Basis of geometry class + PDB dataset sample with H + Reduce Software binary

src/atom.py

@@ -1,41 +1,19 @@
 class Atom:
-
-    def __init__(self, ATOM_ID, ATOM_NAME, ALT_LOCAT, RES_NAME, CHAIN_ID,
-                 RES_SEQ_NB, RES_INSER_CODE, COORD_X, COORD_Y, COORD_Z,
-                 OCCUPANCY, TEMP_FACT, ELEM_SYMBOL, ATOM_CHARGE):
-        
-        self.ATOM_ID = ATOM_ID
-        self.ATOM_NAME = ATOM_NAME
-        self.ALT_LOCAT = ALT_LOCAT 
-        self.RES_NAME = RES_NAME
-        self.CHAIN_ID = CHAIN_ID
-        self.RES_SEQ_NB = RES_SEQ_NB
-        self.RES_INSER_CODE = RES_INSER_CODE
-        self.COORD_X = COORD_X
-        self.COORD_Y = COORD_Y
-        self.COORD_Z = COORD_Z
-        self.OCCUPANCY = OCCUPANCY
-        self.TEMP_FACT = TEMP_FACT
-        self.ELEM_SYMBOL = ELEM_SYMBOL
-        self.ATOM_CHARGE = ATOM_CHARGE
+    def __init__(self, atom_id, atom_name, res_name, chain_id,
+                 res_seq_nb, coordinates):
+        self.atom_id = atom_id
+        self.atom_name = atom_name
+        self.res_name = res_name
+        self.chain_id = chain_id
+        self.res_seq_nb = res_seq_nb
+        self.coord_x = coordinates[0]
+        self.coord_y = coordinates[1]
+        self.coord_z = coordinates[2]             
 
 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
+    def __init__(self, atoms_list):
+        self.atoms = {}
+        for atom in atoms_list:
+            self.atoms[atom.atom_name] = atom
+            
             

src/geometry.py

@@ -0,0 +1,6 @@
+class GeomObject:
+
+    pass
+
+class Distance:
+    

src/pdb.py

@@ -1,12 +1,9 @@
 import sys
 #import collections
-
-
 # custom imports
 from atom import *
 
 class PDBFile:
-
     def getContent(self, filename):
         with open(filename) as f:
             return(f.readlines())
@@ -31,36 +28,31 @@ class PDBFile:
         return(Metadata)
 
     def getAtoms(self):
-        self.ATOMS = []
-        self.RESIDUES = []
-        tempAtoms = []
+        self.atoms = []
+        self.residues = []
+        temp_atoms = []
         for line in self.rawLines:
             if line.startswith("ATOM" or "HETATM"):
-                atom = Atom(ATOM_ID = int(line[6:11].strip()),
-                            ATOM_NAME = line[12:16].strip(),
-                            ALT_LOCAT = line[16:17].strip(),
-                            RES_NAME = line[17:20].strip(),
-                            CHAIN_ID = line[21:22].strip(),
-                            RES_SEQ_NB = int(line[22:26].strip()),
-                            RES_INSER_CODE = line[26:27].strip(),
-                            COORD_X = float(line[30:38].strip()),
-                            COORD_Y = float(line[38:46].strip()),
-                            COORD_Z = float(line[46:54].strip()),
-                            OCCUPANCY = float(line[54:60].strip()),
-                            TEMP_FACT = float(line[60:66].strip()),
-                            ELEM_SYMBOL = line[76:78].strip(),
-                            ATOM_CHARGE = line[78:80].strip())
-                self.ATOMS.append(atom)
+                atom = Atom(atom_id = int(line[6:11].strip()),
+                            atom_name = line[12:16].strip(),
+                            res_name = line[17:20].strip(),
+                            chain_id = line[21:22].strip(),
+                            res_seq_nb = int(line[22:26].strip()),
+                            coordinates = [float(line[30:38].strip()),
+                                     float(line[38:46].strip()),
+                                     float(line[46:54].strip()),
+                            ])
+                self.atoms.append(atom)
                 # get the current indice of atom
-                i = self.ATOMS.index(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)
+                if(len(self.atoms)>1
+                   and atom.res_seq_nb != self.atoms[i-1].res_seq_nb):
+                    self.residues.append(Residue(temp_atoms))
+                    temp_atoms=[]
+                temp_atoms.append(atom)
         # last residue
-        self.RESIDUES.append(Residue(tempAtoms))
+        self.residues.append(Residue(temp_atoms))
        
     def __init__(self, filename):
         self.rawLines = self.getContent(filename)
@@ -76,4 +68,4 @@ if __name__ == "__main__":
               "call structure and parameters.")
     else:
         pdbFile = PDBFile(sys.argv[1])
-        print(pdbFile.RESIDUES[0].ATOMS["N"].COORD_X)
+        print(pdbFile.residues[15].atoms["C"].coord_x)