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

master
Thomas Forest 2019-09-10 19:26:32 +02:00
parent f19f25a3bf
commit d653cbda67
5 changed files with 4270 additions and 66 deletions
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BIN
bin/reduce.3.23.130521.linuxi386 Executable file
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4228
data/1est_H.pdb Normal file
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52
src/atom.py
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@ -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

6
src/geometry.py Normal file
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@ -0,0 +1,6 @@
class GeomObject:
pass
class Distance:

50
src/pdb.py
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@ -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)