def test_pdb_mmcif(self):
"""Test PDB writing with mmcif=True"""
mdl, root_hier = self._make_test_model()
# write PDB and check it's ok
output = IMP.pmi.output.Output(atomistic=True)
output.init_pdb("test_pdb_writing.cif", root_hier, mmcif=True)
output.write_pdbs()
print('init best scoring')
output.init_pdb_best_scoring("test_pdb_writing",
root_hier,
10,
mmcif=True)
print('scoring')
for i in range(20):
score = -float(i)
output.write_pdb_best_scoring(score)
with open('test_pdb_writing.cif') as fh:
s, = ihm.reader.read(fh)
self.assertEqual([x.id for x in s.asym_units],
[' ', ' 1', 'A', 'B', 'A1', 'CA'])
for i in range(10):
os.unlink('test_pdb_writing.' + str(i) + '.cif')
os.unlink('test_pdb_writing.cif')
def test_pdb_writing(self):
"""Test writing of PDB files"""
# input parameter
pdbfile = self.get_input_file_name("mini.pdb")
fastafile = self.get_input_file_name("mini.fasta")
comps = ["P1", "P2", "P3"]
chains = "ABB"
colors = [0., 0.5, 1.0]
beadsize = 20
fastids = IMP.pmi.tools.get_ids_from_fasta_file(fastafile)
m = IMP.Model()
simo = IMP.pmi.representation.Representation(m)
simo.create_component(comps[0], color=colors[0])
simo.add_component_sequence(comps[0], fastafile, id=fastids[0])
simo.autobuild_model(comps[0],
pdbfile,
chains[0],
resolutions=[1],
missingbeadsize=beadsize)
simo.setup_component_sequence_connectivity(comps[0], 1)
simo.create_component(comps[1], color=colors[1])
simo.add_component_sequence(comps[1], fastafile, id=fastids[1])
simo.autobuild_model(comps[1],
pdbfile,
chains[1],
resolutions=[10],
missingbeadsize=beadsize)
simo.setup_component_sequence_connectivity(comps[1], 1)
simo.create_component(comps[2], color=colors[2])
simo.add_component_sequence(comps[2], fastafile, id=fastids[1])
simo.autobuild_model(comps[2],
pdbfile,
chains[2],
resolutions=[1, 10],
missingbeadsize=2)
simo.setup_component_sequence_connectivity(comps[2], 1)
output = IMP.pmi.output.Output()
output.init_pdb("test_pdb_writing.pdb", simo.prot)
output.write_pdbs()
output.init_pdb_best_scoring("test_pdb_writing", simo.prot, 10)
for i in range(20):
score = -float(i)
output.write_pdb_best_scoring(score)
for i in range(10):
os.unlink('test_pdb_writing.' + str(i) + '.pdb')
pdb_content = '''ATOM 1 CA MET A 1 114.370 27.980 -26.088 1.00 3.07 C
ATOM 2 CA VAL A 2 114.370 27.980 -26.088 1.00 2.89 C
ATOM 3 CA GLY A 3 111.506 26.368 -28.075 1.00 2.27 C
ATOM 4 CA GLN A 4 113.468 23.113 -28.639 1.00 3.01 C
ATOM 5 CA GLN A 5 113.808 21.534 -32.168 1.00 3.01 C
ATOM 6 CA TYR A 6 116.743 22.770 -34.259 1.00 3.32 C
ATOM 7 CA SER A 7 116.626 25.161 -37.229 1.00 2.61 C
ATOM 8 CA SER A 8 119.165 25.590 -40.036 1.00 2.61 C
ATOM 9 CA BEA B 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 10 CA BEA B 4 68.799 58.791 50.131 1.00 3.69 C
ATOM 11 CA BEA B 7 68.799 58.791 50.131 1.00 4.76 C
ATOM 12 CA BEA C 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 13 CA ASP C 3 70.427 58.819 51.717 1.00 2.87 C
ATOM 14 CA GLU C 4 68.584 58.274 48.425 1.00 3.00 C
ATOM 15 CA BEA C 6 68.584 58.274 48.425 1.00 3.50 C
ATOM 16 CA BEA C 8 68.584 58.274 48.425 1.00 3.50 C
ATOM 17 CA THR C 9 68.584 58.274 48.425 1.00 2.80 C
ENDMDL'''.split("\n")
with open("test_pdb_writing.pdb") as f:
for nl, l in enumerate(f):
self.assertEqual(pdb_content[nl], l.rstrip('\r\n '))
os.unlink('test_pdb_writing.pdb')
def test_pdb_pmi2(self):
"""Test PDB writing in PMI2"""
mdl = IMP.Model()
pdb_file = self.get_input_file_name("mini.pdb")
fasta_file = self.get_input_file_name("mini.fasta")
seqs = IMP.pmi.topology.Sequences(fasta_file)
s = IMP.pmi.topology.System(mdl)
st = s.create_state()
molA = st.create_molecule("P1", seqs[0], chain_id='A')
aresA = molA.add_structure(pdb_file, chain_id='A', soft_check=True)
molA.add_representation(aresA, [1])
molA.add_representation(molA[:] - aresA, 20)
molB = st.create_molecule("P2", seqs[1], chain_id='B')
aresB = molB.add_structure(pdb_file, chain_id='B', soft_check=True)
molB.add_representation(aresB, [10])
molB.add_representation(molB[:] - aresB, 20)
molC = molB.create_copy(chain_id='C')
aresC = molC.add_structure(pdb_file, chain_id='B', soft_check=True)
molC.add_representation(aresC, [1, 10])
molC.add_representation(molC[:] - aresC, 2)
root_hier = s.build()
# write PDB and check it's ok
output = IMP.pmi.output.Output(atomistic=True)
output.init_pdb("test_pdb_writing.pdb", root_hier)
output.write_pdbs()
print('init best scoring')
output.init_pdb_best_scoring("test_pdb_writing", root_hier, 10)
print('scoring')
for i in range(20):
score = -float(i)
output.write_pdb_best_scoring(score)
pdb_content = '''ATOM 1 CA MET A 1 114.370 27.980 -26.088 1.00 3.07 C
ATOM 2 CA VAL A 2 114.370 27.980 -26.088 1.00 2.89 C
ATOM 3 CA GLY A 3 111.506 26.368 -28.075 1.00 2.27 C
ATOM 4 CA GLN A 4 113.468 23.113 -28.639 1.00 3.01 C
ATOM 5 CA GLN A 5 113.808 21.534 -32.168 1.00 3.01 C
ATOM 6 CA TYR A 6 116.743 22.770 -34.259 1.00 3.32 C
ATOM 7 CA SER A 7 116.626 25.161 -37.229 1.00 2.61 C
ATOM 8 CA SER A 8 119.165 25.590 -40.036 1.00 2.61 C
ATOM 9 CA BEA B 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 10 CA BEA B 4 68.799 58.791 50.131 1.00 3.69 C
ATOM 11 CA BEA B 7 68.584 58.274 48.425 1.00 4.76 C
ATOM 12 CA BEA C 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 13 CA ASP C 3 70.427 58.819 51.717 1.00 2.87 C
ATOM 14 CA GLU C 4 68.584 58.274 48.425 1.00 3.00 C
ATOM 15 CA BEA C 6 68.584 58.274 48.425 1.00 3.50 C
ATOM 16 CA BEA C 8 68.584 58.274 48.425 1.00 3.50 C
ATOM 17 CA THR C 9 68.584 58.274 48.425 1.00 2.80 C
ENDMDL'''.split("\n")
with open("test_pdb_writing.pdb") as f:
for nl, l in enumerate(f):
self.assertEqual(pdb_content[nl], l.rstrip('\r\n '))
with open("test_pdb_writing.0.pdb") as f:
for nl, l in enumerate(f):
self.assertEqual(pdb_content[nl], l.rstrip('\r\n '))
for i in range(10):
os.unlink('test_pdb_writing.' + str(i) + '.pdb')
os.unlink('test_pdb_writing.pdb')
def test_pdb_pmi2(self):
"""Test PDB writing in PMI2"""
mdl, root_hier = self._make_test_model()
# write PDB and check it's ok
output = IMP.pmi.output.Output(atomistic=True)
output.init_pdb("test_pdb_writing.pdb", root_hier)
output.write_pdbs()
print('init best scoring')
output.init_pdb_best_scoring("test_pdb_writing", root_hier, 10)
print('scoring')
for i in range(20):
score = -float(i)
output.write_pdb_best_scoring(score)
pdb_content='''ATOM 1 CA BEA 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 2 CA ASP 3 70.427 58.819 51.717 1.00 2.87 C
ATOM 3 CA GLU 4 68.584 58.274 48.425 1.00 3.00 C
ATOM 4 CA BEA 6 68.584 58.274 48.425 1.00 3.50 C
ATOM 5 CA BEA 8 68.584 58.274 48.425 1.00 3.50 C
ATOM 6 CA THR 9 68.584 58.274 48.425 1.00 2.80 C
ATOM 7 CA MET A 1 114.370 27.980 -26.088 1.00 3.07 C
ATOM 8 CA VAL A 2 114.370 27.980 -26.088 1.00 2.89 C
ATOM 9 CA GLY A 3 111.506 26.368 -28.075 1.00 2.27 C
ATOM 10 CA GLN A 4 113.468 23.113 -28.639 1.00 3.01 C
ATOM 11 CA GLN A 5 113.808 21.534 -32.168 1.00 3.01 C
ATOM 12 CA TYR A 6 116.743 22.770 -34.259 1.00 3.32 C
ATOM 13 CA SER A 7 116.626 25.161 -37.229 1.00 2.61 C
ATOM 14 CA SER A 8 119.165 25.590 -40.036 1.00 2.61 C
ATOM 15 CA BEA B 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 16 CA BEA B 4 68.799 58.791 50.131 1.00 3.69 C
ATOM 17 CA BEA B 7 68.584 58.274 48.425 1.00 4.76 C
ATOM 18 CA MET 1 114.370 27.980 -26.088 1.00 3.07 C
ATOM 19 CA VAL 2 114.370 27.980 -26.088 1.00 2.89 C
ATOM 20 CA GLY 3 111.506 26.368 -28.075 1.00 2.27 C
ATOM 21 CA GLN 4 113.468 23.113 -28.639 1.00 3.01 C
ATOM 22 CA GLN 5 113.808 21.534 -32.168 1.00 3.01 C
ATOM 23 CA TYR 6 116.743 22.770 -34.259 1.00 3.32 C
ATOM 24 CA SER 7 116.626 25.161 -37.229 1.00 2.61 C
ATOM 25 CA SER 8 119.165 25.590 -40.036 1.00 2.61 C
ATOM 26 CA BEA A 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 27 CA ASP A 3 70.427 58.819 51.717 1.00 2.87 C
ATOM 28 CA GLU A 4 68.584 58.274 48.425 1.00 3.00 C
ATOM 29 CA BEA A 6 68.584 58.274 48.425 1.00 3.50 C
ATOM 30 CA BEA A 8 68.584 58.274 48.425 1.00 3.50 C
ATOM 31 CA THR A 9 68.584 58.274 48.425 1.00 2.80 C
ATOM 32 CA BEA C 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 33 CA ASP C 3 70.427 58.819 51.717 1.00 2.87 C
ATOM 34 CA GLU C 4 68.584 58.274 48.425 1.00 3.00 C
ATOM 35 CA BEA C 6 68.584 58.274 48.425 1.00 3.50 C
ATOM 36 CA BEA C 8 68.584 58.274 48.425 1.00 3.50 C
ATOM 37 CA THR C 9 68.584 58.274 48.425 1.00 2.80 C
ENDMDL'''.split("\n")
with open("test_pdb_writing.pdb") as f:
for nl, l in enumerate(f):
self.assertEqual(pdb_content[nl],l.rstrip('\r\n '))
with open("test_pdb_writing.0.pdb") as f:
for nl, l in enumerate(f):
self.assertEqual(pdb_content[nl],l.rstrip('\r\n '))
for i in range(10):
os.unlink('test_pdb_writing.'+str(i)+'.pdb')
os.unlink('test_pdb_writing.pdb')
def test_pdb_writing(self):
"""Test writing of PDB files"""
# input parameter
pdbfile = self.get_input_file_name("mini.pdb")
fastafile = self.get_input_file_name("mini.fasta")
comps = ["P1", "P2", "P3"]
chains = "ABB"
colors = [0., 0.5, 1.0]
beadsize = 20
fastids = IMP.pmi.tools.get_ids_from_fasta_file(fastafile)
m = IMP.Model()
simo = IMP.pmi.representation.Representation(m)
simo.create_component(comps[0], color=colors[0])
simo.add_component_sequence(comps[0], fastafile, id=fastids[0])
simo.autobuild_model(comps[0], pdbfile, chains[0],
resolutions=[1], missingbeadsize=beadsize)
simo.setup_component_sequence_connectivity(comps[0], 1)
simo.create_component(comps[1], color=colors[1])
simo.add_component_sequence(comps[1], fastafile, id=fastids[1])
simo.autobuild_model(comps[1], pdbfile, chains[1],
resolutions=[10], missingbeadsize=beadsize)
simo.setup_component_sequence_connectivity(comps[1], 1)
simo.create_component(comps[2], color=colors[2])
simo.add_component_sequence(comps[2], fastafile, id=fastids[1])
simo.autobuild_model(comps[2], pdbfile, chains[2],
resolutions=[1,10], missingbeadsize=2)
simo.setup_component_sequence_connectivity(comps[2], 1)
output = IMP.pmi.output.Output()
output.init_pdb("test_pdb_writing.pdb", simo.prot)
output.write_pdbs()
output.init_pdb_best_scoring("test_pdb_writing", simo.prot, 10)
for i in range(20):
score = -float(i)
output.write_pdb_best_scoring(score)
for i in range(10):
os.unlink('test_pdb_writing.'+str(i)+'.pdb')
pdb_content='''ATOM 1 CA MET A 1 114.370 27.980 -26.088 1.00 3.07 C
ATOM 2 CA VAL A 2 114.370 27.980 -26.088 1.00 2.89 C
ATOM 3 CA GLY A 3 111.506 26.368 -28.075 1.00 2.27 C
ATOM 4 CA GLN A 4 113.468 23.113 -28.639 1.00 3.01 C
ATOM 5 CA GLN A 5 113.808 21.534 -32.168 1.00 3.01 C
ATOM 6 CA TYR A 6 116.743 22.770 -34.259 1.00 3.32 C
ATOM 7 CA SER A 7 116.626 25.161 -37.229 1.00 2.61 C
ATOM 8 CA SER A 8 119.165 25.590 -40.036 1.00 2.61 C
ATOM 9 CA BEA B 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 10 CA BEA B 4 68.799 58.791 50.131 1.00 3.69 C
ATOM 11 CA BEA B 7 68.799 58.791 50.131 1.00 4.76 C
ATOM 12 CA BEA C 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 13 CA ASP C 3 70.427 58.819 51.717 1.00 2.87 C
ATOM 14 CA GLU C 4 68.584 58.274 48.425 1.00 3.00 C
ATOM 15 CA BEA C 6 68.584 58.274 48.425 1.00 3.50 C
ATOM 16 CA BEA C 8 68.584 58.274 48.425 1.00 3.50 C
ATOM 17 CA THR C 9 68.584 58.274 48.425 1.00 2.80 C
ENDMDL'''.split("\n")
with open("test_pdb_writing.pdb") as f:
for nl, l in enumerate(f):
self.assertEqual(pdb_content[nl],l.rstrip('\r\n '))
os.unlink('test_pdb_writing.pdb')
def test_pdb_pmi2(self):
"""Test PDB writing in PMI2"""
mdl = IMP.Model()
pdb_file = self.get_input_file_name("mini.pdb")
fasta_file = self.get_input_file_name("mini.fasta")
seqs = IMP.pmi.topology.Sequences(fasta_file)
s = IMP.pmi.topology.System(mdl)
st = s.create_state()
molA = st.create_molecule("P1",seqs[0],chain_id='A')
aresA = molA.add_structure(pdb_file,chain_id='A',soft_check=True)
molA.add_representation(aresA,[1])
molA.add_representation(molA[:]-aresA,20)
molB = st.create_molecule("P2",seqs[1],chain_id='B')
aresB = molB.add_structure(pdb_file,chain_id='B',soft_check=True)
molB.add_representation(aresB,[10])
molB.add_representation(molB[:]-aresB,20)
molC = molB.create_copy(chain_id='C')
aresC = molC.add_structure(pdb_file,chain_id='B',soft_check=True)
molC.add_representation(aresC,[1,10])
molC.add_representation(molC[:]-aresC,2)
root_hier = s.build()
# write PDB and check it's ok
output = IMP.pmi.output.Output(atomistic=True)
output.init_pdb("test_pdb_writing.pdb", root_hier)
output.write_pdbs()
print('init best scoring')
output.init_pdb_best_scoring("test_pdb_writing", root_hier, 10)
print('scoring')
for i in range(20):
score = -float(i)
output.write_pdb_best_scoring(score)
pdb_content='''ATOM 1 CA MET A 1 114.370 27.980 -26.088 1.00 3.07 C
ATOM 2 CA VAL A 2 114.370 27.980 -26.088 1.00 2.89 C
ATOM 3 CA GLY A 3 111.506 26.368 -28.075 1.00 2.27 C
ATOM 4 CA GLN A 4 113.468 23.113 -28.639 1.00 3.01 C
ATOM 5 CA GLN A 5 113.808 21.534 -32.168 1.00 3.01 C
ATOM 6 CA TYR A 6 116.743 22.770 -34.259 1.00 3.32 C
ATOM 7 CA SER A 7 116.626 25.161 -37.229 1.00 2.61 C
ATOM 8 CA SER A 8 119.165 25.590 -40.036 1.00 2.61 C
ATOM 9 CA BEA B 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 10 CA BEA B 4 68.799 58.791 50.131 1.00 3.69 C
ATOM 11 CA BEA B 7 68.584 58.274 48.425 1.00 4.76 C
ATOM 12 CA BEA C 2 70.427 58.819 51.717 1.00 3.50 C
ATOM 13 CA ASP C 3 70.427 58.819 51.717 1.00 2.87 C
ATOM 14 CA GLU C 4 68.584 58.274 48.425 1.00 3.00 C
ATOM 15 CA BEA C 6 68.584 58.274 48.425 1.00 3.50 C
ATOM 16 CA BEA C 8 68.584 58.274 48.425 1.00 3.50 C
ATOM 17 CA THR C 9 68.584 58.274 48.425 1.00 2.80 C
ENDMDL'''.split("\n")
with open("test_pdb_writing.pdb") as f:
for nl, l in enumerate(f):
self.assertEqual(pdb_content[nl],l.rstrip('\r\n '))
with open("test_pdb_writing.0.pdb") as f:
for nl, l in enumerate(f):
self.assertEqual(pdb_content[nl],l.rstrip('\r\n '))
for i in range(10):
os.unlink('test_pdb_writing.'+str(i)+'.pdb')
os.unlink('test_pdb_writing.pdb')
simo.add_component_sequence("Rpb1", fastafile, id=fastids[0])
simo.autobuild_model("Rpb1", pdbfile, "A", resolutions=[1], beadsize=beadsize)
simo.setup_component_sequence_connectivity("Rpb1", 1)
simo.add_component_name("Rpb2", color=colors[1])
simo.add_component_sequence("Rpb2", fastafile, id=fastids[1])
simo.autobuild_model("Rpb2", pdbfile, "B", resolutions=[10], beadsize=beadsize)
simo.setup_component_sequence_connectivity("Rpb2", 1)
simo.add_component_name("Rpb3", color=colors[2])
simo.add_component_sequence("Rpb3", fastafile, id=fastids[2])
simo.autobuild_model("Rpb3", pdbfile, "C", resolutions=[0], beadsize=beadsize)
simo.setup_component_sequence_connectivity("Rpb3", 1)
simo.add_component_name("Rpb4", color=colors[3])
simo.add_component_sequence("Rpb4", fastafile, id=fastids[3])
simo.autobuild_model("Rpb4",
pdbfile,
"D",
resolutions=[0, 1],
beadsize=beadsize)
simo.setup_component_sequence_connectivity("Rpb4", 1)
output = IMP.pmi.output.Output()
output.init_pdb("test_pdb_writing.pdb", simo.prot)
output.write_pdbs()
output.init_pdb_best_scoring("test_pdb_writing", simo.prot, 10)
for i in range(20):
score = -float(i)
output.write_pdb_best_scoring(score)
simo.add_component_sequence("Rpb1", fastafile, id=fastids[0])
simo.autobuild_model("Rpb1", pdbfile, "A",
resolutions=[1], beadsize=beadsize)
simo.setup_component_sequence_connectivity("Rpb1", 1)
simo.add_component_name("Rpb2", color=colors[1])
simo.add_component_sequence("Rpb2", fastafile, id=fastids[1])
simo.autobuild_model("Rpb2", pdbfile, "B",
resolutions=[10], beadsize=beadsize)
simo.setup_component_sequence_connectivity("Rpb2", 1)
simo.add_component_name("Rpb3", color=colors[2])
simo.add_component_sequence("Rpb3", fastafile, id=fastids[2])
simo.autobuild_model("Rpb3", pdbfile, "C",
resolutions=[0], beadsize=beadsize)
simo.setup_component_sequence_connectivity("Rpb3", 1)
simo.add_component_name("Rpb4", color=colors[3])
simo.add_component_sequence("Rpb4", fastafile, id=fastids[3])
simo.autobuild_model("Rpb4", pdbfile, "D",
resolutions=[0, 1], beadsize=beadsize)
simo.setup_component_sequence_connectivity("Rpb4", 1)
output = IMP.pmi.output.Output()
output.init_pdb("test_pdb_writing.pdb", simo.prot)
output.write_pdbs()
output.init_pdb_best_scoring("test_pdb_writing", simo.prot, 10)
for i in range(20):
score = -float(i)
output.write_pdb_best_scoring(score)