added beginning of program, md.pdb as toy example and README

README

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+Make sure your current directory is projet_court_nz
+
+Environment
+
+1 - Recreate the conda environment with the config_projet.yml file avaible in the src repository 
+	$ conda env create -f src/config_projet.yml
+2 - Activate the generated environment
+	$ conda activate projet-court
+
+toy-example:
+md.pdb contains structural information of 501 conformations of the calf-1 domain
+
+3 - try the program on md.pdb
+	$ python3 src/projet8 data/md.pdb 
+
+This will generate a md.csv file in the results folder, representing a dataframe of the conformations, each row being a conformation and each column a PB position
+
+Informations:
+
+The pdb was obtained from .trr and .gro files available online (http://www.dsimb.inserm.fr/~tmp/DM_Calf-1_WT_production_long1.tar.gz)
+pbd was generated using gromacs :
+	$ trjconv -f md.trr -s md -o md.pdb

data/barstar_md_traj.PB.fasta

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->test_data/barstar_md_traj.xtc | frame 0
-ZZdddfklpmbfklmmmmmmmmnopafklgoiaklmmmmmmmmpacddddddehklmmmm
-moghilmmmmmmmmmmmmnopacddddZZ
->test_data/barstar_md_traj.xtc | frame 1
-ZZdddfklpcbfklmmmmmmmmnopafkbghiaklmmmmmmmmpccddddddehklmmmm
-moghklmmmmmmmmmmmmnopacddddZZ
->test_data/barstar_md_traj.xtc | frame 2
-ZZdddfklpcbfklmmmmmmmmnopafkbgoiaklmmmmmnopaacddddddehklmmmm
-mpghklmmmmmmmmmmmmnopacddddZZ
->test_data/barstar_md_traj.xtc | frame 3
-ZZdddfklpcbfklmmmmmmmmnopafkbgoiaklmmmmmmmmpccddddddehklmmmm
-mbghilmmmmmmmmmmmmnopacddddZZ
->test_data/barstar_md_traj.xtc | frame 4
-ZZdddfklpcbfklmmmmmmmmnopafkbghiaklmmmmmmmmpccddddddehklmmmm
-mcehilmmmmmmmmmmmmnopacddddZZ
->test_data/barstar_md_traj.xtc | frame 5
-ZZdddfklgcbfklmmmmmmmmnopafkbgoiaklmmmmmmmmpccddddddehklmmmm
-mbghklmmmmmmmmmmmmnopacddddZZ
->test_data/barstar_md_traj.xtc | frame 6
-ZZdddfklpcbfklmmmmmmmmnopafkbghiaklmmmmmmmmpccddddddehklmmmm
-mbghklmmmmmmmmmmmmnopacddddZZ
->test_data/barstar_md_traj.xtc | frame 7
-ZZdddfklpgbfklmmmmmmmmnopafklgoiaklmmmmmmmmpccddddddehkllmmm
-mbghklmmmmmmmmmmmmnopacddddZZ
->test_data/barstar_md_traj.xtc | frame 8
-ZZdddfklpcbfklmmmmmmmmnopafklgoiaklmmmmmmmmpccddddddehklmmmm
-npghklmmmmmmmmmmmmnopacddddZZ
->test_data/barstar_md_traj.xtc | frame 9
-ZZdddfklpcbfklmmmmmmmmnopafkbgoiaklmmmmmmmmmccddddddehkllmmm
-mbghklmmmmmmmmmmmmnopacddddZZ

src/projet8.py

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+#!/bin/python3
+
+import pandas as pd
+import pbxplore as pbx
+import sys
+
+if __name__ == "__main__":
+    if len(sys.argv) != 2:
+        print("Error : usage $ python3 projet8 md.pdb")
+        exit()
+    
+    conformations = [] # list to store PB format chains
+
+    for chain_name, chain in pbx.chains_from_files([sys.argv[1]]): 
+        dihedrals = chain.get_phi_psi_angles() 
+        pb_seq = pbx.assign(dihedrals) 
+        conformations.append(pb_seq) 
+    
+    df = pd.DataFrame() # pandas dataframe to store conformations
+
+    for conf in conformations: 
+        df = df.append(pd.Series(list(conf)), ignore_index=True)
+
+    df.to_csv("results/md.csv", index=False)