class Test(BT.BiskitTest):
"""Test"""
def test_ReduceCoordinates(self):
"""ReduceCoordinates test"""
self.m = PDBModel( T.testRoot()+'/com/1BGS.pdb' )
self.m = self.m.compress( N0.logical_not( self.m.maskH2O() ) )
self.m.atoms.set('test', list(range(len(self.m))))
self.red = ReduceCoordinates( self.m, 4 )
self.mred = self.red.reduceToModel()
if self.local:
print('\nAtoms before reduction %i'% self.m.lenAtoms())
print('Atoms After reduction %i'% self.mred.lenAtoms())
self.assertEqual( self.mred.lenAtoms(), 445 )
class Test(BT.BiskitTest):
"""Test case"""
def test_surfaceRacerTools(self):
"""surfaceRacerTools test"""
from biskit import PDBModel
import biskit.tools as T
## load a structure
self.m = PDBModel(T.testRoot() + '/lig/1A19.pdb')
self.m = self.m.compress(self.m.maskProtein())
self.m = self.m.compress(self.m.maskHeavy())
## some fake surface data
surf = N0.ones(self.m.lenAtoms()) * 10.0
relExp = relExposure(self.m, surf)
## if self.local:
## globals().update( locals() )
self.assertAlmostEqual(N0.sum(relExp), 44276.86085222386, 8)
class Test(BT.BiskitTest):
"""Test case"""
def test_surfaceRacerTools(self):
"""surfaceRacerTools test"""
from biskit import PDBModel
import biskit.tools as T
## load a structure
self.m = PDBModel( T.testRoot()+'/lig/1A19.pdb' )
self.m = self.m.compress( self.m.maskProtein() )
self.m = self.m.compress( self.m.maskHeavy() )
## some fake surface data
surf = N0.ones( self.m.lenAtoms()) * 10.0
relExp = relExposure( self.m, surf )
## if self.local:
## globals().update( locals() )
self.assertAlmostEqual( N0.sum(relExp), 44276.86085222386, 8 )
class AmberCrdParser:
"""
Convert an Amber-generated crd file into a Trajectory object.
"""
def __init__(self,
fcrd,
fref,
box=0,
rnAmber=0,
pdbCode=None,
log=StdLog(),
verbose=0):
"""
:param fcrd: path to input coordinate file
:type fcrd: str
:param fref: PDB or pickled PDBModel with same atom content and order
:type fref: str
:param box: expect line with box info at the end of each frame
(default: 0)
:type box: 1|0
:param rnAmber: rename amber style residues into standard (default: 0)
:type rnAmber: 1|0
:param pdbCode: pdb code to be put into the model (default: None)
:type pdbCode: str
:param log: LogFile instance [Biskit.StdLog]
:type log: biskit.LogFile
:param verbose: print progress to log [0]
:type verbose: int
"""
self.fcrd = T.absfile(fcrd)
self.crd = T.gzopen(self.fcrd)
self.ref = PDBModel(T.absfile(fref), pdbCode=pdbCode)
self.box = box
self.n = self.ref.lenAtoms()
self.log = log
self.verbose = verbose
if rnAmber:
self.ref.renameAmberRes()
## pre-compile pattern for line2numbers
xnumber = "-*\d+\.\d+" # optionally negtive number
xspace = ' *' # one or more space char
self.xnumbers = re.compile('(' + xspace + xnumber + ')')
## pre-compute lines expected per frame
self.lines_per_frame = self.n * 3 // 10
if self.n % 10 != 0: self.lines_per_frame += 1
if self.box: self.lines_per_frame += 1
## mark chains (the TER position might get lost when deleting atoms)
## should not be necessary any longer
## if not self.ref.getAtoms()[0].get('chain_id',''):
## self.ref.addChainId()
def line2numbers(self, l):
"""
convert a line from crd/vel file to list of float numbers
:param l: line
:type l: str
:return: list of floats
:rtype: [float]
"""
match = self.xnumbers.findall(l)
return [round(float(strCrd), 3) for strCrd in match]
def nextLine(self):
"""
extract next 10 coordinates from crd file
:return: coordinates
:rtype: [float]
"""
l = self.crd.readline()
if l == '':
raise EOFError('EOF')
return self.line2numbers(l)
def nextFrame(self):
"""
Collect next complete coordinate frame
:return: coordinate frame
:rtype: array
"""
i = 0
xyz = []
while i != self.lines_per_frame:
if self.box and i + 1 == self.lines_per_frame:
## skip box info
if len(self.nextLine()) != 3:
raise ParseError("BoxInfo must consist of 3 numbers.")
else:
xyz += self.nextLine()
i += 1
return N.reshape(xyz, (len(xyz) // 3, 3)).astype(N.float)
def crd2traj(self):
"""
Convert coordinates into a Trajectory object.
:return: trajectory object
:rtype: Trajectory
"""
## skip first empty line
self.crd.readline()
xyz = []
i = 0
if self.verbose: self.log.write("Reading frames ..")
try:
while 1 == 1:
xyz += [self.nextFrame()]
i += 1
if i % 100 == 0 and self.verbose:
self.log.write('#')
except EOFError:
if self.verbose: self.log.write("Read %i frames.\n" % i)
t = Trajectory(refpdb=self.ref)
t.frames = N0.array(xyz).astype(N0.Float32)
t.setRef(self.ref)
t.ref.disconnect()
return t
class AmberCrdParser:
"""
Convert an Amber-generated crd file into a Trajectory object.
"""
def __init__( self, fcrd, fref, box=0, rnAmber=0, pdbCode=None,
log=StdLog(), verbose=0 ):
"""
:param fcrd: path to input coordinate file
:type fcrd: str
:param fref: PDB or pickled PDBModel with same atom content and order
:type fref: str
:param box: expect line with box info at the end of each frame
(default: 0)
:type box: 1|0
:param rnAmber: rename amber style residues into standard (default: 0)
:type rnAmber: 1|0
:param pdbCode: pdb code to be put into the model (default: None)
:type pdbCode: str
:param log: LogFile instance [Biskit.StdLog]
:type log: biskit.LogFile
:param verbose: print progress to log [0]
:type verbose: int
"""
self.fcrd = T.absfile( fcrd )
self.crd = T.gzopen( self.fcrd )
self.ref = PDBModel( T.absfile(fref), pdbCode=pdbCode )
self.box = box
self.n = self.ref.lenAtoms()
self.log = log
self.verbose = verbose
if rnAmber:
self.ref.renameAmberRes()
## pre-compile pattern for line2numbers
xnumber = "-*\d+\.\d+" # optionally negtive number
xspace = ' *' # one or more space char
self.xnumbers = re.compile('('+xspace+xnumber+')')
## pre-compute lines expected per frame
self.lines_per_frame = self.n * 3 // 10
if self.n % 10 != 0: self.lines_per_frame += 1
if self.box: self.lines_per_frame += 1
## mark chains (the TER position might get lost when deleting atoms)
## should not be necessary any longer
## if not self.ref.getAtoms()[0].get('chain_id',''):
## self.ref.addChainId()
def line2numbers( self, l ):
"""
convert a line from crd/vel file to list of float numbers
:param l: line
:type l: str
:return: list of floats
:rtype: [float]
"""
match = self.xnumbers.findall( l )
return [ round( float(strCrd),3) for strCrd in match ]
def nextLine( self ):
"""
extract next 10 coordinates from crd file
:return: coordinates
:rtype: [float]
"""
l = self.crd.readline()
if l == '':
raise EOFError('EOF')
return self.line2numbers( l )
def nextFrame( self ):
"""
Collect next complete coordinate frame
:return: coordinate frame
:rtype: array
"""
i = 0
xyz = []
while i != self.lines_per_frame:
if self.box and i+1 == self.lines_per_frame:
## skip box info
if len( self.nextLine() ) != 3:
raise ParseError( "BoxInfo must consist of 3 numbers." )
else:
xyz += self.nextLine()
i += 1
return N.reshape( xyz, ( len(xyz) // 3, 3 ) ).astype(N.float)
def crd2traj( self ):
"""
Convert coordinates into a Trajectory object.
:return: trajectory object
:rtype: Trajectory
"""
## skip first empty line
self.crd.readline()
xyz = []
i = 0
if self.verbose: self.log.write( "Reading frames .." )
try:
while 1==1:
xyz += [ self.nextFrame() ]
i += 1
if i % 100 == 0 and self.verbose:
self.log.write( '#' )
except EOFError:
if self.verbose: self.log.write("Read %i frames.\n" % i)
t = Trajectory( refpdb=self.ref )
t.frames = N0.array( xyz ).astype(N0.Float32)
t.setRef( self.ref )
t.ref.disconnect()
return t
