def phil_parse(args=None, log=None):
'''
Contains default parameters, will process commandline params and
changes them
'''
# Default parameters
master_phil = libtbx.phil.parse("""
slice_mtz
{
input
.help = "Input files"
{
mtz_in = None
.type = path
.help = 'File name of PDB containing ensemble to be converted to supercell'
npy_in = None
.type = path
.help = 'File containing 2D numpy array, output of this program'
}
params
.help = "Control running"
{
array = 'Idff'
.type = str
.help = 'Array type, Ibrg, Itot or Idff'
vmin = None
.type = int
.help = 'Minimum value in contour plot'
vmax = None
.type = int
.help = 'Maximum value in contour plot'
}
output
.help = "output files"
{
mtz_out = slice.mtz
.type = path
.help = 'Name of output mtz containing only sliced miller indices'
npy_out = tmp.npy
.type = path
.help = 'Save 2D array to this numpy file'
plt_out = slice.eps
.type = path
.help = 'Save plot to this eps file'
}
}
""")
working_phil = init_command_line_phil(master_phil=master_phil,
args=args,
log=log)
return working_phil.extract()
def phil_parse(args=None, log=None):
'''
Contains default parameters, will process commandline params and
changes them
'''
# Default parameters
master_phil = libtbx.phil.parse("""
additivity_all
{
input
.help = "Input files"
{
single_pdb = None
.type = path
.help = 'PDB file containing single model'
ensemble_pdb = None
.type = path
.help = 'PDB file containing ensemble'
}
params
.help = "Control running"
{
create_ensemble = True
.type = bool
.help = 'wheter to create an ensemble from input or not'
calc_diff = True
.type = bool
.help = 'Calculate diffuse scattering or not'
merge_slices = True
.type = bool
.help = 'Merge 2D slices or not'
plot_all_B_factors = True
.type = bool
.help = 'Plot all B-factors or not'
}
output
.help = "output files"
{
mtz_out = mtz_out.mtz
.type = path
.help = 'file name for output mtz'
}
}
""")
working_phil = init_command_line_phil(master_phil=master_phil,
args=args,
log=log)
return working_phil.extract()
def phil_parse(args=None, log=None):
'''
Contains default parameters, will process commandline params and
changes them
'''
# Default parameters
master_phil = libtbx.phil.parse("""
additivity
{
input
.help = "Input files"
{
mtz_1 = None
.type = path
.help = 'MTZ file, to be converted to map'
mtz_2 = None
.type = path
.help = 'MTZ file, to be converted to map'
}
params
.help = "Control running"
{
array = None
.type = str
.help = 'Array column name'
sf_1 = 1.0
.type = float
.help = 'scale factor for array 1'
sf_2 = 1.0
.type = float
.help = 'scale factor for array 2'
}
output
.help = "output files"
{
mtz_out = mtz_out.mtz
.type = path
.help = 'file name for output mtz'
}
}
""")
working_phil = init_command_line_phil(master_phil=master_phil,
args=args,
log=log)
return working_phil.extract()
def phil_parse(args=None, log=None):
'''
Contains default parameters, will process commandline params and
changes them
'''
# Default parameters
master_phil = libtbx.phil.parse("""
Rfacts
{
input
.help = "Input files"
{
pdb_1 = None
.type = path
.help = 'Calc FFT from this'
mtz_2 = None
.type = path
.help = 'data mtz'
er_mtz = None
.type = path
.help = 'output of ensemble refinement'
}
params
.help = "Control running"
{
array_1 = FMODEL
.type = str
.help = 'array from pdb_1/mtz_1 to use'
array_2 = ITOT2
.type = str
.help = 'Array from data mtz to use in Rfact calc'
}
output
.help = "output files"
{
mtz_out = mtz_out.mtz
.type = path
.help = 'file name for output mtz'
}
}
""")
working_phil = init_command_line_phil(master_phil=master_phil,
args=args,
log=log)
return working_phil.extract()
def phil_parse(args=None, log=None):
'''
Contains default parameters, will process commandline params and
changes them
'''
# Default parameters
master_phil = libtbx.phil.parse("""
sc_reduce
{
input
.help = "Input files"
{
pdb_in = None
.type = path
.help = 'File name of supercell pdb (ensemble or single model)'
ref_pdb = None
.type = path
.help = 'Ref PDB to make reference model (P1) from'
supercell_size = 2
.type = int
.help = 'Size of supercell (x*x*x)'
}
params
.help = "Control running"
{
write_pdb = False
.type = bool
.help = 'write PDB file?'
}
output
.help = "output files"
{
pdb_out = supercell_out.pdb
.type = path
.help = 'Name of output file containing supercell'
}
}
""")
working_phil = init_command_line_phil(master_phil=master_phil,
args=args,
log=log)
return working_phil.extract()
def phil_parse(args=None,log=None):
'''
Contains default parameters, will process commandline params and
changes them
'''
# Default parameters
master_phil = libtbx.phil.parse("""
cypa_helix
{
input
.help = "Input files"
{
pdb_in = None
.type = path
.help = 'MTZ file, to be converted to map'
}
params
.help = "Control running"
{
tmp = None
.type = str
.help = 'placeholder'
}
output
.help = "output files"
{
pdb_out = mtz_out.mtz
.type = path
.help = 'file name for output pdb'
}
}
""")
working_phil = init_command_line_phil(master_phil=master_phil,
args=args,
log=log)
return working_phil.extract()
def phil_parse(args=None,log=None):
'''
Contains default parameters, will process commandline params and
changes them
'''
# Default parameters
master_phil = libtbx.phil.parse("""
sc_er_setup
{
input
.help = "Input files"
{
rb_pdb_in = None
.type = path
.help = 'File name of single PDB (used to generate input for rigid body)'
single_pdb_in = None
.type = path
.help = 'PDB file used for perfect supercell and data'
supercell_num = 100
.type = int
.help = 'supercell number, helps when generating loads of them'
}
params
.help = "Control running"
{
rb_type = "trans"
.type = str
.help = 'Type of rb operations/ method to be used.'
size_h = 2
.type = int
.help = 'number of unit cells stacked in h direction'
size_k = 2
.type = int
.help = 'number of unit cells stacked in k direction'
size_l = 2
.type = int
.help = 'number of unit cells stacked in l direction'
Ncpu = 10
.type = int
.help = 'number of cpu's used for supercell calculations'
make_rb = True
.type = bool
.help = 'Run rigid body module'
prep_single = True
.type = bool
.help = 'Prepare single_pdb'
single_sc = True
.type = bool
.help = 'Calculate scattering and supercell from single_pdb'
single_P1 = True
.type = bool
.help = 'Create mtz and pdb from single_pdb in P1'
rb_sc = True
.type = bool
.help = 'Calculate scattering and supercell from rb_out_pdb'
rb_P1 = True
.type = bool
.help = 'Create mtz and pdb from rb_out_pdb in P1'
add_sigma = True
.type = bool
.help = 'Create new mtz files containing sigma columns'
b_fact_noise = True
.type = bool
.help = 'Create noise between 0.0 and 0.1 in B-factor columns to fool ptls fitting procedure of ensemble refinement'
high_resolution = 2.0
.type = float
.help = "up to what resolution are the structurefactors calculated"
}
output
.help = "output files"
{
rb_pdb_out = rb_pdb_out.pdb
.type = path
.help = 'Name of output file containing rigid body ensemble'
}
}
""")
working_phil = init_command_line_phil(master_phil=master_phil,
args=args,
log=log)
return working_phil.extract()
def phil_parse(args=None,log=None):
'''
Contains default parameters, will process commandline params and
changes them
'''
# Default parameters
master_phil = libtbx.phil.parse("""
addLoes
{
input
.help = "Input files"
{
single_pdb = None
.type = path
.help = 'Single structure PDB file'
internal_pdb = None
.type = path
.help = 'PDB file containing internal motion ensemble'
translation_pdb = trans.pdb
.type = path
.help = 'single translated pdb file'
int_translation_pdb = internal_trans.pdb
.type = path
.help = 'ensemble translated pdb file'
}
params
.help = "Control running"
{
do_rb = False
.type = bool
.help = 'Perform rb action on both single and ensemble pdbs'
trans_sigma = 0.5
.type = float
.help = 'Sigma used in translation of models'
nr_models = 250
.type = int
.help = 'Number of models in rb output'
do_bfactor = False
.type = bool
.help = 'Calculate B-factors from the ensembles'
do_diff_calc = False
.type = bool
.help = 'Calculate diffuse scattering from internal, translation and int_translation'
size_h = 9
.type = int
.help = 'Super parameter in h direction'
size_k = 8
.type = int
.help = 'Super parameter in k direction'
size_l = 5
.type = int
.help = 'Super parameter in l direction'
do_slice = False
.type = bool
.help = 'Slice diffuse scattering mtz files'
vmin = 1000
.type = int
.help = 'plotting minimum'
vmax = 75000000
.type = int
.help = 'plotting maximum'
vmin_internal = 10000
.type = int
.help = 'plotting minimum'
vmax_internal = 25000000
.type = int
.help = 'plotting maximum'
do_subtractions = True
.type = bool
.help = 'subtract translation from translation+internal, and subtract internal from translation+internal'
vmin_sub = 10000
.type = int
.help = 'plotting minimum after subtraction'
vmax_sub = 40000000
.type = int
.help = 'plotting maximumm after subtraction'
}
output
.help = "output files"
{
mtz_out = mtz_out.mtz
.type = path
.help = 'file name for output mtz'
}
}
""")
working_phil = init_command_line_phil(master_phil=master_phil,
args=args,
log=log)
return working_phil.extract()