From f19f25a3bfb23463c2891e7a479b5b7d34d5dda0 Mon Sep 17 00:00:00 2001
From: Thomas Forest <thomas.forest@etu.univ-paris-diderot.fr>
Date: Tue, 10 Sep 2019 00:06:50 +0200
Subject: [PATCH] Residues class creation

---
 src/__pycache__/atom.cpython-36.pyc | Bin 723 -> 0 bytes
 src/atom.py                         |  21 +++++++++++++++++++++
 src/pdb.py                          |  17 ++++++++++++++---
 3 files changed, 35 insertions(+), 3 deletions(-)
 delete mode 100644 src/__pycache__/atom.cpython-36.pyc

diff --git a/src/__pycache__/atom.cpython-36.pyc b/src/__pycache__/atom.cpython-36.pyc
deleted file mode 100644
index 9254d91d75e6e967e1ee786ee8e470c3863f4e2d..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 723
zcmZ{i&5qMB5XYU5HeXFwd>na!UN#b(kPsr9hNV)IEKQKMk<h3#Sy9w9i=D0n@{N5N
z4m=JQUwI2o%%l|cf}{EQpUI5v%=nq_yFbL;`=2^vzu3tzP`^SG4-uEFVwHA}_DwHY
zrRQv7tkM5(VD=&UF^Za%TE$Ae(klI)l}2S?ys6BvYn%1i-yE7LD?$_32&qX1OzKEY
z8c1E5NJ9>grW_&%(n1cUjkKhLw55x5q=$6n2<b^5Ig(?fUoqTSODAJxg+-RYY^t1I
zq+t@HoEI?9qOef*BF>?A+R>YEmQtikzC3;l>4h4To~3!bfGC^B%8IgVF@@`+SRO^G
zoGgmoU4?11R8A2mSMWNF3gyM~IDvebTx4_Q^=H717MJnlOqrtI-f$`gr>b+4Fdz&G
z7QrSs1ef3uMg*TQCQwDcGyVXl-_L`OZBqxLx(k}8A2vaE)ACw$!L(iPn|jxY;Fh<a
z>JHZJo_B%Z>tKc5Iluj)Y=F&f(*e*~#1jNFhuZ(1uReA4{FswspK*cRs;L2#3(&OH
zeoJ};@Oi)59=`BLxN3jW6VOHD8iGtvIc&XuPbXSGpTyEna!OG4i^CQ#`z-XZKerU0
Aod5s;

diff --git a/src/atom.py b/src/atom.py
index 1e417f9..f4a18b8 100644
--- a/src/atom.py
+++ b/src/atom.py
@@ -18,3 +18,24 @@ class Atom:
         self.TEMP_FACT = TEMP_FACT
         self.ELEM_SYMBOL = ELEM_SYMBOL
         self.ATOM_CHARGE = ATOM_CHARGE
+
+class Residue:
+    def __init__(self, atomsList):
+        self.ATOMS = {}
+        for atom in atomsList:
+            self.ATOMS[atom.ATOM_NAME] = atom
+            if atom.ATOM_NAME == "N":
+                self.N = atom
+            if atom.ATOM_NAME == "CA":
+                self.CA = atom
+            if atom.ATOM_NAME == "C":
+                self.C = atom
+            if atom.ATOM_NAME == "O":
+                self.O = atom
+            if atom.ATOM_NAME == "CB":
+                self.CB = atom
+            if atom.ATOM_NAME == "CG1":
+                self.CG1 = atom
+            if atom.ATOM_NAME == "CG2":
+                self.CG2 = atom
+            
diff --git a/src/pdb.py b/src/pdb.py
index 73fda80..96cdbbd 100644
--- a/src/pdb.py
+++ b/src/pdb.py
@@ -32,7 +32,8 @@ class PDBFile:
 
     def getAtoms(self):
         self.ATOMS = []
-        
+        self.RESIDUES = []
+        tempAtoms = []
         for line in self.rawLines:
             if line.startswith("ATOM" or "HETATM"):
                 atom = Atom(ATOM_ID = int(line[6:11].strip()),
@@ -50,8 +51,17 @@ class PDBFile:
                             ELEM_SYMBOL = line[76:78].strip(),
                             ATOM_CHARGE = line[78:80].strip())
                 self.ATOMS.append(atom)
-                      
-    
+                # get the current indice of atom
+                i = self.ATOMS.index(atom)
+                # if this is a brand new residue
+                if(len(self.ATOMS)>1
+                   and atom.RES_SEQ_NB != self.ATOMS[i-1].RES_SEQ_NB):
+                    self.RESIDUES.append(Residue(tempAtoms))
+                    tempAtoms=[]
+                tempAtoms.append(atom)
+        # last residue
+        self.RESIDUES.append(Residue(tempAtoms))
+       
     def __init__(self, filename):
         self.rawLines = self.getContent(filename)
         self.Metadata = self.getHeader()
@@ -66,3 +76,4 @@ if __name__ == "__main__":
               "call structure and parameters.")
     else:
         pdbFile = PDBFile(sys.argv[1])
+        print(pdbFile.RESIDUES[0].ATOMS["N"].COORD_X)