP    19      22.668 -16.487  10.105    0.00     3.79
+ATOM    498    O STP    19      22.623 -16.471  10.089    0.00     3.76
+ATOM    499    O STP    19      22.761 -16.808  10.687    0.00     3.94
+ATOM    500    O STP    19      24.040 -13.911   7.306    0.00     3.54
+ATOM    501    C STP    19      24.558 -13.610   8.244    0.00     4.08
+ATOM    502    O STP    19      24.402 -13.618   8.240    0.00     4.06
+ATOM    503    O STP    19      23.982 -13.022   8.288    0.00     3.77
+ATOM    504    C STP    19      24.023 -12.020   8.383    0.00     3.50
+ATOM    505    O STP    19      22.709 -16.865  10.854    0.00     3.94
+ATOM    506    O STP    19      22.701 -16.860  10.841    0.00     3.93
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket10_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket10_atm.pdb
@@ -0,0 +1,41 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    10:
+HEADER 0  - Pocket Score                      : 0.0405
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of alpha spheres           :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8663
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6124
+HEADER 5  - Mean B-factor of pocket residues  : 0.7690
+HEADER 6  - Hydrophobicity Score              : 9.7000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 3.5000
+HEADER 9  - Pocket volume (Monte Carlo)       : 253.8700
+HEADER 10  -Pocket volume (convex hull)       : 12.1248
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 6.0000
+HEADER 13 - Number of apolar alpha sphere     :     7
+HEADER 14 - Proportion of apolar alpha sphere : 0.4375
+ATOM    434  CD2 HIS E  68      -4.370  16.956   8.208  0.00  0.00           C 0
+ATOM    418    O GLY E  66      -7.767  19.132   6.362  0.14  7.50           O 0
+ATOM    425  OD1 ASN E  67      -8.955  16.520   3.549  0.00  0.00           O 0
+ATOM   2530   CB PRO E 321      -6.517  14.426  10.771  0.00  0.00           C 0
+ATOM    427    N HIS E  68      -4.661  17.016   4.850  0.00  0.00           N 0
+ATOM    431   CB HIS E  68      -2.770  16.341   6.300  0.00  0.00           C 0
+ATOM    430    O HIS E  68      -3.452  15.333   3.304  0.00  0.00           O 0
+ATOM    420   CA ASN E  67      -6.657  18.056   4.121  0.00  0.00           C 0
+ATOM   2533    N GLY E 322      -3.195  14.519  11.020  0.00  0.00           N 0
+ATOM    891  CD2 TYR E 122      -0.618  12.346   7.159  0.00  0.00           C 0
+ATOM   2512   CZ PHE E 318      -4.685  10.281  11.468  0.00  0.00           C 0
+ATOM   2527   CA PRO E 321      -5.396  13.768  11.582  0.00  0.00           C 0
+ATOM    884    N TYR E 122      -0.887  11.623   2.511  0.00  0.00           N 0
+ATOM    887    O TYR E 122      -1.382   9.668   4.729  0.42  5.36           O 0
+ATOM    880   CG GLU E 121      -3.212   9.733   0.513  0.00  0.00           C 0
+ATOM    888   CB TYR E 122      -0.420  12.529   4.688  0.00  0.00           C 0
+ATOM   1344  NE2 GLN E 176      -5.655   7.996   8.723  0.00  0.00           N 0
+ATOM    907   CB ALA E 124      -0.748   8.672   9.338  0.00  0.00           C 0
+ATOM   2511  CE2 PHE E 318      -3.352  10.649  11.639  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket10_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket10_vert.pqr
@@ -0,0 +1,38 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    10:
+HEADER 0  - Pocket Score                      : 0.0405
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of V. Vertices             :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8663
+HEADER 4  - Mean alpha-sphere SA              : 0.6124
+HEADER 5  - Mean B-factor                     : 0.7690
+HEADER 6  - Hydrophobicity Score              : 9.7000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 3.5000
+HEADER 9  - Real volume (approximation)       : 253.8700
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 6.0000
+HEADER 12 - Number of apolar alpha sphere     :     7
+HEADER 13 - Proportion of apolar alpha sphere : 0.4375
+ATOM      1    O STP    10      -7.764  15.242   7.103    0.00     3.96
+ATOM      2    C STP    10      -5.783  13.019   6.568    0.00     4.49
+ATOM      3    O STP    10      -5.788  12.752   6.449    0.00     4.69
+ATOM      4    O STP    10      -7.309  14.474   6.726    0.00     4.12
+ATOM      5    O STP    10      -7.432  15.466   6.755    0.00     3.70
+ATOM      6    O STP    10      -7.395  15.658   6.560    0.00     3.50
+ATOM      7    C STP    10      -4.485  12.252   8.033    0.00     3.97
+ATOM      8    C STP    10      -4.567  13.020   7.587    0.00     3.99
+ATOM      9    C STP    10      -4.565  12.978   7.571    0.00     4.02
+ATOM     10    O STP    10      -4.654  11.597   3.673    0.00     3.94
+ATOM     11    O STP    10      -3.791  12.064   4.278    0.00     3.43
+ATOM     12    O STP    10      -4.242  12.235   5.610    0.00     3.94
+ATOM     13    O STP    10      -3.273  10.191   7.558    0.00     3.44
+ATOM     14    C STP    10      -4.073  12.143   8.369    0.00     3.67
+ATOM     15    C STP    10      -3.693  10.881   8.123    0.00     3.54
+ATOM     16    C STP    10      -3.402  10.565   8.181    0.00     3.46
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket11_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket11_atm.pdb
@@ -0,0 +1,37 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    11:
+HEADER 0  - Pocket Score                      : 0.0334
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.7458
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5051
+HEADER 5  - Mean B-factor of pocket residues  : 0.9475
+HEADER 6  - Hydrophobicity Score              : -5.1429
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 189.3697
+HEADER 10  -Pocket volume (convex hull)       : 4.4609
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     1
+HEADER 14 - Proportion of apolar alpha sphere : 0.0625
+ATOM   2662    C VAL E 337      13.234  31.795  -3.685  0.00  0.00           C 0
+HETATM 2667    N SEP E 338      13.942  31.735  -4.796  0.00  0.00           N 0
+ATOM   2653   CB ARG E 336      14.890  29.572   0.417  0.00  0.00           C 0
+ATOM   2652    O ARG E 336      14.020  28.429  -2.226  0.67  4.29           O 0
+ATOM   2663    O VAL E 337      13.186  32.790  -2.978  0.67  4.29           O 0
+HETATM 2674  O1P SEP E 338      18.260  33.001  -4.713  0.00  0.00           O 0
+ATOM    511  OE1 GLN E  77      21.116  27.144  -6.918  0.74  4.29           O 0
+ATOM   2707   CG LYS E 342      18.487  28.736  -9.104  0.00  0.00           C 0
+ATOM    822   CB SER E 114      14.315  27.704  -5.595  0.00  0.00           C 0
+ATOM   2710   NZ LYS E 342      20.125  30.313  -7.353  0.64  2.19           N 0
+ATOM    494  OD2 ASP E  75      17.923  24.273  -3.807  0.00  0.00           O 0
+ATOM    823   OG SER E 114      14.411  29.102  -5.655  0.64  2.14           O 0
+HETATM 2669   CB SEP E 338      15.948  32.307  -6.020  0.00  0.00           C 0
+ATOM    509   CG GLN E  77      20.051  25.351  -8.083  0.00  0.00           C 0
+ATOM    821    O SER E 114      14.639  24.948  -6.617  0.00  0.00           O 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket11_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket11_vert.pqr
@@ -0,0 +1,38 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    11:
+HEADER 0  - Pocket Score                      : 0.0334
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.7458
+HEADER 4  - Mean alpha-sphere SA              : 0.5051
+HEADER 5  - Mean B-factor                     : 0.9475
+HEADER 6  - Hydrophobicity Score              : -5.1429
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 189.3697
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     1
+HEADER 13 - Proportion of apolar alpha sphere : 0.0625
+ATOM      1    O STP    11      16.399  30.997  -2.408    0.00     3.51
+ATOM      2    O STP    11      16.378  31.564  -2.092    0.00     3.53
+ATOM      3    O STP    11      16.438  31.064  -2.387    0.00     3.53
+ATOM      4    O STP    11      17.895  28.085  -5.613    0.00     3.60
+ATOM      5    O STP    11      18.864  28.710  -3.265    0.00     4.57
+ATOM      6    O STP    11      17.852  28.163  -5.642    0.00     3.57
+ATOM      7    O STP    11      17.748  28.256  -3.638    0.00     3.99
+ATOM      8    O STP    11      18.340  28.694  -3.618    0.00     4.44
+ATOM      9    O STP    11      17.987  28.173  -5.180    0.00     3.72
+ATOM     10    O STP    11      18.227  28.380  -4.224    0.00     4.14
+ATOM     11    O STP    11      18.119  28.193  -4.507    0.00     3.99
+ATOM     12    O STP    11      16.692  30.260  -3.367    0.00     3.43
+ATOM     13    O STP    11      17.772  29.567  -4.909    0.00     3.47
+ATOM     14    C STP    11      17.710  27.065  -6.133    0.00     3.50
+ATOM     15    O STP    11      17.725  26.987  -6.025    0.00     3.51
+ATOM     16    O STP    11      17.545  26.715  -6.183    0.00     3.43
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket12_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket12_atm.pdb
@@ -0,0 +1,48 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    12:
+HEADER 0  - Pocket Score                      : 0.0331
+HEADER 1  - Drug Score                        : 0.2947
+HEADER 2  - Number of alpha spheres           :    35
+HEADER 3  - Mean alpha-sphere radius          : 3.8268
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4500
+HEADER 5  - Mean B-factor of pocket residues  : 0.6250
+HEADER 6  - Hydrophobicity Score              : 67.0909
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 5.7273
+HEADER 9  - Pocket volume (Monte Carlo)       : 306.2977
+HEADER 10  -Pocket volume (convex hull)       : 41.6134
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 32.9412
+HEADER 13 - Number of apolar alpha sphere     :    34
+HEADER 14 - Proportion of apolar alpha sphere : 0.9714
+ATOM    705   CZ PHE E 100      -1.744  -4.441  -7.799  0.00  0.00           C 0
+ATOM   1162  OE1 GLU E 155       0.157 -10.157 -10.045  0.84  5.36           O 0
+ATOM   1136  CD2 LEU E 152      -0.761 -10.147  -6.178  0.00  0.00           C 0
+ATOM   2405  CD2 TYR E 306      -5.142  -5.791  -6.300  0.00  0.00           C 0
+ATOM      7  CG2 VAL E  15      -4.494 -11.830 -11.149  0.00  0.00           C 0
+ATOM      6  CG1 VAL E  15      -2.823 -11.529 -12.987  0.00  0.00           C 0
+ATOM     43  CD1 LEU E  19      -2.165  -6.192 -13.498  0.00  0.00           C 0
+ATOM   2367   CB TRP E 302      -3.282 -13.838  -4.682  0.00  0.00           C 0
+ATOM   2283   NZ LYS E 292      -0.453 -12.979  -9.642  0.76  4.37           N 0
+ATOM   2366    O TRP E 302      -4.842 -11.031  -3.546  0.89  1.07           O 0
+ATOM     33  CD2 PHE E  18      -5.291  -5.668 -12.107  0.00  0.00           C 0
+ATOM    703  CE1 PHE E 100      -2.348  -3.750  -8.845  0.00  0.00           C 0
+ATOM   2403   CG TYR E 306      -6.064  -6.651  -5.700  0.00  0.00           C 0
+ATOM   2404  CD1 TYR E 306      -7.425  -6.424  -5.901  0.00  0.00           C 0
+ATOM   1133   CB LEU E 152      -0.075  -7.803  -5.686  0.00  0.00           C 0
+ATOM   2402   CB TYR E 306      -5.635  -7.781  -4.831  0.00  0.00           C 0
+ATOM     30   CB PHE E  18      -6.759  -7.267 -13.392  0.00  0.00           C 0
+ATOM      1    N VAL E  15      -6.512 -12.177 -13.595  0.00  0.00           N 0
+ATOM      2   CA VAL E  15      -5.276 -11.431 -13.476  0.00  0.00           C 0
+ATOM   2408   CZ TYR E 306      -6.937  -4.519  -7.289  0.00  0.00           C 0
+ATOM   2406  CE1 TYR E 306      -7.867  -5.363  -6.689  0.00  0.00           C 0
+ATOM   1132    O LEU E 152       1.330  -6.256  -8.054  0.66  2.14           O 0
+ATOM   1168   CB TYR E 156       0.836  -4.064 -10.536  0.00  0.00           C 0
+ATOM   2365    C TRP E 302      -5.058 -12.250  -3.632  0.00  0.00           C 0
+ATOM   2382  CG1 ILE E 303      -7.953 -13.342  -6.092  0.00  0.00           C 0
+ATOM     31   CG PHE E  18      -6.523  -5.962 -12.692  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket12_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket12_vert.pqr
@@ -0,0 +1,57 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    12:
+HEADER 0  - Pocket Score                      : 0.0331
+HEADER 1  - Drug Score                        : 0.2947
+HEADER 2  - Number of V. Vertices             :    35
+HEADER 3  - Mean alpha-sphere radius          : 3.8268
+HEADER 4  - Mean alpha-sphere SA              : 0.4500
+HEADER 5  - Mean B-factor                     : 0.6250
+HEADER 6  - Hydrophobicity Score              : 67.0909
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 5.7273
+HEADER 9  - Real volume (approximation)       : 306.2977
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 32.9412
+HEADER 12 - Number of apolar alpha sphere     :    34
+HEADER 13 - Proportion of apolar alpha sphere : 0.9714
+ATOM      1    C STP    12      -3.012  -8.100  -8.760    0.00     3.99
+ATOM      2    C STP    12      -3.458  -8.552  -8.865    0.00     4.13
+ATOM      3    C STP    12      -2.959  -8.581 -10.924    0.00     3.60
+ATOM      4    C STP    12      -3.348 -12.034  -7.768    0.00     3.58
+ATOM      5    C STP    12      -4.265 -11.238  -7.349    0.00     3.85
+ATOM      6    C STP    12      -3.688  -6.964  -9.269    0.00     3.51
+ATOM      7    C STP    12      -2.701  -7.221 -10.008    0.00     3.68
+ATOM      8    C STP    12      -5.618  -8.473  -9.251    0.00     4.02
+ATOM      9    C STP    12      -3.297  -7.983  -9.300    0.00     4.15
+ATOM     10    C STP    12      -3.480  -8.204  -9.300    0.00     4.19
+ATOM     11    C STP    12      -2.711  -7.550  -9.906    0.00     3.88
+ATOM     12    C STP    12      -3.130  -8.353 -10.547    0.00     3.78
+ATOM     13    C STP    12      -6.416  -7.590  -9.212    0.00     3.65
+ATOM     14    C STP    12      -6.562  -8.616  -9.387    0.00     4.21
+ATOM     15    C STP    12      -3.584  -8.558 -11.489    0.00     3.41
+ATOM     16    C STP    12      -2.190  -7.904  -8.566    0.00     3.57
+ATOM     17    C STP    12      -2.781  -7.847  -8.009    0.00     3.57
+ATOM     18    C STP    12      -4.480 -10.505  -7.436    0.00     3.94
+ATOM     19    C STP    12      -4.026  -9.106  -8.251    0.00     4.00
+ATOM     20    C STP    12      -4.477  -9.071  -8.355    0.00     3.93
+ATOM     21    C STP    12      -6.605  -8.625  -9.403    0.00     4.22
+ATOM     22    C STP    12      -7.298  -9.850 -11.196    0.00     3.43
+ATOM     23    C STP    12      -6.455  -7.572  -9.223    0.00     3.65
+ATOM     24    C STP    12      -6.421  -7.573  -9.212    0.00     3.65
+ATOM     25    O STP    12      -1.367  -6.997 -10.176    0.00     3.51
+ATOM     26    C STP    12      -1.239  -6.770 -10.255    0.00     3.42
+ATOM     27    C STP    12      -4.616 -11.435  -7.345    0.00     3.83
+ATOM     28    C STP    12      -4.811 -11.636  -7.371    0.00     3.80
+ATOM     29    C STP    12      -4.913 -11.381  -7.364    0.00     3.83
+ATOM     30    C STP    12      -6.933  -9.877  -8.296    0.00     4.23
+ATOM     31    C STP    12      -6.950  -9.879  -8.185    0.00     4.17
+ATOM     32    C STP    12      -6.960  -7.202  -9.484    0.00     3.47
+ATOM     33    C STP    12      -6.846  -7.861  -9.393    0.00     3.82
+ATOM     34    C STP    12      -7.673  -8.310  -9.533    0.00     4.10
+ATOM     35    C STP    12      -6.670  -8.554  -9.417    0.00     4.18
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket13_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket13_atm.pdb
@@ -0,0 +1,44 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    13:
+HEADER 0  - Pocket Score                      : 0.0233
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of alpha spheres           :    25
+HEADER 3  - Mean alpha-sphere radius          : 4.0661
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5694
+HEADER 5  - Mean B-factor of pocket residues  : 0.5629
+HEADER 6  - Hydrophobicity Score              : 3.2000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.2000
+HEADER 9  - Pocket volume (Monte Carlo)       : 418.0618
+HEADER 10  -Pocket volume (convex hull)       : 21.6391
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 1.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.0800
+ATOM    983   CB ARG E 134      10.740  -0.052  17.353  0.00  0.00           C 0
+ATOM    947    O SER E 130      10.710   0.913  14.300  0.44  3.21           O 0
+ATOM    985   CD ARG E 134       8.529   0.726  18.433  0.00  0.00           C 0
+ATOM   2583  OD1 ASP E 328      12.217   8.079  14.409  0.00  0.00           O 0
+ATOM   2569    O PHE E 327       8.517  10.413  14.152  0.62  3.21           O 0
+ATOM   2561    O ASN E 326       6.724   6.878  12.348  0.72  1.07           O 0
+ATOM   2568    C PHE E 327       8.864   9.938  13.094  0.00  0.00           C 0
+ATOM   2555    O SER E 325       5.460   8.512  16.006  0.50  7.50           O 0
+ATOM   2560    C ASN E 326       6.141   7.798  12.923  0.00  0.00           C 0
+ATOM   2559   CA ASN E 326       4.870   7.517  13.722  0.00  0.00           C 0
+ATOM    988  NH1 ARG E 134       7.122   0.553  15.909  0.00  0.00           N 0
+ATOM    948   CB SER E 130      10.249   3.583  12.410  0.00  0.00           C 0
+ATOM    949   OG SER E 130       8.949   3.497  11.843  0.67  1.07           O 0
+ATOM   2564  OD1 ASN E 326       2.463   5.189  14.371  0.35  5.36           O 0
+ATOM    987   CZ ARG E 134       6.599   0.033  17.017  0.00  0.00           C 0
+ATOM    958  CE1 HIS E 131       5.030   1.759  13.404  0.00  0.00           C 0
+ATOM   2562   CB ASN E 326       3.999   6.458  13.078  0.00  0.00           C 0
+ATOM    989  NH2 ARG E 134       5.422  -0.582  16.939  0.00  0.00           N 0
+ATOM   2477   CZ PHE E 314       2.392  -0.719  14.240  0.00  0.00           C 0
+ATOM   2493    N LYS E 317      -1.434   2.889  15.336  0.00  0.00           N 0
+ATOM   2487   CA PRO E 316      -0.297   1.611  13.669  0.00  0.00           C 0
+ATOM   2496    O LYS E 317      -1.019   5.459  16.446  0.00  0.00           O 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket13_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket13_vert.pqr
@@ -0,0 +1,47 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    13:
+HEADER 0  - Pocket Score                      : 0.0233
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of V. Vertices             :    25
+HEADER 3  - Mean alpha-sphere radius          : 4.0661
+HEADER 4  - Mean alpha-sphere SA              : 0.5694
+HEADER 5  - Mean B-factor                     : 0.5629
+HEADER 6  - Hydrophobicity Score              : 3.2000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.2000
+HEADER 9  - Real volume (approximation)       : 418.0618
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 1.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.0800
+ATOM      1    O STP    13      10.769   4.600  17.144    0.00     4.66
+ATOM      2    O STP    13       8.918   7.040  15.105    0.00     3.53
+ATOM      3    O STP    13       8.811   6.910  15.467    0.00     3.75
+ATOM      4    O STP    13       8.654   7.049  15.351    0.00     3.57
+ATOM      5    O STP    13       7.009   4.684  15.839    0.00     4.13
+ATOM      6    O STP    13      10.267   4.709  16.884    0.00     4.61
+ATOM      7    O STP    13       9.090   4.045  16.233    0.00     4.02
+ATOM      8    O STP    13       8.866   5.705  16.024    0.00     4.41
+ATOM      9    O STP    13       8.485   4.984  16.506    0.00     4.67
+ATOM     10    O STP    13       7.933   4.703  15.769    0.00     4.23
+ATOM     11    O STP    13       8.124   4.913  16.122    0.00     4.48
+ATOM     12    O STP    13       5.406   4.327  17.670    0.00     4.50
+ATOM     13    O STP    13       6.841   4.575  15.663    0.00     4.04
+ATOM     14    C STP    13       6.255   4.603  14.860    0.00     3.42
+ATOM     15    C STP    13       5.811   4.553  15.542    0.00     3.60
+ATOM     16    O STP    13       6.320   4.537  16.081    0.00     4.07
+ATOM     17    O STP    13       5.988   4.465  16.323    0.00     4.09
+ATOM     18    O STP    13       6.008   4.524  16.167    0.00     4.03
+ATOM     19    O STP    13       7.257   4.342  15.204    0.00     3.86
+ATOM     20    O STP    13       4.688   3.338  16.867    0.00     3.82
+ATOM     21    O STP    13       4.288   3.032  16.894    0.00     3.79
+ATOM     22    O STP    13       2.992   2.180  16.473    0.00     3.71
+ATOM     23    O STP    13       2.016   2.191  16.513    0.00     3.71
+ATOM     24    O STP    13       2.230   2.170  17.329    0.00     4.23
+ATOM     25    O STP    13       2.219   2.587  18.277    0.00     4.70
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket14_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket14_atm.pdb
@@ -0,0 +1,46 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    14:
+HEADER 0  - Pocket Score                      : 0.0142
+HEADER 1  - Drug Score                        : 0.0061
+HEADER 2  - Number of alpha spheres           :    25
+HEADER 3  - Mean alpha-sphere radius          : 4.0690
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6169
+HEADER 5  - Mean B-factor of pocket residues  : 0.5743
+HEADER 6  - Hydrophobicity Score              : 19.0000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.0909
+HEADER 9  - Pocket volume (Monte Carlo)       : 370.6070
+HEADER 10  -Pocket volume (convex hull)       : 34.2649
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 11.0000
+HEADER 13 - Number of apolar alpha sphere     :    12
+HEADER 14 - Proportion of apolar alpha sphere : 0.4800
+ATOM   2249  CG1 VAL E 288       3.564 -12.956 -11.539  0.00  0.00           C 0
+ATOM   1160   CG GLU E 155       1.987  -9.808 -11.553  0.00  0.00           C 0
+ATOM     16   NZ LYS E  16      -0.505 -12.557 -16.586  0.00  0.00           N 0
+ATOM   1163  OE2 GLU E 155       0.538 -11.622 -11.655  0.59  1.07           O 0
+ATOM   1198   CB SER E 159       2.184  -5.965 -15.856  0.00  0.00           C 0
+ATOM   1158    O GLU E 155       2.592  -6.882 -13.001  0.00  0.00           O 0
+ATOM     44  CD2 LEU E  19      -0.942  -8.123 -14.318  0.00  0.00           C 0
+ATOM   1188   CB HIS E 158       7.249  -6.299 -13.781  0.00  0.00           C 0
+ATOM   2244    N VAL E 288       6.014 -14.516 -12.342  0.00  0.00           N 0
+ATOM   2206    O GLY E 282      10.358 -13.074 -13.450  0.45  9.64           O 0
+ATOM   2248   CB VAL E 288       4.901 -12.934 -10.819  0.00  0.00           C 0
+ATOM   1705  NE1 TRP E 221       9.870 -10.227 -10.703  0.63  2.19           N 0
+ATOM   1708  CZ2 TRP E 221       7.752 -10.019  -9.370  0.00  0.00           C 0
+ATOM   1191  CD2 HIS E 158       8.957  -7.116 -12.009  0.00  0.00           C 0
+ATOM   1156   CA GLU E 155       3.603  -7.906 -11.008  0.00  0.00           C 0
+ATOM   1675   CE LYS E 217       9.911  -4.369 -16.606  0.00  0.00           C 0
+ATOM   1187    O HIS E 158       6.222  -5.014 -16.513  0.63  6.43           O 0
+ATOM   1673   CG LYS E 217      11.555  -6.094 -15.608  0.00  0.00           C 0
+ATOM   1672   CB LYS E 217      11.906  -6.886 -14.343  0.00  0.00           C 0
+ATOM   1677    N ALA E 218      14.585  -8.461 -13.036  0.52  1.09           N 0
+ATOM   2213  OD1 ASN E 283      14.597 -12.174 -15.706  0.48  4.29           O 0
+ATOM   1194    N SER E 159       4.457  -5.333 -15.179  0.00  0.00           N 0
+ATOM   1186    C HIS E 158       5.736  -5.116 -15.393  0.00  0.00           C 0
+ATOM   1195   CA SER E 159       3.556  -5.471 -16.302  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket14_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket14_vert.pqr
@@ -0,0 +1,47 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    14:
+HEADER 0  - Pocket Score                      : 0.0142
+HEADER 1  - Drug Score                        : 0.0061
+HEADER 2  - Number of V. Vertices             :    25
+HEADER 3  - Mean alpha-sphere radius          : 4.0690
+HEADER 4  - Mean alpha-sphere SA              : 0.6169
+HEADER 5  - Mean B-factor                     : 0.5743
+HEADER 6  - Hydrophobicity Score              : 19.0000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.0909
+HEADER 9  - Real volume (approximation)       : 370.6070
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 11.0000
+HEADER 12 - Number of apolar alpha sphere     :    12
+HEADER 13 - Proportion of apolar alpha sphere : 0.4800
+ATOM      1    O STP    14       2.506 -11.531 -14.753    0.00     3.67
+ATOM      2    O STP    14       3.068 -10.223 -15.746    0.00     4.35
+ATOM      3    O STP    14       2.399  -9.985 -15.545    0.00     4.02
+ATOM      4    O STP    14       2.404  -9.971 -15.570    0.00     4.02
+ATOM      5    C STP    14       5.125 -10.220 -14.880    0.00     4.59
+ATOM      6    O STP    14       6.885 -10.576 -13.808    0.00     4.29
+ATOM      7    C STP    14       5.976 -10.559 -14.490    0.00     4.50
+ATOM      8    O STP    14       6.965 -10.686 -13.636    0.00     4.15
+ATOM      9    C STP    14       6.745 -10.296 -13.292    0.00     4.06
+ATOM     10    C STP    14       6.779 -10.238 -13.247    0.00     4.00
+ATOM     11    O STP    14       6.903 -10.566 -13.771    0.00     4.28
+ATOM     12    O STP    14       7.436 -10.329 -13.922    0.00     4.04
+ATOM     13    C STP    14       5.178  -9.990 -14.394    0.00     4.28
+ATOM     14    C STP    14       6.257  -9.980 -12.969    0.00     3.90
+ATOM     15    C STP    14       5.645 -10.172 -13.886    0.00     4.19
+ATOM     16    C STP    14       5.308 -10.126 -14.302    0.00     4.32
+ATOM     17    C STP    14       6.375  -9.340 -12.443    0.00     3.44
+ATOM     18    C STP    14       8.583  -7.677 -16.792    0.00     3.57
+ATOM     19    O STP    14       9.881  -9.702 -14.137    0.00     3.47
+ATOM     20    C STP    14       8.914  -9.764 -16.244    0.00     4.57
+ATOM     21    C STP    14       9.059  -9.645 -15.171    0.00     4.05
+ATOM     22    O STP    14      12.065 -10.289 -14.422    0.00     3.41
+ATOM     23    O STP    14       5.610  -9.461 -16.514    0.00     4.49
+ATOM     24    O STP    14       5.607  -9.484 -16.523    0.00     4.51
+ATOM     25    O STP    14       4.200  -8.861 -15.470    0.00     3.55
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket15_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket15_atm.pdb
@@ -0,0 +1,49 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    15:
+HEADER 0  - Pocket Score                      : 0.0056
+HEADER 1  - Drug Score                        : 0.0085
+HEADER 2  - Number of alpha spheres           :    29
+HEADER 3  - Mean alpha-sphere radius          : 4.2363
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6830
+HEADER 5  - Mean B-factor of pocket residues  : 0.6083
+HEADER 6  - Hydrophobicity Score              : 21.3636
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 421.6359
+HEADER 10  -Pocket volume (convex hull)       : 21.9768
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 15.0000
+HEADER 13 - Number of apolar alpha sphere     :    16
+HEADER 14 - Proportion of apolar alpha sphere : 0.5517
+ATOM   1819   OH TYR E 235      20.722 -13.511  11.416  0.59  7.50           O 0
+ATOM   2786    N THR I   6      24.752 -13.023  15.286  0.00  0.00           N 0
+ATOM   2793    N TYR I   7      22.704 -11.012  15.175  0.73  1.09           N 0
+ATOM   2783   CB THR I   5      24.155 -13.603  18.177  0.00  0.00           C 0
+ATOM   1817  CE2 TYR E 235      19.985 -11.372  12.216  0.00  0.00           C 0
+ATOM   2797   CB TYR I   7      20.768 -10.287  16.509  0.00  0.00           C 0
+ATOM   2790   CB THR I   6      23.915 -12.886  13.021  0.00  0.00           C 0
+ATOM   2791  OG1 THR I   6      24.715 -14.012  12.684  0.46  6.43           O 0
+ATOM   2023  CD2 HIS E 260      15.149 -16.519  13.733  0.00  0.00           C 0
+ATOM   2803   CZ TYR I   7      17.998  -7.046  17.130  0.00  0.00           C 0
+ATOM   1008   CD ARG E 137      13.015 -12.390  14.489  0.00  0.00           C 0
+ATOM   1001    O GLY E 136      14.004  -7.535  14.180  0.55  1.07           O 0
+ATOM   2801  CE1 TYR I   7      18.129  -7.625  15.869  0.00  0.00           C 0
+ATOM   2802  CE2 TYR I   7      18.768  -7.509  18.203  0.00  0.00           C 0
+ATOM   2800  CD2 TYR I   7      19.671  -8.559  18.021  0.00  0.00           C 0
+ATOM   2007   CB PRO E 258      17.978 -16.703  11.072  0.00  0.00           C 0
+ATOM   2015   OG SER E 259      18.773 -20.147  14.551  0.00  0.00           O 0
+ATOM   2004   CA PRO E 258      18.907 -17.890  10.760  0.00  0.00           C 0
+ATOM   1000    C GLY E 136      13.099  -7.215  14.936  0.00  0.00           C 0
+ATOM   1007   CG ARG E 137      12.064 -11.168  14.522  0.00  0.00           C 0
+ATOM   1006   CB ARG E 137      12.547  -9.944  13.745  0.00  0.00           C 0
+ATOM   1002    N ARG E 137      11.897  -7.755  14.844  0.00  0.00           N 0
+ATOM    993    O ILE E 135      11.277  -6.737  17.844  0.39  8.57           O 0
+ATOM   2025  NE2 HIS E 260      14.962 -15.418  12.941  0.93  2.19           N 0
+ATOM   2798   CG TYR I   7      19.809  -9.148  16.762  0.00  0.00           C 0
+ATOM   2799  CD1 TYR I   7      19.040  -8.667  15.701  0.00  0.00           C 0
+ATOM   1802    O ALA E 233      16.247 -11.091  12.418  0.55  5.36           O 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket15_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket15_vert.pqr
@@ -0,0 +1,51 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    15:
+HEADER 0  - Pocket Score                      : 0.0056
+HEADER 1  - Drug Score                        : 0.0085
+HEADER 2  - Number of V. Vertices             :    29
+HEADER 3  - Mean alpha-sphere radius          : 4.2363
+HEADER 4  - Mean alpha-sphere SA              : 0.6830
+HEADER 5  - Mean B-factor                     : 0.6083
+HEADER 6  - Hydrophobicity Score              : 21.3636
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 421.6359
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 15.0000
+HEADER 12 - Number of apolar alpha sphere     :    16
+HEADER 13 - Proportion of apolar alpha sphere : 0.5517
+ATOM      1    O STP    15      20.762 -15.016  15.628    0.00     4.47
+ATOM      2    O STP    15      20.093 -13.782  15.160    0.00     3.81
+ATOM      3    O STP    15      21.482 -16.110  15.016    0.00     4.50
+ATOM      4    O STP    15      21.091 -14.702  15.246    0.00     4.03
+ATOM      5    C STP    15      18.817 -14.364  15.540    0.00     4.62
+ATOM      6    C STP    15      15.023 -10.073  17.441    0.00     4.26
+ATOM      7    C STP    15      15.741 -10.998  17.957    0.00     4.63
+ATOM      8    O STP    15      20.585 -16.489  14.223    0.00     4.09
+ATOM      9    O STP    15      19.415 -15.607  15.364    0.00     4.66
+ATOM     10    C STP    15      15.015 -10.071  17.451    0.00     4.26
+ATOM     11    C STP    15      14.777 -10.089  16.406    0.00     3.47
+ATOM     12    C STP    15      14.855 -10.051  17.251    0.00     4.06
+ATOM     13    O STP    15      13.277  -9.665  17.514    0.00     3.56
+ATOM     14    C STP    15      14.805 -10.108  17.922    0.00     4.49
+ATOM     15    O STP    15      18.495 -14.244  14.923    0.00     4.22
+ATOM     16    O STP    15      18.480 -14.689  14.307    0.00     3.84
+ATOM     17    C STP    15      18.270 -13.858  15.512    0.00     4.47
+ATOM     18    C STP    15      15.741 -10.998  17.957    0.00     4.63
+ATOM     19    C STP    15      15.742 -10.997  17.953    0.00     4.62
+ATOM     20    C STP    15      15.760 -10.982  17.951    0.00     4.60
+ATOM     21    C STP    15      16.138 -10.636  17.830    0.00     4.10
+ATOM     22    C STP    15      16.014 -10.748  17.869    0.00     4.26
+ATOM     23    O STP    15      17.979 -13.868  13.441    0.00     3.43
+ATOM     24    O STP    15      18.105 -13.657  15.491    0.00     4.41
+ATOM     25    O STP    15      17.165 -13.262  16.453    0.00     4.67
+ATOM     26    O STP    15      15.637 -10.294  15.930    0.00     3.65
+ATOM     27    C STP    15      16.936 -12.523  16.560    0.00     4.44
+ATOM     28    C STP    15      17.083 -12.356  16.365    0.00     4.23
+ATOM     29    C STP    15      16.850 -12.331  16.545    0.00     4.35
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket16_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket16_atm.pdb
@@ -0,0 +1,40 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    16:
+HEADER 0  - Pocket Score                      : -0.0114
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.7471
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5626
+HEADER 5  - Mean B-factor of pocket residues  : 0.3127
+HEADER 6  - Hydrophobicity Score              : -8.1429
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.1429
+HEADER 9  - Pocket volume (Monte Carlo)       : 269.8107
+HEADER 10  -Pocket volume (convex hull)       : 12.6545
+HEADER 11 - Charge Score                      :     3
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     1
+HEADER 14 - Proportion of apolar alpha sphere : 0.0588
+ATOM   2877    O ARG I  18      20.035   5.682   6.907  0.00  0.00           O 0
+ATOM   2901   CG ASN I  20      19.942   9.050   2.872  0.00  0.00           C 0
+ATOM   2903  ND2 ASN I  20      18.976   8.461   3.615  0.72  2.19           N 0
+ATOM   2902  OD1 ASN I  20      20.180  10.277   2.903  0.00  0.00           O 0
+ATOM   2873    O GLY I  17      19.641   2.744   8.748  0.57  1.07           O 0
+ATOM   2851    O GLY I  14      25.837   2.808  10.298  0.00  0.00           O 0
+ATOM   2853   CA ARG I  15      24.354   0.743   9.261  0.00  0.00           C 0
+ATOM    305  CG2 THR E  51      16.648  12.650   5.825  0.00  0.00           C 0
+ATOM   2883  NH1 ARG I  18      15.747   9.018   6.588  0.00  0.00           N 0
+ATOM   2870    N GLY I  17      20.906   2.640  11.216  0.47  2.19           N 0
+ATOM   2871   CA GLY I  17      19.967   3.723  10.956  0.00  0.00           C 0
+ATOM   2872    C GLY I  17      19.396   3.686   9.522  0.00  0.00           C 0
+ATOM   2890   CG ARG I  19      20.455   1.820   5.502  0.00  0.00           C 0
+ATOM   2900   CB ASN I  20      20.719   8.118   1.944  0.00  0.00           C 0
+ATOM   2896    N ASN I  20      20.278   5.891   2.989  0.30  5.47           N 0
+ATOM   2860   CZ ARG I  15      25.245   1.855   4.459  0.00  0.00           C 0
+ATOM   2862  NH2 ARG I  15      25.572   3.087   4.092  0.00  9.84           N 0
+ATOM   2886   CA ARG I  19      19.869   4.126   4.630  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket16_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket16_vert.pqr
@@ -0,0 +1,39 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    16:
+HEADER 0  - Pocket Score                      : -0.0114
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.7471
+HEADER 4  - Mean alpha-sphere SA              : 0.5626
+HEADER 5  - Mean B-factor                     : 0.3127
+HEADER 6  - Hydrophobicity Score              : -8.1429
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 4.1429
+HEADER 9  - Real volume (approximation)       : 269.8107
+HEADER 10 - Charge Score                      :     3
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     1
+HEADER 13 - Proportion of apolar alpha sphere : 0.0588
+ATOM      1    O STP    16      21.605   9.274   6.445    0.00     3.95
+ATOM      2    O STP    16      23.052   4.027   8.218    0.00     3.68
+ATOM      3    O STP    16      20.037  10.202   7.733    0.00     4.60
+ATOM      4    O STP    16      22.942   3.882   8.664    0.00     3.49
+ATOM      5    O STP    16      22.985   4.910   9.082    0.00     3.75
+ATOM      6    O STP    16      22.778   4.706   8.980    0.00     3.57
+ATOM      7    O STP    16      22.932   4.338   8.689    0.00     3.66
+ATOM      8    O STP    16      22.819   4.391   8.749    0.00     3.58
+ATOM      9    O STP    16      22.943   3.580   7.482    0.00     3.63
+ATOM     10    O STP    16      22.800   7.841   5.222    0.00     3.89
+ATOM     11    C STP    16      23.308   3.741   7.149    0.00     3.81
+ATOM     12    O STP    16      23.140   5.515   5.119    0.00     3.59
+ATOM     13    O STP    16      22.972   4.082   6.110    0.00     3.44
+ATOM     14    O STP    16      23.254   3.825   6.901    0.00     3.72
+ATOM     15    O STP    16      23.595   4.080   7.336    0.00     3.93
+ATOM     16    O STP    16      24.143   3.706   7.296    0.00     3.56
+ATOM     17    O STP    16      23.426   3.868   7.200    0.00     3.86
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket17_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket17_atm.pdb
@@ -0,0 +1,36 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    17:
+HEADER 0  - Pocket Score                      : -0.0205
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.9841
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5013
+HEADER 5  - Mean B-factor of pocket residues  : 0.5951
+HEADER 6  - Hydrophobicity Score              : 59.3333
+HEADER 7  - Polarity Score                    :     1
+HEADER 8  - Amino Acid based volume Score     : 4.6667
+HEADER 9  - Pocket volume (Monte Carlo)       : 169.8327
+HEADER 10  -Pocket volume (convex hull)       : 2.1844
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 10.0000
+HEADER 13 - Number of apolar alpha sphere     :    11
+HEADER 14 - Proportion of apolar alpha sphere : 0.6471
+ATOM   2099   CA ARG E 270      17.194 -19.575  -2.168  0.00  0.00           C 0
+ATOM   2129   CB LEU E 273      18.997 -14.631  -2.393  0.00  0.00           C 0
+ATOM   2093    O LEU E 269      16.708 -16.845  -1.937  0.00  0.00           O 0
+ATOM   1978   CB VAL E 255      22.508 -16.367   1.574  0.00  0.00           C 0
+ATOM   2103   CG ARG E 270      18.252 -21.553  -0.888  0.00  0.00           C 0
+ATOM   2128    O LEU E 273      20.651 -16.017  -4.362  0.23  7.50           O 0
+ATOM   2101    O ARG E 270      17.911 -18.997  -4.422  0.00  0.00           O 0
+ATOM   1964    O GLY E 253      26.212 -17.663  -2.433  0.00  0.00           O 0
+ATOM   1974    N VAL E 255      24.871 -17.081   1.353  0.00  0.00           N 0
+ATOM   1977    O VAL E 255      23.715 -18.779   3.313  0.57  6.43           O 0
+ATOM   2001  CE2 PHE E 257      19.271 -19.839   2.946  0.00  0.00           C 0
+ATOM   2107  NH1 ARG E 270      19.684 -23.194   1.662  0.00  0.00           N 0
+ATOM   1980  CG2 VAL E 255      22.744 -15.487   0.360  0.00  0.00           C 0
+ATOM   2002   CZ PHE E 257      18.599 -18.718   2.457  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket17_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket17_vert.pqr
@@ -0,0 +1,39 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    17:
+HEADER 0  - Pocket Score                      : -0.0205
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.9841
+HEADER 4  - Mean alpha-sphere SA              : 0.5013
+HEADER 5  - Mean B-factor                     : 0.5951
+HEADER 6  - Hydrophobicity Score              : 59.3333
+HEADER 7  - Polarity Score                    :     1
+HEADER 8  - Volume Score                      : 4.6667
+HEADER 9  - Real volume (approximation)       : 169.8327
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 10.0000
+HEADER 12 - Number of apolar alpha sphere     :    11
+HEADER 13 - Proportion of apolar alpha sphere : 0.6471
+ATOM      1    C STP    17      20.079 -17.759  -0.802    0.00     3.67
+ATOM      2    O STP    17      21.058 -19.186  -2.154    0.00     3.88
+ATOM      3    O STP    17      22.470 -19.926  -1.235    0.00     4.53
+ATOM      4    O STP    17      22.448 -20.166  -0.692    0.00     4.42
+ATOM      5    C STP    17      21.929 -20.012  -0.119    0.00     4.06
+ATOM      6    O STP    17      21.994 -20.327   0.005    0.00     4.04
+ATOM      7    C STP    17      22.152 -19.454  -1.681    0.00     4.50
+ATOM      8    O STP    17      22.110 -19.403  -1.774    0.00     4.50
+ATOM      9    C STP    17      20.135 -17.782  -0.862    0.00     3.68
+ATOM     10    C STP    17      20.333 -17.868  -1.159    0.00     3.71
+ATOM     11    O STP    17      22.730 -19.052  -1.278    0.00     3.92
+ATOM     12    C STP    17      21.017 -18.682  -1.343    0.00     4.01
+ATOM     13    C STP    17      21.042 -18.693  -1.380    0.00     4.03
+ATOM     14    C STP    17      20.540 -18.564  -0.766    0.00     3.77
+ATOM     15    C STP    17      21.084 -19.267  -0.227    0.00     3.70
+ATOM     16    C STP    17      20.059 -17.765  -0.768    0.00     3.67
+ATOM     17    C STP    17      20.019 -17.679  -0.714    0.00     3.63
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket18_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket18_atm.pdb
@@ -0,0 +1,41 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    18:
+HEADER 0  - Pocket Score                      : -0.0856
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    18
+HEADER 3  - Mean alpha-sphere radius          : 4.0398
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4898
+HEADER 5  - Mean B-factor of pocket residues  : 0.7684
+HEADER 6  - Hydrophobicity Score              : 33.3000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.6000
+HEADER 9  - Pocket volume (Monte Carlo)       : 257.4854
+HEADER 10  -Pocket volume (convex hull)       : 10.9194
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     1
+HEADER 14 - Proportion of apolar alpha sphere : 0.0556
+ATOM    570  NE2 GLN E  84      21.084  10.440  -9.253  0.35  5.47           N 0
+ATOM   1526    O LEU E 198      23.280   4.019  -9.415  0.52  3.21           O 0
+ATOM   2919    C HIS I  23      25.340   8.429  -7.089  0.00  0.00           C 0
+ATOM   2918   CA HIS I  23      23.968   8.408  -6.501  0.00  0.00           C 0
+ATOM   2912    O ILE I  22      22.002   6.740  -5.606  0.50  2.14           O 0
+ATOM   1536   SG CYS E 199      19.889   4.664 -10.584  0.00  0.00           S 0
+ATOM    548    O LEU E  82      23.088  12.682  -9.380  0.41  1.07           O 0
+ATOM    557   CB LYS E  83      23.916  13.115 -12.297  0.00  0.00           C 0
+ATOM   2927    N ASP I  24      25.770   9.592  -7.488  0.60  1.09           N 0
+ATOM   2931   CB ASP I  24      27.519  10.895  -8.641  0.00  0.00           C 0
+HETATM 1515  CG2 TPO E 197      22.109   5.117 -12.962  0.00  0.00           C 0
+ATOM   2920    O HIS I  23      26.014   7.407  -7.167  0.27  8.57           O 0
+ATOM   2933  OD1 ASP I  24      28.705   9.961 -10.427  0.00  0.00           O 0
+ATOM    556    O LYS E  83      21.390  12.223 -12.205  0.29  8.57           O 0
+ATOM    596  CE1 HIS E  87      19.137   7.871 -12.339  0.00  0.00           C 0
+ATOM    560   CE LYS E  83      27.475  12.261 -12.325  0.00  0.00           C 0
+ATOM    559   CD LYS E  83      26.370  13.031 -13.055  0.00  0.00           C 0
+ATOM   1527   CB LEU E 198      25.504   2.342 -10.392  0.00  0.00           C 0
+ATOM   1523    N LEU E 198      23.773   2.787 -12.142  0.00  0.00           N 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket18_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket18_vert.pqr
@@ -0,0 +1,40 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    18:
+HEADER 0  - Pocket Score                      : -0.0856
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    18
+HEADER 3  - Mean alpha-sphere radius          : 4.0398
+HEADER 4  - Mean alpha-sphere SA              : 0.4898
+HEADER 5  - Mean B-factor                     : 0.7684
+HEADER 6  - Hydrophobicity Score              : 33.3000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.6000
+HEADER 9  - Real volume (approximation)       : 257.4854
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     1
+HEADER 13 - Proportion of apolar alpha sphere : 0.0556
+ATOM      1    O STP    18      23.290   7.625 -10.006    0.00     3.65
+ATOM      2    O STP    18      21.998   7.158  -8.997    0.00     3.42
+ATOM      3    O STP    18      21.767   7.080  -9.018    0.00     3.44
+ATOM      4    O STP    18      24.354   9.432 -11.111    0.00     3.89
+ATOM      5    O STP    18      24.924  10.086 -10.852    0.00     3.50
+ATOM      6    O STP    18      24.124   8.241 -11.073    0.00     4.17
+ATOM      7    O STP    18      23.599   7.744 -10.504    0.00     3.89
+ATOM      8    O STP    18      25.034   7.815 -11.334    0.00     4.30
+ATOM      9    O STP    18      24.595   7.493 -10.910    0.00     4.00
+ATOM     10    O STP    18      24.583   8.688 -11.745    0.00     4.51
+ATOM     11    O STP    18      24.433   8.715 -11.668    0.00     4.47
+ATOM     12    O STP    18      24.019   8.832 -11.950    0.00     4.30
+ATOM     13    O STP    18      22.801   8.729 -12.139    0.00     3.77
+ATOM     14    O STP    18      22.207   7.260 -10.194    0.00     3.50
+ATOM     15    C STP    18      24.752   8.793 -13.468    0.00     4.56
+ATOM     16    O STP    18      26.139   6.551 -11.712    0.00     4.46
+ATOM     17    O STP    18      26.177   6.535 -11.779    0.00     4.47
+ATOM     18    O STP    18      26.104   6.506 -11.714    0.00     4.41
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket19_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket19_atm.pdb
@@ -0,0 +1,37 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    19:
+HEADER 0  - Pocket Score                      : -0.0858
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    21
+HEADER 3  - Mean alpha-sphere radius          : 3.8400
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4526
+HEADER 5  - Mean B-factor of pocket residues  : 0.5558
+HEADER 6  - Hydrophobicity Score              : 29.1250
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 5.2500
+HEADER 9  - Pocket volume (Monte Carlo)       : 201.6497
+HEADER 10  -Pocket volume (convex hull)       : 5.4189
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 2.0000
+HEADER 13 - Number of apolar alpha sphere     :     3
+HEADER 14 - Proportion of apolar alpha sphere : 0.1429
+ATOM   1985   CB ARG E 256      24.262 -17.409   6.793  0.00  0.00           C 0
+ATOM   1995    O PHE E 257      20.433 -19.637   9.226  0.00  0.00           O 0
+ATOM   1990  NH1 ARG E 256      26.891 -19.581   8.267  0.00  0.00           N 0
+ATOM   2791  OG1 THR I   6      24.715 -14.012  12.684  0.46  6.43           O 0
+ATOM   1986   CG ARG E 256      25.556 -16.954   6.135  0.00  0.00           C 0
+ATOM   2792  CG2 THR I   6      23.865 -11.906  11.882  0.00  0.00           C 0
+ATOM   1994    C PHE E 257      19.881 -18.647   8.717  0.00  0.00           C 0
+ATOM   1776   OH TYR E 229      20.502 -13.889   7.143  0.19  4.29           O 0
+ATOM   1984    O ARG E 256      21.527 -16.273   6.498  0.35  1.07           O 0
+ATOM   1819   OH TYR E 235      20.722 -13.511  11.416  0.59  7.50           O 0
+ATOM   1816  CE1 TYR E 235      20.944 -11.609  10.005  0.00  0.00           C 0
+ATOM   2003    N PRO E 258      19.173 -17.780   9.368  0.58  1.09           N 0
+ATOM   1830    O PRO E 237      24.002 -11.255   4.963  0.00  0.00           O 0
+ATOM   1854  CE2 PHE E 239      24.254  -8.709   9.507  0.00  0.00           C 0
+ATOM   2004   CA PRO E 258      18.907 -17.890  10.760  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket19_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket19_vert.pqr
@@ -0,0 +1,43 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    19:
+HEADER 0  - Pocket Score                      : -0.0858
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    21
+HEADER 3  - Mean alpha-sphere radius          : 3.8400
+HEADER 4  - Mean alpha-sphere SA              : 0.4526
+HEADER 5  - Mean B-factor                     : 0.5558
+HEADER 6  - Hydrophobicity Score              : 29.1250
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 5.2500
+HEADER 9  - Real volume (approximation)       : 201.6497
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 2.0000
+HEADER 12 - Number of apolar alpha sphere     :     3
+HEADER 13 - Proportion of apolar alpha sphere : 0.1429
+ATOM      1    O STP    19      23.996 -17.991  11.091    0.00     4.35
+ATOM      2    C STP    19      24.960 -14.038   8.738    0.00     3.95
+ATOM      3    O STP    19      22.931 -16.813  10.494    0.00     3.98
+ATOM      4    O STP    19      23.730 -14.416   9.050    0.00     3.79
+ATOM      5    O STP    19      23.534 -14.640   9.195    0.00     3.74
+ATOM      6    O STP    19      23.541 -14.438   9.194    0.00     3.71
+ATOM      7    O STP    19      23.319 -13.996   9.166    0.00     3.47
+ATOM      8    O STP    19      23.506 -14.658   9.215    0.00     3.73
+ATOM      9    O STP    19      22.772 -16.806  10.680    0.00     3.95
+ATOM     10    O STP    19      23.478 -14.756   9.266    0.00     3.71
+ATOM     11    O STP    19      22.867 -16.689  10.427    0.00     3.96
+ATOM     12    O STP    19      22.668 -16.487  10.105    0.00     3.79
+ATOM     13    O STP    19      22.623 -16.471  10.089    0.00     3.76
+ATOM     14    O STP    19      22.761 -16.808  10.687    0.00     3.94
+ATOM     15    O STP    19      24.040 -13.911   7.306    0.00     3.54
+ATOM     16    C STP    19      24.558 -13.610   8.244    0.00     4.08
+ATOM     17    O STP    19      24.402 -13.618   8.240    0.00     4.06
+ATOM     18    O STP    19      23.982 -13.022   8.288    0.00     3.77
+ATOM     19    C STP    19      24.023 -12.020   8.383    0.00     3.50
+ATOM     20    O STP    19      22.709 -16.865  10.854    0.00     3.94
+ATOM     21    O STP    19      22.701 -16.860  10.841    0.00     3.93
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket1_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket1_atm.pdb
@@ -0,0 +1,77 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     1:
+HEADER 0  - Pocket Score                      : 0.9770
+HEADER 1  - Drug Score                        : 0.9590
+HEADER 2  - Number of alpha spheres           :   106
+HEADER 3  - Mean alpha-sphere radius          : 3.9041
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4571
+HEADER 5  - Mean B-factor of pocket residues  : 0.2063
+HEADER 6  - Hydrophobicity Score              : 21.6296
+HEADER 7  - Polarity Score                    :    14
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 585.2505
+HEADER 10  -Pocket volume (convex hull)       : 134.8042
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 38.9500
+HEADER 13 - Number of apolar alpha sphere     :    40
+HEADER 14 - Proportion of apolar alpha sphere : 0.3774
+ATOM    307   CA GLY E  52      16.515  11.229   1.718  0.00  0.00           C 0
+ATOM    302    O THR E  51      15.105  10.533   3.911  0.00  0.00           O 0
+ATOM    470   NZ LYS E  72      11.886  11.415  -3.274  0.62  1.09           N 0
+ATOM   1408  OD2 ASP E 184      13.386   7.180  -2.250  0.00  0.00           O 0
+ATOM    306    N GLY E  52      15.808  12.158   2.525  0.00  0.00           N 0
+ATOM   1279   NZ LYS E 168      16.625   4.590  -0.059  0.00  0.00           N 0
+ATOM   2903  ND2 ASN I  20      18.976   8.461   3.615  0.72  2.19           N 0
+ATOM   2888    O ARG I  19      18.356   4.760   2.859  0.80  2.14           O 0
+ATOM   2884  NH2 ARG I  18      13.846   8.402   5.477  0.64  1.09           N 0
+ATOM   1278   CE LYS E 168      15.628   3.857   0.741  0.00  0.00           C 0
+ATOM   1291   CB GLU E 170      13.987   3.813   4.259  0.00  0.00           C 0
+ATOM    310    N SER E  53      18.416  11.064   0.223  0.00  0.00           N 0
+ATOM   2904    N ALA I  21      19.741   6.551  -0.547  0.00  0.00           N 0
+ATOM   1319  CD2 LEU E 173       6.188   6.273   4.906  0.00  0.00           C 0
+ATOM    291   CB LEU E  49       7.080  13.024   7.073  0.00  0.00           C 0
+ATOM    346   CB VAL E  57       8.724  13.845   2.750  0.00  0.00           C 0
+ATOM    347  CG1 VAL E  57       7.205  13.668   2.731  0.00  0.00           C 0
+ATOM   1318  CD1 LEU E 173       5.187   6.467   2.657  0.00  0.00           C 0
+ATOM    899    O VAL E 123       2.379   7.571   6.588  0.00  0.00           O 0
+ATOM   2576   CZ PHE E 327       4.701   9.108   8.082  0.00  0.00           C 0
+ATOM    348  CG2 VAL E  57       9.375  13.206   1.550  0.00  0.00           C 0
+ATOM    299    N THR E  51      13.468  12.205   5.329  0.00  0.00           N 0
+ATOM    297    C GLY E  50      12.337  12.848   5.580  0.00  0.00           C 0
+ATOM    896    N VAL E 123       0.751   9.121   4.312  0.00  0.00           N 0
+ATOM    890  CD1 TYR E 122       1.561  12.091   6.196  0.00  0.00           C 0
+ATOM   2574  CE1 PHE E 327       6.064   8.851   7.923  0.00  0.00           C 0
+ATOM    290    O LEU E  49       9.471  11.567   8.335  0.39  1.07           O 0
+ATOM    924  OE2 GLU E 127      11.685   6.755   6.599  0.00  0.00           O 0
+ATOM    293  CD1 LEU E  49       4.728  13.522   6.391  0.00  0.00           C 0
+ATOM    323  CD2 PHE E  54      17.672  10.850  -4.138  0.00  0.00           C 0
+ATOM    301    C THR E  51      15.155  11.716   3.603  0.00  0.00           C 0
+ATOM    330    O GLY E  55      14.729  14.598   1.098  0.00  0.00           O 0
+ATOM    469   CE LYS E  72      11.554  12.837  -3.024  0.00  0.00           C 0
+ATOM    296   CA GLY E  50      11.421  12.150   6.532  0.00  0.00           C 0
+ATOM    295    N GLY E  50      10.301  13.000   6.819  0.00  0.00           N 0
+ATOM    289    C LEU E  49       9.418  12.623   7.712  0.00  0.00           C 0
+ATOM   2897   CA ASN I  20      20.003   6.753   1.843  0.00  0.00           C 0
+ATOM    453   CB ALA E  70       3.300  13.315   1.951  0.00  0.00           C 0
+ATOM    878    O GLU E 121       0.705  10.758   1.227  0.00  0.00           O 0
+ATOM   2908   CB ALA I  21      18.886   6.415  -2.821  0.00  0.00           C 0
+ATOM    874   CE MET E 120       5.513  12.462  -1.428  0.00  0.00           C 0
+ATOM   1399  OG1 THR E 183       6.683   8.029  -1.374  0.64  1.07           O 0
+ATOM   1405   CB ASP E 184      11.138   6.567  -2.570  0.00  0.00           C 0
+ATOM   1401    N ASP E 184       8.634   6.825  -2.778  0.38  2.19           N 0
+ATOM   1406   CG ASP E 184      12.368   7.265  -3.077  0.00  0.00           C 0
+ATOM    327    N GLY E  55      15.722  14.519  -1.548  0.00  0.00           N 0
+ATOM    468   CD LYS E  72      10.047  13.080  -2.872  0.00  0.00           C 0
+ATOM    873   SD MET E 120       4.694  11.122  -2.317  0.00  0.00           S 0
+ATOM    737  CG1 VAL E 104       2.360   7.256  -0.876  0.00  0.00           C 0
+ATOM    316    N PHE E  54      18.074  12.798  -1.741  0.00  0.00           N 0
+ATOM   2572  CD1 PHE E 327       6.963   9.283   8.898  0.00  0.00           C 0
+ATOM   1302  OD1 ASN E 171      12.563   5.062  -0.085  0.00  0.00           O 0
+ATOM    921   CG GLU E 127       9.791   5.422   7.060  0.00  0.00           C 0
+ATOM   1290    O GLU E 170      11.096   4.894   3.559  0.00  0.00           O 0
+ATOM   1400  CG2 THR E 183       7.645   6.518   0.354  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket1_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket1_vert.pqr
@@ -0,0 +1,128 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     1:
+HEADER 0  - Pocket Score                      : 0.9770
+HEADER 1  - Drug Score                        : 0.9590
+HEADER 2  - Number of V. Vertices             :   106
+HEADER 3  - Mean alpha-sphere radius          : 3.9041
+HEADER 4  - Mean alpha-sphere SA              : 0.4571
+HEADER 5  - Mean B-factor                     : 0.2063
+HEADER 6  - Hydrophobicity Score              : 21.6296
+HEADER 7  - Polarity Score                    :    14
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 585.2505
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 38.9500
+HEADER 12 - Number of apolar alpha sphere     :    40
+HEADER 13 - Proportion of apolar alpha sphere : 0.3774
+ATOM      1    O STP     1      12.696  10.125   0.572    0.00     4.14
+ATOM      2    O STP     1      12.658  10.336   0.615    0.00     4.11
+ATOM      3    O STP     1      15.748   7.295   2.281    0.00     3.68
+ATOM      4    O STP     1      15.893   7.629   1.836    0.00     3.66
+ATOM      5    O STP     1      15.737   7.221   2.651    0.00     3.60
+ATOM      6    O STP     1      15.587   7.185   2.383    0.00     3.71
+ATOM      7    O STP     1      15.560   7.162   2.428    0.00     3.71
+ATOM      8    O STP     1      15.411   6.698   2.817    0.00     3.53
+ATOM      9    O STP     1      16.502   8.143  -0.698    0.00     3.61
+ATOM     10    O STP     1      16.245   8.195  -0.256    0.00     3.63
+ATOM     11    O STP     1      16.747   8.027   0.402    0.00     3.47
+ATOM     12    C STP     1       8.391   9.917   4.429    0.00     4.28
+ATOM     13    C STP     1       4.608   9.454   4.528    0.00     3.57
+ATOM     14    O STP     1      12.160   9.989   0.796    0.00     4.32
+ATOM     15    C STP     1       8.419   9.736   3.826    0.00     4.26
+ATOM     16    O STP     1      11.311   9.970   2.834    0.00     3.98
+ATOM     17    O STP     1      10.943   9.949   3.228    0.00     3.99
+ATOM     18    O STP     1       3.964  10.063   4.903    0.00     3.40
+ATOM     19    O STP     1       4.493   9.803   4.348    0.00     3.80
+ATOM     20    O STP     1       8.901   9.248   5.088    0.00     4.03
+ATOM     21    C STP     1       7.945   9.977   4.425    0.00     4.13
+ATOM     22    C STP     1       5.641  10.208   4.133    0.00     4.05
+ATOM     23    C STP     1       5.137   9.948   4.335    0.00     3.86
+ATOM     24    C STP     1       5.973  10.461   4.440    0.00     3.84
+ATOM     25    C STP     1       5.539  10.237   4.137    0.00     4.07
+ATOM     26    C STP     1       5.166  10.162   4.234    0.00     4.02
+ATOM     27    C STP     1       4.419  10.241   4.427    0.00     3.84
+ATOM     28    C STP     1       4.642  10.149   4.193    0.00     4.03
+ATOM     29    O STP     1      15.028  10.431  -1.579    0.00     3.70
+ATOM     30    O STP     1      15.448   9.997  -1.468    0.00     3.58
+ATOM     31    O STP     1      11.920  10.913   2.425    0.00     3.54
+ATOM     32    O STP     1      12.555  10.431   0.673    0.00     4.12
+ATOM     33    O STP     1      12.398  10.456   0.747    0.00     4.16
+ATOM     34    O STP     1      12.462  10.651   0.708    0.00     4.10
+ATOM     35    O STP     1      13.408  11.474  -0.038    0.00     3.58
+ATOM     36    O STP     1      12.575  11.875   1.278    0.00     3.48
+ATOM     37    O STP     1      12.622  11.440   0.498    0.00     3.84
+ATOM     38    O STP     1      12.543  11.701   0.360    0.00     3.70
+ATOM     39    O STP     1      10.964   9.954   3.310    0.00     3.93
+ATOM     40    O STP     1      10.084   9.342   3.463    0.00     4.37
+ATOM     41    C STP     1      10.913   9.938   3.249    0.00     3.99
+ATOM     42    C STP     1       8.417   9.911   4.438    0.00     4.29
+ATOM     43    O STP     1       8.933   9.304   4.971    0.00     4.09
+ATOM     44    C STP     1       9.300   9.308   3.778    0.00     4.49
+ATOM     45    C STP     1       8.797   9.677   4.062    0.00     4.37
+ATOM     46    C STP     1       8.647   9.616   4.763    0.00     4.15
+ATOM     47    C STP     1       8.438   9.899   4.628    0.00     4.19
+ATOM     48    C STP     1       8.422   9.882   4.527    0.00     4.26
+ATOM     49    C STP     1       8.477  10.165   4.509    0.00     4.09
+ATOM     50    O STP     1       8.499  10.142   4.794    0.00     3.94
+ATOM     51    O STP     1       8.496  10.107   4.758    0.00     3.98
+ATOM     52    O STP     1      16.898   7.905   0.868    0.00     3.45
+ATOM     53    O STP     1      16.869   7.884   0.943    0.00     3.45
+ATOM     54    C STP     1       4.361  10.400   4.200    0.00     3.83
+ATOM     55    O STP     1       3.879   9.828   2.663    0.00     3.61
+ATOM     56    C STP     1       5.222  10.328   3.927    0.00     4.06
+ATOM     57    C STP     1       4.638  10.187   4.121    0.00     4.04
+ATOM     58    O STP     1      16.512   8.151  -0.730    0.00     3.61
+ATOM     59    O STP     1      16.501   8.709  -1.584    0.00     3.53
+ATOM     60    O STP     1      16.508   8.126  -0.728    0.00     3.60
+ATOM     61    C STP     1       7.098  10.540   1.083    0.00     3.54
+ATOM     62    C STP     1       5.770  10.197   1.723    0.00     3.89
+ATOM     63    C STP     1       5.664  10.226   1.757    0.00     3.89
+ATOM     64    C STP     1       4.772   9.928   1.248    0.00     3.76
+ATOM     65    O STP     1      11.132   9.536   0.429    0.00     4.22
+ATOM     66    O STP     1      10.011   9.555  -0.632    0.00     3.74
+ATOM     67    O STP     1      11.311   9.372  -0.515    0.00     3.48
+ATOM     68    O STP     1      14.016  11.694  -0.593    0.00     3.44
+ATOM     69    O STP     1       9.627  10.169  -0.589    0.00     3.72
+ATOM     70    C STP     1       8.473  10.880  -0.785    0.00     3.42
+ATOM     71    C STP     1       4.769   9.927   1.247    0.00     3.76
+ATOM     72    C STP     1       4.412   9.621   0.996    0.00     3.65
+ATOM     73    C STP     1       4.769   9.927   1.247    0.00     3.76
+ATOM     74    C STP     1       4.289   9.742   1.121    0.00     3.73
+ATOM     75    C STP     1       4.327   9.797   1.169    0.00     3.75
+ATOM     76    O STP     1      15.472  10.546  -1.499    0.00     3.45
+ATOM     77    O STP     1      15.057  10.749  -1.594    0.00     3.65
+ATOM     78    O STP     1      14.976  11.017  -1.509    0.00     3.58
+ATOM     79    O STP     1      15.047  11.161  -1.927    0.00     3.45
+ATOM     80    O STP     1       9.031   8.924   6.153    0.00     3.46
+ATOM     81    O STP     1      14.459   6.786   2.374    0.00     3.55
+ATOM     82    O STP     1      14.767   7.308   1.990    0.00     3.77
+ATOM     83    O STP     1      11.581   9.247   1.361    0.00     4.54
+ATOM     84    O STP     1      11.373   9.098   1.697    0.00     4.57
+ATOM     85    O STP     1      14.886   7.436   1.738    0.00     3.79
+ATOM     86    O STP     1      14.831   7.840   1.220    0.00     3.82
+ATOM     87    O STP     1      14.929   7.783   1.201    0.00     3.83
+ATOM     88    O STP     1      14.927   7.767   1.259    0.00     3.84
+ATOM     89    C STP     1       8.772   8.499   5.722    0.00     3.51
+ATOM     90    O STP     1      10.096   9.193   3.267    0.00     4.42
+ATOM     91    O STP     1      11.325   9.075   1.723    0.00     4.57
+ATOM     92    O STP     1      11.202   9.037   1.672    0.00     4.55
+ATOM     93    C STP     1      11.147   9.165   1.033    0.00     4.44
+ATOM     94    O STP     1      11.183   9.143   1.108    0.00     4.47
+ATOM     95    O STP     1      11.164   9.093   1.052    0.00     4.42
+ATOM     96    O STP     1      10.152   9.628  -0.115    0.00     4.02
+ATOM     97    O STP     1      10.159   9.604  -0.140    0.00     4.01
+ATOM     98    C STP     1      10.214   9.605  -0.074    0.00     4.04
+ATOM     99    O STP     1       9.953   9.182  -0.393    0.00     3.60
+ATOM    100    C STP     1       6.802   9.905   1.993    0.00     3.86
+ATOM    101    C STP     1       7.362  10.012   1.775    0.00     3.78
+ATOM    102    C STP     1       7.845   9.601   3.100    0.00     4.13
+ATOM    103    C STP     1       8.025   9.593   3.157    0.00     4.18
+ATOM    104    C STP     1       9.377   9.170   3.567    0.00     4.51
+ATOM    105    O STP     1       9.399   8.934   3.561    0.00     4.38
+ATOM    106    O STP     1       9.649   9.131   3.392    0.00     4.48
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket2_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket2_atm.pdb
@@ -0,0 +1,45 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     2:
+HEADER 0  - Pocket Score                      : 0.1402
+HEADER 1  - Drug Score                        : 0.0010
+HEADER 2  - Number of alpha spheres           :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.9712
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6139
+HEADER 5  - Mean B-factor of pocket residues  : 0.8934
+HEADER 6  - Hydrophobicity Score              : 12.1667
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.2500
+HEADER 9  - Pocket volume (Monte Carlo)       : 262.3233
+HEADER 10  -Pocket volume (convex hull)       : 7.2454
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 4.0000
+HEADER 13 - Number of apolar alpha sphere     :     5
+HEADER 14 - Proportion of apolar alpha sphere : 0.2632
+ATOM    309    O GLY E  52      18.223  12.904   1.426  0.00  0.00           O 0
+ATOM    330    O GLY E  55      14.729  14.598   1.098  0.00  0.00           O 0
+ATOM    304  OG1 THR E  51      15.944  14.681   4.769  0.00  0.00           O 0
+ATOM    521   NZ LYS E  78      20.649  16.599  -0.867  0.21  4.37           N 0
+ATOM   2648  CD1 ILE E 335      11.727  24.114   3.014  0.00  0.00           C 0
+ATOM   2647  CG2 ILE E 335      10.550  26.263   0.508  0.00  0.00           C 0
+ATOM    831  ND2 ASN E 115      12.293  25.406  -3.370  0.55  1.09           N 0
+ATOM    477  CG2 ILE E  73      11.117  21.494  -1.628  0.00  0.00           C 0
+ATOM   2649    N ARG E 336      13.118  27.889   0.582  0.00  0.00           N 0
+ATOM    340  NH1 ARG E  56      14.550  20.184   4.336  0.00  0.00           N 0
+ATOM    329    C GLY E  55      14.286  15.376   0.253  0.00  0.00           C 0
+ATOM    328   CA GLY E  55      14.897  15.583  -1.082  0.00  0.00           C 0
+ATOM    520   CE LYS E  78      19.997  17.773  -1.474  0.00  0.00           C 0
+ATOM    335   CB ARG E  56      13.027  17.288   2.478  0.00  0.00           C 0
+ATOM   2631  OE2 GLU E 333      16.987  19.040   5.884  0.00  0.00           O 0
+ATOM    319    O PHE E  54      17.192  16.071  -2.246  0.00  0.00           O 0
+ATOM    830  OD1 ASN E 115      14.070  24.389  -4.295  0.00  0.00           O 0
+ATOM    487    N ASP E  75      15.327  20.402  -4.473  0.00  0.00           N 0
+ATOM    491   CB ASP E  75      17.237  21.958  -3.927  0.00  0.00           C 0
+ATOM    337   CD ARG E  56      12.800  19.652   2.652  0.00  0.00           C 0
+ATOM    474    O ILE E  73      12.604  18.077  -2.062  0.72  2.14           O 0
+ATOM    331    N ARG E  56      13.263  16.163   0.423  0.00  0.00           N 0
+ATOM    336   CG ARG E  56      12.385  18.520   1.875  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket2_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket2_vert.pqr
@@ -0,0 +1,41 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     2:
+HEADER 0  - Pocket Score                      : 0.1402
+HEADER 1  - Drug Score                        : 0.0010
+HEADER 2  - Number of V. Vertices             :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.9712
+HEADER 4  - Mean alpha-sphere SA              : 0.6139
+HEADER 5  - Mean B-factor                     : 0.8934
+HEADER 6  - Hydrophobicity Score              : 12.1667
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.2500
+HEADER 9  - Real volume (approximation)       : 262.3233
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 4.0000
+HEADER 12 - Number of apolar alpha sphere     :     5
+HEADER 13 - Proportion of apolar alpha sphere : 0.2632
+ATOM      1    O STP     2      17.904  16.846   2.034    0.00     4.00
+ATOM      2    C STP     2      13.212  24.010  -0.223    0.00     3.56
+ATOM      3    O STP     2      13.590  24.333  -0.124    0.00     3.66
+ATOM      4    C STP     2      16.767  18.684   1.078    0.00     4.22
+ATOM      5    C STP     2      16.715  18.704   1.057    0.00     4.20
+ATOM      6    O STP     2      17.342  17.855   1.830    0.00     4.24
+ATOM      7    O STP     2      17.041  17.846   1.980    0.00     4.08
+ATOM      8    O STP     2      16.580  19.060   0.747    0.00     4.27
+ATOM      9    O STP     2      17.635  17.024   1.403    0.00     3.80
+ATOM     10    O STP     2      17.395  17.419   1.401    0.00     3.89
+ATOM     11    C STP     2      16.900  18.376   1.091    0.00     4.07
+ATOM     12    O STP     2      17.782  16.444   1.256    0.00     3.57
+ATOM     13    O STP     2      14.632  22.244  -1.461    0.00     3.60
+ATOM     14    O STP     2      14.379  23.675  -0.187    0.00     4.18
+ATOM     15    O STP     2      14.950  20.959  -0.498    0.00     4.03
+ATOM     16    O STP     2      16.062  19.544  -0.072    0.00     4.25
+ATOM     17    O STP     2      16.188  19.842  -0.177    0.00     4.42
+ATOM     18    C STP     2      16.044  18.633   0.739    0.00     3.73
+ATOM     19    O STP     2      15.502  19.054  -0.011    0.00     3.68
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket3_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket3_atm.pdb
@@ -0,0 +1,36 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     3:
+HEADER 0  - Pocket Score                      : 0.1266
+HEADER 1  - Drug Score                        : 0.0057
+HEADER 2  - Number of alpha spheres           :    18
+HEADER 3  - Mean alpha-sphere radius          : 3.5428
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4022
+HEADER 5  - Mean B-factor of pocket residues  : 0.6322
+HEADER 6  - Hydrophobicity Score              : 68.8750
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 5.2500
+HEADER 9  - Pocket volume (Monte Carlo)       : 77.2004
+HEADER 10  -Pocket volume (convex hull)       : 0.4010
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 17.0000
+HEADER 13 - Number of apolar alpha sphere     :    18
+HEADER 14 - Proportion of apolar alpha sphere : 1.0000
+ATOM    930   CG MET E 128       8.403  -2.687   7.280  0.00  0.00           C 0
+ATOM    926   CA MET E 128       8.115  -0.207   8.023  0.00  0.00           C 0
+ATOM   1094   OH TYR E 146       3.007  -4.773   9.128  0.69  1.07           O 0
+ATOM   1023   CZ PHE E 138       7.842  -4.944  10.972  0.00  0.00           C 0
+ATOM    954   CB HIS E 131       7.301  -0.869  12.556  0.00  0.00           C 0
+ATOM   2473  CD1 PHE E 314       1.599  -2.313  12.616  0.00  0.00           C 0
+ATOM    997  CD1 ILE E 135       6.961  -4.213  14.925  0.00  0.00           C 0
+ATOM   1325  CG1 ILE E 174       3.748   0.392   8.044  0.00  0.00           C 0
+ATOM   2475  CE1 PHE E 314       1.989  -1.013  12.939  0.00  0.00           C 0
+ATOM   1054  CE1 HIS E 142       4.019  -7.046  11.747  0.00  0.00           C 0
+ATOM   1327  CD1 ILE E 174       3.664  -0.736   7.020  0.00  0.00           C 0
+ATOM    955   CG HIS E 131       6.397   0.292  12.561  0.00  0.00           C 0
+ATOM    957  CD2 HIS E 131       6.036   1.134  11.558  0.00  0.00           C 0
+ATOM   2472   CG PHE E 314       1.571  -3.331  13.568  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket3_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket3_vert.pqr
@@ -0,0 +1,40 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     3:
+HEADER 0  - Pocket Score                      : 0.1266
+HEADER 1  - Drug Score                        : 0.0057
+HEADER 2  - Number of V. Vertices             :    18
+HEADER 3  - Mean alpha-sphere radius          : 3.5428
+HEADER 4  - Mean alpha-sphere SA              : 0.4022
+HEADER 5  - Mean B-factor                     : 0.6322
+HEADER 6  - Hydrophobicity Score              : 68.8750
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 5.2500
+HEADER 9  - Real volume (approximation)       : 77.2004
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 17.0000
+HEADER 12 - Number of apolar alpha sphere     :    18
+HEADER 13 - Proportion of apolar alpha sphere : 1.0000
+ATOM      1    C STP     3       5.666  -2.347   9.650    0.00     3.64
+ATOM      2    C STP     3       5.663  -2.342   9.659    0.00     3.64
+ATOM      3    C STP     3       4.857  -3.237  11.687    0.00     3.51
+ATOM      4    C STP     3       4.909  -3.421  12.179    0.00     3.52
+ATOM      5    C STP     3       4.463  -1.923  10.602    0.00     3.52
+ATOM      6    C STP     3       4.751  -3.640  11.929    0.00     3.49
+ATOM      7    C STP     3       4.816  -3.657  12.202    0.00     3.51
+ATOM      8    C STP     3       5.643  -2.334   9.598    0.00     3.62
+ATOM      9    C STP     3       5.573  -2.273   9.693    0.00     3.63
+ATOM     10    C STP     3       5.625  -2.300   9.658    0.00     3.64
+ATOM     11    C STP     3       5.618  -2.250   9.664    0.00     3.62
+ATOM     12    C STP     3       4.669  -1.977  10.488    0.00     3.53
+ATOM     13    C STP     3       4.819  -1.860  10.403    0.00     3.43
+ATOM     14    C STP     3       4.472  -1.924  10.605    0.00     3.53
+ATOM     15    C STP     3       4.423  -1.750  10.637    0.00     3.43
+ATOM     16    C STP     3       4.474  -1.928  10.609    0.00     3.53
+ATOM     17    C STP     3       4.552  -2.069  10.740    0.00     3.51
+ATOM     18    C STP     3       4.780  -3.687  12.261    0.00     3.48
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket4_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket4_atm.pdb
@@ -0,0 +1,44 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     4:
+HEADER 0  - Pocket Score                      : 0.1199
+HEADER 1  - Drug Score                        : 0.0012
+HEADER 2  - Number of alpha spheres           :    37
+HEADER 3  - Mean alpha-sphere radius          : 3.7030
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4414
+HEADER 5  - Mean B-factor of pocket residues  : 0.3449
+HEADER 6  - Hydrophobicity Score              : 21.3000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 5.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 253.0846
+HEADER 10  -Pocket volume (convex hull)       : 9.3769
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 7.0000
+HEADER 13 - Number of apolar alpha sphere     :     8
+HEADER 14 - Proportion of apolar alpha sphere : 0.2162
+ATOM   2604   OH TYR E 330      13.684  10.354   9.085  0.00  0.00           O 0
+ATOM   2577    N ASP E 328      10.151   9.909  12.765  0.43  2.19           N 0
+ATOM    290    O LEU E  49       9.471  11.567   8.335  0.39  1.07           O 0
+ATOM    924  OE2 GLU E 127      11.685   6.755   6.599  0.00  0.00           O 0
+ATOM    923  OE1 GLU E 127      11.951   5.007   7.989  0.60  1.07           O 0
+ATOM   2584  OD2 ASP E 328      14.041   8.286  13.108  0.00  0.00           O 0
+ATOM   2880   CD ARG I  18      14.991   7.067   8.769  0.00  0.00           C 0
+ATOM   2582   CG ASP E 328      13.020   8.743  13.609  0.00  0.00           C 0
+ATOM    940  CD2 PHE E 129      14.226   2.625   9.854  0.00  0.00           C 0
+ATOM    948   CB SER E 130      10.249   3.583  12.410  0.00  0.00           C 0
+ATOM    942  CE2 PHE E 129      15.500   2.729  10.413  0.00  0.00           C 0
+ATOM   2583  OD1 ASP E 328      12.217   8.079  14.409  0.00  0.00           O 0
+ATOM   2567   CA PHE E 327       7.809   9.376  12.138  0.00  0.00           C 0
+ATOM    949   OG SER E 130       8.949   3.497  11.843  0.67  1.07           O 0
+ATOM   2561    O ASN E 326       6.724   6.878  12.348  0.72  1.07           O 0
+ATOM    972   CB ARG E 133      14.518  -0.467  13.709  0.00  0.00           C 0
+ATOM    945   CA SER E 130      10.922   2.228  12.285  0.00  0.00           C 0
+ATOM    947    O SER E 130      10.710   0.913  14.300  0.44  3.21           O 0
+ATOM    921   CG GLU E 127       9.791   5.422   7.060  0.00  0.00           C 0
+ATOM    916    N GLU E 127       7.291   4.505   8.648  0.00  0.00           N 0
+ATOM   2572  CD1 PHE E 327       6.963   9.283   8.898  0.00  0.00           C 0
+ATOM    922   CD GLU E 127      11.253   5.708   7.267  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket4_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket4_vert.pqr
@@ -0,0 +1,59 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     4:
+HEADER 0  - Pocket Score                      : 0.1199
+HEADER 1  - Drug Score                        : 0.0012
+HEADER 2  - Number of V. Vertices             :    37
+HEADER 3  - Mean alpha-sphere radius          : 3.7030
+HEADER 4  - Mean alpha-sphere SA              : 0.4414
+HEADER 5  - Mean B-factor                     : 0.3449
+HEADER 6  - Hydrophobicity Score              : 21.3000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 5.0000
+HEADER 9  - Real volume (approximation)       : 253.0846
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 7.0000
+HEADER 12 - Number of apolar alpha sphere     :     8
+HEADER 13 - Proportion of apolar alpha sphere : 0.2162
+ATOM      1    O STP     4      10.707   8.465   9.562    0.00     3.56
+ATOM      2    O STP     4      11.897   7.600  10.387    0.00     3.53
+ATOM      3    O STP     4      11.713   7.651  10.429    0.00     3.61
+ATOM      4    O STP     4      11.722   7.673  10.440    0.00     3.59
+ATOM      5    O STP     4      11.706   7.635  10.442    0.00     3.60
+ATOM      6    O STP     4      13.057   5.577  11.209    0.00     3.45
+ATOM      7    C STP     4      13.599   4.782  12.622    0.00     3.56
+ATOM      8    O STP     4      12.926   5.521  11.298    0.00     3.49
+ATOM      9    O STP     4      11.593   6.620  11.138    0.00     3.56
+ATOM     10    O STP     4      11.150   6.837  11.229    0.00     3.58
+ATOM     11    O STP     4      11.203   6.847  11.061    0.00     3.66
+ATOM     12    O STP     4      10.100   6.854  10.639    0.00     3.72
+ATOM     13    O STP     4      10.043   6.829  10.609    0.00     3.72
+ATOM     14    O STP     4      10.008   6.832  11.002    0.00     3.55
+ATOM     15    O STP     4       9.996   6.814  10.721    0.00     3.65
+ATOM     16    O STP     4      14.136   3.921  15.176    0.00     4.64
+ATOM     17    O STP     4      13.450   4.065  15.198    0.00     4.27
+ATOM     18    O STP     4      14.349   4.009  14.805    0.00     4.61
+ATOM     19    O STP     4      13.844   4.358  14.153    0.00     4.07
+ATOM     20    C STP     4      14.400   4.002  14.664    0.00     4.57
+ATOM     21    C STP     4      13.873   4.433  13.491    0.00     3.88
+ATOM     22    C STP     4      13.578   4.355  12.749    0.00     3.43
+ATOM     23    O STP     4       9.524   6.563  10.325    0.00     3.47
+ATOM     24    C STP     4       9.327   7.050  10.077    0.00     3.46
+ATOM     25    O STP     4      10.903   8.245   9.723    0.00     3.55
+ATOM     26    O STP     4      11.424   7.798  10.169    0.00     3.58
+ATOM     27    O STP     4      10.102   6.908  10.584    0.00     3.71
+ATOM     28    O STP     4      10.425   8.337   9.557    0.00     3.58
+ATOM     29    O STP     4      10.324   8.322   9.469    0.00     3.54
+ATOM     30    O STP     4      10.351   8.314   9.560    0.00     3.59
+ATOM     31    C STP     4      10.082   7.855   9.856    0.00     3.56
+ATOM     32    C STP     4       9.763   7.428   9.952    0.00     3.52
+ATOM     33    C STP     4       9.808   6.869  10.405    0.00     3.64
+ATOM     34    O STP     4      10.016   6.824  10.586    0.00     3.71
+ATOM     35    O STP     4       9.960   6.815  10.553    0.00     3.70
+ATOM     36    O STP     4       9.895   6.462  10.350    0.00     3.45
+ATOM     37    O STP     4       9.826   6.743  10.451    0.00     3.64
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket5_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket5_atm.pdb
@@ -0,0 +1,37 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     5:
+HEADER 0  - Pocket Score                      : 0.0990
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    22
+HEADER 3  - Mean alpha-sphere radius          : 3.8005
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4136
+HEADER 5  - Mean B-factor of pocket residues  : 0.4612
+HEADER 6  - Hydrophobicity Score              : 53.5556
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 4.6667
+HEADER 9  - Pocket volume (Monte Carlo)       : 192.6857
+HEADER 10  -Pocket volume (convex hull)       : 3.2029
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     1
+HEADER 14 - Proportion of apolar alpha sphere : 0.0455
+ATOM    683    O VAL E  98      -1.548   5.638 -10.652  0.00  0.00           O 0
+ATOM    751    O LEU E 106      -1.526  12.712  -7.346  0.53  5.36           O 0
+ATOM    669    O GLN E  96      -1.095   9.562 -12.379  0.38  8.57           O 0
+ATOM    694  ND2 ASN E  99      -4.994   4.655  -8.679  0.44  7.66           N 0
+ATOM    744   CG LYS E 105      -3.554   7.695  -4.276  0.00  0.00           C 0
+ATOM    735    O VAL E 104       0.854   6.823  -5.094  0.68  2.14           O 0
+ATOM    727    O LEU E 103      -0.468   4.251  -3.772  0.59  1.07           O 0
+ATOM    698    O PHE E 100      -2.637   1.775  -5.548  0.62  2.14           O 0
+ATOM    743   CB LYS E 105      -2.683   8.936  -4.202  0.00  0.00           C 0
+ATOM    748    N LEU E 106      -0.319  10.587  -5.784  0.55  3.28           N 0
+ATOM    661    O LEU E  95       1.522   8.309 -10.196  0.39  1.07           O 0
+ATOM    695    N PHE E 100      -2.598   1.813  -8.277  0.00  0.00           N 0
+ATOM    688   CA ASN E  99      -2.921   3.314 -10.023  0.00  0.00           C 0
+ATOM    728   CB LEU E 103       1.213   2.937  -5.870  0.00  0.00           C 0
+ATOM    740   CA LYS E 105      -1.217   8.740  -4.554  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket5_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket5_vert.pqr
@@ -0,0 +1,44 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     5:
+HEADER 0  - Pocket Score                      : 0.0990
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    22
+HEADER 3  - Mean alpha-sphere radius          : 3.8005
+HEADER 4  - Mean alpha-sphere SA              : 0.4136
+HEADER 5  - Mean B-factor                     : 0.4612
+HEADER 6  - Hydrophobicity Score              : 53.5556
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 4.6667
+HEADER 9  - Real volume (approximation)       : 192.6857
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     1
+HEADER 13 - Proportion of apolar alpha sphere : 0.0455
+ATOM      1    O STP     5      -3.903   9.091  -8.804    0.00     4.57
+ATOM      2    O STP     5      -3.754   8.992  -8.593    0.00     4.51
+ATOM      3    O STP     5      -2.044   6.009  -7.092    0.00     3.61
+ATOM      4    O STP     5      -2.612   5.104  -6.282    0.00     3.41
+ATOM      5    O STP     5      -2.076   5.517  -6.742    0.00     3.61
+ATOM      6    O STP     5      -1.785   5.216  -7.035    0.00     3.65
+ATOM      7    O STP     5      -3.701   8.983  -8.573    0.00     4.49
+ATOM      8    O STP     5      -3.246   8.932  -8.467    0.00     4.30
+ATOM      9    O STP     5      -1.423   9.628  -8.928    0.00     3.47
+ATOM     10    O STP     5      -2.819   9.025  -8.670    0.00     4.13
+ATOM     11    O STP     5      -1.924   8.885  -8.753    0.00     3.78
+ATOM     12    O STP     5      -1.997   4.980  -6.859    0.00     3.52
+ATOM     13    O STP     5      -1.773   5.141  -7.052    0.00     3.64
+ATOM     14    O STP     5      -1.816   5.091  -7.152    0.00     3.55
+ATOM     15    O STP     5      -1.491   5.021  -7.121    0.00     3.59
+ATOM     16    O STP     5      -1.417   4.986  -7.145    0.00     3.57
+ATOM     17    O STP     5      -1.425   4.982  -7.131    0.00     3.57
+ATOM     18    O STP     5      -2.908   8.645  -8.261    0.00     4.08
+ATOM     19    O STP     5      -1.967   6.532  -7.237    0.00     3.55
+ATOM     20    C STP     5      -2.911   8.402  -8.137    0.00     3.98
+ATOM     21    O STP     5      -1.038   7.720  -7.892    0.00     3.49
+ATOM     22    O STP     5      -1.266   8.004  -8.024    0.00     3.55
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket6_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket6_atm.pdb
@@ -0,0 +1,38 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     6:
+HEADER 0  - Pocket Score                      : 0.0820
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of alpha spheres           :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.6030
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4001
+HEADER 5  - Mean B-factor of pocket residues  : 0.0000
+HEADER 6  - Hydrophobicity Score              : 42.3636
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 4.0909
+HEADER 9  - Pocket volume (Monte Carlo)       : 117.3184
+HEADER 10  -Pocket volume (convex hull)       : 2.2427
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 4.0000
+HEADER 13 - Number of apolar alpha sphere     :     5
+HEADER 14 - Proportion of apolar alpha sphere : 0.2941
+ATOM   1245   CA ARG E 165      14.814  -0.287  -8.335  0.00  0.00           C 0
+ATOM   1686   CB VAL E 219      17.393  -5.524 -10.220  0.00  0.00           C 0
+ATOM   1612  CD1 ILE E 209      20.583  -3.041  -9.258  0.00  0.00           C 0
+ATOM   1685    O VAL E 219      15.724  -6.452  -7.582  0.62  3.21           O 0
+ATOM   1688  CG2 VAL E 219      16.449  -4.471 -10.833  0.00  0.00           C 0
+ATOM   1695  OD1 ASP E 220      12.980  -3.453  -8.516  0.59  3.21           O 0
+ATOM   1729   CB ALA E 223      15.297  -5.551  -4.153  0.00  0.00           C 0
+ATOM   1247    O ARG E 165      15.996   0.577  -6.414  0.42  8.57           O 0
+ATOM   1583  CD2 LEU E 205      21.487  -1.300  -5.351  0.00  0.00           C 0
+ATOM   1534    O CYS E 199      20.416   0.681  -8.038  0.52  1.07           O 0
+ATOM   1567    O TYR E 204      19.201  -4.777  -3.931  0.42  3.21           O 0
+ATOM   1568   CB TYR E 204      18.169  -3.106  -1.552  0.00  0.00           C 0
+ATOM   1541    N THR E 201      20.126   1.181  -3.203  0.32  2.19           N 0
+ATOM   1538   CA GLY E 200      19.720   1.639  -5.452  0.00  0.00           C 0
+ATOM   1263    N LEU E 167      13.718  -0.744  -3.462  0.00  0.00           N 0
+ATOM   1246    C ARG E 165      14.898   0.347  -6.945  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket6_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket6_vert.pqr
@@ -0,0 +1,39 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     6:
+HEADER 0  - Pocket Score                      : 0.0820
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of V. Vertices             :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.6030
+HEADER 4  - Mean alpha-sphere SA              : 0.4001
+HEADER 5  - Mean B-factor                     : 0.0000
+HEADER 6  - Hydrophobicity Score              : 42.3636
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 4.0909
+HEADER 9  - Real volume (approximation)       : 117.3184
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 4.0000
+HEADER 12 - Number of apolar alpha sphere     :     5
+HEADER 13 - Proportion of apolar alpha sphere : 0.2941
+ATOM      1    C STP     6      17.284  -3.003  -7.392    0.00     3.79
+ATOM      2    C STP     6      17.140  -3.037  -7.495    0.00     3.70
+ATOM      3    C STP     6      17.287  -2.942  -7.558    0.00     3.71
+ATOM      4    O STP     6      15.862  -3.114  -6.582    0.00     3.49
+ATOM      5    O STP     6      18.410  -1.869  -6.831    0.00     3.46
+ATOM      6    O STP     6      18.093  -1.568  -4.665    0.00     3.47
+ATOM      7    O STP     6      18.176  -2.391  -6.545    0.00     3.68
+ATOM      8    O STP     6      18.178  -1.260  -4.556    0.00     3.40
+ATOM      9    O STP     6      18.146  -1.324  -4.503    0.00     3.45
+ATOM     10    O STP     6      17.446  -3.009  -6.936    0.00     3.90
+ATOM     11    O STP     6      17.338  -2.967  -7.164    0.00     3.86
+ATOM     12    O STP     6      16.971  -3.071  -6.456    0.00     3.78
+ATOM     13    O STP     6      16.372  -3.033  -6.540    0.00     3.63
+ATOM     14    O STP     6      16.616  -2.342  -4.591    0.00     3.50
+ATOM     15    O STP     6      16.735  -2.388  -4.679    0.00     3.51
+ATOM     16    C STP     6      16.003  -2.925  -6.361    0.00     3.50
+ATOM     17    C STP     6      15.537  -2.940  -6.326    0.00     3.41
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket7_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket7_atm.pdb
@@ -0,0 +1,49 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     7:
+HEADER 0  - Pocket Score                      : 0.0816
+HEADER 1  - Drug Score                        : 0.0045
+HEADER 2  - Number of alpha spheres           :    31
+HEADER 3  - Mean alpha-sphere radius          : 4.0832
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5901
+HEADER 5  - Mean B-factor of pocket residues  : 0.7298
+HEADER 6  - Hydrophobicity Score              : 15.7273
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.1818
+HEADER 9  - Pocket volume (Monte Carlo)       : 340.5146
+HEADER 10  -Pocket volume (convex hull)       : 37.2504
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 14.7500
+HEADER 13 - Number of apolar alpha sphere     :    16
+HEADER 14 - Proportion of apolar alpha sphere : 0.5161
+ATOM   2349   CA THR E 300      -2.136 -16.523   0.940  0.00  0.00           C 0
+ATOM   2348    N THR E 300      -1.897 -17.858   1.436  0.00  0.00           N 0
+ATOM   2353  OG1 THR E 300       0.238 -16.029   1.169  0.00  0.00           O 0
+ATOM   2346  OG1 THR E 299      -0.824 -19.572   4.432  0.76  3.21           O 0
+ATOM   2344    O THR E 299      -3.875 -18.070   2.502  0.36  6.43           O 0
+ATOM   2343    C THR E 299      -2.779 -18.525   2.162  0.00  0.00           C 0
+ATOM   2444  CG1 VAL E 310      -5.465 -11.342   5.087  0.00  0.00           C 0
+ATOM   2359   CB ASP E 301      -6.814 -15.392  -0.021  0.00  0.00           C 0
+ATOM   2445  CG2 VAL E 310      -6.233 -10.529   2.840  0.00  0.00           C 0
+ATOM   2355    N ASP E 301      -4.279 -15.664   0.214  0.00  0.00           N 0
+ATOM   2389   CB ALA E 304      -8.532 -12.091   0.496  0.00  0.00           C 0
+ATOM   2433    O LYS E 309     -10.006  -9.496   4.644  0.00  0.00           O 0
+ATOM   2397  CD1 ILE E 305      -2.545 -11.291   1.475  0.00  0.00           C 0
+ATOM   2454  OE2 GLU E 311      -5.008 -14.364   8.021  0.00  0.00           O 0
+ATOM   2446    N GLU E 311      -6.776  -9.898   7.187  0.00  0.00           N 0
+ATOM   2440   CA VAL E 310      -7.234  -9.583   4.872  0.00  0.00           C 0
+ATOM   1067   CD ARG E 144       2.373 -16.320   3.946  0.00  0.00           C 0
+ATOM   1070  NH1 ARG E 144       2.427 -17.435   6.611  0.00  0.00           N 0
+ATOM   1073   CA PHE E 145       1.537 -10.378   4.578  0.00  0.00           C 0
+ATOM   1076   CB PHE E 145       0.971  -9.866   5.938  0.00  0.00           C 0
+ATOM   1042    O PRO E 141       2.365 -13.029   7.548  0.65  2.14           O 0
+ATOM   1043   CB PRO E 141       2.135 -15.510   9.719  0.00  0.00           C 0
+ATOM   1066   CG ARG E 144       2.651 -14.825   3.866  0.00  0.00           C 0
+ATOM   1072    N PHE E 145       2.605 -11.335   4.829  0.00  0.00           N 0
+ATOM   1064    O ARG E 144       2.912 -11.965   2.698  0.00  0.00           O 0
+ATOM   1078  CD1 PHE E 145      -1.292  -8.937   5.214  0.00  0.00           C 0
+ATOM   2452   CD GLU E 311      -4.896 -13.238   8.497  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket7_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket7_vert.pqr
@@ -0,0 +1,53 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     7:
+HEADER 0  - Pocket Score                      : 0.0816
+HEADER 1  - Drug Score                        : 0.0045
+HEADER 2  - Number of V. Vertices             :    31
+HEADER 3  - Mean alpha-sphere radius          : 4.0832
+HEADER 4  - Mean alpha-sphere SA              : 0.5901
+HEADER 5  - Mean B-factor                     : 0.7298
+HEADER 6  - Hydrophobicity Score              : 15.7273
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.1818
+HEADER 9  - Real volume (approximation)       : 340.5146
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 14.7500
+HEADER 12 - Number of apolar alpha sphere     :    16
+HEADER 13 - Proportion of apolar alpha sphere : 0.5161
+ATOM      1    O STP     7      -1.389 -15.808   4.608    0.00     3.81
+ATOM      2    O STP     7      -1.682 -16.022   4.590    0.00     3.66
+ATOM      3    O STP     7      -1.648 -15.823   4.692    0.00     3.85
+ATOM      4    C STP     7      -5.623 -13.895   2.816    0.00     3.42
+ATOM      5    C STP     7      -7.247 -14.004   3.331    0.00     3.65
+ATOM      6    C STP     7      -8.747 -13.072   4.181    0.00     3.82
+ATOM      7    C STP     7      -3.506 -14.247   3.643    0.00     3.79
+ATOM      8    O STP     7      -3.650 -14.469   3.805    0.00     3.84
+ATOM      9    O STP     7      -5.817 -14.938   3.693    0.00     3.87
+ATOM     10    C STP     7      -2.262 -14.253   4.649    0.00     4.35
+ATOM     11    O STP     7      -8.823 -12.829   5.969    0.00     3.78
+ATOM     12    C STP     7      -8.681 -12.900   4.221    0.00     3.68
+ATOM     13    O STP     7      -1.409 -15.542   5.914    0.00     4.33
+ATOM     14    O STP     7      -1.417 -15.715   4.699    0.00     3.91
+ATOM     15    O STP     7      -1.682 -15.399   5.074    0.00     4.31
+ATOM     16    C STP     7      -1.560 -13.587   5.226    0.00     4.51
+ATOM     17    C STP     7      -1.567 -13.472   5.345    0.00     4.45
+ATOM     18    O STP     7      -1.180 -15.075   6.105    0.00     4.34
+ATOM     19    O STP     7      -1.076 -15.289   7.116    0.00     4.14
+ATOM     20    O STP     7      -1.505 -13.532   5.394    0.00     4.46
+ATOM     21    O STP     7      -0.289 -13.357   5.212    0.00     3.55
+ATOM     22    C STP     7      -0.289 -13.067   3.400    0.00     3.46
+ATOM     23    O STP     7      -1.253 -14.770   5.826    0.00     4.37
+ATOM     24    C STP     7      -1.525 -13.665   5.202    0.00     4.54
+ATOM     25    O STP     7      -1.488 -13.667   5.270    0.00     4.52
+ATOM     26    C STP     7      -1.739 -14.231   4.832    0.00     4.53
+ATOM     27    C STP     7      -1.647 -14.742   4.977    0.00     4.44
+ATOM     28    C STP     7      -1.682 -14.732   5.030    0.00     4.49
+ATOM     29    C STP     7      -1.616 -13.199   5.185    0.00     4.27
+ATOM     30    C STP     7      -1.612 -13.209   5.227    0.00     4.28
+ATOM     31    C STP     7      -1.726 -13.041   5.798    0.00     4.17
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket8_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket8_atm.pdb
@@ -0,0 +1,36 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     8:
+HEADER 0  - Pocket Score                      : 0.0798
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of alpha spheres           :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.6298
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.3583
+HEADER 5  - Mean B-factor of pocket residues  : 0.0681
+HEADER 6  - Hydrophobicity Score              : 19.9000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.2000
+HEADER 9  - Pocket volume (Monte Carlo)       : 110.9388
+HEADER 10  -Pocket volume (convex hull)       : 2.3995
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 1.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.1333
+ATOM    321   CG PHE E  54      17.995  12.178  -4.417  0.00  0.00           C 0
+ATOM    569  OE1 GLN E  84      18.789  10.413  -9.405  0.00  0.00           O 0
+ATOM    323  CD2 PHE E  54      17.672  10.850  -4.138  0.00  0.00           C 0
+ATOM    628  OE1 GLU E  91      11.799  11.798  -7.613  0.61  4.29           O 0
+ATOM    320   CB PHE E  54      17.100  13.280  -3.954  0.00  0.00           C 0
+ATOM    470   NZ LYS E  72      11.886  11.415  -3.274  0.62  1.09           N 0
+ATOM   1421   CA GLY E 186      12.913   8.374  -7.628  0.00  0.00           C 0
+ATOM   1407  OD1 ASP E 184      12.373   7.897  -4.139  0.00  0.00           O 0
+ATOM    603  OG1 THR E  88      14.838  14.429  -9.929  0.79  2.14           O 0
+ATOM    485  CD1 LEU E  74      13.945  15.900  -4.565  0.00  0.00           C 0
+ATOM    566   CB GLN E  84      18.752  13.052  -9.731  0.00  0.00           C 0
+ATOM   1423    O GLY E 186      14.353   8.217  -9.471  0.00  0.00           O 0
+ATOM    592   CB HIS E  87      16.234   9.885 -11.768  0.00  0.00           C 0
+ATOM   1432  CE1 PHE E 187      17.677   7.326  -7.166  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket8_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket8_vert.pqr
@@ -0,0 +1,37 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     8:
+HEADER 0  - Pocket Score                      : 0.0798
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of V. Vertices             :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.6298
+HEADER 4  - Mean alpha-sphere SA              : 0.3583
+HEADER 5  - Mean B-factor                     : 0.0681
+HEADER 6  - Hydrophobicity Score              : 19.9000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.2000
+HEADER 9  - Real volume (approximation)       : 110.9388
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 1.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.1333
+ATOM      1    O STP     8      15.640  11.395  -7.384    0.00     3.87
+ATOM      2    O STP     8      14.547  11.507  -5.506    0.00     3.47
+ATOM      3    C STP     8      15.133  11.716  -6.441    0.00     3.54
+ATOM      4    O STP     8      14.464  10.763  -5.571    0.00     3.51
+ATOM      5    O STP     8      14.467  10.370  -5.296    0.00     3.44
+ATOM      6    O STP     8      14.848  13.223  -6.639    0.00     3.50
+ATOM      7    O STP     8      15.418  12.203  -7.050    0.00     3.68
+ATOM      8    O STP     8      15.660  11.576  -7.445    0.00     3.87
+ATOM      9    O STP     8      16.047  11.948  -7.515    0.00     3.67
+ATOM     10    O STP     8      15.521  11.388  -7.841    0.00     3.75
+ATOM     11    O STP     8      15.570  11.317  -8.748    0.00     3.41
+ATOM     12    O STP     8      15.604  11.206  -7.376    0.00     3.86
+ATOM     13    O STP     8      15.544  11.122  -7.297    0.00     3.82
+ATOM     14    O STP     8      15.979  10.444  -7.233    0.00     3.55
+ATOM     15    C STP     8      15.792  10.270  -7.031    0.00     3.50
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket9_atm.pdb
+++ b/tests/reference_output/1ATP_out/pockets/pocket9_atm.pdb
@@ -0,0 +1,41 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     9:
+HEADER 0  - Pocket Score                      : 0.0433
+HEADER 1  - Drug Score                        : 0.0090
+HEADER 2  - Number of alpha spheres           :    22
+HEADER 3  - Mean alpha-sphere radius          : 3.7189
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4354
+HEADER 5  - Mean B-factor of pocket residues  : 0.6548
+HEADER 6  - Hydrophobicity Score              : 61.3000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 5.2000
+HEADER 9  - Pocket volume (Monte Carlo)       : 257.6532
+HEADER 10  -Pocket volume (convex hull)       : 20.1196
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 15.0000
+HEADER 13 - Number of apolar alpha sphere     :    16
+HEADER 14 - Proportion of apolar alpha sphere : 0.7273
+ATOM    211    O LEU E  40       1.756  26.553  -0.763  0.56  1.07           O 0
+ATOM    216    N ASP E  41       1.737  28.499  -1.964  0.00  0.00           N 0
+ATOM    217   CA ASP E  41       0.826  29.328  -1.179  0.00  0.00           C 0
+ATOM    214  CD1 LEU E  40       6.287  27.704  -0.907  0.00  0.00           C 0
+ATOM    371  CG2 VAL E  60       2.938  21.371   3.082  0.00  0.00           C 0
+ATOM    215  CD2 LEU E  40       4.920  25.611  -0.876  0.00  0.00           C 0
+ATOM    256   CB ARG E  45       5.477  24.448   5.841  0.00  0.00           C 0
+ATOM    460   SD MET E  71       5.246  21.433  -0.548  0.00  0.00           S 0
+ATOM    252    N ARG E  45       3.004  24.807   5.734  0.36  2.19           N 0
+ATOM    355   SD MET E  58       8.463  21.425   5.189  0.00  0.00           S 0
+ATOM    356   CE MET E  58       9.807  22.030   4.159  0.00  0.00           C 0
+ATOM    210    C LEU E  40       2.136  27.238  -1.696  0.00  0.00           C 0
+ATOM   2646  CG1 ILE E 335      10.465  24.754   2.439  0.00  0.00           C 0
+ATOM    236    O PHE E  43       0.880  26.519   2.621  0.59  5.36           O 0
+ATOM    237   CB PHE E  43       0.553  23.837   1.182  0.00  0.00           C 0
+ATOM    478  CD1 ILE E  73       9.538  21.094   1.013  0.00  0.00           C 0
+ATOM    849  CE2 TYR E 117       8.106  23.530  -2.859  0.00  0.00           C 0
+ATOM   2645   CB ILE E 335      10.671  26.195   2.001  0.00  0.00           C 0
+ATOM    261  NH1 ARG E  45       9.719  25.580   5.861  0.00  0.00           N 0
+TER
+END
--- a/tests/reference_output/1ATP_out/pockets/pocket9_vert.pqr
+++ b/tests/reference_output/1ATP_out/pockets/pocket9_vert.pqr
@@ -0,0 +1,44 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     9:
+HEADER 0  - Pocket Score                      : 0.0433
+HEADER 1  - Drug Score                        : 0.0090
+HEADER 2  - Number of V. Vertices             :    22
+HEADER 3  - Mean alpha-sphere radius          : 3.7189
+HEADER 4  - Mean alpha-sphere SA              : 0.4354
+HEADER 5  - Mean B-factor                     : 0.6548
+HEADER 6  - Hydrophobicity Score              : 61.3000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 5.2000
+HEADER 9  - Real volume (approximation)       : 257.6532
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 15.0000
+HEADER 12 - Number of apolar alpha sphere     :    16
+HEADER 13 - Proportion of apolar alpha sphere : 0.7273
+ATOM      1    O STP     9       3.602  29.013   1.016    0.00     3.55
+ATOM      2    C STP     9       5.556  23.790   2.238    0.00     3.66
+ATOM      3    C STP     9       4.374  24.558   2.469    0.00     3.55
+ATOM      4    C STP     9       6.248  22.839   2.662    0.00     3.65
+ATOM      5    C STP     9       6.687  23.325   2.417    0.00     3.80
+ATOM      6    O STP     9       3.605  28.995   0.988    0.00     3.53
+ATOM      7    C STP     9       6.666  23.871   2.160    0.00     3.91
+ATOM      8    C STP     9       6.778  23.571   2.298    0.00     3.87
+ATOM      9    C STP     9       6.777  25.942   2.510    0.00     3.88
+ATOM     10    O STP     9       3.851  24.675   2.332    0.00     3.51
+ATOM     11    C STP     9       3.757  24.628   2.235    0.00     3.46
+ATOM     12    O STP     9       3.932  27.786   1.618    0.00     3.45
+ATOM     13    O STP     9       4.637  26.459   2.777    0.00     3.76
+ATOM     14    C STP     9       4.889  27.180   2.881    0.00     4.07
+ATOM     15    O STP     9       3.599  29.091   1.545    0.00     3.89
+ATOM     16    C STP     9       7.492  23.806   0.509    0.00     3.43
+ATOM     17    C STP     9       7.257  23.839   1.162    0.00     3.57
+ATOM     18    C STP     9       7.637  23.976   0.562    0.00     3.48
+ATOM     19    C STP     9       6.839  23.523   2.245    0.00     3.83
+ATOM     20    C STP     9       6.757  23.101   2.378    0.00     3.69
+ATOM     21    C STP     9       6.868  27.794   3.414    0.00     4.36
+ATOM     22    C STP     9       6.830  26.126   2.605    0.00     3.89
+TER
+END
--- a/tests/reference_output/1UYD_out/1UYD.pml
+++ b/tests/reference_output/1UYD_out/1UYD.pml
@@ -0,0 +1,15 @@
+from pymol import cmd,stored
+load 1UYD_out.pdb
+#select pockets, resn STP
+stored.list=[]
+cmd.iterate("(resn STP)","stored.list.append(resi)")	#read info about residues STP
+#print stored.list
+lastSTP=stored.list[-1]	#get the index of the last residu
+hide lines, resn STP
+
+#show spheres, resn STP
+for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
+for my_index in range(2,int(lastSTP)+2): cmd.color(my_index,"pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.3","pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
--- a/tests/reference_output/1UYD_out/1UYD.tcl
+++ b/tests/reference_output/1UYD_out/1UYD.tcl
@@ -0,0 +1,24 @@
+proc highlighting { colorId representation id selection } {
+   puts "highlighting $id"
+   mol representation $representation
+   mol material "Diffuse" 
+    mol color $colorId
+   mol selection $selection
+   mol addrep $id
+}
+
+set id [mol new 1UYD_out.pdb type pdb]
+mol delrep top $id
+highlighting Name "Lines" $id "protein"
+highlighting Name "Licorice" $id "not protein and not resname STP"
+highlighting Element "NewCartoon" $id "protein"
+highlighting "ColorID 7" "VdW 0.4" $id "protein and occupancy>0.95"
+set id [mol new 1UYD_pockets.pqr type pqr]
+                        mol selection "all" 
+                         mol material "Glass3" 
+                         mol delrep top $id 
+                         mol representation "QuickSurf 0.3" 
+                         mol color ResId $id 
+                         mol addrep $id 
+highlighting Index "Points 1" $id "resname STP"
+display rendermode GLSL
--- a/tests/reference_output/1UYD_out/1UYD_PYMOL.sh
+++ b/tests/reference_output/1UYD_out/1UYD_PYMOL.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+pymol 1UYD.pml
--- a/tests/reference_output/1UYD_out/1UYD_VMD.sh
+++ b/tests/reference_output/1UYD_out/1UYD_VMD.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+vmd 1UYD_out.pdb -e 1UYD.tcl
--- a/tests/reference_output/1UYD_out/1UYD_info.txt
+++ b/tests/reference_output/1UYD_out/1UYD_info.txt
@@ -0,0 +1,252 @@
+Pocket 1 :
+	Score : 	0.664
+	Druggability Score : 	0.855
+	Number of Alpha Spheres : 	143
+	Total SASA : 	214.924
+	Polar SASA : 	111.068
+	Apolar SASA : 	103.856
+	Volume : 	1437.686
+	Mean local hydrophobic density : 	53.083
+	Mean alpha sphere radius :	3.977
+	Mean alp. sph. solvent access : 	0.451
+	Apolar alpha sphere proportion : 	0.503
+	Hydrophobicity score:	39.727
+	Volume score: 	 3.939
+	Polarity score:	 13
+	Charge score :	 -2
+	Proportion of polar atoms: 	36.905
+	Alpha sphere density : 	8.233
+	Cent. of mass - Alpha Sphere max dist: 	21.512
+	Flexibility : 	0.227
+
+Pocket 2 :
+	Score : 	0.122
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	24
+	Total SASA : 	94.066
+	Polar SASA : 	68.706
+	Apolar SASA : 	25.360
+	Volume : 	425.424
+	Mean local hydrophobic density : 	2.000
+	Mean alpha sphere radius :	4.011
+	Mean alp. sph. solvent access : 	0.544
+	Apolar alpha sphere proportion : 	0.125
+	Hydrophobicity score:	-15.727
+	Volume score: 	 3.727
+	Polarity score:	 10
+	Charge score :	 -1
+	Proportion of polar atoms: 	52.174
+	Alpha sphere density : 	4.862
+	Cent. of mass - Alpha Sphere max dist: 	10.651
+	Flexibility : 	0.601
+
+Pocket 3 :
+	Score : 	0.050
+	Druggability Score : 	0.014
+	Number of Alpha Spheres : 	31
+	Total SASA : 	124.126
+	Polar SASA : 	31.139
+	Apolar SASA : 	92.987
+	Volume : 	438.371
+	Mean local hydrophobic density : 	19.455
+	Mean alpha sphere radius :	3.914
+	Mean alp. sph. solvent access : 	0.605
+	Apolar alpha sphere proportion : 	0.710
+	Hydrophobicity score:	39.909
+	Volume score: 	 4.818
+	Polarity score:	 6
+	Charge score :	 1
+	Proportion of polar atoms: 	34.483
+	Alpha sphere density : 	5.097
+	Cent. of mass - Alpha Sphere max dist: 	11.542
+	Flexibility : 	0.285
+
+Pocket 4 :
+	Score : 	0.042
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	19
+	Total SASA : 	75.497
+	Polar SASA : 	24.776
+	Apolar SASA : 	50.720
+	Volume : 	275.129
+	Mean local hydrophobic density : 	3.000
+	Mean alpha sphere radius :	3.801
+	Mean alp. sph. solvent access : 	0.490
+	Apolar alpha sphere proportion : 	0.211
+	Hydrophobicity score:	27.750
+	Volume score: 	 2.625
+	Polarity score:	 2
+	Charge score :	 0
+	Proportion of polar atoms: 	35.294
+	Alpha sphere density : 	3.508
+	Cent. of mass - Alpha Sphere max dist: 	6.460
+	Flexibility : 	0.230
+
+Pocket 5 :
+	Score : 	-0.012
+	Druggability Score : 	0.011
+	Number of Alpha Spheres : 	28
+	Total SASA : 	92.394
+	Polar SASA : 	25.737
+	Apolar SASA : 	66.657
+	Volume : 	314.367
+	Mean local hydrophobic density : 	23.000
+	Mean alpha sphere radius :	3.858
+	Mean alp. sph. solvent access : 	0.522
+	Apolar alpha sphere proportion : 	0.857
+	Hydrophobicity score:	-4.429
+	Volume score: 	 4.571
+	Polarity score:	 6
+	Charge score :	 0
+	Proportion of polar atoms: 	38.095
+	Alpha sphere density : 	3.282
+	Cent. of mass - Alpha Sphere max dist: 	7.261
+	Flexibility : 	0.748
+
+Pocket 6 :
+	Score : 	-0.021
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	16
+	Total SASA : 	82.319
+	Polar SASA : 	70.242
+	Apolar SASA : 	12.076
+	Volume : 	256.757
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.889
+	Mean alp. sph. solvent access : 	0.547
+	Apolar alpha sphere proportion : 	0.000
+	Hydrophobicity score:	-4.000
+	Volume score: 	 4.714
+	Polarity score:	 6
+	Charge score :	 1
+	Proportion of polar atoms: 	71.429
+	Alpha sphere density : 	3.223
+	Cent. of mass - Alpha Sphere max dist: 	7.463
+	Flexibility : 	0.620
+
+Pocket 7 :
+	Score : 	-0.034
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	15
+	Total SASA : 	76.174
+	Polar SASA : 	20.623
+	Apolar SASA : 	55.551
+	Volume : 	262.364
+	Mean local hydrophobic density : 	5.000
+	Mean alpha sphere radius :	3.728
+	Mean alp. sph. solvent access : 	0.402
+	Apolar alpha sphere proportion : 	0.400
+	Hydrophobicity score:	7.714
+	Volume score: 	 4.000
+	Polarity score:	 4
+	Charge score :	 -1
+	Proportion of polar atoms: 	37.500
+	Alpha sphere density : 	2.882
+	Cent. of mass - Alpha Sphere max dist: 	6.933
+	Flexibility : 	0.716
+
+Pocket 8 :
+	Score : 	-0.039
+	Druggability Score : 	0.009
+	Number of Alpha Spheres : 	25
+	Total SASA : 	97.119
+	Polar SASA : 	15.000
+	Apolar SASA : 	82.119
+	Volume : 	292.064
+	Mean local hydrophobic density : 	18.500
+	Mean alpha sphere radius :	4.046
+	Mean alp. sph. solvent access : 	0.563
+	Apolar alpha sphere proportion : 	0.800
+	Hydrophobicity score:	46.556
+	Volume score: 	 4.333
+	Polarity score:	 4
+	Charge score :	 -1
+	Proportion of polar atoms: 	25.000
+	Alpha sphere density : 	3.371
+	Cent. of mass - Alpha Sphere max dist: 	8.654
+	Flexibility : 	0.688
+
+Pocket 9 :
+	Score : 	-0.060
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	17
+	Total SASA : 	85.530
+	Polar SASA : 	40.848
+	Apolar SASA : 	44.682
+	Volume : 	280.765
+	Mean local hydrophobic density : 	6.000
+	Mean alpha sphere radius :	3.890
+	Mean alp. sph. solvent access : 	0.593
+	Apolar alpha sphere proportion : 	0.412
+	Hydrophobicity score:	-11.375
+	Volume score: 	 3.375
+	Polarity score:	 4
+	Charge score :	 -1
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	2.895
+	Cent. of mass - Alpha Sphere max dist: 	6.688
+	Flexibility : 	0.637
+
+Pocket 10 :
+	Score : 	-0.063
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	19
+	Total SASA : 	66.665
+	Polar SASA : 	36.474
+	Apolar SASA : 	30.191
+	Volume : 	188.758
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.982
+	Mean alp. sph. solvent access : 	0.596
+	Apolar alpha sphere proportion : 	0.000
+	Hydrophobicity score:	10.625
+	Volume score: 	 3.375
+	Polarity score:	 6
+	Charge score :	 0
+	Proportion of polar atoms: 	57.143
+	Alpha sphere density : 	1.979
+	Cent. of mass - Alpha Sphere max dist: 	4.058
+	Flexibility : 	0.138
+
+Pocket 11 :
+	Score : 	-0.085
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	24
+	Total SASA : 	104.600
+	Polar SASA : 	55.087
+	Apolar SASA : 	49.513
+	Volume : 	314.715
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.941
+	Mean alp. sph. solvent access : 	0.631
+	Apolar alpha sphere proportion : 	0.042
+	Hydrophobicity score:	1.286
+	Volume score: 	 3.571
+	Polarity score:	 5
+	Charge score :	 0
+	Proportion of polar atoms: 	60.870
+	Alpha sphere density : 	3.147
+	Cent. of mass - Alpha Sphere max dist: 	7.973
+	Flexibility : 	0.419
+
+Pocket 12 :
+	Score : 	-0.094
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	17
+	Total SASA : 	93.149
+	Polar SASA : 	56.920
+	Apolar SASA : 	36.229
+	Volume : 	258.996
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.969
+	Mean alp. sph. solvent access : 	0.469
+	Apolar alpha sphere proportion : 	0.059
+	Hydrophobicity score:	17.125
+	Volume score: 	 4.375
+	Polarity score:	 4
+	Charge score :	 0
+	Proportion of polar atoms: 	46.667
+	Alpha sphere density : 	2.873
+	Cent. of mass - Alpha Sphere max dist: 	7.632
+	Flexibility : 	0.681
+
--- a/tests/reference_output/1UYD_out/1UYD_out.pdb
+++ b/tests/reference_output/1UYD_out/1UYD_out.pdb
--- a/tests/reference_output/1UYD_out/1UYD_pockets.pqr
+++ b/tests/reference_output/1UYD_out/1UYD_pockets.pqr
@@ -0,0 +1,383 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It contains all the pocket vertices found by fpocket.                    
+ATOM      1    C STP     1       7.785   6.838  24.439    0.00     3.59
+ATOM      2    C STP     1       5.774   9.979  23.751    0.00     4.47
+ATOM      3    C STP     1       4.349   9.667  23.812    0.00     4.63
+ATOM      4    O STP     1      -1.508  10.969  24.938    0.00     3.99
+ATOM      5    O STP     1       6.817   8.930  24.068    0.00     4.02
+ATOM      6    C STP     1       5.854   9.885  23.690    0.00     4.50
+ATOM      7    O STP     1       4.623   9.304  23.580    0.00     4.68
+ATOM      8    O STP     1       7.615   6.878  24.306    0.00     3.76
+ATOM      9    O STP     1       7.083   7.215  24.474    0.00     3.93
+ATOM     10    O STP     1       3.114   6.284  29.706    0.00     4.08
+ATOM     11    C STP     1       6.727   6.176  30.320    0.00     3.43
+ATOM     12    O STP     1       6.590   4.208  31.665    0.00     4.58
+ATOM     13    O STP     1       4.754   4.946  29.971    0.00     4.33
+ATOM     14    O STP     1      13.912  14.330  27.259    0.00     4.00
+ATOM     15    O STP     1      16.020  12.287  30.152    0.00     4.01
+ATOM     16    O STP     1      16.084  11.656  30.325    0.00     4.03
+ATOM     17    O STP     1       8.887  11.600  24.709    0.00     3.43
+ATOM     18    C STP     1      -0.732  13.051  21.091    0.00     3.58
+ATOM     19    C STP     1      -0.386  13.047  21.225    0.00     3.58
+ATOM     20    O STP     1      -1.558  11.234  24.081    0.00     3.83
+ATOM     21    O STP     1      -1.802  11.344  23.665    0.00     3.62
+ATOM     22    O STP     1      -1.699  12.544  22.872    0.00     3.86
+ATOM     23    O STP     1      -1.739  12.698  22.218    0.00     3.70
+ATOM     24    O STP     1      -1.975  11.852  23.036    0.00     3.54
+ATOM     25    C STP     1       0.563  12.588  23.454    0.00     4.19
+ATOM     26    O STP     1      -0.950  10.812  25.145    0.00     4.16
+ATOM     27    C STP     1       0.277  13.297  21.360    0.00     3.50
+ATOM     28    C STP     1       0.736  12.678  23.430    0.00     4.18
+ATOM     29    O STP     1       0.753   6.534  22.979    0.00     3.53
+ATOM     30    O STP     1       0.730   6.506  22.916    0.00     3.49
+ATOM     31    O STP     1       1.477   7.589  24.040    0.00     4.21
+ATOM     32    O STP     1       0.889   7.396  23.257    0.00     3.49
+ATOM     33    C STP     1      11.631  14.628  26.606    0.00     3.96
+ATOM     34    C STP     1      12.945  13.969  25.376    0.00     3.56
+ATOM     35    C STP     1      13.913  14.874  26.698    0.00     3.67
+ATOM     36    C STP     1      13.708  14.441  26.773    0.00     3.98
+ATOM     37    O STP     1      13.827  14.182  26.170    0.00     3.82
+ATOM     38    C STP     1      13.822  14.141  26.067    0.00     3.80
+ATOM     39    O STP     1      13.857  14.157  26.064    0.00     3.79
+ATOM     40    C STP     1       7.381  10.470  21.326    0.00     3.51
+ATOM     41    O STP     1       7.972  11.066  23.806    0.00     3.97
+ATOM     42    O STP     1       8.295  11.024  23.750    0.00     3.81
+ATOM     43    O STP     1       7.478  10.337  23.282    0.00     4.27
+ATOM     44    O STP     1       7.280  10.418  23.358    0.00     4.38
+ATOM     45    C STP     1       7.156  10.473  23.341    0.00     4.42
+ATOM     46    O STP     1       8.724   6.926  23.719    0.00     3.43
+ATOM     47    O STP     1      16.251  10.521  30.258    0.00     3.97
+ATOM     48    O STP     1      16.016  10.444  30.032    0.00     3.76
+ATOM     49    O STP     1      16.674  10.615  30.805    0.00     4.40
+ATOM     50    O STP     1      16.395   8.912  33.152    0.00     4.55
+ATOM     51    O STP     1      15.810   9.633  32.174    0.00     3.94
+ATOM     52    O STP     1      17.109  10.453  31.017    0.00     4.60
+ATOM     53    C STP     1       1.424  11.066  24.202    0.00     4.18
+ATOM     54    C STP     1       2.034   9.777  24.491    0.00     4.45
+ATOM     55    C STP     1       3.535  10.777  24.109    0.00     4.44
+ATOM     56    C STP     1       2.895  11.680  23.923    0.00     4.23
+ATOM     57    C STP     1       2.330  11.918  23.906    0.00     4.17
+ATOM     58    C STP     1       0.249  10.171  25.029    0.00     4.31
+ATOM     59    C STP     1      -0.088  10.016  25.481    0.00     4.28
+ATOM     60    C STP     1       1.463  14.193  23.946    0.00     3.61
+ATOM     61    C STP     1       3.864  14.031  24.821    0.00     3.91
+ATOM     62    C STP     1       0.172  12.525  23.583    0.00     4.14
+ATOM     63    C STP     1      -1.579  12.507  23.063    0.00     3.90
+ATOM     64    O STP     1      -1.912  11.626  24.998    0.00     3.45
+ATOM     65    O STP     1      -0.989  11.052  24.874    0.00     4.19
+ATOM     66    C STP     1      -0.879  11.128  24.694    0.00     4.20
+ATOM     67    O STP     1      -1.354  11.116  24.781    0.00     4.07
+ATOM     68    O STP     1      -1.288  11.285  24.407    0.00     4.07
+ATOM     69    O STP     1      -1.482  10.096  27.670    0.00     3.55
+ATOM     70    O STP     1       1.783   6.931  28.759    0.00     4.60
+ATOM     71    O STP     1       1.714   6.908  28.614    0.00     4.66
+ATOM     72    O STP     1      15.581  12.421  30.019    0.00     3.95
+ATOM     73    O STP     1      15.750  12.621  30.007    0.00     4.00
+ATOM     74    O STP     1      16.662  14.424  30.372    0.00     4.33
+ATOM     75    O STP     1      14.219  12.652  28.837    0.00     3.48
+ATOM     76    O STP     1      14.087  14.330  27.578    0.00     4.00
+ATOM     77    O STP     1      14.631  14.244  28.046    0.00     3.87
+ATOM     78    O STP     1      13.939  14.281  27.501    0.00     4.01
+ATOM     79    O STP     1      14.756  14.840  28.269    0.00     3.78
+ATOM     80    O STP     1      15.299  14.577  28.703    0.00     3.82
+ATOM     81    O STP     1      16.054  10.122  29.656    0.00     3.46
+ATOM     82    O STP     1      16.456   9.802  29.471    0.00     3.42
+ATOM     83    C STP     1      16.445   9.833  29.519    0.00     3.45
+ATOM     84    C STP     1      16.465   9.812  29.510    0.00     3.44
+ATOM     85    C STP     1       1.618   7.073  28.344    0.00     4.66
+ATOM     86    C STP     1      -0.008   8.421  27.485    0.00     4.02
+ATOM     87    O STP     1       1.812   7.179  28.734    0.00     4.49
+ATOM     88    O STP     1      -1.242  10.098  27.540    0.00     3.66
+ATOM     89    C STP     1      -0.795  10.331  26.577    0.00     3.87
+ATOM     90    C STP     1      -0.351  10.061  26.183    0.00     4.04
+ATOM     91    C STP     1       5.216  14.534  25.639    0.00     4.31
+ATOM     92    C STP     1       6.844  13.993  25.301    0.00     4.31
+ATOM     93    C STP     1       4.953  13.937  25.159    0.00     4.18
+ATOM     94    C STP     1       6.895  13.161  24.861    0.00     4.13
+ATOM     95    C STP     1       6.336  11.714  24.056    0.00     4.19
+ATOM     96    C STP     1       7.101  11.566  23.730    0.00     4.23
+ATOM     97    C STP     1       7.064  11.491  23.691    0.00     4.25
+ATOM     98    C STP     1       4.397  14.033  24.909    0.00     4.08
+ATOM     99    C STP     1       4.395  14.034  24.909    0.00     4.08
+ATOM    100    C STP     1       4.116  14.428  25.075    0.00     4.00
+ATOM    101    C STP     1       4.854  14.788  25.584    0.00     4.24
+ATOM    102    C STP     1       3.927  14.727  25.118    0.00     3.90
+ATOM    103    C STP     1       4.371  15.015  25.725    0.00     4.02
+ATOM    104    C STP     1       4.329  14.825  25.421    0.00     4.07
+ATOM    105    C STP     1       4.599  14.941  25.596    0.00     4.17
+ATOM    106    C STP     1      11.147  15.077  26.485    0.00     3.81
+ATOM    107    C STP     1       4.407  14.017  24.905    0.00     4.09
+ATOM    108    C STP     1       4.436  13.999  24.911    0.00     4.09
+ATOM    109    C STP     1       4.748  13.478  24.902    0.00     4.10
+ATOM    110    C STP     1       3.975  11.754  24.269    0.00     4.18
+ATOM    111    C STP     1       3.151  11.816  24.008    0.00     4.17
+ATOM    112    C STP     1       5.894  11.911  24.134    0.00     4.08
+ATOM    113    C STP     1       3.984  15.311  26.029    0.00     3.70
+ATOM    114    C STP     1       1.548  14.653  24.159    0.00     3.52
+ATOM    115    C STP     1       1.551  14.776  24.130    0.00     3.45
+ATOM    116    C STP     1       1.848  14.707  24.298    0.00     3.47
+ATOM    117    C STP     1       4.926  15.350  25.662    0.00     4.10
+ATOM    118    C STP     1       6.620  14.280  27.401    0.00     3.53
+ATOM    119    O STP     1      10.896  15.156  26.541    0.00     3.85
+ATOM    120    O STP     1      10.721  14.194  26.674    0.00     3.81
+ATOM    121    O STP     1      11.490  13.931  27.857    0.00     3.51
+ATOM    122    O STP     1      11.366  14.623  26.733    0.00     4.01
+ATOM    123    O STP     1       9.184  13.635  26.450    0.00     3.80
+ATOM    124    O STP     1      11.789  14.458  27.414    0.00     3.84
+ATOM    125    O STP     1      11.772  14.543  27.511    0.00     3.75
+ATOM    126    O STP     1      10.363  15.394  26.388    0.00     3.75
+ATOM    127    O STP     1      10.557  15.655  26.584    0.00     3.67
+ATOM    128    O STP     1       6.897  14.234  25.492    0.00     4.38
+ATOM    129    O STP     1       7.349  14.139  25.864    0.00     4.27
+ATOM    130    O STP     1       7.403  14.166  26.142    0.00     4.18
+ATOM    131    O STP     1       7.664  14.151  26.041    0.00     4.19
+ATOM    132    O STP     1       6.658  14.520  26.744    0.00     3.94
+ATOM    133    C STP     1       5.424  15.941  26.511    0.00     3.40
+ATOM    134    C STP     1       5.487  15.835  26.436    0.00     3.49
+ATOM    135    C STP     1       7.227  14.775  25.129    0.00     3.96
+ATOM    136    O STP     1       7.217  14.760  25.143    0.00     3.97
+ATOM    137    O STP     1       7.249  14.785  25.136    0.00     3.95
+ATOM    138    C STP     1       5.482  15.772  26.370    0.00     3.54
+ATOM    139    C STP     1       5.091  15.244  25.653    0.00     4.15
+ATOM    140    C STP     1       5.067  15.273  25.656    0.00     4.14
+ATOM    141    C STP     1       5.814  14.647  25.758    0.00     4.34
+ATOM    142    C STP     1       5.861  14.632  25.749    0.00     4.33
+ATOM    143    C STP     1       5.829  14.647  25.770    0.00     4.33
+ATOM    144    O STP     2      -3.991   5.938  38.283    0.00     3.50
+ATOM    145    O STP     2      -3.568   5.524  37.917    0.00     3.47
+ATOM    146    C STP     2      -3.931   5.923  38.105    0.00     3.54
+ATOM    147    C STP     2      -4.180   5.886  37.623    0.00     3.52
+ATOM    148    O STP     2      -4.420   5.879  37.503    0.00     3.45
+ATOM    149    O STP     2      -4.377   6.059  37.115    0.00     3.41
+ATOM    150    O STP     2      -7.842   6.647  41.105    0.00     3.88
+ATOM    151    O STP     2      -7.652   7.448  41.790    0.00     4.41
+ATOM    152    O STP     2      -4.666   6.404  35.706    0.00     3.43
+ATOM    153    C STP     2      -5.556   6.104  39.988    0.00     3.43
+ATOM    154    O STP     2      -6.919   6.642  41.684    0.00     4.41
+ATOM    155    O STP     2      -6.980   6.668  41.645    0.00     4.39
+ATOM    156    O STP     2      -6.526   5.836  41.929    0.00     4.31
+ATOM    157    O STP     2      -6.378   5.700  41.831    0.00     4.22
+ATOM    158    O STP     2      -7.822   6.625  41.102    0.00     3.88
+ATOM    159    O STP     2      -7.825   7.749  41.660    0.00     4.29
+ATOM    160    O STP     2      -8.100   8.674  42.098    0.00     4.62
+ATOM    161    O STP     2      -8.659   9.530  41.927    0.00     4.66
+ATOM    162    O STP     2      -8.737  12.631  40.804    0.00     4.50
+ATOM    163    O STP     2     -11.049  12.429  41.049    0.00     4.29
+ATOM    164    O STP     2     -11.267  12.028  41.036    0.00     4.03
+ATOM    165    O STP     2     -10.890  12.386  41.380    0.00     4.60
+ATOM    166    O STP     2      -9.951  10.626  40.848    0.00     4.18
+ATOM    167    O STP     2     -10.041   9.901  40.431    0.00     3.83
+ATOM    168    O STP     3     -13.394   8.035  11.699    0.00     3.75
+ATOM    169    O STP     3     -13.866   8.149  12.756    0.00     4.22
+ATOM    170    O STP     3     -13.235   6.985  13.878    0.00     3.71
+ATOM    171    C STP     3     -13.396  13.376  12.554    0.00     3.64
+ATOM    172    O STP     3     -14.773   7.681  13.727    0.00     4.61
+ATOM    173    C STP     3     -14.552   8.323  12.854    0.00     4.64
+ATOM    174    C STP     3     -14.690   7.717  13.852    0.00     4.48
+ATOM    175    C STP     3     -13.947  10.342   9.126    0.00     3.72
+ATOM    176    C STP     3     -12.889   8.488   9.768    0.00     3.44
+ATOM    177    O STP     3     -14.059  10.991   9.026    0.00     3.83
+ATOM    178    C STP     3     -12.850  13.648  12.578    0.00     3.53
+ATOM    179    C STP     3     -12.635  13.830  12.726    0.00     3.42
+ATOM    180    C STP     3     -15.321  12.050   6.421    0.00     3.91
+ATOM    181    C STP     3     -15.149  12.299   5.990    0.00     3.77
+ATOM    182    C STP     3     -14.138  13.128   4.148    0.00     3.73
+ATOM    183    O STP     3     -13.842  12.966   4.202    0.00     3.54
+ATOM    184    C STP     3     -14.202  12.998   4.431    0.00     3.63
+ATOM    185    C STP     3     -15.071  12.945  11.123    0.00     4.55
+ATOM    186    C STP     3     -15.181  12.284   7.101    0.00     3.70
+ATOM    187    C STP     3     -14.069  13.525  10.889    0.00     4.05
+ATOM    188    C STP     3     -14.486  12.345   9.698    0.00     4.10
+ATOM    189    C STP     3     -15.581  11.691   7.702    0.00     4.30
+ATOM    190    C STP     3     -13.744  12.589   9.720    0.00     3.59
+ATOM    191    C STP     3     -13.903  13.601  10.918    0.00     3.98
+ATOM    192    C STP     3     -13.004  13.765  11.916    0.00     3.53
+ATOM    193    C STP     3     -12.804  14.399  11.014    0.00     3.51
+ATOM    194    O STP     3     -14.691   7.701  13.857    0.00     4.48
+ATOM    195    O STP     3     -14.353   7.367  13.918    0.00     4.32
+ATOM    196    O STP     3     -14.766   7.663  13.746    0.00     4.60
+ATOM    197    C STP     3     -13.822  14.302  10.714    0.00     3.55
+ATOM    198    C STP     3     -12.793  14.411  11.014    0.00     3.51
+ATOM    199    O STP     4      16.547  23.639  13.890    0.00     4.14
+ATOM    200    O STP     4      16.092  23.630  14.033    0.00     4.24
+ATOM    201    C STP     4      15.859  23.404  14.170    0.00     4.10
+ATOM    202    C STP     4      15.557  23.398  14.576    0.00     4.15
+ATOM    203    O STP     4      16.011  22.871  13.482    0.00     3.59
+ATOM    204    C STP     4      15.928  23.207  13.765    0.00     3.90
+ATOM    205    O STP     4      17.691  22.245  18.072    0.00     3.56
+ATOM    206    O STP     4      19.529  21.954  18.755    0.00     4.34
+ATOM    207    C STP     4      15.011  22.229  15.825    0.00     3.58
+ATOM    208    O STP     4      15.135  20.552  18.741    0.00     3.44
+ATOM    209    O STP     4      19.253  21.725  18.788    0.00     4.16
+ATOM    210    O STP     4      17.650  21.048  18.652    0.00     3.48
+ATOM    211    O STP     4      16.195  21.162  18.168    0.00     3.43
+ATOM    212    O STP     4      15.398  20.983  17.666    0.00     3.45
+ATOM    213    O STP     4      15.138  20.557  18.735    0.00     3.44
+ATOM    214    O STP     4      16.943  21.983  17.981    0.00     3.42
+ATOM    215    O STP     4      15.182  22.714  15.737    0.00     3.78
+ATOM    216    O STP     4      15.741  24.064  14.855    0.00     4.60
+ATOM    217    O STP     4      15.109  20.220  19.179    0.00     3.40
+ATOM    218    C STP     5      20.605   6.618  21.102    0.00     3.76
+ATOM    219    O STP     5      19.082   9.114  16.906    0.00     3.51
+ATOM    220    C STP     5      19.211   8.868  16.477    0.00     3.41
+ATOM    221    O STP     5      19.141   9.065  16.855    0.00     3.52
+ATOM    222    C STP     5      20.411   8.950  16.497    0.00     4.01
+ATOM    223    C STP     5      21.278   7.286  15.271    0.00     3.95
+ATOM    224    C STP     5      21.737   8.273  15.966    0.00     4.55
+ATOM    225    C STP     5      19.545   9.253  17.348    0.00     3.83
+ATOM    226    C STP     5      19.605   9.305  17.253    0.00     3.89
+ATOM    227    C STP     5      19.361   9.202  17.087    0.00     3.71
+ATOM    228    O STP     5      21.005   6.678  13.902    0.00     3.49
+ATOM    229    C STP     5      21.887   7.048  14.721    0.00     4.32
+ATOM    230    C STP     5      21.576   8.462  17.094    0.00     4.39
+ATOM    231    C STP     5      21.237   8.164  17.688    0.00     3.98
+ATOM    232    C STP     5      19.823   9.314  17.205    0.00     3.96
+ATOM    233    C STP     5      19.842   9.288  17.195    0.00     3.97
+ATOM    234    C STP     5      19.813   9.293  17.207    0.00     3.96
+ATOM    235    C STP     5      23.114   7.517  18.754    0.00     4.38
+ATOM    236    C STP     5      23.216   7.267  19.612    0.00     4.27
+ATOM    237    C STP     5      21.455   7.159  19.578    0.00     3.62
+ATOM    238    C STP     5      19.601   8.988  17.728    0.00     3.65
+ATOM    239    C STP     5      20.637   6.657  21.076    0.00     3.77
+ATOM    240    C STP     5      21.991   6.742  21.095    0.00     3.92
+ATOM    241    C STP     5      20.614   6.661  21.080    0.00     3.77
+ATOM    242    C STP     5      20.578   6.679  21.067    0.00     3.75
+ATOM    243    C STP     5      20.573   6.576  21.121    0.00     3.74
+ATOM    244    O STP     5      19.279  10.317  17.326    0.00     3.47
+ATOM    245    C STP     5      19.218  10.275  17.340    0.00     3.46
+ATOM    246    O STP     6       0.606  30.613  17.291    0.00     3.76
+ATOM    247    O STP     6       0.349  29.933  16.102    0.00     3.64
+ATOM    248    O STP     6       0.398  29.825  16.006    0.00     3.59
+ATOM    249    O STP     6       0.310  30.058  15.886    0.00     3.64
+ATOM    250    O STP     6      -2.704  33.369  14.954    0.00     3.46
+ATOM    251    O STP     6       0.267  30.094  15.812    0.00     3.62
+ATOM    252    O STP     6       0.297  30.167  15.803    0.00     3.64
+ATOM    253    O STP     6      -1.603  34.311  14.914    0.00     4.52
+ATOM    254    O STP     6      -1.370  34.089  14.976    0.00     4.40
+ATOM    255    O STP     6       0.328  30.306  15.653    0.00     3.60
+ATOM    256    O STP     6       0.297  30.561  15.738    0.00     3.64
+ATOM    257    O STP     6      -0.300  32.461  15.359    0.00     3.76
+ATOM    258    O STP     6      -1.581  33.922  14.529    0.00     4.09
+ATOM    259    O STP     6      -2.185  34.279  14.137    0.00     4.26
+ATOM    260    O STP     6      -3.286  34.022  12.999    0.00     4.08
+ATOM    261    O STP     6      -3.344  34.741  12.491    0.00     4.54
+ATOM    262    O STP     7      -6.625  24.421  30.057    0.00     3.72
+ATOM    263    O STP     7      -5.799  26.309  29.404    0.00     4.28
+ATOM    264    O STP     7      -8.308  22.685  29.725    0.00     3.61
+ATOM    265    O STP     7      -7.037  21.813  30.245    0.00     3.44
+ATOM    266    C STP     7     -10.258  22.548  28.497    0.00     4.05
+ATOM    267    C STP     7      -9.562  22.615  29.037    0.00     3.80
+ATOM    268    C STP     7      -7.102  21.786  30.244    0.00     3.44
+ATOM    269    C STP     7      -8.874  22.184  29.811    0.00     3.72
+ATOM    270    C STP     7      -9.225  22.114  29.661    0.00     3.78
+ATOM    271    C STP     7      -6.839  21.824  30.201    0.00     3.40
+ATOM    272    O STP     7      -6.761  22.668  29.984    0.00     3.54
+ATOM    273    O STP     7      -6.848  22.141  30.159    0.00     3.46
+ATOM    274    O STP     7      -6.421  23.405  30.062    0.00     3.58
+ATOM    275    O STP     7      -5.071  24.416  29.230    0.00     3.41
+ATOM    276    O STP     7      -4.870  26.897  28.843    0.00     4.69
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+ATOM    278    C STP     8      18.473  10.489   8.873    0.00     3.90
+ATOM    279    C STP     8      18.698  10.488   9.792    0.00     3.67
+ATOM    280    C STP     8      14.943  10.866   4.541    0.00     4.51
+ATOM    281    O STP     8      14.875  10.843   4.459    0.00     4.53
+ATOM    282    O STP     8      14.864  10.355   4.722    0.00     4.07
+ATOM    283    C STP     8      17.917  10.225   9.354    0.00     3.49
+ATOM    284    C STP     8      14.939  11.399   5.926    0.00     4.03
+ATOM    285    C STP     8      16.088  11.832   6.354    0.00     4.19
+ATOM    286    C STP     8      17.345  11.079   8.062    0.00     3.54
+ATOM    287    C STP     8      14.302  11.614   6.290    0.00     3.81
+ATOM    288    C STP     8      14.169  11.576   6.426    0.00     3.68
+ATOM    289    C STP     8      13.282  11.035   4.472    0.00     4.30
+ATOM    290    O STP     8      13.297  11.009   4.410    0.00     4.33
+ATOM    291    C STP     8      13.187  11.021   4.702    0.00     4.11
+ATOM    292    C STP     8      12.553  11.402   3.811    0.00     4.29
+ATOM    293    C STP     8      12.615  11.331   3.695    0.00     4.37
+ATOM    294    C STP     8      16.085  11.834   6.357    0.00     4.19
+ATOM    295    C STP     8      15.342  12.249   7.345    0.00     3.56
+ATOM    296    C STP     8      14.506  12.196   7.034    0.00     3.62
+ATOM    297    C STP     8      14.353  12.486   7.796    0.00     3.41
+ATOM    298    O STP     8      13.277  10.973   4.430    0.00     4.29
+ATOM    299    C STP     8      13.182  11.064   3.370    0.00     4.59
+ATOM    300    O STP     8      13.287  11.012   4.386    0.00     4.34
+ATOM    301    C STP     8      12.716  11.267   3.730    0.00     4.38
+ATOM    302    O STP     9      -5.987  21.597  39.224    0.00     4.67
+ATOM    303    C STP     9      -6.191  22.298  37.656    0.00     3.79
+ATOM    304    O STP     9      -6.290  22.862  37.242    0.00     3.57
+ATOM    305    C STP     9      -6.076  21.951  37.687    0.00     3.87
+ATOM    306    O STP     9      -4.027  21.397  38.848    0.00     3.60
+ATOM    307    O STP     9      -5.569  19.993  39.101    0.00     4.01
+ATOM    308    C STP     9      -6.315  20.503  39.256    0.00     4.60
+ATOM    309    C STP     9      -6.095  21.897  37.670    0.00     3.85
+ATOM    310    C STP     9      -6.531  20.110  38.511    0.00     4.14
+ATOM    311    O STP     9      -5.839  22.040  37.133    0.00     3.50
+ATOM    312    O STP     9      -6.021  22.227  37.054    0.00     3.55
+ATOM    313    O STP     9      -6.062  21.968  37.603    0.00     3.83
+ATOM    314    O STP     9      -8.206  18.652  36.918    0.00     3.45
+ATOM    315    O STP     9      -8.120  18.521  37.184    0.00     3.65
+ATOM    316    C STP     9      -6.229  19.490  37.843    0.00     3.48
+ATOM    317    O STP     9      -9.377  17.540  38.316    0.00     4.06
+ATOM    318    C STP     9      -9.701  17.858  38.776    0.00     4.51
+ATOM    319    O STP    10       7.964  27.871  24.200    0.00     3.67
+ATOM    320    O STP    10       9.060  27.846  24.971    0.00     4.48
+ATOM    321    O STP    10       8.457  27.440  25.735    0.00     3.83
+ATOM    322    O STP    10       8.568  27.505  25.590    0.00     3.93
+ATOM    323    O STP    10       8.418  27.411  25.750    0.00     3.79
+ATOM    324    O STP    10       9.084  27.764  24.955    0.00     4.46
+ATOM    325    O STP    10      10.654  26.047  25.364    0.00     3.76
+ATOM    326    O STP    10      10.424  27.853  24.712    0.00     4.67
+ATOM    327    O STP    10       9.439  27.576  24.860    0.00     4.44
+ATOM    328    O STP    10      10.404  26.714  24.932    0.00     4.18
+ATOM    329    O STP    10      10.731  27.817  24.294    0.00     4.46
+ATOM    330    O STP    10      10.476  26.400  24.885    0.00     4.02
+ATOM    331    O STP    10      11.588  27.014  23.248    0.00     3.77
+ATOM    332    O STP    10      11.536  26.189  23.460    0.00     3.42
+ATOM    333    O STP    10       8.935  27.351  24.682    0.00     4.15
+ATOM    334    O STP    10      10.729  25.699  25.632    0.00     3.55
+ATOM    335    O STP    10      10.887  25.711  25.706    0.00     3.52
+ATOM    336    O STP    10      10.424  26.232  24.837    0.00     3.90
+ATOM    337    O STP    10       8.612  26.736  24.470    0.00     3.66
+ATOM    338    O STP    11       3.065   1.680  14.257    0.00     3.59
+ATOM    339    O STP    11      -0.262   5.672  13.713    0.00     3.61
+ATOM    340    O STP    11       0.191   4.442  13.421    0.00     4.24
+ATOM    341    O STP    11       2.560   3.835  10.859    0.00     4.30
+ATOM    342    O STP    11      -0.316   5.894  13.740    0.00     3.52
+ATOM    343    O STP    11       3.457   4.032   6.967    0.00     3.95
+ATOM    344    O STP    11       2.663   3.891  10.841    0.00     4.26
+ATOM    345    O STP    11       4.096   4.245  10.995    0.00     3.57
+ATOM    346    O STP    11       4.136   4.217  10.924    0.00     3.55
+ATOM    347    O STP    11       3.244   4.177  11.181    0.00     3.96
+ATOM    348    O STP    11       3.188   4.166  11.182    0.00     3.99
+ATOM    349    O STP    11       2.014   3.532  11.198    0.00     4.50
+ATOM    350    O STP    11       2.518   3.690  10.662    0.00     4.31
+ATOM    351    O STP    11       2.689   3.819  10.691    0.00     4.24
+ATOM    352    O STP    11       2.118   3.108   9.175    0.00     4.30
+ATOM    353    O STP    11       3.327   3.642   7.482    0.00     4.08
+ATOM    354    O STP    11       4.123   4.188  10.873    0.00     3.55
+ATOM    355    O STP    11       4.234   4.163  10.882    0.00     3.47
+ATOM    356    O STP    11       2.703   1.870  14.067    0.00     3.79
+ATOM    357    C STP    11       2.011   3.354  12.335    0.00     4.36
+ATOM    358    O STP    11       1.265   3.803  14.371    0.00     4.24
+ATOM    359    O STP    11       1.313   3.846  14.395    0.00     4.19
+ATOM    360    O STP    11       4.151   4.474  11.146    0.00     3.47
+ATOM    361    O STP    11       3.883   4.476  11.221    0.00     3.57
+ATOM    362    O STP    12     -12.188  31.839  16.593    0.00     3.49
+ATOM    363    O STP    12     -14.197  27.278  17.645    0.00     4.05
+ATOM    364    O STP    12     -14.250  26.710  18.687    0.00     4.47
+ATOM    365    O STP    12     -14.909  26.223  19.335    0.00     4.57
+ATOM    366    C STP    12     -14.382  24.675  18.050    0.00     3.53
+ATOM    367    O STP    12     -14.022  26.981  18.887    0.00     4.51
+ATOM    368    O STP    12     -13.149  28.055  17.189    0.00     3.54
+ATOM    369    O STP    12     -13.848  27.808  17.708    0.00     4.07
+ATOM    370    O STP    12     -13.798  28.442  17.460    0.00     3.88
+ATOM    371    O STP    12     -13.798  28.303  17.460    0.00     3.92
+ATOM    372    O STP    12     -13.804  28.284  17.472    0.00     3.93
+ATOM    373    O STP    12     -13.734  30.649  17.420    0.00     3.89
+ATOM    374    O STP    12     -13.444  31.621  17.292    0.00     4.09
+ATOM    375    O STP    12     -13.757  31.663  17.802    0.00     4.23
+ATOM    376    O STP    12     -12.392  31.711  16.849    0.00     3.60
+ATOM    377    O STP    12     -14.320  27.344  17.475    0.00     3.92
+ATOM    378    O STP    12     -14.498  27.355  17.384    0.00     3.78
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket10_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket10_atm.pdb
@@ -0,0 +1,36 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    10:
+HEADER 0  - Pocket Score                      : -0.0628
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.9820
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5960
+HEADER 5  - Mean B-factor of pocket residues  : 0.1384
+HEADER 6  - Hydrophobicity Score              : 10.6250
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 3.3750
+HEADER 9  - Pocket volume (Monte Carlo)       : 188.7581
+HEADER 10  -Pocket volume (convex hull)       : 5.5840
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     0
+HEADER 14 - Proportion of apolar alpha sphere : 0.0000
+ATOM   1154  OE1 GLU A 163       4.650  27.819  25.764  0.43  6.43           O 0
+ATOM   1152   CG GLU A 163       5.161  25.638  24.967  0.00  0.00           C 0
+ATOM   1016   CD LYS A 147       5.052  27.779  21.976  0.00  0.00           C 0
+ATOM   1167   OG SER A 165       8.291  27.410  20.578  0.68  6.43           O 0
+ATOM   1204  CG2 THR A 171       9.908  26.194  29.049  0.00  0.00           C 0
+ATOM   1150    O GLU A 163       7.888  23.714  26.395  0.70  2.14           O 0
+ATOM   1203  OG1 THR A 171       7.661  25.327  28.824  0.56  4.29           O 0
+ATOM   1184    O SER A 169      12.438  22.965  24.150  0.58  1.07           O 0
+ATOM   1186   OG SER A 169      14.353  25.376  25.217  0.00  0.00           O 0
+ATOM   1162    N SER A 165       9.174  24.740  21.459  0.65  2.19           N 0
+ATOM   1166   CB SER A 165       9.474  26.784  20.137  0.00  0.00           C 0
+ATOM   1171    O ALA A 166      13.261  24.393  21.119  0.42  5.36           O 0
+ATOM   1188   CA PHE A 170      11.288  22.362  26.702  0.00  0.00           C 0
+ATOM   1157   CA SER A 164       8.406  23.292  23.261  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket10_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket10_vert.pqr
@@ -0,0 +1,41 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    10:
+HEADER 0  - Pocket Score                      : -0.0628
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.9820
+HEADER 4  - Mean alpha-sphere SA              : 0.5960
+HEADER 5  - Mean B-factor                     : 0.1384
+HEADER 6  - Hydrophobicity Score              : 10.6250
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 3.3750
+HEADER 9  - Real volume (approximation)       : 188.7581
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     0
+HEADER 13 - Proportion of apolar alpha sphere : 0.0000
+ATOM      1    O STP    10       7.964  27.871  24.200    0.00     3.67
+ATOM      2    O STP    10       9.060  27.846  24.971    0.00     4.48
+ATOM      3    O STP    10       8.457  27.440  25.735    0.00     3.83
+ATOM      4    O STP    10       8.568  27.505  25.590    0.00     3.93
+ATOM      5    O STP    10       8.418  27.411  25.750    0.00     3.79
+ATOM      6    O STP    10       9.084  27.764  24.955    0.00     4.46
+ATOM      7    O STP    10      10.654  26.047  25.364    0.00     3.76
+ATOM      8    O STP    10      10.424  27.853  24.712    0.00     4.67
+ATOM      9    O STP    10       9.439  27.576  24.860    0.00     4.44
+ATOM     10    O STP    10      10.404  26.714  24.932    0.00     4.18
+ATOM     11    O STP    10      10.731  27.817  24.294    0.00     4.46
+ATOM     12    O STP    10      10.476  26.400  24.885    0.00     4.02
+ATOM     13    O STP    10      11.588  27.014  23.248    0.00     3.77
+ATOM     14    O STP    10      11.536  26.189  23.460    0.00     3.42
+ATOM     15    O STP    10       8.935  27.351  24.682    0.00     4.15
+ATOM     16    O STP    10      10.729  25.699  25.632    0.00     3.55
+ATOM     17    O STP    10      10.887  25.711  25.706    0.00     3.52
+ATOM     18    O STP    10      10.424  26.232  24.837    0.00     3.90
+ATOM     19    O STP    10       8.612  26.736  24.470    0.00     3.66
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket11_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket11_atm.pdb
@@ -0,0 +1,45 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    11:
+HEADER 0  - Pocket Score                      : -0.0850
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    24
+HEADER 3  - Mean alpha-sphere radius          : 3.9413
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6305
+HEADER 5  - Mean B-factor of pocket residues  : 0.4193
+HEADER 6  - Hydrophobicity Score              : 1.2857
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 3.5714
+HEADER 9  - Pocket volume (Monte Carlo)       : 314.7152
+HEADER 10  -Pocket volume (convex hull)       : 23.7268
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     1
+HEADER 14 - Proportion of apolar alpha sphere : 0.0417
+ATOM    905   CG GLN A 133       5.839   1.301  12.015  0.00  0.00           C 0
+ATOM    900    N GLN A 133       6.065   3.614  13.906  0.65  2.19           N 0
+ATOM    899    O GLY A 132       5.184   4.004  15.981  0.41  9.64           O 0
+ATOM    901   CA GLN A 133       6.602   2.274  14.225  0.00  0.00           C 0
+ATOM    288   CB SER A  50      -2.318   6.388  16.587  0.00  0.00           C 0
+ATOM    266  OE1 GLU A  47       2.544   7.847  14.341  0.46  3.21           O 0
+ATOM    289   OG SER A  50      -1.198   5.792  17.193  0.42  8.57           O 0
+ATOM    254   CD ARG A  46      -1.055   7.401  10.651  0.00  0.00           C 0
+ATOM    267  OE2 GLU A  47       2.264   7.922  12.168  0.62  2.14           O 0
+ATOM    256   CZ ARG A  46       0.655   7.138   8.868  0.00  0.00           C 0
+ATOM    258  NH2 ARG A  46       1.902   7.340   8.454  0.00  0.00           N 0
+ATOM    251    O ARG A  46      -2.341   8.640  14.586  0.42  1.07           O 0
+ATOM    877    O SER A 129       4.713   7.157   9.023  0.00  0.00           O 0
+ATOM    885   CG MET A 130       7.387   4.013   7.315  0.00  0.00           C 0
+ATOM    879   OG SER A 129       5.275   7.233   5.546  0.00  0.00           O 0
+ATOM    883    O MET A 130       7.577   4.779  11.583  0.00  0.00           O 0
+ATOM    881   CA MET A 130       7.027   5.523   9.334  0.00  0.00           C 0
+ATOM    897   CA GLY A 132       5.029   5.773  14.338  0.00  0.00           C 0
+ATOM    255   NE ARG A  46       0.290   7.541  10.087  0.49  1.09           N 0
+ATOM    908  NE2 GLN A 133       6.088   1.519   9.608  0.00  0.00           N 0
+ATOM    257  NH1 ARG A  46      -0.217   6.541   8.063  0.00  0.00           N 0
+ATOM    898    C GLY A 132       5.444   4.381  14.811  0.00  0.00           C 0
+ATOM    896    N GLY A 132       5.940   6.411  13.397  0.00  0.00           N 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket11_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket11_vert.pqr
@@ -0,0 +1,46 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    11:
+HEADER 0  - Pocket Score                      : -0.0850
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    24
+HEADER 3  - Mean alpha-sphere radius          : 3.9413
+HEADER 4  - Mean alpha-sphere SA              : 0.6305
+HEADER 5  - Mean B-factor                     : 0.4193
+HEADER 6  - Hydrophobicity Score              : 1.2857
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 3.5714
+HEADER 9  - Real volume (approximation)       : 314.7152
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     1
+HEADER 13 - Proportion of apolar alpha sphere : 0.0417
+ATOM      1    O STP    11       3.065   1.680  14.257    0.00     3.59
+ATOM      2    O STP    11      -0.262   5.672  13.713    0.00     3.61
+ATOM      3    O STP    11       0.191   4.442  13.421    0.00     4.24
+ATOM      4    O STP    11       2.560   3.835  10.859    0.00     4.30
+ATOM      5    O STP    11      -0.316   5.894  13.740    0.00     3.52
+ATOM      6    O STP    11       3.457   4.032   6.967    0.00     3.95
+ATOM      7    O STP    11       2.663   3.891  10.841    0.00     4.26
+ATOM      8    O STP    11       4.096   4.245  10.995    0.00     3.57
+ATOM      9    O STP    11       4.136   4.217  10.924    0.00     3.55
+ATOM     10    O STP    11       3.244   4.177  11.181    0.00     3.96
+ATOM     11    O STP    11       3.188   4.166  11.182    0.00     3.99
+ATOM     12    O STP    11       2.014   3.532  11.198    0.00     4.50
+ATOM     13    O STP    11       2.518   3.690  10.662    0.00     4.31
+ATOM     14    O STP    11       2.689   3.819  10.691    0.00     4.24
+ATOM     15    O STP    11       2.118   3.108   9.175    0.00     4.30
+ATOM     16    O STP    11       3.327   3.642   7.482    0.00     4.08
+ATOM     17    O STP    11       4.123   4.188  10.873    0.00     3.55
+ATOM     18    O STP    11       4.234   4.163  10.882    0.00     3.47
+ATOM     19    O STP    11       2.703   1.870  14.067    0.00     3.79
+ATOM     20    C STP    11       2.011   3.354  12.335    0.00     4.36
+ATOM     21    O STP    11       1.265   3.803  14.371    0.00     4.24
+ATOM     22    O STP    11       1.313   3.846  14.395    0.00     4.19
+ATOM     23    O STP    11       4.151   4.474  11.146    0.00     3.47
+ATOM     24    O STP    11       3.883   4.476  11.221    0.00     3.57
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket12_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket12_atm.pdb
@@ -0,0 +1,37 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    12:
+HEADER 0  - Pocket Score                      : -0.0943
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.9685
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4690
+HEADER 5  - Mean B-factor of pocket residues  : 0.6813
+HEADER 6  - Hydrophobicity Score              : 17.1250
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 4.3750
+HEADER 9  - Pocket volume (Monte Carlo)       : 258.9960
+HEADER 10  -Pocket volume (convex hull)       : 6.1907
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     1
+HEADER 14 - Proportion of apolar alpha sphere : 0.0588
+ATOM    546  OD1 ASN A  83      -9.060  30.353  17.010  0.00  0.00           O 0
+ATOM    564  OE1 GLN A  85     -11.154  34.993  17.665  0.00  0.00           O 0
+ATOM    561   CB GLN A  85      -9.191  33.552  16.094  0.00  0.00           C 0
+ATOM   1635  OE1 GLU A 223     -12.191  29.432  14.068  0.69  6.43           O 0
+ATOM   1624    O VAL A 222     -16.483  24.967  15.232  0.41  9.64           O 0
+ATOM    536    O PRO A  82     -10.987  25.587  15.850  0.58  5.36           O 0
+ATOM   1633   CG GLU A 223     -13.156  27.273  13.733  0.00  0.00           C 0
+ATOM   1640    O LYS A 224     -17.476  29.652  17.739  0.00  0.00           O 0
+ATOM    531  CG2 ILE A  81     -11.338  23.371  19.262  0.00  0.00           C 0
+ATOM   1617  CD2 PHE A 221     -15.287  21.681  19.679  0.00  0.00           C 0
+ATOM   1614   CB PHE A 221     -14.726  21.255  17.261  0.00  0.00           C 0
+ATOM    547  ND2 ASN A  83     -10.255  29.459  18.675  0.00  0.00           N 0
+ATOM   1638   CA LYS A 224     -16.885  29.440  15.328  0.00  0.00           C 0
+ATOM   1641   CB LYS A 224     -16.523  30.812  14.719  0.00  0.00           C 0
+ATOM   1629   CA GLU A 223     -15.616  27.088  13.785  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket12_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket12_vert.pqr
@@ -0,0 +1,39 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    12:
+HEADER 0  - Pocket Score                      : -0.0943
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.9685
+HEADER 4  - Mean alpha-sphere SA              : 0.4690
+HEADER 5  - Mean B-factor                     : 0.6813
+HEADER 6  - Hydrophobicity Score              : 17.1250
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 4.3750
+HEADER 9  - Real volume (approximation)       : 258.9960
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     1
+HEADER 13 - Proportion of apolar alpha sphere : 0.0588
+ATOM      1    O STP    12     -12.188  31.839  16.593    0.00     3.49
+ATOM      2    O STP    12     -14.197  27.278  17.645    0.00     4.05
+ATOM      3    O STP    12     -14.250  26.710  18.687    0.00     4.47
+ATOM      4    O STP    12     -14.909  26.223  19.335    0.00     4.57
+ATOM      5    C STP    12     -14.382  24.675  18.050    0.00     3.53
+ATOM      6    O STP    12     -14.022  26.981  18.887    0.00     4.51
+ATOM      7    O STP    12     -13.149  28.055  17.189    0.00     3.54
+ATOM      8    O STP    12     -13.848  27.808  17.708    0.00     4.07
+ATOM      9    O STP    12     -13.798  28.442  17.460    0.00     3.88
+ATOM     10    O STP    12     -13.798  28.303  17.460    0.00     3.92
+ATOM     11    O STP    12     -13.804  28.284  17.472    0.00     3.93
+ATOM     12    O STP    12     -13.734  30.649  17.420    0.00     3.89
+ATOM     13    O STP    12     -13.444  31.621  17.292    0.00     4.09
+ATOM     14    O STP    12     -13.757  31.663  17.802    0.00     4.23
+ATOM     15    O STP    12     -12.392  31.711  16.849    0.00     3.60
+ATOM     16    O STP    12     -14.320  27.344  17.475    0.00     3.92
+ATOM     17    O STP    12     -14.498  27.355  17.384    0.00     3.78
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket1_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket1_atm.pdb
@@ -0,0 +1,106 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     1:
+HEADER 0  - Pocket Score                      : 0.6640
+HEADER 1  - Drug Score                        : 0.8551
+HEADER 2  - Number of alpha spheres           :   143
+HEADER 3  - Mean alpha-sphere radius          : 3.9767
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4511
+HEADER 5  - Mean B-factor of pocket residues  : 0.2270
+HEADER 6  - Hydrophobicity Score              : 39.7273
+HEADER 7  - Polarity Score                    :    13
+HEADER 8  - Amino Acid based volume Score     : 3.9394
+HEADER 9  - Pocket volume (Monte Carlo)       : 1437.6858
+HEADER 10  -Pocket volume (convex hull)       : 806.5479
+HEADER 11 - Charge Score                      :    -2
+HEADER 12 - Local hydrophobic density Score   : 53.0833
+HEADER 13 - Number of apolar alpha sphere     :    72
+HEADER 14 - Proportion of apolar alpha sphere : 0.5035
+ATOM    745   CB ILE A 110      10.451   5.101  26.110  0.00  0.00           C 0
+ATOM    725    O LEU A 107      10.269   8.807  26.132  0.57  1.07           O 0
+ATOM    747  CG2 ILE A 110       9.941   4.043  25.116  0.00  0.00           C 0
+ATOM    748  CD1 ILE A 110       8.312   5.037  27.504  0.00  0.00           C 0
+ATOM    939   CB PHE A 138       4.805  12.603  20.262  0.00  0.00           C 0
+ATOM    729  CD2 LEU A 107       6.011   8.589  27.995  0.00  0.00           C 0
+ATOM    726   CB LEU A 107       7.835  10.315  27.706  0.00  0.00           C 0
+ATOM    728  CD1 LEU A 107       5.486  11.007  28.094  0.00  0.00           C 0
+ATOM    297  ND2 ASN A  51       1.685  10.358  20.090  0.00  0.00           N 0
+ATOM    322   CB ALA A  55      -3.732   7.859  26.069  0.00  0.00           C 0
+ATOM    629  OD2 ASP A  93      -5.250  12.211  24.343  0.00  0.00           O 0
+ATOM   1297  OG1 THR A 184      -2.825  13.382  27.826  0.00  0.00           O 0
+ATOM    293    O ASN A  51      -2.550   7.762  22.810  0.62  1.07           O 0
+ATOM    923    O GLY A 135       7.398   7.044  20.561  0.37  1.07           O 0
+ATOM    688  OD1 ASP A 102       5.273   8.543  32.326  0.00  0.00           O 0
+ATOM    689  OD2 ASP A 102       3.245   9.344  32.398  0.05  9.64           O 0
+ATOM    347   NZ LYS A  58       1.037   3.136  31.258  0.48  9.84           N 0
+ATOM    718   CB ASN A 106       8.903   8.135  32.100  0.00  0.00           C 0
+ATOM    721  ND2 ASN A 106       7.640   7.886  34.181  0.62  6.56           N 0
+ATOM     67  OE1 GLN A  23      16.065  11.089  26.331  0.48  3.21           O 0
+ATOM     60    N GLN A  23      17.367  15.515  25.627  0.62  2.19           N 0
+ATOM    731   CA GLY A 108      12.285  10.723  26.676  0.00  0.00           C 0
+ATOM   1196  CE2 PHE A 170      12.833  18.086  28.115  0.00  0.00           C 0
+ATOM     66   CD GLN A  23      17.284  11.258  26.494  0.00  0.00           C 0
+ATOM     65   CG GLN A  23      17.841  12.642  26.603  0.00  0.00           C 0
+ATOM    712  OD1 ASN A 105      14.376  12.949  33.744  0.00  0.00           O 0
+ATOM    709    O ASN A 105      12.294  10.288  30.522  0.00  0.00           O 0
+ATOM    724    C LEU A 107      10.170   9.520  27.110  0.00  0.00           C 0
+ATOM    957   OH TYR A 139      10.408  14.067  22.882  0.74  2.14           O 0
+ATOM   1314  CG2 VAL A 186      -1.059  16.328  22.486  0.00  0.00           C 0
+ATOM    294   CB ASN A  51      -0.500   9.491  20.841  0.00  0.00           C 0
+ATOM    271    O LEU A  48      -2.902  10.967  19.157  0.00  0.00           O 0
+ATOM    275  CD2 LEU A  48       0.650  14.227  18.009  0.00  0.00           C 0
+ATOM    292    C ASN A  51      -2.566   8.364  21.757  0.00  0.00           C 0
+ATOM    298    N SER A  52      -3.580   9.144  21.406  0.00  0.00           N 0
+ATOM    303   OG SER A  52      -5.207  11.547  21.613  0.48  2.14           O 0
+ATOM    660   CE MET A  98       1.031  13.622  27.487  0.00  0.00           C 0
+ATOM    941  CD1 PHE A 138       3.473  14.667  20.982  0.00  0.00           C 0
+ATOM    314   CB ASP A  54      -1.972   4.306  22.744  0.00  0.00           C 0
+ATOM    296  OD1 ASN A  51       1.250   8.116  19.865  0.28  9.64           O 0
+ATOM    291   CA ASN A  51      -1.395   8.242  20.762  0.00  0.00           C 0
+ATOM    317  OD2 ASP A  54      -0.471   3.918  20.908  0.06  4.29           O 0
+ATOM    295   CG ASN A  51       0.891   9.265  20.218  0.00  0.00           C 0
+ATOM     55  CD1 PHE A  22      13.087  17.262  24.033  0.00  0.00           C 0
+ATOM     88  CG1 ILE A  26      14.985  12.652  22.774  0.00  0.00           C 0
+ATOM     50   CA PHE A  22      16.075  17.574  25.463  0.00  0.00           C 0
+ATOM    955  CE2 TYR A 139       9.897  12.867  20.832  0.00  0.00           C 0
+ATOM    925   CA VAL A 136       8.331   8.608  18.506  0.00  0.00           C 0
+ATOM    753   CB ALA A 111      11.602   9.225  23.194  0.00  0.00           C 0
+ATOM    749    N ALA A 111      12.059   7.141  24.480  0.00  0.00           N 0
+ATOM    738   CB THR A 109      14.279   7.151  29.525  0.00  0.00           C 0
+ATOM    734    N THR A 109      13.309   8.871  27.955  0.67  1.09           N 0
+ATOM    710   CB ASN A 105      12.609  11.390  33.652  0.00  0.00           C 0
+ATOM    739  OG1 THR A 109      15.393   6.242  29.602  0.00  0.00           O 0
+ATOM     68  NE2 GLN A  23      18.164  10.249  26.547  0.26  5.47           N 0
+ATOM    659   SD MET A  98       2.323  12.442  28.046  0.00  0.00           S 0
+ATOM    943  CE1 PHE A 138       3.386  15.978  21.463  0.00  0.00           C 0
+ATOM   1298  CG2 THR A 184      -2.118  14.890  26.102  0.00  0.00           C 0
+ATOM   1296   CB THR A 184      -3.360  14.202  26.782  0.00  0.00           C 0
+ATOM    649    N GLY A  97      -3.592  10.108  30.530  0.00  0.00           N 0
+ATOM    652    O GLY A  97      -0.982   9.715  31.168  0.50  2.14           O 0
+ATOM    647  CG2 ILE A  96      -2.705   6.940  30.078  0.00  0.00           C 0
+ATOM    701    O ILE A 104      12.410  14.458  31.203  0.45  4.29           O 0
+ATOM     47    O ALA A  21      16.676  18.084  28.053  0.00  0.00           O 0
+ATOM    735   CA THR A 109      14.166   7.683  28.081  0.00  0.00           C 0
+ATOM    658   CG MET A  98       1.514  11.608  29.411  0.00  0.00           C 0
+ATOM    944  CE2 PHE A 138       5.823  16.040  21.651  0.00  0.00           C 0
+ATOM    697  CD2 LEU A 103       4.295  15.610  29.705  0.00  0.00           C 0
+ATOM    942  CD2 PHE A 138       5.899  14.705  21.159  0.00  0.00           C 0
+ATOM    945   CZ PHE A 138       4.564  16.672  21.797  0.00  0.00           C 0
+ATOM   1039  CG2 VAL A 150       2.163  18.153  24.511  0.00  0.00           C 0
+ATOM     57  CE1 PHE A  22      11.774  17.738  23.825  0.00  0.00           C 0
+ATOM    940   CG PHE A 138       4.730  14.010  20.833  0.00  0.00           C 0
+ATOM   1038  CG1 VAL A 150       0.847  17.227  26.458  0.00  0.00           C 0
+ATOM   1140  CD2 TRP A 162       6.147  19.241  26.093  0.00  0.00           C 0
+ATOM    693    O LEU A 103       8.948  15.292  29.858  0.34  4.29           O 0
+ATOM    691   CA LEU A 103       6.946  14.622  30.902  0.00  0.00           C 0
+ATOM    730    N GLY A 108      11.053  10.476  27.422  0.44  1.09           N 0
+ATOM   1197   CZ PHE A 170      12.116  17.841  29.257  0.00  0.00           C 0
+ATOM   1141  NE1 TRP A 162       7.972  18.233  26.915  0.00  0.00           N 0
+ATOM   1139  CD1 TRP A 162       7.121  18.505  27.971  0.00  0.00           C 0
+ATOM   1138   CG TRP A 162       6.008  19.134  27.536  0.00  0.00           C 0
+ATOM   1144  CZ2 TRP A 162       7.884  18.614  24.422  0.00  0.00           C 0
+ATOM   1142  CE2 TRP A 162       7.409  18.680  25.751  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket1_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket1_vert.pqr
@@ -0,0 +1,165 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     1:
+HEADER 0  - Pocket Score                      : 0.6640
+HEADER 1  - Drug Score                        : 0.8551
+HEADER 2  - Number of V. Vertices             :   143
+HEADER 3  - Mean alpha-sphere radius          : 3.9767
+HEADER 4  - Mean alpha-sphere SA              : 0.4511
+HEADER 5  - Mean B-factor                     : 0.2270
+HEADER 6  - Hydrophobicity Score              : 39.7273
+HEADER 7  - Polarity Score                    :    13
+HEADER 8  - Volume Score                      : 3.9394
+HEADER 9  - Real volume (approximation)       : 1437.6858
+HEADER 10 - Charge Score                      :    -2
+HEADER 11 - Local hydrophobic density Score   : 53.0833
+HEADER 12 - Number of apolar alpha sphere     :    72
+HEADER 13 - Proportion of apolar alpha sphere : 0.5035
+ATOM      1    C STP     1       7.785   6.838  24.439    0.00     3.59
+ATOM      2    C STP     1       5.774   9.979  23.751    0.00     4.47
+ATOM      3    C STP     1       4.349   9.667  23.812    0.00     4.63
+ATOM      4    O STP     1      -1.508  10.969  24.938    0.00     3.99
+ATOM      5    O STP     1       6.817   8.930  24.068    0.00     4.02
+ATOM      6    C STP     1       5.854   9.885  23.690    0.00     4.50
+ATOM      7    O STP     1       4.623   9.304  23.580    0.00     4.68
+ATOM      8    O STP     1       7.615   6.878  24.306    0.00     3.76
+ATOM      9    O STP     1       7.083   7.215  24.474    0.00     3.93
+ATOM     10    O STP     1       3.114   6.284  29.706    0.00     4.08
+ATOM     11    C STP     1       6.727   6.176  30.320    0.00     3.43
+ATOM     12    O STP     1       6.590   4.208  31.665    0.00     4.58
+ATOM     13    O STP     1       4.754   4.946  29.971    0.00     4.33
+ATOM     14    O STP     1      13.912  14.330  27.259    0.00     4.00
+ATOM     15    O STP     1      16.020  12.287  30.152    0.00     4.01
+ATOM     16    O STP     1      16.084  11.656  30.325    0.00     4.03
+ATOM     17    O STP     1       8.887  11.600  24.709    0.00     3.43
+ATOM     18    C STP     1      -0.732  13.051  21.091    0.00     3.58
+ATOM     19    C STP     1      -0.386  13.047  21.225    0.00     3.58
+ATOM     20    O STP     1      -1.558  11.234  24.081    0.00     3.83
+ATOM     21    O STP     1      -1.802  11.344  23.665    0.00     3.62
+ATOM     22    O STP     1      -1.699  12.544  22.872    0.00     3.86
+ATOM     23    O STP     1      -1.739  12.698  22.218    0.00     3.70
+ATOM     24    O STP     1      -1.975  11.852  23.036    0.00     3.54
+ATOM     25    C STP     1       0.563  12.588  23.454    0.00     4.19
+ATOM     26    O STP     1      -0.950  10.812  25.145    0.00     4.16
+ATOM     27    C STP     1       0.277  13.297  21.360    0.00     3.50
+ATOM     28    C STP     1       0.736  12.678  23.430    0.00     4.18
+ATOM     29    O STP     1       0.753   6.534  22.979    0.00     3.53
+ATOM     30    O STP     1       0.730   6.506  22.916    0.00     3.49
+ATOM     31    O STP     1       1.477   7.589  24.040    0.00     4.21
+ATOM     32    O STP     1       0.889   7.396  23.257    0.00     3.49
+ATOM     33    C STP     1      11.631  14.628  26.606    0.00     3.96
+ATOM     34    C STP     1      12.945  13.969  25.376    0.00     3.56
+ATOM     35    C STP     1      13.913  14.874  26.698    0.00     3.67
+ATOM     36    C STP     1      13.708  14.441  26.773    0.00     3.98
+ATOM     37    O STP     1      13.827  14.182  26.170    0.00     3.82
+ATOM     38    C STP     1      13.822  14.141  26.067    0.00     3.80
+ATOM     39    O STP     1      13.857  14.157  26.064    0.00     3.79
+ATOM     40    C STP     1       7.381  10.470  21.326    0.00     3.51
+ATOM     41    O STP     1       7.972  11.066  23.806    0.00     3.97
+ATOM     42    O STP     1       8.295  11.024  23.750    0.00     3.81
+ATOM     43    O STP     1       7.478  10.337  23.282    0.00     4.27
+ATOM     44    O STP     1       7.280  10.418  23.358    0.00     4.38
+ATOM     45    C STP     1       7.156  10.473  23.341    0.00     4.42
+ATOM     46    O STP     1       8.724   6.926  23.719    0.00     3.43
+ATOM     47    O STP     1      16.251  10.521  30.258    0.00     3.97
+ATOM     48    O STP     1      16.016  10.444  30.032    0.00     3.76
+ATOM     49    O STP     1      16.674  10.615  30.805    0.00     4.40
+ATOM     50    O STP     1      16.395   8.912  33.152    0.00     4.55
+ATOM     51    O STP     1      15.810   9.633  32.174    0.00     3.94
+ATOM     52    O STP     1      17.109  10.453  31.017    0.00     4.60
+ATOM     53    C STP     1       1.424  11.066  24.202    0.00     4.18
+ATOM     54    C STP     1       2.034   9.777  24.491    0.00     4.45
+ATOM     55    C STP     1       3.535  10.777  24.109    0.00     4.44
+ATOM     56    C STP     1       2.895  11.680  23.923    0.00     4.23
+ATOM     57    C STP     1       2.330  11.918  23.906    0.00     4.17
+ATOM     58    C STP     1       0.249  10.171  25.029    0.00     4.31
+ATOM     59    C STP     1      -0.088  10.016  25.481    0.00     4.28
+ATOM     60    C STP     1       1.463  14.193  23.946    0.00     3.61
+ATOM     61    C STP     1       3.864  14.031  24.821    0.00     3.91
+ATOM     62    C STP     1       0.172  12.525  23.583    0.00     4.14
+ATOM     63    C STP     1      -1.579  12.507  23.063    0.00     3.90
+ATOM     64    O STP     1      -1.912  11.626  24.998    0.00     3.45
+ATOM     65    O STP     1      -0.989  11.052  24.874    0.00     4.19
+ATOM     66    C STP     1      -0.879  11.128  24.694    0.00     4.20
+ATOM     67    O STP     1      -1.354  11.116  24.781    0.00     4.07
+ATOM     68    O STP     1      -1.288  11.285  24.407    0.00     4.07
+ATOM     69    O STP     1      -1.482  10.096  27.670    0.00     3.55
+ATOM     70    O STP     1       1.783   6.931  28.759    0.00     4.60
+ATOM     71    O STP     1       1.714   6.908  28.614    0.00     4.66
+ATOM     72    O STP     1      15.581  12.421  30.019    0.00     3.95
+ATOM     73    O STP     1      15.750  12.621  30.007    0.00     4.00
+ATOM     74    O STP     1      16.662  14.424  30.372    0.00     4.33
+ATOM     75    O STP     1      14.219  12.652  28.837    0.00     3.48
+ATOM     76    O STP     1      14.087  14.330  27.578    0.00     4.00
+ATOM     77    O STP     1      14.631  14.244  28.046    0.00     3.87
+ATOM     78    O STP     1      13.939  14.281  27.501    0.00     4.01
+ATOM     79    O STP     1      14.756  14.840  28.269    0.00     3.78
+ATOM     80    O STP     1      15.299  14.577  28.703    0.00     3.82
+ATOM     81    O STP     1      16.054  10.122  29.656    0.00     3.46
+ATOM     82    O STP     1      16.456   9.802  29.471    0.00     3.42
+ATOM     83    C STP     1      16.445   9.833  29.519    0.00     3.45
+ATOM     84    C STP     1      16.465   9.812  29.510    0.00     3.44
+ATOM     85    C STP     1       1.618   7.073  28.344    0.00     4.66
+ATOM     86    C STP     1      -0.008   8.421  27.485    0.00     4.02
+ATOM     87    O STP     1       1.812   7.179  28.734    0.00     4.49
+ATOM     88    O STP     1      -1.242  10.098  27.540    0.00     3.66
+ATOM     89    C STP     1      -0.795  10.331  26.577    0.00     3.87
+ATOM     90    C STP     1      -0.351  10.061  26.183    0.00     4.04
+ATOM     91    C STP     1       5.216  14.534  25.639    0.00     4.31
+ATOM     92    C STP     1       6.844  13.993  25.301    0.00     4.31
+ATOM     93    C STP     1       4.953  13.937  25.159    0.00     4.18
+ATOM     94    C STP     1       6.895  13.161  24.861    0.00     4.13
+ATOM     95    C STP     1       6.336  11.714  24.056    0.00     4.19
+ATOM     96    C STP     1       7.101  11.566  23.730    0.00     4.23
+ATOM     97    C STP     1       7.064  11.491  23.691    0.00     4.25
+ATOM     98    C STP     1       4.397  14.033  24.909    0.00     4.08
+ATOM     99    C STP     1       4.395  14.034  24.909    0.00     4.08
+ATOM    100    C STP     1       4.116  14.428  25.075    0.00     4.00
+ATOM    101    C STP     1       4.854  14.788  25.584    0.00     4.24
+ATOM    102    C STP     1       3.927  14.727  25.118    0.00     3.90
+ATOM    103    C STP     1       4.371  15.015  25.725    0.00     4.02
+ATOM    104    C STP     1       4.329  14.825  25.421    0.00     4.07
+ATOM    105    C STP     1       4.599  14.941  25.596    0.00     4.17
+ATOM    106    C STP     1      11.147  15.077  26.485    0.00     3.81
+ATOM    107    C STP     1       4.407  14.017  24.905    0.00     4.09
+ATOM    108    C STP     1       4.436  13.999  24.911    0.00     4.09
+ATOM    109    C STP     1       4.748  13.478  24.902    0.00     4.10
+ATOM    110    C STP     1       3.975  11.754  24.269    0.00     4.18
+ATOM    111    C STP     1       3.151  11.816  24.008    0.00     4.17
+ATOM    112    C STP     1       5.894  11.911  24.134    0.00     4.08
+ATOM    113    C STP     1       3.984  15.311  26.029    0.00     3.70
+ATOM    114    C STP     1       1.548  14.653  24.159    0.00     3.52
+ATOM    115    C STP     1       1.551  14.776  24.130    0.00     3.45
+ATOM    116    C STP     1       1.848  14.707  24.298    0.00     3.47
+ATOM    117    C STP     1       4.926  15.350  25.662    0.00     4.10
+ATOM    118    C STP     1       6.620  14.280  27.401    0.00     3.53
+ATOM    119    O STP     1      10.896  15.156  26.541    0.00     3.85
+ATOM    120    O STP     1      10.721  14.194  26.674    0.00     3.81
+ATOM    121    O STP     1      11.490  13.931  27.857    0.00     3.51
+ATOM    122    O STP     1      11.366  14.623  26.733    0.00     4.01
+ATOM    123    O STP     1       9.184  13.635  26.450    0.00     3.80
+ATOM    124    O STP     1      11.789  14.458  27.414    0.00     3.84
+ATOM    125    O STP     1      11.772  14.543  27.511    0.00     3.75
+ATOM    126    O STP     1      10.363  15.394  26.388    0.00     3.75
+ATOM    127    O STP     1      10.557  15.655  26.584    0.00     3.67
+ATOM    128    O STP     1       6.897  14.234  25.492    0.00     4.38
+ATOM    129    O STP     1       7.349  14.139  25.864    0.00     4.27
+ATOM    130    O STP     1       7.403  14.166  26.142    0.00     4.18
+ATOM    131    O STP     1       7.664  14.151  26.041    0.00     4.19
+ATOM    132    O STP     1       6.658  14.520  26.744    0.00     3.94
+ATOM    133    C STP     1       5.424  15.941  26.511    0.00     3.40
+ATOM    134    C STP     1       5.487  15.835  26.436    0.00     3.49
+ATOM    135    C STP     1       7.227  14.775  25.129    0.00     3.96
+ATOM    136    O STP     1       7.217  14.760  25.143    0.00     3.97
+ATOM    137    O STP     1       7.249  14.785  25.136    0.00     3.95
+ATOM    138    C STP     1       5.482  15.772  26.370    0.00     3.54
+ATOM    139    C STP     1       5.091  15.244  25.653    0.00     4.15
+ATOM    140    C STP     1       5.067  15.273  25.656    0.00     4.14
+ATOM    141    C STP     1       5.814  14.647  25.758    0.00     4.34
+ATOM    142    C STP     1       5.861  14.632  25.749    0.00     4.33
+ATOM    143    C STP     1       5.829  14.647  25.770    0.00     4.33
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket2_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket2_atm.pdb
@@ -0,0 +1,45 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     2:
+HEADER 0  - Pocket Score                      : 0.1222
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    24
+HEADER 3  - Mean alpha-sphere radius          : 4.0106
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5440
+HEADER 5  - Mean B-factor of pocket residues  : 0.6012
+HEADER 6  - Hydrophobicity Score              : -15.7273
+HEADER 7  - Polarity Score                    :    10
+HEADER 8  - Amino Acid based volume Score     : 3.7273
+HEADER 9  - Pocket volume (Monte Carlo)       : 425.4238
+HEADER 10  -Pocket volume (convex hull)       : 41.3760
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 2.0000
+HEADER 13 - Number of apolar alpha sphere     :     3
+HEADER 14 - Proportion of apolar alpha sphere : 0.1250
+ATOM    437   CE LYS A  69      -5.696   2.915  38.737  0.00  0.00           C 0
+ATOM   1078   CB ASN A 155      -5.607   9.043  38.223  0.00  0.00           C 0
+ATOM   1088  OD1 ASP A 156      -2.629   7.495  41.107  0.57  7.50           O 0
+ATOM   1089  OD2 ASP A 156      -1.007   6.604  39.987  0.45  5.36           O 0
+ATOM   1072  CE1 HIS A 154      -1.594   7.833  36.249  0.00  0.00           C 0
+ATOM    386  OE1 GLU A  62      -4.122   3.018  35.589  0.61  3.21           O 0
+ATOM   1081  ND2 ASN A 155      -7.367   7.680  37.395  0.83  2.19           N 0
+ATOM    427    O SER A  68     -11.565   6.414  40.037  0.41  5.36           O 0
+ATOM    429   OG SER A  68     -10.440   4.092  42.438  0.00  0.00           O 0
+ATOM    431   CA LYS A  69      -9.876   5.253  38.109  0.00  0.00           C 0
+ATOM    646  CG1 ILE A  96      -3.578   6.400  32.452  0.00  0.00           C 0
+ATOM    435   CG LYS A  69      -7.660   4.136  38.129  0.00  0.00           C 0
+ATOM    416  OD2 ASP A  66      -7.632   1.680  41.581  0.65  8.57           O 0
+ATOM   1079   CG ASN A 155      -6.996   8.917  37.616  0.00  0.00           C 0
+ATOM   1077    O ASN A 155      -4.519  11.110  40.482  0.00  0.00           O 0
+ATOM   1080  OD1 ASN A 155      -7.743   9.903  37.372  0.64  4.29           O 0
+ATOM   1063   NZ LYS A 153      -5.356  14.633  38.620  0.00  0.00           N 0
+ATOM    459   CB SER A  72     -10.631  11.640  36.849  0.00  0.00           C 0
+ATOM    456   CA SER A  72     -12.159  11.609  36.983  0.00  0.00           C 0
+ATOM    455    N SER A  72     -12.600  10.355  37.624  0.00  0.00           N 0
+ATOM    450    O ASP A  71     -14.393  11.297  38.605  0.00  0.00           O 0
+ATOM    451   CB ASP A  71     -13.738   8.920  40.362  0.00  0.00           C 0
+ATOM    449    C ASP A  71     -13.715  10.304  38.343  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket2_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket2_vert.pqr
@@ -0,0 +1,46 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     2:
+HEADER 0  - Pocket Score                      : 0.1222
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    24
+HEADER 3  - Mean alpha-sphere radius          : 4.0106
+HEADER 4  - Mean alpha-sphere SA              : 0.5440
+HEADER 5  - Mean B-factor                     : 0.6012
+HEADER 6  - Hydrophobicity Score              : -15.7273
+HEADER 7  - Polarity Score                    :    10
+HEADER 8  - Volume Score                      : 3.7273
+HEADER 9  - Real volume (approximation)       : 425.4238
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 2.0000
+HEADER 12 - Number of apolar alpha sphere     :     3
+HEADER 13 - Proportion of apolar alpha sphere : 0.1250
+ATOM      1    O STP     2      -3.991   5.938  38.283    0.00     3.50
+ATOM      2    O STP     2      -3.568   5.524  37.917    0.00     3.47
+ATOM      3    C STP     2      -3.931   5.923  38.105    0.00     3.54
+ATOM      4    C STP     2      -4.180   5.886  37.623    0.00     3.52
+ATOM      5    O STP     2      -4.420   5.879  37.503    0.00     3.45
+ATOM      6    O STP     2      -4.377   6.059  37.115    0.00     3.41
+ATOM      7    O STP     2      -7.842   6.647  41.105    0.00     3.88
+ATOM      8    O STP     2      -7.652   7.448  41.790    0.00     4.41
+ATOM      9    O STP     2      -4.666   6.404  35.706    0.00     3.43
+ATOM     10    C STP     2      -5.556   6.104  39.988    0.00     3.43
+ATOM     11    O STP     2      -6.919   6.642  41.684    0.00     4.41
+ATOM     12    O STP     2      -6.980   6.668  41.645    0.00     4.39
+ATOM     13    O STP     2      -6.526   5.836  41.929    0.00     4.31
+ATOM     14    O STP     2      -6.378   5.700  41.831    0.00     4.22
+ATOM     15    O STP     2      -7.822   6.625  41.102    0.00     3.88
+ATOM     16    O STP     2      -7.825   7.749  41.660    0.00     4.29
+ATOM     17    O STP     2      -8.100   8.674  42.098    0.00     4.62
+ATOM     18    O STP     2      -8.659   9.530  41.927    0.00     4.66
+ATOM     19    O STP     2      -8.737  12.631  40.804    0.00     4.50
+ATOM     20    O STP     2     -11.049  12.429  41.049    0.00     4.29
+ATOM     21    O STP     2     -11.267  12.028  41.036    0.00     4.03
+ATOM     22    O STP     2     -10.890  12.386  41.380    0.00     4.60
+ATOM     23    O STP     2      -9.951  10.626  40.848    0.00     4.18
+ATOM     24    O STP     2     -10.041   9.901  40.431    0.00     3.83
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket3_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket3_atm.pdb
@@ -0,0 +1,51 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     3:
+HEADER 0  - Pocket Score                      : 0.0502
+HEADER 1  - Drug Score                        : 0.0138
+HEADER 2  - Number of alpha spheres           :    31
+HEADER 3  - Mean alpha-sphere radius          : 3.9139
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6054
+HEADER 5  - Mean B-factor of pocket residues  : 0.2848
+HEADER 6  - Hydrophobicity Score              : 39.9091
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.8182
+HEADER 9  - Pocket volume (Monte Carlo)       : 438.3710
+HEADER 10  -Pocket volume (convex hull)       : 60.7327
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 19.4545
+HEADER 13 - Number of apolar alpha sphere     :    22
+HEADER 14 - Proportion of apolar alpha sphere : 0.7097
+ATOM   1500  CG1 VAL A 207     -11.010  10.906  11.334  0.00  0.00           C 0
+ATOM   1533    O SER A 211      -9.891   6.827  12.276  0.55  1.07           O 0
+ATOM   1539    O GLN A 212     -12.672   4.377  11.298  0.00  0.00           O 0
+ATOM   1537   CA GLN A 212     -11.070   5.585  10.068  0.00  0.00           C 0
+ATOM   1594  CD1 ILE A 218     -10.824   9.348  15.419  0.00  0.00           C 0
+ATOM   1559    O ILE A 214     -12.563   4.175  16.207  0.48  6.43           O 0
+ATOM   1606   CB LEU A 220     -14.074  16.914  13.109  0.00  0.00           C 0
+ATOM   1593  CG2 ILE A 218     -11.852  12.231  15.651  0.00  0.00           C 0
+ATOM   1590    O ILE A 218     -15.064  12.371  15.635  0.00  0.00           O 0
+ATOM   1587    N ILE A 218     -14.467  10.181  17.586  0.59  5.47           N 0
+ATOM   1591   CB ILE A 218     -12.641  10.969  16.152  0.00  0.00           C 0
+ATOM   1592  CG1 ILE A 218     -11.762   9.770  16.549  0.00  0.00           C 0
+ATOM   1503   CA LYS A 208     -11.107   9.334   6.950  0.00  0.00           C 0
+ATOM   1502    N LYS A 208     -10.517  10.430   7.696  0.00  0.00           N 0
+ATOM   1506   CB LYS A 208     -12.107   9.883   5.929  0.00  0.00           C 0
+ATOM   1498    O VAL A 207      -9.553   9.082   9.177  0.00  0.00           O 0
+ATOM   1472    O LYS A 204     -11.546  12.938   6.899  0.55  4.29           O 0
+ATOM   1501  CG2 VAL A 207      -9.586  13.044  11.381  0.00  0.00           C 0
+ATOM    523  CD1 LEU A  80      -9.898  15.086  14.356  0.00  0.00           C 0
+ATOM   1508   CD LYS A 208     -13.692   9.431   4.022  0.00  0.00           C 0
+ATOM   1475   CD LYS A 204     -16.021  15.874   6.811  0.00  0.00           C 0
+ATOM   1473   CB LYS A 204     -13.540  15.591   6.878  0.00  0.00           C 0
+ATOM   1478    N GLU A 205     -11.077  14.716   5.558  0.00  0.00           N 0
+ATOM   1471    C LYS A 204     -11.587  14.151   6.663  0.00  0.00           C 0
+ATOM   1474   CG LYS A 204     -14.759  15.911   7.688  0.00  0.00           C 0
+ATOM   1470   CA LYS A 204     -12.281  15.108   7.616  0.00  0.00           C 0
+ATOM   1499   CB VAL A 207     -10.284  12.010  10.498  0.00  0.00           C 0
+ATOM   1571    O TYR A 216     -13.684   6.959  18.163  0.00  0.00           O 0
+ATOM   1609  CD2 LEU A 220     -13.507  17.839  10.826  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket3_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket3_vert.pqr
@@ -0,0 +1,53 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     3:
+HEADER 0  - Pocket Score                      : 0.0502
+HEADER 1  - Drug Score                        : 0.0138
+HEADER 2  - Number of V. Vertices             :    31
+HEADER 3  - Mean alpha-sphere radius          : 3.9139
+HEADER 4  - Mean alpha-sphere SA              : 0.6054
+HEADER 5  - Mean B-factor                     : 0.2848
+HEADER 6  - Hydrophobicity Score              : 39.9091
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.8182
+HEADER 9  - Real volume (approximation)       : 438.3710
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 19.4545
+HEADER 12 - Number of apolar alpha sphere     :    22
+HEADER 13 - Proportion of apolar alpha sphere : 0.7097
+ATOM      1    O STP     3     -13.394   8.035  11.699    0.00     3.75
+ATOM      2    O STP     3     -13.866   8.149  12.756    0.00     4.22
+ATOM      3    O STP     3     -13.235   6.985  13.878    0.00     3.71
+ATOM      4    C STP     3     -13.396  13.376  12.554    0.00     3.64
+ATOM      5    O STP     3     -14.773   7.681  13.727    0.00     4.61
+ATOM      6    C STP     3     -14.552   8.323  12.854    0.00     4.64
+ATOM      7    C STP     3     -14.690   7.717  13.852    0.00     4.48
+ATOM      8    C STP     3     -13.947  10.342   9.126    0.00     3.72
+ATOM      9    C STP     3     -12.889   8.488   9.768    0.00     3.44
+ATOM     10    O STP     3     -14.059  10.991   9.026    0.00     3.83
+ATOM     11    C STP     3     -12.850  13.648  12.578    0.00     3.53
+ATOM     12    C STP     3     -12.635  13.830  12.726    0.00     3.42
+ATOM     13    C STP     3     -15.321  12.050   6.421    0.00     3.91
+ATOM     14    C STP     3     -15.149  12.299   5.990    0.00     3.77
+ATOM     15    C STP     3     -14.138  13.128   4.148    0.00     3.73
+ATOM     16    O STP     3     -13.842  12.966   4.202    0.00     3.54
+ATOM     17    C STP     3     -14.202  12.998   4.431    0.00     3.63
+ATOM     18    C STP     3     -15.071  12.945  11.123    0.00     4.55
+ATOM     19    C STP     3     -15.181  12.284   7.101    0.00     3.70
+ATOM     20    C STP     3     -14.069  13.525  10.889    0.00     4.05
+ATOM     21    C STP     3     -14.486  12.345   9.698    0.00     4.10
+ATOM     22    C STP     3     -15.581  11.691   7.702    0.00     4.30
+ATOM     23    C STP     3     -13.744  12.589   9.720    0.00     3.59
+ATOM     24    C STP     3     -13.903  13.601  10.918    0.00     3.98
+ATOM     25    C STP     3     -13.004  13.765  11.916    0.00     3.53
+ATOM     26    C STP     3     -12.804  14.399  11.014    0.00     3.51
+ATOM     27    O STP     3     -14.691   7.701  13.857    0.00     4.48
+ATOM     28    O STP     3     -14.353   7.367  13.918    0.00     4.32
+ATOM     29    O STP     3     -14.766   7.663  13.746    0.00     4.60
+ATOM     30    C STP     3     -13.822  14.302  10.714    0.00     3.55
+ATOM     31    C STP     3     -12.793  14.411  11.014    0.00     3.51
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket4_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket4_atm.pdb
@@ -0,0 +1,39 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     4:
+HEADER 0  - Pocket Score                      : 0.0422
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of alpha spheres           :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.8010
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4900
+HEADER 5  - Mean B-factor of pocket residues  : 0.2299
+HEADER 6  - Hydrophobicity Score              : 27.7500
+HEADER 7  - Polarity Score                    :     2
+HEADER 8  - Amino Acid based volume Score     : 2.6250
+HEADER 9  - Pocket volume (Monte Carlo)       : 275.1293
+HEADER 10  -Pocket volume (convex hull)       : 12.3309
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 3.0000
+HEADER 13 - Number of apolar alpha sphere     :     4
+HEADER 14 - Proportion of apolar alpha sphere : 0.2105
+ATOM    125   CB SER A  31      17.326  19.576  14.038  0.00  0.00           C 0
+ATOM    126   OG SER A  31      17.732  19.950  15.347  0.00  0.00           O 0
+ATOM    158  ND2 ASN A  35      17.494  21.267  10.632  0.00  0.00           N 0
+ATOM    157  OD1 ASN A  35      15.956  22.734   9.894  0.00  0.00           O 0
+ATOM    149  CG2 ILE A  34      12.680  22.906  11.627  0.00  0.00           C 0
+ATOM    122   CA SER A  31      15.810  19.311  13.908  0.00  0.00           C 0
+ATOM    150  CD1 ILE A  34      11.667  21.954  14.572  0.00  0.00           C 0
+ATOM   1177    N GLY A 168      16.023  22.831  21.164  0.73  2.19           N 0
+ATOM   1175    C GLY A 167      16.348  24.073  20.818  0.00  0.00           C 0
+ATOM   1174   CA GLY A 167      15.573  24.649  19.628  0.00  0.00           C 0
+ATOM   1178   CA GLY A 168      16.782  22.051  22.118  0.00  0.00           C 0
+ATOM   1172   CB ALA A 166      12.281  22.382  18.138  0.00  0.00           C 0
+ATOM     94    O ALA A  27      16.870  17.872  17.453  0.55  1.07           O 0
+ATOM    117   CB MET A  30      13.128  18.094  17.405  0.00  0.00           C 0
+ATOM     95   CB ALA A  27      18.043  18.164  20.565  0.00  0.00           C 0
+ATOM   1173    N GLY A 167      14.393  23.879  19.246  0.38  2.19           N 0
+ATOM     92   CA ALA A  27      16.913  17.410  19.844  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket4_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket4_vert.pqr
@@ -0,0 +1,41 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     4:
+HEADER 0  - Pocket Score                      : 0.0422
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of V. Vertices             :    19
+HEADER 3  - Mean alpha-sphere radius          : 3.8010
+HEADER 4  - Mean alpha-sphere SA              : 0.4900
+HEADER 5  - Mean B-factor                     : 0.2299
+HEADER 6  - Hydrophobicity Score              : 27.7500
+HEADER 7  - Polarity Score                    :     2
+HEADER 8  - Volume Score                      : 2.6250
+HEADER 9  - Real volume (approximation)       : 275.1293
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 3.0000
+HEADER 12 - Number of apolar alpha sphere     :     4
+HEADER 13 - Proportion of apolar alpha sphere : 0.2105
+ATOM      1    O STP     4      16.547  23.639  13.890    0.00     4.14
+ATOM      2    O STP     4      16.092  23.630  14.033    0.00     4.24
+ATOM      3    C STP     4      15.859  23.404  14.170    0.00     4.10
+ATOM      4    C STP     4      15.557  23.398  14.576    0.00     4.15
+ATOM      5    O STP     4      16.011  22.871  13.482    0.00     3.59
+ATOM      6    C STP     4      15.928  23.207  13.765    0.00     3.90
+ATOM      7    O STP     4      17.691  22.245  18.072    0.00     3.56
+ATOM      8    O STP     4      19.529  21.954  18.755    0.00     4.34
+ATOM      9    C STP     4      15.011  22.229  15.825    0.00     3.58
+ATOM     10    O STP     4      15.135  20.552  18.741    0.00     3.44
+ATOM     11    O STP     4      19.253  21.725  18.788    0.00     4.16
+ATOM     12    O STP     4      17.650  21.048  18.652    0.00     3.48
+ATOM     13    O STP     4      16.195  21.162  18.168    0.00     3.43
+ATOM     14    O STP     4      15.398  20.983  17.666    0.00     3.45
+ATOM     15    O STP     4      15.138  20.557  18.735    0.00     3.44
+ATOM     16    O STP     4      16.943  21.983  17.981    0.00     3.42
+ATOM     17    O STP     4      15.182  22.714  15.737    0.00     3.78
+ATOM     18    O STP     4      15.741  24.064  14.855    0.00     4.60
+ATOM     19    O STP     4      15.109  20.220  19.179    0.00     3.40
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket5_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket5_atm.pdb
@@ -0,0 +1,43 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     5:
+HEADER 0  - Pocket Score                      : -0.0120
+HEADER 1  - Drug Score                        : 0.0106
+HEADER 2  - Number of alpha spheres           :    28
+HEADER 3  - Mean alpha-sphere radius          : 3.8577
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5218
+HEADER 5  - Mean B-factor of pocket residues  : 0.7484
+HEADER 6  - Hydrophobicity Score              : -4.4286
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.5714
+HEADER 9  - Pocket volume (Monte Carlo)       : 314.3672
+HEADER 10  -Pocket volume (convex hull)       : 22.9942
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 23.0000
+HEADER 13 - Number of apolar alpha sphere     :    24
+HEADER 14 - Proportion of apolar alpha sphere : 0.8571
+ATOM    784   CB LYS A 116      19.005   4.904  18.162  0.00  0.00           C 0
+ATOM    761   CE LYS A 112      20.763   7.806  24.667  0.00  0.00           C 0
+ATOM    759   CG LYS A 112      18.345   7.905  23.819  0.00  0.00           C 0
+ATOM    786   CD LYS A 116      21.107   3.626  18.880  0.00  0.00           C 0
+ATOM    779  CG2 THR A 115      15.826   9.929  17.943  0.00  0.00           C 0
+ATOM    811   SD MET A 119      17.851  11.068  14.259  0.00  0.00           S 0
+ATOM    780    N LYS A 116      17.048   6.386  17.780  0.61  1.09           N 0
+ATOM    776    O THR A 115      16.217   7.347  15.900  0.00  0.00           O 0
+ATOM    781   CA LYS A 116      18.173   5.688  17.126  0.00  0.00           C 0
+ATOM    809   CB MET A 119      18.047   8.438  13.304  0.00  0.00           C 0
+ATOM    103  OE1 GLN A  28      21.519  12.799  16.414  0.00  0.00           O 0
+ATOM    783    O LYS A 116      18.078   5.007  14.822  0.00  0.00           O 0
+ATOM    785   CG LYS A 116      20.367   4.281  17.674  0.00  0.00           C 0
+ATOM     78   CB GLU A  25      19.262  11.053  20.713  0.00  0.00           C 0
+ATOM    818   CG GLU A 120      20.403   3.337  13.075  0.00  0.00           C 0
+ATOM    813    N GLU A 120      18.338   5.404  12.039  0.00  0.00           N 0
+ATOM     79   CG GLU A  25      20.650  10.425  20.910  0.00  0.00           C 0
+ATOM    787   CE LYS A 116      22.558   3.176  18.577  0.00  0.00           C 0
+ATOM     81  OE1 GLU A  25      22.506  10.395  22.432  0.00  0.00           O 0
+ATOM    757    O LYS A 112      16.831   6.525  21.054  0.75  2.14           O 0
+ATOM     77    O GLU A  25      17.500  12.958  18.695  0.00  0.00           O 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket5_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket5_vert.pqr
@@ -0,0 +1,50 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     5:
+HEADER 0  - Pocket Score                      : -0.0120
+HEADER 1  - Drug Score                        : 0.0106
+HEADER 2  - Number of V. Vertices             :    28
+HEADER 3  - Mean alpha-sphere radius          : 3.8577
+HEADER 4  - Mean alpha-sphere SA              : 0.5218
+HEADER 5  - Mean B-factor                     : 0.7484
+HEADER 6  - Hydrophobicity Score              : -4.4286
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.5714
+HEADER 9  - Real volume (approximation)       : 314.3672
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 23.0000
+HEADER 12 - Number of apolar alpha sphere     :    24
+HEADER 13 - Proportion of apolar alpha sphere : 0.8571
+ATOM      1    C STP     5      20.605   6.618  21.102    0.00     3.76
+ATOM      2    O STP     5      19.082   9.114  16.906    0.00     3.51
+ATOM      3    C STP     5      19.211   8.868  16.477    0.00     3.41
+ATOM      4    O STP     5      19.141   9.065  16.855    0.00     3.52
+ATOM      5    C STP     5      20.411   8.950  16.497    0.00     4.01
+ATOM      6    C STP     5      21.278   7.286  15.271    0.00     3.95
+ATOM      7    C STP     5      21.737   8.273  15.966    0.00     4.55
+ATOM      8    C STP     5      19.545   9.253  17.348    0.00     3.83
+ATOM      9    C STP     5      19.605   9.305  17.253    0.00     3.89
+ATOM     10    C STP     5      19.361   9.202  17.087    0.00     3.71
+ATOM     11    O STP     5      21.005   6.678  13.902    0.00     3.49
+ATOM     12    C STP     5      21.887   7.048  14.721    0.00     4.32
+ATOM     13    C STP     5      21.576   8.462  17.094    0.00     4.39
+ATOM     14    C STP     5      21.237   8.164  17.688    0.00     3.98
+ATOM     15    C STP     5      19.823   9.314  17.205    0.00     3.96
+ATOM     16    C STP     5      19.842   9.288  17.195    0.00     3.97
+ATOM     17    C STP     5      19.813   9.293  17.207    0.00     3.96
+ATOM     18    C STP     5      23.114   7.517  18.754    0.00     4.38
+ATOM     19    C STP     5      23.216   7.267  19.612    0.00     4.27
+ATOM     20    C STP     5      21.455   7.159  19.578    0.00     3.62
+ATOM     21    C STP     5      19.601   8.988  17.728    0.00     3.65
+ATOM     22    C STP     5      20.637   6.657  21.076    0.00     3.77
+ATOM     23    C STP     5      21.991   6.742  21.095    0.00     3.92
+ATOM     24    C STP     5      20.614   6.661  21.080    0.00     3.77
+ATOM     25    C STP     5      20.578   6.679  21.067    0.00     3.75
+ATOM     26    C STP     5      20.573   6.576  21.121    0.00     3.74
+ATOM     27    O STP     5      19.279  10.317  17.326    0.00     3.47
+ATOM     28    C STP     5      19.218  10.275  17.340    0.00     3.46
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket6_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket6_atm.pdb
@@ -0,0 +1,36 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     6:
+HEADER 0  - Pocket Score                      : -0.0207
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of alpha spheres           :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8891
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5474
+HEADER 5  - Mean B-factor of pocket residues  : 0.6196
+HEADER 6  - Hydrophobicity Score              : -4.0000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.7143
+HEADER 9  - Pocket volume (Monte Carlo)       : 256.7571
+HEADER 10  -Pocket volume (convex hull)       : 6.4999
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     0
+HEADER 14 - Proportion of apolar alpha sphere : 0.0000
+ATOM   1335   CB HIS A 189       1.397  27.011  18.007  0.00  0.00           C 0
+ATOM   1009  OE2 GLU A 146       3.925  30.351  15.551  0.00  0.00           O 0
+ATOM    569    O ASP A  86      -3.134  30.577  16.949  0.33  9.64           O 0
+ATOM   1337  ND1 HIS A 189       0.040  27.983  19.913  0.77  5.47           N 0
+ATOM    577    O ARG A  87      -2.431  27.764  15.190  0.00  0.00           O 0
+ATOM   1344    O LEU A 190       1.574  28.168  13.041  0.74  1.07           O 0
+ATOM    578   CB ARG A  87      -2.813  30.073  13.913  0.00  0.00           C 0
+ATOM    560    O GLN A  85      -5.938  33.818  16.095  0.00  0.00           O 0
+ATOM    568    C ASP A  86      -4.287  30.742  16.552  0.00  0.00           C 0
+ATOM    584  NH2 ARG A  87       0.614  32.921  11.229  0.09  5.47           N 0
+ATOM    582   CZ ARG A  87       0.454  31.713  11.756  0.00  0.00           C 0
+ATOM    583  NH1 ARG A  87       1.503  31.117  12.350  0.41  2.19           N 0
+ATOM    581   NE ARG A  87      -0.749  31.111  11.680  0.24  2.19           N 0
+ATOM    551    O LYS A  84      -6.645  31.712  13.194  0.00  0.00           O 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket6_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket6_vert.pqr
@@ -0,0 +1,38 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     6:
+HEADER 0  - Pocket Score                      : -0.0207
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of V. Vertices             :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8891
+HEADER 4  - Mean alpha-sphere SA              : 0.5474
+HEADER 5  - Mean B-factor                     : 0.6196
+HEADER 6  - Hydrophobicity Score              : -4.0000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.7143
+HEADER 9  - Real volume (approximation)       : 256.7571
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     0
+HEADER 13 - Proportion of apolar alpha sphere : 0.0000
+ATOM      1    O STP     6       0.606  30.613  17.291    0.00     3.76
+ATOM      2    O STP     6       0.349  29.933  16.102    0.00     3.64
+ATOM      3    O STP     6       0.398  29.825  16.006    0.00     3.59
+ATOM      4    O STP     6       0.310  30.058  15.886    0.00     3.64
+ATOM      5    O STP     6      -2.704  33.369  14.954    0.00     3.46
+ATOM      6    O STP     6       0.267  30.094  15.812    0.00     3.62
+ATOM      7    O STP     6       0.297  30.167  15.803    0.00     3.64
+ATOM      8    O STP     6      -1.603  34.311  14.914    0.00     4.52
+ATOM      9    O STP     6      -1.370  34.089  14.976    0.00     4.40
+ATOM     10    O STP     6       0.328  30.306  15.653    0.00     3.60
+ATOM     11    O STP     6       0.297  30.561  15.738    0.00     3.64
+ATOM     12    O STP     6      -0.300  32.461  15.359    0.00     3.76
+ATOM     13    O STP     6      -1.581  33.922  14.529    0.00     4.09
+ATOM     14    O STP     6      -2.185  34.279  14.137    0.00     4.26
+ATOM     15    O STP     6      -3.286  34.022  12.999    0.00     4.08
+ATOM     16    O STP     6      -3.344  34.741  12.491    0.00     4.54
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket7_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket7_atm.pdb
@@ -0,0 +1,38 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     7:
+HEADER 0  - Pocket Score                      : -0.0338
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of alpha spheres           :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.7280
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4019
+HEADER 5  - Mean B-factor of pocket residues  : 0.7160
+HEADER 6  - Hydrophobicity Score              : 7.7143
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 262.3640
+HEADER 10  -Pocket volume (convex hull)       : 6.7930
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 5.0000
+HEADER 13 - Number of apolar alpha sphere     :     6
+HEADER 14 - Proportion of apolar alpha sphere : 0.4000
+ATOM   1307   NZ LYS A 185      -6.814  23.332  26.506  0.00  0.00           N 0
+ATOM   1237  OD2 ASP A 175      -3.713  23.987  32.328  0.00  0.00           O 0
+ATOM   1249    N GLU A 178      -7.967  26.111  33.085  0.00  0.00           N 0
+ATOM   1252    O GLU A 178      -7.954  23.140  33.285  0.64  2.14           O 0
+ATOM   1246   CA GLY A 177      -5.755  26.984  33.627  0.00  0.00           C 0
+ATOM   1253   CB GLU A 178      -9.877  25.079  31.919  0.00  0.00           C 0
+ATOM   1305   CD LYS A 185      -6.913  20.867  26.939  0.00  0.00           C 0
+ATOM   1271   SD MET A 180      -5.989  18.540  30.424  0.00  0.00           S 0
+ATOM   1115  NE2 GLN A 159      -5.515  21.745  33.331  0.00  0.00           N 0
+ATOM   1254   CG GLU A 178     -11.190  24.323  32.022  0.00  0.00           C 0
+ATOM   1306   CE LYS A 185      -7.179  21.983  25.920  0.00  0.00           C 0
+ATOM   1269   CB MET A 180      -8.472  18.896  31.501  0.00  0.00           C 0
+ATOM   1046  CG2 ILE A 151      -3.467  21.394  30.249  0.00  0.00           C 0
+ATOM   1047  CD1 ILE A 151      -1.923  23.263  28.606  0.00  0.00           C 0
+ATOM   1045  CG1 ILE A 151      -2.748  22.280  27.937  0.00  0.00           C 0
+ATOM   1236  OD1 ASP A 175      -2.222  25.511  32.451  0.50  2.14           O 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket7_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket7_vert.pqr
@@ -0,0 +1,37 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     7:
+HEADER 0  - Pocket Score                      : -0.0338
+HEADER 1  - Drug Score                        : 0.0006
+HEADER 2  - Number of V. Vertices             :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.7280
+HEADER 4  - Mean alpha-sphere SA              : 0.4019
+HEADER 5  - Mean B-factor                     : 0.7160
+HEADER 6  - Hydrophobicity Score              : 7.7143
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 262.3640
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 5.0000
+HEADER 12 - Number of apolar alpha sphere     :     6
+HEADER 13 - Proportion of apolar alpha sphere : 0.4000
+ATOM      1    O STP     7      -6.625  24.421  30.057    0.00     3.72
+ATOM      2    O STP     7      -5.799  26.309  29.404    0.00     4.28
+ATOM      3    O STP     7      -8.308  22.685  29.725    0.00     3.61
+ATOM      4    O STP     7      -7.037  21.813  30.245    0.00     3.44
+ATOM      5    C STP     7     -10.258  22.548  28.497    0.00     4.05
+ATOM      6    C STP     7      -9.562  22.615  29.037    0.00     3.80
+ATOM      7    C STP     7      -7.102  21.786  30.244    0.00     3.44
+ATOM      8    C STP     7      -8.874  22.184  29.811    0.00     3.72
+ATOM      9    C STP     7      -9.225  22.114  29.661    0.00     3.78
+ATOM     10    C STP     7      -6.839  21.824  30.201    0.00     3.40
+ATOM     11    O STP     7      -6.761  22.668  29.984    0.00     3.54
+ATOM     12    O STP     7      -6.848  22.141  30.159    0.00     3.46
+ATOM     13    O STP     7      -6.421  23.405  30.062    0.00     3.58
+ATOM     14    O STP     7      -5.071  24.416  29.230    0.00     3.41
+ATOM     15    O STP     7      -4.870  26.897  28.843    0.00     4.69
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket8_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket8_atm.pdb
@@ -0,0 +1,42 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     8:
+HEADER 0  - Pocket Score                      : -0.0391
+HEADER 1  - Drug Score                        : 0.0087
+HEADER 2  - Number of alpha spheres           :    25
+HEADER 3  - Mean alpha-sphere radius          : 4.0460
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5630
+HEADER 5  - Mean B-factor of pocket residues  : 0.6875
+HEADER 6  - Hydrophobicity Score              : 46.5556
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 4.3333
+HEADER 9  - Pocket volume (Monte Carlo)       : 292.0643
+HEADER 10  -Pocket volume (convex hull)       : 11.0907
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 18.5000
+HEADER 13 - Number of apolar alpha sphere     :    20
+HEADER 14 - Proportion of apolar alpha sphere : 0.8000
+ATOM    134  CD2 LEU A  32      15.972  12.683  10.900  0.00  0.00           C 0
+ATOM    831   CB LEU A 122      15.645   7.979   7.938  0.00  0.00           C 0
+ATOM    133  CD1 LEU A  32      17.260  14.294   9.535  0.00  0.00           C 0
+ATOM    840   CG GLN A 123      20.411   7.331   7.673  0.00  0.00           C 0
+ATOM    808    O MET A 119      18.239   6.888  10.339  0.59  1.07           O 0
+ATOM    810   CG MET A 119      17.406   9.804  13.159  0.00  0.00           C 0
+ATOM    812   CE MET A 119      18.896  12.204  13.031  0.00  0.00           C 0
+ATOM    830    O LEU A 122      16.827   6.812   5.159  0.00  0.00           O 0
+ATOM    834  CD2 LEU A 122      13.141   8.318   7.801  0.00  0.00           C 0
+ATOM    165  CG2 THR A  36      13.954  15.228   5.144  0.00  0.00           C 0
+ATOM    856    O ALA A 126      13.064   6.701   4.796  0.00  0.00           O 0
+ATOM    833  CD1 LEU A 122      14.496   9.519   9.463  0.00  0.00           C 0
+ATOM    873  CD1 ILE A 128      11.138  13.485   7.280  0.00  0.00           C 0
+ATOM    871  CG1 ILE A 128      10.835  12.117   7.893  0.00  0.00           C 0
+ATOM    866    N ILE A 128       9.827   9.471   6.497  0.00  0.00           N 0
+ATOM    183  CD1 TYR A  38       8.575  12.993   3.679  0.00  0.00           C 0
+ATOM    862   CB ASP A 127       9.804   7.990   3.839  0.00  0.00           C 0
+ATOM    164  OG1 THR A  36      14.951  15.781   7.174  0.77  3.21           O 0
+ATOM    132   CG LEU A  32      15.981  14.083  10.326  0.00  0.00           C 0
+ATOM    859   CA ASP A 127      10.629   7.660   5.095  0.00  0.00           C 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket8_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket8_vert.pqr
@@ -0,0 +1,47 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     8:
+HEADER 0  - Pocket Score                      : -0.0391
+HEADER 1  - Drug Score                        : 0.0087
+HEADER 2  - Number of V. Vertices             :    25
+HEADER 3  - Mean alpha-sphere radius          : 4.0460
+HEADER 4  - Mean alpha-sphere SA              : 0.5630
+HEADER 5  - Mean B-factor                     : 0.6875
+HEADER 6  - Hydrophobicity Score              : 46.5556
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 4.3333
+HEADER 9  - Real volume (approximation)       : 292.0643
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 18.5000
+HEADER 12 - Number of apolar alpha sphere     :    20
+HEADER 13 - Proportion of apolar alpha sphere : 0.8000
+ATOM      1    C STP     8      18.480  10.647   8.623    0.00     3.95
+ATOM      2    C STP     8      18.473  10.489   8.873    0.00     3.90
+ATOM      3    C STP     8      18.698  10.488   9.792    0.00     3.67
+ATOM      4    C STP     8      14.943  10.866   4.541    0.00     4.51
+ATOM      5    O STP     8      14.875  10.843   4.459    0.00     4.53
+ATOM      6    O STP     8      14.864  10.355   4.722    0.00     4.07
+ATOM      7    C STP     8      17.917  10.225   9.354    0.00     3.49
+ATOM      8    C STP     8      14.939  11.399   5.926    0.00     4.03
+ATOM      9    C STP     8      16.088  11.832   6.354    0.00     4.19
+ATOM     10    C STP     8      17.345  11.079   8.062    0.00     3.54
+ATOM     11    C STP     8      14.302  11.614   6.290    0.00     3.81
+ATOM     12    C STP     8      14.169  11.576   6.426    0.00     3.68
+ATOM     13    C STP     8      13.282  11.035   4.472    0.00     4.30
+ATOM     14    O STP     8      13.297  11.009   4.410    0.00     4.33
+ATOM     15    C STP     8      13.187  11.021   4.702    0.00     4.11
+ATOM     16    C STP     8      12.553  11.402   3.811    0.00     4.29
+ATOM     17    C STP     8      12.615  11.331   3.695    0.00     4.37
+ATOM     18    C STP     8      16.085  11.834   6.357    0.00     4.19
+ATOM     19    C STP     8      15.342  12.249   7.345    0.00     3.56
+ATOM     20    C STP     8      14.506  12.196   7.034    0.00     3.62
+ATOM     21    C STP     8      14.353  12.486   7.796    0.00     3.41
+ATOM     22    O STP     8      13.277  10.973   4.430    0.00     4.29
+ATOM     23    C STP     8      13.182  11.064   3.370    0.00     4.59
+ATOM     24    O STP     8      13.287  11.012   4.386    0.00     4.34
+ATOM     25    C STP     8      12.716  11.267   3.730    0.00     4.38
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket9_atm.pdb
+++ b/tests/reference_output/1UYD_out/pockets/pocket9_atm.pdb
@@ -0,0 +1,38 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     9:
+HEADER 0  - Pocket Score                      : -0.0597
+HEADER 1  - Drug Score                        : 0.0005
+HEADER 2  - Number of alpha spheres           :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.8905
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5932
+HEADER 5  - Mean B-factor of pocket residues  : 0.6375
+HEADER 6  - Hydrophobicity Score              : -11.3750
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 3.3750
+HEADER 9  - Pocket volume (Monte Carlo)       : 280.7654
+HEADER 10  -Pocket volume (convex hull)       : 12.8403
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 6.0000
+HEADER 13 - Number of apolar alpha sphere     :     7
+HEADER 14 - Proportion of apolar alpha sphere : 0.4118
+ATOM   1262   CB PRO A 179      -9.732  21.711  36.429  0.00  0.00           C 0
+ATOM   1111   CB GLN A 159      -3.563  19.835  35.636  0.00  0.00           C 0
+ATOM   1233    O ASP A 175      -2.967  23.964  36.554  0.34  7.50           O 0
+ATOM   1106  OE2 GLU A 158      -2.440  19.673  41.584  0.00  0.00           O 0
+ATOM   1259   CA PRO A 179      -8.962  21.849  35.105  0.00  0.00           C 0
+ATOM   1263   CG PRO A 179      -9.842  23.072  36.977  0.00  0.00           C 0
+ATOM   1248    O GLY A 177      -7.087  25.609  35.109  0.40  4.29           O 0
+ATOM   1107    N GLN A 159      -2.228  18.673  37.326  0.63  2.19           N 0
+ATOM   1062   CE LYS A 153      -5.591  16.089  38.200  0.00  0.00           C 0
+ATOM   1114  OE1 GLN A 159      -6.210  19.893  34.388  0.76  2.14           O 0
+ATOM   1113   CD GLN A 159      -5.304  20.600  33.983  0.00  0.00           C 0
+ATOM   1273    N GLY A 181      -9.984  17.239  34.316  0.59  3.28           N 0
+ATOM   1265    N MET A 180      -8.985  19.796  33.754  0.61  1.09           N 0
+ATOM   1061   CD LYS A 153      -4.956  16.412  36.840  0.00  0.00           C 0
+ATOM   1274   CA GLY A 181     -10.573  15.994  34.761  0.00  0.00           C 0
+ATOM   1276    O GLY A 181      -9.088  14.413  35.748  0.70  5.36           O 0
+TER
+END
--- a/tests/reference_output/1UYD_out/pockets/pocket9_vert.pqr
+++ b/tests/reference_output/1UYD_out/pockets/pocket9_vert.pqr
@@ -0,0 +1,39 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     9:
+HEADER 0  - Pocket Score                      : -0.0597
+HEADER 1  - Drug Score                        : 0.0005
+HEADER 2  - Number of V. Vertices             :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.8905
+HEADER 4  - Mean alpha-sphere SA              : 0.5932
+HEADER 5  - Mean B-factor                     : 0.6375
+HEADER 6  - Hydrophobicity Score              : -11.3750
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 3.3750
+HEADER 9  - Real volume (approximation)       : 280.7654
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 6.0000
+HEADER 12 - Number of apolar alpha sphere     :     7
+HEADER 13 - Proportion of apolar alpha sphere : 0.4118
+ATOM      1    O STP     9      -5.987  21.597  39.224    0.00     4.67
+ATOM      2    C STP     9      -6.191  22.298  37.656    0.00     3.79
+ATOM      3    O STP     9      -6.290  22.862  37.242    0.00     3.57
+ATOM      4    C STP     9      -6.076  21.951  37.687    0.00     3.87
+ATOM      5    O STP     9      -4.027  21.397  38.848    0.00     3.60
+ATOM      6    O STP     9      -5.569  19.993  39.101    0.00     4.01
+ATOM      7    C STP     9      -6.315  20.503  39.256    0.00     4.60
+ATOM      8    C STP     9      -6.095  21.897  37.670    0.00     3.85
+ATOM      9    C STP     9      -6.531  20.110  38.511    0.00     4.14
+ATOM     10    O STP     9      -5.839  22.040  37.133    0.00     3.50
+ATOM     11    O STP     9      -6.021  22.227  37.054    0.00     3.55
+ATOM     12    O STP     9      -6.062  21.968  37.603    0.00     3.83
+ATOM     13    O STP     9      -8.206  18.652  36.918    0.00     3.45
+ATOM     14    O STP     9      -8.120  18.521  37.184    0.00     3.65
+ATOM     15    C STP     9      -6.229  19.490  37.843    0.00     3.48
+ATOM     16    O STP     9      -9.377  17.540  38.316    0.00     4.06
+ATOM     17    C STP     9      -9.701  17.858  38.776    0.00     4.51
+TER
+END
--- a/tests/reference_output/3LKF_out/3LKF.pml
+++ b/tests/reference_output/3LKF_out/3LKF.pml
@@ -0,0 +1,15 @@
+from pymol import cmd,stored
+load 3LKF_out.pdb
+#select pockets, resn STP
+stored.list=[]
+cmd.iterate("(resn STP)","stored.list.append(resi)")	#read info about residues STP
+#print stored.list
+lastSTP=stored.list[-1]	#get the index of the last residu
+hide lines, resn STP
+
+#show spheres, resn STP
+for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
+for my_index in range(2,int(lastSTP)+2): cmd.color(my_index,"pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.3","pocket"+str(my_index))
+for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
--- a/tests/reference_output/3LKF_out/3LKF.tcl
+++ b/tests/reference_output/3LKF_out/3LKF.tcl
@@ -0,0 +1,24 @@
+proc highlighting { colorId representation id selection } {
+   puts "highlighting $id"
+   mol representation $representation
+   mol material "Diffuse" 
+    mol color $colorId
+   mol selection $selection
+   mol addrep $id
+}
+
+set id [mol new 3LKF_out.pdb type pdb]
+mol delrep top $id
+highlighting Name "Lines" $id "protein"
+highlighting Name "Licorice" $id "not protein and not resname STP"
+highlighting Element "NewCartoon" $id "protein"
+highlighting "ColorID 7" "VdW 0.4" $id "protein and occupancy>0.95"
+set id [mol new 3LKF_pockets.pqr type pqr]
+                        mol selection "all" 
+                         mol material "Glass3" 
+                         mol delrep top $id 
+                         mol representation "QuickSurf 0.3" 
+                         mol color ResId $id 
+                         mol addrep $id 
+highlighting Index "Points 1" $id "resname STP"
+display rendermode GLSL
--- a/tests/reference_output/3LKF_out/3LKF_PYMOL.sh
+++ b/tests/reference_output/3LKF_out/3LKF_PYMOL.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+pymol 3LKF.pml
--- a/tests/reference_output/3LKF_out/3LKF_VMD.sh
+++ b/tests/reference_output/3LKF_out/3LKF_VMD.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+vmd 3LKF_out.pdb -e 3LKF.tcl
--- a/tests/reference_output/3LKF_out/3LKF_info.txt
+++ b/tests/reference_output/3LKF_out/3LKF_info.txt
@@ -0,0 +1,210 @@
+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 : 	276.494
+	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
+	Volume score: 	 4.556
+	Polarity score:	 6
+	Charge score :	 0
+	Proportion of polar atoms: 	45.833
+	Alpha sphere density : 	3.065
+	Cent. of mass - Alpha Sphere max dist: 	8.406
+	Flexibility : 	0.841
+
+Pocket 2 :
+	Score : 	0.398
+	Druggability Score : 	0.284
+	Number of Alpha Spheres : 	31
+	Total SASA : 	67.280
+	Polar SASA : 	41.920
+	Apolar SASA : 	25.360
+	Volume : 	198.225
+	Mean local hydrophobic density : 	9.000
+	Mean alpha sphere radius :	3.806
+	Mean alp. sph. solvent access : 	0.459
+	Apolar alpha sphere proportion : 	0.323
+	Hydrophobicity score:	27.875
+	Volume score: 	 4.500
+	Polarity score:	 7
+	Charge score :	 -1
+	Proportion of polar atoms: 	42.105
+	Alpha sphere density : 	2.392
+	Cent. of mass - Alpha Sphere max dist: 	6.011
+	Flexibility : 	0.724
+
+Pocket 3 :
+	Score : 	0.251
+	Druggability Score : 	0.004
+	Number of Alpha Spheres : 	27
+	Total SASA : 	143.193
+	Polar SASA : 	71.943
+	Apolar SASA : 	71.250
+	Volume : 	365.406
+	Mean local hydrophobic density : 	3.000
+	Mean alpha sphere radius :	3.909
+	Mean alp. sph. solvent access : 	0.517
+	Apolar alpha sphere proportion : 	0.148
+	Hydrophobicity score:	6.333
+	Volume score: 	 3.917
+	Polarity score:	 8
+	Charge score :	 0
+	Proportion of polar atoms: 	58.333
+	Alpha sphere density : 	4.731
+	Cent. of mass - Alpha Sphere max dist: 	10.832
+	Flexibility : 	0.426
+
+Pocket 4 :
+	Score : 	0.244
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	26
+	Total SASA : 	137.813
+	Polar SASA : 	85.885
+	Apolar SASA : 	51.928
+	Volume : 	439.429
+	Mean local hydrophobic density : 	3.000
+	Mean alpha sphere radius :	4.138
+	Mean alp. sph. solvent access : 	0.537
+	Apolar alpha sphere proportion : 	0.154
+	Hydrophobicity score:	0.875
+	Volume score: 	 4.500
+	Polarity score:	 7
+	Charge score :	 3
+	Proportion of polar atoms: 	52.174
+	Alpha sphere density : 	4.603
+	Cent. of mass - Alpha Sphere max dist: 	10.727
+	Flexibility : 	0.625
+
+Pocket 5 :
+	Score : 	0.173
+	Druggability Score : 	0.002
+	Number of Alpha Spheres : 	26
+	Total SASA : 	120.199
+	Polar SASA : 	62.233
+	Apolar SASA : 	57.966
+	Volume : 	343.696
+	Mean local hydrophobic density : 	3.000
+	Mean alpha sphere radius :	3.909
+	Mean alp. sph. solvent access : 	0.498
+	Apolar alpha sphere proportion : 	0.154
+	Hydrophobicity score:	23.800
+	Volume score: 	 4.400
+	Polarity score:	 5
+	Charge score :	 1
+	Proportion of polar atoms: 	52.381
+	Alpha sphere density : 	3.092
+	Cent. of mass - Alpha Sphere max dist: 	7.422
+	Flexibility : 	0.655
+
+Pocket 6 :
+	Score : 	0.162
+	Druggability Score : 	0.097
+	Number of Alpha Spheres : 	15
+	Total SASA : 	74.562
+	Polar SASA : 	34.552
+	Apolar SASA : 	40.010
+	Volume : 	232.871
+	Mean local hydrophobic density : 	7.000
+	Mean alpha sphere radius :	3.804
+	Mean alp. sph. solvent access : 	0.500
+	Apolar alpha sphere proportion : 	0.533
+	Hydrophobicity score:	38.100
+	Volume score: 	 4.500
+	Polarity score:	 3
+	Charge score :	 1
+	Proportion of polar atoms: 	41.176
+	Alpha sphere density : 	2.977
+	Cent. of mass - Alpha Sphere max dist: 	6.539
+	Flexibility : 	0.411
+
+Pocket 7 :
+	Score : 	0.147
+	Druggability Score : 	0.004
+	Number of Alpha Spheres : 	15
+	Total SASA : 	76.071
+	Polar SASA : 	28.974
+	Apolar SASA : 	47.097
+	Volume : 	225.706
+	Mean local hydrophobic density : 	4.000
+	Mean alpha sphere radius :	3.866
+	Mean alp. sph. solvent access : 	0.563
+	Apolar alpha sphere proportion : 	0.333
+	Hydrophobicity score:	9.250
+	Volume score: 	 4.125
+	Polarity score:	 6
+	Charge score :	 0
+	Proportion of polar atoms: 	33.333
+	Alpha sphere density : 	2.890
+	Cent. of mass - Alpha Sphere max dist: 	5.567
+	Flexibility : 	0.666
+
+Pocket 8 :
+	Score : 	0.143
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	17
+	Total SASA : 	72.675
+	Polar SASA : 	49.730
+	Apolar SASA : 	22.945
+	Volume : 	223.272
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	3.812
+	Mean alp. sph. solvent access : 	0.546
+	Apolar alpha sphere proportion : 	0.118
+	Hydrophobicity score:	9.375
+	Volume score: 	 4.250
+	Polarity score:	 5
+	Charge score :	 1
+	Proportion of polar atoms: 	62.500
+	Alpha sphere density : 	2.318
+	Cent. of mass - Alpha Sphere max dist: 	5.305
+	Flexibility : 	0.664
+
+Pocket 9 :
+	Score : 	0.096
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	18
+	Total SASA : 	101.127
+	Polar SASA : 	93.881
+	Apolar SASA : 	7.246
+	Volume : 	353.058
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.989
+	Mean alp. sph. solvent access : 	0.458
+	Apolar alpha sphere proportion : 	0.000
+	Hydrophobicity score:	-11.000
+	Volume score: 	 4.250
+	Polarity score:	 6
+	Charge score :	 2
+	Proportion of polar atoms: 	66.667
+	Alpha sphere density : 	2.808
+	Cent. of mass - Alpha Sphere max dist: 	6.209
+	Flexibility : 	0.503
+
+Pocket 10 :
+	Score : 	0.081
+	Druggability Score : 	0.002
+	Number of Alpha Spheres : 	15
+	Total SASA : 	61.676
+	Polar SASA : 	37.523
+	Apolar SASA : 	24.153
+	Volume : 	133.564
+	Mean local hydrophobic density : 	4.000
+	Mean alpha sphere radius :	3.817
+	Mean alp. sph. solvent access : 	0.581
+	Apolar alpha sphere proportion : 	0.333
+	Hydrophobicity score:	32.000
+	Volume score: 	 5.000
+	Polarity score:	 3
+	Charge score :	 0
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	1.545
+	Cent. of mass - Alpha Sphere max dist: 	3.327
+	Flexibility : 	0.616
+
--- a/tests/reference_output/3LKF_out/3LKF_out.pdb
+++ b/tests/reference_output/3LKF_out/3LKF_out.pdb
--- a/tests/reference_output/3LKF_out/3LKF_pockets.pqr
+++ b/tests/reference_output/3LKF_out/3LKF_pockets.pqr
@@ -0,0 +1,216 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It contains all the pocket vertices found by fpocket.                    
+ATOM      1    O STP     1      27.849  33.435 123.906    0.00     3.75
+ATOM      2    C STP     1      29.108  33.195 122.206    0.00     4.30
+ATOM      3    O STP     1      28.611  33.141 119.797    0.00     4.31
+ATOM      4    O STP     1      26.830  32.143 118.779    0.00     3.64
+ATOM      5    O STP     1      27.981  32.070 118.273    0.00     4.26
+ATOM      6    C STP     1      29.018  31.922 119.605    0.00     3.83
+ATOM      7    C STP     1      25.761  31.354 118.617    0.00     3.40
+ATOM      8    C STP     1      29.406  33.448 121.564    0.00     4.64
+ATOM      9    O STP     1      26.515  31.932 118.543    0.00     3.68
+ATOM     10    O STP     1      27.025  31.909 118.334    0.00     3.88
+ATOM     11    O STP     1      27.874  32.028 117.817    0.00     4.24
+ATOM     12    O STP     1      26.955  30.624 116.168    0.00     3.51
+ATOM     13    O STP     1      26.317  31.846 118.575    0.00     3.61
+ATOM     14    O STP     1      25.803  31.523 118.608    0.00     3.48
+ATOM     15    O STP     1      25.827  31.451 118.562    0.00     3.48
+ATOM     16    O STP     1      27.861  32.048 116.485    0.00     3.77
+ATOM     17    O STP     1      27.844  33.032 116.741    0.00     3.73
+ATOM     18    O STP     1      27.849  32.717 116.552    0.00     3.69
+ATOM     19    O STP     1      27.760  31.246 116.561    0.00     3.93
+ATOM     20    O STP     1      26.786  30.585 116.070    0.00     3.40
+ATOM     21    O STP     1      27.336  30.561 116.050    0.00     3.61
+ATOM     22    O STP     2      16.357  36.496 127.915    0.00     3.52
+ATOM     23    O STP     2      15.069  34.269 127.149    0.00     3.58
+ATOM     24    O STP     2      15.398  33.710 126.598    0.00     3.51
+ATOM     25    O STP     2      16.800  34.223 126.970    0.00     3.60
+ATOM     26    O STP     2      16.457  35.880 127.865    0.00     3.70
+ATOM     27    O STP     2      16.654  35.109 128.041    0.00     4.08
+ATOM     28    O STP     2      16.856  35.430 127.555    0.00     3.60
+ATOM     29    C STP     2      16.024  33.908 126.891    0.00     3.58
+ATOM     30    O STP     2      14.366  33.559 129.013    0.00     3.41
+ATOM     31    C STP     2      19.620  35.296 129.784    0.00     3.91
+ATOM     32    O STP     2      16.748  34.346 127.230    0.00     3.71
+ATOM     33    O STP     2      16.631  34.977 128.037    0.00     4.11
+ATOM     34    O STP     2      15.971  34.428 127.681    0.00     3.91
+ATOM     35    O STP     2      16.629  34.948 129.488    0.00     4.11
+ATOM     36    O STP     2      16.707  35.039 128.175    0.00     4.13
+ATOM     37    C STP     2      17.194  34.979 128.410    0.00     3.96
+ATOM     38    O STP     2      16.883  35.175 128.841    0.00     4.20
+ATOM     39    O STP     2      16.883  35.175 128.855    0.00     4.20
+ATOM     40    C STP     2      16.890  35.174 128.844    0.00     4.20
+ATOM     41    C STP     2      15.877  34.086 127.313    0.00     3.78
+ATOM     42    C STP     2      15.879  34.090 127.319    0.00     3.78
+ATOM     43    O STP     2      15.878  34.091 127.321    0.00     3.78
+ATOM     44    O STP     2      15.461  33.937 127.079    0.00     3.69
+ATOM     45    O STP     2      14.880  33.815 128.268    0.00     3.47
+ATOM     46    O STP     2      15.423  34.131 127.372    0.00     3.80
+ATOM     47    O STP     2      15.621  34.204 127.486    0.00     3.85
+ATOM     48    C STP     2      19.788  35.314 130.003    0.00     4.00
+ATOM     49    C STP     2      20.088  35.294 129.633    0.00     3.85
+ATOM     50    C STP     2      19.637  35.293 129.780    0.00     3.91
+ATOM     51    O STP     2      19.922  35.097 128.959    0.00     3.52
+ATOM     52    C STP     2      19.053  34.999 128.886    0.00     3.54
+ATOM     53    O STP     3      23.576  36.881  88.227    0.00     4.49
+ATOM     54    O STP     3      24.927  36.631  88.169    0.00     3.79
+ATOM     55    O STP     3      24.040  36.991  88.136    0.00     4.39
+ATOM     56    O STP     3      22.322  35.083  91.112    0.00     3.60
+ATOM     57    O STP     3      22.600  35.297  90.868    0.00     3.69
+ATOM     58    O STP     3      21.779  35.252  92.569    0.00     3.79
+ATOM     59    O STP     3      19.324  35.169  84.734    0.00     3.87
+ATOM     60    O STP     3      20.484  34.728  85.452    0.00     3.44
+ATOM     61    O STP     3      19.456  35.266  84.853    0.00     3.94
+ATOM     62    O STP     3      19.382  35.248  84.731    0.00     3.94
+ATOM     63    O STP     3      20.495  34.717  85.464    0.00     3.43
+ATOM     64    O STP     3      23.172  35.707  88.032    0.00     3.74
+ATOM     65    O STP     3      22.101  35.518  86.307    0.00     3.57
+ATOM     66    O STP     3      20.519  34.730  85.471    0.00     3.43
+ATOM     67    O STP     3      23.177  35.492  88.772    0.00     3.63
+ATOM     68    O STP     3      22.473  34.494  90.586    0.00     3.43
+ATOM     69    O STP     3      22.554  34.566  90.521    0.00     3.46
+ATOM     70    C STP     3      20.676  37.730  95.171    0.00     3.58
+ATOM     71    O STP     3      21.572  37.594  93.840    0.00     4.38
+ATOM     72    O STP     3      21.560  37.466  93.844    0.00     4.36
+ATOM     73    O STP     3      22.294  36.811  93.529    0.00     4.50
+ATOM     74    O STP     3      21.699  35.258  92.616    0.00     3.77
+ATOM     75    O STP     3      22.745  35.623  91.096    0.00     3.75
+ATOM     76    C STP     3      22.471  37.475  93.461    0.00     4.61
+ATOM     77    C STP     3      23.072  37.407  93.857    0.00     4.23
+ATOM     78    C STP     3      22.312  36.813  93.521    0.00     4.50
+ATOM     79    O STP     3      22.319  36.261  93.081    0.00     4.23
+ATOM     80    O STP     4      22.024  14.444  95.703    0.00     4.20
+ATOM     81    O STP     4      23.411  15.006  95.440    0.00     4.40
+ATOM     82    O STP     4      22.629  15.257  94.360    0.00     4.17
+ATOM     83    O STP     4      22.345  15.581  93.999    0.00     4.00
+ATOM     84    O STP     4      25.210  14.642  94.766    0.00     4.33
+ATOM     85    O STP     4      25.465  14.766  95.480    0.00     4.50
+ATOM     86    O STP     4      26.206  14.383  94.887    0.00     4.53
+ATOM     87    O STP     4      22.533  15.549  93.878    0.00     3.91
+ATOM     88    O STP     4      22.855  15.215  94.221    0.00     4.07
+ATOM     89    O STP     4      25.201  14.646  94.737    0.00     4.32
+ATOM     90    O STP     4      27.217  12.711  92.749    0.00     4.44
+ATOM     91    O STP     4      26.822  14.169  94.372    0.00     4.63
+ATOM     92    O STP     4      27.498  14.405  93.712    0.00     4.44
+ATOM     93    O STP     4      26.394  13.908  94.209    0.00     4.39
+ATOM     94    O STP     4      26.370  13.871  94.166    0.00     4.36
+ATOM     95    O STP     4      26.325  14.255  94.554    0.00     4.54
+ATOM     96    O STP     4      25.291  14.608  94.730    0.00     4.33
+ATOM     97    O STP     4      28.259  15.430  92.085    0.00     3.97
+ATOM     98    C STP     4      29.326  16.482  88.113    0.00     3.42
+ATOM     99    C STP     4      29.328  16.476  88.116    0.00     3.42
+ATOM    100    C STP     4      29.326  16.480  88.119    0.00     3.42
+ATOM    101    O STP     4      29.514  15.087  90.402    0.00     4.63
+ATOM    102    O STP     4      29.475  16.293  88.529    0.00     3.62
+ATOM    103    C STP     4      29.328  16.600  88.491    0.00     3.45
+ATOM    104    O STP     4      29.521  15.074  90.429    0.00     4.65
+ATOM    105    O STP     4      28.679  16.817  91.761    0.00     3.43
+ATOM    106    O STP     5      29.635  35.275 104.417    0.00     4.55
+ATOM    107    O STP     5      30.559  34.516 104.012    0.00     4.22
+ATOM    108    O STP     5      31.807  32.492 102.943    0.00     3.92
+ATOM    109    O STP     5      26.555  35.915 100.036    0.00     3.50
+ATOM    110    O STP     5      29.466  34.343 104.595    0.00     3.97
+ATOM    111    O STP     5      30.183  33.588 104.297    0.00     3.68
+ATOM    112    O STP     5      26.774  35.761 103.700    0.00     3.45
+ATOM    113    O STP     5      29.216  35.520 104.371    0.00     4.59
+ATOM    114    O STP     5      27.252  34.633 104.079    0.00     3.68
+ATOM    115    O STP     5      27.402  34.055 104.653    0.00     3.67
+ATOM    116    O STP     5      27.866  37.514 103.235    0.00     4.54
+ATOM    117    O STP     5      26.643  36.474 100.631    0.00     3.72
+ATOM    118    O STP     5      27.030  34.647 103.478    0.00     3.41
+ATOM    119    C STP     5      27.229  35.248 101.256    0.00     3.50
+ATOM    120    O STP     5      27.453  35.364 103.563    0.00     3.96
+ATOM    121    O STP     5      27.140  35.794 103.487    0.00     3.79
+ATOM    122    O STP     5      27.418  35.515 101.749    0.00     3.68
+ATOM    123    O STP     5      27.057  36.943 101.661    0.00     4.08
+ATOM    124    C STP     5      26.582  35.766 100.199    0.00     3.52
+ATOM    125    C STP     5      26.715  35.527 100.357    0.00     3.45
+ATOM    126    O STP     5      27.768  35.942 103.238    0.00     4.31
+ATOM    127    O STP     5      27.710  36.120 103.185    0.00     4.32
+ATOM    128    O STP     5      27.291  38.285 101.884    0.00     4.51
+ATOM    129    O STP     5      26.239  37.052 101.194    0.00     3.65
+ATOM    130    O STP     5      26.654  36.790 100.832    0.00     3.85
+ATOM    131    C STP     5      26.833  37.125 101.294    0.00     4.08
+ATOM    132    O STP     6      17.155  39.542 115.152    0.00     3.44
+ATOM    133    O STP     6      16.074  39.330 112.829    0.00     4.50
+ATOM    134    O STP     6      15.927  39.002 110.584    0.00     4.33
+ATOM    135    C STP     6      16.444  36.421 109.986    0.00     3.73
+ATOM    136    C STP     6      16.294  37.192 109.876    0.00     3.82
+ATOM    137    C STP     6      16.916  36.082 109.608    0.00     3.59
+ATOM    138    C STP     6      17.018  36.641 109.307    0.00     3.53
+ATOM    139    O STP     6      16.163  38.436 113.238    0.00     3.97
+ATOM    140    O STP     6      16.242  38.507 112.872    0.00     4.05
+ATOM    141    C STP     6      16.210  37.483 111.779    0.00     3.62
+ATOM    142    C STP     6      16.467  36.258 110.711    0.00     3.55
+ATOM    143    C STP     6      14.927  37.895 109.272    0.00     3.44
+ATOM    144    C STP     6      15.152  37.916 109.363    0.00     3.53
+ATOM    145    O STP     6      15.702  39.501 110.680    0.00     4.54
+ATOM    146    O STP     6      16.408  37.882 114.305    0.00     3.42
+ATOM    147    O STP     7      20.645  17.503 111.071    0.00     4.37
+ATOM    148    C STP     7      15.820  19.177 113.039    0.00     3.54
+ATOM    149    O STP     7      20.635  19.938 112.308    0.00     3.73
+ATOM    150    O STP     7      20.913  18.616 111.749    0.00     4.12
+ATOM    151    O STP     7      20.843  19.644 111.761    0.00     3.70
+ATOM    152    O STP     7      20.897  18.566 111.803    0.00     4.15
+ATOM    153    O STP     7      20.610  19.852 112.395    0.00     3.77
+ATOM    154    O STP     7      19.110  19.000 113.516    0.00     3.90
+ATOM    155    O STP     7      20.637  19.946 112.316    0.00     3.73
+ATOM    156    O STP     7      20.622  19.901 112.431    0.00     3.75
+ATOM    157    C STP     7      16.334  18.498 113.698    0.00     4.16
+ATOM    158    O STP     7      18.320  18.736 113.928    0.00     4.14
+ATOM    159    C STP     7      16.075  19.168 113.443    0.00     3.76
+ATOM    160    C STP     7      16.021  19.691 113.267    0.00     3.47
+ATOM    161    C STP     7      18.721  19.401 114.167    0.00     3.70
+ATOM    162    O STP     8      29.362  22.473 114.305    0.00     4.01
+ATOM    163    O STP     8      29.526  22.621 114.800    0.00     4.07
+ATOM    164    O STP     8      27.490  23.333 114.463    0.00     3.53
+ATOM    165    O STP     8      28.626  22.816 114.473    0.00     3.73
+ATOM    166    O STP     8      26.805  23.688 113.987    0.00     3.40
+ATOM    167    O STP     8      27.117  23.488 114.139    0.00     3.47
+ATOM    168    C STP     8      26.996  23.584 114.077    0.00     3.44
+ATOM    169    O STP     8      29.877  22.219 113.882    0.00     4.25
+ATOM    170    C STP     8      30.995  22.326 112.654    0.00     4.50
+ATOM    171    O STP     8      31.065  25.368 116.666    0.00     3.68
+ATOM    172    O STP     8      27.689  24.002 115.360    0.00     3.41
+ATOM    173    O STP     8      27.771  23.642 115.116    0.00     3.49
+ATOM    174    O STP     8      29.396  23.937 115.791    0.00     3.57
+ATOM    175    O STP     8      30.156  22.567 114.990    0.00     4.34
+ATOM    176    O STP     8      30.107  22.253 115.370    0.00     4.02
+ATOM    177    O STP     8      29.633  22.634 114.893    0.00     4.12
+ATOM    178    O STP     8      29.528  22.353 115.230    0.00     3.77
+ATOM    179    O STP     9      25.199  18.226 102.932    0.00     4.17
+ATOM    180    O STP     9      25.326  16.386 101.266    0.00     4.69
+ATOM    181    O STP     9      25.788  19.373 101.422    0.00     3.76
+ATOM    182    O STP     9      25.705  17.371 102.299    0.00     4.63
+ATOM    183    O STP     9      25.906  18.450 102.503    0.00     4.44
+ATOM    184    O STP     9      24.018  19.385 103.636    0.00     3.63
+ATOM    185    O STP     9      25.933  20.105 101.001    0.00     3.58
+ATOM    186    O STP     9      25.897  19.725 101.681    0.00     3.91
+ATOM    187    O STP     9      26.028  19.445 102.420    0.00     4.32
+ATOM    188    O STP     9      24.536  20.354 103.313    0.00     3.70
+ATOM    189    O STP     9      24.560  20.478 103.397    0.00     3.64
+ATOM    190    O STP     9      24.145  20.692 103.141    0.00     3.40
+ATOM    191    O STP     9      27.092  20.122 102.715    0.00     4.19
+ATOM    192    O STP     9      27.217  20.540 102.988    0.00     4.02
+ATOM    193    O STP     9      28.526  19.406 103.321    0.00     4.32
+ATOM    194    O STP     9      29.585  19.821 104.201    0.00     4.47
+ATOM    195    O STP     9      26.471  21.638 103.888    0.00     3.41
+ATOM    196    O STP     9      27.293  21.174 102.683    0.00     3.51
+ATOM    197    O STP    10      29.588  17.664  79.254    0.00     3.67
+ATOM    198    C STP    10      28.147  15.706  79.363    0.00     3.50
+ATOM    199    O STP    10      27.964  14.902  79.498    0.00     3.44
+ATOM    200    O STP    10      28.650  15.745  79.406    0.00     3.79
+ATOM    201    O STP    10      29.000  15.290  79.529    0.00     4.01
+ATOM    202    O STP    10      29.829  15.757  79.981    0.00     4.37
+ATOM    203    O STP    10      29.587  17.657  79.261    0.00     3.68
+ATOM    204    O STP    10      29.593  17.661  79.258    0.00     3.68
+ATOM    205    O STP    10      29.732  15.881  82.059    0.00     3.48
+ATOM    206    C STP    10      29.621  15.938  80.677    0.00     3.87
+ATOM    207    O STP    10      29.123  16.675  79.719    0.00     3.96
+ATOM    208    C STP    10      29.211  16.534  79.762    0.00     4.01
+ATOM    209    O STP    10      29.069  16.638  79.701    0.00     3.95
+ATOM    210    C STP    10      29.064  16.625  79.701    0.00     3.94
+ATOM    211    C STP    10      29.034  16.637  79.702    0.00     3.92
+TER
+END
--- a/tests/reference_output/3LKF_out/pockets/pocket10_atm.pdb
+++ b/tests/reference_output/3LKF_out/pockets/pocket10_atm.pdb
@@ -0,0 +1,34 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket    10:
+HEADER 0  - Pocket Score                      : 0.0813
+HEADER 1  - Drug Score                        : 0.0018
+HEADER 2  - Number of alpha spheres           :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.8170
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5812
+HEADER 5  - Mean B-factor of pocket residues  : 0.6158
+HEADER 6  - Hydrophobicity Score              : 32.0000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 5.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 133.5639
+HEADER 10  -Pocket volume (convex hull)       : 1.9142
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 4.0000
+HEADER 13 - Number of apolar alpha sphere     :     5
+HEADER 14 - Proportion of apolar alpha sphere : 0.3333
+ATOM    764    O TYR A  99      27.955  20.779  80.311  0.70  1.07           O 0
+ATOM    761    N TYR A  99      26.358  19.300  78.639  0.64  1.09           N 0
+ATOM    967  CD1 ILE A 124      30.114  21.018  77.854  0.00  0.00           C 0
+ATOM    759  OD1 ASP A  98      29.154  16.631  75.757  0.00  0.00           O 0
+ATOM    749    O VAL A  97      26.637  14.844  76.325  0.00  0.00           O 0
+ATOM    771   CZ TYR A  99      26.046  15.958  82.151  0.00  0.00           C 0
+ATOM    754   CA ASP A  98      26.374  17.537  76.964  0.00  0.00           C 0
+ATOM    770  CE2 TYR A  99      25.133  15.993  81.119  0.00  0.00           C 0
+ATOM    772   OH TYR A  99      26.489  14.737  82.601  0.48  9.64           O 0
+ATOM    789   CB LYS A 102      30.136  19.311  82.498  0.00  0.00           C 0
+ATOM    769  CE1 TYR A  99      26.549  17.140  82.695  0.00  0.00           C 0
+ATOM    788    O LYS A 102      30.089  17.692  85.011  0.48  8.57           O 0
+TER
+END
--- a/tests/reference_output/3LKF_out/pockets/pocket10_vert.pqr
+++ b/tests/reference_output/3LKF_out/pockets/pocket10_vert.pqr
@@ -0,0 +1,37 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket    10:
+HEADER 0  - Pocket Score                      : 0.0813
+HEADER 1  - Drug Score                        : 0.0018
+HEADER 2  - Number of V. Vertices             :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.8170
+HEADER 4  - Mean alpha-sphere SA              : 0.5812
+HEADER 5  - Mean B-factor                     : 0.6158
+HEADER 6  - Hydrophobicity Score              : 32.0000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 5.0000
+HEADER 9  - Real volume (approximation)       : 133.5639
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 4.0000
+HEADER 12 - Number of apolar alpha sphere     :     5
+HEADER 13 - Proportion of apolar alpha sphere : 0.3333
+ATOM      1    O STP    10      29.588  17.664  79.254    0.00     3.67
+ATOM      2    C STP    10      28.147  15.706  79.363    0.00     3.50
+ATOM      3    O STP    10      27.964  14.902  79.498    0.00     3.44
+ATOM      4    O STP    10      28.650  15.745  79.406    0.00     3.79
+ATOM      5    O STP    10      29.000  15.290  79.529    0.00     4.01
+ATOM      6    O STP    10      29.829  15.757  79.981    0.00     4.37
+ATOM      7    O STP    10      29.587  17.657  79.261    0.00     3.68
+ATOM      8    O STP    10      29.593  17.661  79.258    0.00     3.68
+ATOM      9    O STP    10      29.732  15.881  82.059    0.00     3.48
+ATOM     10    C STP    10      29.621  15.938  80.677    0.00     3.87
+ATOM     11    O STP    10      29.123  16.675  79.719    0.00     3.96
+ATOM     12    C STP    10      29.211  16.534  79.762    0.00     4.01
+ATOM     13    O STP    10      29.069  16.638  79.701    0.00     3.95
+ATOM     14    C STP    10      29.064  16.625  79.701    0.00     3.94
+ATOM     15    C STP    10      29.034  16.637  79.702    0.00     3.92
+TER
+END
--- a/tests/reference_output/3LKF_out/pockets/pocket1_atm.pdb
+++ b/tests/reference_output/3LKF_out/pockets/pocket1_atm.pdb
@@ -0,0 +1,46 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     1:
+HEADER 0  - Pocket Score                      : 0.4900
+HEADER 1  - Drug Score                        : 0.0185
+HEADER 2  - Number of alpha spheres           :    21
+HEADER 3  - Mean alpha-sphere radius          : 3.8164
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5193
+HEADER 5  - Mean B-factor of pocket residues  : 0.8414
+HEADER 6  - Hydrophobicity Score              : 23.8889
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.5556
+HEADER 9  - Pocket volume (Monte Carlo)       : 276.4945
+HEADER 10  -Pocket volume (convex hull)       : 13.4057
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 3.0000
+HEADER 13 - Number of apolar alpha sphere     :     4
+HEADER 14 - Proportion of apolar alpha sphere : 0.1905
+ATOM   1502   CG GLN A 198      25.855  32.230 126.839  0.00  0.00           C 0
+ATOM   1490   CB ARG A 197      25.882  30.425 122.858  0.00  0.00           C 0
+ATOM   1497    N GLN A 198      24.213  32.753 124.492  0.55  2.19           N 0
+ATOM   1486    N ARG A 197      24.896  32.396 121.850  0.00  0.00           N 0
+ATOM   1492   CD ARG A 197      27.769  29.119 121.892  0.00  0.00           C 0
+ATOM   1491   CG ARG A 197      26.479  29.848 121.580  0.00  0.00           C 0
+ATOM   1324  NE1 TRP A 176      31.876  33.211 116.985  0.72  3.28           N 0
+ATOM   1480    O ALA A 195      25.325  35.396 118.156  0.48  9.64           O 0
+ATOM   1483   CA GLY A 196      24.378  34.259 120.436  0.00  0.00           C 0
+ATOM   1448  OE1 GLU A 191      26.586  28.056 118.540  0.00  0.00           O 0
+ATOM   1493   NE ARG A 197      28.310  28.346 120.770  0.00  0.00           N 0
+ATOM   1325  CE2 TRP A 176      32.250  32.029 117.559  0.00  0.00           C 0
+ATOM   1474   CG LEU A 194      22.458  30.664 118.196  0.00  0.00           C 0
+ATOM   1476  CD2 LEU A 194      22.990  29.401 118.883  0.00  0.00           C 0
+ATOM   1327  CZ2 TRP A 176      32.768  31.772 118.841  0.00  0.00           C 0
+ATOM   1472    O LEU A 194      24.241  32.824 115.786  0.00  0.00           O 0
+ATOM   1322  CD1 TRP A 176      31.434  32.964 115.716  0.00  0.00           C 0
+ATOM   1306  ND2 ASN A 173      25.717  32.413 113.408  0.00  0.00           N 0
+ATOM   1445   CB GLU A 191      25.579  27.436 115.621  0.00  0.00           C 0
+ATOM   1304   CG ASN A 173      26.777  33.145 113.047  0.00  0.00           C 0
+ATOM   1305  OD1 ASN A 173      26.910  34.319 113.363  0.42  5.36           O 0
+ATOM   1321   CG TRP A 176      31.511  31.634 115.439  0.00  0.00           C 0
+ATOM   1444    O GLU A 191      24.684  29.324 113.711  0.00  0.00           O 0
+ATOM   1352   OH TYR A 179      29.515  28.039 114.662  0.72  4.29           O 0
+TER
+END
--- a/tests/reference_output/3LKF_out/pockets/pocket1_vert.pqr
+++ b/tests/reference_output/3LKF_out/pockets/pocket1_vert.pqr
@@ -0,0 +1,43 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     1:
+HEADER 0  - Pocket Score                      : 0.4900
+HEADER 1  - Drug Score                        : 0.0185
+HEADER 2  - Number of V. Vertices             :    21
+HEADER 3  - Mean alpha-sphere radius          : 3.8164
+HEADER 4  - Mean alpha-sphere SA              : 0.5193
+HEADER 5  - Mean B-factor                     : 0.8414
+HEADER 6  - Hydrophobicity Score              : 23.8889
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.5556
+HEADER 9  - Real volume (approximation)       : 276.4945
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 3.0000
+HEADER 12 - Number of apolar alpha sphere     :     4
+HEADER 13 - Proportion of apolar alpha sphere : 0.1905
+ATOM      1    O STP     1      27.849  33.435 123.906    0.00     3.75
+ATOM      2    C STP     1      29.108  33.195 122.206    0.00     4.30
+ATOM      3    O STP     1      28.611  33.141 119.797    0.00     4.31
+ATOM      4    O STP     1      26.830  32.143 118.779    0.00     3.64
+ATOM      5    O STP     1      27.981  32.070 118.273    0.00     4.26
+ATOM      6    C STP     1      29.018  31.922 119.605    0.00     3.83
+ATOM      7    C STP     1      25.761  31.354 118.617    0.00     3.40
+ATOM      8    C STP     1      29.406  33.448 121.564    0.00     4.64
+ATOM      9    O STP     1      26.515  31.932 118.543    0.00     3.68
+ATOM     10    O STP     1      27.025  31.909 118.334    0.00     3.88
+ATOM     11    O STP     1      27.874  32.028 117.817    0.00     4.24
+ATOM     12    O STP     1      26.955  30.624 116.168    0.00     3.51
+ATOM     13    O STP     1      26.317  31.846 118.575    0.00     3.61
+ATOM     14    O STP     1      25.803  31.523 118.608    0.00     3.48
+ATOM     15    O STP     1      25.827  31.451 118.562    0.00     3.48
+ATOM     16    O STP     1      27.861  32.048 116.485    0.00     3.77
+ATOM     17    O STP     1      27.844  33.032 116.741    0.00     3.73
+ATOM     18    O STP     1      27.849  32.717 116.552    0.00     3.69
+ATOM     19    O STP     1      27.760  31.246 116.561    0.00     3.93
+ATOM     20    O STP     1      26.786  30.585 116.070    0.00     3.40
+ATOM     21    O STP     1      27.336  30.561 116.050    0.00     3.61
+TER
+END
--- a/tests/reference_output/3LKF_out/pockets/pocket2_atm.pdb
+++ b/tests/reference_output/3LKF_out/pockets/pocket2_atm.pdb
@@ -0,0 +1,41 @@
+HEADER
+HEADER This is a pdb format file writen by the programm fpocket.                 
+HEADER It represents the atoms contacted by the voronoi vertices of the pocket.  
+HEADER                                                                           
+HEADER Information about the pocket     2:
+HEADER 0  - Pocket Score                      : 0.3979
+HEADER 1  - Drug Score                        : 0.2835
+HEADER 2  - Number of alpha spheres           :    31
+HEADER 3  - Mean alpha-sphere radius          : 3.8059
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4586
+HEADER 5  - Mean B-factor of pocket residues  : 0.7238
+HEADER 6  - Hydrophobicity Score              : 27.8750
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.5000
+HEADER 9  - Pocket volume (Monte Carlo)       : 198.2249
+HEADER 10  -Pocket volume (convex hull)       : 10.3917
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 9.0000
+HEADER 13 - Number of apolar alpha sphere     :    10
+HEADER 14 - Proportion of apolar alpha sphere : 0.3226
+ATOM   1513   CA SER A 200      19.413  37.860 126.837  0.00  0.00           C 0
+ATOM   1518    N ALA A 201      17.864  37.756 124.999  0.00  0.00           N 0
+ATOM    547   OH TYR A  71      12.955  36.655 128.787  0.00  0.00           O 0
+ATOM   1517   OG SER A 200      18.672  38.973 128.845  0.60  8.57           O 0
+ATOM   1521    O ALA A 201      15.676  36.319 124.272  0.57  4.29           O 0
+ATOM    546   CZ TYR A  71      12.108  36.179 127.804  0.00  0.00           C 0
+ATOM    554  OD1 ASP A  72      12.388  31.920 126.772  0.81  1.07           O 0
+ATOM   1972   CG TRP A 256      16.287  30.343 127.002  0.00  0.00           C 0
+ATOM   2027  CZ2 TRP A 261      16.999  33.252 123.513  0.00  0.00           C 0
+ATOM   1509    O SER A 199      19.788  35.550 125.470  0.54  1.07           O 0
+ATOM   1974  CD2 TRP A 256      17.632  30.740 127.302  0.00  0.00           C 0
+ATOM    545  CE2 TYR A  71      11.443  34.960 127.956  0.00  0.00           C 0
+ATOM   1975  NE1 TRP A 256      16.431  30.852 129.192  0.55  5.47           N 0
+ATOM   1978  CZ2 TRP A 256      18.849  31.492 129.304  0.00  0.00           C 0
+ATOM   1516   CB SER A 200      19.791  38.775 128.004  0.00  0.00           C 0
+ATOM   1976  CE2 TRP A 256      17.679  31.056 128.679  0.00  0.00           C 0
+ATOM   1973  CD1 TRP A 256      15.596  30.421 128.186  0.00  0.00           C 0
+ATOM   1980  CH2 TRP A 256      19.975  31.602 128.532  0.00  0.00           C 0
+ATOM   1500    O GLN A 198      22.727  35.092 126.831  0.36  6.43           O 0
+TER
+END
--- a/tests/reference_output/3LKF_out/pockets/pocket2_vert.pqr
+++ b/tests/reference_output/3LKF_out/pockets/pocket2_vert.pqr
@@ -0,0 +1,53 @@
+HEADER
+HEADER This is a pqr format file writen by the programm fpocket.                 
+HEADER It represent the voronoi vertices of a single pocket found by the         
+HEADER algorithm.                                                                
+HEADER                                                                           
+HEADER Information about the pocket     2:
+HEADER 0  - Pocket Score                      : 0.3979
+HEADER 1  - Drug Score                        : 0.2835
+HEADER 2  - Number of V. Vertices             :    31
+HEADER 3  - Mean alpha-sphere radius          : 3.8059
+HEADER 4  - Mean alpha-sphere SA              : 0.4586
+HEADER 5  - Mean B-factor                     : 0.7238
+HEADER 6  - Hydrophobicity Score              : 27.8750
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.5000
+HEADER 9  - Real volume (approximation)       : 198.2249
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 9.0000
+HEADER 12 - Number of apolar alpha sphere     :    10
+HEADER 13 - Proportion of apolar alpha sphere : 0.3226
+ATOM      1    O STP     2      16.357  36.496 127.915    0.00     3.52
+ATOM      2    O STP     2      15.069  34.269 127.149    0.00     3.58
+ATOM      3    O STP     2      15.398  33.710 126.598    0.00     3.51
+ATOM      4    O STP     2      16.800  34.223 126.970    0.00     3.60
+ATOM      5    O STP     2      16.457  35.880 127.865    0.00     3.70
+ATOM      6    O STP     2      16.654  35.109 128.041    0.00     4.08
+ATOM      7    O STP     2      16.856  35.430 127.555    0.00     3.60
+ATOM      8    C STP     2      16.024  33.908 126.891    0.00     3.58
+ATOM      9    O STP     2      14.366  33.559 129.013    0.00     3.41
+ATOM     10    C STP     2      19.620  35.296 129.784    0.00     3.91
+ATOM     11    O STP     2      16.748  34.346 127.230    0.00     3.71
+ATOM     12    O STP     2      16.631  34.977 128.037    0.00     4.11
+ATOM     13    O STP     2      15.971  34.428 127.681    0.00     3.91
+ATOM     14    O STP     2      16.629  34.948 129.488    0.00     4.11
+ATOM     15    O STP     2      16.707  35.039 128.175    0.00     4.13
+ATOM     16    C STP     2      17.194  34.979 128.410    0.00     3.96
+ATOM     17    O STP     2      16.883  35.175 128.841    0.00     4.20
+ATOM     18    O STP     2      16.883  35.175 128.855    0.00     4.20
+ATOM     19    C STP     2      16.890  35.174 128.844    0.00     4.20
+ATOM     20    C STP     2      15.877  34.086 127.313    0.00     3.78
+ATOM     21    C STP     2      15.879  34.090 127.319    0.00     3.78
+ATOM     22    O STP     2      15.878  34.091 127.321    0.00     3.78
+ATOM     23    O STP     2      15.461  33.937 127.079    0.00     3.69
+ATOM     24    O STP     2      14.880  33.815 128.268    0.00     3.47
+ATOM     25    O STP     2      15.423  34.131 127.372    0.00     3.80
+ATOM     26    O STP     2      15.621  34.204 127.486    0.00     3.85
+ATOM     27    C STP     2      19.788  35.314 130.003    0.00     4.00
+ATOM     28    C STP     2      20.088  35.294 129.633    0.00     3.85
+ATOM     29    C STP     2      19.637  35.293 129.780    0.00     3.91
+ATOM     30    O STP     2      19.922  35.097 128.959    0.00     3.52
+ATOM     31    C STP     2      19.053  34.999 128.886    0.00     3.54
+TER
+END
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
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
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