def test_length_one_stems(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1byj.pdb',
intermediate_file_dir='tmp', remove_pseudoknots=False)
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/2QBZ.pdb',
intermediate_file_dir='tmp', remove_pseudoknots=False)
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
def test_from_mmcif(self):
import Bio.PDB as bpdb
cg = ftmc.from_pdb('test/forgi/threedee/data/1Y26.cif',
parser=bpdb.MMCIFParser())
cg2 = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
self.assertEqual(cg.defines, cg2.defines)
self.assertGreater(len(cg.defines), 3)
for d in cg.defines:
nptest.assert_almost_equal(cg.coords[d], cg2.coords[d])
def setUp(self):
pdbfile1 = "test/forgi/threedee/data/3FU2.pdb"
self.cg1 = ftmc.from_pdb(pdbfile1)
pdbfile2 = "test/forgi/threedee/data/3V2F.pdb" #Takes some time. Big structure
self.cg2 = ftmc.from_pdb(pdbfile2)
pdbfile3 = "test/forgi/threedee/data/1X8W.pdb"
self.cg3 = ftmc.from_pdb(pdbfile3)
pdbfile4 = "test/forgi/threedee/data/2QBZ.pdb"
self.cg4 = ftmc.from_pdb(pdbfile4)
def test_length_one_stems(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1byj.pdb',
intermediate_file_dir='tmp',
remove_pseudoknots=False)
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/2QBZ.pdb',
intermediate_file_dir='tmp',
remove_pseudoknots=False)
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
def main():
usage = """
usage
"""
num_args = 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
cg = ftmc.from_pdb(args[0])
angles = []
for loop in it.chain(cg.iloop_iterator(), cg.mloop_iterator()):
conn = cg.connections(loop)
(s1b, s1e) = cg.get_sides(conn[0], loop)
(s2b, s2e) = cg.get_sides(conn[1], loop)
angle = ftuv.vec_angle(
cg.coords[conn[0]][s1b] - cg.coords[conn[0]][s1e],
cg.coords[conn[1]][s2e] - cg.coords[conn[1]][s2b])
for rn in cg.define_residue_num_iterator(loop, adjacent=True):
angles += [(rn, angle)]
for rn, angle in sorted(angles):
print "{}:{}".format(rn, angle)
def test_angle_between_twists(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
self.verify_virtual_twist_angles(cg, 's0')
self.verify_virtual_twist_angles(cg, 's1')
self.verify_virtual_twist_angles(cg, 's2')
self.verify_virtual_twist_angles(cg, 's3')
def main():
usage = """
python interior_loop_angles.py pdb_file
Iterate over the interior loop angles and calculate how much of a kink
they introduce between the two adjacent stems.
"""
num_args = 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
cg = ftmc.from_pdb(op.expanduser(args[0]))
for iloop in cg.iloop_iterator():
conn = cg.connections(iloop)
angle = ftuv.vec_angle(cg.coords[conn[0]][1] - cg.coords[conn[0]][0],
cg.coords[conn[1]][1] - cg.coords[conn[1]][0])
fud.pv('iloop, angle')
def test_get_node_from_residue_num(self):
cg = cmc.from_pdb('test/forgi/threedee/data/1X8W.pdb',
intermediate_file_dir='tmp',
chain_id='A')
self.check_cg_integrity(cg)
elem_name = cg.get_node_from_residue_num(247, seq_id=True)
def main():
usage = """
./pdb_to_ss_fasta.py pdb_file
Take a pdb file, extract the secondary structure and print it out
as a fasta file like this:
>id
sequence
secondary structure
Where the id will be the part of the filename without the extension.
"""
num_args= 1
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-c', '--chain', dest='chain', default=None, help="Extract the secondary structure of a particular chain in the PDB file")
parser.add_option('-p', '--pseudoknots', dest='pseudoknots', default=False, action='store_true', help='Include pseudoknots?')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
#pdb_id = op.basename(op.splitext(args[0])[0])
cg = ftmc.from_pdb(args[0], chain_id=options.chain, remove_pseudoknots = not options.pseudoknots)
print cg.to_fasta_string()
def test_proj_longest_axis_vs_img_diameter(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_two_chains.pdb')
ref_proj = fpp.Projection2D(cg, [1., 1., 1. ], project_virtual_atoms=True)
ref_box=ref_proj.get_bounding_square(margin=30)
scale=ref_box[1]-ref_box[0]
ref_img, _=ref_proj.rasterize(70, bounding_square=ref_box, rotate=0)
self.assertAlmostEqual(ref_proj.longest_axis, fph.get_longest_img_diameter(ref_img, scale), places=-1)
def main():
usage = """
python loop_variation.py pdb_file|cg_file
Calculate how much the geometry of each loop-associated nucleotide can
vary based on the size of the loop that it is in.
Whether the input is a pdb or a cg file depends on the extension.
"""
num_args = 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
fn, fe = op.splitext(args[0])
if fe == '.cg':
cg = ftmc.CoarseGrainRNA(args[0])
else:
cg = ftmc.from_pdb(args[0])
angle_stats = ftms.get_angle_stats()
for loop in it.chain(cg.iloop_iterator(), cg.mloop_iterator()):
calculate_variation(angle_stats, cg.get_bulge_dimensions(loop))
def test_virtual_residue_atoms(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
ftug.add_virtual_residues(cg, 's1')
bases_to_test = []
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's0', 1, 0))
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's0', 2, 1))
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's1', 0, 0))
#Assert that any two atoms of the same base within reasonable distance to each other
#(https://en.wikipedia.org/wiki/Bond_length says than a CH-bond is >= 1.06A)
for va in bases_to_test:
for k1, v1 in va.items():
for k2, v2 in va.items():
dist = ftuv.magnitude(v1 - v2)
self.assertLess(dist,
30,
msg="Nucleotide too big: "
"Distance between {} and {} is {}".format(
k1, k2, dist))
if k1 != k2:
dist = ftuv.magnitude(v1 - v2)
self.assertGreater(
dist,
0.8,
msg="Nucleotide too small: "
"Distance between {} and {} is {}".format(
k1, k2, dist))
def test_get_angle_stats(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/2mis.pdb',
intermediate_file_dir='tmp')
for d in cg.defines:
if d[0] in "mi":
cg.get_bulge_angle_stats(d)
cg = ftmc.from_pdb('test/forgi/threedee/data/1byj.pdb')
for d in cg.defines:
if d[0] in "mi":
cg.get_bulge_angle_stats(d)
cg = ftmc.from_pdb('test/forgi/threedee/data/2QBZ.pdb')
for d in cg.defines:
if d[0] in "mi":
cg.get_bulge_angle_stats(d)
def test_get_node_from_residue_num(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1X8W.pdb',
intermediate_file_dir='tmp',
chain_id='A')
self.check_cg_integrity(cg)
elem_name = cg.get_node_from_residue_num(10)
self.assertEqual(elem_name, "f0")
def main():
usage = """
usage
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
cg = ftmc.from_pdb(args[0])
angles = []
for loop in it.chain(cg.iloop_iterator(), cg.mloop_iterator()):
conn = cg.connections(loop)
(s1b, s1e) = cg.get_sides(conn[0], loop)
(s2b, s2e) = cg.get_sides(conn[1], loop)
angle = ftuv.vec_angle(cg.coords[conn[0]][s1b] - cg.coords[conn[0]][s1e],
cg.coords[conn[1]][s2e] - cg.coords[conn[1]][s2b])
for rn in cg.define_residue_num_iterator(loop, adjacent=True):
angles += [(rn, angle)]
for rn, angle in sorted(angles):
print "{}:{}".format(rn, angle)
def test_first_virtual_res_basis(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
basis = ftug.virtual_res_basis(cg, "s0", 0)
nptest.assert_array_equal(
basis,
ftuv.create_orthonormal_basis(
cg.coords["s0"][1] - cg.coords["s0"][0], cg.twists["s0"][0]))
def main():
usage = """
python loop_variation.py pdb_file|cg_file
Calculate how much the geometry of each loop-associated nucleotide can
vary based on the size of the loop that it is in.
Whether the input is a pdb or a cg file depends on the extension.
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
fn, fe = op.splitext(args[0])
if fe == '.cg':
cg = ftmc.CoarseGrainRNA(args[0])
else:
cg = ftmc.from_pdb(args[0])
angle_stats = ftms.get_angle_stats()
for loop in it.chain(cg.iloop_iterator(), cg.mloop_iterator()):
calculate_variation(angle_stats, cg.get_bulge_dimensions(loop))
def test_define_residue_num_iterator(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/2mis.pdb', intermediate_file_dir='tmp')
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
self.assertEqual(list(cg.define_range_iterator('i0', adjacent=True, seq_ids=True)),
[[(' ', 6, ' '), (' ', 10, ' ')], [(' ', 19, ' '), (' ', 21, ' ')]])
def main():
usage = """
python interior_loop_angles.py pdb_file
Iterate over the interior loop angles and calculate how much of a kink
they introduce between the two adjacent stems.
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
cg = ftmc.from_pdb(op.expanduser(args[0]))
for iloop in cg.iloop_iterator():
conn = cg.connections(iloop)
angle = ftuv.vec_angle(cg.coords[conn[0]][1] - cg.coords[conn[0]][0], cg.coords[conn[1]][1] - cg.coords[conn[1]][0])
fud.pv('iloop, angle')
def test_plot(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_two_chains.pdb')
for dire in [(1., 0., 0.), (0., 0., 1.), (0., 1., 0.), (1., 1., 0.),
(1., 0., 1.), (0., 1., 1.), (1., 1., 1.)]:
self.proj = fpp.Projection2D(cg, dire)
self.proj.condense_points(1)
self.proj.plot(show=True, add_labels=True)
def test_virtual_residue_atom_exact_match(self):
#This test serves to detect unwanted changes in the virtual atom calculation algorithm.
#It is allowed to fail, if the virtual atom calculation changes.
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
vres= ftug.virtual_residue_atoms(cg, 's0', 1, 0)
nptest.assert_allclose(vres['C8'], np.array([ 5.60052258, -2.31817798, -2.74075904]))
nptest.assert_allclose(vres['N2'], np.array([ 7.27932017, 2.84403948, -2.83806392]))
def test_get_loop_stat(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/2mis.pdb', intermediate_file_dir='tmp')
cg.get_loop_stat("h0")
cg = ftmc.CoarseGrainRNA('test/forgi/threedee/data/4GXY_A.cg')
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
cg.get_loop_stat('h3')
def test_angle_between_twists(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb',
dissolve_length_one_stems=False)
self.verify_virtual_twist_angles(cg, 's0')
self.verify_virtual_twist_angles(cg, 's1')
self.verify_virtual_twist_angles(cg, 's2')
self.verify_virtual_twist_angles(cg, 's3')
def test_get_loop_stat(self):
cg = cmc.from_pdb('test/forgi/threedee/data/2mis.pdb',
intermediate_file_dir='tmp')
cg.get_loop_stat("h0")
cg = ftmc.CoarseGrainRNA('test/forgi/threedee/data/4GXY_A.cg')
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
cg.get_loop_stat('h3')
def test_proj_longest_axis_vs_img_diameter(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_two_chains.pdb')
ref_proj = fpp.Projection2D(
cg, [1., 1., 1.], project_virtual_atoms=True)
ref_box = ref_proj.get_bounding_square(margin=30)
scale = ref_box[1] - ref_box[0]
ref_img, _ = ref_proj.rasterize(70, bounding_square=ref_box, rotate=0)
self.assertAlmostEqual(
ref_proj.longest_axis, fph.get_longest_img_diameter(ref_img, scale), places=-1)
def test_total_length(self):
cg = ftmc.CoarseGrainRNA('test/forgi/threedee/data/1y26.cg')
self.assertEqual(cg.total_length(), cg.seq_length)
cg = ftmc.from_pdb('test/forgi/threedee/data/2X1F.pdb')
self.assertEqual(cg.total_length(), cg.seq_length)
cg = ftmc.CoarseGrainRNA()
cg.from_dotbracket('..((..((...))..))..((..))..')
self.assertEqual(cg.total_length(), cg.seq_length)
self.assertEqual(cg.total_length(), 27)
def test_from_pdb(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/4GV9.pdb', chain_id='E')
cg = ftmc.from_pdb('test/forgi/threedee/data/RS_363_S_5.pdb')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/RS_118_S_0.pdb',
intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
self.assertTrue(len(cg.defines) > 1)
cg = ftmc.from_pdb('test/forgi/threedee/data/ideal_1_4_5_8.pdb',
intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/ideal_1_4_5_8.pdb',
intermediate_file_dir=None)
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_missing.pdb',
intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_two_chains.pdb',
intermediate_file_dir='tmp',
chain_id='Y')
self.assertEqual(len(cg.defines), 1)
self.assertIn("f0", cg.defines)
self.assertEqual(cg.seq, "U")
cg = ftmc.from_pdb('test/forgi/threedee/data/1X8W.pdb',
intermediate_file_dir='tmp',
chain_id='A')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/1FJG_reduced.pdb',
intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb',
intermediate_file_dir='tmp')
for d in cg.defines:
for r in cg.define_residue_num_iterator(d):
# make sure all the seq_ids are there
print(cg.seq_ids[r - 1])
def test_init_projection(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/2X1F.pdb')
proj = fpp.Projection2D(cg, [1., 1., 1.])
self.assertTrue(
ftuv.is_almost_colinear(proj.proj_direction, np.array([1., 1.,
1.])),
msg=
"The projection direction was not stored correctly. Should be coliniar"
" with {}, got {}".format(np.array([1., 1., 1.]),
proj.proj_direction))
def test_define_residue_num_iterator(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/2mis.pdb',
intermediate_file_dir='tmp')
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
self.assertEqual(
list(cg.define_range_iterator('i0', adjacent=True, seq_ids=True)),
[[(' ', 6, ' '), (' ', 10, ' ')], [(' ', 19, ' '),
(' ', 21, ' ')]])
def setUp(self):
self.rs_random_281=ftmc.from_pdb('test/forgi/threedee/data/RS_random_281_S_0.pdb')
for key in self.rs_random_281.defines.keys():
if key[0] =="s":
ftug.add_virtual_residues(self.rs_random_281, key)
self.minimal_multiloop = ftmc.CoarseGrainRNA()
self.minimal_multiloop.from_file('test/forgi/threedee/data/minimal_multiloop.cg')
for key in self.minimal_multiloop.defines.keys():
if key[0] =="s":
ftug.add_virtual_residues(self.minimal_multiloop, key)
def setUp(self):
self.rs_random_281=ftmc.from_pdb('test/forgi/threedee/data/RS_random_281_S_0.pdb')
for key in self.rs_random_281.defines.keys():
if key[0] =="s":
ftug.add_virtual_residues(self.rs_random_281, key)
self.minimal_multiloop = ftmc.CoarseGrainRNA()
self.minimal_multiloop.from_file('test/forgi/threedee/data/minimal_multiloop.cg')
for key in self.minimal_multiloop.defines.keys():
if key[0] =="s":
ftug.add_virtual_residues(self.minimal_multiloop, key)
def test_virtual_residue_atom_exact_match(self):
#This test serves to detect unwanted changes in the virtual atom calculation algorithm.
#It is allowed to fail, if the virtual atom calculation changes.
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
vres = ftug.virtual_residue_atoms(cg, 's0', 1, 0)
nptest.assert_allclose(vres['C8'],
np.array([5.23455929, -2.9606417, -2.18156476]))
nptest.assert_allclose(vres['N2'],
np.array([6.99285237, 2.32505693, -1.95868568]))
def test_pseudoknot(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1YMO.pdb', intermediate_file_dir='tmp')
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
cg = ftmc.CoarseGrainRNA('test/forgi/threedee/data/3D0U_A.cg')
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
cg.traverse_graph()
self.assertEqual(cg.get_angle_type("i3"), 1)
def test_pseudoknot(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1ymo.pdb',
intermediate_file_dir='tmp')
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
cg = ftmc.CoarseGrainRNA('test/forgi/threedee/data/3D0U_A.cg')
self.check_graph_integrity(cg)
self.check_cg_integrity(cg)
cg.traverse_graph()
self.assertEqual(cg.get_angle_type("i3"), 1)
def test_multiple_chain_to_cg(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/4GV9.pdb', chain_id='all')
log.debug("======= FIRST IS LOADED =========")
cg_str = cg.to_cg_string()
log.debug("\n" + cg_str)
print(cg_str)
cg2 = ftmc.CoarseGrainRNA()
cg2.from_cg_string(cg_str)
self.assertEqual(cg.defines, cg2.defines)
self.assertAlmostEqual(ftme.cg_rmsd(cg, cg2),
0) #This only looks at stems
self.assertEqual(cg.backbone_breaks_after, cg2.backbone_breaks_after)
cg = ftmc.from_pdb('test/forgi/threedee/data/3CQS.pdb', chain_id='all')
cg.log(logging.WARNING)
cg_str = cg.to_cg_string()
cg2 = ftmc.CoarseGrainRNA()
cg2.from_cg_string(cg_str)
self.assertEqual(cg.defines, cg2.defines)
self.assertAlmostEqual(ftme.cg_rmsd(cg, cg2),
0) #This only looks at stems
self.assertEqual(cg.backbone_breaks_after, cg2.backbone_breaks_after)
def main():
usage = """
./pdb_to_cg_fasta.py pdb_file
Take a pdb file, extract the secondary structure and print it out
as a fasta file like this:
>id
sequence
secondary structure
Where the id will be the part of the filename without the extension.
"""
num_args = 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-p',
'--pseudoknots',
dest='pseudoknots',
default=False,
help='Keep pseudoknots in the structure',
action='store_true')
parser.add_option('-d',
'--dump-all',
dest='dump_all',
default=None,
help='Enter a directory where to dump all of \
temporary and intermediate files.',
type='str')
parser.add_option('-c',
'--chain',
dest='chain',
default=None,
help='Specify the chain to coarse-grain',
type='str')
(options, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
sys.exit(1)
pdb_id = op.basename(op.splitext(args[0])[0])
cg = ftmc.from_pdb(args[0],
intermediate_file_dir=options.dump_all,
remove_pseudoknots=not options.pseudoknots,
chain_id=options.chain)
print cg.to_cg_string()
def test_get_longest_img_diameter_resolution_invariant(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_two_chains.pdb')
ref_proj = fpp.Projection2D(cg, [1., 1., 1. ], project_virtual_atoms=True)
ref_box=ref_proj.get_bounding_square(margin=30)
scale=ref_box[1]-ref_box[0]
img1, _=ref_proj.rasterize(70, bounding_square=ref_box, rotate=0)
img2, _=ref_proj.rasterize(40, bounding_square=ref_box, rotate=0)
img3, _=ref_proj.rasterize(60, bounding_square=ref_box, rotate=10)
d1 = fph.get_longest_img_diameter(img1, scale)
d2 = fph.get_longest_img_diameter(img2, scale)
d3 = fph.get_longest_img_diameter(img3, scale)
self.assertAlmostEqual(d1, d2, places=-1 )
self.assertAlmostEqual(d1, d3, places=-1 )
self.assertAlmostEqual(d3, d2, places=-1 )
def test_basis_transformation_for_virtual_residues(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
offset=cg.vposs["s0"][0]
vbasis=cg.vbases["s0"][0]
local_pos=np.array([0,0,1])
global_pos = np.dot(vbasis.transpose(), local_pos) + offset
#Checking dimensions of vectors, just in case...
self.assertEqual(len(global_pos),3)
self.assertEqual(len(vbasis),3)
self.assertEqual(len(vbasis[0]),3)
#Analytically true:
self.assertTrue(all(global_pos[x]-vbasis[2][x]-offset[x]<0.0000001 for x in [0,1,2]),
msg="global pos for (0,0,1) should be {}+{}={}, but is {} instead.".format(
vbasis[2], offset, vbasis[2]+offset, global_pos))
def test_get_longest_img_diameter_resolution_invariant(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_two_chains.pdb')
ref_proj = fpp.Projection2D(
cg, [1., 1., 1.], project_virtual_atoms=True)
ref_box = ref_proj.get_bounding_square(margin=30)
scale = ref_box[1] - ref_box[0]
img1, _ = ref_proj.rasterize(70, bounding_square=ref_box, rotate=0)
img2, _ = ref_proj.rasterize(40, bounding_square=ref_box, rotate=0)
img3, _ = ref_proj.rasterize(60, bounding_square=ref_box, rotate=10)
d1 = fph.get_longest_img_diameter(img1, scale)
d2 = fph.get_longest_img_diameter(img2, scale)
d3 = fph.get_longest_img_diameter(img3, scale)
self.assertAlmostEqual(d1, d2, places=-1)
self.assertAlmostEqual(d1, d3, places=-1)
self.assertAlmostEqual(d3, d2, places=-1)
def test_from_pdb(self):
cg = cmc.from_pdb('test/forgi/threedee/data/RS_363_S_5.pdb')
self.check_cg_integrity(cg)
cg = cmc.from_pdb('test/forgi/threedee/data/1ymo.pdb',
intermediate_file_dir='tmp',
remove_pseudoknots=False)
self.check_cg_integrity(cg)
node = cg.get_node_from_residue_num(25)
self.assertFalse(node[0] == 'h')
cg = cmc.from_pdb('test/forgi/threedee/data/RS_118_S_0.pdb',
intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
self.assertTrue(len(cg.defines) > 1)
cg = cmc.from_pdb('test/forgi/threedee/data/ideal_1_4_5_8.pdb',
intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
cg = cmc.from_pdb('test/forgi/threedee/data/ideal_1_4_5_8.pdb',
intermediate_file_dir=None)
cg = cmc.from_pdb('test/forgi/threedee/data/1y26_missing.pdb',
intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
cg = cmc.from_pdb('test/forgi/threedee/data/1y26_two_chains.pdb',
intermediate_file_dir='tmp',
chain_id='Y')
self.check_cg_integrity(cg)
cg = cmc.from_pdb('test/forgi/threedee/data/1X8W.pdb',
intermediate_file_dir='tmp',
chain_id='A')
self.check_cg_integrity(cg)
cg = cmc.from_pdb('test/forgi/threedee/data/1FJG_reduced.pdb',
intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
def test_basis_transformation_for_virtual_residues(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
offset=cg.vposs["s0"][0]
vbasis=cg.vbases["s0"][0]
local_pos=np.array([0,0,1])
global_pos = np.dot(vbasis.transpose(), local_pos) + offset
#Checking dimensions of vectors, just in case...
self.assertEqual(len(global_pos),3)
self.assertEqual(len(vbasis),3)
self.assertEqual(len(vbasis[0]),3)
#Analytically true:
self.assertTrue(all(global_pos[x]-vbasis[2][x]-offset[x]<0.0000001 for x in [0,1,2]),
msg="global pos for (0,0,1) should be {}+{}={}, but is {} instead.".format(
vbasis[2], offset, vbasis[2]+offset, global_pos))
def test_coordinates_for_add_virtual_residues(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
#XYZ coordinate for first residue are ok:
self.assertAlmostEqual(cg.vposs["s0"][0][0], 2.3, delta=3,
msg="Wrong x-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][0]))
self.assertAlmostEqual(cg.vposs["s0"][0][1], 1.3, delta=3,
msg="Wrong y-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][1]))
self.assertAlmostEqual(cg.vposs["s0"][0][2], 1.0, delta=3,
msg="Wrong z-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][2]))
last_residue=cg.stem_length("s0") - 1
self.assertAlmostEqual(cg.vposs["s0"][last_residue][0], 16, delta=4,
msg="Wrong x-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][0]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][1], -13, delta=4,
msg="Wrong y-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][1]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][2], 8, delta=4,
msg="Wrong z-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][2]))
def test_coordinates_for_add_virtual_residues(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
#XYZ coordinate for first residue are ok:
self.assertAlmostEqual(cg.vposs["s0"][0][0], 2.3, delta=3,
msg="Wrong x-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][0]))
self.assertAlmostEqual(cg.vposs["s0"][0][1], 1.3, delta=3,
msg="Wrong y-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][1]))
self.assertAlmostEqual(cg.vposs["s0"][0][2], 1.0, delta=3,
msg="Wrong z-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][2]))
last_residue=cg.stem_length("s0") - 1
self.assertAlmostEqual(cg.vposs["s0"][last_residue][0], 16, delta=4,
msg="Wrong x-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][0]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][1], -13, delta=4,
msg="Wrong y-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][1]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][2], 8, delta=4,
msg="Wrong z-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][2]))
def test_traverse_and_build(self):
return
sm = fbm.SpatialModel(self.cg, conf_stats=self.conf_stats)
sm.sample_stats()
sm.traverse_and_build()
cg = ftmc.CoarseGrainRNA('test/fess/data/1ymo_pk.cg')
sm = fbm.SpatialModel(cg, conf_stats=self.conf_stats)
sm.sample_stats()
sm.traverse_and_build()
sm.bg.to_file('temp1.cg')
#pseudoknot
cg = ftmc.CoarseGrainRNA(op.expanduser('~/doarse/4LVV_A/temp.cg'))
cg = ftmc.from_pdb(op.expanduser('~/doarse/4LVV_A/temp.pdb'),
remove_pseudoknots=False)
sm = fbm.SpatialModel(cg, conf_stats=self.conf_stats)
sm.sample_stats()
sm.traverse_and_build()
def main():
usage = """
./pdb_to_cg_fasta.py pdb_file
Take a pdb file, extract the secondary structure and print it out
as a fasta file like this:
>id
sequence
secondary structure
Where the id will be the part of the filename without the extension.
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-p', '--pseudoknots', dest='pseudoknots', default=False,
help='Keep pseudoknots in the structure',
action='store_true')
parser.add_option('-d', '--dump-all', dest='dump_all',
default=None, help='Enter a directory where to dump all of \
temporary and intermediate files.',
type = 'str')
parser.add_option('-c', '--chain', dest='chain',
default=None, help='Specify the chain to coarse-grain',
type = 'str')
(options, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
sys.exit(1)
pdb_id = op.basename(op.splitext(args[0])[0])
cg = ftmc.from_pdb(args[0], intermediate_file_dir=options.dump_all,
remove_pseudoknots=not options.pseudoknots,
chain_id = options.chain)
print cg.to_cg_string()
def test_virtual_residue_atoms(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
ftug.add_virtual_residues(cg, 's1')
bases_to_test=[]
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's0', 1, 0))
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's0', 2, 1))
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's1', 0, 0))
#Assert that any two atoms of the same base within reasonable distance to each other
#(https://en.wikipedia.org/wiki/Bond_length says than a CH-bond is >= 1.06A)
for va in bases_to_test:
for k1, v1 in va.items():
for k2, v2 in va.items():
dist=ftuv.magnitude(v1-v2)
self.assertLess(dist, 30, msg="Nucleotide too big: "
"Distance between {} and {} is {}".format(k1, k2, dist))
if k1!=k2:
dist=ftuv.magnitude(v1-v2)
self.assertGreater(dist, 0.8, msg="Nucleotide too small: "
"Distance between {} and {} is {}".format(k1, k2, dist))
def get_cg_from_pdb(pdb_file, chain_id, temp_dir=None, cg_filename=None):
'''
Get a BulgeGraph from a pdb file.
@param pdb_file: The filename of the pdb file
@param chain_id: The chain within the file for which to load the BulgeGraph.
'''
if temp_dir is not None:
temp_dir = op.join(temp_dir, 'cg_temp')
print("Creating CG RNA for:", pdb_file, file=sys.stderr)
cg = ftmc.from_pdb(pdb_file, chain_id=chain_id,
intermediate_file_dir=temp_dir,
remove_pseudoknots=False)
if cg_filename is not None:
if not op.exists(op.dirname(cg_filename)):
os.makedirs(op.dirname(cg_filename))
with open(cg_filename, 'w') as f:
f.write(cg.to_cg_string())
#print >>sys.stderr, "Loading cg representation from pdb:", pdb_file, "chain id:", chain_id
return cg
def main():
usage = """
python average_atom_positions.py file1.pdb file2.pdb ...
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-a', '--all', dest='all_entries', default=False, action='store_true', help='Store all positions')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
poss = c.defaultdict(list)
sources = c.defaultdict(list)
for i,arg in enumerate(args):
cg = ftmc.from_pdb(arg)
for d in cg.defines.keys():
origin, basis = ftug.element_coord_system(cg, d)
if d[0] == 'i' or d[0] == 'm':
conn = cg.connections(d)
conn_type = cg.connection_type(d, conn)
else:
conn_type = 0
for i, r in it.izip(it.count(),
cg.define_residue_num_iterator(d)):
# add only the base atoms which are relevant to the calculation
# of the chi torsion angle
resname = cg.chain[r].resname.strip()
atoms = ftup.nonsidechain_atoms + ftup.chi_torsion_atoms[resname][-2:]
for aname in atoms:
try:
a = cg.chain[r][aname]
except KeyError as ke:
# missing an atom
continue
# The C1'->B1 and B1->B2 vectors define the plane of the base
# The O4'->C1'->B1->B2 sequence defines the torsion
# angle chi
if aname == ftup.chi_torsion_atoms[resname][-2]:
aname = 'B1'
elif aname == ftup.chi_torsion_atoms[resname][-1]:
aname = 'B2'
avec = a.get_vector().get_array()
atom_pos = ftuv.change_basis(avec - origin, basis, ftuv.standard_basis)
identifier = "%s %s %d %d %s" % (d[0],
" ".join(map(str, cg.get_node_dimensions(d))),
conn_type,
i, aname)
poss[identifier] += [atom_pos]
sources[identifier] += [d]
print "import collections as co"
if options.all_entries:
print "all_atom_poss = dict()"
for key in poss.keys():
print 'all_atom_poss["%s"] = [%s] #%d' % (key,
",".join(["[%s]" % (",".join(map(str, pos))) for pos in poss[key]]), len(poss[key]))
else:
print "avg_atom_poss = dict()"
for key in poss.keys():
pos = np.mean(poss[key], axis=0)
print 'avg_atom_poss["%s"] = [%s] #%d' % (key, ",".join(map(str, pos)), len(poss[key]))
print "sources = dict()"
for key in sources.keys():
print 'sources["%s"] = [%s]' % (key, ",".join(sources[key]))
def setUp(self):
self.cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_two_chains.pdb')
self.ref_proj = fpp.Projection2D(self.cg, [1., 1., 1. ], project_virtual_atoms=True)
self.ref_proj_na = fpp.Projection2D(self.cg, [1., 1., 1. ], project_virtual_atoms=False)
def test_from_pdb(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/4GV9.pdb', chain_id='E')
cg = ftmc.from_pdb('test/forgi/threedee/data/RS_363_S_5.pdb')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/1ymo.pdb',
intermediate_file_dir='tmp',
remove_pseudoknots=False)
self.check_cg_integrity(cg)
node = cg.get_node_from_residue_num(25)
self.assertFalse(node[0] == 'h')
cg = ftmc.from_pdb('test/forgi/threedee/data/RS_118_S_0.pdb', intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
self.assertTrue(len(cg.defines) > 1)
cg = ftmc.from_pdb('test/forgi/threedee/data/ideal_1_4_5_8.pdb', intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/ideal_1_4_5_8.pdb', intermediate_file_dir=None)
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_missing.pdb', intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26_two_chains.pdb',
intermediate_file_dir='tmp', chain_id='Y')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/1X8W.pdb',
intermediate_file_dir='tmp', chain_id='A')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/1FJG_reduced.pdb',
intermediate_file_dir='tmp')
self.check_cg_integrity(cg)
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb',
intermediate_file_dir='tmp')
for d in cg.defines:
for r in cg.define_residue_num_iterator(d):
# make sure all the seq_ids are there
print (cg.seq_ids[r - 1])
def test_from_mmcif(self):
import Bio.PDB as bpdb
cg = ftmc.from_pdb('test/forgi/threedee/data/1Y26.cif', parser=bpdb.MMCIFParser())
def main():
usage = """
python average_atom_positions.py file1.pdb file2.pdb ...
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-p', '--pseudoknots', dest='pseudoknots', default=False, action='store_true', help='Allow pseudoknots in the CG structure')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
poss = c.defaultdict(list)
sources = c.defaultdict(list)
for i,arg in enumerate(args):
cg = ftmc.from_pdb(arg, remove_pseudoknots=not options.pseudoknots)
if len(list(cg.stem_iterator())) == 0:
print >>sys.stderr, "skipping {}: no stems".format(arg)
continue
for d in cg.defines.keys():
if np.allclose(cg.coords[d][0], cg.coords[d][1]):
print >>sys.stderr, "File {}: Degenerate coordinates for element: {}".format(i, d)
continue
origin, basis = ftug.element_coord_system(cg, d)
if d[0] == 'i' or d[0] == 'm':
conn = cg.connections(d)
conn_type = cg.connection_type(d, conn)
else:
conn_type = 0
for i, r in it.izip(it.count(),
cg.define_residue_num_iterator(d)):
# add only the base atoms which are relevant to the calculation
# of the chi torsion angle
resname = cg.chain[cg.seq_ids[r-1]].resname.strip()
if resname not in ftup.chi_torsion_atoms.keys():
print >>sys.stderr, "Unknown nucleotide name:", resname
continue
atoms = ftup.nonsidechain_atoms + ftup.chi_torsion_atoms[resname][-2:]
scatoms=ftup.side_chain_atoms[resname]
for aname in atoms+scatoms:
try:
a = cg.chain[cg.seq_ids[r-1]][aname]
except KeyError as ke:
# missing an atom
continue
# The C1'->B1 and B1->B2 vectors define the plane of the base
# The O4'->C1'->B1->B2 sequence defines the torsion
# angle chi
if aname == ftup.chi_torsion_atoms[resname][-2]:
aname = 'B1'
elif aname == ftup.chi_torsion_atoms[resname][-1]:
aname = 'B2'
elif aname in scatoms:
aname=resname+"."+aname
avec = a.get_vector().get_array()
atom_pos = ftuv.change_basis(avec - origin, basis, ftuv.standard_basis)
identifier = "%s %s %d %d %s" % (d[0],
" ".join(map(str, cg.get_node_dimensions(d))),
conn_type,
i, aname)
poss[identifier] += [atom_pos]
sources[identifier] += [d]
print "{}:{}".format(identifier, ",".join(map(str, atom_pos)))
def test_add_loop_information_from_pdb_chain(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1A34.pdb')
def test_angle_between_twists(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
self.verify_virtual_twist_angles(cg, 's2')
self.verify_virtual_twist_angles(cg, 's0')
def test_get_node_from_residue_num(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1X8W.pdb',
intermediate_file_dir='tmp', chain_id='A')
self.check_cg_integrity(cg)
elem_name = cg.get_node_from_residue_num(247, seq_id=True)
def main():
usage = """
python disturb_multiloop.py
Add (default) or remove a basepair from a random multiloop in the fast file.
Print out the resulting structure. An input file must be specified using
one of the options (fasta or pdb).
"""
num_args = 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
parser.add_option('-p', '--pdb', dest='pdb', default='',
help='PDB File to use as input.', type='str')
parser.add_option('-f', '--fasta', dest='fasta', default='',
help='Fasta file to use as input.', type='str')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
bg = None
filename = ''
if len(options.fasta) > 0:
filename = options.fasta
with open(options.fastq, 'r'):
lines = bg.readlines()
bg = cgb.BulgeGraph()
bg.from_fasta("".join(lines), False)
elif len(options.pdb) > 0:
filename = options.pdb
cg = cmc.from_pdb(options.pdb)
bg = cg.bg
if bg is None:
parser.print_help()
sys.exit(1)
pdb_id = op.basename(op.splitext(filename)[0])
print ">%s" % (pdb_id)
print bg.seq
print bg.to_dotbracket_string()
multiloops = bg.find_multiloop_loops()
for multi in multiloops:
shortened = set()
for m in [d for d in multi if d[0] == 'm']:
connected_stems = list(bg.edges[m])
for to_shorten in connected_stems:
if to_shorten in shortened:
continue
shortened.add(to_shorten)
# find the stems which are connected to this multiloop
# and pick a random one
db = list(bg.to_dotbracket_string())
# get the side of the stem which is connected to the
# multiloop
(s1b, s1e) = bg.get_sides(to_shorten, m)
#print to_shorten, s1b, "(", bg.defines[to_shorten], ")"
# the nucleotides that need to be changed
to_change = bg.get_side_nucleotides(to_shorten, s1b)
#print bg.defines[to_shorten], to_change
db[to_change[0] - 1] = '.'
db[to_change[1] - 1] = '.'
print "".join(db)
import Bio.PDB as bpdb
import sys
import itertools as it
import forgi.graph.bulge_graph as cgb
import forgi.threedee.model.coarse_grain as cmc
# load the pdb structure
s = bpdb.PDBParser().get_structure('blah', sys.argv[1])
# load a bulge-graph representation
m = cmc.from_pdb(sys.argv[1])
bg = m.bg
# little function to see if a given residue number corresponds
# to a particular named element of the bulge graph
def is_inelement(bg, element, resnum):
d = bg.defines[element]
for i in range(0, len(d), 2):
if resnum > d[i] and resnum < d[i+1]:
return True
return False
# take only the C1' atom of the structure and make sure it's not in
# the fiveprime or threeprime element
atoms = [a for a in bpdb.Selection.unfold_entities(s, 'A') if (a.name == "C1'" and not is_inelement(bg, 'f1', a.parent.id[1]) and not is_inelement(bg, 't1', a.parent.id[1]))]
def main():
usage = './bounding_box_coords.py temp.pdb [temp2.pdb ...]'
usage += "Print out the positions of the atoms in coordinates "
usage += "respective to the virtual residue coordinate system."
parser = OptionParser()
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
parser.add_option('-e', '--edge', dest='edge', default=True, action='store_true', help='Include the edge nucleotides in the statistics.')
parser.add_option('-p', '--pymol', dest='pymol', default=False, action='store_true', help='Output in pymol cgo format.')
parser.add_option('-a', '--averages', dest='averages', default=False, action='store_true', help='Output the average coordinates')
parser.add_option('-r', '--residue', dest='residue', default='AUGC', help="The type of residue to calculate the averages for.", type='str')
(options, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
sys.exit(1)
all_coords = [co.defaultdict(list),
co.defaultdict(list)]
pp = cvp.PymolPrinter()
pp.draw_axes = True
for pdbfile in args:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
chain = list(bp.PDBParser().get_structure('temp', pdbfile).get_chains())[0]
bg = ttmc.from_pdb(pdbfile)
for s in bg.stem_iterator():
for i in range(bg.stem_length(s)):
if i == 0 or i == bg.stem_length(s) - 1:
if not options.edge:
continue
(origin, basis, coords) = cgg.stem_vres_reference_atoms(bg, chain, s, i)
# subtract one because the sequence is 0-based
(p1, p2) = (bg.defines[s][0] + i - 1, bg.defines[s][3] - i - 1)
(r1, r2) = (bg.seq[p1], bg.seq[p2])
all_coords[0][r1] += [coords[0]]
all_coords[1][r2] += [coords[1]]
'''
if options.pymol:
if not options.averages:
add_pymol_coords(coords)
else:
print_atom_positions(coords)
'''
if options.averages:
if options.pymol:
print_average_atom_positions(all_coords, list(options.residue), pp)
pp.output_pymol_file()
else:
print_average_atom_positions(all_coords, list(options.residue), None)
else:
for i, c in enumerate(all_coords):
for k in c.keys():
for coords in c[k]:
for atom in coords.keys():
print i, k, atom, " ".join(map(str, coords[atom]))
def test_get_angle_stats(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/2mis.pdb', intermediate_file_dir='tmp')
cg.get_bulge_angle_stats("i0")
def test_small_molecule(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/2X1F.pdb')
self.assertTrue('f1' in cg.coords)
