update readme

README.md

@@ -1,5 +1,8 @@
 # PRODIGY-cryst
 
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@@ -10,14 +13,69 @@ Collection of scripts to predict whether an interface in a protein-protein compl
 ## Installation
 
 ```bash
-> git clone http://github.com/haddocking/prodigy-cryst
-> python setup.py install
+pip install prodigy-cryst
 ```
 
 ## Usage
 
+Type --help to get a list of all the possible options.
+
+```bash
+$ prodigy_cryst --help
+usage: prodigy_cryst [-h] [--contact_list] [-q] [--selection A B [A,B C ...]] structf
+
+Biological/crystallographic interface classifier based on Intermolecular Contacts (ICs).
+
+positional arguments:
+  structf               Structure to analyse in PDB or mmCIF format
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --contact_list        Output a list of contacts
+  -q, --quiet           Outputs only the predicted interface class
+
+Selection Options:
+
+      By default, all intermolecular contacts are taken into consideration,
+      a molecule being defined as an isolated group of amino acids sharing
+      a common chain identifier. In specific cases, for example
+      antibody-antigen complexes, some chains should be considered as a
+      single molecule.
+
+      Use the --selection option to provide collections of chains that should
+      be considered for the calculation. Separate by a space the chains that
+      are to be considered _different_ molecules. Use commas to include multiple
+      chains as part of a single group:
+
+      --selection A B => Contacts calculated (only) between chains A and B.
+      --selection A,B C => Contacts calculated (only) between chains A and C; and B and C.
+      --selection A B C => Contacts calculated (only) between chains A and B; B and C; and A and C.
+
+
+  --selection A B [A,B C ...]
+```
+
+## Examples
+
+Download PDB file 1ppe from the PDB and run the script on it.
+
 ```bash
-prodigy_cryst <pdb file> [--selection <chain1><chain2>]
+wget https://files.rcsb.org/download/1PPE.pdb
 ```
 
-Type --help to get a list of all the possible options.
+Check how PRODIGY-cryst works on the 1PPE.pdb file. The script will output the number of intermolecular contacts, the number of contacts of each type, the link density, and the predicted interface class.
+
+```bash
+$ prodigy_cryst 1PPE.pdb
+[+] Reading structure file: /home/rodrigo/1PPE.pdb
+[+] Selection: E, I
+[+] No. of intermolecular contacts: 71
+[+] No. of charged-charged contacts: 4
+[+] No. of charged-polar contacts: 8
+[+] No. of charged-apolar contacts: 24
+[+] No. of polar-polar contacts: 0
+[+] No. of apolar-polar contacts: 15
+[+] No. of apolar-apolar contacts: 20
+[+] Link density: 0.14
+[+] Class: BIO 0.804 0.196
+```