def go(self, model_list = None, reference = None):
"""
Run benchmarking.
@param model_list: list of models
(default: None S{->} outFolder/L{F_PDBModels})
@type model_list: ModelList
@param reference: reference model
(default: None S{->} outFolder/L{F_INPUT_REFERENCE})
@type reference: PDBModel
"""
model_list = model_list or self.outFolder + self.F_PDBModels
reference = reference or self.outFolder + self.F_INPUT_REFERENCE
pdb_list = T.load('%s'%model_list)
reference = PDBModel(reference)
# check with python 2.4
iref, imodel = reference.compareAtoms(pdb_list[0])
mask_casting = N.zeros(len(pdb_list[0]))
N.put(mask_casting, imodel, 1)
reference = reference.take(iref)
#reference_mask_CA = reference_rmsd.maskCA()
atom_mask = N.zeros(len(pdb_list[0]))
N.put(atom_mask,imodel,1)
rmask = pdb_list[0].profile2mask("n_templates", 1,1000)
amask = pdb_list[0].res2atomMask(rmask)
mask_final_ref = N.compress(mask_casting, amask)
mask_final = mask_casting * amask
reference = reference.compress(mask_final_ref)
for i in range(len(pdb_list)):
#self.cad(reference, pdb_list[i])
pdb_list[i], pdb_wo_if = self.output_fittedStructures(\
pdb_list[i], reference, i, mask_final)
fitted_model_if = pdb_list[i].compress(mask_final)
fitted_model_wo_if = pdb_wo_if.compress(mask_final)
coord1 = reference.getXyz()
coord2 = fitted_model_if.getXyz()
aprofile = self.rmsd_res(coord1,coord2)
self.calc_rmsd(fitted_model_if, fitted_model_wo_if,
reference, pdb_list[i])
pdb_list[i].atoms.set('rmsd2ref_if', aprofile,
mask=mask_final, default = -1,
comment="rmsd to known reference structure")
self.output_rmsd_aa(pdb_list)
self.output_rmsd_ca(pdb_list)
self.output_rmsd_res(pdb_list)
self.write_PDBModels(pdb_list)
def parmMirror( self, f_out, f_out_crd=None, fmod=['frcmod.ionsjc_tip3p'],
fprep=[], **kw ):
"""
Create a parm7 file whose atom content (and order) exactly mirrors
the given PDBModel. This requires two leap runs. First we get a
temporary topology, then we identify all atoms added by leap and
build a final topology where these atoms are deleted.
This parm is hence NOT suited for simulations but can be used to parse
e.g. a trajectory or PDB into ptraj.
@param f_out: target parm file
@type f_out: str
@param f_out_crd: target crd file (default: f_out but ending .crd)
@type f_out_crd: str
@param fmod : list of amber Mod files (loaded with loadAmberParams)
@type fmod : [str]
@param fmod : list of amber Prep files (loaded with loadAmberPrep)
@type fmod : [str]
"""
f_out = t.absfile( f_out )
f_out_crd = t.absfile( f_out_crd ) or t.stripSuffix( f_out ) + '.crd'
## if there are hydrogens, recast them to standard amber names
aatm = 'HA' in self.m.atomNames() ## 'HB2' in self.m.atomNames()
## First leap round ##
m_ref = self.m.clone()
m_ref.xplor2amber( aatm=aatm, parm10=True )
tmp_in = tempfile.mktemp( 'leap_in0.pdb' )
m_ref.writePdb( tmp_in, ter=3 )
tmp_parm = tempfile.mktemp( '_parm0' )
tmp_crd = tempfile.mktemp( '_crd0' )
leap_mod = self.__fLines( 'm = loadAmberParams %s\n', fmod )
leap_prep= self.__fLines( 'loadAmberPrep %s\n', fprep )
self.__runLeap( self.script_mirror_pdb,
leaprc=self.leaprc, fmod=leap_mod, fprep=leap_prep,
in_pdb=tmp_in, out_parm=tmp_parm, out_crd=tmp_crd,
delete_atoms='' )
tmp_pdb = self.parm2pdb( tmp_parm, tmp_crd,
tempfile.mktemp( 'leap_out.pdb' ), aatm=aatm )
if not self.debug:
t.tryRemove( tmp_parm )
t.tryRemove( tmp_crd )
t.tryRemove( tmp_in )
## load model with missing atoms added by leap
m_leap = PDBModel( tmp_pdb )
## compare atom content
iLeap, iRef = m_leap.compareAtoms( m_ref )
## check that ref model doesn't need any change
if iRef != range( len( m_ref ) ):
uLeap, uRef = m_leap.unequalAtoms( m_ref, iLeap, iRef )
atms = m_ref.reportAtoms( uRef, n=6 )
raise AmberError, "Cannot create exact mirror of %s.\n" % tmp_in +\
"Leap has renamed/deleted original atoms in %s:\n"% tmp_pdb+\
atms
## indices of atoms that were added by leap
delStr = self.__deleteAtoms( m_leap,
self.__inverseIndices( m_leap, iLeap ) )
## Second leap round ##
self.__runLeap( self.script_mirror_pdb, leaprc=self.leaprc,
in_pdb=tmp_pdb, fmod=leap_mod, fprep=leap_prep,
out_parm=f_out, out_crd=f_out_crd,
delete_atoms=delStr )
if not self.debug:
t.tryRemove( tmp_pdb )
def go(self, model_list=None, reference=None):
"""
Run benchmarking.
@param model_list: list of models
(default: None S{->} outFolder/L{F_PDBModels})
@type model_list: ModelList
@param reference: reference model
(default: None S{->} outFolder/L{F_INPUT_REFERENCE})
@type reference: PDBModel
"""
model_list = model_list or self.outFolder + self.F_PDBModels
reference = reference or self.outFolder + self.F_INPUT_REFERENCE
pdb_list = T.load('%s' % model_list)
reference = PDBModel(reference)
# check with python 2.4
iref, imodel = reference.compareAtoms(pdb_list[0])
mask_casting = N0.zeros(len(pdb_list[0]))
N0.put(mask_casting, imodel, 1)
reference = reference.take(iref)
#reference_mask_CA = reference_rmsd.maskCA()
atom_mask = N0.zeros(len(pdb_list[0]))
N0.put(atom_mask, imodel, 1)
rmask = pdb_list[0].profile2mask("n_templates", 1, 1000)
amask = pdb_list[0].res2atomMask(rmask)
mask_final_ref = N0.compress(mask_casting, amask)
mask_final = mask_casting * amask
reference = reference.compress(mask_final_ref)
for i in range(len(pdb_list)):
#self.cad(reference, pdb_list[i])
pdb_list[i], pdb_wo_if = self.output_fittedStructures(\
pdb_list[i], reference, i, mask_final)
fitted_model_if = pdb_list[i].compress(mask_final)
fitted_model_wo_if = pdb_wo_if.compress(mask_final)
coord1 = reference.getXyz()
coord2 = fitted_model_if.getXyz()
aprofile = self.rmsd_res(coord1, coord2)
self.calc_rmsd(fitted_model_if, fitted_model_wo_if, reference,
pdb_list[i])
pdb_list[i].atoms.set('rmsd2ref_if',
aprofile,
mask=mask_final,
default=-1,
comment="rmsd to known reference structure")
self.output_rmsd_aa(pdb_list)
self.output_rmsd_ca(pdb_list)
self.output_rmsd_res(pdb_list)
self.write_PDBModels(pdb_list)
def parmMirror(self,
f_out,
f_out_crd=None,
fmod=['frcmod.ionsjc_tip3p'],
fprep=[],
**kw):
"""
Create a parm7 file whose atom content (and order) exactly mirrors
the given PDBModel. This requires two leap runs. First we get a
temporary topology, then we identify all atoms added by leap and
build a final topology where these atoms are deleted.
This parm is hence NOT suited for simulations but can be used to parse
e.g. a trajectory or PDB into ptraj.
@param f_out: target parm file
@type f_out: str
@param f_out_crd: target crd file (default: f_out but ending .crd)
@type f_out_crd: str
@param fmod : list of amber Mod files (loaded with loadAmberParams)
@type fmod : [str]
@param fmod : list of amber Prep files (loaded with loadAmberPrep)
@type fmod : [str]
"""
f_out = t.absfile(f_out)
f_out_crd = t.absfile(f_out_crd) or t.stripSuffix(f_out) + '.crd'
## if there are hydrogens, recast them to standard amber names
aatm = 'HA' in self.m.atomNames() ## 'HB2' in self.m.atomNames()
## First leap round ##
m_ref = self.m.clone()
m_ref.xplor2amber(aatm=aatm, parm10=True)
tmp_in = tempfile.mktemp('leap_in0.pdb')
m_ref.writePdb(tmp_in, ter=3)
tmp_parm = tempfile.mktemp('_parm0')
tmp_crd = tempfile.mktemp('_crd0')
leap_mod = self.__fLines('m = loadAmberParams %s\n', fmod)
leap_prep = self.__fLines('loadAmberPrep %s\n', fprep)
self.__runLeap(self.script_mirror_pdb,
leaprc=self.leaprc,
fmod=leap_mod,
fprep=leap_prep,
in_pdb=tmp_in,
out_parm=tmp_parm,
out_crd=tmp_crd,
delete_atoms='')
tmp_pdb = self.parm2pdb(tmp_parm,
tmp_crd,
tempfile.mktemp('leap_out.pdb'),
aatm=aatm)
if not self.debug:
t.tryRemove(tmp_parm)
t.tryRemove(tmp_crd)
t.tryRemove(tmp_in)
## load model with missing atoms added by leap
m_leap = PDBModel(tmp_pdb)
## compare atom content
iLeap, iRef = m_leap.compareAtoms(m_ref)
## check that ref model doesn't need any change
if iRef != range(len(m_ref)):
uLeap, uRef = m_leap.unequalAtoms(m_ref, iLeap, iRef)
atms = m_ref.reportAtoms(uRef, n=6)
raise AmberError, "Cannot create exact mirror of %s.\n" % tmp_in +\
"Leap has renamed/deleted original atoms in %s:\n"% tmp_pdb+\
atms
## indices of atoms that were added by leap
delStr = self.__deleteAtoms(m_leap,
self.__inverseIndices(m_leap, iLeap))
## Second leap round ##
self.__runLeap(self.script_mirror_pdb,
leaprc=self.leaprc,
in_pdb=tmp_pdb,
fmod=leap_mod,
fprep=leap_prep,
out_parm=f_out,
out_crd=f_out_crd,
delete_atoms=delStr)
if not self.debug:
t.tryRemove(tmp_pdb)
