def test_superimposer_atoms():
from Bio.PDB.PDBParser import PDBParser
code = '1ptq'
fileName = testFilePath + code + '.pdb'
fixedS = PDBParser().get_structure(code, fileName)
movingS = PDBParser().get_structure(code, fileName)
# TODO transform moving
sup = Superimposer()
sup.set_atoms(list(fixedS.get_atoms()), list(movingS.get_atoms()))
assert sup.rms == approx(0.)
return
def test_compare():
"""
Compare the result of the diSTruct superimposer to the biopython one.
"""
from Bio import SeqIO
from Bio.PDB import Superimposer as BPSuperimposer
from Bio.PDB import PDBParser
from distruct.tools.pdb import get_contacts
code = '1ptq'
fileName = testFilePath + code + '.pdb'
refStructure = PDBParser().get_structure(code, fileName)
contacts = get_contacts(refStructure[0], cutOff=5., minSeqDist=0)
sequences = []
with open(fileName, 'r') as f:
sequences = [r.seq for r in SeqIO.parse(f, "pdb-seqres")]
pass
ds = Distructure('test', sequences,
[[r.get_id() for r in c if r.get_id()[0] == ' ']
for c in refStructure[0]])
ds.generate_primary_contacts()
ds.set_tertiary_contacts(contacts)
ds.run()
refStructure = PDBParser().get_structure(code, fileName)
tempStructure = ds.copy()
refAtoms = list(cull_atoms(refStructure.get_atoms(), ds))
resAtoms = list(cull_atoms(tempStructure.get_atoms(), refStructure))
assert len(refAtoms) > 3
assert len(refAtoms) == len(resAtoms)
dssup = Superimposer()
dssup.set_atoms(refAtoms, resAtoms)
dsRMSD = dssup.rms
bpsup = BPSuperimposer()
bpsup.set_atoms(refAtoms, resAtoms)
bpRMSD = bpsup.rms
for atom in resAtoms:
atom.set_coord(-1 * atom.get_coord())
pass
bpsup.set_atoms(refAtoms, resAtoms)
if bpsup.rms < bpRMSD:
bpRMSD = bpsup.rms
pass
assert dsRMSD == approx(bpRMSD)
return
if pdb_match:
PDB = pdb_match.group(1)
pdb_biomol_match = re.search(PDB_BIOMOL_REGEX, INPUT_FILENAME)
if pdb_biomol_match:
PDB = pdb_biomol_match.group(1)
BIOMOL_ID = pdb_biomol_match.group(2)
pdb_rcsb_asm_match = re.search(PDB_RCSB_ASM_REGEX, INPUT_FILENAME)
if pdb_rcsb_asm_match:
PDB = pdb_rcsb_asm_match.group(1)
BIOMOL_ID = pdb_rcsb_asm_match.group(2)
# LOAD STRUCTURE
structure = PDBParser().get_structure('structure', INPUT_FILE)
structure_atoms = list(structure.get_atoms())
logging.info('Loaded PDB structure (BioPython).')
# CONSTRUCT KDTREE
neighborsearch = NeighborSearch(structure_atoms)
logging.info('Constructured NeighborSearch.')
# GET INTERACTIONS
logging.info('Calculating interactions...')
for interaction_level in 'ARC':
if interaction_level in OUTPUTS:
logging.info('Calculating interactions for {}s...'.format(
if pdb_match:
PDB = pdb_match.group(1)
pdb_biomol_match = re.search(PDB_BIOMOL_REGEX, INPUT_FILENAME)
if pdb_biomol_match:
PDB = pdb_biomol_match.group(1)
BIOMOL_ID = pdb_biomol_match.group(2)
pdb_rcsb_asm_match = re.search(PDB_RCSB_ASM_REGEX, INPUT_FILENAME)
if pdb_rcsb_asm_match:
PDB = pdb_rcsb_asm_match.group(1)
BIOMOL_ID = pdb_rcsb_asm_match.group(2)
# LOAD STRUCTURE
structure = PDBParser().get_structure('structure', INPUT_FILE)
structure_atoms = list(structure.get_atoms())
logging.info('Loaded PDB structure (BioPython).')
# CONSTRUCT KDTREE
neighborsearch = NeighborSearch(structure_atoms)
logging.info('Constructured NeighborSearch.')
# GET INTERACTIONS
logging.info('Calculating interactions...')
for interaction_level in 'ARC':
if interaction_level in OUTPUTS:
logging.info('Calculating interactions for {}s...'.format(