mmtbx.command_line.interpolate
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/command_line/interpolate.py

 
Modules
       
os
sys

 
Classes
       
__builtin__.object
morph

 
class morph(__builtin__.object)
    Container for interpolated sites.
 
  Methods defined here:
__init__(self, pdb_hierarchy)
add_frame(self, sites_cart)
write_pdb_files(self, output_base, serial, serial_format='%04d', pause=0, pause_at_end=False, log=None)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
Functions
       
StringIO(...)
StringIO([s]) -- Return a StringIO-like stream for reading or writing
adiabatic_mapping(pdb_hierarchy, restraints_manager, start_coords, end_coords, params, nsteps=10, verbose=False, out=None)
Linear interpolation with energy minimization.  The number of minimizer
cycles should be kept low to prevent each "frame" from snapping back to the
starting coordinates.  Interpolating the dihedral restraint target angles
may help remediate this problem.
fit_sites(sites_fixed, sites_moving, selection)
Simple least-squares superposition of sites on reference structure
homogenize_structures(pdb_hierarchies, delete_heteroatoms=False, delete_waters=True, debug=False, log=None)
Eliminate atoms not present in all models.  This ignores residue names, so
corresponding mainchain atoms should be preserved in most cases.
morph_models(params, out=None, debug=False)
run(args, out=None)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
morph_params_str = '\ndebug = False\n .type = bool\nmorph {\n pdb_file...nomer_library.pdb_interpretation.master_params\n}\n'