fixed typo and deleted mod 2POR

lilely not working

.gitattributes

@@ -0,0 +1,2 @@
+*.tcl linguist-detectable=false
+*.c linguist-detectable=true

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,10 @@
+---
+name: Question
+about: Custom question
+title: ''
+labels: question
+assignees: ''
+
+---
+
+

.github/workflows/c-cpp.yml

@@ -0,0 +1,23 @@
+name: C/C++ CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build-and-test-linux:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: netcdf
+      run: sudo apt-get install libnetcdf-dev
+    - name: make
+      run: make fpocket
+    - name: create conda environment
+      run: conda env update -f ./tests/environment.yml
+    - name: activate conda environment
+      run: conda activate fpocket_test
+    - name: Run pytest
+      run: pytest

Dockerfile

@@ -0,0 +1,24 @@
+FROM centos:7
+
+#RUN yum -y install epel-release && yum -y update && yum -y install gcc gcc-c++ make netcdf-devel; yum clean all
+RUN yum -y install gcc gcc-c++ make netcdf-devel; yum clean all
+
+# all of this mess is essentially to have a minimalistic build at the end
+COPY makefile /opt/fpocket/
+COPY src /opt/fpocket/src
+COPY man /opt/fpocket/man
+COPY headers /opt/fpocket/headers
+COPY obj /opt/fpocket/obj
+COPY scripts /opt/fpocket/scripts
+COPY bin /opt/fpocket/bin
+COPY plugins/LINUXAMD64 /opt/fpocket/plugins/LINUXAMD64
+COPY plugins/include /opt/fpocket/plugins/include
+COPY plugins/noarch /opt/fpocket/plugins/noarch
+
+WORKDIR /opt/fpocket
+
+RUN make; make install; make clean
+
+WORKDIR /WORKDIR
+
+CMD ["fpocket"]

README.md

@@ -1,5 +1,8 @@
 
-![fpocket logo](doc/images/fpocket_logo.png)
+![fpocket logo](doc/images/fpocket_logo.png) 
+
+[![Build Status](https://dev.azure.com/3decision/fpocket/_apis/build/status/Discngine.fpocket?branchName=master)](https://dev.azure.com/3decision/fpocket/_build/latest?definitionId=2&branchName=master)
+[![Join the chat at https://gitter.im/fpocket/community](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/fpocket-official/community?utm_source=badge&utm_medium=badge&utm_content=badge)
 
 The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.
 
@@ -29,7 +32,7 @@ mdpocket:
 
 ## Getting Started
 
-### Prerequisites
+### Prerequisites (if you want to compile it)
 
 The most recent versions (starting with fpocket 3.0) make use of the molfile plugin from VMD. This plugin is shipped with fpocket. However, now you need to install the netcdf library on your system. This is typically called netcdf-devel or so, depending on you linux distribution.
 fpocket needs to be compiled to run on your machine. For this you'll need the gnu c compiler (or another one).
@@ -52,6 +55,35 @@ sudo port install netcdf
 export LIBRARY_PATH=/opt/local/lib
 ```
 
+### Docker Image
+
+#### Using the official fpocket docker image
+
+The following command will pull the latest fpocket docker image from the dockerhub. 
+
+```bash
+docker pull fpocket/fpocket
+```
+
+#### Building the docker image
+
+
+You can create a docker image with fpocket using the provided Dockerfile of the repo (obviously you'd need docker to do that): 
+
+```bash
+docker build -t fpocket/fpocket .
+```
+
+#### Using the docker image
+
+This will build fpocket into your local fpocket/fpocket image. You can then run fpocket/mdpocket etc using: 
+
+```bash
+docker run -v `pwd`:/WORKDIR fpocket/fpocket fpocket -f data/sample/1UYD.pdb
+```
+
+Here you mount your current directory with your input files into the preconfigured `/WORKDIR` in the docker container and then run fpocket on a file in that mounted folder.
+
 ### Installing
 
 Download the sources from github via the website or using git clone and then build and deploy fpocket using the following commands.
@@ -142,6 +174,7 @@ Please read [CONTRIBUTING.md](https://gist.github.com/PurpleBooth/b24679402957c6
 
 * **Peter Schmidtke** - *Initial work* - [pschmidtke](https://github.com/pschmidtke)
 * **Vincent Le Guilloux** - *Initial work* - [leguilv](https://github.com/leguilv)
+* **Mael Shorkar** - *Chain handling* - [leguilv](https://github.com/shorkarmael)
 
 
 ## License

azure-pipelines.yml

@@ -0,0 +1,49 @@
+# C/C++ with GCC
+# Build your C/C++ project with GCC using make.
+# Add steps that publish test results, save build artifacts, deploy, and more:
+# https://docs.microsoft.com/azure/devops/pipelines/apps/c-cpp/gcc
+
+trigger: none                       # will disable CI builds entirely i.e. merges, check-ins do not trigger this build
+
+pr:
+  - master                          # trigger on a PR to master
+
+jobs:
+ - job: build_and_test_linux
+   pool:
+      vmImage: 'ubuntu-latest'
+   steps:
+      - script: conda env create --file tests/environment.yml --name fpocket_test
+        displayName: Create Anaconda environment
+      - script: conda env list
+        displayName:  environment installation verification
+      - task: Bash@3
+        inputs:
+          targetType: 'inline'
+          script: |
+            eval "$(conda shell.bash hook)"
+            sudo apt-get install libnetcdf-dev
+            conda activate fpocket_test
+            make
+            pytest
+        displayName: Active
+
+ - job: build_and_test_mac
+   pool:
+      vmImage: 'macOS-10.14'
+   steps:
+      - bash: sudo chown -R $USER $CONDA
+      - script: conda env create --file tests/environment.yml --name fpocket_test
+        displayName: Create Anaconda environment
+      - script: conda env list
+        displayName:  environment installation verification
+      - task: Bash@3
+        inputs:
+          targetType: 'inline'
+          script: |
+            eval "$(conda shell.bash hook)"
+            conda activate fpocket_test
+            make fpocket ARCH=MACOSXX86_64
+            pytest
+        displayName: Active
+

doc/GETTINGSTARTED.md

@@ -220,7 +220,7 @@ You can extract these grid points using a python script that is available in the
 ##### or : 
 
 	-L: a mdpocket input file, this file has to contain the paths to the PDB files of all snapshots (one path per line)
-    --selected_pocket   : a PDB file containing the sitepoints in the pocket to be selected
+	--selected_pocket   : a PDB file containing the sitepoints in the pocket to be selected
 
 #### Optional:
 
@@ -414,17 +414,17 @@ The simplest way to run fpocket is either by providing a single pdb file, or by
 #### Optional:
 
     -m float: (default 3.4Å) This flag enables the user to modify the minimum radius an alpha sphere might have in a binding pocket. An alpha sphere is a contact sphere, that touches 4 atoms in 3D space without having any internal atoms. Here 3Å allow filtering of too small (protein internal) alpha spheres. I you want to analyze internal interstices, lower this parameter. In the contrary, if you want to analyze more solvent exposed cavities, you can raise this parameter in order to filter out too buried cavities.
-
+    
     -M float: (default 6.2Å) Here you can modify the maximum radius of alpha spheres in a pocket. An alpha sphere is a contact sphere, that touches 4 atoms in 3D space without having any internal atoms. Here 7Å allow to filter out too large contact spheres, that are lying on the protein surface. If you want to analyze very flat and solvent exposed surface depressions, raise this parameter. For analysis of buried parts of the protein you can lower this parameter. Higher radii might be more interesting for identification of protein protein binding sites or polysaccharide binding sites. Smaller radii enable detection of buried cavities for small organic molecules (drugs, for instance).
-
+    
     -l int: (None) If you have an input PDB file of an NMR structure or one with multiple models you can specify which model (conformation) you'd like to analyse
-
+    
     -C char: (default s) The clustering method to be used here. By default a pairwise single linkage clustering is used here. 
         's': pairwise single linkage clustering,
         'm': pairwise maximum- (or complete-) linkage clustering, 
         'a': pairwise average-linkage clustering, 
         'c': pairwise centroid-linkage clustering
-
+    
     -e char: (default e) The distance measure used for the clustering algorithm. 
         'e': Euclidean distance
         'b': City-block distance
@@ -434,29 +434,35 @@ The simplest way to run fpocket is either by providing a single pdb file, or by
         'x': absolute uncentered correlation
         's': Spearman's rank correlation
         'k': Kendall's tau
-
+    
     -i int: (default 15) This flag indicates how many alpha spheres a pocket must contain at least in order to figure in the results provided by fpocket. This parameter enables filtering of too small cavities. Thus, if you want to analyze smaller cavities also, lower this parameter, if you are only interested in huge cavities, like NADP binding sites, you can raise it in order to retain only very few pockets in the end. To give you an idea, a rather big cavity, like a NADP binding site, can have hundreds of alpha spheres. Thus, 30 as standard parameter enables also to keep smaller binding sites.
-
+    
     -A int: (default 3) Fpocket distinguishes between two types of alpha spheres. Polar alpha spheres and apolar alpha spheres. This flag ranges from 0 to 4 and modifies the definition of the alpha sphere type. By default, an alpha sphere contacting at least 3 apolar atoms (having an electronegativity below 2.8) is considered as apolar. If this is not the case it is considered as polar.
-
+    
     -D float: (default 2.4Å) this parameter changed compared to the previous versions of fpocket as we completely replaced the clustering algorithms entirely. This measure is now used to analyze a hierarchical distance and cut sub-trees at the desired distance. The bigger the distance, the larger the clusters you'll get. 
-
+    
     -p float: (default 0.0) This is another parameter for filtering unwanted pockets. It defines the maximum ratio of apolar alpha spheres and the number of alpha spheres in a pocket in order to keep the pocket in the results list. That is to say, by default every pocket is kept (0.0). Now, if you would like to filter rather hydrophobic pockets, raise this parameter and very polar cavities will be filtered out. This parameter is a ratio, not a percentage, thus it ranges from 0 to 1.
-
+    
     -v int: (default 2500) By default, pockets volume are calculated using a monte-carlo algorithm. Basically, the algorithm picks a random point in the space and check if it is included in any alpha sphere, and stores this status. This is repeated N times, and we estimate the volume of the pocket using ratio between the number of hit and the number of iteration, scaled by the size of the box. This parameter defines the number of iteration to perform. Of course, the higher the value is, the greater the accuracy will be, but the performance will be slowed down.
-
+    
     -b (none): (NOT USED BY DEFAULT) This option allows the user to chose a discrete algorithm  to calculate  the  volume of each pocket instead of the Monte Carlo method. This algorithm puts each pocket into a grid of  dimention (1/N*X  ;  1/N*Y  ;  1/N*Z),  N being the value given using this option, and X, Y and Z being the box dimensions,  determined using coordinates of vertices. Then, a triple iteration on each dimensions is used to estimate the volume, checking if each points  given  by the iteration is in one of the pocket’s vertices. This parameter defines the grid discretization. If this parameter is used, this algorithm will be used instead of the Monte Carlo algorithm. 
     Warning: Although this algorithm could be more accurate, a high value might dramatically slow down the program, as this algorithm has a maximum complexity of N*N*N*nb_vertices, and a minimum of N*N*N !!!
-    
+
 
     -d (none): Option allowing you to output pockets and properties in a condensed format. This will put to the stdout pocket properties in a tab separated string and write pocket files in a subfolder
-
+    
     -r string: (None) This parameter allows you to run fpocket in a restricted mode. Let's suppose you have a very shallow or large pocket with a ligand inside and the automatic pocket prediction always splits up you pocket or you have only a part of the pocket found. Specifying your ligand residue with -r allows you to detect and characterize you ligand binding site explicitely. For instance for `1UYD.pdb` you can specify `-r 1224:PU8:A` (residue number of the ligand: residue name of the ligand: chain of the ligand)
-
+    
     -y string: (filename) EXPERIMENTAL: here you can specify a topology filename in the Amber prmtop format. This can then be used by fpocket & mdpocket to calculate energy grids for your pockets. NB: you have to specify the -x flag to run energy calculations
-
+    
     -x None: (None) EXPERIMENTAL: specify this flag if you want to run energy calculations on calculated pockets. That's not fully functional and only one or two probes are currently generated and output density grids written. Use with caution
     
+    -c char : (Default is none): Use this flag to choose which chains you want to delete before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-c B,D' or '-c B:D'. You can delete up to 20 different chains.
+    
+    -k char : (Default is none): Use this flag to choose which chains you want to keep before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-k A,B,E' or '-k A:B:E'. You can keep up to 20 different chains.
+    
+    -a char : (Default is none): With this flag you can select a chain you want to be considered as a ligand. Works the same way as the "-r" flag but with a whole chain. Only a single chain can be chosen, for example '-a D'.
+
 
 ###  Output files description
 
@@ -571,11 +577,11 @@ See the [Getting started section of dpocket](#dpocket-descriptor-extraction) for
 ### Optional:
 
     -o : (default dpout) the prefix you want to give to dpocket output files. The standard will produce three output files named dpout_fpocketnp.txt, dpout_fpocketp.txt, dpout_explicitp.txt.
-
+    
     -e : Use the first explicit interface definition (default): we define  the explicit pocket  as  being  all  atoms  contacted  by  alpha spheres situated at a distance of d A° from any ligand atom.
-
+    
     -E : Use  the  second  explicit  interface  definition: we define the explicit pocket as being all atoms situated at a distance  of  d A° from any ligand atom.
-
+    
     -d : The distance criteria used for the explicit pocket definition.
     Last, all optional parameters used by fpocket are also accessible on command line through dpocket. Refer to the preceding paragraph to see details about fpocket parameters.
 

headers/fparams.h

@@ -55,6 +55,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 #define M_DB_RUN 0  /**< default value for running fpocket for populating a database, 0 default*/
 
+#define M_MAX_CHAINS_DELETE 20 
 
 #define M_MIN_AS_DENSITY 0.7
 
@@ -107,6 +108,16 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define M_PAR_CUSTOM_LIGAND 'r' /**flag, to define detection of explicit pockets around the specified ligand*/
 #define M_PAR_CUSTOM_LIGAND_LONG "custom_ligand"
 
+#define M_PAR_DROP_CHAINS 'c' /**flag, to define which chain are dropped before the pocket detection*/
+#define M_PAR_DROP_CHAINS_LONG "drop_chains"
+
+#define M_PAR_KEEP_CHAINS 'k' /**flag, to define which chains are kept before the pocket detection*/
+#define M_PAR_KEEP_CHAINS_LONG "keep_chains"
+
+#define M_PAR_CHAIN_AS_LIGAND 'a' /**flag, to define which chains are defined as a ligand*/
+#define M_PAR_CHAIN_AS_LIGAND_LONG "chain_as_ligand"
+
+
 
 #define M_FP_USAGE "\n\
 ***** USAGE (fpocket) *****\n\
@@ -189,8 +200,9 @@ typedef struct s_fparams
 		  asph_min_size,	 	/**< Minimum size of alpha spheres to keep */
                 min_as_density,                 /**<Minimum alpha sphere density for a pocket to be retained*/
 		  asph_max_size ;		/**< Maximum size of alpha spheres to keep */
-
-
+	char chain_delete[M_MAX_CHAINS_DELETE]; /*chosen chain to delete before calculation*/
+	char chain_as_ligand[M_MAX_CHAINS_DELETE];
+	int chain_is_kept;/* To choose if we keep the chains or not*/
 
 } s_fparams ;
 

headers/rpdb.h

@@ -141,5 +141,5 @@ s_atom_ptr_list *init_atom_ptr_list(void);
 
 
 short get_mm_type_from_element(char *symbol);
-
+int chains_to_delete(char *chains_selected, char *current_line_chain, int is_chain_kept);
 #endif

src/fparams.c

@@ -80,6 +80,7 @@ s_fparams* init_def_fparams(void) {
     par->topology_path[0] = 0;
     par->fpocket_running = 0;
     par->xlig_resnumber = - 1;
+    par->chain_is_kept = 0;
     return par;
 }
 
@@ -101,14 +102,15 @@ s_fparams* init_def_fparams(void) {
  */
 s_fparams* get_fpocket_args(int nargs, char **args) {
     int status = 0;
-    s_fparams *par = init_def_fparams();
+    s_fparams *par = init_def_fparams(); /*default param initialy*/
     int c = 0;
     short j = 0;
     short xflag;
     opterr = 0;
     char *pt;
     short custom_ligand_i=0;
-    static struct option fplong_options[] = {
+    
+    static struct option fplong_options[] = {  /*long options args located in fparams.h*/
         {"file", required_argument, 0, M_PAR_PDB_FILE},
         {"min_alpha_size", required_argument, 0, M_PAR_MIN_ASHAPE_SIZE},
         {"max_alpha_size", required_argument, 0, M_PAR_MAX_ASHAPE_SIZE},
@@ -124,6 +126,9 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
         {"topology_file", required_argument, 0, M_PAR_TOPOLOGY},
         {"model_number", required_argument, 0, M_PAR_MODEL_FLAG},
         {"custom_ligand", required_argument, 0, M_PAR_CUSTOM_LIGAND},
+        {M_PAR_DROP_CHAINS_LONG, required_argument, 0, M_PAR_DROP_CHAINS}, /*drop chains*/
+        {M_PAR_CHAIN_AS_LIGAND_LONG, required_argument, 0, M_PAR_CHAIN_AS_LIGAND}, /*chain as ligand*/
+        {M_PAR_KEEP_CHAINS_LONG, required_argument, 0, M_PAR_KEEP_CHAINS}, /*chain as ligand*/
         {0, 0, 0, 0}
     };
 
@@ -132,13 +137,67 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
         /* getopt_long stores the option index here. */
         int option_index = 0;
         optarg = 0;
-        c = getopt_long(nargs, args, "f:m:M:i:p:D:C:e:dxp:v:y:l:r:",
+        c = getopt_long(nargs, args, "f:m:M:i:p:D:C:e:dxp:v:y:l:r:c:a:k:",
                 fplong_options, &option_index);
         //        printf("C: %d nargs : %d optindex:%d\n", c, nargs, option_index);
 
         switch (c) {
             case 0:
                 break;
+
+            case M_PAR_CHAIN_AS_LIGAND :
+                /*select the chains as ligand*/
+                status++;
+                strcpy(par->chain_as_ligand, optarg); /*par->chain_as_ligand contains the arg given in cmd line*/
+                const char  *separatorss  = ",:"; /* defining separators*/
+                pt = strtok( par->chain_as_ligand, separatorss);
+                int nn = 0;
+                while (pt != NULL) {
+                    strncpy(&(par->chain_as_ligand[nn]), pt, 1);
+                    nn++;
+                    pt = strtok(NULL, separatorss);
+                }
+                par->xlig_resnumber = 0;
+                //printf("lig %s\n",par->chain_as_ligand);
+                
+                
+                break;
+
+            case M_PAR_DROP_CHAINS :
+            /*drop the selected chains from the pdb file*/
+                strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
+                //printf("%s and %s",par->custom_ligand,optarg);
+                const char  *separators  = ",:"; /* defining separators for drop chains args*/
+                pt = strtok( par->chain_delete, separators);
+                int n = 0;
+                while (pt != NULL) {
+                    strncpy(&(par->chain_delete[n]), pt, 1);
+                    n++;
+                    pt = strtok(NULL, separators);
+                }
+                par->chain_is_kept = 0;
+                //printf("%s\n",par->chain_delete);
+                status++;
+                break;
+                
+            case M_PAR_KEEP_CHAINS :
+            /*drop the selected chains from the pdb file*/
+                
+                strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
+                //printf("%s and %s",par->custom_ligand,optarg);
+                const char  *separator  = ",:"; /* defining separators for drop chains args*/
+                pt = strtok( par->chain_delete, separator);
+                int nk = 0;
+                while (pt != NULL) {
+                    strncpy(&(par->chain_delete[nk]), pt, 1);
+                    nk++;
+                    pt = strtok(NULL, separator);
+                }
+                //printf("%s\n",par->chain_delete);
+                par->chain_is_kept = 1;
+                status++;
+                break;
+
             case M_PAR_CUSTOM_LIGAND:
 
                 //parse ligand specification that has to be given as 
@@ -146,9 +205,11 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
                 //for 1uyd for instance 1224:PU8:A
                 
                 status++;
-                strcpy(par->custom_ligand, optarg);
                 
+                strcpy(par->custom_ligand, optarg);
+                //printf("%s and %s",par->custom_ligand,optarg);
                 pt = strtok( par->custom_ligand, ":");
+
                 while (pt != NULL) {
                     custom_ligand_i++;
                     if(custom_ligand_i==1) par->xlig_resnumber =atoi(pt);
@@ -728,6 +789,7 @@ void print_pocket_usage(FILE *f) {
     fprintf(f, "\t-%c --%s (int)\t\t\t: Number of Model to analyze.\t\n", M_PAR_MODEL_FLAG, M_PAR_MODEL_FLAG_LONG);
     fprintf(f, "\t-%c --%s (string)\t\t: File name of a topology file (Amber prmtop).\t\n", M_PAR_TOPOLOGY, M_PAR_LONG_TOPOLOGY);
     fprintf(f, "\t-%c --%s (string)\t\t: String specifying a ligand like: residuenumber:residuename:chain_code (ie. 1224:PU8:A).\t\n", M_PAR_CUSTOM_LIGAND, M_PAR_CUSTOM_LIGAND_LONG);
+    fprintf(f, "\t-%c --%s (char)\t\t: Character specifying a chain as a ligand\t\n", M_PAR_CHAIN_AS_LIGAND, M_PAR_CHAIN_AS_LIGAND_LONG);
 
     fprintf(f, "\n\n\033[1mOptional pocket detection parameters\033[0m (default parameters)           \n\
 \t-%c --%s (float)\t\t: Minimum radius of an alpha-sphere.\t(%.1f)\n", M_PAR_MIN_ASHAPE_SIZE, M_PAR_LONG_MIN_ASHAPE_SIZE, M_MAX_ASHAPE_SIZE_DEFAULT);
@@ -749,7 +811,10 @@ void print_pocket_usage(FILE *f) {
 \t\t\t\t\t\t  an a-sphere to be considered as apolar.   (%d)\n", M_PAR_MIN_APOL_NEIGH, M_PAR_LONG_MIN_APOL_NEIGH, M_MIN_APOL_NEIGH_DEFAULT);
     fprintf(f, "\t-%c --%s (integer)\t: Number of Monte-Carlo iteration for the      \n\
 \t\t\t\t\t\t  calculation of each pocket volume.(%d)\n", M_PAR_MC_ITER, M_PAR_LONG_MC_ITER, M_MC_ITER);
-
+fprintf(f, "\t-%c --%s (char)\t\t\t: Name of the chains to be deleted before pocket detection,      \n\
+\t\t\t\t\t\t  able to delete up to (%d) chains (ie : -c A,B,E)\n", M_PAR_DROP_CHAINS, M_PAR_DROP_CHAINS_LONG, M_MAX_CHAINS_DELETE);
+fprintf(f, "\t-%c --%s (char)\t\t\t: Name of the chains to be kept before pocket detection,      \n\
+\t\t\t\t\t\t  able to keep up to (%d) chains (ie : -k A,B,C,E)\n", M_PAR_KEEP_CHAINS, M_PAR_KEEP_CHAINS_LONG, M_MAX_CHAINS_DELETE);
     fprintf(f, "\n\033[1mFor more information: http://fpocket.sourceforge.net\033[0m\n");
 
 }

src/fpmain.c

@@ -61,7 +61,7 @@ int main(int argc, char *argv[])
                     for (i = 0 ; i < params->npdb ; i++) {
 
                                         printf("> Protein %d / %d : %s", i, params->npdb,
-                                                                                                           params->pdb_lst[i]) ;
+                                                                        params->pdb_lst[i]) ;
                                         if(i == params->npdb - 1) fprintf(stdout, "\n") ;
                                         else fprintf(stdout, "\r") ;
                                         fflush(stdout) ;

src/voronoi.c

@@ -93,10 +93,12 @@ s_lst_vvertice* load_vvertices_DEPRECATED(s_pdb *pdb, int min_apol_neigh, float
     FILE *fvoro = fopen(tmpn1, "w+");
     FILE *ftmp = fopen(tmpn2, "w");
 
+    
     if (fvoro != NULL) {
         lvvert = (s_lst_vvertice *) my_malloc(sizeof (s_lst_vvertice));
         lvvert->h_tr = NULL;
         /* Loop a first time to get out how many heavy atoms are in the file */
+        
         for (i = 0; i < pdb->natoms; i++) {
             ca = (pdb->latoms) + i;
             if (strcmp(ca->symbol, "H") != 0) {
@@ -181,7 +183,6 @@ s_lst_vvertice* load_vvertices(s_pdb *pdb, int min_apol_neigh, float asph_min_si
 
     pid_t pid = getpid();
 
-
     sprintf(tmpn1, "/tmp/qvoro_in_fpocket_%d.dat", pid);
     sprintf(tmpn2, "/tmp/qvoro_out_fpocket_%d.dat", pid);
 //    fprintf(stdout, tmpn1);
@@ -601,7 +602,9 @@ void fill_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, in
                     else v->type = M_POLAR_AS;
 
                     v->qhullId = i; /* Set index in the qhull file */
-                    if(pdb->n_xlig_atoms>0) v->resid=1;
+                    if(pdb->n_xlig_atoms>0) {
+                        v->resid=1;
+                    }
                     
                     else v->resid = -1; /* Initialize internal index */
 
@@ -1080,9 +1083,12 @@ float testVvertice(float xyz[3], int curNbIdx[4], s_atm *atoms,
                     printf("here %d\n",dist(xlig_x,xlig_y,xlig_z, x,y,z));*/
                     if(dist(xlig_x, xlig_y, xlig_z, x,y,z)<=(distVatom1)){
                         /*TODO, debug why not working here*/
+                        //printf("xl:%.2f|yl:%.2f|zl:%.2f\t x:%.2f|y:%.2f|z:%.2f\n", xlig_x, xlig_y, xlig_z,x,y,z);
+                        //printf("here %f\t %f\n",dist(xlig_x,xlig_y,xlig_z, x,y,z),distVatom1);
                         /*TODO: add manual clustering for explicit pockets*/
                         return distVatom1;
                     };
+                    
                 }
                 return(-1.0);
             }

tests/reference_output/2P0R_mod_out/2P0R_mod.pml

@@ -0,0 +1,15 @@
+from pymol import cmd,stored
+load 2P0R_mod_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))

tests/reference_output/2P0R_mod_out/2P0R_mod.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 2P0R_mod_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 2P0R_mod_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

tests/reference_output/2P0R_mod_out/2P0R_mod_PYMOL.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+pymol 2P0R_mod.pml

tests/reference_output/2P0R_mod_out/2P0R_mod_VMD.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+vmd 2P0R_mod_out.pdb -e 2P0R_mod.tcl

tests/reference_output/2P0R_mod_out/2P0R_mod_info.txt

@@ -0,0 +1,21 @@
+Pocket 1 :
+	Score : 	0.156
+	Druggability Score : 	0.421
+	Number of Alpha Spheres : 	100
+	Total SASA : 	195.984
+	Polar SASA : 	87.297
+	Apolar SASA : 	108.687
+	Volume : 	1933.883
+	Mean local hydrophobic density : 	19.643
+	Mean alpha sphere radius :	4.224
+	Mean alp. sph. solvent access : 	0.508
+	Apolar alpha sphere proportion : 	0.280
+	Hydrophobicity score:	12.962
+	Volume score: 	 3.462
+	Polarity score:	 15
+	Charge score :	 -2
+	Proportion of polar atoms: 	46.970
+	Alpha sphere density : 	7.636
+	Cent. of mass - Alpha Sphere max dist: 	20.089
+	Flexibility : 	0.000
+

tests/reference_output/2P0R_mod_out/2P0R_mod_pockets.pqr

@@ -0,0 +1,105 @@
+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      -7.927  25.710  29.491    0.00     5.17
+ATOM      2    O STP     1      -0.944  21.557  24.346    0.00     3.44
+ATOM      3    C STP     1      -0.390  21.119  25.163    0.00     3.64
+ATOM      4    C STP     1      -0.497  19.750  26.137    0.00     3.65
+ATOM      5    O STP     1      -1.505  21.560  24.468    0.00     3.47
+ATOM      6    O STP     1      -7.006  23.099  31.939    0.00     4.34
+ATOM      7    C STP     1      -2.421  19.598  26.681    0.00     4.15
+ATOM      8    O STP     1      -1.904  20.950  25.868    0.00     3.94
+ATOM      9    O STP     1      -1.138  19.994  26.698    0.00     4.16
+ATOM     10    O STP     1      -0.610  21.340  26.848    0.00     3.56
+ATOM     11    O STP     1      -1.105  20.703  26.217    0.00     4.05
+ATOM     12    C STP     1      -2.450  19.593  26.684    0.00     4.15
+ATOM     13    C STP     1      -0.703  20.660  31.637    0.00     3.51
+ATOM     14    O STP     1      -0.812  20.704  31.050    0.00     3.49
+ATOM     15    C STP     1      -0.219  20.522  28.381    0.00     3.59
+ATOM     16    O STP     1      -0.246  20.464  28.365    0.00     3.61
+ATOM     17    O STP     1       2.253  18.734  33.805    0.00     3.49
+ATOM     18    O STP     1       2.716  18.560  34.058    0.00     3.45
+ATOM     19    O STP     1      -2.017  21.009  25.831    0.00     3.92
+ATOM     20    C STP     1      -7.684  25.074  29.391    0.00     4.87
+ATOM     21    C STP     1      -5.738  21.726  22.846    0.00     4.15
+ATOM     22    O STP     1      -4.802  20.822  26.086    0.00     4.22
+ATOM     23    O STP     1      -3.784  20.874  25.890    0.00     3.98
+ATOM     24    O STP     1      -2.002  21.755  24.422    0.00     3.47
+ATOM     25    O STP     1      -3.770  21.486  26.150    0.00     3.48
+ATOM     26    O STP     1      -3.053  21.034  25.802    0.00     3.86
+ATOM     27    O STP     1      -2.286  21.303  25.452    0.00     3.76
+ATOM     28    C STP     1      -2.467  19.582  26.696    0.00     4.15
+ATOM     29    C STP     1      -3.065  18.013  27.593    0.00     4.08
+ATOM     30    O STP     1      -4.069  15.575  26.940    0.00     3.56
+ATOM     31    O STP     1      -3.587  13.987  38.073    0.00     4.16
+ATOM     32    O STP     1      -3.704  14.174  38.166    0.00     4.28
+ATOM     33    O STP     1      -5.656  15.984  36.278    0.00     4.39
+ATOM     34    O STP     1      -5.504  16.518  38.204    0.00     5.63
+ATOM     35    C STP     1      -6.227  18.398  36.193    0.00     6.02
+ATOM     36    O STP     1      -3.847  18.514  36.288    0.00     4.85
+ATOM     37    O STP     1      -5.712  16.109  39.065    0.00     5.80
+ATOM     38    O STP     1      -3.819  14.133  38.275    0.00     4.27
+ATOM     39    O STP     1      -4.642  15.555  38.606    0.00     5.18
+ATOM     40    O STP     1      -4.979  16.043  38.743    0.00     5.59
+ATOM     41    O STP     1      -4.914  16.042  38.749    0.00     5.56
+ATOM     42    O STP     1      -4.641  18.226  28.432    0.00     5.06
+ATOM     43    C STP     1      -3.129  18.059  27.644    0.00     4.13
+ATOM     44    O STP     1      -2.825  18.832  27.555    0.00     4.37
+ATOM     45    C STP     1      -3.030  18.141  27.600    0.00     4.12
+ATOM     46    O STP     1      -1.764  19.741  31.334    0.00     3.95
+ATOM     47    O STP     1      -1.278  19.903  31.356    0.00     3.93
+ATOM     48    O STP     1      -1.286  19.922  31.268    0.00     3.93
+ATOM     49    O STP     1      -0.653  19.833  28.635    0.00     3.77
+ATOM     50    O STP     1      -1.291  18.558  33.444    0.00     4.21
+ATOM     51    O STP     1       0.141  18.540  33.212    0.00     3.88
+ATOM     52    O STP     1      -0.337  17.740  33.506    0.00     3.75
+ATOM     53    O STP     1      -0.856  18.760  27.475    0.00     3.57
+ATOM     54    O STP     1      -2.728  14.181  37.978    0.00     3.82
+ATOM     55    O STP     1      -0.221  17.529  33.664    0.00     3.59
+ATOM     56    C STP     1      -3.437  18.918  36.407    0.00     4.47
+ATOM     57    O STP     1      -2.278  19.673  36.184    0.00     3.62
+ATOM     58    C STP     1      -4.398  20.219  36.733    0.00     4.08
+ATOM     59    O STP     1      -1.215  19.866  26.768    0.00     4.18
+ATOM     60    C STP     1      -2.296  19.575  26.726    0.00     4.15
+ATOM     61    C STP     1      -0.463  19.697  26.108    0.00     3.61
+ATOM     62    O STP     1      -0.646  18.417  26.693    0.00     3.44
+ATOM     63    O STP     1      -1.504  19.313  27.220    0.00     4.28
+ATOM     64    O STP     1      -1.799  19.199  27.242    0.00     4.28
+ATOM     65    O STP     1      -1.195  18.862  27.071    0.00     3.93
+ATOM     66    C STP     1      -1.255  18.277  26.909    0.00     3.58
+ATOM     67    O STP     1      -1.374  19.085  27.170    0.00     4.12
+ATOM     68    C STP     1      -1.665  18.991  27.195    0.00     4.13
+ATOM     69    C STP     1       0.538  20.926  24.251    0.00     3.40
+ATOM     70    O STP     1      -4.253  16.196  38.650    0.00     5.21
+ATOM     71    C STP     1      -0.660  17.674  41.151    0.00     3.82
+ATOM     72    O STP     1      -0.665  17.381  41.718    0.00     4.21
+ATOM     73    O STP     1      -2.320  14.385  37.937    0.00     3.72
+ATOM     74    O STP     1      -3.527  17.299  37.574    0.00     4.60
+ATOM     75    O STP     1       1.896  18.908  33.762    0.00     3.44
+ATOM     76    C STP     1      -0.502  20.722  31.885    0.00     3.42
+ATOM     77    O STP     1      -0.828  18.820  33.297    0.00     4.14
+ATOM     78    O STP     1      -0.715  19.279  32.645    0.00     3.96
+ATOM     79    O STP     1      -0.068  18.700  33.204    0.00     3.95
+ATOM     80    O STP     1       2.761  18.546  34.093    0.00     3.44
+ATOM     81    O STP     1       2.783  18.567  34.049    0.00     3.45
+ATOM     82    C STP     1      -4.983  18.148  28.557    0.00     5.25
+ATOM     83    C STP     1      -6.697  18.281  32.723    0.00     6.16
+ATOM     84    O STP     1      -6.877  15.226  26.592    0.00     3.64
+ATOM     85    O STP     1      -5.571  16.002  26.870    0.00     3.92
+ATOM     86    O STP     1      -4.952  18.143  28.746    0.00     5.22
+ATOM     87    C STP     1      -4.516  15.952  27.324    0.00     3.90
+ATOM     88    C STP     1      -6.455  17.186  32.808    0.00     5.30
+ATOM     89    C STP     1      -6.466  17.333  32.806    0.00     5.42
+ATOM     90    O STP     1      -5.335  18.346  31.496    0.00     5.69
+ATOM     91    O STP     1      -5.324  18.315  31.552    0.00     5.68
+ATOM     92    O STP     1      -3.887  15.796  31.076    0.00     3.86
+ATOM     93    C STP     1      -3.831  15.614  31.082    0.00     3.77
+ATOM     94    O STP     1      -5.263  16.341  42.194    0.00     5.12
+ATOM     95    O STP     1      -4.438  16.373  40.937    0.00     4.86
+ATOM     96    O STP     1      -4.111  16.415  42.058    0.00     4.74
+ATOM     97    O STP     1      -6.809  16.200  40.052    0.00     6.13
+ATOM     98    O STP     1      -6.390  16.221  39.684    0.00     6.00
+ATOM     99    O STP     1       2.836  18.727  33.815    0.00     3.49
+ATOM    100    O STP     1       2.888  18.613  33.980    0.00     3.47
+TER
+END

tests/reference_output/2P0R_mod_out/pockets/pocket1_atm.pdb

@@ -0,0 +1,88 @@
+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                      : 0.1562
+HEADER 1  - Drug Score                        : 0.4209
+HEADER 2  - Number of alpha spheres           :   100
+HEADER 3  - Mean alpha-sphere radius          : 4.2242
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5076
+HEADER 5  - Mean B-factor of pocket residues  : 0.0000
+HEADER 6  - Hydrophobicity Score              : 12.9615
+HEADER 7  - Polarity Score                    :    15
+HEADER 8  - Amino Acid based volume Score     : 3.4615
+HEADER 9  - Pocket volume (Monte Carlo)       : 1933.8832
+HEADER 10  -Pocket volume (convex hull)       : 700.1219
+HEADER 11 - Charge Score                      :    -2
+HEADER 12 - Local hydrophobic density Score   : 19.6429
+HEADER 13 - Number of apolar alpha sphere     :    28
+HEADER 14 - Proportion of apolar alpha sphere : 0.2800
+ATOM   1378   CA GLY A 190      -3.069  24.572  30.848  0.00  0.00           C 0
+ATOM   1385   CB SER A 191      -3.958  24.958  26.264  0.00  0.00           C 0
+ATOM   1407  OE1 GLU A 194      -3.709  28.683  29.816  0.00  0.00           O 0
+ATOM   1381    N SER A 191      -2.905  25.010  28.479  0.00  0.00           N 0
+ATOM   1387    N ALA A 192      -0.717  24.707  25.707  0.00  0.00           N 0
+ATOM   1708  CD1 PHE A 233      -1.372  18.506  22.820  0.00  0.00           C 0
+ATOM   2514  OE2 GLU A 332      -1.745  20.996  21.050  0.94  2.14           O 0
+ATOM   1391   CB ALA A 192       1.169  24.266  24.193  0.00  0.00           C 0
+ATOM   1875   CB ALA A 255       2.918  20.919  26.678  0.00  0.00           C 0
+ATOM   1871    N ALA A 255       2.705  18.589  27.448  0.00  0.00           N 0
+ATOM   1872   CA ALA A 255       3.134  19.444  26.343  0.00  0.00           C 0
+ATOM   1710  CE1 PHE A 233      -2.716  18.891  22.605  0.00  0.00           C 0
+ATOM   1375    C GLY A 189      -2.873  23.712  33.124  0.00  0.00           C 0
+ATOM   1377    N GLY A 190      -2.688  23.547  31.816  0.00  0.00           N 0
+ATOM   1376    O GLY A 189      -3.355  24.744  33.620  0.59  1.07           O 0
+ATOM   1380    O GLY A 190      -2.803  22.883  29.185  0.00  0.00           O 0
+ATOM   1709  CD2 PHE A 233      -2.136  16.521  23.915  0.00  0.00           C 0
+ATOM    629   CB TRP A  98       1.005  23.879  28.745  0.00  0.00           C 0
+ATOM   1712   CZ PHE A 233      -3.744  18.091  23.041  0.00  0.00           C 0
+ATOM    624   SG CYS A  97       2.577  20.007  30.576  0.00  0.00           S 0
+ATOM   1374   CA GLY A 189      -2.458  22.559  34.008  0.00  0.00           C 0
+ATOM    631  CD1 TRP A  98       0.531  23.921  31.248  0.00  0.00           C 0
+ATOM    608   CA GLY A  95       2.503  21.248  36.208  0.00  0.00           C 0
+ATOM   2906  NE2 GLN B  62       0.939  18.225  36.994  0.00  0.00           N 0
+ATOM   1786  OE2 GLU A 243       2.492  15.584  32.332  0.00  0.00           O 0
+ATOM   1784   CD GLU A 243       2.694  15.158  33.499  0.00  0.00           C 0
+ATOM   1382   CA SER A 191      -2.701  24.663  27.080  0.00  0.00           C 0
+ATOM   1379    C GLY A 190      -2.921  24.081  29.426  0.00  0.00           C 0
+ATOM   1386   OG SER A 191      -3.724  24.727  24.886  0.57  6.43           O 0
+ATOM   1399  CD1 ILE A 193      -4.273  25.106  20.935  0.00  0.00           C 0
+ATOM   1711  CE2 PHE A 233      -3.457  16.897  23.692  0.00  0.00           C 0
+ATOM   1859    C GLY A 253      -0.072  15.654  29.040  0.00  0.00           C 0
+ATOM   1858   CA GLY A 253      -1.116  14.599  28.671  0.00  0.00           C 0
+ATOM   1716    O ILE A 234      -1.778  13.371  25.339  0.00  0.00           O 0
+ATOM   1729    N THR A 236      -4.945  12.140  26.625  0.51  2.19           N 0
+ATOM   2873    C GLU B  59      -0.834  12.124  40.583  0.00  0.00           C 0
+ATOM   1777   OG SER A 242      -2.074  14.501  34.227  0.55  6.43           O 0
+ATOM   1776   CB SER A 242      -2.940  13.400  34.001  0.00  0.00           C 0
+ATOM   1756    O ALA A 239      -5.685  11.711  35.287  0.52  7.50           O 0
+ATOM   2874    O GLU B  59      -0.742  13.219  41.098  0.45  8.57           O 0
+ATOM   1757   CB ALA A 239      -8.655  12.980  35.171  0.00  0.00           C 0
+ATOM   1371   CE LYS A 188      -2.628  20.847  40.357  0.00  0.00           C 0
+ATOM   2871    N GLU B  59      -2.827  11.860  41.757  0.00  0.00           N 0
+ATOM   1860    O GLY A 253      -0.215  16.355  30.028  0.00  0.00           O 0
+ATOM   1861    N HIS A 254       0.956  15.779  28.210  0.00  0.00           N 0
+ATOM   2880    N ARG B  60      -0.178  11.767  39.486  0.41  4.37           N 0
+ATOM   1783   CG GLU A 243       1.575  14.473  34.258  0.00  0.00           C 0
+ATOM   1369   CG LYS A 188      -1.361  22.226  38.580  0.00  0.00           C 0
+ATOM   1373    N GLY A 189      -1.500  23.000  34.991  0.00  0.00           N 0
+ATOM   1367    O LYS A 188      -3.008  24.033  36.303  0.50  3.21           O 0
+ATOM   1707   CG PHE A 233      -1.075  17.309  23.466  0.00  0.00           C 0
+ATOM   1706   CB PHE A 233       0.351  16.918  23.763  0.00  0.00           C 0
+ATOM   2513  OE1 GLU A 332       0.238  22.000  21.040  0.69  2.14           O 0
+ATOM   2905  OE1 GLN B  62       0.920  16.211  37.999  0.65  3.21           O 0
+ATOM   2903   CG GLN B  62       2.406  17.910  38.889  0.00  0.00           C 0
+ATOM   2904   CD GLN B  62       1.349  17.373  37.919  0.00  0.00           C 0
+ATOM    610    O GLY A  95       1.251  22.223  34.411  0.00  0.00           O 0
+ATOM   1785  OE1 GLU A 243       3.783  15.261  34.092  0.00  0.00           O 0
+ATOM   1735  CG2 THR A 236      -6.115  13.099  29.447  0.00  0.00           C 0
+ATOM   1727  OD1 ASP A 235      -5.761  14.755  23.158  0.70  4.29           O 0
+ATOM   1732    O THR A 236      -7.509  11.799  27.646  0.44  5.36           O 0
+ATOM   1754   CA ALA A 239      -7.769  12.233  34.170  0.00  0.00           C 0
+ATOM   2868    O SER B  58      -2.600  12.325  43.922  0.61  4.29           O 0
+ATOM   1372   NZ LYS A 188      -3.438  21.085  41.590  0.00  0.00           N 0
+ATOM   2869   CB SER B  58      -5.491  11.456  43.707  0.00  0.00           C 0
+ATOM    585  NE2 GLN A  91       5.950  20.196  34.395  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_mod_out/pockets/pocket1_vert.pqr

@@ -0,0 +1,122 @@
+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                      : 0.1562
+HEADER 1  - Drug Score                        : 0.4209
+HEADER 2  - Number of V. Vertices             :   100
+HEADER 3  - Mean alpha-sphere radius          : 4.2242
+HEADER 4  - Mean alpha-sphere SA              : 0.5076
+HEADER 5  - Mean B-factor                     : 0.0000
+HEADER 6  - Hydrophobicity Score              : 12.9615
+HEADER 7  - Polarity Score                    :    15
+HEADER 8  - Volume Score                      : 3.4615
+HEADER 9  - Real volume (approximation)       : 1933.8832
+HEADER 10 - Charge Score                      :    -2
+HEADER 11 - Local hydrophobic density Score   : 19.6429
+HEADER 12 - Number of apolar alpha sphere     :    28
+HEADER 13 - Proportion of apolar alpha sphere : 0.2800
+ATOM      1    O STP     1      -7.927  25.710  29.491    0.00     5.17
+ATOM      2    O STP     1      -0.944  21.557  24.346    0.00     3.44
+ATOM      3    C STP     1      -0.390  21.119  25.163    0.00     3.64
+ATOM      4    C STP     1      -0.497  19.750  26.137    0.00     3.65
+ATOM      5    O STP     1      -1.505  21.560  24.468    0.00     3.47
+ATOM      6    O STP     1      -7.006  23.099  31.939    0.00     4.34
+ATOM      7    C STP     1      -2.421  19.598  26.681    0.00     4.15
+ATOM      8    O STP     1      -1.904  20.950  25.868    0.00     3.94
+ATOM      9    O STP     1      -1.138  19.994  26.698    0.00     4.16
+ATOM     10    O STP     1      -0.610  21.340  26.848    0.00     3.56
+ATOM     11    O STP     1      -1.105  20.703  26.217    0.00     4.05
+ATOM     12    C STP     1      -2.450  19.593  26.684    0.00     4.15
+ATOM     13    C STP     1      -0.703  20.660  31.637    0.00     3.51
+ATOM     14    O STP     1      -0.812  20.704  31.050    0.00     3.49
+ATOM     15    C STP     1      -0.219  20.522  28.381    0.00     3.59
+ATOM     16    O STP     1      -0.246  20.464  28.365    0.00     3.61
+ATOM     17    O STP     1       2.253  18.734  33.805    0.00     3.49
+ATOM     18    O STP     1       2.716  18.560  34.058    0.00     3.45
+ATOM     19    O STP     1      -2.017  21.009  25.831    0.00     3.92
+ATOM     20    C STP     1      -7.684  25.074  29.391    0.00     4.87
+ATOM     21    C STP     1      -5.738  21.726  22.846    0.00     4.15
+ATOM     22    O STP     1      -4.802  20.822  26.086    0.00     4.22
+ATOM     23    O STP     1      -3.784  20.874  25.890    0.00     3.98
+ATOM     24    O STP     1      -2.002  21.755  24.422    0.00     3.47
+ATOM     25    O STP     1      -3.770  21.486  26.150    0.00     3.48
+ATOM     26    O STP     1      -3.053  21.034  25.802    0.00     3.86
+ATOM     27    O STP     1      -2.286  21.303  25.452    0.00     3.76
+ATOM     28    C STP     1      -2.467  19.582  26.696    0.00     4.15
+ATOM     29    C STP     1      -3.065  18.013  27.593    0.00     4.08
+ATOM     30    O STP     1      -4.069  15.575  26.940    0.00     3.56
+ATOM     31    O STP     1      -3.587  13.987  38.073    0.00     4.16
+ATOM     32    O STP     1      -3.704  14.174  38.166    0.00     4.28
+ATOM     33    O STP     1      -5.656  15.984  36.278    0.00     4.39
+ATOM     34    O STP     1      -5.504  16.518  38.204    0.00     5.63
+ATOM     35    C STP     1      -6.227  18.398  36.193    0.00     6.02
+ATOM     36    O STP     1      -3.847  18.514  36.288    0.00     4.85
+ATOM     37    O STP     1      -5.712  16.109  39.065    0.00     5.80
+ATOM     38    O STP     1      -3.819  14.133  38.275    0.00     4.27
+ATOM     39    O STP     1      -4.642  15.555  38.606    0.00     5.18
+ATOM     40    O STP     1      -4.979  16.043  38.743    0.00     5.59
+ATOM     41    O STP     1      -4.914  16.042  38.749    0.00     5.56
+ATOM     42    O STP     1      -4.641  18.226  28.432    0.00     5.06
+ATOM     43    C STP     1      -3.129  18.059  27.644    0.00     4.13
+ATOM     44    O STP     1      -2.825  18.832  27.555    0.00     4.37
+ATOM     45    C STP     1      -3.030  18.141  27.600    0.00     4.12
+ATOM     46    O STP     1      -1.764  19.741  31.334    0.00     3.95
+ATOM     47    O STP     1      -1.278  19.903  31.356    0.00     3.93
+ATOM     48    O STP     1      -1.286  19.922  31.268    0.00     3.93
+ATOM     49    O STP     1      -0.653  19.833  28.635    0.00     3.77
+ATOM     50    O STP     1      -1.291  18.558  33.444    0.00     4.21
+ATOM     51    O STP     1       0.141  18.540  33.212    0.00     3.88
+ATOM     52    O STP     1      -0.337  17.740  33.506    0.00     3.75
+ATOM     53    O STP     1      -0.856  18.760  27.475    0.00     3.57
+ATOM     54    O STP     1      -2.728  14.181  37.978    0.00     3.82
+ATOM     55    O STP     1      -0.221  17.529  33.664    0.00     3.59
+ATOM     56    C STP     1      -3.437  18.918  36.407    0.00     4.47
+ATOM     57    O STP     1      -2.278  19.673  36.184    0.00     3.62
+ATOM     58    C STP     1      -4.398  20.219  36.733    0.00     4.08
+ATOM     59    O STP     1      -1.215  19.866  26.768    0.00     4.18
+ATOM     60    C STP     1      -2.296  19.575  26.726    0.00     4.15
+ATOM     61    C STP     1      -0.463  19.697  26.108    0.00     3.61
+ATOM     62    O STP     1      -0.646  18.417  26.693    0.00     3.44
+ATOM     63    O STP     1      -1.504  19.313  27.220    0.00     4.28
+ATOM     64    O STP     1      -1.799  19.199  27.242    0.00     4.28
+ATOM     65    O STP     1      -1.195  18.862  27.071    0.00     3.93
+ATOM     66    C STP     1      -1.255  18.277  26.909    0.00     3.58
+ATOM     67    O STP     1      -1.374  19.085  27.170    0.00     4.12
+ATOM     68    C STP     1      -1.665  18.991  27.195    0.00     4.13
+ATOM     69    C STP     1       0.538  20.926  24.251    0.00     3.40
+ATOM     70    O STP     1      -4.253  16.196  38.650    0.00     5.21
+ATOM     71    C STP     1      -0.660  17.674  41.151    0.00     3.82
+ATOM     72    O STP     1      -0.665  17.381  41.718    0.00     4.21
+ATOM     73    O STP     1      -2.320  14.385  37.937    0.00     3.72
+ATOM     74    O STP     1      -3.527  17.299  37.574    0.00     4.60
+ATOM     75    O STP     1       1.896  18.908  33.762    0.00     3.44
+ATOM     76    C STP     1      -0.502  20.722  31.885    0.00     3.42
+ATOM     77    O STP     1      -0.828  18.820  33.297    0.00     4.14
+ATOM     78    O STP     1      -0.715  19.279  32.645    0.00     3.96
+ATOM     79    O STP     1      -0.068  18.700  33.204    0.00     3.95
+ATOM     80    O STP     1       2.761  18.546  34.093    0.00     3.44
+ATOM     81    O STP     1       2.783  18.567  34.049    0.00     3.45
+ATOM     82    C STP     1      -4.983  18.148  28.557    0.00     5.25
+ATOM     83    C STP     1      -6.697  18.281  32.723    0.00     6.16
+ATOM     84    O STP     1      -6.877  15.226  26.592    0.00     3.64
+ATOM     85    O STP     1      -5.571  16.002  26.870    0.00     3.92
+ATOM     86    O STP     1      -4.952  18.143  28.746    0.00     5.22
+ATOM     87    C STP     1      -4.516  15.952  27.324    0.00     3.90
+ATOM     88    C STP     1      -6.455  17.186  32.808    0.00     5.30
+ATOM     89    C STP     1      -6.466  17.333  32.806    0.00     5.42
+ATOM     90    O STP     1      -5.335  18.346  31.496    0.00     5.69
+ATOM     91    O STP     1      -5.324  18.315  31.552    0.00     5.68
+ATOM     92    O STP     1      -3.887  15.796  31.076    0.00     3.86
+ATOM     93    C STP     1      -3.831  15.614  31.082    0.00     3.77
+ATOM     94    O STP     1      -5.263  16.341  42.194    0.00     5.12
+ATOM     95    O STP     1      -4.438  16.373  40.937    0.00     4.86
+ATOM     96    O STP     1      -4.111  16.415  42.058    0.00     4.74
+ATOM     97    O STP     1      -6.809  16.200  40.052    0.00     6.13
+ATOM     98    O STP     1      -6.390  16.221  39.684    0.00     6.00
+ATOM     99    O STP     1       2.836  18.727  33.815    0.00     3.49
+ATOM    100    O STP     1       2.888  18.613  33.980    0.00     3.47
+TER
+END

tests/reference_output/2P0R_out/2P0R.pml

@@ -0,0 +1,15 @@
+from pymol import cmd,stored
+load 2P0R_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))

tests/reference_output/2P0R_out/2P0R.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 2P0R_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 2P0R_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

tests/reference_output/2P0R_out/2P0R_PYMOL.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+pymol 2P0R.pml

tests/reference_output/2P0R_out/2P0R_VMD.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+vmd 2P0R_out.pdb -e 2P0R.tcl

tests/reference_output/2P0R_out/2P0R_info.txt

@@ -0,0 +1,924 @@
+Pocket 1 :
+	Score : 	0.358
+	Druggability Score : 	0.054
+	Number of Alpha Spheres : 	46
+	Total SASA : 	56.959
+	Polar SASA : 	36.430
+	Apolar SASA : 	20.530
+	Volume : 	386.650
+	Mean local hydrophobic density : 	14.625
+	Mean alpha sphere radius :	3.873
+	Mean alp. sph. solvent access : 	0.467
+	Apolar alpha sphere proportion : 	0.348
+	Hydrophobicity score:	10.143
+	Volume score: 	 3.429
+	Polarity score:	 7
+	Charge score :	 0
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	3.695
+	Cent. of mass - Alpha Sphere max dist: 	8.946
+	Flexibility : 	0.704
+
+Pocket 2 :
+	Score : 	0.322
+	Druggability Score : 	0.023
+	Number of Alpha Spheres : 	82
+	Total SASA : 	228.206
+	Polar SASA : 	123.142
+	Apolar SASA : 	105.064
+	Volume : 	933.613
+	Mean local hydrophobic density : 	9.059
+	Mean alpha sphere radius :	4.049
+	Mean alp. sph. solvent access : 	0.543
+	Apolar alpha sphere proportion : 	0.207
+	Hydrophobicity score:	26.800
+	Volume score: 	 4.600
+	Polarity score:	 10
+	Charge score :	 2
+	Proportion of polar atoms: 	49.020
+	Alpha sphere density : 	7.507
+	Cent. of mass - Alpha Sphere max dist: 	20.590
+	Flexibility : 	0.533
+
+Pocket 3 :
+	Score : 	0.308
+	Druggability Score : 	0.014
+	Number of Alpha Spheres : 	71
+	Total SASA : 	175.232
+	Polar SASA : 	94.974
+	Apolar SASA : 	80.258
+	Volume : 	801.518
+	Mean local hydrophobic density : 	14.000
+	Mean alpha sphere radius :	3.962
+	Mean alp. sph. solvent access : 	0.466
+	Apolar alpha sphere proportion : 	0.225
+	Hydrophobicity score:	25.316
+	Volume score: 	 4.316
+	Polarity score:	 11
+	Charge score :	 1
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	6.192
+	Cent. of mass - Alpha Sphere max dist: 	15.864
+	Flexibility : 	0.538
+
+Pocket 4 :
+	Score : 	0.236
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	46
+	Total SASA : 	59.367
+	Polar SASA : 	27.969
+	Apolar SASA : 	31.398
+	Volume : 	273.478
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	4.070
+	Mean alp. sph. solvent access : 	0.587
+	Apolar alpha sphere proportion : 	0.043
+	Hydrophobicity score:	35.667
+	Volume score: 	 5.500
+	Polarity score:	 3
+	Charge score :	 1
+	Proportion of polar atoms: 	46.667
+	Alpha sphere density : 	2.572
+	Cent. of mass - Alpha Sphere max dist: 	6.347
+	Flexibility : 	0.466
+
+Pocket 5 :
+	Score : 	0.181
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	18
+	Total SASA : 	86.033
+	Polar SASA : 	58.257
+	Apolar SASA : 	27.775
+	Volume : 	419.163
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	3.979
+	Mean alp. sph. solvent access : 	0.692
+	Apolar alpha sphere proportion : 	0.111
+	Hydrophobicity score:	0.300
+	Volume score: 	 3.100
+	Polarity score:	 7
+	Charge score :	 -2
+	Proportion of polar atoms: 	65.000
+	Alpha sphere density : 	4.911
+	Cent. of mass - Alpha Sphere max dist: 	10.576
+	Flexibility : 	0.580
+
+Pocket 6 :
+	Score : 	0.152
+	Druggability Score : 	0.006
+	Number of Alpha Spheres : 	27
+	Total SASA : 	70.207
+	Polar SASA : 	30.355
+	Apolar SASA : 	39.852
+	Volume : 	252.148
+	Mean local hydrophobic density : 	6.667
+	Mean alpha sphere radius :	3.668
+	Mean alp. sph. solvent access : 	0.402
+	Apolar alpha sphere proportion : 	0.333
+	Hydrophobicity score:	49.333
+	Volume score: 	 4.778
+	Polarity score:	 5
+	Charge score :	 1
+	Proportion of polar atoms: 	40.000
+	Alpha sphere density : 	3.400
+	Cent. of mass - Alpha Sphere max dist: 	8.144
+	Flexibility : 	0.719
+
+Pocket 7 :
+	Score : 	0.151
+	Druggability Score : 	0.348
+	Number of Alpha Spheres : 	59
+	Total SASA : 	179.558
+	Polar SASA : 	88.590
+	Apolar SASA : 	90.968
+	Volume : 	645.087
+	Mean local hydrophobic density : 	25.000
+	Mean alpha sphere radius :	3.965
+	Mean alp. sph. solvent access : 	0.500
+	Apolar alpha sphere proportion : 	0.475
+	Hydrophobicity score:	23.067
+	Volume score: 	 4.200
+	Polarity score:	 9
+	Charge score :	 2
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	5.590
+	Cent. of mass - Alpha Sphere max dist: 	14.341
+	Flexibility : 	0.408
+
+Pocket 8 :
+	Score : 	0.138
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	42
+	Total SASA : 	132.756
+	Polar SASA : 	90.489
+	Apolar SASA : 	42.267
+	Volume : 	477.150
+	Mean local hydrophobic density : 	2.800
+	Mean alpha sphere radius :	3.936
+	Mean alp. sph. solvent access : 	0.547
+	Apolar alpha sphere proportion : 	0.119
+	Hydrophobicity score:	4.500
+	Volume score: 	 4.429
+	Polarity score:	 10
+	Charge score :	 -2
+	Proportion of polar atoms: 	55.172
+	Alpha sphere density : 	4.899
+	Cent. of mass - Alpha Sphere max dist: 	14.694
+	Flexibility : 	0.915
+
+Pocket 9 :
+	Score : 	0.129
+	Druggability Score : 	0.006
+	Number of Alpha Spheres : 	18
+	Total SASA : 	51.800
+	Polar SASA : 	20.402
+	Apolar SASA : 	31.398
+	Volume : 	216.365
+	Mean local hydrophobic density : 	10.000
+	Mean alpha sphere radius :	3.909
+	Mean alp. sph. solvent access : 	0.554
+	Apolar alpha sphere proportion : 	0.611
+	Hydrophobicity score:	48.500
+	Volume score: 	 4.750
+	Polarity score:	 2
+	Charge score :	 -1
+	Proportion of polar atoms: 	29.412
+	Alpha sphere density : 	2.994
+	Cent. of mass - Alpha Sphere max dist: 	6.481
+	Flexibility : 	0.699
+
+Pocket 10 :
+	Score : 	0.097
+	Druggability Score : 	0.020
+	Number of Alpha Spheres : 	33
+	Total SASA : 	70.487
+	Polar SASA : 	36.673
+	Apolar SASA : 	33.814
+	Volume : 	241.612
+	Mean local hydrophobic density : 	17.000
+	Mean alpha sphere radius :	4.036
+	Mean alp. sph. solvent access : 	0.559
+	Apolar alpha sphere proportion : 	0.545
+	Hydrophobicity score:	39.667
+	Volume score: 	 4.667
+	Polarity score:	 3
+	Charge score :	 -2
+	Proportion of polar atoms: 	30.435
+	Alpha sphere density : 	2.440
+	Cent. of mass - Alpha Sphere max dist: 	5.602
+	Flexibility : 	0.482
+
+Pocket 11 :
+	Score : 	0.093
+	Druggability Score : 	0.002
+	Number of Alpha Spheres : 	59
+	Total SASA : 	233.274
+	Polar SASA : 	106.473
+	Apolar SASA : 	126.801
+	Volume : 	832.296
+	Mean local hydrophobic density : 	3.556
+	Mean alpha sphere radius :	4.073
+	Mean alp. sph. solvent access : 	0.681
+	Apolar alpha sphere proportion : 	0.153
+	Hydrophobicity score:	5.105
+	Volume score: 	 3.368
+	Polarity score:	 12
+	Charge score :	 -3
+	Proportion of polar atoms: 	47.059
+	Alpha sphere density : 	6.966
+	Cent. of mass - Alpha Sphere max dist: 	19.633
+	Flexibility : 	0.409
+
+Pocket 12 :
+	Score : 	0.087
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	25
+	Total SASA : 	52.033
+	Polar SASA : 	38.750
+	Apolar SASA : 	13.284
+	Volume : 	130.401
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.639
+	Mean alp. sph. solvent access : 	0.469
+	Apolar alpha sphere proportion : 	0.040
+	Hydrophobicity score:	23.200
+	Volume score: 	 4.400
+	Polarity score:	 5
+	Charge score :	 0
+	Proportion of polar atoms: 	52.632
+	Alpha sphere density : 	2.073
+	Cent. of mass - Alpha Sphere max dist: 	4.278
+	Flexibility : 	0.509
+
+Pocket 13 :
+	Score : 	0.082
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	21
+	Total SASA : 	38.749
+	Polar SASA : 	27.880
+	Apolar SASA : 	10.869
+	Volume : 	119.578
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	3.723
+	Mean alp. sph. solvent access : 	0.436
+	Apolar alpha sphere proportion : 	0.095
+	Hydrophobicity score:	12.444
+	Volume score: 	 4.556
+	Polarity score:	 7
+	Charge score :	 -1
+	Proportion of polar atoms: 	56.250
+	Alpha sphere density : 	1.703
+	Cent. of mass - Alpha Sphere max dist: 	3.731
+	Flexibility : 	0.378
+
+Pocket 14 :
+	Score : 	0.080
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	25
+	Total SASA : 	42.368
+	Polar SASA : 	29.084
+	Apolar SASA : 	13.284
+	Volume : 	118.943
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.698
+	Mean alp. sph. solvent access : 	0.488
+	Apolar alpha sphere proportion : 	0.000
+	Hydrophobicity score:	12.444
+	Volume score: 	 4.556
+	Polarity score:	 7
+	Charge score :	 -1
+	Proportion of polar atoms: 	68.750
+	Alpha sphere density : 	1.567
+	Cent. of mass - Alpha Sphere max dist: 	3.471
+	Flexibility : 	0.729
+
+Pocket 15 :
+	Score : 	0.077
+	Druggability Score : 	0.003
+	Number of Alpha Spheres : 	47
+	Total SASA : 	135.418
+	Polar SASA : 	78.659
+	Apolar SASA : 	56.759
+	Volume : 	508.468
+	Mean local hydrophobic density : 	8.000
+	Mean alpha sphere radius :	3.823
+	Mean alp. sph. solvent access : 	0.435
+	Apolar alpha sphere proportion : 	0.191
+	Hydrophobicity score:	10.929
+	Volume score: 	 4.214
+	Polarity score:	 8
+	Charge score :	 0
+	Proportion of polar atoms: 	48.387
+	Alpha sphere density : 	3.920
+	Cent. of mass - Alpha Sphere max dist: 	10.386
+	Flexibility : 	0.795
+
+Pocket 16 :
+	Score : 	0.074
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	20
+	Total SASA : 	63.026
+	Polar SASA : 	40.892
+	Apolar SASA : 	22.133
+	Volume : 	166.282
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	3.696
+	Mean alp. sph. solvent access : 	0.392
+	Apolar alpha sphere proportion : 	0.100
+	Hydrophobicity score:	9.000
+	Volume score: 	 2.900
+	Polarity score:	 5
+	Charge score :	 -1
+	Proportion of polar atoms: 	60.000
+	Alpha sphere density : 	2.748
+	Cent. of mass - Alpha Sphere max dist: 	5.469
+	Flexibility : 	0.476
+
+Pocket 17 :
+	Score : 	0.073
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	17
+	Total SASA : 	98.912
+	Polar SASA : 	71.137
+	Apolar SASA : 	27.775
+	Volume : 	320.310
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	3.874
+	Mean alp. sph. solvent access : 	0.623
+	Apolar alpha sphere proportion : 	0.118
+	Hydrophobicity score:	19.625
+	Volume score: 	 4.250
+	Polarity score:	 6
+	Charge score :	 1
+	Proportion of polar atoms: 	52.941
+	Alpha sphere density : 	4.470
+	Cent. of mass - Alpha Sphere max dist: 	10.659
+	Flexibility : 	0.614
+
+Pocket 18 :
+	Score : 	0.070
+	Druggability Score : 	0.039
+	Number of Alpha Spheres : 	25
+	Total SASA : 	78.181
+	Polar SASA : 	26.986
+	Apolar SASA : 	51.195
+	Volume : 	284.181
+	Mean local hydrophobic density : 	16.000
+	Mean alpha sphere radius :	3.875
+	Mean alp. sph. solvent access : 	0.568
+	Apolar alpha sphere proportion : 	0.680
+	Hydrophobicity score:	21.875
+	Volume score: 	 4.000
+	Polarity score:	 5
+	Charge score :	 0
+	Proportion of polar atoms: 	28.571
+	Alpha sphere density : 	3.012
+	Cent. of mass - Alpha Sphere max dist: 	7.183
+	Flexibility : 	0.775
+
+Pocket 19 :
+	Score : 	0.054
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	34
+	Total SASA : 	104.741
+	Polar SASA : 	74.550
+	Apolar SASA : 	30.191
+	Volume : 	370.999
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	4.001
+	Mean alp. sph. solvent access : 	0.533
+	Apolar alpha sphere proportion : 	0.000
+	Hydrophobicity score:	20.833
+	Volume score: 	 4.833
+	Polarity score:	 7
+	Charge score :	 1
+	Proportion of polar atoms: 	56.000
+	Alpha sphere density : 	3.323
+	Cent. of mass - Alpha Sphere max dist: 	7.437
+	Flexibility : 	0.801
+
+Pocket 20 :
+	Score : 	0.048
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	23
+	Total SASA : 	82.549
+	Polar SASA : 	55.981
+	Apolar SASA : 	26.568
+	Volume : 	279.142
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	4.020
+	Mean alp. sph. solvent access : 	0.698
+	Apolar alpha sphere proportion : 	0.087
+	Hydrophobicity score:	12.000
+	Volume score: 	 4.625
+	Polarity score:	 5
+	Charge score :	 3
+	Proportion of polar atoms: 	57.895
+	Alpha sphere density : 	3.081
+	Cent. of mass - Alpha Sphere max dist: 	6.744
+	Flexibility : 	0.509
+
+Pocket 21 :
+	Score : 	0.047
+	Druggability Score : 	0.014
+	Number of Alpha Spheres : 	27
+	Total SASA : 	113.874
+	Polar SASA : 	47.454
+	Apolar SASA : 	66.420
+	Volume : 	359.691
+	Mean local hydrophobic density : 	12.000
+	Mean alpha sphere radius :	3.928
+	Mean alp. sph. solvent access : 	0.660
+	Apolar alpha sphere proportion : 	0.481
+	Hydrophobicity score:	-9.375
+	Volume score: 	 3.875
+	Polarity score:	 5
+	Charge score :	 2
+	Proportion of polar atoms: 	47.826
+	Alpha sphere density : 	4.119
+	Cent. of mass - Alpha Sphere max dist: 	11.144
+	Flexibility : 	0.448
+
+Pocket 22 :
+	Score : 	0.044
+	Druggability Score : 	0.005
+	Number of Alpha Spheres : 	18
+	Total SASA : 	55.714
+	Polar SASA : 	19.485
+	Apolar SASA : 	36.229
+	Volume : 	231.692
+	Mean local hydrophobic density : 	12.000
+	Mean alpha sphere radius :	4.067
+	Mean alp. sph. solvent access : 	0.673
+	Apolar alpha sphere proportion : 	0.722
+	Hydrophobicity score:	0.333
+	Volume score: 	 4.667
+	Polarity score:	 5
+	Charge score :	 1
+	Proportion of polar atoms: 	41.176
+	Alpha sphere density : 	2.248
+	Cent. of mass - Alpha Sphere max dist: 	5.161
+	Flexibility : 	0.522
+
+Pocket 23 :
+	Score : 	0.043
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	26
+	Total SASA : 	110.639
+	Polar SASA : 	65.956
+	Apolar SASA : 	44.682
+	Volume : 	373.423
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	4.152
+	Mean alp. sph. solvent access : 	0.666
+	Apolar alpha sphere proportion : 	0.077
+	Hydrophobicity score:	7.500
+	Volume score: 	 4.333
+	Polarity score:	 5
+	Charge score :	 1
+	Proportion of polar atoms: 	42.857
+	Alpha sphere density : 	4.071
+	Cent. of mass - Alpha Sphere max dist: 	10.454
+	Flexibility : 	0.621
+
+Pocket 24 :
+	Score : 	0.040
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	22
+	Total SASA : 	52.460
+	Polar SASA : 	25.892
+	Apolar SASA : 	26.568
+	Volume : 	201.565
+	Mean local hydrophobic density : 	6.000
+	Mean alpha sphere radius :	3.959
+	Mean alp. sph. solvent access : 	0.551
+	Apolar alpha sphere proportion : 	0.318
+	Hydrophobicity score:	-26.286
+	Volume score: 	 4.143
+	Polarity score:	 7
+	Charge score :	 -1
+	Proportion of polar atoms: 	53.333
+	Alpha sphere density : 	1.785
+	Cent. of mass - Alpha Sphere max dist: 	3.872
+	Flexibility : 	0.657
+
+Pocket 25 :
+	Score : 	0.039
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	16
+	Total SASA : 	52.442
+	Polar SASA : 	35.535
+	Apolar SASA : 	16.907
+	Volume : 	238.630
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.883
+	Mean alp. sph. solvent access : 	0.594
+	Apolar alpha sphere proportion : 	0.062
+	Hydrophobicity score:	35.556
+	Volume score: 	 4.889
+	Polarity score:	 5
+	Charge score :	 1
+	Proportion of polar atoms: 	57.143
+	Alpha sphere density : 	2.162
+	Cent. of mass - Alpha Sphere max dist: 	4.767
+	Flexibility : 	0.324
+
+Pocket 26 :
+	Score : 	0.035
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	27
+	Total SASA : 	91.621
+	Polar SASA : 	60.223
+	Apolar SASA : 	31.398
+	Volume : 	357.614
+	Mean local hydrophobic density : 	1.000
+	Mean alpha sphere radius :	3.998
+	Mean alp. sph. solvent access : 	0.463
+	Apolar alpha sphere proportion : 	0.074
+	Hydrophobicity score:	-1.400
+	Volume score: 	 4.000
+	Polarity score:	 6
+	Charge score :	 0
+	Proportion of polar atoms: 	60.000
+	Alpha sphere density : 	3.042
+	Cent. of mass - Alpha Sphere max dist: 	6.995
+	Flexibility : 	0.440
+
+Pocket 27 :
+	Score : 	0.030
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	15
+	Total SASA : 	49.108
+	Polar SASA : 	12.880
+	Apolar SASA : 	36.229
+	Volume : 	197.723
+	Mean local hydrophobic density : 	4.000
+	Mean alpha sphere radius :	3.928
+	Mean alp. sph. solvent access : 	0.629
+	Apolar alpha sphere proportion : 	0.333
+	Hydrophobicity score:	22.429
+	Volume score: 	 3.714
+	Polarity score:	 4
+	Charge score :	 -1
+	Proportion of polar atoms: 	42.857
+	Alpha sphere density : 	2.002
+	Cent. of mass - Alpha Sphere max dist: 	4.999
+	Flexibility : 	0.702
+
+Pocket 28 :
+	Score : 	0.028
+	Druggability Score : 	0.007
+	Number of Alpha Spheres : 	37
+	Total SASA : 	95.771
+	Polar SASA : 	37.567
+	Apolar SASA : 	58.204
+	Volume : 	272.798
+	Mean local hydrophobic density : 	13.000
+	Mean alpha sphere radius :	3.876
+	Mean alp. sph. solvent access : 	0.490
+	Apolar alpha sphere proportion : 	0.378
+	Hydrophobicity score:	30.000
+	Volume score: 	 3.300
+	Polarity score:	 4
+	Charge score :	 0
+	Proportion of polar atoms: 	33.333
+	Alpha sphere density : 	2.525
+	Cent. of mass - Alpha Sphere max dist: 	5.760
+	Flexibility : 	0.428
+
+Pocket 29 :
+	Score : 	0.024
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	31
+	Total SASA : 	113.046
+	Polar SASA : 	71.987
+	Apolar SASA : 	41.059
+	Volume : 	382.428
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	4.070
+	Mean alp. sph. solvent access : 	0.694
+	Apolar alpha sphere proportion : 	0.000
+	Hydrophobicity score:	6.222
+	Volume score: 	 3.556
+	Polarity score:	 7
+	Charge score :	 -3
+	Proportion of polar atoms: 	57.143
+	Alpha sphere density : 	3.541
+	Cent. of mass - Alpha Sphere max dist: 	7.664
+	Flexibility : 	0.809
+
+Pocket 30 :
+	Score : 	0.022
+	Druggability Score : 	0.003
+	Number of Alpha Spheres : 	22
+	Total SASA : 	126.450
+	Polar SASA : 	43.124
+	Apolar SASA : 	83.326
+	Volume : 	415.124
+	Mean local hydrophobic density : 	7.000
+	Mean alpha sphere radius :	4.025
+	Mean alp. sph. solvent access : 	0.620
+	Apolar alpha sphere proportion : 	0.364
+	Hydrophobicity score:	17.800
+	Volume score: 	 4.700
+	Polarity score:	 7
+	Charge score :	 -1
+	Proportion of polar atoms: 	47.826
+	Alpha sphere density : 	4.752
+	Cent. of mass - Alpha Sphere max dist: 	12.329
+	Flexibility : 	0.419
+
+Pocket 31 :
+	Score : 	0.013
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	23
+	Total SASA : 	105.586
+	Polar SASA : 	54.866
+	Apolar SASA : 	50.720
+	Volume : 	376.423
+	Mean local hydrophobic density : 	3.000
+	Mean alpha sphere radius :	3.971
+	Mean alp. sph. solvent access : 	0.594
+	Apolar alpha sphere proportion : 	0.174
+	Hydrophobicity score:	8.889
+	Volume score: 	 3.444
+	Polarity score:	 6
+	Charge score :	 -1
+	Proportion of polar atoms: 	42.857
+	Alpha sphere density : 	3.649
+	Cent. of mass - Alpha Sphere max dist: 	9.255
+	Flexibility : 	0.610
+
+Pocket 32 :
+	Score : 	0.011
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	18
+	Total SASA : 	84.302
+	Polar SASA : 	51.696
+	Apolar SASA : 	32.606
+	Volume : 	243.039
+	Mean local hydrophobic density : 	4.000
+	Mean alpha sphere radius :	3.851
+	Mean alp. sph. solvent access : 	0.583
+	Apolar alpha sphere proportion : 	0.278
+	Hydrophobicity score:	17.400
+	Volume score: 	 4.600
+	Polarity score:	 3
+	Charge score :	 -1
+	Proportion of polar atoms: 	44.444
+	Alpha sphere density : 	3.116
+	Cent. of mass - Alpha Sphere max dist: 	6.911
+	Flexibility : 	0.754
+
+Pocket 33 :
+	Score : 	0.006
+	Druggability Score : 	0.010
+	Number of Alpha Spheres : 	17
+	Total SASA : 	78.442
+	Polar SASA : 	28.929
+	Apolar SASA : 	49.513
+	Volume : 	227.359
+	Mean local hydrophobic density : 	11.000
+	Mean alpha sphere radius :	3.905
+	Mean alp. sph. solvent access : 	0.622
+	Apolar alpha sphere proportion : 	0.706
+	Hydrophobicity score:	42.000
+	Volume score: 	 4.667
+	Polarity score:	 3
+	Charge score :	 0
+	Proportion of polar atoms: 	33.333
+	Alpha sphere density : 	2.894
+	Cent. of mass - Alpha Sphere max dist: 	6.487
+	Flexibility : 	0.378
+
+Pocket 34 :
+	Score : 	-0.002
+	Druggability Score : 	0.034
+	Number of Alpha Spheres : 	27
+	Total SASA : 	81.212
+	Polar SASA : 	40.153
+	Apolar SASA : 	41.059
+	Volume : 	281.548
+	Mean local hydrophobic density : 	20.000
+	Mean alpha sphere radius :	4.025
+	Mean alp. sph. solvent access : 	0.619
+	Apolar alpha sphere proportion : 	0.778
+	Hydrophobicity score:	31.000
+	Volume score: 	 4.600
+	Polarity score:	 3
+	Charge score :	 1
+	Proportion of polar atoms: 	27.778
+	Alpha sphere density : 	2.216
+	Cent. of mass - Alpha Sphere max dist: 	6.237
+	Flexibility : 	0.813
+
+Pocket 35 :
+	Score : 	-0.020
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	16
+	Total SASA : 	55.577
+	Polar SASA : 	11.786
+	Apolar SASA : 	43.791
+	Volume : 	155.436
+	Mean local hydrophobic density : 	5.000
+	Mean alpha sphere radius :	3.819
+	Mean alp. sph. solvent access : 	0.487
+	Apolar alpha sphere proportion : 	0.375
+	Hydrophobicity score:	-3.000
+	Volume score: 	 3.143
+	Polarity score:	 4
+	Charge score :	 -1
+	Proportion of polar atoms: 	41.667
+	Alpha sphere density : 	1.680
+	Cent. of mass - Alpha Sphere max dist: 	4.107
+	Flexibility : 	0.271
+
+Pocket 36 :
+	Score : 	-0.021
+	Druggability Score : 	0.194
+	Number of Alpha Spheres : 	26
+	Total SASA : 	93.206
+	Polar SASA : 	26.786
+	Apolar SASA : 	66.420
+	Volume : 	302.742
+	Mean local hydrophobic density : 	21.000
+	Mean alpha sphere radius :	4.066
+	Mean alp. sph. solvent access : 	0.589
+	Apolar alpha sphere proportion : 	0.846
+	Hydrophobicity score:	22.900
+	Volume score: 	 3.400
+	Polarity score:	 5
+	Charge score :	 -2
+	Proportion of polar atoms: 	40.000
+	Alpha sphere density : 	2.663
+	Cent. of mass - Alpha Sphere max dist: 	7.896
+	Flexibility : 	0.760
+
+Pocket 37 :
+	Score : 	-0.026
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	16
+	Total SASA : 	53.873
+	Polar SASA : 	23.683
+	Apolar SASA : 	30.191
+	Volume : 	165.159
+	Mean local hydrophobic density : 	5.000
+	Mean alpha sphere radius :	4.147
+	Mean alp. sph. solvent access : 	0.584
+	Apolar alpha sphere proportion : 	0.375
+	Hydrophobicity score:	-32.833
+	Volume score: 	 4.333
+	Polarity score:	 6
+	Charge score :	 -1
+	Proportion of polar atoms: 	53.333
+	Alpha sphere density : 	1.534
+	Cent. of mass - Alpha Sphere max dist: 	3.589
+	Flexibility : 	0.901
+
+Pocket 38 :
+	Score : 	-0.028
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	21
+	Total SASA : 	118.852
+	Polar SASA : 	64.509
+	Apolar SASA : 	54.343
+	Volume : 	373.641
+	Mean local hydrophobic density : 	6.000
+	Mean alpha sphere radius :	3.944
+	Mean alp. sph. solvent access : 	0.571
+	Apolar alpha sphere proportion : 	0.333
+	Hydrophobicity score:	23.750
+	Volume score: 	 4.000
+	Polarity score:	 5
+	Charge score :	 0
+	Proportion of polar atoms: 	42.857
+	Alpha sphere density : 	3.875
+	Cent. of mass - Alpha Sphere max dist: 	9.016
+	Flexibility : 	0.547
+
+Pocket 39 :
+	Score : 	-0.029
+	Druggability Score : 	0.001
+	Number of Alpha Spheres : 	23
+	Total SASA : 	108.466
+	Polar SASA : 	42.858
+	Apolar SASA : 	65.608
+	Volume : 	289.661
+	Mean local hydrophobic density : 	2.000
+	Mean alpha sphere radius :	3.867
+	Mean alp. sph. solvent access : 	0.434
+	Apolar alpha sphere proportion : 	0.130
+	Hydrophobicity score:	3.100
+	Volume score: 	 3.800
+	Polarity score:	 6
+	Charge score :	 -1
+	Proportion of polar atoms: 	42.105
+	Alpha sphere density : 	3.379
+	Cent. of mass - Alpha Sphere max dist: 	6.950
+	Flexibility : 	0.612
+
+Pocket 40 :
+	Score : 	-0.030
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	17
+	Total SASA : 	80.399
+	Polar SASA : 	45.377
+	Apolar SASA : 	35.021
+	Volume : 	265.301
+	Mean local hydrophobic density : 	5.000
+	Mean alpha sphere radius :	4.033
+	Mean alp. sph. solvent access : 	0.543
+	Apolar alpha sphere proportion : 	0.353
+	Hydrophobicity score:	13.857
+	Volume score: 	 4.429
+	Polarity score:	 5
+	Charge score :	 -1
+	Proportion of polar atoms: 	40.000
+	Alpha sphere density : 	2.550
+	Cent. of mass - Alpha Sphere max dist: 	4.655
+	Flexibility : 	0.731
+
+Pocket 41 :
+	Score : 	-0.030
+	Druggability Score : 	0.014
+	Number of Alpha Spheres : 	20
+	Total SASA : 	63.323
+	Polar SASA : 	5.357
+	Apolar SASA : 	57.966
+	Volume : 	196.956
+	Mean local hydrophobic density : 	14.000
+	Mean alpha sphere radius :	3.894
+	Mean alp. sph. solvent access : 	0.592
+	Apolar alpha sphere proportion : 	0.750
+	Hydrophobicity score:	51.000
+	Volume score: 	 3.857
+	Polarity score:	 2
+	Charge score :	 0
+	Proportion of polar atoms: 	26.667
+	Alpha sphere density : 	1.653
+	Cent. of mass - Alpha Sphere max dist: 	4.670
+	Flexibility : 	0.499
+
+Pocket 42 :
+	Score : 	-0.033
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	23
+	Total SASA : 	104.224
+	Polar SASA : 	51.089
+	Apolar SASA : 	53.136
+	Volume : 	285.535
+	Mean local hydrophobic density : 	6.000
+	Mean alpha sphere radius :	3.937
+	Mean alp. sph. solvent access : 	0.636
+	Apolar alpha sphere proportion : 	0.304
+	Hydrophobicity score:	-1.667
+	Volume score: 	 4.833
+	Polarity score:	 4
+	Charge score :	 1
+	Proportion of polar atoms: 	50.000
+	Alpha sphere density : 	3.185
+	Cent. of mass - Alpha Sphere max dist: 	8.525
+	Flexibility : 	0.631
+
+Pocket 43 :
+	Score : 	-0.034
+	Druggability Score : 	0.000
+	Number of Alpha Spheres : 	17
+	Total SASA : 	105.087
+	Polar SASA : 	70.065
+	Apolar SASA : 	35.021
+	Volume : 	265.080
+	Mean local hydrophobic density : 	0.000
+	Mean alpha sphere radius :	3.836
+	Mean alp. sph. solvent access : 	0.381
+	Apolar alpha sphere proportion : 	0.000
+	Hydrophobicity score:	-3.143
+	Volume score: 	 4.000
+	Polarity score:	 6
+	Charge score :	 -2
+	Proportion of polar atoms: 	58.824
+	Alpha sphere density : 	3.579
+	Cent. of mass - Alpha Sphere max dist: 	8.402
+	Flexibility : 	0.506
+
+Pocket 44 :
+	Score : 	-0.068
+	Druggability Score : 	0.007
+	Number of Alpha Spheres : 	24
+	Total SASA : 	99.271
+	Polar SASA : 	36.474
+	Apolar SASA : 	62.797
+	Volume : 	258.754
+	Mean local hydrophobic density : 	12.000
+	Mean alpha sphere radius :	3.905
+	Mean alp. sph. solvent access : 	0.573
+	Apolar alpha sphere proportion : 	0.542
+	Hydrophobicity score:	34.556
+	Volume score: 	 3.444
+	Polarity score:	 2
+	Charge score :	 0
+	Proportion of polar atoms: 	38.095
+	Alpha sphere density : 	2.492
+	Cent. of mass - Alpha Sphere max dist: 	5.483
+	Flexibility : 	0.656
+

tests/reference_output/2P0R_out/pockets/pocket10_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    10:
+HEADER 0  - Pocket Score                      : 0.0965
+HEADER 1  - Drug Score                        : 0.0202
+HEADER 2  - Number of alpha spheres           :    33
+HEADER 3  - Mean alpha-sphere radius          : 4.0358
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5593
+HEADER 5  - Mean B-factor of pocket residues  : 0.4816
+HEADER 6  - Hydrophobicity Score              : 39.6667
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 4.6667
+HEADER 9  - Pocket volume (Monte Carlo)       : 241.6115
+HEADER 10  -Pocket volume (convex hull)       : 12.6017
+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 : 0.5455
+ATOM    360  CG1 ILE A  63       7.931  23.368  50.604  0.00  0.00           C 0
+ATOM    354  NE2 GLN A  62       1.217  20.100  50.698  0.46  9.84           N 0
+ATOM    299  CE2 PHE A  56       3.087  25.696  46.582  0.00  0.00           C 0
+ATOM   3149  OE1 GLU B  93       8.651  19.729  46.632  0.69  6.43           O 0
+ATOM    300   CZ PHE A  56       3.043  25.108  45.318  0.00  0.00           C 0
+ATOM   1126  CG1 VAL A 158       9.646  23.743  44.107  0.00  0.00           C 0
+ATOM    593    O GLU A  93       5.835  22.348  41.499  0.71  5.36           O 0
+ATOM   1136  CE1 PHE A 159       6.673  25.502  42.416  0.00  0.00           C 0
+ATOM    343   CB PRO A  61       3.846  25.554  50.314  0.00  0.00           C 0
+ATOM    380   CZ PHE A  65       7.519  25.919  47.113  0.00  0.00           C 0
+ATOM    594   CB GLU A  93       8.061  20.768  42.117  0.00  0.00           C 0
+ATOM    327  OE2 GLU A  59      -1.461  21.832  49.069  0.44  9.64           O 0
+ATOM   3146   CB GLU B  93       8.285  17.935  49.039  0.00  0.00           C 0
+ATOM    340   CA PRO A  61       2.685  24.927  51.096  0.00  0.00           C 0
+ATOM   3144    C GLU B  93       6.819  17.141  50.867  0.00  0.00           C 0
+ATOM    350   CB GLN A  62       3.501  20.694  53.139  0.00  0.00           C 0
+ATOM    379  CE2 PHE A  65       6.859  25.938  48.344  0.00  0.00           C 0
+ATOM    362  CD1 ILE A  63       8.975  23.356  49.460  0.00  0.00           C 0
+ATOM   3145    O GLU B  93       6.194  16.566  50.007  0.00  0.00           O 0
+ATOM    346    N GLN A  62       3.496  22.986  52.297  0.36  2.19           N 0
+ATOM    361  CG2 ILE A  63       8.424  21.275  51.799  0.00  0.00           C 0
+ATOM   3143   CA GLU B  93       8.083  17.899  50.541  0.00  0.00           C 0
+ATOM    355    N ILE A  63       6.134  22.975  52.943  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket10_vert.pqr

@@ -0,0 +1,55 @@
+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                      : 0.0965
+HEADER 1  - Drug Score                        : 0.0202
+HEADER 2  - Number of V. Vertices             :    33
+HEADER 3  - Mean alpha-sphere radius          : 4.0358
+HEADER 4  - Mean alpha-sphere SA              : 0.5593
+HEADER 5  - Mean B-factor                     : 0.4816
+HEADER 6  - Hydrophobicity Score              : 39.6667
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 4.6667
+HEADER 9  - Real volume (approximation)       : 241.6115
+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 : 0.5455
+ATOM      1    O STP    10       4.621  21.560  47.942    0.00     4.62
+ATOM      2    O STP    10       4.504  21.449  47.739    0.00     4.62
+ATOM      3    O STP    10       6.096  22.555  45.468    0.00     3.98
+ATOM      4    C STP    10       6.137  23.026  45.157    0.00     3.73
+ATOM      5    C STP    10       4.567  21.675  48.074    0.00     4.54
+ATOM      6    C STP    10       6.104  22.569  45.494    0.00     3.98
+ATOM      7    C STP    10       6.145  23.054  45.172    0.00     3.72
+ATOM      8    O STP    10       6.500  22.202  45.066    0.00     3.63
+ATOM      9    O STP    10       2.054  22.106  47.519    0.00     3.85
+ATOM     10    O STP    10       5.022  20.760  48.748    0.00     4.33
+ATOM     11    C STP    10       3.264  22.323  48.364    0.00     3.82
+ATOM     12    O STP    10       1.967  22.721  48.316    0.00     3.62
+ATOM     13    C STP    10       5.099  20.584  49.309    0.00     4.15
+ATOM     14    C STP    10       5.136  20.596  49.343    0.00     4.13
+ATOM     15    C STP    10       4.933  22.352  48.025    0.00     4.08
+ATOM     16    C STP    10       5.158  22.058  47.584    0.00     4.30
+ATOM     17    C STP    10       5.241  22.134  47.395    0.00     4.24
+ATOM     18    C STP    10       5.571  22.361  46.916    0.00     4.06
+ATOM     19    C STP    10       5.692  22.228  47.524    0.00     3.97
+ATOM     20    C STP    10       6.115  22.438  47.207    0.00     3.75
+ATOM     21    O STP    10       5.007  20.400  49.155    0.00     4.10
+ATOM     22    O STP    10       4.739  20.193  48.283    0.00     4.27
+ATOM     23    O STP    10       3.496  22.230  48.633    0.00     3.74
+ATOM     24    O STP    10       4.566  21.677  48.106    0.00     4.52
+ATOM     25    O STP    10       5.098  20.617  49.261    0.00     4.17
+ATOM     26    O STP    10       5.101  20.590  49.306    0.00     4.15
+ATOM     27    C STP    10       5.126  20.599  49.330    0.00     4.14
+ATOM     28    C STP    10       5.176  20.591  49.409    0.00     4.09
+ATOM     29    C STP    10       5.200  20.586  49.391    0.00     4.08
+ATOM     30    C STP    10       5.336  20.515  49.469    0.00     3.94
+ATOM     31    C STP    10       5.205  20.682  49.557    0.00     3.97
+ATOM     32    O STP    10       5.406  21.082  50.173    0.00     3.43
+ATOM     33    O STP    10       5.375  20.955  50.298    0.00     3.41
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket11_atm.pdb

@@ -0,0 +1,73 @@
+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                      : 0.0932
+HEADER 1  - Drug Score                        : 0.0020
+HEADER 2  - Number of alpha spheres           :    59
+HEADER 3  - Mean alpha-sphere radius          : 4.0734
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6811
+HEADER 5  - Mean B-factor of pocket residues  : 0.4088
+HEADER 6  - Hydrophobicity Score              : 5.1053
+HEADER 7  - Polarity Score                    :    12
+HEADER 8  - Amino Acid based volume Score     : 3.3684
+HEADER 9  - Pocket volume (Monte Carlo)       : 832.2958
+HEADER 10  -Pocket volume (convex hull)       : 222.1873
+HEADER 11 - Charge Score                      :    -3
+HEADER 12 - Local hydrophobic density Score   : 3.5556
+HEADER 13 - Number of apolar alpha sphere     :     9
+HEADER 14 - Proportion of apolar alpha sphere : 0.1525
+ATOM   2203  OE1 GLU A 295      16.931   2.735  15.283  0.71  2.14           O 0
+ATOM   2195   CD PRO A 294      18.794   0.530  17.609  0.00  0.00           C 0
+ATOM   2204  OE2 GLU A 295      15.495   1.877  13.893  0.57  4.29           O 0
+ATOM   2194   CG PRO A 294      18.698  -0.318  16.393  0.00  0.00           C 0
+ATOM   2181   CB SER A 292      21.258   4.639  22.889  0.00  0.00           C 0
+ATOM   2180    O SER A 292      21.011   2.867  20.728  0.00  0.00           O 0
+ATOM   2134    O ASN A 286      13.789   2.876  22.101  0.00  0.00           O 0
+ATOM   2179    C SER A 292      20.537   3.997  20.585  0.00  0.00           C 0
+ATOM   2168   OG SER A 290      15.804   5.485  20.672  0.00  0.00           O 0
+ATOM   2143    N SER A 288      12.966   3.830  17.423  0.67  1.09           N 0
+ATOM   2187   CB SER A 293      17.687   3.782  18.185  0.00  0.00           C 0
+ATOM   2148   OG SER A 288      12.645   2.630  14.846  0.00  0.00           O 0
+ATOM   2184   CA SER A 293      18.992   3.262  18.815  0.00  0.00           C 0
+ATOM   2135   CB ASN A 286      13.213   4.148  24.648  0.00  0.00           C 0
+ATOM   2132   CA ASN A 286      13.240   4.900  23.302  0.00  0.00           C 0
+ATOM   2141    C GLY A 287      13.309   4.128  18.670  0.00  0.00           C 0
+ATOM   2140   CA GLY A 287      12.414   3.575  19.770  0.00  0.00           C 0
+ATOM   2120    O TRP A 285      13.831   7.561  23.460  0.00  0.00           O 0
+ATOM   2182   OG SER A 292      21.741   5.701  23.697  0.00  0.00           O 0
+ATOM   2183    N SER A 293      19.587   4.285  19.695  0.00  0.00           N 0
+ATOM   2167   CB SER A 290      15.457   6.840  20.853  0.00  0.00           C 0
+ATOM   2169    N ASP A 291      18.106   8.314  21.061  0.44  1.09           N 0
+ATOM   2106  CG1 VAL A 283      10.962  10.217  30.543  0.00  0.00           C 0
+ATOM   2107  CG2 VAL A 283      12.381  11.489  32.204  0.00  0.00           C 0
+ATOM   1801  NH1 ARG A 245      10.700   7.731  33.691  0.00  0.00           N 0
+ATOM   2102   CA VAL A 283      13.066  11.415  29.782  0.00  0.00           C 0
+ATOM   2111    O GLU A 284      12.515   8.181  26.134  0.00  0.00           O 0
+ATOM   2108    N GLU A 284      12.957  10.502  27.570  0.41  1.09           N 0
+ATOM   1798   CD ARG A 245       8.751   6.999  31.761  0.00  0.00           C 0
+ATOM   1829   CA GLY A 249       9.497   6.604  27.181  0.00  0.00           C 0
+ATOM   2333    N LEU A 312      22.322  12.114  24.942  0.76  1.09           N 0
+ATOM   2173   CB ASP A 291      19.744   9.320  22.593  0.00  0.00           C 0
+ATOM   2332   CB ALA A 311      24.193   9.373  23.541  0.00  0.00           C 0
+ATOM   2177    N SER A 292      20.136   6.287  21.474  0.57  1.09           N 0
+ATOM   2348  OD2 ASP A 313      17.520  11.229  31.403  0.00  0.00           O 0
+ATOM   2939  CG2 VAL B  66      14.443   9.165  37.938  0.00  0.00           C 0
+ATOM   2099  OE1 GLN A 282      15.542  13.818  34.600  0.50  9.64           O 0
+ATOM   2347  OD1 ASP A 313      16.728  11.876  29.447  0.73  3.21           O 0
+ATOM   2115  OE1 GLU A 284      16.642  11.840  24.435  0.69  3.21           O 0
+ATOM   2176  OD2 ASP A 291      19.604  11.508  23.547  0.67  2.14           O 0
+ATOM   2342   CA ASP A 313      19.209  12.682  28.487  0.00  0.00           C 0
+ATOM   2336    O LEU A 312      19.860  12.995  25.837  0.00  0.00           O 0
+ATOM   2345   CB ASP A 313      19.115  11.846  29.764  0.00  0.00           C 0
+ATOM   2112   CB GLU A 284      14.297  10.854  25.555  0.00  0.00           C 0
+ATOM   2330    C ALA A 311      23.459  11.543  24.584  0.00  0.00           C 0
+ATOM   2341    N ASP A 313      20.543  12.584  27.911  0.61  4.37           N 0
+ATOM   2331    O ALA A 311      24.482  11.680  25.217  0.00  0.00           O 0
+ATOM   2334   CA LEU A 312      22.190  12.928  26.160  0.00  0.00           C 0
+ATOM   2114   CD GLU A 284      16.274  12.456  25.461  0.00  0.00           C 0
+ATOM   2113   CG GLU A 284      15.041  11.981  26.236  0.00  0.00           C 0
+ATOM   2335    C LEU A 312      20.761  12.839  26.631  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket11_vert.pqr

@@ -0,0 +1,81 @@
+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                      : 0.0932
+HEADER 1  - Drug Score                        : 0.0020
+HEADER 2  - Number of V. Vertices             :    59
+HEADER 3  - Mean alpha-sphere radius          : 4.0734
+HEADER 4  - Mean alpha-sphere SA              : 0.6811
+HEADER 5  - Mean B-factor                     : 0.4088
+HEADER 6  - Hydrophobicity Score              : 5.1053
+HEADER 7  - Polarity Score                    :    12
+HEADER 8  - Volume Score                      : 3.3684
+HEADER 9  - Real volume (approximation)       : 832.2958
+HEADER 10 - Charge Score                      :    -3
+HEADER 11 - Local hydrophobic density Score   : 3.5556
+HEADER 12 - Number of apolar alpha sphere     :     9
+HEADER 13 - Proportion of apolar alpha sphere : 0.1525
+ATOM      1    O STP    11      14.894   0.063  17.335    0.00     3.94
+ATOM      2    O STP    11      17.745   2.488  23.233    0.00     4.13
+ATOM      3    O STP    11      17.649   2.937  23.138    0.00     4.00
+ATOM      4    O STP    11      15.261   1.116  18.040    0.00     3.61
+ATOM      5    O STP    11      14.697   0.092  17.520    0.00     4.12
+ATOM      6    O STP    11      14.467  -0.295  17.569    0.00     4.39
+ATOM      7    O STP    11      14.516  -0.226  17.566    0.00     4.34
+ATOM      8    C STP    11      16.479   1.119  20.369    0.00     3.65
+ATOM      9    O STP    11      17.484   0.381  21.874    0.00     4.46
+ATOM     10    O STP    11      16.632   4.083  23.797    0.00     3.52
+ATOM     11    O STP    11      17.360   3.713  24.147    0.00     4.20
+ATOM     12    C STP    11      15.242   1.089  18.158    0.00     3.64
+ATOM     13    C STP    11      14.563  -0.084  18.626    0.00     4.39
+ATOM     14    C STP    11      15.345   0.940  19.199    0.00     3.82
+ATOM     15    C STP    11      14.842   0.229  19.010    0.00     4.20
+ATOM     16    O STP    11      17.384   5.389  24.727    0.00     4.35
+ATOM     17    O STP    11      17.481   5.540  25.209    0.00     4.52
+ATOM     18    O STP    11      17.086   5.374  24.527    0.00     4.06
+ATOM     19    O STP    11      17.528   2.596  22.345    0.00     3.76
+ATOM     20    O STP    11      17.410   2.501  22.005    0.00     3.64
+ATOM     21    O STP    11      17.552   2.278  22.217    0.00     3.81
+ATOM     22    O STP    11      17.548   2.258  22.195    0.00     3.81
+ATOM     23    O STP    11      17.328   6.149  24.121    0.00     3.83
+ATOM     24    C STP    11      14.187   7.860  31.517    0.00     4.11
+ATOM     25    O STP    11      14.267   6.931  30.276    0.00     4.67
+ATOM     26    C STP    11      12.742   6.231  30.110    0.00     4.39
+ATOM     27    O STP    11      12.818   6.210  30.099    0.00     4.44
+ATOM     28    O STP    11      21.395   8.679  25.794    0.00     3.66
+ATOM     29    O STP    11      17.385   5.392  24.725    0.00     4.35
+ATOM     30    O STP    11      17.355   6.121  24.161    0.00     3.87
+ATOM     31    O STP    11      17.525   5.700  24.972    0.00     4.40
+ATOM     32    O STP    11      17.689   6.403  25.040    0.00     4.33
+ATOM     33    O STP    11      17.616   6.502  24.746    0.00     4.14
+ATOM     34    O STP    11      14.745   7.675  31.680    0.00     4.52
+ATOM     35    O STP    11      15.084   8.303  33.650    0.00     4.42
+ATOM     36    O STP    11      15.266   9.992  34.269    0.00     3.85
+ATOM     37    O STP    11      15.407   7.777  29.871    0.00     4.33
+ATOM     38    O STP    11      18.622   8.742  26.751    0.00     4.35
+ATOM     39    O STP    11      18.656   9.561  26.559    0.00     3.71
+ATOM     40    O STP    11      18.240   9.021  26.935    0.00     4.09
+ATOM     41    C STP    11      18.610   8.718  26.764    0.00     4.36
+ATOM     42    O STP    11      17.395   7.831  25.930    0.00     4.34
+ATOM     43    O STP    11      16.308   8.024  27.882    0.00     4.18
+ATOM     44    O STP    11      21.857   8.418  26.921    0.00     4.22
+ATOM     45    O STP    11      18.977   8.753  26.777    0.00     4.29
+ATOM     46    O STP    11      18.957   9.421  26.616    0.00     3.77
+ATOM     47    C STP    11      18.982   8.723  26.794    0.00     4.31
+ATOM     48    O STP    11      19.657   8.109  27.070    0.00     4.64
+ATOM     49    O STP    11      20.755   8.577  26.618    0.00     4.22
+ATOM     50    O STP    11      21.952   8.321  27.375    0.00     4.52
+ATOM     51    O STP    11      22.598   9.481  27.579    0.00     3.74
+ATOM     52    O STP    11      22.612   9.548  27.577    0.00     3.69
+ATOM     53    O STP    11      17.999   9.762  26.934    0.00     3.52
+ATOM     54    O STP    11      17.399   8.979  26.949    0.00     3.88
+ATOM     55    O STP    11      17.432   9.402  26.946    0.00     3.59
+ATOM     56    O STP    11      20.518   9.056  26.309    0.00     3.80
+ATOM     57    O STP    11      20.225   8.974  26.454    0.00     3.91
+ATOM     58    O STP    11      20.605   8.824  26.489    0.00     4.02
+ATOM     59    O STP    11      19.536   9.570  26.455    0.00     3.50
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket12_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    12:
+HEADER 0  - Pocket Score                      : 0.0874
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of alpha spheres           :    25
+HEADER 3  - Mean alpha-sphere radius          : 3.6388
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4694
+HEADER 5  - Mean B-factor of pocket residues  : 0.5092
+HEADER 6  - Hydrophobicity Score              : 23.2000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.4000
+HEADER 9  - Pocket volume (Monte Carlo)       : 130.4008
+HEADER 10  -Pocket volume (convex hull)       : 4.9318
+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 : 0.0400
+ATOM    117   NE ARG A  33      18.170  49.202  35.022  0.73  3.28           N 0
+ATOM    866    O ILE A 130      15.298  44.095  36.691  0.62  3.21           O 0
+ATOM    841    O GLY A 126      20.226  48.322  36.864  0.00  0.00           O 0
+ATOM    116   CD ARG A  33      16.763  49.002  35.333  0.00  0.00           C 0
+ATOM    840    C GLY A 126      21.404  48.005  36.803  0.00  0.00           C 0
+ATOM    120  NH2 ARG A  33      19.957  50.213  34.017  0.20  4.37           N 0
+ATOM    839   CA GLY A 126      22.389  48.846  36.014  0.00  0.00           C 0
+ATOM    834    O PRO A 125      24.174  47.560  34.327  0.00  5.36           O 0
+ATOM    813    O SER A 122      21.000  42.632  35.595  0.52  6.43           O 0
+ATOM    843   CA TYR A 127      21.055  45.994  38.154  0.00  0.00           C 0
+ATOM    810    N SER A 122      20.516  42.185  32.999  0.57  1.09           N 0
+ATOM    879  CE1 PHE A 131      17.486  40.671  34.971  0.00  0.00           C 0
+ATOM     83   CZ PHE A  29      14.464  46.875  33.397  0.00  0.00           C 0
+ATOM    796    O ASP A 120      19.612  45.254  30.451  0.38  5.36           O 0
+ATOM    815   OG SER A 122      23.443  43.047  33.410  0.49  3.21           O 0
+ATOM    802   CA GLN A 121      18.880  42.770  31.373  0.00  0.00           C 0
+ATOM    808  OE1 GLN A 121      14.698  42.916  32.392  0.00  0.00           O 0
+ATOM    806   CG GLN A 121      16.460  42.917  30.847  0.00  0.00           C 0
+ATOM    805   CB GLN A 121      17.533  42.096  31.492  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket12_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    12:
+HEADER 0  - Pocket Score                      : 0.0874
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of V. Vertices             :    25
+HEADER 3  - Mean alpha-sphere radius          : 3.6388
+HEADER 4  - Mean alpha-sphere SA              : 0.4694
+HEADER 5  - Mean B-factor                     : 0.5092
+HEADER 6  - Hydrophobicity Score              : 23.2000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 4.4000
+HEADER 9  - Real volume (approximation)       : 130.4008
+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 : 0.0400
+ATOM      1    O STP    12      18.068  45.891  35.833    0.00     3.41
+ATOM      2    O STP    12      20.292  46.808  33.788    0.00     3.43
+ATOM      3    O STP    12      20.895  46.958  33.594    0.00     3.41
+ATOM      4    O STP    12      18.548  45.342  35.576    0.00     3.65
+ATOM      5    O STP    12      18.487  45.430  35.144    0.00     3.79
+ATOM      6    O STP    12      18.022  44.083  34.519    0.00     3.48
+ATOM      7    O STP    12      17.792  45.571  34.379    0.00     3.71
+ATOM      8    O STP    12      21.054  45.773  33.754    0.00     3.64
+ATOM      9    O STP    12      21.022  45.635  33.692    0.00     3.56
+ATOM     10    O STP    12      20.936  45.870  33.835    0.00     3.69
+ATOM     11    O STP    12      20.775  46.757  33.497    0.00     3.59
+ATOM     12    O STP    12      20.058  45.881  34.078    0.00     3.71
+ATOM     13    O STP    12      20.306  46.666  33.668    0.00     3.58
+ATOM     14    O STP    12      20.220  46.547  33.744    0.00     3.59
+ATOM     15    O STP    12      19.505  45.784  34.177    0.00     3.77
+ATOM     16    O STP    12      17.994  44.086  34.479    0.00     3.49
+ATOM     17    C STP    12      17.265  44.889  33.544    0.00     3.44
+ATOM     18    O STP    12      18.063  44.276  34.478    0.00     3.55
+ATOM     19    O STP    12      18.305  45.286  34.389    0.00     3.97
+ATOM     20    O STP    12      18.766  45.359  34.160    0.00     3.81
+ATOM     21    O STP    12      18.646  45.418  34.223    0.00     3.90
+ATOM     22    O STP    12      18.006  45.380  34.164    0.00     3.92
+ATOM     23    O STP    12      18.022  45.502  33.954    0.00     3.85
+ATOM     24    O STP    12      17.339  44.814  33.856    0.00     3.57
+ATOM     25    O STP    12      17.346  44.592  33.916    0.00     3.48
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket13_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    13:
+HEADER 0  - Pocket Score                      : 0.0820
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of alpha spheres           :    21
+HEADER 3  - Mean alpha-sphere radius          : 3.7225
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4364
+HEADER 5  - Mean B-factor of pocket residues  : 0.3783
+HEADER 6  - Hydrophobicity Score              : 12.4444
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.5556
+HEADER 9  - Pocket volume (Monte Carlo)       : 119.5779
+HEADER 10  -Pocket volume (convex hull)       : 2.2755
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 1.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.0952
+ATOM   2326  OG1 THR A 310      23.627  14.948  21.980  0.19  1.07           O 0
+ATOM   2364    O GLU A 316      16.868  14.413  22.498  0.75  3.21           O 0
+ATOM   2308    O CYS A 308      22.353  16.541  17.977  0.52  6.43           O 0
+ATOM   2324    O THR A 310      22.136  12.406  21.546  0.51  1.07           O 0
+ATOM   2035   CD ARG A 275      16.219  17.938  17.519  0.00  0.00           C 0
+ATOM   2389  NE1 TRP A 318      18.042  14.969  15.742  0.88  1.09           N 0
+ATOM   2368  OE1 GLU A 316      17.497  19.414  20.501  0.39  5.36           O 0
+ATOM   2175  OD1 ASP A 291      18.718  11.210  21.579  0.45  5.36           O 0
+ATOM   2356  OD2 ASP A 314      20.129  16.993  24.467  0.89  2.14           O 0
+ATOM   2366   CG GLU A 316      15.874  17.823  21.140  0.00  0.00           C 0
+ATOM   2318  CD2 HIS A 309      21.843  10.869  17.925  0.00  0.00           C 0
+ATOM   2387  CD1 TRP A 318      17.614  13.778  16.247  0.00  0.00           C 0
+ATOM   2312   CA HIS A 309      22.628  13.955  17.104  0.00  0.00           C 0
+ATOM   2365   CB GLU A 316      16.239  17.397  22.573  0.00  0.00           C 0
+ATOM   2371   CA PHE A 317      15.124  13.309  20.636  0.00  0.00           C 0
+ATOM   2321    N THR A 310      23.295  13.549  19.385  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket13_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    13:
+HEADER 0  - Pocket Score                      : 0.0820
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of V. Vertices             :    21
+HEADER 3  - Mean alpha-sphere radius          : 3.7225
+HEADER 4  - Mean alpha-sphere SA              : 0.4364
+HEADER 5  - Mean B-factor                     : 0.3783
+HEADER 6  - Hydrophobicity Score              : 12.4444
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.5556
+HEADER 9  - Real volume (approximation)       : 119.5779
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 1.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.0952
+ATOM      1    O STP    13      20.074  15.488  20.804    0.00     3.78
+ATOM      2    O STP    13      18.833  15.811  19.452    0.00     3.89
+ATOM      3    O STP    13      18.852  15.914  19.523    0.00     3.88
+ATOM      4    O STP    13      19.473  14.481  19.602    0.00     3.90
+ATOM      5    O STP    13      20.112  15.395  21.213    0.00     3.63
+ATOM      6    O STP    13      19.699  16.288  20.727    0.00     3.83
+ATOM      7    O STP    13      20.064  15.701  20.893    0.00     3.80
+ATOM      8    O STP    13      18.822  15.922  19.532    0.00     3.86
+ATOM      9    C STP    13      19.729  13.459  19.054    0.00     3.53
+ATOM     10    O STP    13      18.978  15.423  19.445    0.00     3.85
+ATOM     11    O STP    13      19.471  14.481  19.600    0.00     3.90
+ATOM     12    O STP    13      19.474  14.477  19.597    0.00     3.90
+ATOM     13    O STP    13      18.393  15.596  19.357    0.00     3.69
+ATOM     14    O STP    13      19.267  16.512  21.150    0.00     3.46
+ATOM     15    C STP    13      17.511  15.325  19.280    0.00     3.41
+ATOM     16    O STP    13      19.842  13.414  19.155    0.00     3.46
+ATOM     17    O STP    13      19.801  13.457  19.116    0.00     3.51
+ATOM     18    O STP    13      19.601  14.108  19.393    0.00     3.74
+ATOM     19    O STP    13      19.694  13.744  19.198    0.00     3.61
+ATOM     20    O STP    13      19.543  14.407  19.520    0.00     3.85
+ATOM     21    O STP    13      19.652  14.346  19.318    0.00     3.73
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket14_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    14:
+HEADER 0  - Pocket Score                      : 0.0796
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    25
+HEADER 3  - Mean alpha-sphere radius          : 3.6975
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4878
+HEADER 5  - Mean B-factor of pocket residues  : 0.7292
+HEADER 6  - Hydrophobicity Score              : 12.4444
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.5556
+HEADER 9  - Pocket volume (Monte Carlo)       : 118.9432
+HEADER 10  -Pocket volume (convex hull)       : 3.9774
+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   4939  CD1 TRP B 318      17.137  27.686  74.036  0.00  0.00           C 0
+ATOM   4864   CA HIS B 309      22.129  28.277  73.108  0.00  0.00           C 0
+ATOM   4876    O THR B 310      21.382  29.646  69.077  0.00  0.00           O 0
+ATOM   4869  ND1 HIS B 309      20.537  30.941  72.382  0.31  1.09           N 0
+ATOM   4860    O CYS B 308      22.565  25.688  72.144  0.42  6.43           O 0
+ATOM   4873    N THR B 310      22.749  28.547  70.824  0.58  1.09           N 0
+ATOM   4727  OD1 ASP B 291      18.000  30.080  68.274  0.15  2.14           O 0
+ATOM   4941  NE1 TRP B 318      17.808  26.621  74.561  0.71  2.19           N 0
+ATOM   4587   CD ARG B 275      16.125  23.579  73.215  0.00  0.00           C 0
+ATOM   4590  NH1 ARG B 275      18.492  22.362  74.246  0.64  7.66           N 0
+ATOM   4920  OE1 GLU B 316      17.612  21.822  70.107  0.20  5.36           O 0
+ATOM   4918   CG GLU B 316      15.839  23.221  69.462  0.00  0.00           C 0
+ATOM   4908  OD2 ASP B 314      19.680  25.558  66.699  0.69  5.36           O 0
+ATOM   4916    O GLU B 316      16.330  26.515  67.848  0.57  1.07           O 0
+ATOM   4922    N PHE B 317      14.575  26.203  69.228  0.00  0.00           N 0
+ATOM   4923   CA PHE B 317      14.621  27.498  69.883  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_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                      : 0.0796
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    25
+HEADER 3  - Mean alpha-sphere radius          : 3.6975
+HEADER 4  - Mean alpha-sphere SA              : 0.4878
+HEADER 5  - Mean B-factor                     : 0.7292
+HEADER 6  - Hydrophobicity Score              : 12.4444
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.5556
+HEADER 9  - Real volume (approximation)       : 118.9432
+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    14      19.202  27.917  71.211    0.00     3.51
+ATOM      2    O STP    14      19.226  27.067  70.896    0.00     3.82
+ATOM      3    O STP    14      19.250  27.087  70.944    0.00     3.79
+ATOM      4    O STP    14      19.241  27.175  70.952    0.00     3.77
+ATOM      5    O STP    14      18.907  28.142  71.048    0.00     3.50
+ATOM      6    O STP    14      19.359  26.926  71.426    0.00     3.51
+ATOM      7    O STP    14      19.125  24.843  71.770    0.00     3.56
+ATOM      8    O STP    14      19.137  24.723  71.603    0.00     3.60
+ATOM      9    O STP    14      18.922  25.192  71.235    0.00     3.79
+ATOM     10    O STP    14      18.640  25.480  70.938    0.00     3.89
+ATOM     11    O STP    14      20.007  26.598  69.989    0.00     3.47
+ATOM     12    O STP    14      17.514  25.927  71.062    0.00     3.48
+ATOM     13    O STP    14      17.483  25.806  70.995    0.00     3.43
+ATOM     14    O STP    14      17.495  25.990  71.053    0.00     3.45
+ATOM     15    O STP    14      17.983  27.601  70.684    0.00     3.46
+ATOM     16    O STP    14      17.934  25.831  71.026    0.00     3.62
+ATOM     17    O STP    14      18.310  25.659  70.946    0.00     3.77
+ATOM     18    O STP    14      18.926  26.344  70.799    0.00     3.93
+ATOM     19    O STP    14      18.880  27.185  70.646    0.00     3.84
+ATOM     20    O STP    14      19.074  26.857  70.683    0.00     3.96
+ATOM     21    O STP    14      19.256  26.680  70.385    0.00     3.88
+ATOM     22    O STP    14      18.794  25.563  70.841    0.00     3.99
+ATOM     23    O STP    14      18.727  25.552  70.855    0.00     3.96
+ATOM     24    O STP    14      18.974  25.479  70.563    0.00     3.93
+ATOM     25    O STP    14      18.711  25.164  70.059    0.00     3.52
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket15_atm.pdb

@@ -0,0 +1,53 @@
+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                      : 0.0767
+HEADER 1  - Drug Score                        : 0.0028
+HEADER 2  - Number of alpha spheres           :    47
+HEADER 3  - Mean alpha-sphere radius          : 3.8227
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4346
+HEADER 5  - Mean B-factor of pocket residues  : 0.7955
+HEADER 6  - Hydrophobicity Score              : 10.9286
+HEADER 7  - Polarity Score                    :     8
+HEADER 8  - Amino Acid based volume Score     : 4.2143
+HEADER 9  - Pocket volume (Monte Carlo)       : 508.4681
+HEADER 10  -Pocket volume (convex hull)       : 68.0182
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 8.0000
+HEADER 13 - Number of apolar alpha sphere     :     9
+HEADER 14 - Proportion of apolar alpha sphere : 0.1915
+ATOM   3340   CB GLN B 119      20.968  -3.150  67.588  0.00  0.00           C 0
+ATOM   3345    N ASP B 120      21.895  -3.307  64.522  0.60  1.09           N 0
+ATOM   3352  OD2 ASP B 120      24.066  -5.749  66.236  0.00  0.00           O 0
+ATOM   3336    N GLN B 119      19.288  -2.776  65.888  0.00  0.00           N 0
+ATOM   3333   CB PRO B 118      16.585  -3.387  64.207  0.00  0.00           C 0
+ATOM   3443  NE2 HIS B 132      16.137  -5.443  61.564  0.00  0.00           N 0
+ATOM   2670   CZ ARG B  33      22.246  -9.303  57.891  0.00  0.00           C 0
+ATOM   3348    O ASP B 120      23.769  -3.742  61.455  0.68  7.50           O 0
+ATOM   2669   NE ARG B  33      21.040  -8.787  57.635  0.81  2.19           N 0
+ATOM   2672  NH2 ARG B  33      22.477  -9.904  59.050  0.00  0.00           N 0
+ATOM   2671  NH1 ARG B  33      23.222  -9.251  56.989  0.34  2.19           N 0
+ATOM   3386    O PRO B 125      27.689  -6.119  57.236  0.36  6.43           O 0
+ATOM   2668   CD ARG B  33      20.660  -8.098  56.396  0.00  0.00           C 0
+ATOM   2635   CZ PHE B  29      17.935  -6.111  58.385  0.00  0.00           C 0
+ATOM   3393    O GLY B 126      23.860  -7.034  55.091  0.77  3.21           O 0
+ATOM   3392    C GLY B 126      25.046  -6.746  54.929  0.00  0.00           C 0
+ATOM   3358   CG GLN B 121      19.504  -2.194  61.058  0.00  0.00           C 0
+ATOM   2632  CD2 PHE B  29      16.798  -7.827  59.607  0.00  0.00           C 0
+ATOM   2643  OE1 GLU B  30      19.847 -10.965  60.128  0.00  0.00           O 0
+ATOM   3442  CE1 HIS B 132      15.063  -5.865  62.209  0.00  0.00           C 0
+ATOM   3349   CB ASP B 120      23.838  -4.752  64.075  0.00  0.00           C 0
+ATOM   3362    N SER B 122      23.495  -1.062  58.798  0.00  0.00           N 0
+ATOM   3367   OG SER B 122      26.708  -1.325  58.264  0.64  2.14           O 0
+ATOM   3357   CB GLN B 121      20.552  -1.329  60.376  0.00  0.00           C 0
+ATOM   3431  CE1 PHE B 131      20.125   0.149  56.725  0.00  0.00           C 0
+ATOM   3418    O ILE B 130      18.446  -3.972  55.259  0.54  5.36           O 0
+ATOM   2634  CE2 PHE B  29      17.923  -7.041  59.405  0.00  0.00           C 0
+ATOM   3347    C ASP B 120      23.081  -3.126  62.271  0.00  0.00           C 0
+ATOM   3365    O SER B 122      24.001  -1.391  56.171  0.55  4.29           O 0
+ATOM   3395   CA TYR B 127      24.465  -4.797  53.556  0.00  0.00           C 0
+ATOM   3354   CA GLN B 121      21.990  -1.836  60.536  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket15_vert.pqr

@@ -0,0 +1,69 @@
+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                      : 0.0767
+HEADER 1  - Drug Score                        : 0.0028
+HEADER 2  - Number of V. Vertices             :    47
+HEADER 3  - Mean alpha-sphere radius          : 3.8227
+HEADER 4  - Mean alpha-sphere SA              : 0.4346
+HEADER 5  - Mean B-factor                     : 0.7955
+HEADER 6  - Hydrophobicity Score              : 10.9286
+HEADER 7  - Polarity Score                    :     8
+HEADER 8  - Volume Score                      : 4.2143
+HEADER 9  - Real volume (approximation)       : 508.4681
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 8.0000
+HEADER 12 - Number of apolar alpha sphere     :     9
+HEADER 13 - Proportion of apolar alpha sphere : 0.1915
+ATOM      1    O STP    15      20.194  -6.669  65.857    0.00     4.00
+ATOM      2    O STP    15      19.302  -6.705  64.169    0.00     4.29
+ATOM      3    O STP    15      22.214  -6.564  60.076    0.00     3.50
+ATOM      4    O STP    15      24.769  -6.899  59.562    0.00     3.81
+ATOM      5    O STP    15      24.498  -6.814  59.491    0.00     3.72
+ATOM      6    O STP    15      21.625  -5.139  58.615    0.00     3.82
+ATOM      7    O STP    15      22.531  -5.336  58.228    0.00     3.81
+ATOM      8    O STP    15      22.934  -5.701  58.422    0.00     3.71
+ATOM      9    O STP    15      23.613  -5.988  58.581    0.00     3.65
+ATOM     10    O STP    15      24.268  -6.113  58.655    0.00     3.70
+ATOM     11    O STP    15      24.337  -4.756  57.953    0.00     3.69
+ATOM     12    O STP    15      19.351  -5.149  62.950    0.00     3.51
+ATOM     13    O STP    15      18.113  -8.925  63.931    0.00     4.65
+ATOM     14    O STP    15      22.242  -9.055  63.581    0.00     4.62
+ATOM     15    O STP    15      24.776  -4.293  58.101    0.00     3.54
+ATOM     16    O STP    15      21.046  -3.142  57.435    0.00     3.49
+ATOM     17    O STP    15      18.742  -8.387  63.488    0.00     4.38
+ATOM     18    O STP    15      21.067  -7.471  62.275    0.00     4.28
+ATOM     19    C STP    15      20.683  -6.316  62.196    0.00     3.99
+ATOM     20    O STP    15      21.305  -7.029  61.758    0.00     4.12
+ATOM     21    C STP    15      20.346  -5.774  62.062    0.00     3.81
+ATOM     22    O STP    15      19.835  -5.733  62.428    0.00     3.81
+ATOM     23    C STP    15      20.890  -6.442  61.996    0.00     3.98
+ATOM     24    O STP    15      21.330  -5.775  59.666    0.00     3.64
+ATOM     25    O STP    15      21.452  -6.672  60.764    0.00     3.80
+ATOM     26    C STP    15      20.902  -5.288  60.104    0.00     3.53
+ATOM     27    C STP    15      20.692  -5.588  61.185    0.00     3.60
+ATOM     28    O STP    15      21.180  -3.123  57.227    0.00     3.47
+ATOM     29    O STP    15      24.771  -4.286  58.065    0.00     3.54
+ATOM     30    O STP    15      21.904  -4.215  55.911    0.00     3.53
+ATOM     31    O STP    15      21.808  -4.454  57.172    0.00     3.90
+ATOM     32    O STP    15      21.993  -4.533  57.561    0.00     3.98
+ATOM     33    O STP    15      24.306  -4.656  57.902    0.00     3.71
+ATOM     34    O STP    15      23.585  -4.634  57.880    0.00     3.69
+ATOM     35    O STP    15      24.352  -4.649  57.907    0.00     3.71
+ATOM     36    O STP    15      24.699  -4.344  58.058    0.00     3.57
+ATOM     37    C STP    15      20.988  -5.124  59.814    0.00     3.51
+ATOM     38    C STP    15      21.626  -5.116  58.595    0.00     3.83
+ATOM     39    C STP    15      20.713  -3.944  57.986    0.00     3.55
+ATOM     40    O STP    15      21.051  -3.158  57.441    0.00     3.49
+ATOM     41    C STP    15      21.439  -4.500  57.723    0.00     3.91
+ATOM     42    O STP    15      22.256  -4.833  57.963    0.00     3.96
+ATOM     43    O STP    15      22.061  -4.599  57.674    0.00     3.98
+ATOM     44    O STP    15      22.399  -4.726  57.910    0.00     3.93
+ATOM     45    O STP    15      21.734  -4.407  57.488    0.00     4.00
+ATOM     46    O STP    15      21.704  -4.339  57.480    0.00     3.96
+ATOM     47    O STP    15      21.781  -4.430  57.507    0.00     3.99
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket16_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    16:
+HEADER 0  - Pocket Score                      : 0.0741
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    20
+HEADER 3  - Mean alpha-sphere radius          : 3.6964
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.3921
+HEADER 5  - Mean B-factor of pocket residues  : 0.4762
+HEADER 6  - Hydrophobicity Score              : 9.0000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 2.9000
+HEADER 9  - Pocket volume (Monte Carlo)       : 166.2820
+HEADER 10  -Pocket volume (convex hull)       : 4.5717
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 1.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.1000
+ATOM    624   SG CYS A  97       2.577  20.007  30.576  0.00  0.00           S 0
+ATOM   1377    N GLY A 190      -2.688  23.547  31.816  0.00  0.00           N 0
+ATOM   1374   CA GLY A 189      -2.458  22.559  34.008  0.00  0.00           C 0
+ATOM    631  CD1 TRP A  98       0.531  23.921  31.248  0.00  0.00           C 0
+ATOM   1380    O GLY A 190      -2.803  22.883  29.185  0.00  0.00           O 0
+ATOM    608   CA GLY A  95       2.503  21.248  36.208  0.00  0.00           C 0
+ATOM   2906  NE2 GLN B  62       0.939  18.225  36.994  0.61  8.75           N 0
+ATOM   1786  OE2 GLU A 243       2.492  15.584  32.332  0.67  2.14           O 0
+ATOM   1784   CD GLU A 243       2.694  15.158  33.499  0.00  0.00           C 0
+ATOM   1860    O GLY A 253      -0.215  16.355  30.028  0.71  7.50           O 0
+ATOM   1777   OG SER A 242      -2.074  14.501  34.227  0.63  6.43           O 0
+ATOM   1783   CG GLU A 243       1.575  14.473  34.258  0.00  0.00           C 0
+ATOM    610    O GLY A  95       1.251  22.223  34.411  0.36  3.21           O 0
+ATOM   1785  OE1 GLU A 243       3.783  15.261  34.092  0.00  0.00           O 0
+ATOM    585  NE2 GLN A  91       5.950  20.196  34.395  0.18  1.09           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket16_vert.pqr

@@ -0,0 +1,42 @@
+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                      : 0.0741
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    20
+HEADER 3  - Mean alpha-sphere radius          : 3.6964
+HEADER 4  - Mean alpha-sphere SA              : 0.3921
+HEADER 5  - Mean B-factor                     : 0.4762
+HEADER 6  - Hydrophobicity Score              : 9.0000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 2.9000
+HEADER 9  - Real volume (approximation)       : 166.2820
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 1.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.1000
+ATOM      1    C STP    16      -0.703  20.660  31.637    0.00     3.51
+ATOM      2    O STP    16      -0.812  20.704  31.050    0.00     3.49
+ATOM      3    O STP    16       2.253  18.734  33.805    0.00     3.49
+ATOM      4    O STP    16       2.716  18.560  34.058    0.00     3.45
+ATOM      5    O STP    16      -1.764  19.741  31.334    0.00     3.95
+ATOM      6    O STP    16      -1.278  19.903  31.356    0.00     3.93
+ATOM      7    O STP    16      -1.286  19.922  31.268    0.00     3.93
+ATOM      8    O STP    16      -1.291  18.558  33.444    0.00     4.21
+ATOM      9    O STP    16       0.141  18.540  33.212    0.00     3.88
+ATOM     10    O STP    16      -0.337  17.740  33.506    0.00     3.75
+ATOM     11    O STP    16      -0.221  17.529  33.664    0.00     3.59
+ATOM     12    O STP    16       1.896  18.908  33.762    0.00     3.44
+ATOM     13    C STP    16      -0.502  20.722  31.885    0.00     3.42
+ATOM     14    O STP    16      -0.828  18.820  33.297    0.00     4.14
+ATOM     15    O STP    16      -0.715  19.279  32.645    0.00     3.96
+ATOM     16    O STP    16      -0.068  18.700  33.204    0.00     3.95
+ATOM     17    O STP    16       2.761  18.546  34.093    0.00     3.44
+ATOM     18    O STP    16       2.783  18.567  34.049    0.00     3.45
+ATOM     19    O STP    16       2.836  18.727  33.815    0.00     3.49
+ATOM     20    O STP    16       2.888  18.613  33.980    0.00     3.47
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket17_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    17:
+HEADER 0  - Pocket Score                      : 0.0734
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.8737
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6227
+HEADER 5  - Mean B-factor of pocket residues  : 0.6140
+HEADER 6  - Hydrophobicity Score              : 19.6250
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.2500
+HEADER 9  - Pocket volume (Monte Carlo)       : 320.3098
+HEADER 10  -Pocket volume (convex hull)       : 15.2698
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 1.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.1176
+ATOM   2564   CD ARG B  20       1.895  -9.042  63.508  0.00  0.00           C 0
+ATOM   3544  CD2 LEU B 142       2.332  -5.441  63.968  0.00  0.00           C 0
+ATOM   3543  CD1 LEU B 142       1.940  -3.858  62.018  0.00  0.00           C 0
+ATOM   2567  NH1 ARG B  20      -0.615 -10.157  62.593  0.00  0.00           N 0
+ATOM   2566   CZ ARG B  20      -0.197 -10.360  63.845  0.00  0.00           C 0
+ATOM   3492    O GLN B 137      -1.090  -3.041  67.202  0.32  7.50           O 0
+ATOM   2582  OG1 THR B  22       3.332  -6.306  58.107  0.65  7.50           O 0
+ATOM   2572    O ILE B  21       4.190 -10.199  60.500  0.00  0.00           O 0
+ATOM   3522  OE2 GLU B 140      -0.399  -9.585  67.558  0.50  3.21           O 0
+ATOM   3518   CB GLU B 140       1.528  -6.941  68.115  0.00  0.00           C 0
+ATOM   3513   OG SER B 139      -2.891  -5.975  69.521  0.69  5.36           O 0
+ATOM   3493   CB GLN B 137       0.258  -1.769  65.012  0.00  0.00           C 0
+ATOM   2565   NE ARG B  20       0.961  -9.856  64.292  0.00  0.00           N 0
+ATOM   2578   CA THR B  22       4.441  -8.458  58.374  0.00  0.00           C 0
+ATOM   2580    O THR B  22       3.562  -8.297  56.123  0.00  0.00           O 0
+ATOM   2579    C THR B  22       4.499  -8.641  56.836  0.00  0.00           C 0
+ATOM   2587    O HIS B  23       4.816 -11.612  54.959  0.52  8.57           O 0
+TER
+END

tests/reference_output/2P0R_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                      : 0.0734
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.8737
+HEADER 4  - Mean alpha-sphere SA              : 0.6227
+HEADER 5  - Mean B-factor                     : 0.6140
+HEADER 6  - Hydrophobicity Score              : 19.6250
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.2500
+HEADER 9  - Real volume (approximation)       : 320.3098
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 1.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.1176
+ATOM      1    C STP    17      -0.180  -6.713  61.783    0.00     3.56
+ATOM      2    O STP    17      -1.988  -6.341  64.382    0.00     4.43
+ATOM      3    O STP    17       0.439  -7.079  60.530    0.00     3.85
+ATOM      4    O STP    17       1.165  -8.346  60.082    0.00     3.57
+ATOM      5    O STP    17      -1.174  -6.469  65.339    0.00     3.90
+ATOM      6    O STP    17      -1.627  -6.540  64.913    0.00     4.22
+ATOM      7    O STP    17      -1.480  -6.449  66.302    0.00     3.55
+ATOM      8    C STP    17      -2.174  -5.247  63.374    0.00     4.55
+ATOM      9    O STP    17      -1.471  -6.621  64.938    0.00     4.10
+ATOM     10    O STP    17      -0.849  -6.895  63.839    0.00     3.50
+ATOM     11    O STP    17      -1.005  -6.836  63.974    0.00     3.62
+ATOM     12    O STP    17      -0.638  -6.853  65.304    0.00     3.55
+ATOM     13    O STP    17       0.908  -8.760  59.500    0.00     3.72
+ATOM     14    O STP    17       0.471  -9.896  58.519    0.00     4.22
+ATOM     15    O STP    17       0.320  -9.172  58.629    0.00     4.19
+ATOM     16    O STP    17       2.072 -11.479  57.601    0.00     3.81
+ATOM     17    O STP    17       2.092 -10.999  57.807    0.00     3.51
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket18_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    18:
+HEADER 0  - Pocket Score                      : 0.0703
+HEADER 1  - Drug Score                        : 0.0394
+HEADER 2  - Number of alpha spheres           :    25
+HEADER 3  - Mean alpha-sphere radius          : 3.8751
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5679
+HEADER 5  - Mean B-factor of pocket residues  : 0.7752
+HEADER 6  - Hydrophobicity Score              : 21.8750
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 284.1812
+HEADER 10  -Pocket volume (convex hull)       : 16.8484
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 16.0000
+HEADER 13 - Number of apolar alpha sphere     :    17
+HEADER 14 - Proportion of apolar alpha sphere : 0.6800
+ATOM     64   CD GLN A  27       7.532  56.165  38.625  0.00  0.00           C 0
+ATOM     65  OE1 GLN A  27       8.118  57.065  38.005  0.56  7.50           O 0
+ATOM     66  NE2 GLN A  27       6.755  56.406  39.684  0.65  6.56           N 0
+ATOM    137  OE1 GLU A  35      12.803  57.554  42.729  0.42  6.43           O 0
+ATOM    103   CA MET A  32      11.298  52.230  38.954  0.00  0.00           C 0
+ATOM    106   CB MET A  32      10.293  51.085  38.931  0.00  0.00           C 0
+ATOM    105    O MET A  32      13.242  51.655  40.239  0.00  0.00           O 0
+ATOM    135   CG GLU A  35      12.793  55.209  43.256  0.00  0.00           C 0
+ATOM    107   CG MET A  32       8.869  51.543  39.025  0.00  0.00           C 0
+ATOM    108   SD MET A  32       7.639  50.225  39.105  0.00  0.00           S 0
+ATOM    200  CE1 PHE A  43       9.337  47.743  41.664  0.00  0.00           C 0
+ATOM     52   CB SER A  25       3.884  52.452  40.968  0.00  0.00           C 0
+ATOM     53   OG SER A  25       4.606  52.130  39.791  0.00  0.00           O 0
+ATOM     62   CB GLN A  27       6.397  53.887  38.237  0.00  0.00           C 0
+ATOM    136   CD GLU A  35      12.821  56.694  43.667  0.00  0.00           C 0
+ATOM     40  CE1 HIS A  23       4.985  48.601  41.019  0.00  0.00           C 0
+ATOM    198  CD1 PHE A  43      10.676  47.759  42.042  0.00  0.00           C 0
+ATOM    144   SG CYS A  36      14.203  50.056  43.160  0.00  0.00           S 0
+ATOM    134   CB GLU A  35      13.206  54.987  41.765  0.00  0.00           C 0
+ATOM     96    O GLN A  31      12.787  54.534  38.268  0.68  4.29           O 0
+ATOM     63   CG GLN A  27       7.693  54.702  38.207  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket18_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    18:
+HEADER 0  - Pocket Score                      : 0.0703
+HEADER 1  - Drug Score                        : 0.0394
+HEADER 2  - Number of V. Vertices             :    25
+HEADER 3  - Mean alpha-sphere radius          : 3.8751
+HEADER 4  - Mean alpha-sphere SA              : 0.5679
+HEADER 5  - Mean B-factor                     : 0.7752
+HEADER 6  - Hydrophobicity Score              : 21.8750
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 284.1812
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 16.0000
+HEADER 12 - Number of apolar alpha sphere     :    17
+HEADER 13 - Proportion of apolar alpha sphere : 0.6800
+ATOM      1    O STP    18       9.873  57.110  40.970    0.00     3.45
+ATOM      2    C STP    18      10.169  52.129  42.859    0.00     4.07
+ATOM      3    C STP    18       7.693  51.678  43.525    0.00     4.65
+ATOM      4    C STP    18      10.114  52.177  42.844    0.00     4.07
+ATOM      5    O STP    18       7.428  53.447  42.016    0.00     3.83
+ATOM      6    C STP    18       7.283  51.988  42.326    0.00     3.69
+ATOM      7    O STP    18       7.372  53.467  41.688    0.00     3.61
+ATOM      8    O STP    18       9.261  56.285  42.497    0.00     3.77
+ATOM      9    C STP    18       7.496  51.434  43.419    0.00     4.48
+ATOM     10    C STP    18      10.089  51.870  43.152    0.00     4.30
+ATOM     11    C STP    18      10.351  51.770  43.309    0.00     4.22
+ATOM     12    C STP    18       9.453  51.972  43.635    0.00     4.67
+ATOM     13    C STP    18       9.783  51.221  42.496    0.00     3.60
+ATOM     14    C STP    18      10.040  51.881  43.170    0.00     4.32
+ATOM     15    O STP    18       9.814  56.056  41.486    0.00     3.57
+ATOM     16    O STP    18       9.925  56.172  41.221    0.00     3.53
+ATOM     17    O STP    18      10.367  56.496  40.544    0.00     3.44
+ATOM     18    O STP    18      10.877  56.777  40.009    0.00     3.42
+ATOM     19    C STP    18       9.526  54.137  41.691    0.00     3.78
+ATOM     20    C STP    18       9.607  54.831  41.293    0.00     3.63
+ATOM     21    C STP    18       9.469  54.324  41.547    0.00     3.80
+ATOM     22    C STP    18       7.565  53.586  41.433    0.00     3.42
+ATOM     23    C STP    18       9.335  54.317  41.713    0.00     3.89
+ATOM     24    C STP    18       9.418  54.448  41.615    0.00     3.83
+ATOM     25    C STP    18       9.414  54.325  41.632    0.00     3.85
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket19_atm.pdb

@@ -0,0 +1,47 @@
+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                      : 0.0540
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    34
+HEADER 3  - Mean alpha-sphere radius          : 4.0010
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5332
+HEADER 5  - Mean B-factor of pocket residues  : 0.8006
+HEADER 6  - Hydrophobicity Score              : 20.8333
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.8333
+HEADER 9  - Pocket volume (Monte Carlo)       : 370.9989
+HEADER 10  -Pocket volume (convex hull)       : 31.4529
+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   2948  NE1 TRP B  67       9.537   5.577  42.941  0.65  1.09           N 0
+ATOM   2806    O ALA B  50       9.410   2.025  41.759  0.43  8.57           O 0
+ATOM   2809   CA SER B  51       6.756   2.911  41.996  0.00  0.00           C 0
+ATOM   2946  CD1 TRP B  67      10.791   5.409  42.408  0.00  0.00           C 0
+ATOM   1801  NH1 ARG A 245      10.700   7.731  33.691  0.00  0.00           N 0
+ATOM   1802  NH2 ARG A 245       9.503   9.619  34.228  0.49  5.47           N 0
+ATOM   1800   CZ ARG A 245       9.637   8.511  33.508  0.00  0.00           C 0
+ATOM   2925    O PHE B  65      10.933   8.937  39.657  0.00  0.00           O 0
+ATOM   1799   NE ARG A 245       8.712   8.199  32.602  0.65  1.09           N 0
+ATOM   1796   CB ARG A 245       6.200   6.917  31.895  0.00  0.00           C 0
+ATOM   1798   CD ARG A 245       8.751   6.999  31.761  0.00  0.00           C 0
+ATOM   2821  ND2 ASN B  52       3.713   7.082  38.405  0.43  9.84           N 0
+ATOM   2820  OD1 ASN B  52       5.252   7.290  40.034  0.00  0.00           O 0
+ATOM   2922    N PHE B  65      10.275  11.638  39.510  0.58  1.09           N 0
+ATOM   2897   CD PRO B  61       4.112  11.356  40.072  0.00  0.00           C 0
+ATOM   2910    O ILE B  63       7.957  13.483  38.714  0.62  1.07           O 0
+ATOM   2916   CA PRO B  64      10.051  12.487  37.216  0.00  0.00           C 0
+ATOM   2087  CH2 TRP A 280       7.593  13.169  33.391  0.00  0.00           C 0
+ATOM   2896   CG PRO B  61       5.266  11.804  40.867  0.00  0.00           C 0
+ATOM   1781    O GLU A 243       3.039  10.509  33.721  0.38  7.50           O 0
+ATOM   1792    N ARG A 245       3.836   7.552  31.936  0.45  3.28           N 0
+ATOM   2894    O PRO B  61       4.125  13.873  37.996  0.70  1.07           O 0
+ATOM   2884   CB ARG B  60       1.662  10.959  38.119  0.00  0.00           C 0
+ATOM   2814    N ASN B  52       5.026   4.545  41.543  0.73  2.19           N 0
+ATOM   2819   CG ASN B  52       4.173   6.853  39.640  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket19_vert.pqr

@@ -0,0 +1,56 @@
+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                      : 0.0540
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    34
+HEADER 3  - Mean alpha-sphere radius          : 4.0010
+HEADER 4  - Mean alpha-sphere SA              : 0.5332
+HEADER 5  - Mean B-factor                     : 0.8006
+HEADER 6  - Hydrophobicity Score              : 20.8333
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.8333
+HEADER 9  - Real volume (approximation)       : 370.9989
+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    19       8.646   4.843  39.309    0.00     3.81
+ATOM      2    O STP    19       8.670   6.888  37.050    0.00     4.01
+ATOM      3    O STP    19       7.690   5.224  35.649    0.00     4.38
+ATOM      4    O STP    19       7.729   5.195  35.566    0.00     4.33
+ATOM      5    O STP    19       6.998   6.418  35.945    0.00     4.16
+ATOM      6    O STP    19       6.716   7.405  35.892    0.00     3.93
+ATOM      7    O STP    19       6.324   7.901  35.649    0.00     3.88
+ATOM      8    O STP    19       7.562   9.442  37.663    0.00     3.95
+ATOM      9    O STP    19       8.541   5.065  38.991    0.00     4.11
+ATOM     10    O STP    19       8.716   5.807  39.170    0.00     3.87
+ATOM     11    O STP    19       8.297   6.788  37.136    0.00     4.23
+ATOM     12    O STP    19       7.336   7.058  36.540    0.00     4.07
+ATOM     13    O STP    19       6.456   9.849  37.015    0.00     4.14
+ATOM     14    O STP    19       6.645   9.900  37.174    0.00     4.11
+ATOM     15    O STP    19       8.633   4.965  38.698    0.00     4.31
+ATOM     16    O STP    19       8.378   6.510  37.138    0.00     4.33
+ATOM     17    O STP    19       7.632   9.458  37.646    0.00     3.90
+ATOM     18    O STP    19       7.323   9.732  37.778    0.00     3.92
+ATOM     19    O STP    19       7.543   9.464  37.657    0.00     3.95
+ATOM     20    O STP    19       7.104   9.759  37.454    0.00     4.02
+ATOM     21    O STP    19       6.861  11.062  36.249    0.00     3.63
+ATOM     22    O STP    19       6.936   9.973  38.113    0.00     3.70
+ATOM     23    O STP    19       7.237   9.911  38.442    0.00     3.65
+ATOM     24    O STP    19       6.029   8.863  34.953    0.00     3.63
+ATOM     25    O STP    19       5.300   8.068  35.254    0.00     3.66
+ATOM     26    O STP    19       5.939   8.512  35.487    0.00     3.94
+ATOM     27    O STP    19       6.064  10.050  36.594    0.00     4.20
+ATOM     28    O STP    19       6.176  10.709  36.316    0.00     4.08
+ATOM     29    O STP    19       6.129  10.789  36.315    0.00     4.04
+ATOM     30    O STP    19       4.902  10.083  36.786    0.00     3.61
+ATOM     31    O STP    19       4.863  10.694  36.711    0.00     3.51
+ATOM     32    O STP    19       6.122  10.436  36.533    0.00     4.17
+ATOM     33    O STP    19       6.064  10.538  36.529    0.00     4.13
+ATOM     34    O STP    19       6.918   3.876  37.341    0.00     4.66
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket1_atm.pdb

@@ -0,0 +1,50 @@
+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                      : 0.3579
+HEADER 1  - Drug Score                        : 0.0540
+HEADER 2  - Number of alpha spheres           :    46
+HEADER 3  - Mean alpha-sphere radius          : 3.8728
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4671
+HEADER 5  - Mean B-factor of pocket residues  : 0.7038
+HEADER 6  - Hydrophobicity Score              : 10.1429
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 3.4286
+HEADER 9  - Pocket volume (Monte Carlo)       : 386.6498
+HEADER 10  -Pocket volume (convex hull)       : 47.0975
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 14.6250
+HEADER 13 - Number of apolar alpha sphere     :    16
+HEADER 14 - Proportion of apolar alpha sphere : 0.3478
+ATOM   4329   OG SER B 242      -2.458  22.779  57.442  0.46  2.14           O 0
+ATOM   4308    O ALA B 239      -6.176  24.381  55.461  0.52  7.50           O 0
+ATOM   4328   CB SER B 242      -3.494  23.750  57.388  0.00  0.00           C 0
+ATOM    326  OE1 GLU A  59      -3.044  21.598  50.555  0.00  0.00           O 0
+ATOM    323   CB GLU A  59      -3.538  24.430  50.590  0.00  0.00           C 0
+ATOM   5142    O LEU E 356      -3.779  19.268  60.303  0.71  2.14           O 0
+ATOM   5143   CB LEU E 356      -4.971  16.227  60.338  0.00  0.00           C 0
+HETATM 5137    O ACE E 355      -7.922  17.564  59.708  0.00  0.00           O 0
+ATOM   3926   CA GLY B 189      -1.806  15.347  57.587  0.00  0.00           C 0
+ATOM   3919    O LYS B 188      -2.310  13.999  55.215  0.16  8.57           O 0
+ATOM   5145  CD1 LEU E 356      -5.131  13.800  59.853  0.00  0.00           C 0
+ATOM   5150    O LEU E 357      -0.739  17.137  59.981  0.00  0.00           O 0
+ATOM   3162    O GLY B  95       1.796  16.322  56.982  0.00  0.00           O 0
+ATOM   3925    N GLY B 189      -0.844  15.092  56.538  0.00  0.00           N 0
+ATOM   3921   CG LYS B 188      -1.076  15.859  52.881  0.00  0.00           C 0
+ATOM   3923   CE LYS B 188      -2.528  17.163  51.213  0.00  0.00           C 0
+ATOM   4335   CG GLU B 243       1.200  23.713  56.721  0.00  0.00           C 0
+ATOM   3160   CA GLY B  95       3.021  17.527  55.300  0.00  0.00           C 0
+ATOM   4336   CD GLU B 243       2.401  23.261  57.540  0.00  0.00           C 0
+ATOM   4338  OE2 GLU B 243       3.328  22.668  56.956  0.00  0.00           O 0
+ATOM   3176   SG CYS B  97       2.842  18.748  60.855  0.00  0.00           S 0
+ATOM   4327    O SER B 242      -1.793  25.960  56.221  0.37  1.07           O 0
+ATOM   5149    C LEU E 357      -0.704  18.267  60.447  0.00  0.00           C 0
+ATOM    351   CG GLN A  62       1.945  20.477  53.022  0.00  0.00           C 0
+ATOM    353  OE1 GLN A  62       1.389  18.286  52.065  0.59  2.14           O 0
+ATOM    352   CD GLN A  62       1.503  19.518  51.878  0.00  0.00           C 0
+ATOM    331    O ARG A  60       0.082  24.654  51.811  0.56  2.14           O 0
+ATOM   4412    O GLY B 253      -0.409  21.779  61.354  0.00  0.00           O 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket1_vert.pqr

@@ -0,0 +1,68 @@
+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                      : 0.3579
+HEADER 1  - Drug Score                        : 0.0540
+HEADER 2  - Number of V. Vertices             :    46
+HEADER 3  - Mean alpha-sphere radius          : 3.8728
+HEADER 4  - Mean alpha-sphere SA              : 0.4671
+HEADER 5  - Mean B-factor                     : 0.7038
+HEADER 6  - Hydrophobicity Score              : 10.1429
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 3.4286
+HEADER 9  - Real volume (approximation)       : 386.6498
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 14.6250
+HEADER 12 - Number of apolar alpha sphere     :    16
+HEADER 13 - Proportion of apolar alpha sphere : 0.3478
+ATOM      1    O STP     1      -3.432  22.587  53.988    0.00     3.59
+ATOM      2    O STP     1      -3.260  22.979  53.876    0.00     3.60
+ATOM      3    O STP     1      -3.021  23.020  53.879    0.00     3.62
+ATOM      4    O STP     1      -5.139  18.000  56.241    0.00     4.47
+ATOM      5    C STP     1      -5.520  15.759  56.519    0.00     3.89
+ATOM      6    O STP     1      -6.092  15.865  56.176    0.00     4.33
+ATOM      7    O STP     1      -5.689  16.686  56.029    0.00     4.39
+ATOM      8    O STP     1      -1.988  19.065  56.992    0.00     3.77
+ATOM      9    O STP     1      -1.054  19.135  56.359    0.00     4.05
+ATOM     10    O STP     1      -1.030  19.140  56.509    0.00     4.02
+ATOM     11    C STP     1      -4.106  17.799  55.060    0.00     4.21
+ATOM     12    O STP     1      -1.993  19.036  55.522    0.00     4.23
+ATOM     13    C STP     1      -3.377  18.910  55.294    0.00     4.52
+ATOM     14    O STP     1       0.134  19.899  56.615    0.00     3.96
+ATOM     15    C STP     1       0.576  19.947  56.972    0.00     3.83
+ATOM     16    C STP     1       0.711  20.023  56.817    0.00     3.72
+ATOM     17    O STP     1       1.860  19.667  57.707    0.00     3.42
+ATOM     18    O STP     1       0.843  19.911  57.140    0.00     3.72
+ATOM     19    O STP     1      -3.137  23.728  53.950    0.00     3.46
+ATOM     20    O STP     1      -2.696  23.368  53.911    0.00     3.59
+ATOM     21    O STP     1      -1.985  19.068  56.996    0.00     3.77
+ATOM     22    C STP     1       0.222  20.436  57.761    0.00     3.57
+ATOM     23    O STP     1      -0.922  19.206  56.582    0.00     3.98
+ATOM     24    O STP     1       0.204  19.918  56.995    0.00     3.93
+ATOM     25    C STP     1       0.449  19.944  57.157    0.00     3.87
+ATOM     26    C STP     1       1.216  19.842  57.802    0.00     3.63
+ATOM     27    O STP     1       1.221  19.822  57.782    0.00     3.64
+ATOM     28    O STP     1       1.172  19.834  57.741    0.00     3.65
+ATOM     29    C STP     1       0.813  20.142  56.427    0.00     3.60
+ATOM     30    C STP     1       0.101  19.921  56.477    0.00     3.96
+ATOM     31    O STP     1      -0.077  19.777  56.374    0.00     3.98
+ATOM     32    O STP     1      -0.991  19.219  55.754    0.00     4.20
+ATOM     33    C STP     1      -0.569  18.753  55.281    0.00     3.79
+ATOM     34    C STP     1      -0.570  18.754  55.282    0.00     3.80
+ATOM     35    O STP     1      -1.252  19.193  55.508    0.00     4.25
+ATOM     36    C STP     1      -1.917  19.656  54.605    0.00     4.25
+ATOM     37    C STP     1      -1.637  19.484  54.228    0.00     3.91
+ATOM     38    C STP     1      -1.629  19.517  54.148    0.00     3.87
+ATOM     39    O STP     1      -2.038  19.977  54.317    0.00     4.22
+ATOM     40    C STP     1      -1.829  19.936  53.875    0.00     3.91
+ATOM     41    O STP     1      -0.779  18.887  55.413    0.00     3.96
+ATOM     42    O STP     1      -1.409  21.924  53.930    0.00     3.76
+ATOM     43    O STP     1      -0.928  22.231  54.249    0.00     3.58
+ATOM     44    O STP     1      -2.523  23.108  53.821    0.00     3.64
+ATOM     45    O STP     1      -2.556  23.326  53.879    0.00     3.61
+ATOM     46    O STP     1       0.191  20.674  58.137    0.00     3.45
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket20_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    20:
+HEADER 0  - Pocket Score                      : 0.0475
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    23
+HEADER 3  - Mean alpha-sphere radius          : 4.0202
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6976
+HEADER 5  - Mean B-factor of pocket residues  : 0.5092
+HEADER 6  - Hydrophobicity Score              : 12.0000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.6250
+HEADER 9  - Pocket volume (Monte Carlo)       : 279.1420
+HEADER 10  -Pocket volume (convex hull)       : 12.8866
+HEADER 11 - Charge Score                      :     3
+HEADER 12 - Local hydrophobic density Score   : 1.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.0870
+ATOM    702    O LEU A 108      14.548  29.949  16.096  0.55  6.43           O 0
+ATOM    713  OD1 ASN A 109      12.412  34.568  15.449  0.59  5.36           O 0
+ATOM   1649    O LYS A 225      11.870  29.904   9.315  0.00  0.00           O 0
+ATOM    712   CG ASN A 109      11.575  33.694  15.586  0.00  0.00           C 0
+ATOM    708   CA ASN A 109      13.280  32.318  16.913  0.00  0.00           C 0
+ATOM    715    N GLN A 110      15.067  33.877  17.482  0.65  1.09           N 0
+ATOM    719   CB GLN A 110      17.157  35.173  17.626  0.00  0.00           C 0
+ATOM    724    N LYS A 111      14.241  36.438  17.493  0.00  0.00           N 0
+ATOM    728   CB LYS A 111      13.511  37.947  15.851  0.00  0.00           C 0
+ATOM    723  NE2 GLN A 110      19.045  32.911  15.556  0.35  8.75           N 0
+ATOM    721   CD GLN A 110      19.054  33.984  16.354  0.00  0.00           C 0
+ATOM    722  OE1 GLN A 110      19.786  34.960  16.149  0.00  0.00           O 0
+ATOM   1657    C ARG A 226       9.181  31.258  10.733  0.00  0.00           C 0
+ATOM   1656   CA ARG A 226       9.354  30.859   9.257  0.00  0.00           C 0
+ATOM   1658    O ARG A 226       8.635  32.310  11.019  0.47  7.50           O 0
+ATOM    714  ND2 ASN A 109      10.420  33.697  14.917  0.61  2.19           N 0
+ATOM   1641    O LEU A 224      10.763  27.660  11.810  0.53  6.43           O 0
+ATOM   1667   CA GLY A 227       9.730  30.788  13.074  0.00  0.00           C 0
+ATOM   1666    N GLY A 227       9.646  30.420  11.660  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket20_vert.pqr

@@ -0,0 +1,45 @@
+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    20:
+HEADER 0  - Pocket Score                      : 0.0475
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    23
+HEADER 3  - Mean alpha-sphere radius          : 4.0202
+HEADER 4  - Mean alpha-sphere SA              : 0.6976
+HEADER 5  - Mean B-factor                     : 0.5092
+HEADER 6  - Hydrophobicity Score              : 12.0000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 4.6250
+HEADER 9  - Real volume (approximation)       : 279.1420
+HEADER 10 - Charge Score                      :     3
+HEADER 11 - Local hydrophobic density Score   : 1.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.0870
+ATOM      1    O STP    20      13.785  31.936  12.465    0.00     4.21
+ATOM      2    O STP    20      13.798  32.093  13.542    0.00     3.42
+ATOM      3    O STP    20      15.442  32.888  13.789    0.00     3.84
+ATOM      4    O STP    20      15.721  35.515  14.317    0.00     3.62
+ATOM      5    O STP    20      15.723  35.519  14.313    0.00     3.63
+ATOM      6    O STP    20      15.554  32.921  13.654    0.00     3.98
+ATOM      7    O STP    20      16.076  35.013  13.683    0.00     4.09
+ATOM      8    C STP    20      16.562  36.007  13.352    0.00     4.39
+ATOM      9    C STP    20      16.195  35.486  13.292    0.00     4.45
+ATOM     10    O STP    20      16.202  35.490  13.241    0.00     4.48
+ATOM     11    O STP    20      16.183  35.418  13.338    0.00     4.40
+ATOM     12    O STP    20      11.849  33.659   9.595    0.00     3.77
+ATOM     13    O STP    20      12.722  33.663  11.246    0.00     4.31
+ATOM     14    O STP    20      12.707  33.515  11.359    0.00     4.23
+ATOM     15    O STP    20      12.675  33.622  11.307    0.00     4.26
+ATOM     16    O STP    20      13.303  30.142  12.667    0.00     3.65
+ATOM     17    O STP    20      13.716  31.885  12.492    0.00     4.17
+ATOM     18    O STP    20      13.510  32.175  12.307    0.00     4.10
+ATOM     19    O STP    20      12.826  32.797  12.091    0.00     3.82
+ATOM     20    O STP    20      12.822  33.037  11.713    0.00     4.06
+ATOM     21    O STP    20      12.647  33.160  11.584    0.00     4.04
+ATOM     22    O STP    20      12.561  33.001  11.572    0.00     3.89
+ATOM     23    O STP    20      12.088  33.204  11.724    0.00     3.64
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket21_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    21:
+HEADER 0  - Pocket Score                      : 0.0465
+HEADER 1  - Drug Score                        : 0.0142
+HEADER 2  - Number of alpha spheres           :    27
+HEADER 3  - Mean alpha-sphere radius          : 3.9281
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6600
+HEADER 5  - Mean B-factor of pocket residues  : 0.4483
+HEADER 6  - Hydrophobicity Score              : -9.3750
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 3.8750
+HEADER 9  - Pocket volume (Monte Carlo)       : 359.6914
+HEADER 10  -Pocket volume (convex hull)       : 34.3167
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 12.0000
+HEADER 13 - Number of apolar alpha sphere     :    13
+HEADER 14 - Proportion of apolar alpha sphere : 0.4815
+ATOM   2424   CG LYS A 322       5.133   5.657   9.702  0.00  0.00           C 0
+ATOM   2426   CE LYS A 322       4.989   3.124   9.316  0.00  0.00           C 0
+ATOM   2460   CB ALA A 326       1.969   5.869  15.007  0.00  0.00           C 0
+ATOM   2427   NZ LYS A 322       4.063   3.369   8.180  0.00  0.00           N 0
+ATOM   2422    O LYS A 322       4.086   7.520  12.471  0.67  5.36           O 0
+ATOM   2434  OD1 ASP A 323       7.277   4.557  13.455  0.67  9.64           O 0
+ATOM   2451   CB LYS A 325       1.910  10.505  12.327  0.00  0.00           C 0
+ATOM   2457   CA ALA A 326       1.238   7.178  15.369  0.00  0.00           C 0
+ATOM   1525   CG LYS A 210      -3.295   8.952  13.937  0.00  0.00           C 0
+ATOM   1527   CE LYS A 210      -2.765   7.664  16.012  0.00  0.00           C 0
+ATOM   2455   NZ LYS A 325       1.878  10.755   7.855  0.00  5.47           N 0
+ATOM   1521   CA LYS A 210      -3.872  10.844  12.313  0.00  0.00           C 0
+ATOM   2453   CD LYS A 325       1.829  11.818  10.143  0.00  0.00           C 0
+ATOM   1516    O THR A 209      -1.667  12.542  11.972  0.00  0.00           O 0
+ATOM   1523    O LYS A 210      -5.188  10.334  10.406  0.00  0.00           O 0
+ATOM   1541    O ALA A 212      -3.631  14.355   6.775  0.67  7.50           O 0
+ATOM   1538    N ALA A 212      -4.369  14.239   9.363  0.00  0.00           N 0
+ATOM   2454   CE LYS A 325       2.590  10.873   9.182  0.00  0.00           C 0
+ATOM   1542   CB ALA A 212      -2.278  15.543   9.525  0.00  0.00           C 0
+ATOM   1546    O PRO A 213      -1.160  15.349   5.530  0.31  3.21           O 0
+ATOM   2456    N ALA A 326       1.926   8.328  14.798  0.00  0.00           N 0
+ATOM   2449    C LYS A 325       1.316   9.500  14.591  0.00  0.00           C 0
+ATOM   2450    O LYS A 325       0.172   9.754  14.989  0.00  0.00           O 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket21_vert.pqr

@@ -0,0 +1,49 @@
+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    21:
+HEADER 0  - Pocket Score                      : 0.0465
+HEADER 1  - Drug Score                        : 0.0142
+HEADER 2  - Number of V. Vertices             :    27
+HEADER 3  - Mean alpha-sphere radius          : 3.9281
+HEADER 4  - Mean alpha-sphere SA              : 0.6600
+HEADER 5  - Mean B-factor                     : 0.4483
+HEADER 6  - Hydrophobicity Score              : -9.3750
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 3.8750
+HEADER 9  - Real volume (approximation)       : 359.6914
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 12.0000
+HEADER 12 - Number of apolar alpha sphere     :    13
+HEADER 13 - Proportion of apolar alpha sphere : 0.4815
+ATOM      1    C STP    21       1.680   4.310  11.297    0.00     4.03
+ATOM      2    O STP    21       1.055   4.865  10.902    0.00     4.32
+ATOM      3    O STP    21       3.837   3.939  12.621    0.00     3.59
+ATOM      4    C STP    21       3.410   4.053  12.339    0.00     3.53
+ATOM      5    O STP    21       3.902   3.990  12.567    0.00     3.54
+ATOM      6    C STP    21      -0.096   6.696  11.133    0.00     4.47
+ATOM      7    C STP    21      -1.463   5.468  12.812    0.00     4.09
+ATOM      8    C STP    21      -1.136   7.929   9.962    0.00     4.64
+ATOM      9    C STP    21      -1.076   8.957  10.019    0.00     4.08
+ATOM     10    C STP    21      -1.069   9.073  10.088    0.00     3.99
+ATOM     11    O STP    21      -1.444   9.448   9.535    0.00     3.95
+ATOM     12    O STP    21      -1.137   9.130   9.937    0.00     4.01
+ATOM     13    O STP    21      -2.164  11.358   8.461    0.00     3.74
+ATOM     14    O STP    21      -1.983  11.165   8.325    0.00     3.91
+ATOM     15    C STP    21      -0.255   9.002  10.015    0.00     3.51
+ATOM     16    O STP    21       0.311   6.933   9.896    0.00     4.61
+ATOM     17    O STP    21       1.006   6.881   9.527    0.00     4.31
+ATOM     18    O STP    21      -1.256  12.316   8.452    0.00     3.55
+ATOM     19    O STP    21      -1.253  12.318   8.453    0.00     3.55
+ATOM     20    O STP    21      -0.738  12.949   7.923    0.00     3.42
+ATOM     21    O STP    21       0.021   6.788  11.259    0.00     4.30
+ATOM     22    O STP    21       0.171   6.770  11.404    0.00     4.13
+ATOM     23    C STP    21      -0.405   7.244  11.663    0.00     4.05
+ATOM     24    C STP    21      -0.408   7.337  11.746    0.00     3.97
+ATOM     25    C STP    21      -0.424   7.347  11.850    0.00     3.90
+ATOM     26    C STP    21      -0.533   7.551  12.446    0.00     3.44
+ATOM     27    C STP    21      -0.544   8.113  12.054    0.00     3.44
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket22_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    22:
+HEADER 0  - Pocket Score                      : 0.0438
+HEADER 1  - Drug Score                        : 0.0050
+HEADER 2  - Number of alpha spheres           :    18
+HEADER 3  - Mean alpha-sphere radius          : 4.0675
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6726
+HEADER 5  - Mean B-factor of pocket residues  : 0.5220
+HEADER 6  - Hydrophobicity Score              : 0.3333
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.6667
+HEADER 9  - Pocket volume (Monte Carlo)       : 231.6918
+HEADER 10  -Pocket volume (convex hull)       : 2.1721
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 12.0000
+HEADER 13 - Number of apolar alpha sphere     :    13
+HEADER 14 - Proportion of apolar alpha sphere : 0.7222
+ATOM   1989   CB ARG A 270      14.526  10.413   1.557  0.00  0.00           C 0
+ATOM   1986   CA ARG A 270      14.943   9.218   2.406  0.00  0.00           C 0
+ATOM   1985    N ARG A 270      15.069   8.035   1.583  0.00  0.00           N 0
+ATOM   1949   OG SER A 265      20.042   7.618   2.078  0.00  0.00           O 0
+ATOM   1948   CB SER A 265      20.277   8.526   3.146  0.00  0.00           C 0
+ATOM   1990   CG ARG A 270      14.807  11.769   2.229  0.00  0.00           C 0
+ATOM   1991   CD ARG A 270      14.705  12.910   1.238  0.00  0.00           C 0
+ATOM   2267  OE2 GLU A 303      22.137  12.354   5.350  0.51  5.36           O 0
+ATOM   1944    N SER A 265      19.144   9.655   4.973  0.00  0.00           N 0
+ATOM   1945   CA SER A 265      19.139   8.470   4.160  0.00  0.00           C 0
+ATOM   1938   CA VAL A 264      18.268  11.226   6.534  0.00  0.00           C 0
+ATOM   1939    C VAL A 264      18.042  10.116   5.554  0.00  0.00           C 0
+ATOM   1932   CB GLN A 263      15.315  14.288   5.397  0.00  0.00           C 0
+ATOM   1931    O GLN A 263      18.007  13.940   7.141  0.28  2.14           O 0
+ATOM   2296  NH2 ARG A 306      20.721  15.505   6.846  0.50  7.66           N 0
+ATOM   1937    N VAL A 264      17.022  11.951   6.758  0.00  0.00           N 0
+ATOM   1930    C GLN A 263      16.998  13.269   6.924  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket22_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    22:
+HEADER 0  - Pocket Score                      : 0.0438
+HEADER 1  - Drug Score                        : 0.0050
+HEADER 2  - Number of V. Vertices             :    18
+HEADER 3  - Mean alpha-sphere radius          : 4.0675
+HEADER 4  - Mean alpha-sphere SA              : 0.6726
+HEADER 5  - Mean B-factor                     : 0.5220
+HEADER 6  - Hydrophobicity Score              : 0.3333
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 4.6667
+HEADER 9  - Real volume (approximation)       : 231.6918
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 12.0000
+HEADER 12 - Number of apolar alpha sphere     :    13
+HEADER 13 - Proportion of apolar alpha sphere : 0.7222
+ATOM      1    O STP    22      17.854   9.911   0.584    0.00     3.50
+ATOM      2    C STP    22      18.031  10.363   1.133    0.00     3.53
+ATOM      3    O STP    22      19.020  13.203   2.289    0.00     4.45
+ATOM      4    C STP    22      19.178  12.590   1.567    0.00     4.50
+ATOM      5    C STP    22      18.084  10.855   1.960    0.00     3.41
+ATOM      6    C STP    22      18.015  10.603   1.478    0.00     3.49
+ATOM      7    O STP    22      18.779  13.396   2.819    0.00     4.33
+ATOM      8    C STP    22      18.772  13.389   2.824    0.00     4.32
+ATOM      9    C STP    22      18.666  11.331   0.170    0.00     4.40
+ATOM     10    C STP    22      18.415  11.002   0.505    0.00     4.07
+ATOM     11    C STP    22      18.562  11.205   0.035    0.00     4.39
+ATOM     12    O STP    22      19.036  14.478   2.676    0.00     4.61
+ATOM     13    C STP    22      18.786  13.596   2.765    0.00     4.41
+ATOM     14    O STP    22      18.766  13.524   2.901    0.00     4.33
+ATOM     15    C STP    22      18.758  13.496   2.848    0.00     4.36
+ATOM     16    C STP    22      17.859  12.903   3.585    0.00     3.42
+ATOM     17    C STP    22      18.290  13.169   3.184    0.00     3.87
+ATOM     18    C STP    22      18.434  13.383   3.387    0.00     3.82
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket23_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    23:
+HEADER 0  - Pocket Score                      : 0.0425
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    26
+HEADER 3  - Mean alpha-sphere radius          : 4.1515
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6662
+HEADER 5  - Mean B-factor of pocket residues  : 0.6215
+HEADER 6  - Hydrophobicity Score              : 7.5000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.3333
+HEADER 9  - Pocket volume (Monte Carlo)       : 373.4230
+HEADER 10  -Pocket volume (convex hull)       : 14.4928
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 0.0000
+HEADER 13 - Number of apolar alpha sphere     :     2
+HEADER 14 - Proportion of apolar alpha sphere : 0.0769
+ATOM    946    N HIS A 138      -4.980  41.020  26.242  0.71  4.37           N 0
+ATOM    952  ND1 HIS A 138      -8.760  40.087  27.971  0.00  0.00           N 0
+ATOM    951   CG HIS A 138      -7.632  39.853  27.212  0.00  0.00           C 0
+ATOM    953  CD2 HIS A 138      -6.914  38.923  27.886  0.00  0.00           C 0
+ATOM    942   CG GLN A 137      -3.192  39.180  28.919  0.00  0.00           C 0
+ATOM    991  CD1 LEU A 142      -1.285  42.907  30.241  0.00  0.00           C 0
+ATOM     16  NH2 ARG A  20      -3.523  46.470  30.335  0.39  6.56           N 0
+ATOM    992  CD2 LEU A 142      -1.176  44.692  28.544  0.00  0.00           C 0
+ATOM    950   CB HIS A 138      -7.368  40.553  25.917  0.00  0.00           C 0
+ATOM    955  NE2 HIS A 138      -7.616  38.616  29.028  0.00  0.00           N 0
+ATOM    954  CE1 HIS A 138      -8.725  39.333  29.054  0.00  0.00           C 0
+ATOM    941   CB GLN A 137      -2.452  40.010  27.942  0.00  0.00           C 0
+ATOM    969  OE1 GLU A 140      -3.869  46.477  26.485  0.00  0.00           O 0
+ATOM    956    N SER A 139      -5.695  42.080  23.651  0.00  0.00           N 0
+ATOM    961   OG SER A 139      -7.884  42.715  22.532  0.52  8.57           O 0
+ATOM    966   CB GLU A 140      -3.061  44.958  24.340  0.00  0.00           C 0
+ATOM    960   CB SER A 139      -6.763  43.066  21.741  0.00  0.00           C 0
+ATOM    959    O SER A 139      -4.246  44.175  21.351  0.00  0.00           O 0
+ATOM    968   CD GLU A 140      -3.066  47.054  25.726  0.00  0.00           C 0
+ATOM    967   CG GLU A 140      -2.367  46.262  24.643  0.00  0.00           C 0
+ATOM    970  OE2 GLU A 140      -2.795  48.262  25.823  0.00  0.00           O 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket23_vert.pqr

@@ -0,0 +1,48 @@
+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    23:
+HEADER 0  - Pocket Score                      : 0.0425
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    26
+HEADER 3  - Mean alpha-sphere radius          : 4.1515
+HEADER 4  - Mean alpha-sphere SA              : 0.6662
+HEADER 5  - Mean B-factor                     : 0.6215
+HEADER 6  - Hydrophobicity Score              : 7.5000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 4.3333
+HEADER 9  - Real volume (approximation)       : 373.4230
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 0.0000
+HEADER 12 - Number of apolar alpha sphere     :     2
+HEADER 13 - Proportion of apolar alpha sphere : 0.0769
+ATOM      1    O STP    23      -5.887  42.426  30.265    0.00     4.36
+ATOM      2    O STP    23      -5.782  42.563  30.407    0.00     4.51
+ATOM      3    O STP    23      -4.476  43.427  28.792    0.00     3.54
+ATOM      4    O STP    23      -6.982  43.330  28.360    0.00     3.72
+ATOM      5    O STP    23      -5.876  42.441  30.298    0.00     4.39
+ATOM      6    O STP    23      -5.818  42.409  30.325    0.00     4.39
+ATOM      7    O STP    23      -5.828  42.531  30.565    0.00     4.57
+ATOM      8    O STP    23      -5.856  42.577  30.415    0.00     4.54
+ATOM      9    O STP    23      -5.862  42.498  30.360    0.00     4.46
+ATOM     10    O STP    23      -5.832  42.556  30.435    0.00     4.55
+ATOM     11    O STP    23      -5.830  42.541  30.513    0.00     4.56
+ATOM     12    O STP    23      -5.833  42.540  30.424    0.00     4.53
+ATOM     13    O STP    23      -5.840  42.520  30.664    0.00     4.59
+ATOM     14    C STP    23      -4.561  42.294  29.406    0.00     3.44
+ATOM     15    O STP    23      -4.526  43.675  28.480    0.00     3.50
+ATOM     16    O STP    23      -6.906  44.248  26.483    0.00     3.77
+ATOM     17    O STP    23      -7.710  44.748  26.226    0.00     4.22
+ATOM     18    O STP    23      -7.032  44.175  28.706    0.00     4.50
+ATOM     19    O STP    23      -7.165  44.214  28.437    0.00     4.45
+ATOM     20    O STP    23      -6.555  45.426  24.351    0.00     3.53
+ATOM     21    O STP    23      -6.614  45.570  24.331    0.00     3.61
+ATOM     22    O STP    23      -6.591  45.441  24.431    0.00     3.56
+ATOM     23    C STP    23      -5.477  47.472  22.807    0.00     3.81
+ATOM     24    O STP    23      -5.395  48.505  22.105    0.00     4.54
+ATOM     25    O STP    23      -6.628  46.833  23.431    0.00     4.13
+ATOM     26    O STP    23      -6.436  47.165  23.268    0.00     4.17
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket24_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    24:
+HEADER 0  - Pocket Score                      : 0.0398
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of alpha spheres           :    22
+HEADER 3  - Mean alpha-sphere radius          : 3.9590
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5510
+HEADER 5  - Mean B-factor of pocket residues  : 0.6573
+HEADER 6  - Hydrophobicity Score              : -26.2857
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.1429
+HEADER 9  - Pocket volume (Monte Carlo)       : 201.5648
+HEADER 10  -Pocket volume (convex hull)       : 2.9696
+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 : 0.3182
+ATOM   2498   NZ LYS A 330      -6.789  15.298  20.001  0.43  3.28           N 0
+ATOM   2486   CB ASP A 329      -3.288  12.352  20.005  0.00  0.00           C 0
+ATOM   1728  OD2 ASP A 235      -6.229  13.417  21.468  0.00  0.00           O 0
+ATOM   1512  NE2 GLN A 208      -9.045  14.188  15.423  0.00  0.00           N 0
+ATOM   1534   CG GLU A 211      -8.380  12.009  11.266  0.00  0.00           C 0
+ATOM   1535   CD GLU A 211      -9.563  12.480  12.138  0.00  0.00           C 0
+ATOM   1524   CB LYS A 210      -4.393   9.695  13.175  0.00  0.00           C 0
+ATOM   1537  OE2 GLU A 211     -10.448  11.643  12.451  0.00  0.00           O 0
+ATOM   1526   CD LYS A 210      -3.862   8.154  15.100  0.00  0.00           C 0
+ATOM   1529    N GLU A 211      -5.398  12.413  11.242  0.00  0.00           N 0
+ATOM   2488  OD1 ASP A 329      -3.227  10.002  19.487  0.41  4.29           O 0
+ATOM   2485    O ASP A 329      -3.347  14.364  17.406  0.00  0.00           O 0
+ATOM   1519  CG2 THR A 209      -2.026  11.910  15.685  0.00  0.00           C 0
+ATOM   1509   CG GLN A 208      -6.896  15.192  15.196  0.00  0.00           C 0
+ATOM   1520    N LYS A 210      -3.535  11.999  13.144  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket24_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    24:
+HEADER 0  - Pocket Score                      : 0.0398
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of V. Vertices             :    22
+HEADER 3  - Mean alpha-sphere radius          : 3.9590
+HEADER 4  - Mean alpha-sphere SA              : 0.5510
+HEADER 5  - Mean B-factor                     : 0.6573
+HEADER 6  - Hydrophobicity Score              : -26.2857
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.1429
+HEADER 9  - Real volume (approximation)       : 201.5648
+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 : 0.3182
+ATOM      1    O STP    24      -6.583  11.987  17.723    0.00     4.02
+ATOM      2    C STP    24      -7.273  11.244  14.547    0.00     3.55
+ATOM      3    O STP    24      -7.695  10.609  14.944    0.00     3.86
+ATOM      4    C STP    24      -7.695  10.414  14.422    0.00     3.60
+ATOM      5    O STP    24      -8.088   9.734  15.878    0.00     4.58
+ATOM      6    O STP    24      -6.814  11.838  14.309    0.00     3.43
+ATOM      7    O STP    24      -6.741  11.529  17.738    0.00     4.21
+ATOM      8    O STP    24      -6.580  11.990  17.721    0.00     4.02
+ATOM      9    O STP    24      -6.464  11.606  17.421    0.00     4.16
+ATOM     10    C STP    24      -5.988  11.335  16.581    0.00     4.10
+ATOM     11    O STP    24      -5.920  11.282  16.709    0.00     4.08
+ATOM     12    O STP    24      -6.565  12.214  17.659    0.00     3.88
+ATOM     13    O STP    24      -6.760  11.879  14.338    0.00     3.42
+ATOM     14    O STP    24      -6.729  11.893  14.341    0.00     3.41
+ATOM     15    C STP    24      -6.241  11.282  16.607    0.00     4.21
+ATOM     16    C STP    24      -6.121  11.333  16.616    0.00     4.18
+ATOM     17    C STP    24      -5.859  11.594  16.230    0.00     3.88
+ATOM     18    C STP    24      -5.934  11.505  16.380    0.00     3.99
+ATOM     19    O STP    24      -5.742  11.758  16.167    0.00     3.75
+ATOM     20    O STP    24      -6.227  11.285  16.752    0.00     4.26
+ATOM     21    O STP    24      -6.236  11.313  16.793    0.00     4.25
+ATOM     22    O STP    24      -6.213  11.292  16.747    0.00     4.25
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket25_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    25:
+HEADER 0  - Pocket Score                      : 0.0393
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of alpha spheres           :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8832
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5940
+HEADER 5  - Mean B-factor of pocket residues  : 0.3243
+HEADER 6  - Hydrophobicity Score              : 35.5556
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.8889
+HEADER 9  - Pocket volume (Monte Carlo)       : 238.6296
+HEADER 10  -Pocket volume (convex hull)       : 3.9526
+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   1915    O ILE A 261      13.856  19.579   9.511  0.52  6.43           O 0
+ATOM   1645  CD2 LEU A 224      11.587  22.875  12.978  0.00  0.00           C 0
+ATOM   1912    N ILE A 261      12.689  19.674  12.107  0.61  2.19           N 0
+ATOM   1909   CA GLY A 260      13.270  20.237  14.391  0.00  0.00           C 0
+ATOM   2298   CA LEU A 307      21.227  16.759  12.632  0.00  0.00           C 0
+ATOM   2300    O LEU A 307      20.489  16.933  14.864  0.00  0.00           O 0
+ATOM   2289    O ARG A 306      22.157  19.171  11.626  0.00  0.00           O 0
+ATOM   2392  CZ2 TRP A 318      17.107  16.601  14.075  0.00  0.00           C 0
+ATOM   2039  NH2 ARG A 275      16.578  21.454  16.505  0.00  0.00           N 0
+ATOM   1904    O THR A 259      13.861  22.310  16.199  0.68  3.21           O 0
+ATOM   1927  OD2 ASP A 262      17.732  18.746   9.225  0.00  0.00           O 0
+ATOM   2394  CH2 TRP A 318      16.034  16.802  13.247  0.00  0.00           C 0
+ATOM   2037   CZ ARG A 275      16.901  20.193  16.712  0.00  0.00           C 0
+ATOM   2038  NH1 ARG A 275      18.104  19.777  16.363  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket25_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    25:
+HEADER 0  - Pocket Score                      : 0.0393
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of V. Vertices             :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8832
+HEADER 4  - Mean alpha-sphere SA              : 0.5940
+HEADER 5  - Mean B-factor                     : 0.3243
+HEADER 6  - Hydrophobicity Score              : 35.5556
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 4.8889
+HEADER 9  - Real volume (approximation)       : 238.6296
+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    25      15.822  22.733  11.841    0.00     4.39
+ATOM      2    O STP    25      18.908  19.363  12.907    0.00     3.50
+ATOM      3    O STP    25      16.073  23.152  12.322    0.00     4.54
+ATOM      4    O STP    25      18.778  19.253  12.524    0.00     3.50
+ATOM      5    O STP    25      16.634  22.160  12.016    0.00     4.54
+ATOM      6    O STP    25      16.371  20.891  12.156    0.00     3.88
+ATOM      7    O STP    25      16.213  20.170  12.111    0.00     3.56
+ATOM      8    O STP    25      16.353  20.400  12.281    0.00     3.74
+ATOM      9    O STP    25      16.811  20.662  12.601    0.00     3.99
+ATOM     10    C STP    25      16.544  20.225  13.269    0.00     3.46
+ATOM     11    O STP    25      18.893  19.425  12.942    0.00     3.53
+ATOM     12    O STP    25      18.599  22.106  12.348    0.00     4.67
+ATOM     13    O STP    25      18.643  19.681  12.696    0.00     3.71
+ATOM     14    O STP    25      16.982  20.609  12.648    0.00     3.97
+ATOM     15    O STP    25      16.632  20.242  13.231    0.00     3.49
+ATOM     16    O STP    25      17.912  19.907  12.701    0.00     3.67
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket26_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    26:
+HEADER 0  - Pocket Score                      : 0.0350
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of alpha spheres           :    27
+HEADER 3  - Mean alpha-sphere radius          : 3.9976
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4632
+HEADER 5  - Mean B-factor of pocket residues  : 0.4396
+HEADER 6  - Hydrophobicity Score              : -1.4000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 357.6136
+HEADER 10  -Pocket volume (convex hull)       : 21.9863
+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 : 0.0741
+ATOM   4652  NE2 GLN B 282      14.150  27.253  55.385  0.85  3.28           N 0
+ATOM    409   CE LYS A  68      18.254  31.448  50.478  0.00  0.00           C 0
+ATOM   4900  OD2 ASP B 313      16.384  29.050  58.944  0.42  5.36           O 0
+ATOM   1100  OD1 ASP A 155      20.250  27.822  51.013  0.57  1.07           O 0
+ATOM    410   NZ LYS A  68      19.569  30.745  50.425  0.19  3.28           N 0
+ATOM    387  CG2 VAL A  66      13.559  30.359  53.421  0.00  0.00           C 0
+ATOM    386  CG1 VAL A  66      14.645  32.072  51.961  0.00  0.00           C 0
+ATOM    385   CB VAL A  66      13.773  30.833  51.980  0.00  0.00           C 0
+ATOM   4651  OE1 GLN B 282      14.736  25.106  55.785  0.00  0.00           O 0
+ATOM   1084   CA ARG A 154      17.114  23.994  50.463  0.00  0.00           C 0
+ATOM   1101  OD2 ASP A 155      21.258  25.877  51.114  0.00  0.00           O 0
+ATOM   4643    O GLY B 281      16.226  23.524  60.154  0.44  7.50           O 0
+ATOM   4649   CG GLN B 282      14.693  26.562  57.678  0.00  0.00           C 0
+ATOM   4896    O ASP B 313      18.290  25.931  61.054  0.00  0.00           O 0
+ATOM   4650   CD GLN B 282      14.530  26.244  56.194  0.00  0.00           C 0
+ATOM   1083    N ARG A 154      15.829  24.665  50.316  0.45  4.37           N 0
+ATOM    366    O PRO A  64      11.438  26.826  52.838  0.00  0.00           O 0
+ATOM   1073   CA PHE A 153      13.847  25.443  49.191  0.00  0.00           C 0
+ATOM   1094    N ASP A 155      18.096  25.949  49.425  0.60  1.09           N 0
+ATOM   1070  OG1 THR A 152      15.063  29.696  48.354  0.74  1.07           O 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket26_vert.pqr

@@ -0,0 +1,49 @@
+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    26:
+HEADER 0  - Pocket Score                      : 0.0350
+HEADER 1  - Drug Score                        : 0.0001
+HEADER 2  - Number of V. Vertices             :    27
+HEADER 3  - Mean alpha-sphere radius          : 3.9976
+HEADER 4  - Mean alpha-sphere SA              : 0.4632
+HEADER 5  - Mean B-factor                     : 0.4396
+HEADER 6  - Hydrophobicity Score              : -1.4000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 357.6136
+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 : 0.0741
+ATOM      1    O STP    26      18.076  29.569  54.686    0.00     4.61
+ATOM      2    O STP    26      18.364  29.744  54.799    0.00     4.65
+ATOM      3    C STP    26      17.830  30.804  54.981    0.00     4.57
+ATOM      4    O STP    26      17.896  29.763  54.701    0.00     4.56
+ATOM      5    O STP    26      17.476  29.106  53.788    0.00     4.13
+ATOM      6    C STP    26      16.793  28.538  52.488    0.00     3.83
+ATOM      7    O STP    26      17.408  26.575  53.363    0.00     3.89
+ATOM      8    O STP    26      18.324  25.740  53.947    0.00     4.08
+ATOM      9    O STP    26      18.197  25.142  57.343    0.00     3.80
+ATOM     10    O STP    26      19.172  26.252  56.511    0.00     4.64
+ATOM     11    O STP    26      19.115  26.317  56.460    0.00     4.59
+ATOM     12    O STP    26      18.605  27.885  55.204    0.00     4.50
+ATOM     13    O STP    26      18.020  26.909  54.261    0.00     4.04
+ATOM     14    O STP    26      17.287  26.534  53.318    0.00     3.83
+ATOM     15    O STP    26      14.714  27.449  51.998    0.00     3.44
+ATOM     16    O STP    26      17.345  26.637  53.285    0.00     3.87
+ATOM     17    O STP    26      14.651  27.514  51.833    0.00     3.44
+ATOM     18    O STP    26      14.638  27.516  51.809    0.00     3.43
+ATOM     19    O STP    26      16.001  28.077  51.416    0.00     3.59
+ATOM     20    O STP    26      16.628  28.365  51.926    0.00     3.77
+ATOM     21    O STP    26      16.459  28.459  51.459    0.00     3.62
+ATOM     22    O STP    26      16.566  28.108  52.313    0.00     3.92
+ATOM     23    O STP    26      16.381  27.980  52.243    0.00     3.87
+ATOM     24    O STP    26      17.395  26.650  52.908    0.00     3.62
+ATOM     25    O STP    26      16.568  28.046  52.384    0.00     3.93
+ATOM     26    O STP    26      16.836  27.482  52.684    0.00     3.82
+ATOM     27    O STP    26      16.413  27.962  52.299    0.00     3.89
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket27_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    27:
+HEADER 0  - Pocket Score                      : 0.0302
+HEADER 1  - Drug Score                        : 0.0009
+HEADER 2  - Number of alpha spheres           :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.9279
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6292
+HEADER 5  - Mean B-factor of pocket residues  : 0.7018
+HEADER 6  - Hydrophobicity Score              : 22.4286
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 3.7143
+HEADER 9  - Pocket volume (Monte Carlo)       : 197.7227
+HEADER 10  -Pocket volume (convex hull)       : 2.8968
+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 : 0.3333
+ATOM   3549   CB ASP B 143       9.245  -6.724  62.289  0.00  0.00           C 0
+ATOM   2574  CG1 ILE B  21       8.379 -12.237  60.819  0.00  0.00           C 0
+ATOM   3550   CG ASP B 143      10.624  -6.575  61.710  0.00  0.00           C 0
+ATOM   2556    O ALA B  19       8.411  -9.573  65.074  0.00  0.00           O 0
+ATOM   2623   CB SER B  28      12.713 -13.225  59.637  0.00  0.00           C 0
+ATOM   3551  OD1 ASP B 143      11.555  -6.209  62.466  0.54  1.07           O 0
+ATOM   2625    N PHE B  29      13.227 -10.546  58.376  0.53  2.19           N 0
+ATOM   2629   CB PHE B  29      14.473  -8.531  59.010  0.00  0.00           C 0
+ATOM   2640   CB GLU B  30      17.560 -12.626  59.846  0.00  0.00           C 0
+ATOM   2636    N GLU B  30      16.012 -11.157  58.626  0.00  0.00           N 0
+ATOM   2624   OG SER B  28      13.987 -13.731  59.249  0.78  1.07           O 0
+ATOM   3552  OD2 ASP B 143      10.768  -6.801  60.489  0.54  3.21           O 0
+ATOM   2632  CD2 PHE B  29      16.798  -7.827  59.607  0.00  0.00           C 0
+ATOM   3442  CE1 HIS B 132      15.063  -5.865  62.209  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket27_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    27:
+HEADER 0  - Pocket Score                      : 0.0302
+HEADER 1  - Drug Score                        : 0.0009
+HEADER 2  - Number of V. Vertices             :    15
+HEADER 3  - Mean alpha-sphere radius          : 3.9279
+HEADER 4  - Mean alpha-sphere SA              : 0.6292
+HEADER 5  - Mean B-factor                     : 0.7018
+HEADER 6  - Hydrophobicity Score              : 22.4286
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 3.7143
+HEADER 9  - Real volume (approximation)       : 197.7227
+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 : 0.3333
+ATOM      1    C STP    27      10.428  -9.941  62.327    0.00     3.43
+ATOM      2    C STP    27      11.720 -10.507  62.672    0.00     4.19
+ATOM      3    O STP    27      12.035 -10.480  62.903    0.00     4.32
+ATOM      4    O STP    27      12.376 -10.199  62.347    0.00     4.08
+ATOM      5    O STP    27      12.942 -10.199  62.578    0.00     4.23
+ATOM      6    O STP    27      12.536  -9.744  61.930    0.00     3.71
+ATOM      7    O STP    27      14.875 -11.603  62.007    0.00     3.59
+ATOM      8    O STP    27      14.328 -10.820  61.825    0.00     3.63
+ATOM      9    O STP    27      11.650 -10.281  61.877    0.00     3.85
+ATOM     10    C STP    27      11.545 -10.312  61.870    0.00     3.85
+ATOM     11    O STP    27      11.519 -10.306  61.770    0.00     3.81
+ATOM     12    O STP    27      12.513  -9.712  61.874    0.00     3.67
+ATOM     13    O STP    27      12.546  -9.632  61.863    0.00     3.61
+ATOM     14    C STP    27      15.310 -10.353  63.139    0.00     4.59
+ATOM     15    C STP    27      15.380 -10.356  62.869    0.00     4.36
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket28_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    28:
+HEADER 0  - Pocket Score                      : 0.0282
+HEADER 1  - Drug Score                        : 0.0072
+HEADER 2  - Number of alpha spheres           :    37
+HEADER 3  - Mean alpha-sphere radius          : 3.8758
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4899
+HEADER 5  - Mean B-factor of pocket residues  : 0.4277
+HEADER 6  - Hydrophobicity Score              : 30.0000
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 3.3000
+HEADER 9  - Pocket volume (Monte Carlo)       : 272.7978
+HEADER 10  -Pocket volume (convex hull)       : 19.6950
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 13.0000
+HEADER 13 - Number of apolar alpha sphere     :    14
+HEADER 14 - Proportion of apolar alpha sphere : 0.3784
+ATOM   1387    N ALA A 192      -0.717  24.707  25.707  0.55  1.09           N 0
+ATOM   1708  CD1 PHE A 233      -1.372  18.506  22.820  0.00  0.00           C 0
+ATOM   2514  OE2 GLU A 332      -1.745  20.996  21.050  0.89  3.21           O 0
+ATOM   1391   CB ALA A 192       1.169  24.266  24.193  0.00  0.00           C 0
+ATOM   1875   CB ALA A 255       2.918  20.919  26.678  0.00  0.00           C 0
+ATOM   1871    N ALA A 255       2.705  18.589  27.448  0.73  1.09           N 0
+ATOM   1872   CA ALA A 255       3.134  19.444  26.343  0.00  0.00           C 0
+ATOM   1710  CE1 PHE A 233      -2.716  18.891  22.605  0.00  0.00           C 0
+ATOM   1380    O GLY A 190      -2.803  22.883  29.185  0.00  0.00           O 0
+ATOM   1709  CD2 PHE A 233      -2.136  16.521  23.915  0.00  0.00           C 0
+ATOM    629   CB TRP A  98       1.005  23.879  28.745  0.00  0.00           C 0
+ATOM   1712   CZ PHE A 233      -3.744  18.091  23.041  0.00  0.00           C 0
+ATOM    624   SG CYS A  97       2.577  20.007  30.576  0.00  0.00           S 0
+ATOM   1382   CA SER A 191      -2.701  24.663  27.080  0.00  0.00           C 0
+ATOM   1386   OG SER A 191      -3.724  24.727  24.886  0.41  7.50           O 0
+ATOM   1385   CB SER A 191      -3.958  24.958  26.264  0.00  0.00           C 0
+ATOM   1711  CE2 PHE A 233      -3.457  16.897  23.692  0.00  0.00           C 0
+ATOM   1859    C GLY A 253      -0.072  15.654  29.040  0.00  0.00           C 0
+ATOM   1858   CA GLY A 253      -1.116  14.599  28.671  0.00  0.00           C 0
+ATOM   1860    O GLY A 253      -0.215  16.355  30.028  0.71  7.50           O 0
+ATOM   1861    N HIS A 254       0.956  15.779  28.210  0.97  1.09           N 0
+ATOM   1707   CG PHE A 233      -1.075  17.309  23.466  0.00  0.00           C 0
+ATOM   1706   CB PHE A 233       0.351  16.918  23.763  0.00  0.00           C 0
+ATOM   2513  OE1 GLU A 332       0.238  22.000  21.040  0.68  3.21           O 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket28_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    28:
+HEADER 0  - Pocket Score                      : 0.0282
+HEADER 1  - Drug Score                        : 0.0072
+HEADER 2  - Number of V. Vertices             :    37
+HEADER 3  - Mean alpha-sphere radius          : 3.8758
+HEADER 4  - Mean alpha-sphere SA              : 0.4899
+HEADER 5  - Mean B-factor                     : 0.4277
+HEADER 6  - Hydrophobicity Score              : 30.0000
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 3.3000
+HEADER 9  - Real volume (approximation)       : 272.7978
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 13.0000
+HEADER 12 - Number of apolar alpha sphere     :    14
+HEADER 13 - Proportion of apolar alpha sphere : 0.3784
+ATOM      1    O STP    28      -0.944  21.557  24.346    0.00     3.44
+ATOM      2    C STP    28      -0.390  21.119  25.163    0.00     3.64
+ATOM      3    C STP    28      -0.497  19.750  26.137    0.00     3.65
+ATOM      4    O STP    28      -1.505  21.560  24.468    0.00     3.47
+ATOM      5    C STP    28      -2.421  19.598  26.681    0.00     4.15
+ATOM      6    O STP    28      -1.904  20.950  25.868    0.00     3.94
+ATOM      7    O STP    28      -1.138  19.994  26.698    0.00     4.16
+ATOM      8    O STP    28      -0.610  21.340  26.848    0.00     3.56
+ATOM      9    O STP    28      -1.105  20.703  26.217    0.00     4.05
+ATOM     10    C STP    28      -2.450  19.593  26.684    0.00     4.15
+ATOM     11    C STP    28      -0.219  20.522  28.381    0.00     3.59
+ATOM     12    O STP    28      -0.246  20.464  28.365    0.00     3.61
+ATOM     13    O STP    28      -2.017  21.009  25.831    0.00     3.92
+ATOM     14    O STP    28      -4.802  20.822  26.086    0.00     4.22
+ATOM     15    O STP    28      -3.784  20.874  25.890    0.00     3.98
+ATOM     16    O STP    28      -2.002  21.755  24.422    0.00     3.47
+ATOM     17    O STP    28      -3.770  21.486  26.150    0.00     3.48
+ATOM     18    O STP    28      -3.053  21.034  25.802    0.00     3.86
+ATOM     19    O STP    28      -2.286  21.303  25.452    0.00     3.76
+ATOM     20    C STP    28      -2.467  19.582  26.696    0.00     4.15
+ATOM     21    C STP    28      -3.065  18.013  27.593    0.00     4.08
+ATOM     22    C STP    28      -3.129  18.059  27.644    0.00     4.13
+ATOM     23    O STP    28      -2.825  18.832  27.555    0.00     4.37
+ATOM     24    C STP    28      -3.030  18.141  27.600    0.00     4.12
+ATOM     25    O STP    28      -0.653  19.833  28.635    0.00     3.77
+ATOM     26    O STP    28      -0.856  18.760  27.475    0.00     3.57
+ATOM     27    O STP    28      -1.215  19.866  26.768    0.00     4.18
+ATOM     28    C STP    28      -2.296  19.575  26.726    0.00     4.15
+ATOM     29    C STP    28      -0.463  19.697  26.108    0.00     3.61
+ATOM     30    O STP    28      -0.646  18.417  26.693    0.00     3.44
+ATOM     31    O STP    28      -1.504  19.313  27.220    0.00     4.28
+ATOM     32    O STP    28      -1.799  19.199  27.242    0.00     4.28
+ATOM     33    O STP    28      -1.195  18.862  27.071    0.00     3.93
+ATOM     34    C STP    28      -1.255  18.277  26.909    0.00     3.58
+ATOM     35    O STP    28      -1.374  19.085  27.170    0.00     4.12
+ATOM     36    C STP    28      -1.665  18.991  27.195    0.00     4.13
+ATOM     37    C STP    28       0.538  20.926  24.251    0.00     3.40
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket29_atm.pdb

@@ -0,0 +1,50 @@
+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    29:
+HEADER 0  - Pocket Score                      : 0.0235
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of alpha spheres           :    31
+HEADER 3  - Mean alpha-sphere radius          : 4.0696
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6937
+HEADER 5  - Mean B-factor of pocket residues  : 0.8090
+HEADER 6  - Hydrophobicity Score              : 6.2222
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 3.5556
+HEADER 9  - Pocket volume (Monte Carlo)       : 382.4278
+HEADER 10  -Pocket volume (convex hull)       : 35.2325
+HEADER 11 - Charge Score                      :    -3
+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   4720   OG SER B 290      14.143  35.520  69.099  0.58  2.14           O 0
+ATOM   4733   CB SER B 292      19.445  36.766  66.578  0.00  0.00           C 0
+ATOM   4686    O ASN B 286      12.107  37.205  68.015  0.61  8.57           O 0
+ATOM   4732    O SER B 292      18.267  38.589  68.261  0.27  6.43           O 0
+ATOM   4731    C SER B 292      18.441  37.480  68.748  0.00  0.00           C 0
+ATOM   4729    N SER B 292      18.612  35.138  68.164  0.73  1.09           N 0
+ATOM   4721    N ASP B 291      16.864  32.945  69.050  0.53  1.09           N 0
+ATOM   4719   CB SER B 290      14.020  34.117  69.161  0.00  0.00           C 0
+ATOM   4883    O ALA B 311      23.352  30.563  64.936  0.00  0.00           O 0
+ATOM   4882    C ALA B 311      22.374  30.391  65.655  0.00  0.00           C 0
+ATOM   4884   CB ALA B 311      22.655  32.629  66.765  0.00  0.00           C 0
+ATOM   4734   OG SER B 292      20.112  35.697  65.929  0.53  4.29           O 0
+ATOM   4725   CB ASP B 291      18.575  32.259  67.408  0.00  0.00           C 0
+ATOM   4672    O TRP B 285      12.271  33.162  66.827  0.50  3.21           O 0
+ATOM   4667  OE1 GLU B 284      15.654  29.021  66.187  0.56  2.14           O 0
+ATOM   4897   CB ASP B 313      18.144  28.731  60.508  0.00  0.00           C 0
+ATOM   4899  OD1 ASP B 313      15.797  29.070  61.046  0.59  7.50           O 0
+ATOM   4893    N ASP B 313      19.681  28.522  62.424  0.00  0.00           N 0
+ATOM   4728  OD2 ASP B 291      18.823  30.181  66.267  0.63  2.14           O 0
+ATOM   4666   CD GLU B 284      15.459  28.410  65.119  0.00  0.00           C 0
+ATOM   4885    N LEU B 312      21.439  29.504  65.363  0.00  0.00           N 0
+ATOM   4894   CA ASP B 313      18.353  28.179  61.934  0.00  0.00           C 0
+ATOM   4664   CB GLU B 284      13.244  29.659  64.915  0.00  0.00           C 0
+ATOM   4660    N GLU B 284      11.901  29.684  62.863  0.37  5.47           N 0
+ATOM   4663    O GLU B 284      10.784  31.858  64.225  0.47  2.14           O 0
+ATOM   4689  OD1 ASN B 286      10.750  35.841  64.041  0.00  0.00           O 0
+ATOM   4684   CA ASN B 286      10.825  35.656  66.761  0.00  0.00           C 0
+ATOM   4886   CA LEU B 312      21.407  28.933  64.027  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket29_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    29:
+HEADER 0  - Pocket Score                      : 0.0235
+HEADER 1  - Drug Score                        : 0.0000
+HEADER 2  - Number of V. Vertices             :    31
+HEADER 3  - Mean alpha-sphere radius          : 4.0696
+HEADER 4  - Mean alpha-sphere SA              : 0.6937
+HEADER 5  - Mean B-factor                     : 0.8090
+HEADER 6  - Hydrophobicity Score              : 6.2222
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 3.5556
+HEADER 9  - Real volume (approximation)       : 382.4278
+HEADER 10 - Charge Score                      :    -3
+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    29      15.444  37.217  65.530    0.00     4.16
+ATOM      2    O STP    29      15.976  36.744  66.415    0.00     3.47
+ATOM      3    O STP    29      16.039  36.619  66.485    0.00     3.41
+ATOM      4    O STP    29      15.726  34.529  65.845    0.00     3.75
+ATOM      5    O STP    29      21.032  33.076  63.427    0.00     3.74
+ATOM      6    O STP    29      15.486  32.418  65.979    0.00     3.41
+ATOM      7    O STP    29      15.707  34.495  65.724    0.00     3.85
+ATOM      8    O STP    29      15.803  34.332  65.510    0.00     3.95
+ATOM      9    O STP    29      15.699  34.526  65.718    0.00     3.85
+ATOM     10    O STP    29      15.930  34.586  64.535    0.00     4.55
+ATOM     11    O STP    29      15.855  34.821  64.544    0.00     4.56
+ATOM     12    O STP    29      15.608  35.341  64.947    0.00     4.41
+ATOM     13    O STP    29      17.930  32.528  62.679    0.00     4.38
+ATOM     14    O STP    29      16.460  31.903  63.664    0.00     3.91
+ATOM     15    O STP    29      20.014  32.645  63.377    0.00     3.98
+ATOM     16    O STP    29      17.808  32.079  62.846    0.00     4.04
+ATOM     17    O STP    29      17.867  32.084  62.682    0.00     4.01
+ATOM     18    O STP    29      16.156  32.013  63.657    0.00     3.95
+ATOM     19    O STP    29      15.610  32.667  65.020    0.00     3.83
+ATOM     20    O STP    29      16.211  32.573  63.834    0.00     4.30
+ATOM     21    O STP    29      16.265  32.437  63.664    0.00     4.29
+ATOM     22    O STP    29      16.252  32.697  63.616    0.00     4.47
+ATOM     23    O STP    29      14.711  33.136  62.532    0.00     4.46
+ATOM     24    O STP    29      14.155  35.881  65.317    0.00     3.64
+ATOM     25    O STP    29      15.245  36.470  64.743    0.00     4.59
+ATOM     26    O STP    29      14.605  35.952  65.139    0.00     4.01
+ATOM     27    O STP    29      15.342  35.849  64.639    0.00     4.63
+ATOM     28    O STP    29      19.786  32.677  63.029    0.00     4.20
+ATOM     29    O STP    29      19.975  32.647  63.264    0.00     4.05
+ATOM     30    O STP    29      20.036  32.660  63.257    0.00     4.05
+ATOM     31    O STP    29      20.550  32.907  62.731    0.00     4.27
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket2_atm.pdb

@@ -0,0 +1,73 @@
+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                      : 0.3221
+HEADER 1  - Drug Score                        : 0.0229
+HEADER 2  - Number of alpha spheres           :    82
+HEADER 3  - Mean alpha-sphere radius          : 4.0489
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5430
+HEADER 5  - Mean B-factor of pocket residues  : 0.5335
+HEADER 6  - Hydrophobicity Score              : 26.8000
+HEADER 7  - Polarity Score                    :    10
+HEADER 8  - Amino Acid based volume Score     : 4.6000
+HEADER 9  - Pocket volume (Monte Carlo)       : 933.6125
+HEADER 10  -Pocket volume (convex hull)       : 270.6384
+HEADER 11 - Charge Score                      :     2
+HEADER 12 - Local hydrophobic density Score   : 9.0588
+HEADER 13 - Number of apolar alpha sphere     :    17
+HEADER 14 - Proportion of apolar alpha sphere : 0.2073
+ATOM    302   CA TYR A  57      -4.097  30.042  46.474  0.00  0.00           C 0
+ATOM    274   CB SER A  53      -0.980  35.033  48.721  0.00  0.00           C 0
+ATOM    305   CB TYR A  57      -4.906  30.640  45.281  0.00  0.00           C 0
+ATOM    304    O TYR A  57      -5.728  29.366  48.072  0.00  0.00           O 0
+ATOM    271   CA SER A  53      -0.212  33.784  48.339  0.00  0.00           C 0
+ATOM    338  NH2 ARG A  60      -3.037  32.401  54.903  0.52  5.47           N 0
+ATOM    270    N SER A  53       0.947  33.625  49.220  0.69  2.19           N 0
+ATOM    273    O SER A  53      -0.662  33.608  45.990  0.64  3.21           O 0
+ATOM    261   OG SER A  51       3.138  36.925  50.302  0.61  7.50           O 0
+ATOM    266   CB ASN A  52       2.382  31.823  51.583  0.00  0.00           C 0
+ATOM    262    N ASN A  52       3.487  33.687  50.476  0.00  0.00           N 0
+ATOM    260   CB SER A  51       4.367  36.518  50.847  0.00  0.00           C 0
+ATOM    320   CA GLU A  59      -3.590  25.966  50.435  0.00  0.00           C 0
+ATOM   4314   CB ALA B 240      -8.170  27.920  54.288  0.00  0.00           C 0
+ATOM   4313    O ALA B 240      -5.400  28.635  55.225  0.70  5.36           O 0
+ATOM    293    O PHE A  56      -1.438  30.433  47.567  0.65  4.29           O 0
+ATOM    337  NH1 ARG A  60      -3.437  30.209  55.296  0.49  2.19           N 0
+ATOM    315    C SER A  58      -5.341  26.069  48.700  0.00  0.00           C 0
+ATOM    319    N GLU A  59      -4.119  26.383  49.130  0.00  0.00           N 0
+ATOM    316    O SER A  58      -6.101  25.321  49.319  0.00  6.43           O 0
+ATOM   4350   CD ARG B 245       6.007  31.438  57.723  0.00  0.00           C 0
+ATOM   4351   NE ARG B 245       6.412  30.699  56.543  0.45  1.09           N 0
+ATOM   4353  NH1 ARG B 245       8.649  31.313  56.653  0.00  0.00           N 0
+ATOM   4352   CZ ARG B 245       7.654  30.656  56.059  0.00  0.00           C 0
+ATOM    257   CA SER A  51       5.067  35.461  49.965  0.00  0.00           C 0
+ATOM    265    O ASN A  52       1.290  31.468  48.668  0.00  0.00           O 0
+ATOM    333   CG ARG A  60      -1.093  28.749  53.682  0.00  0.00           C 0
+ATOM    264    C ASN A  52       1.602  32.471  49.310  0.00  0.00           C 0
+ATOM    267   CG ASN A  52       3.399  30.847  52.116  0.00  0.00           C 0
+ATOM    328    N ARG A  60      -1.723  26.657  51.789  0.00  0.00           N 0
+ATOM    382   CA VAL A  66      12.394  31.077  51.245  0.00  0.00           C 0
+ATOM    387  CG2 VAL A  66      13.559  30.359  53.421  0.00  0.00           C 0
+ATOM    386  CG1 VAL A  66      14.645  32.072  51.961  0.00  0.00           C 0
+ATOM    373    O PHE A  65      10.109  30.046  52.567  0.46  3.21           O 0
+ATOM    388    N TRP A  67      12.117  32.977  49.763  0.00  0.00           N 0
+ATOM    254    O ALA A  50       7.466  36.688  50.064  0.56  7.50           O 0
+ATOM    394  CD1 TRP A  67       8.947  33.607  48.971  0.00  0.00           C 0
+ATOM   4354  NH2 ARG B 245       7.908  29.942  54.969  0.41  1.09           N 0
+ATOM   4349   CG ARG B 245       4.537  31.274  57.985  0.00  0.00           C 0
+ATOM    336   CZ ARG A  60      -2.584  31.170  54.997  0.00  0.00           C 0
+ATOM    269  ND2 ASN A  52       3.031  30.136  53.165  0.21  1.09           N 0
+ATOM    321    C GLU A  59      -2.187  26.519  50.558  0.00  0.00           C 0
+ATOM    391    O TRP A  67      14.098  34.902  49.533  0.59  3.21           O 0
+ATOM    392   CB TRP A  67      11.179  34.821  48.441  0.00  0.00           C 0
+ATOM   1048  NH1 ARG A 149      10.790  40.952  49.175  0.00  0.00           N 0
+ATOM   1045   CD ARG A 149      12.466  39.543  47.415  0.00  0.00           C 0
+ATOM    255   CB ALA A  50       8.969  37.814  48.070  0.00  0.00           C 0
+ATOM    268  OD1 ASN A  52       4.499  30.717  51.577  0.51  6.43           O 0
+ATOM   4344    N ARG B 245       1.807  31.214  58.848  0.00  0.00           N 0
+ATOM   4348   CB ARG B 245       4.065  32.186  59.080  0.00  0.00           C 0
+ATOM    335   NE ARG A  60      -1.292  30.918  54.777  0.61  2.19           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket2_vert.pqr

@@ -0,0 +1,104 @@
+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                      : 0.3221
+HEADER 1  - Drug Score                        : 0.0229
+HEADER 2  - Number of V. Vertices             :    82
+HEADER 3  - Mean alpha-sphere radius          : 4.0489
+HEADER 4  - Mean alpha-sphere SA              : 0.5430
+HEADER 5  - Mean B-factor                     : 0.5335
+HEADER 6  - Hydrophobicity Score              : 26.8000
+HEADER 7  - Polarity Score                    :    10
+HEADER 8  - Volume Score                      : 4.6000
+HEADER 9  - Real volume (approximation)       : 933.6125
+HEADER 10 - Charge Score                      :     2
+HEADER 11 - Local hydrophobic density Score   : 9.0588
+HEADER 12 - Number of apolar alpha sphere     :    17
+HEADER 13 - Proportion of apolar alpha sphere : 0.2073
+ATOM      1    C STP     2      -5.558  34.040  48.448    0.00     4.69
+ATOM      2    O STP     2      -1.809  32.763  51.472    0.00     3.66
+ATOM      3    C STP     2      -4.146  33.673  47.306    0.00     3.73
+ATOM      4    O STP     2      -0.180  35.614  53.228    0.00     4.61
+ATOM      5    O STP     2       1.708  35.335  54.150    0.00     4.40
+ATOM      6    O STP     2       0.102  35.379  53.375    0.00     4.59
+ATOM      7    O STP     2       0.700  35.156  52.842    0.00     3.94
+ATOM      8    O STP     2      -5.804  28.589  51.617    0.00     3.63
+ATOM      9    O STP     2      -4.099  32.712  49.375    0.00     3.94
+ATOM     10    O STP     2      -3.869  32.376  50.622    0.00     4.36
+ATOM     11    O STP     2      -2.983  32.230  50.854    0.00     4.05
+ATOM     12    O STP     2      -5.704  31.177  51.877    0.00     4.21
+ATOM     13    O STP     2      -4.363  29.515  51.646    0.00     3.83
+ATOM     14    O STP     2      -6.095  28.215  51.343    0.00     3.49
+ATOM     15    O STP     2      -6.283  28.192  51.337    0.00     3.51
+ATOM     16    C STP     2      -6.148  28.219  51.396    0.00     3.54
+ATOM     17    C STP     2      -6.169  28.138  51.412    0.00     3.51
+ATOM     18    O STP     2       4.806  34.310  54.621    0.00     4.39
+ATOM     19    O STP     2       6.541  34.957  54.659    0.00     4.66
+ATOM     20    O STP     2       6.515  35.038  54.752    0.00     4.70
+ATOM     21    O STP     2       6.084  34.013  53.859    0.00     4.28
+ATOM     22    C STP     2       6.207  34.077  53.880    0.00     4.31
+ATOM     23    C STP     2      -1.083  31.302  51.261    0.00     3.52
+ATOM     24    O STP     2      -1.472  31.620  50.953    0.00     3.59
+ATOM     25    O STP     2      -1.417  31.678  50.762    0.00     3.43
+ATOM     26    O STP     2       4.609  34.165  54.645    0.00     4.34
+ATOM     27    O STP     2      -4.262  29.384  51.757    0.00     3.73
+ATOM     28    O STP     2      -4.161  29.251  51.941    0.00     3.56
+ATOM     29    C STP     2      11.379  34.401  54.403    0.00     4.70
+ATOM     30    O STP     2      11.188  33.770  54.298    0.00     4.25
+ATOM     31    O STP     2      10.654  34.442  53.899    0.00     4.63
+ATOM     32    O STP     2       6.958  34.762  54.177    0.00     4.57
+ATOM     33    C STP     2       6.907  34.506  53.922    0.00     4.47
+ATOM     34    O STP     2       9.779  34.536  53.371    0.00     4.57
+ATOM     35    O STP     2       8.100  33.873  53.247    0.00     4.30
+ATOM     36    O STP     2       7.427  33.574  52.896    0.00     4.21
+ATOM     37    O STP     2       7.326  33.750  53.147    0.00     4.26
+ATOM     38    O STP     2       8.199  33.840  53.192    0.00     4.29
+ATOM     39    O STP     2       8.218  33.854  53.211    0.00     4.30
+ATOM     40    C STP     2       4.159  34.257  54.781    0.00     4.39
+ATOM     41    C STP     2       4.396  34.225  54.737    0.00     4.39
+ATOM     42    C STP     2       4.436  33.896  54.753    0.00     4.16
+ATOM     43    C STP     2       3.755  34.595  54.946    0.00     4.57
+ATOM     44    C STP     2       4.386  34.417  54.801    0.00     4.48
+ATOM     45    O STP     2      -4.513  30.898  51.532    0.00     3.97
+ATOM     46    O STP     2      -3.881  30.297  51.402    0.00     3.92
+ATOM     47    O STP     2      -3.536  31.217  51.006    0.00     4.10
+ATOM     48    O STP     2      -3.416  30.765  51.069    0.00     4.04
+ATOM     49    C STP     2       3.550  33.709  54.939    0.00     4.02
+ATOM     50    O STP     2       4.280  33.180  54.836    0.00     3.69
+ATOM     51    O STP     2      -3.285  30.158  50.895    0.00     3.82
+ATOM     52    O STP     2      -4.171  29.646  51.570    0.00     3.84
+ATOM     53    O STP     2      -4.188  29.486  51.690    0.00     3.75
+ATOM     54    O STP     2      -4.288  29.543  51.619    0.00     3.83
+ATOM     55    O STP     2      -4.250  29.426  51.721    0.00     3.75
+ATOM     56    O STP     2      11.950  37.731  50.616    0.00     3.71
+ATOM     57    C STP     2      11.662  37.747  50.329    0.00     3.52
+ATOM     58    O STP     2      11.165  36.318  52.819    0.00     4.63
+ATOM     59    O STP     2      11.427  37.529  52.026    0.00     4.50
+ATOM     60    O STP     2      11.231  37.577  51.523    0.00     4.13
+ATOM     61    O STP     2      10.270  35.264  51.984    0.00     3.68
+ATOM     62    O STP     2       7.530  32.965  52.542    0.00     3.90
+ATOM     63    O STP     2       7.363  33.479  52.827    0.00     4.17
+ATOM     64    O STP     2       7.062  33.630  53.165    0.00     4.19
+ATOM     65    O STP     2       5.407  33.819  54.090    0.00     4.09
+ATOM     66    O STP     2       6.126  33.962  53.813    0.00     4.26
+ATOM     67    O STP     2       6.170  33.951  53.796    0.00     4.26
+ATOM     68    C STP     2       2.169  34.320  55.456    0.00     4.61
+ATOM     69    O STP     2       2.165  33.605  55.396    0.00     4.21
+ATOM     70    O STP     2      -2.232  31.897  51.107    0.00     3.91
+ATOM     71    O STP     2      -2.465  31.621  51.131    0.00     3.89
+ATOM     72    O STP     2      -1.802  32.379  51.394    0.00     3.72
+ATOM     73    O STP     2      -1.680  31.694  51.110    0.00     3.77
+ATOM     74    O STP     2      -0.603  33.695  52.518    0.00     3.64
+ATOM     75    O STP     2      -2.531  31.262  51.156    0.00     3.84
+ATOM     76    O STP     2      -1.546  31.592  51.114    0.00     3.73
+ATOM     77    O STP     2      -1.100  31.869  51.428    0.00     3.49
+ATOM     78    C STP     2      -1.101  31.333  51.276    0.00     3.53
+ATOM     79    O STP     2       1.925  33.486  55.367    0.00     4.16
+ATOM     80    O STP     2      -1.502  31.524  51.118    0.00     3.72
+ATOM     81    O STP     2      -1.176  31.344  51.240    0.00     3.56
+ATOM     82    O STP     2      -1.450  31.376  51.127    0.00     3.68
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket30_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    30:
+HEADER 0  - Pocket Score                      : 0.0220
+HEADER 1  - Drug Score                        : 0.0034
+HEADER 2  - Number of alpha spheres           :    22
+HEADER 3  - Mean alpha-sphere radius          : 4.0255
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6195
+HEADER 5  - Mean B-factor of pocket residues  : 0.4194
+HEADER 6  - Hydrophobicity Score              : 17.8000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Amino Acid based volume Score     : 4.7000
+HEADER 9  - Pocket volume (Monte Carlo)       : 415.1244
+HEADER 10  -Pocket volume (convex hull)       : 32.8138
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 7.0000
+HEADER 13 - Number of apolar alpha sphere     :     8
+HEADER 14 - Proportion of apolar alpha sphere : 0.3636
+ATOM   2425   CD LYS A 322       5.902   4.315   9.555  0.00  0.00           C 0
+ATOM   2002  CG2 ILE A 271      12.991   7.718   8.149  0.00  0.00           C 0
+ATOM   2003  CD1 ILE A 271      13.393   5.749   6.018  0.00  0.00           C 0
+ATOM   2423   CB LYS A 322       6.127   6.811   9.910  0.00  0.00           C 0
+ATOM   1957  CD2 PHE A 266      16.408   3.328   8.177  0.00  0.00           C 0
+ATOM   2157  NE1 TRP A 289      14.633   6.315  11.961  0.00  0.00           N 0
+ATOM   1959  CE2 PHE A 266      16.467   2.245   9.053  0.00  0.00           C 0
+ATOM   2148   OG SER A 288      12.645   2.630  14.846  0.00  0.00           O 0
+ATOM   2204  OE2 GLU A 295      15.495   1.877  13.893  0.57  4.29           O 0
+ATOM   2407   CB ALA A 320      10.463   7.470  11.981  0.00  0.00           C 0
+ATOM   2004    N GLU A 272      11.835  10.646   6.665  0.45  2.19           N 0
+ATOM   2008   CB GLU A 272       9.976  12.205   6.834  0.00  0.00           C 0
+ATOM   2011  OE1 GLU A 272       7.448  12.227   5.684  0.59  5.36           O 0
+ATOM   1997   CA ILE A 271      13.385   8.955   5.927  0.00  0.00           C 0
+ATOM   1988    O ARG A 270      12.882   8.375   3.223  0.35  5.36           O 0
+ATOM   2147   CB SER A 288      12.960   4.000  14.966  0.00  0.00           C 0
+ATOM   2435  OD2 ASP A 323       9.168   4.811  14.506  0.82  1.07           O 0
+ATOM   2419    N LYS A 322       6.663   9.052  10.744  0.68  3.28           N 0
+ATOM   2007    O GLU A 272      10.837  10.995   9.347  0.00  0.00           O 0
+ATOM   2009   CG GLU A 272       9.787  12.438   5.352  0.00  0.00           C 0
+ATOM   2010   CD GLU A 272       8.360  12.758   5.019  0.00  0.00           C 0
+ATOM   1994  NH1 ARG A 270      11.913  13.050   1.890  0.00  0.00           N 0
+ATOM   2012  OE2 GLU A 272       8.158  13.552   4.090  0.00  0.00           O 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket30_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    30:
+HEADER 0  - Pocket Score                      : 0.0220
+HEADER 1  - Drug Score                        : 0.0034
+HEADER 2  - Number of V. Vertices             :    22
+HEADER 3  - Mean alpha-sphere radius          : 4.0255
+HEADER 4  - Mean alpha-sphere SA              : 0.6195
+HEADER 5  - Mean B-factor                     : 0.4194
+HEADER 6  - Hydrophobicity Score              : 17.8000
+HEADER 7  - Polarity Score                    :     7
+HEADER 8  - Volume Score                      : 4.7000
+HEADER 9  - Real volume (approximation)       : 415.1244
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 7.0000
+HEADER 12 - Number of apolar alpha sphere     :     8
+HEADER 13 - Proportion of apolar alpha sphere : 0.3636
+ATOM      1    C STP    30       9.367   5.590   7.419    0.00     4.27
+ATOM      2    C STP    30      13.026   4.228   9.367    0.00     3.70
+ATOM      3    C STP    30      12.152   3.375   9.631    0.00     4.50
+ATOM      4    O STP    30      13.085   2.852  10.952    0.00     3.93
+ATOM      5    C STP    30       9.690   5.396   8.579    0.00     4.06
+ATOM      6    C STP    30      11.611   3.550   9.727    0.00     4.67
+ATOM      7    C STP    30      10.363   4.145   8.942    0.00     4.51
+ATOM      8    O STP    30       8.394   8.416   6.885    0.00     4.11
+ATOM      9    C STP    30       9.722   7.340   5.869    0.00     4.00
+ATOM     10    O STP    30       9.549   7.330   5.528    0.00     4.19
+ATOM     11    O STP    30      11.711   3.880  11.318    0.00     3.86
+ATOM     12    O STP    30      11.332   3.934  11.698    0.00     3.65
+ATOM     13    O STP    30       8.271   8.661   7.161    0.00     3.95
+ATOM     14    O STP    30       9.089   7.939   7.545    0.00     3.95
+ATOM     15    C STP    30       9.361   7.764   8.515    0.00     3.65
+ATOM     16    O STP    30       9.284   7.867   8.643    0.00     3.56
+ATOM     17    O STP    30       8.527   8.534   7.258    0.00     3.97
+ATOM     18    O STP    30       8.505   8.561   7.279    0.00     3.95
+ATOM     19    O STP    30       8.637   8.809   3.415    0.00     4.27
+ATOM     20    O STP    30       8.858   8.323   4.662    0.00     4.27
+ATOM     21    O STP    30       9.192   9.919   2.103    0.00     4.15
+ATOM     22    O STP    30       9.344  10.869   2.365    0.00     3.40
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket31_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    31:
+HEADER 0  - Pocket Score                      : 0.0126
+HEADER 1  - Drug Score                        : 0.0005
+HEADER 2  - Number of alpha spheres           :    23
+HEADER 3  - Mean alpha-sphere radius          : 3.9707
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5940
+HEADER 5  - Mean B-factor of pocket residues  : 0.6103
+HEADER 6  - Hydrophobicity Score              : 8.8889
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 3.4444
+HEADER 9  - Pocket volume (Monte Carlo)       : 376.4228
+HEADER 10  -Pocket volume (convex hull)       : 30.5078
+HEADER 11 - Charge Score                      :    -1
+HEADER 12 - Local hydrophobic density Score   : 3.0000
+HEADER 13 - Number of apolar alpha sphere     :     4
+HEADER 14 - Proportion of apolar alpha sphere : 0.1739
+ATOM    949    O HIS A 138      -6.013  40.021  22.998  0.00  0.00           O 0
+ATOM    950   CB HIS A 138      -7.368  40.553  25.917  0.00  0.00           C 0
+ATOM    951   CG HIS A 138      -7.632  39.853  27.212  0.00  0.00           C 0
+ATOM    953  CD2 HIS A 138      -6.914  38.923  27.886  0.00  0.00           C 0
+ATOM    957   CA SER A 139      -5.518  42.391  22.272  0.00  0.00           C 0
+ATOM    934  CZ2 TRP A 136      -2.780  41.060  19.984  0.00  0.00           C 0
+ATOM    960   CB SER A 139      -6.763  43.066  21.741  0.00  0.00           C 0
+ATOM   1429  OE1 GLU A 197      -4.752  32.145  21.963  0.56  7.50           O 0
+ATOM    931  NE1 TRP A 136      -2.749  38.969  21.389  0.00  0.00           N 0
+ATOM   1471  CG2 VAL A 203      -5.666  34.276  16.511  0.00  0.00           C 0
+ATOM   1460    O GLY A 201      -1.543  37.709  17.569  0.67  3.21           O 0
+ATOM    929  CD1 TRP A 136      -1.859  38.424  22.267  0.00  0.00           C 0
+ATOM   1464    O GLY A 202      -2.588  34.164  18.501  0.75  3.21           O 0
+ATOM   1437  OD1 ASP A 198      -1.702  34.795  26.267  0.62  6.43           O 0
+ATOM    926    O TRP A 136      -1.154  37.827  25.553  0.00  0.00           O 0
+ATOM    938   CA GLN A 137      -2.879  39.850  26.496  0.00  0.00           C 0
+ATOM    944  OE1 GLN A 137      -2.015  37.362  28.052  0.72  1.07           O 0
+ATOM    943   CD GLN A 137      -2.740  37.781  28.923  0.00  0.00           C 0
+ATOM    945  NE2 GLN A 137      -3.185  37.029  29.895  0.38  6.56           N 0
+ATOM   1426   CB GLU A 197      -2.071  32.888  21.966  0.00  0.00           C 0
+ATOM    947   CA HIS A 138      -5.949  40.350  25.383  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket31_vert.pqr

@@ -0,0 +1,45 @@
+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    31:
+HEADER 0  - Pocket Score                      : 0.0126
+HEADER 1  - Drug Score                        : 0.0005
+HEADER 2  - Number of V. Vertices             :    23
+HEADER 3  - Mean alpha-sphere radius          : 3.9707
+HEADER 4  - Mean alpha-sphere SA              : 0.5940
+HEADER 5  - Mean B-factor                     : 0.6103
+HEADER 6  - Hydrophobicity Score              : 8.8889
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 3.4444
+HEADER 9  - Real volume (approximation)       : 376.4228
+HEADER 10 - Charge Score                      :    -1
+HEADER 11 - Local hydrophobic density Score   : 3.0000
+HEADER 12 - Number of apolar alpha sphere     :     4
+HEADER 13 - Proportion of apolar alpha sphere : 0.1739
+ATOM      1    C STP    31      -8.032  36.598  24.507    0.00     4.25
+ATOM      2    C STP    31      -6.317  40.316  19.354    0.00     3.67
+ATOM      3    O STP    31      -6.241  36.196  20.577    0.00     4.53
+ATOM      4    O STP    31      -5.894  38.358  18.290    0.00     4.46
+ATOM      5    O STP    31      -5.085  36.061  23.011    0.00     4.07
+ATOM      6    O STP    31      -5.997  36.118  20.506    0.00     4.41
+ATOM      7    O STP    31      -4.992  37.054  19.004    0.00     3.79
+ATOM      8    O STP    31      -4.682  36.520  24.300    0.00     3.97
+ATOM      9    O STP    31      -4.977  35.973  23.815    0.00     4.26
+ATOM     10    O STP    31      -5.969  35.699  24.686    0.00     4.64
+ATOM     11    O STP    31      -4.825  36.766  25.651    0.00     3.74
+ATOM     12    O STP    31      -4.611  36.817  25.615    0.00     3.60
+ATOM     13    O STP    31      -5.217  35.714  27.069    0.00     3.72
+ATOM     14    O STP    31      -5.187  35.774  27.014    0.00     3.70
+ATOM     15    O STP    31      -5.094  35.710  27.122    0.00     3.62
+ATOM     16    O STP    31      -4.308  35.750  22.030    0.00     3.63
+ATOM     17    O STP    31      -4.289  35.685  21.321    0.00     3.63
+ATOM     18    O STP    31      -4.287  35.669  23.512    0.00     3.88
+ATOM     19    O STP    31      -5.766  35.921  24.773    0.00     4.47
+ATOM     20    C STP    31      -4.838  36.764  25.611    0.00     3.76
+ATOM     21    C STP    31      -7.525  36.946  24.679    0.00     3.82
+ATOM     22    O STP    31      -4.818  36.627  24.650    0.00     3.96
+ATOM     23    O STP    31      -4.757  36.793  25.400    0.00     3.75
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket32_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    32:
+HEADER 0  - Pocket Score                      : 0.0114
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of alpha spheres           :    18
+HEADER 3  - Mean alpha-sphere radius          : 3.8510
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5826
+HEADER 5  - Mean B-factor of pocket residues  : 0.7545
+HEADER 6  - Hydrophobicity Score              : 17.4000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 4.6000
+HEADER 9  - Pocket volume (Monte Carlo)       : 243.0391
+HEADER 10  -Pocket volume (convex hull)       : 8.3578
+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 : 0.2778
+ATOM   4206   NZ LYS B 225      18.332  15.278  83.603  0.82  7.66           N 0
+ATOM   4467    O ILE B 261      14.531  21.888  81.244  0.00  0.00           O 0
+ATOM   4175  OE2 GLU B 221      13.472  20.921  85.571  0.00  0.00           O 0
+ATOM   4479  OD2 ASP B 262      18.355  23.633  81.552  0.00  0.00           O 0
+ATOM   4204   CD LYS B 225      15.907  14.880  83.535  0.00  0.00           C 0
+ATOM   4172   CG GLU B 221      11.745  19.532  84.684  0.00  0.00           C 0
+ATOM   4478  OD1 ASP B 262      17.451  24.799  83.175  0.48  6.43           O 0
+ATOM   4477   CG ASP B 262      17.424  24.321  82.021  0.00  0.00           C 0
+ATOM   4197  CD2 LEU B 224      12.544  18.193  77.956  0.00  0.00           C 0
+ATOM   4170    O GLU B 221      10.908  16.644  83.047  0.00  0.00           O 0
+ATOM   4195   CG LEU B 224      11.982  16.770  78.015  0.00  0.00           C 0
+ATOM   4199   CA LYS B 225      13.263  13.840  82.010  0.00  0.00           C 0
+ATOM   4193    O LEU B 224      12.524  13.636  79.310  0.20  4.29           O 0
+ATOM   4198    N LYS B 225      12.171  14.554  81.337  0.78  1.09           N 0
+ATOM   4202   CB LYS B 225      13.453  14.385  83.430  0.00  0.00           C 0
+ATOM   4194   CB LEU B 224      11.038  16.598  79.207  0.00  0.00           C 0
+ATOM   4192    C LEU B 224      11.877  14.375  80.051  0.00  0.00           C 0
+ATOM   4468   CB ILE B 261      11.524  21.661  80.476  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket32_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    32:
+HEADER 0  - Pocket Score                      : 0.0114
+HEADER 1  - Drug Score                        : 0.0002
+HEADER 2  - Number of V. Vertices             :    18
+HEADER 3  - Mean alpha-sphere radius          : 3.8510
+HEADER 4  - Mean alpha-sphere SA              : 0.5826
+HEADER 5  - Mean B-factor                     : 0.7545
+HEADER 6  - Hydrophobicity Score              : 17.4000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 4.6000
+HEADER 9  - Real volume (approximation)       : 243.0391
+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 : 0.2778
+ATOM      1    O STP    32      17.596  19.789  83.926    0.00     4.58
+ATOM      2    O STP    32      15.034  18.555  83.023    0.00     3.81
+ATOM      3    O STP    32      16.481  18.986  83.474    0.00     4.15
+ATOM      4    O STP    32      16.976  21.120  84.072    0.00     3.82
+ATOM      5    O STP    32      16.949  21.192  84.004    0.00     3.74
+ATOM      6    O STP    32      14.344  17.920  81.495    0.00     3.98
+ATOM      7    O STP    32      14.358  18.153  82.201    0.00     3.86
+ATOM      8    C STP    32      15.591  16.240  79.747    0.00     4.04
+ATOM      9    C STP    32      15.607  16.224  79.729    0.00     4.05
+ATOM     10    C STP    32      15.639  16.219  79.705    0.00     4.07
+ATOM     11    O STP    32      15.143  16.197  79.858    0.00     3.70
+ATOM     12    C STP    32      15.196  16.406  79.995    0.00     3.79
+ATOM     13    C STP    32      15.194  16.592  80.194    0.00     3.82
+ATOM     14    O STP    32      14.329  17.871  81.476    0.00     3.96
+ATOM     15    O STP    32      14.171  17.513  81.797    0.00     3.60
+ATOM     16    O STP    32      13.661  17.688  81.205    0.00     3.47
+ATOM     17    O STP    32      14.792  16.125  79.830    0.00     3.41
+ATOM     18    O STP    32      13.135  18.704  81.345    0.00     3.48
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket33_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    33:
+HEADER 0  - Pocket Score                      : 0.0056
+HEADER 1  - Drug Score                        : 0.0098
+HEADER 2  - Number of alpha spheres           :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.9046
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6220
+HEADER 5  - Mean B-factor of pocket residues  : 0.3783
+HEADER 6  - Hydrophobicity Score              : 42.0000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 4.6667
+HEADER 9  - Pocket volume (Monte Carlo)       : 227.3591
+HEADER 10  -Pocket volume (convex hull)       : 4.3371
+HEADER 11 - Charge Score                      :     0
+HEADER 12 - Local hydrophobic density Score   : 11.0000
+HEADER 13 - Number of apolar alpha sphere     :    12
+HEADER 14 - Proportion of apolar alpha sphere : 0.7059
+ATOM   1618    O GLU A 221       9.633  24.324   8.108  0.60  1.07           O 0
+ATOM   1651   CG LYS A 225      12.595  26.168   7.409  0.00  0.00           C 0
+ATOM   1642   CB LEU A 224       9.952  24.392  11.875  0.00  0.00           C 0
+ATOM   1645  CD2 LEU A 224      11.587  22.875  12.978  0.00  0.00           C 0
+ATOM   1653   CE LYS A 225      13.634  24.531   5.773  0.00  0.00           C 0
+ATOM   1915    O ILE A 261      13.856  19.579   9.511  0.52  6.43           O 0
+ATOM   1916   CB ILE A 261      10.921  19.633  10.305  0.00  0.00           C 0
+ATOM   1643   CG LEU A 224      10.843  24.201  13.096  0.00  0.00           C 0
+ATOM    706  CD2 LEU A 108      15.143  25.813  18.025  0.00  0.00           C 0
+ATOM   1904    O THR A 259      13.861  22.310  16.199  0.68  3.21           O 0
+ATOM    705  CD1 LEU A 108      12.705  25.190  17.699  0.00  0.00           C 0
+ATOM    703   CB LEU A 108      13.411  27.619  17.589  0.00  0.00           C 0
+ATOM   1641    O LEU A 224      10.763  27.660  11.810  0.53  6.43           O 0
+ATOM    702    O LEU A 108      14.548  29.949  16.096  0.55  6.43           O 0
+ATOM   1620   CG GLU A 221      10.570  21.677   6.115  0.00  0.00           C 0
+ATOM   1646    N LYS A 225      10.430  26.718   9.800  0.00  0.00           N 0
+ATOM   1647   CA LYS A 225      11.347  27.613   9.082  0.00  0.00           C 0
+ATOM   1640    C LEU A 224      10.250  26.796  11.114  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket33_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    33:
+HEADER 0  - Pocket Score                      : 0.0056
+HEADER 1  - Drug Score                        : 0.0098
+HEADER 2  - Number of V. Vertices             :    17
+HEADER 3  - Mean alpha-sphere radius          : 3.9046
+HEADER 4  - Mean alpha-sphere SA              : 0.6220
+HEADER 5  - Mean B-factor                     : 0.3783
+HEADER 6  - Hydrophobicity Score              : 42.0000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 4.6667
+HEADER 9  - Real volume (approximation)       : 227.3591
+HEADER 10 - Charge Score                      :     0
+HEADER 11 - Local hydrophobic density Score   : 11.0000
+HEADER 12 - Number of apolar alpha sphere     :    12
+HEADER 13 - Proportion of apolar alpha sphere : 0.7059
+ATOM      1    C STP    33      12.580  23.652   9.768    0.00     3.45
+ATOM      2    O STP    33      12.819  22.916   8.838    0.00     3.56
+ATOM      3    O STP    33      12.358  22.726   9.582    0.00     3.49
+ATOM      4    O STP    33      12.842  23.135   9.509    0.00     3.70
+ATOM      5    C STP    33      15.204  25.744  13.391    0.00     4.64
+ATOM      6    C STP    33      14.383  25.657  14.136    0.00     3.97
+ATOM      7    C STP    33      14.330  25.875  14.110    0.00     4.00
+ATOM      8    C STP    33      14.566  25.576  11.265    0.00     4.37
+ATOM      9    O STP    33      14.509  26.436  13.581    0.00     4.32
+ATOM     10    C STP    33      14.854  26.238  13.535    0.00     4.52
+ATOM     11    O STP    33      12.716  22.769   8.649    0.00     3.50
+ATOM     12    C STP    33      13.018  24.580  10.396    0.00     3.41
+ATOM     13    C STP    33      13.550  25.050  10.770    0.00     3.67
+ATOM     14    C STP    33      14.356  25.543  11.189    0.00     4.22
+ATOM     15    C STP    33      13.917  25.498  11.096    0.00     3.89
+ATOM     16    C STP    33      13.848  25.359  10.969    0.00     3.86
+ATOM     17    C STP    33      13.828  25.416  11.014    0.00     3.84
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket34_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    34:
+HEADER 0  - Pocket Score                      : -0.0022
+HEADER 1  - Drug Score                        : 0.0343
+HEADER 2  - Number of alpha spheres           :    27
+HEADER 3  - Mean alpha-sphere radius          : 4.0246
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.6186
+HEADER 5  - Mean B-factor of pocket residues  : 0.8132
+HEADER 6  - Hydrophobicity Score              : 31.0000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Amino Acid based volume Score     : 4.6000
+HEADER 9  - Pocket volume (Monte Carlo)       : 281.5477
+HEADER 10  -Pocket volume (convex hull)       : 14.7681
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 20.0000
+HEADER 13 - Number of apolar alpha sphere     :    21
+HEADER 14 - Proportion of apolar alpha sphere : 0.7778
+ATOM      5   CB ALA A  19       5.485  47.447  25.036  0.00  0.00           C 0
+ATOM    977  CD1 TRP A 141       2.410  43.570  21.034  0.00  0.00           C 0
+ATOM    976   CG TRP A 141       2.673  43.406  22.354  0.00  0.00           C 0
+ATOM    975   CB TRP A 141       2.419  44.378  23.429  0.00  0.00           C 0
+ATOM      1    N ALA A  19       4.342  49.417  24.066  0.00  0.00           N 0
+ATOM    911  NE2 GLN A 134       8.391  45.322  25.385  0.00  0.00           N 0
+ATOM    909   CD GLN A 134       7.588  44.650  26.196  0.00  0.00           C 0
+ATOM    756   CG ARG A 115       9.521  40.950  19.563  0.00  0.00           C 0
+ATOM    755   CB ARG A 115       8.999  40.309  20.841  0.00  0.00           C 0
+ATOM    754    O ARG A 115       8.800  41.147  23.920  0.59  5.36           O 0
+ATOM    978  CD2 TRP A 141       3.250  42.099  22.495  0.00  0.00           C 0
+ATOM    907   CB GLN A 134       6.750  42.233  26.226  0.00  0.00           C 0
+ATOM    981  CE3 TRP A 141       3.714  41.354  23.584  0.00  0.00           C 0
+ATOM    752   CA ARG A 115       9.982  40.563  21.962  0.00  0.00           C 0
+ATOM    749    O ALA A 114      12.408  41.249  22.955  0.33  9.64           O 0
+ATOM    980  CE2 TRP A 141       3.312  41.533  21.211  0.00  0.00           C 0
+ATOM    757   CD ARG A 115       8.652  40.619  18.350  0.00  0.00           C 0
+ATOM    979  NE1 TRP A 141       2.796  42.450  20.338  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket34_vert.pqr

@@ -0,0 +1,49 @@
+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    34:
+HEADER 0  - Pocket Score                      : -0.0022
+HEADER 1  - Drug Score                        : 0.0343
+HEADER 2  - Number of V. Vertices             :    27
+HEADER 3  - Mean alpha-sphere radius          : 4.0246
+HEADER 4  - Mean alpha-sphere SA              : 0.6186
+HEADER 5  - Mean B-factor                     : 0.8132
+HEADER 6  - Hydrophobicity Score              : 31.0000
+HEADER 7  - Polarity Score                    :     3
+HEADER 8  - Volume Score                      : 4.6000
+HEADER 9  - Real volume (approximation)       : 281.5477
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 20.0000
+HEADER 12 - Number of apolar alpha sphere     :    21
+HEADER 13 - Proportion of apolar alpha sphere : 0.7778
+ATOM      1    C STP    34       5.176  46.122  21.496    0.00     3.79
+ATOM      2    C STP    34       4.695  46.705  21.302    0.00     3.89
+ATOM      3    C STP    34       6.671  45.344  21.102    0.00     4.62
+ATOM      4    C STP    34       5.867  44.408  23.210    0.00     3.46
+ATOM      5    C STP    34       5.823  44.543  23.278    0.00     3.41
+ATOM      6    C STP    34       5.891  44.597  23.044    0.00     3.50
+ATOM      7    C STP    34       6.982  44.650  20.954    0.00     4.70
+ATOM      8    C STP    34       6.967  44.386  21.149    0.00     4.57
+ATOM      9    O STP    34       7.490  44.296  21.318    0.00     4.29
+ATOM     10    C STP    34       5.990  44.166  23.131    0.00     3.49
+ATOM     11    C STP    34       6.319  43.697  23.068    0.00     3.51
+ATOM     12    O STP    34       6.427  43.613  22.970    0.00     3.55
+ATOM     13    C STP    34       6.398  43.488  23.002    0.00     3.48
+ATOM     14    C STP    34       6.966  44.383  21.152    0.00     4.56
+ATOM     15    O STP    34       6.967  44.253  21.296    0.00     4.46
+ATOM     16    C STP    34       6.964  44.381  21.146    0.00     4.56
+ATOM     17    C STP    34       8.491  43.852  21.504    0.00     3.64
+ATOM     18    O STP    34       8.778  44.348  21.529    0.00     4.00
+ATOM     19    O STP    34      10.265  44.159  22.483    0.00     3.64
+ATOM     20    O STP    34      10.484  45.071  21.318    0.00     4.58
+ATOM     21    C STP    34       6.851  44.163  20.991    0.00     4.42
+ATOM     22    C STP    34       6.526  42.887  20.217    0.00     3.63
+ATOM     23    C STP    34       6.848  44.282  20.938    0.00     4.49
+ATOM     24    C STP    34       6.857  44.320  20.938    0.00     4.51
+ATOM     25    C STP    34       5.977  43.937  21.065    0.00     3.59
+ATOM     26    C STP    34       6.855  44.311  20.941    0.00     4.51
+ATOM     27    C STP    34       6.533  43.305  20.098    0.00     3.84
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket35_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    35:
+HEADER 0  - Pocket Score                      : -0.0201
+HEADER 1  - Drug Score                        : 0.0007
+HEADER 2  - Number of alpha spheres           :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8193
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4869
+HEADER 5  - Mean B-factor of pocket residues  : 0.2711
+HEADER 6  - Hydrophobicity Score              : -3.0000
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Amino Acid based volume Score     : 3.1429
+HEADER 9  - Pocket volume (Monte Carlo)       : 155.4362
+HEADER 10  -Pocket volume (convex hull)       : 1.5830
+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 : 0.3750
+ATOM   1167   CB ALA A 163      20.931  22.647  31.840  0.00  0.00           C 0
+ATOM   2344    O ASP A 313      18.861  14.595  29.914  0.00  0.00           O 0
+ATOM   2091    O GLY A 281      16.614  16.985  30.335  0.33  4.29           O 0
+ATOM   2350   CA ASP A 314      18.405  16.344  27.714  0.00  0.00           C 0
+ATOM    551    O THR A  87      18.666  23.823  29.423  0.65  1.07           O 0
+ATOM   2058  NH2 ARG A 277      15.434  21.460  27.932  0.00  0.00           N 0
+ATOM   2352    O ASP A 314      16.543  17.844  27.274  0.00  0.00           O 0
+ATOM    549   CA THR A  87      18.617  23.744  27.032  0.00  0.00           C 0
+ATOM    554  CG2 THR A  87      20.315  22.397  25.602  0.00  0.00           C 0
+ATOM    576   SG CYS A  90      16.781  22.002  32.323  0.00  0.00           S 0
+ATOM   2353   CB ASP A 314      19.371  17.085  26.766  0.00  0.00           C 0
+ATOM    552   CB THR A  87      20.117  23.528  26.669  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket35_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    35:
+HEADER 0  - Pocket Score                      : -0.0201
+HEADER 1  - Drug Score                        : 0.0007
+HEADER 2  - Number of V. Vertices             :    16
+HEADER 3  - Mean alpha-sphere radius          : 3.8193
+HEADER 4  - Mean alpha-sphere SA              : 0.4869
+HEADER 5  - Mean B-factor                     : 0.2711
+HEADER 6  - Hydrophobicity Score              : -3.0000
+HEADER 7  - Polarity Score                    :     4
+HEADER 8  - Volume Score                      : 3.1429
+HEADER 9  - Real volume (approximation)       : 155.4362
+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 : 0.3750
+ATOM      1    O STP    35      20.683  18.448  30.757    0.00     4.34
+ATOM      2    O STP    35      18.535  20.086  29.509    0.00     3.74
+ATOM      3    O STP    35      18.850  20.396  28.335    0.00     3.60
+ATOM      4    O STP    35      18.700  20.431  27.894    0.00     3.42
+ATOM      5    O STP    35      18.468  20.119  29.602    0.00     3.71
+ATOM      6    O STP    35      18.957  20.005  29.849    0.00     3.85
+ATOM      7    O STP    35      18.876  19.363  29.298    0.00     3.44
+ATOM      8    O STP    35      19.053  19.923  29.451    0.00     3.92
+ATOM      9    C STP    35      20.153  20.272  28.858    0.00     3.89
+ATOM     10    O STP    35      18.969  20.354  28.334    0.00     3.65
+ATOM     11    C STP    35      18.958  20.356  28.271    0.00     3.62
+ATOM     12    C STP    35      19.013  20.359  28.333    0.00     3.65
+ATOM     13    C STP    35      20.207  18.928  30.314    0.00     4.08
+ATOM     14    O STP    35      19.202  19.893  29.565    0.00     3.97
+ATOM     15    C STP    35      20.954  18.400  30.663    0.00     4.41
+ATOM     16    C STP    35      20.241  20.412  28.843    0.00     3.80
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket36_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    36:
+HEADER 0  - Pocket Score                      : -0.0206
+HEADER 1  - Drug Score                        : 0.1939
+HEADER 2  - Number of alpha spheres           :    26
+HEADER 3  - Mean alpha-sphere radius          : 4.0665
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5888
+HEADER 5  - Mean B-factor of pocket residues  : 0.7603
+HEADER 6  - Hydrophobicity Score              : 22.9000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 3.4000
+HEADER 9  - Pocket volume (Monte Carlo)       : 302.7416
+HEADER 10  -Pocket volume (convex hull)       : 7.2399
+HEADER 11 - Charge Score                      :    -2
+HEADER 12 - Local hydrophobic density Score   : 21.0000
+HEADER 13 - Number of apolar alpha sphere     :    22
+HEADER 14 - Proportion of apolar alpha sphere : 0.8462
+HETATM 5138  CH3 ACE E 355      -8.464  18.770  61.674  0.00  0.00           C 0
+ATOM   4263  CE2 PHE B 233      -3.280  20.740  68.083  0.00  0.00           C 0
+ATOM   5139    N LEU E 356      -6.229  18.339  60.905  0.64  1.09           N 0
+ATOM   4287  CG2 THR B 236      -5.683  23.029  62.738  0.00  0.00           C 0
+ATOM   4279  OD1 ASP B 235      -6.029  23.334  68.270  0.00  0.00           O 0
+ATOM   4284    O THR B 236      -8.487  24.993  63.383  0.43  9.64           O 0
+ATOM   5152   CG LEU E 357      -1.271  18.582  64.323  0.00  0.00           C 0
+ATOM   3932    O GLY B 190      -1.981  14.926  62.479  0.60  1.07           O 0
+ATOM   3934   CA SER B 191      -1.996  12.972  64.518  0.00  0.00           C 0
+ATOM   5146  CD2 LEU E 356      -5.122  14.513  62.278  0.00  0.00           C 0
+ATOM   5140   CA LEU E 356      -5.070  17.475  61.230  0.00  0.00           C 0
+ATOM   5147    N LEU E 357      -2.747  17.886  61.760  0.00  0.00           N 0
+ATOM   4264   CZ PHE B 233      -3.093  19.582  68.806  0.00  0.00           C 0
+ATOM   5154  CD2 LEU E 357      -1.370  20.078  64.523  0.00  0.00           C 0
+ATOM   5153  CD1 LEU E 357      -0.477  17.951  65.443  0.00  0.00           C 0
+ATOM   5141    C LEU E 356      -3.801  18.294  61.060  0.00  0.00           C 0
+ATOM   3937   CB SER B 191      -3.056  12.010  65.083  0.00  0.00           C 0
+ATOM   3938   OG SER B 191      -3.103  12.025  66.501  0.00  0.00           O 0
+ATOM   5066  OE2 GLU B 332      -2.537  15.738  70.156  0.57  5.36           O 0
+ATOM   3939    N ALA B 192      -0.163  13.704  65.941  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket36_vert.pqr

@@ -0,0 +1,48 @@
+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    36:
+HEADER 0  - Pocket Score                      : -0.0206
+HEADER 1  - Drug Score                        : 0.1939
+HEADER 2  - Number of V. Vertices             :    26
+HEADER 3  - Mean alpha-sphere radius          : 4.0665
+HEADER 4  - Mean alpha-sphere SA              : 0.5888
+HEADER 5  - Mean B-factor                     : 0.7603
+HEADER 6  - Hydrophobicity Score              : 22.9000
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 3.4000
+HEADER 9  - Real volume (approximation)       : 302.7416
+HEADER 10 - Charge Score                      :    -2
+HEADER 11 - Local hydrophobic density Score   : 21.0000
+HEADER 12 - Number of apolar alpha sphere     :    22
+HEADER 13 - Proportion of apolar alpha sphere : 0.8462
+ATOM      1    C STP    36      -5.900  19.435  64.999    0.00     4.25
+ATOM      2    C STP    36      -6.847  19.898  65.623    0.00     4.41
+ATOM      3    O STP    36      -8.589  21.079  65.449    0.00     4.43
+ATOM      4    C STP    36      -3.938  16.114  65.559    0.00     3.84
+ATOM      5    C STP    36      -4.561  17.072  64.827    0.00     3.65
+ATOM      6    C STP    36      -5.332  17.381  65.663    0.00     4.44
+ATOM      7    C STP    36      -4.829  19.097  64.431    0.00     3.60
+ATOM      8    C STP    36      -5.381  17.975  65.511    0.00     4.32
+ATOM      9    C STP    36      -5.257  18.993  64.993    0.00     4.06
+ATOM     10    C STP    36      -6.262  17.976  65.741    0.00     4.69
+ATOM     11    C STP    36      -5.925  19.066  65.133    0.00     4.30
+ATOM     12    C STP    36      -5.559  19.453  64.853    0.00     4.16
+ATOM     13    C STP    36      -5.433  19.479  64.808    0.00     4.12
+ATOM     14    C STP    36      -4.338  16.187  66.168    0.00     4.31
+ATOM     15    C STP    36      -3.511  16.057  65.508    0.00     3.58
+ATOM     16    C STP    36      -5.192  19.682  64.157    0.00     3.67
+ATOM     17    C STP    36      -5.136  19.636  64.350    0.00     3.80
+ATOM     18    C STP    36      -4.829  19.165  64.377    0.00     3.58
+ATOM     19    C STP    36      -4.498  15.199  65.711    0.00     3.56
+ATOM     20    O STP    36      -3.083  15.554  66.671    0.00     3.53
+ATOM     21    O STP    36      -3.086  15.728  66.585    0.00     3.61
+ATOM     22    O STP    36      -4.393  16.179  66.238    0.00     4.36
+ATOM     23    C STP    36      -4.385  16.189  66.234    0.00     4.36
+ATOM     24    C STP    36      -4.486  16.284  66.252    0.00     4.40
+ATOM     25    C STP    36      -4.410  16.220  66.237    0.00     4.37
+ATOM     26    C STP    36      -4.403  16.306  66.281    0.00     4.34
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket37_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    37:
+HEADER 0  - Pocket Score                      : -0.0257
+HEADER 1  - Drug Score                        : 0.0004
+HEADER 2  - Number of alpha spheres           :    16
+HEADER 3  - Mean alpha-sphere radius          : 4.1475
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5838
+HEADER 5  - Mean B-factor of pocket residues  : 0.9013
+HEADER 6  - Hydrophobicity Score              : -32.8333
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 4.3333
+HEADER 9  - Pocket volume (Monte Carlo)       : 165.1588
+HEADER 10  -Pocket volume (convex hull)       : 1.0501
+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 : 0.3750
+ATOM   5040  OD1 ASP B 329      -4.110  28.263  71.437  0.44  3.21           O 0
+ATOM   4280  OD2 ASP B 235      -6.824  24.823  69.708  0.00  0.00           O 0
+ATOM   5038   CB ASP B 329      -3.793  25.907  71.086  0.00  0.00           C 0
+ATOM   5037    O ASP B 329      -3.449  24.343  74.036  0.69  2.14           O 0
+ATOM   4064  NE2 GLN B 208      -9.127  22.189  74.752  0.00  0.00           N 0
+ATOM   5050   NZ LYS B 330      -7.354  22.505  71.342  0.64  2.19           N 0
+ATOM   4076   CB LYS B 210      -5.462  28.842  77.518  0.00  0.00           C 0
+ATOM   4072    N LYS B 210      -3.856  26.964  77.789  0.00  0.00           N 0
+ATOM   4060   CB GLN B 208      -6.383  22.970  77.037  0.00  0.00           C 0
+ATOM   4062   CD GLN B 208      -8.648  22.456  75.968  0.00  0.00           C 0
+ATOM   4063  OE1 GLN B 208      -9.306  23.049  76.822  0.74  7.50           O 0
+ATOM   4087   CD GLU B 211      -9.985  27.355  80.115  0.00  0.00           C 0
+ATOM   4085   CB GLU B 211      -7.953  25.859  80.562  0.00  0.00           C 0
+ATOM   4077   CG LYS B 210      -4.830  29.399  76.245  0.00  0.00           C 0
+ATOM   4081    N GLU B 211      -5.741  26.429  79.713  0.00  0.00           N 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket37_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    37:
+HEADER 0  - Pocket Score                      : -0.0257
+HEADER 1  - Drug Score                        : 0.0004
+HEADER 2  - Number of V. Vertices             :    16
+HEADER 3  - Mean alpha-sphere radius          : 4.1475
+HEADER 4  - Mean alpha-sphere SA              : 0.5838
+HEADER 5  - Mean B-factor                     : 0.9013
+HEADER 6  - Hydrophobicity Score              : -32.8333
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 4.3333
+HEADER 9  - Real volume (approximation)       : 165.1588
+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 : 0.3750
+ATOM      1    O STP    37      -7.102  26.313  73.597    0.00     4.17
+ATOM      2    O STP    37      -7.421  26.061  73.817    0.00     4.33
+ATOM      3    O STP    37      -6.330  26.133  75.287    0.00     3.61
+ATOM      4    C STP    37      -7.608  26.361  74.944    0.00     4.17
+ATOM      5    O STP    37      -7.525  26.375  73.934    0.00     4.56
+ATOM      6    C STP    37      -8.269  26.555  76.983    0.00     3.66
+ATOM      7    O STP    37      -6.096  26.318  75.184    0.00     3.50
+ATOM      8    O STP    37      -7.522  26.471  73.942    0.00     4.60
+ATOM      9    O STP    37      -7.546  26.457  73.959    0.00     4.61
+ATOM     10    C STP    37      -6.961  26.277  74.736    0.00     4.07
+ATOM     11    C STP    37      -7.338  26.325  74.390    0.00     4.38
+ATOM     12    C STP    37      -7.421  26.365  74.546    0.00     4.34
+ATOM     13    O STP    37      -7.645  26.511  73.951    0.00     4.64
+ATOM     14    C STP    37      -8.015  26.697  74.397    0.00     4.57
+ATOM     15    O STP    37      -7.748  26.231  76.799    0.00     3.54
+ATOM     16    O STP    37      -8.132  26.462  77.003    0.00     3.61
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket38_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    38:
+HEADER 0  - Pocket Score                      : -0.0283
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of alpha spheres           :    21
+HEADER 3  - Mean alpha-sphere radius          : 3.9440
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5710
+HEADER 5  - Mean B-factor of pocket residues  : 0.5466
+HEADER 6  - Hydrophobicity Score              : 23.7500
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.0000
+HEADER 9  - Pocket volume (Monte Carlo)       : 373.6409
+HEADER 10  -Pocket volume (convex hull)       : 39.7338
+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 : 0.3333
+ATOM   3543  CD1 LEU B 142       1.940  -3.858  62.018  0.00  0.00           C 0
+ATOM   3859    O LEU B 180       0.332   1.044  57.200  0.19  5.36           O 0
+ATOM   3497  NE2 GLN B 137      -0.618   0.150  62.689  0.00  0.00           N 0
+ATOM   3862  CD1 LEU B 180       2.448  -0.287  60.303  0.00  0.00           C 0
+ATOM   2582  OG1 THR B  22       3.332  -6.306  58.107  0.65  7.50           O 0
+ATOM   3854   CE LYS B 179       6.326  -3.168  53.519  0.00  0.00           C 0
+ATOM   3558  CG1 VAL B 144       7.424  -1.547  57.561  0.00  0.00           C 0
+ATOM   2583  CG2 THR B  22       5.643  -6.282  58.518  0.00  0.00           C 0
+ATOM   2580    O THR B  22       3.562  -8.297  56.123  0.00  0.00           O 0
+ATOM   2595   CA SER B  24       3.690 -11.388  52.407  0.00  0.00           C 0
+ATOM   2598   CB SER B  24       3.226 -10.813  51.075  0.00  0.00           C 0
+ATOM   2594    N SER B  24       4.530 -10.400  53.093  0.00  0.00           N 0
+ATOM   2784  OD2 ASP B  47       5.311  -7.628  52.003  0.74  2.14           O 0
+ATOM   2781   CB ASP B  47       4.744  -5.693  50.745  0.00  0.00           C 0
+ATOM   2782   CG ASP B  47       4.849  -7.202  50.933  0.00  0.00           C 0
+ATOM   3857   CA LEU B 180       2.718   0.998  57.180  0.00  0.00           C 0
+ATOM   3559  CG2 VAL B 144       6.230  -2.247  59.644  0.00  0.00           C 0
+ATOM   3852   CG LYS B 179       5.547  -0.800  53.662  0.00  0.00           C 0
+ATOM   3856    N LEU B 180       3.721   1.328  56.173  0.00  0.00           N 0
+ATOM   3850    O LYS B 179       2.545   0.669  54.382  0.00  0.00           O 0
+ATOM   2780    O ASP B  47       3.769  -3.158  49.491  0.44  8.57           O 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket38_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    38:
+HEADER 0  - Pocket Score                      : -0.0283
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of V. Vertices             :    21
+HEADER 3  - Mean alpha-sphere radius          : 3.9440
+HEADER 4  - Mean alpha-sphere SA              : 0.5710
+HEADER 5  - Mean B-factor                     : 0.5466
+HEADER 6  - Hydrophobicity Score              : 23.7500
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 373.6409
+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 : 0.3333
+ATOM      1    O STP    38      -1.172  -2.506  59.261    0.00     4.37
+ATOM      2    O STP    38       0.132  -3.277  58.041    0.00     4.41
+ATOM      3    C STP    38       4.766  -3.543  56.588    0.00     3.46
+ATOM      4    O STP    38       1.257  -8.946  53.438    0.00     3.60
+ATOM      5    O STP    38       1.750  -7.974  52.921    0.00     3.69
+ATOM      6    O STP    38       3.518  -5.330  54.101    0.00     3.59
+ATOM      7    O STP    38       2.106  -4.530  54.178    0.00     4.48
+ATOM      8    O STP    38       1.520  -7.803  52.851    0.00     3.89
+ATOM      9    O STP    38       1.921  -6.346  53.258    0.00     3.84
+ATOM     10    O STP    38       1.452  -2.825  57.335    0.00     4.03
+ATOM     11    C STP    38       3.201  -2.650  57.558    0.00     3.70
+ATOM     12    C STP    38       3.922  -2.824  56.529    0.00     3.87
+ATOM     13    C STP    38       4.164  -2.073  56.557    0.00     3.45
+ATOM     14    C STP    38       3.817  -2.726  56.599    0.00     3.91
+ATOM     15    C STP    38       3.815  -2.712  56.602    0.00     3.91
+ATOM     16    C STP    38       3.808  -2.720  56.601    0.00     3.92
+ATOM     17    O STP    38       3.212  -2.825  56.175    0.00     3.98
+ATOM     18    O STP    38       2.978  -3.087  55.734    0.00     4.02
+ATOM     19    O STP    38       2.348  -3.142  53.219    0.00     3.99
+ATOM     20    O STP    38       1.441  -2.958  56.300    0.00     4.25
+ATOM     21    O STP    38       1.890  -3.659  53.508    0.00     4.46
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket39_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    39:
+HEADER 0  - Pocket Score                      : -0.0286
+HEADER 1  - Drug Score                        : 0.0007
+HEADER 2  - Number of alpha spheres           :    23
+HEADER 3  - Mean alpha-sphere radius          : 3.8671
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4339
+HEADER 5  - Mean B-factor of pocket residues  : 0.6124
+HEADER 6  - Hydrophobicity Score              : 3.1000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Amino Acid based volume Score     : 3.8000
+HEADER 9  - Pocket volume (Monte Carlo)       : 289.6613
+HEADER 10  -Pocket volume (convex hull)       : 21.1800
+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 : 0.1304
+ATOM   4904    O ASP B 314      16.529  23.016  63.132  0.58  6.43           O 0
+ATOM   3103    O THR B  87      19.372  17.149  61.547  0.45  2.14           O 0
+ATOM   3101   CA THR B  87      19.174  17.345  63.917  0.00  0.00           C 0
+ATOM   4610  NH2 ARG B 277      15.594  19.205  63.155  0.00  0.00           N 0
+ATOM   3104   CB THR B  87      20.666  17.812  64.182  0.00  0.00           C 0
+ATOM   3128   SG CYS B  90      17.210  18.693  58.624  0.00  0.00           S 0
+ATOM   3719   CB ALA B 163      21.283  18.472  58.972  0.00  0.00           C 0
+ATOM   3094   CG ARG B  86      16.638  17.478  67.527  0.00  0.00           C 0
+ATOM   3106  CG2 THR B  87      20.818  18.552  65.535  0.00  0.00           C 0
+ATOM   4607   NE ARG B 277      15.127  19.672  65.336  0.00  0.00           N 0
+ATOM   4920  OE1 GLU B 316      17.612  21.822  70.107  0.20  5.36           O 0
+ATOM   4917   CB GLU B 316      15.920  23.484  67.971  0.00  0.00           C 0
+ATOM   4907  OD1 ASP B 314      20.199  23.991  65.220  0.68  7.50           O 0
+ATOM   4891  CD1 LEU B 312      23.717  25.794  63.419  0.00  0.00           C 0
+ATOM   4896    O ASP B 313      18.290  25.931  61.054  0.00  0.00           O 0
+ATOM   4902   CA ASP B 314      17.950  24.860  63.695  0.00  0.00           C 0
+ATOM   4890   CG LEU B 312      22.474  26.424  64.044  0.00  0.00           C 0
+ATOM   4643    O GLY B 281      16.226  23.524  60.154  0.44  7.50           O 0
+ATOM   4905   CB ASP B 314      18.035  24.811  65.227  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket39_vert.pqr

@@ -0,0 +1,45 @@
+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    39:
+HEADER 0  - Pocket Score                      : -0.0286
+HEADER 1  - Drug Score                        : 0.0007
+HEADER 2  - Number of V. Vertices             :    23
+HEADER 3  - Mean alpha-sphere radius          : 3.8671
+HEADER 4  - Mean alpha-sphere SA              : 0.4339
+HEADER 5  - Mean B-factor                     : 0.6124
+HEADER 6  - Hydrophobicity Score              : 3.1000
+HEADER 7  - Polarity Score                    :     6
+HEADER 8  - Volume Score                      : 3.8000
+HEADER 9  - Real volume (approximation)       : 289.6613
+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 : 0.1304
+ATOM      1    O STP    39      18.749  20.447  62.424    0.00     3.47
+ATOM      2    O STP    39      19.235  20.676  62.445    0.00     3.64
+ATOM      3    O STP    39      18.366  20.535  61.411    0.00     3.53
+ATOM      4    O STP    39      20.111  21.256  61.869    0.00     4.19
+ATOM      5    O STP    39      19.185  21.026  61.064    0.00     3.91
+ATOM      6    O STP    39      18.213  20.583  66.835    0.00     3.55
+ATOM      7    C STP    39      19.002  20.735  63.658    0.00     3.40
+ATOM      8    O STP    39      18.315  21.056  66.569    0.00     3.69
+ATOM      9    O STP    39      18.352  21.025  65.355    0.00     3.50
+ATOM     10    O STP    39      18.324  21.089  66.518    0.00     3.69
+ATOM     11    O STP    39      18.355  21.095  66.568    0.00     3.69
+ATOM     12    O STP    39      19.436  21.037  63.444    0.00     3.53
+ATOM     13    O STP    39      20.231  21.357  61.896    0.00     4.24
+ATOM     14    C STP    39      22.988  21.407  62.842    0.00     4.48
+ATOM     15    C STP    39      22.616  21.487  62.195    0.00     4.61
+ATOM     16    O STP    39      20.314  22.196  61.359    0.00     4.26
+ATOM     17    O STP    39      20.389  22.091  61.276    0.00     4.38
+ATOM     18    O STP    39      21.122  24.069  61.862    0.00     3.48
+ATOM     19    O STP    39      21.451  22.588  61.021    0.00     4.60
+ATOM     20    O STP    39      19.196  21.107  60.987    0.00     3.92
+ATOM     21    O STP    39      20.168  22.065  61.052    0.00     4.30
+ATOM     22    O STP    39      18.000  21.449  65.775    0.00     3.41
+ATOM     23    O STP    39      18.003  21.454  66.087    0.00     3.47
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket3_atm.pdb

@@ -0,0 +1,66 @@
+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                      : 0.3076
+HEADER 1  - Drug Score                        : 0.0140
+HEADER 2  - Number of alpha spheres           :    71
+HEADER 3  - Mean alpha-sphere radius          : 3.9619
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.4660
+HEADER 5  - Mean B-factor of pocket residues  : 0.5381
+HEADER 6  - Hydrophobicity Score              : 25.3158
+HEADER 7  - Polarity Score                    :    11
+HEADER 8  - Amino Acid based volume Score     : 4.3158
+HEADER 9  - Pocket volume (Monte Carlo)       : 801.5175
+HEADER 10  -Pocket volume (convex hull)       : 168.0013
+HEADER 11 - Charge Score                      :     1
+HEADER 12 - Local hydrophobic density Score   : 14.0000
+HEADER 13 - Number of apolar alpha sphere     :    16
+HEADER 14 - Proportion of apolar alpha sphere : 0.2254
+ATOM   3734  ND1 HIS B 165      25.824  14.663  50.708  0.81  2.19           N 0
+ATOM   3008  CG2 VAL B  74      25.238  11.476  49.047  0.00  0.00           C 0
+ATOM   2997    O ILE B  73      24.298  10.690  45.514  0.37  5.36           O 0
+ATOM   3736  CE1 HIS B 165      27.020  15.205  50.577  0.00  0.00           C 0
+ATOM   3649    O ASP B 155      20.687  13.728  44.830  0.00  0.00           O 0
+ATOM   3000  CG2 ILE B  73      21.629  10.622  47.251  0.00  0.00           C 0
+ATOM   3731    O HIS B 165      23.254  12.112  52.333  0.62  1.07           O 0
+ATOM   3665    N LEU B 157      17.181  13.651  47.729  0.55  2.19           N 0
+ATOM   3670   CG LEU B 157      17.079  11.384  50.094  0.00  0.00           C 0
+ATOM   3664  NH2 ARG B 156      21.438  21.111  47.819  0.00  0.00           N 0
+ATOM   3737  NE2 HIS B 165      27.054  16.312  51.297  0.00  0.00           N 0
+ATOM   3732   CB HIS B 165      23.638  15.094  51.917  0.00  0.00           C 0
+ATOM   3659   CG ARG B 156      19.505  17.075  46.176  0.00  0.00           C 0
+ATOM   3655   CA ARG B 156      18.378  14.804  45.948  0.00  0.00           C 0
+ATOM   1093  NH2 ARG A 154      18.333  17.804  50.685  0.00  0.00           N 0
+ATOM   3671  CD1 LEU B 157      17.493  11.401  51.571  0.00  0.00           C 0
+ATOM   3765   CZ PHE B 168      21.589   9.140  51.135  0.00  0.00           C 0
+ATOM   3703   CB HIS B 161      16.847  14.497  53.748  0.00  0.00           C 0
+ATOM   3661   NE ARG B 156      20.352  19.249  47.022  0.00  0.00           N 0
+ATOM   3733   CG HIS B 165      25.064  15.427  51.573  0.00  0.00           C 0
+ATOM   3749    O GLU B 167      20.648  10.491  55.780  0.74  1.07           O 0
+ATOM   3729   CA HIS B 165      23.442  14.298  53.239  0.00  0.00           C 0
+ATOM   3723    O ASP B 164      22.768  13.672  55.837  0.00  0.00           O 0
+ATOM   3718    O ALA B 163      23.028  17.937  56.383  0.00  0.00           O 0
+ATOM   3716   CA ALA B 163      21.053  17.633  57.714  0.00  0.00           C 0
+ATOM   1090   NE ARG A 154      17.020  19.651  51.040  0.47  2.19           N 0
+ATOM   3708  NE2 HIS B 161      16.170  18.104  53.754  0.79  2.19           N 0
+ATOM   3706  CD2 HIS B 161      17.083  17.082  53.816  0.00  0.00           C 0
+ATOM   3128   SG CYS B  90      17.210  18.693  58.624  0.00  0.00           S 0
+ATOM   3669   CB LEU B 157      16.258  12.648  49.804  0.00  0.00           C 0
+ATOM   1080  CE1 PHE A 153      12.506  22.724  52.407  0.00  0.00           C 0
+ATOM   3132    O GLN B  91      12.002  18.926  54.715  0.00  0.00           O 0
+ATOM   4629    O TRP B 280      13.400  21.678  58.236  0.47  4.29           O 0
+ATOM   3735  CD2 HIS B 165      25.842  16.481  51.921  0.00  0.00           C 0
+ATOM   3127   CB CYS B  90      15.835  18.457  57.569  0.00  0.00           C 0
+ATOM   4643    O GLY B 281      16.226  23.524  60.154  0.44  7.50           O 0
+ATOM   4651  OE1 GLN B 282      14.736  25.106  55.785  0.00  0.00           O 0
+ATOM   3712    O SER B 162      19.816  15.854  55.881  0.69  3.21           O 0
+ATOM   3709    N SER B 162      18.256  13.740  56.606  0.00  0.00           N 0
+ATOM   1086    O ARG A 154      19.034  23.933  48.988  0.00  0.00           O 0
+ATOM   1101  OD2 ASP A 155      21.258  25.877  51.114  0.00  0.00           O 0
+ATOM   1087   CB ARG A 154      16.943  22.487  50.267  0.00  0.00           C 0
+ATOM   1084   CA ARG A 154      17.114  23.994  50.463  0.00  0.00           C 0
+ATOM   1088   CG ARG A 154      15.993  21.884  51.307  0.00  0.00           C 0
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket3_vert.pqr

@@ -0,0 +1,93 @@
+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                      : 0.3076
+HEADER 1  - Drug Score                        : 0.0140
+HEADER 2  - Number of V. Vertices             :    71
+HEADER 3  - Mean alpha-sphere radius          : 3.9619
+HEADER 4  - Mean alpha-sphere SA              : 0.4660
+HEADER 5  - Mean B-factor                     : 0.5381
+HEADER 6  - Hydrophobicity Score              : 25.3158
+HEADER 7  - Polarity Score                    :    11
+HEADER 8  - Volume Score                      : 4.3158
+HEADER 9  - Real volume (approximation)       : 801.5175
+HEADER 10 - Charge Score                      :     1
+HEADER 11 - Local hydrophobic density Score   : 14.0000
+HEADER 12 - Number of apolar alpha sphere     :    16
+HEADER 13 - Proportion of apolar alpha sphere : 0.2254
+ATOM      1    O STP     3      25.914  14.961  46.113    0.00     4.61
+ATOM      2    O STP     3      24.623  15.027  46.442    0.00     4.45
+ATOM      3    O STP     3      23.346  13.654  47.087    0.00     3.49
+ATOM      4    O STP     3      20.476  13.338  49.842    0.00     3.93
+ATOM      5    O STP     3      24.738  17.937  47.695    0.00     4.58
+ATOM      6    C STP     3      22.346  13.343  49.243    0.00     3.45
+ATOM      7    O STP     3      22.861  14.505  48.064    0.00     3.97
+ATOM      8    C STP     3      22.640  14.304  48.195    0.00     3.93
+ATOM      9    O STP     3      22.931  15.458  47.852    0.00     4.14
+ATOM     10    O STP     3      20.656  13.624  49.701    0.00     4.00
+ATOM     11    C STP     3      21.266  14.519  48.726    0.00     4.02
+ATOM     12    C STP     3      20.758  14.727  49.164    0.00     4.00
+ATOM     13    C STP     3      21.208  14.331  48.787    0.00     4.04
+ATOM     14    C STP     3      20.985  14.220  48.988    0.00     4.05
+ATOM     15    O STP     3      20.642  14.865  49.295    0.00     3.99
+ATOM     16    C STP     3      20.480  13.077  49.918    0.00     3.80
+ATOM     17    C STP     3      20.546  12.329  50.116    0.00     3.51
+ATOM     18    O STP     3      20.435  13.428  49.926    0.00     3.93
+ATOM     19    O STP     3      20.377  13.716  50.100    0.00     3.98
+ATOM     20    C STP     3      19.900  14.384  51.430    0.00     3.84
+ATOM     21    O STP     3      20.053  14.224  50.424    0.00     3.98
+ATOM     22    O STP     3      22.135  18.234  50.277    0.00     3.85
+ATOM     23    O STP     3      21.498  16.519  49.250    0.00     3.70
+ATOM     24    O STP     3      24.749  17.878  47.547    0.00     4.64
+ATOM     25    O STP     3      24.539  17.871  47.849    0.00     4.48
+ATOM     26    O STP     3      23.145  18.015  49.413    0.00     3.88
+ATOM     27    O STP     3      23.181  16.357  47.982    0.00     4.16
+ATOM     28    O STP     3      23.186  16.368  47.988    0.00     4.16
+ATOM     29    O STP     3      20.025  13.018  53.408    0.00     3.52
+ATOM     30    C STP     3      20.144  13.959  51.631    0.00     3.68
+ATOM     31    C STP     3      20.057  13.525  52.697    0.00     3.51
+ATOM     32    C STP     3      20.003  14.183  51.745    0.00     3.75
+ATOM     33    O STP     3      20.161  13.153  53.574    0.00     3.49
+ATOM     34    O STP     3      20.111  13.169  53.544    0.00     3.53
+ATOM     35    O STP     3      20.114  13.184  53.569    0.00     3.53
+ATOM     36    C STP     3      20.077  15.140  52.332    0.00     3.59
+ATOM     37    O STP     3      19.875  20.811  54.526    0.00     4.65
+ATOM     38    O STP     3      19.886  20.547  54.482    0.00     4.51
+ATOM     39    C STP     3      18.954  19.779  55.538    0.00     3.71
+ATOM     40    O STP     3      20.242  19.977  53.846    0.00     4.29
+ATOM     41    O STP     3      19.917  20.570  54.402    0.00     4.53
+ATOM     42    O STP     3      19.417  14.323  50.533    0.00     3.65
+ATOM     43    C STP     3      18.870  14.461  51.013    0.00     3.40
+ATOM     44    O STP     3      14.781  21.290  54.878    0.00     3.65
+ATOM     45    O STP     3      24.691  17.943  47.778    0.00     4.54
+ATOM     46    O STP     3      24.567  17.893  47.855    0.00     4.49
+ATOM     47    C STP     3      23.174  18.282  49.791    0.00     3.86
+ATOM     48    O STP     3      22.386  19.528  52.042    0.00     4.61
+ATOM     49    O STP     3      22.386  19.569  52.089    0.00     4.64
+ATOM     50    O STP     3      22.379  19.538  52.095    0.00     4.62
+ATOM     51    O STP     3      16.744  21.846  57.076    0.00     3.54
+ATOM     52    O STP     3      15.832  21.515  55.347    0.00     3.78
+ATOM     53    O STP     3      16.893  22.044  56.666    0.00     3.85
+ATOM     54    O STP     3      17.946  21.905  55.497    0.00     4.54
+ATOM     55    O STP     3      17.063  22.058  56.613    0.00     3.92
+ATOM     56    O STP     3      20.054  19.405  54.471    0.00     3.83
+ATOM     57    O STP     3      20.115  13.217  53.577    0.00     3.51
+ATOM     58    O STP     3      20.082  15.179  52.376    0.00     3.58
+ATOM     59    O STP     3      21.295  17.840  53.029    0.00     3.78
+ATOM     60    O STP     3      20.448  18.984  53.700    0.00     3.87
+ATOM     61    O STP     3      20.106  15.221  52.385    0.00     3.56
+ATOM     62    O STP     3      20.042  13.183  53.702    0.00     3.45
+ATOM     63    O STP     3      20.098  13.193  53.616    0.00     3.51
+ATOM     64    O STP     3      20.952  21.515  52.307    0.00     4.53
+ATOM     65    O STP     3      20.365  21.375  51.439    0.00     3.78
+ATOM     66    O STP     3      20.760  21.645  52.389    0.00     4.45
+ATOM     67    O STP     3      19.989  22.657  52.272    0.00     3.65
+ATOM     68    O STP     3      14.998  21.461  54.875    0.00     3.73
+ATOM     69    O STP     3      15.099  21.491  54.914    0.00     3.74
+ATOM     70    O STP     3      15.010  21.502  54.881    0.00     3.73
+ATOM     71    O STP     3      18.195  21.973  55.435    0.00     4.68
+TER
+END

tests/reference_output/2P0R_out/pockets/pocket40_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    40:
+HEADER 0  - Pocket Score                      : -0.0299
+HEADER 1  - Drug Score                        : 0.0003
+HEADER 2  - Number of alpha spheres           :    17
+HEADER 3  - Mean alpha-sphere radius          : 4.0333
+HEADER 4  - Mean alpha-sphere Solvent Acc.    : 0.5431
+HEADER 5  - Mean B-factor of pocket residues  : 0.7315
+HEADER 6  - Hydrophobicity Score              : 13.8571
+HEADER 7  - Polarity Score                    :     5
+HEADER 8  - Amino Acid based volume Score     : 4.4286
+HEADER 9  - Pocket volume (Monte Carlo)       : 265.3010
+HEADER 10  -Pocket volume (convex hull)       : 10.1933
+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 : 0.3529
+ATOM   3922   CD LYS B 188      -1.622  15.955  51.452  0.00  0.00           C 0
+ATOM   2850  CE1 PHE B  56       2.378  12.753  46.755  0.00  0.00           C 0
+ATOM   3157  CD1 LEU B  94       3.656  13.994  51.957  0.00  0.00           C 0
+ATOM   3899   CG GLU B 185      -1.228  11.605  49.092  0.00  0.00           C 0
+ATOM   3920   CB LYS B 188      -0.327  14.528  53.052  0.00  0.00           C 0
+ATOM   2868    O SER B  58      -2.600  12.325  43.922  0.32  8.57           O 0
+ATOM   3902  OE2 GLU B 185      -3.259  12.131  47.991  0.33  4.29           O 0
+ATOM   3900   CD GLU B 185      -2.159  11.549  47.897  0.00  0.00           C 0
+ATOM   2848  CD1 PHE B  56       1.475  11.829  46.324  0.00  0.00           C 0
+ATOM   3924   NZ LYS B 188      -3.354  16.996  49.960  0.06  9.84           N 0
+ATOM    354  NE2 GLN A  62       1.217  20.100  50.698  0.46  9.84           N 0
+ATOM   3923   CE LYS B 188      -2.528  17.163  51.213  0.00  0.00           C 0
+ATOM    353  OE1 GLN A  62       1.389  18.286  52.065  0.59  2.14           O 0
+ATOM   3145    O GLU B  93       6.194  16.566  50.007  0.00  0.00           O 0
+ATOM   2852   CZ PHE B  56       3.514  12.979  46.047  0.00  0.00           C 0
+TER
+END