def get_atom_list_from_pdb_frame (frame):
""" Function doc """
#print ('\nstarting: parse_pdb - building atom list')
#initial = time.time()
pdb_file_lines = frame.split('\n')
atoms = []
for line in pdb_file_lines:
if line[:4] == 'ATOM' or line[:6] == 'HETATM':
at_name = line[12:16].strip()
at_pos = np.array([float(line[30:38]), float(line[38:46]), float(line[46:54])])
at_res_i = int(line[22:26])
at_res_n = line[17:20].strip()
at_ch = line[21]
atom = mm.Atom(name = at_name,
#index = index,
pos = at_pos,
resi = at_res_i,
resn = at_res_n,
chain = at_ch,
#atom_id = counter,
)
#Vobject.atoms.append(atom)
atoms.append(atom)
print ('Numeber of atoms: ', len(atoms))
#print ('ending parse_pdb: - building atom list', final - initial, '\n')
return atoms
def parse_pdb_old(infile = None, counter = 0, atom_dic_id = None, Vobject_id = None):
""" Function doc """
print ('\nstarting pdb parser')
initial = time.time()
with open(infile, 'r') as pdb_file:
label = os.path.basename(infile)
Vobject = mm.Vobject(label = label)
pdb_file_lines = pdb_file.readlines()
atoms = []
frame = []
#for line in pdb_file:
for line in pdb_file_lines:
if line[:4] == 'ATOM' or line[:6] == 'HETATM':
at_name = line[12:16].strip()
#at_index = int(line[6:11])
at_pos = np.array([float(line[30:38]), float(line[38:46]), float(line[46:54])])
at_res_i = int(line[22:26])
at_res_n = line[17:20].strip()
at_ch = line[21]
atom = mm.Atom(name = at_name,
#index = index,
pos = at_pos,
resi = at_res_i,
resn = at_res_n,
chain = at_ch,
#atom_id = counter,
Vobject = Vobject,
)
Vobject.atoms.append(atom)
if 'ENDMDL' in line:
break
atom_dic_id = Vobject.generate_chain_structure(counter = counter, atom_dic_id = atom_dic_id)
final = time.time()
print ('ending pdb parser: ', final - initial, '\n')
return Vobject, atom_dic_id
def parse_pdb_old (infile = None, counter = 0, atom_dic_id = None, Vobject_id = None ):
""" Function doc """
#frames = []
with open(infile, 'r') as pdb_file:
label = os.path.basename(infile)
Vobject = mm.Vobject()
Vobject.label = label.split('.')
Vobject.label = Vobject.label[0]
chains_m = {}
residues = {}
atoms = []
index = 1
sum_x = 0
sum_y = 0
sum_z = 0
frame = []
residue_list = []
parser_resi = None
parser_resn = None
for line in pdb_file:
if line[:4] == 'ATOM' or line[:6] == 'HETATM':
at_name = line[12:16].strip()
#at_index = int(line[6:11])
at_pos = np.array([float(line[30:38]), float(line[38:46]), float(line[46:54])])
at_res_i = int(line[22:26])
at_res_n = line[17:20].strip()
at_ch = line[21]
atm = mm.Atom(name = at_name,
index = index,
pos = at_pos,
resi = at_res_i,
resn = at_res_n,
chain = at_ch,
atom_id = counter,
#Vobject_id = Vobject_id,
#Vobject_name = Vobject.label,
Vobject = Vobject,
)
if atom_dic_id is not None:
atom_dic_id[counter] = atm
counter += 1
index += 1
if at_ch in chains_m.keys():
ch = chains_m[at_ch]
#print 'existe'
else:
ch = mm.Chain(name=at_ch, label = 'UNK')
chains_m[at_ch] = ch
#print 'n existe'
if at_res_i == parser_resi:# and at_res_n == parser_resn:
atm.residue = ch.residues[-1]
ch.residues[-1].atoms.append(atm)
#res.atoms.append(atm)
Vobject.atoms.append(atm)
frame.append([atm.pos[0],atm.pos[1],atm.pos[2]])
#ch.residues[at_res_i].atoms.append(atm)
#Vobject.atoms.append(atm)
else:
residue = mm.Residue(name=at_res_n, index=at_res_i, chain=at_ch)
atm.residue = residue
residue.atoms.append(atm)
ch.residues.append(residue)
#ch.residues[at_res_i] = res
#ch.residues[at_res_i].atoms.append(atm)
Vobject.atoms.append(atm)
frame.append([atm.pos[0],atm.pos[1],atm.pos[2]])
parser_resi = at_res_i
parser_resn = at_res_n
#if at_res_i in ch.residues.keys():
# res = ch.residues[at_res_i]
# #print 'existe'
# ch.residues[at_res_i].atoms.append(atm)
# Vobject.atoms.append(atm)
# frame.append([atm.pos[0],atm.pos[1],atm.pos[2]])
#else:
# #print at_res_n, at_res_i, at_ch
# res = mm.Residue(name=at_res_n, index=at_res_i, chain=at_ch)
# ch.residues[at_res_i] = res
# ch.residues[at_res_i].atoms.append(atm)
# Vobject.atoms.append(atm)
# frame.append([atm.pos[0],atm.pos[1],atm.pos[2]])
if atm.name == 'CA':
ch.backbone.append(atm)
#ch.backbone.append(atm.pos[0])
#ch.backbone.append(atm.pos[1])
#ch.backbone.append(atm.pos[2])
sum_x += atm.pos[0]
sum_y += atm.pos[1]
sum_z += atm.pos[2]
# add a new frame to frames list
Vobject.frames.append(frame)
Vobject.chains = chains_m
total = len(Vobject.atoms)
Vobject.list_atom_lines = [True] *total
Vobject.list_atom_ribbons = [False]*total
Vobject.list_atom_dots = [False]*total
Vobject.list_atom_sticks = [False]*total
Vobject.list_atom_spheres = [False]*total
Vobject.list_atom_surface = [False]*total
Vobject.list_atom_ball_and_stick = [False]*total
Vobject.mass_center[0] = sum_x / total
Vobject.mass_center[1] = sum_y / total
Vobject.mass_center[2] = sum_z / total
#print Vobject.mass_center
for chain in Vobject.chains:
print('number_of_residues', len(Vobject.chains[chain].residues))
#print('number_of_residues', len())
return Vobject, atom_dic_id
def parse_xyz(infile = None, counter = 0, atom_dic_id = None, Vobject_id = None ):
""" Function doc """
#frames = []
with open(infile, 'r') as xyz_file:
label = os.path.basename(infile)
xyz_lines = xyz_file.readlines()
total_size = len(xyz_lines)
xyz_model_size = int(xyz_lines[0])
model_size = xyz_model_size+2 # include first and secound lines in a xyzfile
models = []
for i in range(0, int(total_size/model_size)):
#print (i*model_size) , (i+1)*model_size
model = xyz_lines[(i*model_size) : (i+1)*model_size]
models.append(model)
pprint (models[-1][2:])
Vobject = mm.Vobject()
Vobject.label = label.split('.')
Vobject.label = Vobject.label[0]
chains_m = {}
residues = {}
atoms = []
index = 1
sum_x = 0
sum_y = 0
sum_z = 0
residue_list = []
parser_resi = None
parser_resn = None
frame = []
for line in models[0][2:]:
line2 = line.split()
#print line2, [float(line[1]), float(line[2]), float(line[3])]
at_name = line2[0].strip()
at_pos = np.array([float(line2[1]), float(line2[2]), float(line2[3])])
at_res_i = 1
at_res_n = 'UNK'
at_ch = 'A'
#print at_name, '<--------'
atm = mm.Atom(name = at_name,
index = index,
pos = at_pos,
resi = at_res_i,
resn = at_res_n,
chain = at_ch,
atom_id = counter,
#Vobject_id = Vobject_id,
#Vobject_name = Vobject.label,
Vobject = Vobject
)
if atom_dic_id is not None:
atom_dic_id[counter] = atm
counter += 1
index += 1
coords = []
if at_ch in chains_m.keys():
ch = chains_m[at_ch]
else:
ch = mm.Chain(name=at_ch, label = 'UNK')
chains_m[at_ch] = ch
if at_res_i == parser_resi:# and at_res_n == parser_resn:
atm.residue = ch.residues[-1]
ch.residues[-1].atoms.append(atm)
#res.atoms.append(atm)
Vobject.atoms.append(atm)
frame.append([atm.pos[0],atm.pos[1],atm.pos[2]])
#ch.residues[at_res_i].atoms.append(atm)
#Vobject.atoms.append(atm)
else:
residue = mm.Residue(name=at_res_n, index=at_res_i, chain=at_ch)
atm.residue = residue
residue.atoms.append(atm)
ch.residues.append(residue)
Vobject.atoms.append(atm)
frame.append([atm.pos[0],atm.pos[1],atm.pos[2]])
parser_resi = at_res_i
parser_resn = at_res_n
#if at_res_i in ch.residues.keys():
# res = ch.residues[at_res_i]
# ch.residues[at_res_i].atoms.append(atm)
# Vobject.atoms.append(atm)
# frame.append([atm.pos[0],atm.pos[1],atm.pos[2]])
#
#else:
# res = mm.Residue(name=at_res_n, index=at_res_i, chain=at_ch)
# ch.residues[at_res_i] = res
# ch.residues[at_res_i].atoms.append(atm)
# Vobject.atoms.append(atm)
# frame.append([atm.pos[0],atm.pos[1],atm.pos[2]])
sum_x += atm.pos[0]
sum_y += atm.pos[1]
sum_z += atm.pos[2]
# add a new frame to frames list
Vobject.frames.append(frame)
Vobject.chains = chains_m
total = len(Vobject.atoms)
Vobject.list_atom_lines = [True] *total
Vobject.list_atom_ribbons = [False]*total
Vobject.list_atom_dots = [False]*total
Vobject.list_atom_sticks = [False]*total
Vobject.list_atom_spheres = [False]*total
Vobject.list_atom_surface = [False]*total
Vobject.list_atom_ball_and_stick = [False]*total
Vobject.mass_center[0] = sum_x / total
Vobject.mass_center[1] = sum_y / total
Vobject.mass_center[2] = sum_z / total
n = 1
for model_i in models[1:]:
frame = []
for line in model_i[2:]:
line2 = line.split()
#print line2, [float(line[1]), float(line[2]), float(line[3])]
#at_name = line2[0].strip()
#at_pos = np.array([float(line2[1]), float(line2[2]), float(line2[3])])
frame.append([float(line2[1]), float(line2[2]), float(line2[3])])
#pprint (n)
#pprint (frame)
Vobject.frames.append(frame)
n += 1
#print atom_dic_id
return Vobject, atom_dic_id
def parse_pdb(infile):
"""
"""
frames = []
with open(infile, 'r') as pdb_file:
frame = mm.Frame()
chains_m = {}
frame.chains = chains_m
atoms = []
for line in pdb_file:
if line[:4] == 'ATOM' or line[:6] == 'HETATM':
at_name = line[12:16].strip()
at_index = int(line[6:11])
at_pos = np.array([
float(line[30:38]),
float(line[38:46]),
float(line[46:54])
])
at_res_i = int(line[22:26])
at_res_n = line[17:20].strip()
at_ch = line[21]
atm = mm.Atom(name=at_name,
index=at_index,
pos=at_pos,
residue=at_res_i)
atm.sphere = True
atm.ball = True
atm.vdw = True
atm.pretty_vdw = True
atm.dot = True
atm.wires = True
if at_ch == ' ':
at_ch = 'A'
#if chains_m.has_key(at_ch):
if at_ch in chains_m:
ch = chains_m[at_ch]
else:
ch = mm.Chain(name=at_ch, frame=frame)
chains_m[at_ch] = ch
#if ch.residues.has_key(at_res_i):
if at_res_i in ch.residues:
res = ch.residues[at_res_i]
else:
res = mm.Residue(name=at_res_n,
index=at_res_i,
chain=at_ch)
ch.residues[at_res_i] = res
if atm.name == 'CA':
ch.backbone.append(atm)
#if not res.atoms.has_key(at_index):
if at_index not in res.atoms:
res.atoms[at_index] = atm
atoms.append(atm)
elif line[:6] == 'ENDMDL':
frame.chains = chains_m
frame.atoms = atoms
frame.load_bonds()
frame.load_ribbons()
frames.append(frame)
frame = mm.Frame()
chains_m = {}
atoms = []
if len(frame.chains.values()) > 0 and len(frames) == 0:
frame.atoms = atoms
frame.load_bonds()
frame.load_ribbons()
frames.append(frame)
return frames