def generate(fin='rna.pdb', fout='rna.dcd', frames=1000):
path = os.path.dirname(os.path.realpath(__file__))
fin = os.path.join(path, '../', 'data', 'pdb_common', fin)
if not os.path.exists(fin):
raise Exception, fin + ' does not exist while generating huge rna dcd files'
return
#fout = os.path.join(path,'../','data','dcd_common',fout)
fout = os.path.join('/tmp/', fout)
if os.path.exists(fout):
return
o = s.SasMol(0)
o.read_pdb(fin)
outfile = dcdio.open_dcd_write(fout)
nset = frames
natoms = o._coor[0, :, 0].shape[0]
istart = 0
nsavc = 1
delta = 1.0
o.write_dcd_header(outfile, frames)
tx = o.coor()[0, :, 0].astype(np.float32)
ty = o.coor()[0, :, 1].astype(np.float32)
tz = o.coor()[0, :, 2].astype(np.float32)
for i in range(frames):
dcdio.write_dcdstep(outfile, tx, ty, tz, i + 1)
o.close_dcd_write(outfile)
def test_file_doesnt_exist(self):
'''
test a dcd which doent exist
'''
filename = 'file-notexist.dcd'
dcdFile = moduleDataPath+'test-results/'+filename
stdoutFile = filename+'.stdiout'
pf = dcdio.open_dcd_write(dcdFile)
sys.stdout = open(stdoutFile,'w')
self.o.close_dcd_write(pf)
sys.stdout = sys.__stdout__
code=string.split(open(stdoutFile).read())[2]
self.assertEqual(int(code), 0)
os.remove(stdoutFile)
os.remove(dcdFile)
def test_1CRN(self):
'''
test a dcd from a small protein (crambin)
'''
#
pdbFileName = DataPath+'1CRN.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath+'test-results/1CRN-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize>0)
os.remove(dcdFileName)
def test_2AAD(self):
'''
test a dcd with 3 frames based on a 2-aa pdb
'''
#
pdbFileName = DataPath+'2AAD.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath+'test-results/2AAD-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize>0)
os.remove(dcdFileName)
def test_rna_1to10frames(self):
'''
test a dcd of 10 frames based on a rna molecule
'''
#
pdbFileName = DataPath+'rna.pdb'
self.o.read_pdb(pdbFileName)
nset = 10
#
dcdFileName = moduleDataPath+'test-results/rna-1to10-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize>0)
os.remove(dcdFileName)
def test_1KP8(self):
'''
test a dcd from a large protein complex (groel)
'''
#
pdbFileName = DataPath+'1KP8.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath+'test-results/1KP8-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize>0)
os.remove(dcdFileName)
def test_1CRN(self):
'''
test a dcd from a small protein (crambin)
'''
#
pdbFileName = DataPath + '1CRN.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath + 'test-results/1CRN-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize > 0)
os.remove(dcdFileName)
def test_2AAD(self):
'''
test a dcd with 3 frames based on a 2-aa pdb
'''
#
pdbFileName = DataPath + '2AAD.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath + 'test-results/2AAD-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize > 0)
os.remove(dcdFileName)
def test_rna_1to10frames(self):
'''
test a dcd of 10 frames based on a rna molecule
'''
#
pdbFileName = DataPath + 'rna.pdb'
self.o.read_pdb(pdbFileName)
nset = 10
#
dcdFileName = moduleDataPath + 'test-results/rna-1to10-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize > 0)
os.remove(dcdFileName)
def test_1KP8(self):
'''
test a dcd from a large protein complex (groel)
'''
#
pdbFileName = DataPath + '1KP8.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath + 'test-results/1KP8-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize > 0)
os.remove(dcdFileName)
def test_1ATM(self):
'''
test a dcd with 2 frames based on an 1-atom pdb
'''
#
filename = '1ATM.dcd'
dcdFile = commonDcdDataPath+filename
tmpDcdFile = moduleDataPath+'test-results/'+filename
shutil.copy(dcdFile, tmpDcdFile)
stdoutFile = filename+'.stdiout'
pf = dcdio.open_dcd_write(tmpDcdFile)
sys.stdout = open(stdoutFile,'w')
self.o.close_dcd_write(pf)
sys.stdout = sys.__stdout__
code=string.split(open(stdoutFile).read())[2]
self.assertEqual(int(code), 0)
os.remove(stdoutFile)
os.remove(tmpDcdFile)
def test_rna_6point4gb(self):
'''
test a dcd of size 6.4gb based on a rna molecule
'''
#
filename = "rna-6.4g.dcd"
dcdFile = os.path.join('/tmp/',filename)
tmpDcdFile = moduleDataPath+'test-results/'+filename
shutil.copy(dcdFile, tmpDcdFile)
stdoutFile = filename+'.stdiout'
pf = dcdio.open_dcd_write(tmpDcdFile)
sys.stdout = open(stdoutFile,'w')
self.o.close_dcd_write(pf)
sys.stdout = sys.__stdout__
code=string.split(open(stdoutFile).read())[2]
self.assertEqual(int(code), 0)
os.remove(stdoutFile)
os.remove(tmpDcdFile)
def generate(fin='rna.pdb', fout='rna.dcd', frames=1000):
path = os.path.dirname(os.path.realpath(__file__))
fin = os.path.join(path,'../','data','pdb_common',fin)
if not os.path.exists(fin):
raise Exception,fin+' does not exist while generating huge rna dcd files'
return
#fout = os.path.join(path,'../','data','dcd_common',fout)
fout = os.path.join('/tmp/',fout)
if os.path.exists(fout):
return
o=s.SasMol(0)
o.read_pdb(fin)
outfile = dcdio.open_dcd_write(fout)
nset = frames
natoms = o._coor[0,:,0].shape[0]
istart = 0 ; nsavc = 1 ; delta = 1.0
o.write_dcd_header(outfile,frames)
tx=o.coor()[0,:,0].astype(np.float32)
ty=o.coor()[0,:,1].astype(np.float32)
tz=o.coor()[0,:,2].astype(np.float32)
for i in range(frames):
dcdio.write_dcdstep(outfile,tx,ty,tz,i+1)
o.close_dcd_write(outfile)
