def get_mmtfstr(selection='all', state=1, _self=cmd):
'''
DESCRIPTION
DEPRECATED: Use cmd.get_bytes('mmtf')
Export an atom selection to MMTF format.
'''
import simplemmtf
try:
# register PyMOL-specific spec extensions
simplemmtf.levels[u'atom'][u'pymolReps'] = 0
simplemmtf.levels[u'atom'][u'pymolColor'] = 0
simplemmtf.encodingrules[u'pymolRepsList'] = (7, 0)
except Exception as e:
print(e)
mmtfstr = simplemmtf.mmtfstr
ss_map = {
'H': 2, # alpha helix
'S': 3, # extended
}
def callback(state, segi, chain, resv, resi, resn, name, elem, x, y, z,
reps, color, alt, formal_charge, b, q, ss):
atoms.append({
u'modelIndex': state,
u'chainId': mmtfstr(segi),
u'chainName': mmtfstr(chain),
u'groupId': resv,
u'groupName': mmtfstr(resn),
u'atomName': mmtfstr(name),
u'element': mmtfstr(elem),
u'coords': (x, y, z),
u'altLoc': mmtfstr(alt),
u'formalCharge': formal_charge,
u'bFactor': b,
u'occupancy': q,
u'secStruct': ss_map.get(ss, -1),
u'insCode': mmtfstr(resi.lstrip('0123456789')),
u'pymolReps': reps,
u'pymolColor': color,
})
atoms = []
_self.iterate_state(
state,
selection,
'callback(state, segi, chain, resv, resi, resn, name, elem, '
'x, y, z, reps, color, alt, formal_charge, b, q, ss)',
space={'callback': callback})
bonds = _self.get_bonds(selection, state)
d_out = simplemmtf.from_atoms(atoms, bonds)
return d_out.encode()
def get_mmtfstr(selection='all', state=1, _self=cmd):
'''
DESCRIPTION
DEPRECATED: Use cmd.get_bytes('mmtf')
Export an atom selection to MMTF format.
'''
import simplemmtf
try:
# register PyMOL-specific spec extensions
simplemmtf.levels[u'atom'][u'pymolReps'] = 0
simplemmtf.levels[u'atom'][u'pymolColor'] = 0
simplemmtf.encodingrules[u'pymolRepsList'] = (7, 0)
except Exception as e:
print(e)
mmtfstr = simplemmtf.mmtfstr
ss_map = {
'H': 2, # alpha helix
'S': 3, # extended
}
def callback(state, segi, chain, resv, resi, resn, name, elem,
x, y, z, reps, color, alt, formal_charge, b, q, ss):
atoms.append({
u'modelIndex': state,
u'chainId': mmtfstr(segi),
u'chainName': mmtfstr(chain),
u'groupId': resv,
u'groupName': mmtfstr(resn),
u'atomName': mmtfstr(name),
u'element': mmtfstr(elem),
u'coords': (x, y, z),
u'altLoc': mmtfstr(alt),
u'formalCharge': formal_charge,
u'bFactor': b,
u'occupancy': q,
u'secStruct': ss_map.get(ss, -1),
u'insCode': mmtfstr(resi.lstrip('0123456789')),
u'pymolReps': reps,
u'pymolColor': color,
})
atoms = []
_self.iterate_state(state, selection,
'callback(state, segi, chain, resv, resi, resn, name, elem, '
'x, y, z, reps, color, alt, formal_charge, b, q, ss)',
space={'callback': callback})
bonds = _self.get_bonds(selection, state)
d_out = simplemmtf.from_atoms(atoms, bonds)
return d_out.encode()
def test_encodable():
atoms = [{
u'atomName': u'N',
u'chainId': u'A',
u'coords': (12.284, 42.763, 10.037),
u'element': u'N',
u'groupName': u'MET',
}]
# len('A') <= 4: encodable -> binary
d = simplemmtf.from_atoms(atoms)
assert d.get(u'chainIdList') == ['A']
assert isinstance(d._data[u'chainIdList'], bytes)
atoms[0][u'chainId'] = u'ABCDE'
# len('ABCDE') > 4: not encodable -> array
d = simplemmtf.from_atoms(atoms)
assert d.get(u'chainIdList') == ['ABCDE']
assert isinstance(d._data[u'chainIdList'], list)
def pdb2mmtf(handle):
'''
@type handle: open file handle for reading
@rtype: bytes
'''
from simplemmtf import mmtfstr, from_atoms
def atom_gen():
state = 0
for line in handle:
rec = line[:6]
if rec == 'MODEL ':
state += 1
elif rec in ('ATOM ', 'HETATM'):
yield {
u'modelIndex': state,
u'atomId': int(line[6:11]),
u'atomName': mmtfstr(line[12:16].strip()),
u'altLoc': mmtfstr(line[16:17].rstrip()),
u'groupName': mmtfstr(line[17:20].strip()),
u'chainName': mmtfstr(line[21:22].rstrip()),
u'groupId': int(line[22:26]),
u'insCode': mmtfstr(line[26:27].rstrip()),
u'xCoord': float(line[30:38]),
u'yCoord': float(line[38:46]),
u'zCoord': float(line[46:54]),
u'bFactor': float(line[60:66]),
u'occupancy': float(line[54:60]),
u'chainId': mmtfstr(line[72:76].strip()),
u'element': mmtfstr(line[76:78].lstrip()),
}
d_out = from_atoms(atom_gen())
return d_out.encode()
def get_mmtfstr(selection='all', state=1, _self=pymol.cmd):
'''
DESCRIPTION
Get an atom selection as MMTF format.
'''
from simplemmtf import mmtfstr, from_atoms
state = int(state)
if state == 0:
states = range(1, _self.count_states(selection) + 1)
else:
states = [state]
ss_map = {
'H': 2, # alpha helix
'S': 3, # extended
}
bonds = []
atoms = []
if True:
numBonds = 0
for state in states:
m = _self.get_model(selection, state)
for a in m.atom:
atom = {
u'modelIndex': state,
u'chainId': mmtfstr(a.segi),
u'chainName': mmtfstr(a.chain),
u'groupId': a.resi_number,
u'groupName': mmtfstr(a.resn),
u'atomName': mmtfstr(a.name),
u'element': mmtfstr(a.symbol),
u'coords': a.coord,
}
if a.resi[-1:].isalpha():
atom[u'insCode'] = mmtfstr(a.resi[-1])
if a.alt:
atom[u'altLoc'] = mmtfstr(a.alt)
if a.formal_charge:
atom[u'formalCharge'] = int(a.formal_charge)
if a.b:
atom[u'bFactor'] = a.b
if a.q != 1.0:
atom[u'occupancy'] = a.q
if a.ss:
atom[u'secStruct'] = ss_map.get(a.ss, -1)
atoms.append(atom)
for b in m.bond:
bonds.append(
(b.index[0] + numBonds, b.index[1] + numBonds, b.order))
numBonds += len(m.atom)
d_out = from_atoms(atoms, bonds)
return d_out.encode()