Modules

acme_supplement

class acme_supplement.DotDict(*args, **kwargs)

Bases: dict

Use dots to access dictionary items.

Methods

class acme_supplement.SafeDictHook(*args, **kwargs)

Bases: dict

Hook for json.loads object_pairs_hook to catch repeated keys.

Methods

acme_supplement.check_repeated_keys(text, verbose=False)

Confirm that dict literals pass through non-redundant json checker.

acme_supplement.checker(fn)

Check a file for evaluation from the command line. ! Less generic name.

acme_supplement.jsonify(text)

Convert python to JSON by replacing single quotes with double quotes and stripping trailing commas Note that this checker might be oversensitive if additional JSON errors with the nested dictionary Used before SafeDictHook to check for redundant keys. We use a placeholder in block text because JSON cannot process it and the point of this function is to use SafeDictHook to prevent redundant keys.

acme_supplement.yamlb(text, style=None, ignore_json=False)

Basic YAML parser. Development note: missing colons are hard to troubleshoot. Predict them? Development note: doesn’t prevent errors with multiple keys in a dictionary!

examples_omnicalc_interface

batch_original

Combined automacs (classic, original) and omnicalc execution for making standard videos. See runner.py for the updated, acme-inflected version. Or see the examples for some alternate ways of using VMDWrap.

batch_original.remove_box_jumps_DEPRECATED()

Convert the trajectory to reassemble broken molecules. Requires items frm state.last_mdrun_output. Note that this is customized for vmdmake but it could be generalized and added to automacs.py.

batch_original.view_routine_original(**kwargs)

Function which interprets incoming video requests for VMDWrap and then executes them. Note that this function prepares a local viewer script for each video so users can tune/rerender.

batch

Automatic execution of VMDWrap for the acme-inflected automacs. Note that alternate runner scripts can be used to interface with other systems like automacs classic, omnicalc Or better yet you can just write your own VMDWrap-flavored scripts (see examples for examples)

batch.create_unbroken_trajectory(vmdstate)

Get the last frame from the state and make an unbroken trajectory. Note that the typ

batch.prepare_viewer_scripts(vmdstate)

key variables

show_trajectory : necessary for loading a video

batch.render_video(vmdstate)

batch.run_vmd(vmdstate)

batch.view_routine()

Manage incoming video requests. This function performs the four steps required to make images with VMD. It is designed to rerender videos without rerendering snapshots if desired.

quickview

quickview.martiniview(*args, **kwargs)

Quickly view a martini structure. !Needs more fine-tuning.

makeface_supplement

execpython-B$0$@

makeface_supplement.abspath(path)

Get the right path.

makeface_supplement.fab(text, *flags)

Colorize the text.

makeface_supplement.fab_deprecated(text, *flags)

On the chopping block.

makeface_supplement.import_local(fn)

Import a local script manually.

makeface_supplement.import_remote(script, is_script=False)

Import a script as a module, directly, iff it is not in the path.

makeface_supplement.makeface(*arglist)

### M2P “Makefile to python” ### Ryan Bradley’s ultra-hackish way of making CLI’s for python

makeface_supplement.str_or_list(x)

Turn a string or a list into a list.

makeface_supplement.strip_builtins(obj)

Remove builtins from a hash in place.

makeface_supplement.tracebacker(e)

commons

This module contains important constants used by VMDMake.

vmdmake

class vmdmake.VMDWrap(name=’vmd’, **kwargs)

Methods

command(text)

Add a raw command to the script if necessary.

do(*names)

Use a set of prescribed code blocks defined in commons.

i = ‘black’

ii = 16

martini_secondary_structure(itp, style=’all’, name=’protein_subject’, back_color=None, mers=1)

Color a MARTINI protein by secondary structure.

recipe(recipe, **kwargs)

Add from a set of predefined selections.

render(name=’video’, rate=1.0, codec=None, size=50.0, duration=0.0, webm=False)

Render a video from snapshots.

select(**kwargs)

Create a new selection with string substitutions.

set_color_cursor(color)

The $color_cursor variable in tcl is set to black (16) by the standard package but can be changed to use coloring by a particular ColorID, on the fly.

show(**kwargs)

Run VMD. The pipe option will feed commands directly to VMD for systems with a wonky setup. !option to remove everything when done (clean)? !dispdev text option (text)?

trajectory(target, first=0, last=-1, step=1)

Load a trajectory. Most functions are handled in the commons.py, however it makes more sense to do this manually.

video(traces=None, snapshot=False, pause=False, cwd=”, dn=None)

Prepare to render a video by writing an add-on script.

vmd_colors = {‘blue’: 0, ‘gray’: 2, ‘purple’: 11, ‘mauve’: 13, ‘white’: 8, ‘yellow’: 4, ‘black’: 16, ‘pink’: 9, ‘green’: 7, ‘iceblue’: 15, ‘orange’: 3, ‘cyan’: 10, ‘tan’: 5, ‘ochre’: 14, ‘silver’: 6, ‘red’: 1, ‘lime’: 12}

write()

Write the script.

yamlparse(text)

Try yamlparse (comes from yamlb in acme) first otherwise treat it like python.

vmdmake.nospaces(text)