def test_reorderAllCoordinatesByChainLen(self):
input = StringIO.StringIO(chain_padding_proto_3)
structure = prody.parsePDBStream(input)
group_lens = {1: ['A'], 2: ['B', 'D'], 3: ['C', 'E']}
result = ChainMappingRMSDMatrixCalculator.getReorderedCoordinatesByLenGroups(structure, "all", group_lens)
expected =[[[1.0, 2.0, 3.0],
[4.0, 5.0, 6.0],
[7.0, 8.0, 9.0],
[19.0, 20.0, 21.0],
[22.0, 23.0, 24.0],
[10.0, 11.0, 12.0],
[13.0, 14.0, 15.0],
[16.0, 17.0, 18.0],
[25.0, 26.0, 27.0],
[28.0, 29.0, 30.0],
[31.0, 32.0, 33.0]],
[[41.0, 42.0, 43.0],
[44.0, 45.0, 46.0],
[47.0, 48.0, 49.0],
[59.0, 60.0, 61.0],
[62.0, 63.0, 64.0],
[50.0, 51.0, 52.0],
[53.0, 54.0, 55.0],
[56.0, 57.0, 58.0],
[65.0, 66.0, 67.0],
[68.0, 69.0, 70.0],
[71.0, 72.0, 73.0]]]
numpy.testing.assert_array_equal(expected, result)
def normalmodes_prody(selection, cutoff=15, first=7, last=10, guide=1,
prefix='prody', states=7, factor=-1, quiet=1):
'''
DESCRIPTION
Anisotropic Network Model (ANM) analysis with ProDy.
Based on:
http://www.csb.pitt.edu/prody/examples/dynamics/enm/anm.html
'''
try:
import prody
except ImportError:
print('Failed to import prody, please add to PYTHONPATH')
raise CmdException
first, last, guide = int(first), int(last), int(guide)
states, factor, quiet = int(states), float(factor), int(quiet)
assert first > 6
if guide:
selection = '(%s) and guide and alt A+' % (selection)
tmpsele = cmd.get_unused_name('_')
cmd.select(tmpsele, selection)
f = StringIO(cmd.get_pdbstr(tmpsele))
conf = prody.parsePDBStream(f)
modes = prody.ANM()
modes.buildHessian(conf, float(cutoff))
modes.calcModes(last - first + 1)
if factor < 0:
from math import log
natoms = modes.numAtoms()
factor = log(natoms) * 10
if not quiet:
print(' set factor to %.2f' % (factor))
for mode in range(first, last + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d' % (name, mode))
for state in range(1, states+1):
xyz_it = iter(modes[mode-7].getArrayNx3() * (factor *
((state-1.0)/(states-1.0) - 0.5)))
cmd.create(name, tmpsele, 1, state, zoom=0)
cmd.alter_state(state, name, '(x,y,z) = next(xyz_it) + (x,y,z)',
space={'xyz_it': xyz_it, 'next': next})
cmd.delete(tmpsele)
if guide:
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
def normalmodes_prody(selection, cutoff=15, first=7, last=10, guide=1,
prefix='prody', states=7, factor=-1, quiet=1):
'''
DESCRIPTION
Anisotropic Network Model (ANM) analysis with ProDy.
Based on:
http://www.csb.pitt.edu/prody/examples/dynamics/enm/anm.html
'''
try:
import prody
except ImportError:
print('Failed to import prody, please add to PYTHONPATH')
raise CmdException
first, last, guide = int(first), int(last), int(guide)
states, factor, quiet = int(states), float(factor), int(quiet)
assert first > 6
if guide:
selection = '(%s) and guide and alt A+' % (selection)
tmpsele = cmd.get_unused_name('_')
cmd.select(tmpsele, selection)
f = StringIO(cmd.get_pdbstr(tmpsele))
conf = prody.parsePDBStream(f)
modes = prody.ANM()
modes.buildHessian(conf, float(cutoff))
modes.calcModes(last - first + 1)
if factor < 0:
from math import log
natoms = modes.numAtoms()
factor = log(natoms) * 10
if not quiet:
print(' set factor to %.2f' % (factor))
for mode in range(first, last + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d' % (name, mode))
for state in range(1, states+1):
xyz_it = iter(modes[mode-7].getArrayNx3() * (factor *
((state-1.0)/(states-1.0) - 0.5)))
cmd.create(name, tmpsele, 1, state, zoom=0)
cmd.alter_state(state, name, '(x,y,z) = xyz_it.next() + (x,y,z)',
space=locals())
cmd.delete(tmpsele)
if guide:
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
def test_removeAllCoordsetsFromStructureLeavingFirst(self):
input = StringIO.StringIO(switched_pdb_data)
pdb_structure = prody.parsePDBStream(input)
removeAllCoordsetsFromStructureLeavingFirst(pdb_structure)
expected = [[[1.0, 2.0, 3.0], [-33.115, 1.294, -1.163]]]
numpy.testing.assert_array_equal(expected,
pdb_structure.getCoordsets())
def test_getStructureChains(self):
expected = [{
'A': numpy.array([[1., 2., 3.]]),
'X': numpy.array([[-33.115, 1.294, -1.163]])
}, {
'A': numpy.array([[4., 5., 6.]]),
'X': numpy.array([[-32.555, -2.5, -5.367]])
}, {
'A': numpy.array([[7., 8., 9.]]),
'X': numpy.array([[-33.257, 5.28, -8.441]])
}, {
'A': numpy.array([[10., 11., 12.]]),
'X': numpy.array([[32.306, 6.517, -1.544]])
}, {
'A': numpy.array([[13., 14., 15.]]),
'X': numpy.array([[30.494, 10.39, -3.066]])
}]
input = StringIO.StringIO(pdb_data)
pdb_structure = prody.parsePDBStream(input)
result = ChainMappingRMSDMatrixCalculator.getStructureChains(
pdb_structure, "all")
for i in range(len(expected)):
numpy.testing.assert_array_equal(expected[i]['A'], result[i]['A'])
numpy.testing.assert_array_equal(expected[i]['X'], result[i]['X'])
def add_mol(self, mol, keep_chains=False, keep_resi=False):
"""
This behaves bad when molecules have same chain names
"""
ag1 = self.ag.copy()
ag2 = mol.ag.copy()
if ag1.numCoordsets() != ag2.numCoordsets():
raise RuntimeError('Atom groups have different numbers of coordinate sets')
nsets = ag1.numCoordsets()
chains1 = list(set(ag1.getChids()))
chains2 = list(set(ag2.getChids()))
all_chains = chains1 + chains2
if len(set(all_chains)) != len(all_chains) and keep_chains:
logger.warning('Two atom groups contain same chain IDs, merging can go wrong')
if keep_resi and len(set(ag1.getResnums()).intersection(set(ag2.getResnums()))) > 0:
raise RuntimeError('Refusing to merge atom groups which contain same chain IDs AND residue IDs')
if not keep_chains:
if len(chains1) + len(chains2) > len(self._chain_order):
raise RuntimeError('Total number of chains is too large, out of chain ID letters')
iter_chains = iter(self._chain_order)
map1 = {x: next(iter_chains) for x in chains1}
map2 = {x: next(iter_chains) for x in chains2}
for old, new in map1.items():
ag1.select('chain ' + old).setChids(new)
for old, new in map2.items():
ag2.select('chain ' + old).setChids(new)
if not keep_resi:
resi = 1
for r in ag1.getHierView().iterResidues():
r.setResnum(resi)
resi += 1
for r in ag2.getHierView().iterResidues():
r.setResnum(resi)
resi += 1
buf = StringIO()
for i in range(nsets):
if nsets > 1:
buf.write('MODEL \n' + str(i + 1))
prody.writePDBStream(buf, ag1, csets=i)
prody.writePDBStream(buf, ag2, csets=i)
if nsets > 1:
buf.write('ENDMDL\n')
else:
buf.write('END\n')
buf.seek(0)
joint = BasePDB(ag=prody.parsePDBStream(buf))
joint.renumber(keep_resi=True, keep_chains=True)
buf.close()
return joint
def test_get_dihedrals(self):
input = StringIO.StringIO(pdb1)
pdb_structure = prody.parsePDBStream(input)
dihedrals = DihedralRMSDMatrixCalculator.calculateDihedralsForCoordset(
pdb_structure,
pdb_structure.getCoordsets()[0])
# We have to get rid off the unknown values!
numpy.testing.assert_array_almost_equal(
numpy.array(expected_dihedrals[1:-1]),
numpy.array(dihedrals[2:-2]), 2)
def test_getChainLengths(self):
input = StringIO.StringIO(chain_padding_proto_3)
structure = prody.parsePDBStream(input)
self.assertDictEqual({
'A': 1,
'C': 3,
'B': 2,
'E': 3,
'D': 2
}, ChainMappingRMSDMatrixCalculator.getChainLengths(structure, "all"))
def _from_str(string):
"""
Load a ProDy AtomGroup form a string representation.
Parameters:
string - a string containing the contents of a ProDy AtomGroup
Returns:
A ProDy AtomGroup
"""
ss = io_tools.StringStream(string)
return prody.parsePDBStream(ss)
def test_getStructureChains(self):
expected = [{'A': numpy.array([[ 1., 2., 3.]]), 'X': numpy.array([[-33.115, 1.294, -1.163]])},
{'A': numpy.array([[ 4., 5., 6.]]), 'X': numpy.array([[-32.555, -2.5 , -5.367]])},
{'A': numpy.array([[ 7., 8., 9.]]), 'X': numpy.array([[-33.257, 5.28 , -8.441]])},
{'A': numpy.array([[ 10., 11., 12.]]), 'X': numpy.array([[ 32.306, 6.517, -1.544]])},
{'A': numpy.array([[ 13., 14., 15.]]), 'X': numpy.array([[ 30.494, 10.39 , -3.066]])}]
input = StringIO.StringIO(pdb_data)
pdb_structure = prody.parsePDBStream(input)
result = ChainMappingRMSDMatrixCalculator.getStructureChains(pdb_structure,"all")
for i in range(len(expected)):
numpy.testing.assert_array_equal(expected[i]['A'], result[i]['A'])
numpy.testing.assert_array_equal(expected[i]['X'], result[i]['X'])
def add_hydrogens(self, trim=True, csets=None):
raise NotImplementedError()
output = []
natoms = -1
csets = self._make_csets(csets)
for i in csets:
if trim:
p_start = Popen([define.REDUCE_EXE, '-Quiet', '-Trim', '-'], stdin=PIPE, stdout=PIPE, stderr=STDOUT)
p_finish = Popen([define.REDUCE_EXE, '-Quiet', '-FLIP', '-'], stdin=p_start.stdout, stdout=PIPE,
stderr=STDOUT)
else:
p_start = Popen([define.REDUCE_EXE, '-Quiet', '-FLIP', '-'], stdin=PIPE, stdout=PIPE, stderr=STDOUT)
p_finish = p_start
prody.writePDBStream(p_start.stdin, self.ag, csets=i)
p_start.stdin.close()
output += ['MODEL%9i\n' % (i + 1)]
reduced = []
while p_finish.poll() is None:
reduced = p_finish.stdout.readlines()
p_start.wait()
p_finish.wait()
print(reduced)
natoms_cur = len(list(filter(lambda x: x.startswith('ATOM') or x.startswith('HETATM'), reduced)))
if i == csets[0]:
natoms = natoms_cur
elif natoms != natoms_cur:
raise RuntimeError('Number of atoms in reduced model %i is different from the first model (%i, %i)' % (
i, natoms_cur, natoms))
output += reduced
output += ['ENDMDL\n']
status = p_finish.poll()
if status != 0:
logger.error('Called process returned ' + str(status))
self.ag = prody.parsePDBStream(StringIO(''.join(output)))
self.renumber()
return self
def read_result(self, seq):
fname = "%s.dok" % seq
with open(fname, 'r') as f:
raw = f.readlines()
res = self.split_result(raw)
pres = list()
for r in res:
e_ = self.get_energy(r)
r_ = prody.parsePDBStream(StringIO.StringIO(r))
c_ = r_.getCoords()
pres.append((c_, e_))
if self.cleanup:
os.remove(fname)
os.remove("%s.mol2" % seq)
os.remove(self.llist_fname)
os.remove(self.config.fname)
return pres
def test_reorderAllCoordinatesByChainLen(self):
input = StringIO.StringIO(chain_padding_proto_3)
structure = prody.parsePDBStream(input)
group_lens = {1: ['A'], 2: ['B', 'D'], 3: ['C', 'E']}
result = ChainMappingRMSDMatrixCalculator.getReorderedCoordinatesByLenGroups(
structure, "all", group_lens)
expected = [[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0],
[19.0, 20.0, 21.0], [22.0, 23.0,
24.0], [10.0, 11.0, 12.0],
[13.0, 14.0, 15.0], [16.0, 17.0,
18.0], [25.0, 26.0, 27.0],
[28.0, 29.0, 30.0], [31.0, 32.0, 33.0]],
[[41.0, 42.0, 43.0], [44.0, 45.0,
46.0], [47.0, 48.0, 49.0],
[59.0, 60.0, 61.0], [62.0, 63.0,
64.0], [50.0, 51.0, 52.0],
[53.0, 54.0, 55.0], [56.0, 57.0,
58.0], [65.0, 66.0, 67.0],
[68.0, 69.0, 70.0], [71.0, 72.0, 73.0]]]
numpy.testing.assert_array_equal(expected, result)
def identify_best_chain(pdbid, aaseq, chain_str):
"""Determine PDB file and chain that best matches the aa sequence
"""
files = glob.glob(DOWNLOADDIR + pdbid + "*pdb*")
chains = chain_str.split(',')
chain_scores = []
for file_path in files:
if file_path.split('.')[-1] == "gz":
f = gzip.open(file_path, 'rt')
filter_chains = True
else:
f = open(file_path, "r")
filter_chains = False
try:
mol, header = prody.parsePDBStream(f, header=True)
except ValueError as e:
print("PDB Error: %s: %s" % (pdbid, e))
return None
f.close()
for chain in mol.iterChains():
if filter_chains and chain.getChid() not in chains:
continue
chain_sequence = chain.getSequence()
# score = pairwise2.align.globalms(aaseq, chain_sequence, 2, -1, -1, -.5, score_only=True)
# ms: https://biopython.org/DIST/docs/api/Bio.pairwise2-module.html
# 2 for identity, -1 for non-identity, -1 for gap, -0.5 for extending gap
score = pairwise2.align.globalxx(aaseq, chain_sequence, score_only=True)
# xx: no parameters
if isinstance(score, list):
# case [], doesn't align at all
continue
chain_scores.append((chain, score, file_path))
best = sorted(chain_scores, key=lambda x: x[1], reverse=True)[0]
best_chain = best[0]
best_file = best[2].lstrip(DOWNLOADDIR)
best_chain_id = best_chain.getChid()
best_score = best[1] / float(len(aaseq))
return best_file, best_chain_id, best_score
def _from_str(string):
ss = io.StringStream(string)
return prody.parsePDBStream(ss)
def test_removeAllCoordsetsFromStructure(self):
input = StringIO.StringIO(switched_pdb_data)
pdb_structure = prody.parsePDBStream(input)
removeAllCoordsetsFromStructure(pdb_structure)
self.assertEqual(pdb_structure.getCoordsets(), None)
def __init__(self,
user_defined_dir,
current_fragment,
fragment_smiles_sanitized,
verify_substructure=True
): # todo: fragment_string really shouldn't be a string...
# --- Paths --- #
self.current_fragment = current_fragment
self.frag_rigid_pdb_name = f'{current_fragment}-rigid.pdb'
self.user_defined_dir = user_defined_dir
self.inputs_dir = os.path.join(self.user_defined_dir, 'Inputs')
self.fragment_inputs_path = os.path.join(self.inputs_dir,
'Fragment_Inputs')
self.rosetta_inputs_path = os.path.join(self.inputs_dir,
'Rosetta_Inputs')
# Select rigid atoms from fragment map for alignments if rigid atoms are defined in the Fragment_Inputs directory
self.frag_inputs_dir = os.path.join(self.fragment_inputs_path,
'Rigid_Fragment_Atoms')
# --- Fragment-related variables --- #
self.fragment_string = open(
os.path.join(self.fragment_inputs_path,
'{}.pdb'.format(current_fragment))).read()
self.fragment_smiles_sanitized = fragment_smiles_sanitized
self.fragment_prody = prody.parsePDBStream(
io.StringIO(self.fragment_string)).select('not hydrogen')
self.ideal_fragment_mapping = None # Assigned in _init_map_fragment_smiles_onto_ideal()
# RDKit Mol representations of fragment
self.fragment_ideal_rdkit_mol = Chem.MolFromSmiles(
self.fragment_smiles_sanitized)
if self.fragment_ideal_rdkit_mol is None:
print(
'Unable to parse SMILES from Fragment_Inputs.csv, generating fragment Mol from file!'
)
try:
fragment_pdb_path = os.path.join(self.fragment_inputs_path,
f'{current_fragment}.pdb')
self.fragment_ideal_rdkit_mol = Chem.MolFromPDBFile(
fragment_pdb_path)
print(Chem.MolToSmiles(self.fragment_ideal_rdkit_mol))
except Exception as e:
print(e)
self.fragment_pdb_rdkit_mol = Chem.MolFromPDBBlock(
self.fragment_string, removeHs=False)
# Assert that mol objects were loaded properly
assert not any([
self.fragment_pdb_rdkit_mol is None,
self.fragment_ideal_rdkit_mol is None
])
# --- Run initialization functions --- #
self._init_map_fragment_smiles_onto_ideal()
# --- Fragment Mapping options --- #
self.verify_substructure = verify_substructure
if verify_substructure:
reference_ligand_path = os.path.join(
self.rosetta_inputs_path,
f'{os.path.basename(user_defined_dir)[:3]}_0001.pdb')
self.reference_ligand_rdkit_mol = Chem.MolFromPDBFile(
reference_ligand_path, removeHs=True)
# Map ref_fragment_index > ref_fragment name > ref_ligand name > ref_ligand degree
ref_ligand_atomname_degree_map = {
atom.GetMonomerInfo().GetName(): atom.GetDegree()
for atom in self.reference_ligand_rdkit_mol.GetAtoms()
}
self.pdbfrag_refdegree_map = dict()
for ideal_idx, pdb_idx in self.ideal_fragment_mapping.items():
fragment_pdb_atom = self.fragment_pdb_rdkit_mol.GetAtomWithIdx(
pdb_idx)
fragment_pdb_atom_name = fragment_pdb_atom.GetMonomerInfo(
).GetName()
self.pdbfrag_refdegree_map[
pdb_idx] = ref_ligand_atomname_degree_map[
fragment_pdb_atom_name]
def test_getChainLengths(self):
input = StringIO.StringIO(chain_padding_proto_3)
structure = prody.parsePDBStream(input)
self.assertDictEqual({'A': 1, 'C': 3, 'B': 2, 'E': 3, 'D': 2},
ChainMappingRMSDMatrixCalculator.getChainLengths(structure, "all"))
def test_get_dihedrals(self):
input = StringIO.StringIO(pdb1)
pdb_structure = prody.parsePDBStream(input)
dihedrals = DihedralRMSDMatrixCalculator.calculateDihedralsForCoordset(pdb_structure,pdb_structure.getCoordsets()[0])
# We have to get rid off the unknown values!
numpy.testing.assert_array_almost_equal(numpy.array(expected_dihedrals[1:-1]), numpy.array(dihedrals[2:-2]), 2)
def test_removeAllCoordsetsFromStructureLeavingFirst(self):
input = StringIO.StringIO(switched_pdb_data)
pdb_structure = prody.parsePDBStream(input)
removeAllCoordsetsFromStructureLeavingFirst(pdb_structure)
expected = [[[1.0, 2.0, 3.0], [-33.115, 1.294, -1.163]]]
numpy.testing.assert_array_equal(expected, pdb_structure.getCoordsets())
def test_removeAllCoordsetsFromStructure(self):
input = StringIO.StringIO(switched_pdb_data)
pdb_structure = prody.parsePDBStream(input)
removeAllCoordsetsFromStructure(pdb_structure)
self.assertEqual(pdb_structure.getCoordsets(),None)
def _from_str(string):
ss = io.StringStream(string)
return prody.parsePDBStream(ss)
