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

Nicolas Zimmermann 2 years ago
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88d52b8e8f
4 changed files with 1069180 additions and 30 deletions
  1. 22 0
      README
  2. 0 30
      data/barstar_md_traj.PB.fasta
  3. 1069134 0
      data/md.pdb
  4. 24 0
      src/projet8.py

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README View File

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+Make sure your current directory is projet_court_nz
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+
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+Environment
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+
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+1 - Recreate the conda environment with the config_projet.yml file avaible in the src repository 
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+	$ conda env create -f src/config_projet.yml
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+2 - Activate the generated environment
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+	$ conda activate projet-court
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+
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+toy-example:
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+md.pdb contains structural information of 501 conformations of the calf-1 domain
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+
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+3 - try the program on md.pdb
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+	$ python3 src/projet8 data/md.pdb 
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+
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+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
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+
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+Informations:
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+
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+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)
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+pbd was generated using gromacs :
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+	$ trjconv -f md.trr -s md -o md.pdb

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data/barstar_md_traj.PB.fasta View File

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->test_data/barstar_md_traj.xtc | frame 0
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-ZZdddfklpmbfklmmmmmmmmnopafklgoiaklmmmmmmmmpacddddddehklmmmm
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-moghilmmmmmmmmmmmmnopacddddZZ
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->test_data/barstar_md_traj.xtc | frame 1
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-ZZdddfklpcbfklmmmmmmmmnopafkbghiaklmmmmmmmmpccddddddehklmmmm
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-ZZdddfklpcbfklmmmmmmmmnopafkbgoiaklmmmmmnopaacddddddehklmmmm
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->test_data/barstar_md_traj.xtc | frame 3
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-ZZdddfklpcbfklmmmmmmmmnopafkbgoiaklmmmmmmmmpccddddddehklmmmm
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->test_data/barstar_md_traj.xtc | frame 4
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-ZZdddfklpcbfklmmmmmmmmnopafkbghiaklmmmmmmmmpccddddddehklmmmm
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-ZZdddfklgcbfklmmmmmmmmnopafkbgoiaklmmmmmmmmpccddddddehklmmmm
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->test_data/barstar_md_traj.xtc | frame 6
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-ZZdddfklpcbfklmmmmmmmmnopafkbghiaklmmmmmmmmpccddddddehklmmmm
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->test_data/barstar_md_traj.xtc | frame 7
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-ZZdddfklpgbfklmmmmmmmmnopafklgoiaklmmmmmmmmpccddddddehkllmmm
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-mbghklmmmmmmmmmmmmnopacddddZZ
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->test_data/barstar_md_traj.xtc | frame 8
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-ZZdddfklpcbfklmmmmmmmmnopafklgoiaklmmmmmmmmpccddddddehklmmmm
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->test_data/barstar_md_traj.xtc | frame 9
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-ZZdddfklpcbfklmmmmmmmmnopafkbgoiaklmmmmmmmmmccddddddehkllmmm
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-mbghklmmmmmmmmmmmmnopacddddZZ

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data/md.pdb


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src/projet8.py View File

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