def optimize(self):
span = self.__update_schedule()
self.__check_schedule()
ometh = self.__get_optimization_method()
AutoCommands.optimize(self,
residue_span_range=span,
optimization_method=ometh)
def pick_restraints(self):
if not self.vars['add_restraints']:
mdl = self.get_mdl()
rsr = _modeller.mod_model_rsr_get(mdl)
_modeller.mod_restraints_unpick_all(rsr)
span = self.__update_schedule()
AutoCommands.pick_restraints(self, residue_span_range=span)
def read_parameters(self):
if not self.vars['add_parameters']:
# Clear both CHARMM parameters and group restraint parameters
_modeller.mod_parameters_clear(self.get_prm())
_modeller.mod_group_restraints_clear(self.get_gprsr())
self.__default_file('file', '.toplib', ('', '.lib'))
AutoCommands.read_parameters(self)
def sequence_comparison(self):
self.__default_file('rr_file', '.A', ('', '.mat'))
self.__default_file('matrix_file', '.M')
self.__default_file('variability_file', '.V')
AutoCommands.sequence_comparison(
self,
matrix_file=self.__add_outdir('matrix_file'),
variability_file=self.__add_outdir('variability_file'))
def read_alignment(self):
if not self.vars['add_sequence']:
_modeller.mod_alignment_clear(self.get_aln())
self.__default_file('file', '.A', ('', '.ali'))
fh = modfile.File(self.vars['file'], 'r')
AutoCommands.read_alignment(self,
allow_alternates=False,
fh=fh.file_pointer)
fh.close()
def generate_topology(self):
seq = self.vars['sequence']
iseq = _modeller.mod_alignment_find_code(self.get_aln(), seq)
if iseq < 0:
log.error('generate_topology',
"Sequence '%s' not found in alignment" % seq)
if not self.vars['add_segment']:
_modeller.mod_model_topology_clear(self.get_mdl())
AutoCommands.generate_topology(self, iseq=iseq)
def read_model(self):
self.__default_file('file', 'B')
(file, model_segment) = self.__seg_from_aln('model_segment')
io = self.get_io()
file = _modeller.mod_pdb_filename_get(file, io.atom_files_directory)
fh = modfile.File(file, 'r')
AutoCommands.read_model(self,
fh=fh.file_pointer,
model_segment=model_segment,
keep_disulfides=False)
fh.close()
self.__pickall()
def delete_restraint(self):
atom_names = self.vars['atom_ids']
mdl = self.get_mdl(1)
cd = _modeller.mod_model_cd_get(mdl)
seq = _modeller.mod_model_seq_get(mdl)
atom_ids = [_modeller.mod_coordinates_find_atom(cd, seq, a) \
for a in atom_names]
if 0 in atom_ids:
log.warning("delete_restraint",
"One or more atoms absent from MODEL: " \
+ " ".join(atom_names))
else:
AutoCommands.unpick_restraints(self, atom_ids=atom_ids)
def make_restraints(self):
if not self.vars['add_restraints']:
_modeller.mod_restraints_clear(self.get_mdl())
span = self.__update_schedule()
rsrtype = self.vars['restraint_type'].lower()
if rsrtype == 'alpha':
self.__make_sstruc_restraints(_modeller.mod_restraints_make_alpha)
elif rsrtype == 'strand':
self.__make_sstruc_restraints(_modeller.mod_restraints_make_strand)
elif rsrtype == 'sheet':
self.__make_sheet_restraints()
else:
AutoCommands.make_restraints(self,
residue_span_range=span,
exclude_distance=0.0)
def sequence_to_ali(self):
aln = self.get_aln()
if not self.vars['add_sequence']:
_modeller.mod_alignment_clear(aln)
nseq = _modeller.mod_alignment_nseq_get(aln)
try:
align_codes = self.vars['align_codes'][nseq]
except IndexError:
align_codes = ''
try:
atom_files = self.vars['atom_files'][nseq]
except IndexError:
atom_files = ''
AutoCommands.sequence_to_ali(self,
align_codes=align_codes,
atom_files=atom_files)
def read_sequence_db(self):
chains = self.vars['chains_list']
if chains.upper() != 'ALL':
self.__default_file('chains_list', 'H', ('', '.list'))
self.__default_file('seq_database_file', 'H', ('', '.seq'))
AutoCommands.read_sequence_db(self)
def read_restyp_lib(self):
fh = modfile.File(self.vars['restyp_lib_file'], 'r')
AutoCommands.read_restyp_lib(self, fh=fh.file_pointer)
def prof_to_aln(self):
if not self.vars['append_aln']:
_modeller.mod_alignment_clear(self.get_aln())
AutoCommands.prof_to_aln(self)
def read_alignment2(self):
if not self.vars['add_sequence']:
_modeller.mod_alignment_clear(self.get_aln(2))
self.__default_file('file', '.A', ('', '.ali'))
AutoCommands.read_alignment2(self)
def principal_components(self):
self.__default_file('matrix_file', '.G')
self.__default_file('file', '.dat')
AutoCommands.principal_components(self)
def edit_alignment(self):
AutoCommands.edit_alignment(self, by_chain=False)
def read_density(self):
fh = modfile.File(self.vars['file'], 'rb')
AutoCommands.read_density(self, fh=fh.file_pointer, read_origin=False)
fh.close()
def salign(self):
AutoCommands.salign(self,
rms_cutoff=self.vars['rms_cutoffs'][0],
break_break_bonus=0.)
def patch(self):
mdl = self.get_mdl()
resids = self.__parse_residue_ids(mdl, self.vars['residue_ids'])
AutoCommands.patch(self, residue_ids=resids)
def build_profile(self):
self.__default_file('rr_file', '.mat', ('', '.mat'))
AutoCommands.build_profile(self, window_size=1024)
def write_pdb_xref(self):
self.__default_file('file', '.X')
(file, model_segment) = self.__seg_from_aln('model_segment')
AutoCommands.write_pdb_xref(self,
model_segment=model_segment,
file=self.__add_outdir('file'))
def align2d(self):
self.__default_file('rr_file', '.A', ('', '.mat'))
AutoCommands.align2d(self, break_break_bonus=0.)
def superpose(self):
AutoCommands.superpose(self, rms_cutoff=self.vars['rms_cutoffs'][0])
def write_sequence_db(self):
self.__default_file('chains_list', 'H')
self.__default_file('seq_database_file', 'H')
AutoCommands.write_sequence_db(self, window_size=1024)
def compare(self):
AutoCommands.compare(self, varatom=self.vars['distance_atoms'][0])
def seqfilter(self):
self.__default_file('rr_file', '.mat', ('', '.mat'))
AutoCommands.seqfilter(self, window_size=512)
def make_chains(self):
AutoCommands.make_chains(self, chop_nonstd_termini= \
self.vars['chop_nonstd_terminii'])
def open(self):
self.__default_file('objects_file', 'TOP')
AutoCommands.open(self)
def read_atom_classes(self):
fh = modfile.File(self.vars['atom_classes_file'], 'r')
AutoCommands.read_atom_classes(self, fh=fh.file_pointer)
fh.close()
def inquire(self):
self.__default_file('file', '.B')
AutoCommands.inquire(self)