symexp module

Expansion of molecular & crystal symmetry.

usage: - SymExp [options] [input-pdb-file]

• symexp.py [options] [input-pdb-file]

For help in stand-alone usage:

• Command-line options: symmetry.py -h

• Commands: at the (Cmd) prompt: help or help <command>

This is a front-end for module symmetry.py that is called by several packages.

Module author: Michael S. Chapman <chapmanms@missouri.edu>

Authors:

Michael S. Chapman <chapmanms@missouri.edu>

Oregon Health & Science University & University of Missouri

Changed in version 0.1.1: 09/09/11 refactoring into python, support of rsref / use of modules

Changed in version 0.4.1: 07/01/13 Space group / lattice symmetry

Changed in version 0.5.0: 03/12/15 Restructured text documentation

Changed in version 0.5.5: 10/20/15 Riding anisotropic Us

Changed in version 1.0.0: 11/06/20 Python 2.7 –> 3.6

class symexp.Tasks

Bases: object

Program-specific tasks, supporting just-in-time execution.

Methods with names ending _prereq define tasks whose prerequisites will be met, if possible, prior to execution.

read_coords(new_file=None)

Read coordinates without recalculating statistics

Parameters:

new_file (string) – PDB file to be read.

read_coords_prereq(*args, **kwargs)

Pass-through, trying to meet the prerequisites.

symmetry_expand(target_atoms=None, center=None, distance=None)

Identify self.atom neighbors of target (or self.atoms) + symm equivs.

Pass through for Symmetry.neighbors.

Parameters:

• center ([float, float, float]) – atoms w/in distance of this point instead of other atoms.

• distance (float) – within which considered close (Å).

symmetry_expand_prereq(*args, **kwargs)

Pass-through, trying to meet the prerequisites.

symmetry_init(distance=None)

Initialize symmetry calculation & identify neighbors.

Parameters:

distance (float) – neighbor cut-off; default (None) is 3.5 Å, different from RSRef.

symmetry_init_prereq(*args, **kwargs)

Pass-through, trying to meet the prerequisites.

write_coords(new_file=None, header=None, neighbors_only=False, anisotropic=False)

Parameters:

• new_file (str) – PDB file to be written.

• header (str) – to be inserted at top of PDB file.

• boolneighbors_only – output atoms that are close, but not selected evaluation (non-standard), noting “close” can contain “evaluation” atoms after residue or chain completion.

• anisotropic (bool) – Write riding anisotropic Us.

write_coords_prereq(*args, **kwargs)

Pass-through, trying to meet the prerequisites.

class symexp.TopCommands(tasks, initial_commands=None, py_locals={}, parser=None)

Bases: TopCmd, ProgCmd

Top-level commands for Program Prog.

Parameters:

• tasks (Control) – class instance that defines methods to be called.

• initial_commands (str or list of str) – file(s) of commands to run before interactive loop at the top level, and before any command-line commands.

• py_locals (dict) – objects added to the local namespace in the python interpreter invoked by ‘py’ commands.

• parser (ArgumentParser (argparse) or OptionParser (optparse)) – to which -t / –test option will be added for cmd2 regression testing. Should only be used once / program.

do_neighbors(args)

Identify neighbors within distance of (selected) atoms.

do_pdbout(args)

Write coordinates (symmetry expansion as per command-line arguments).

do_sphere(args)

Find atoms & symmetry equivalents near given point.

do_test(rest)

Run a program developer’s test.

help_test()

neighbors_parser = ArgumentParser(prog='sphinx-build', usage=None, description=None, formatter_class=<class 'argparse.HelpFormatter'>, conflict_handler='error', add_help=True)

pdbout_parser = ArgumentParser(prog='sphinx-build', usage=None, description=None, formatter_class=<class 'argparse.HelpFormatter'>, conflict_handler='error', add_help=True)

sphere_parser = ArgumentParser(prog='sphinx-build', usage=None, description=None, formatter_class=<class 'argparse.HelpFormatter'>, conflict_handler='error', add_help=True)

symexp.startup()

Program initialization, reading options etc..

Returns:

parser

Return type:

Arguments.ArgumentParser