Module pml_menus

Show and restart the progress bar on the Toggle Table if the TT is defined

Parameters:

• maximum (int) - The maximum value of the progress bar

Show the current progress on the progress bar on the Toggle Table if the TT is defined

Parameters:

• inc (int) - The amount to increment the progress bar value
• total (int) - The absolute value to set the progress bar to

Get the atoms in the workspace structure that match the given asl

Parameters:

• asl (str) - the asl this action will apply to
• extract (bool) - True if a structure containing the matching atoms should be extracted and returned, False if not

Returns: tuple

workspace structure (schrodinger.Structure), list of matching atom indicies, matching structure (or None)

Get the entries in the workspace structure are affected by the given asl

Parameters:

• owner (ToggleTableObject) - the object this command will operate on
• asl (str) - the asl this action will apply to

Returns: list or None

Each item of the list is a workspace entry (Structure) that is affected by asl. In case of error - normally caused by multiple Scratch entries - None is returned. An empty list is returned if ASL does not affect any workspace entries.

Return list of the the Visible workspace atoms

Returns: list

list of atom indexes of visible workspace atoms

Return an ASL that represents the Visible workspace atoms

Returns: str

an ASL expression that represents the Visible workspace objects, or None if no atoms are visible

Joins 2 asls with the given joiner (default is AND)

Parameters:

• asl1 (str) - the first asl
• asl2 (str) - the second asl
• joiner (str) - the linking logic (AND, AND NOT, OR...)

Returns: str

the two asls joined by the joiner

Puts a modifier in front of asl - which it protects in ()'s to make sure the modifier applies to the whole asl

Parameters:

• modifier (str) - the modifier to prepend to the asl (NOT, FILLRES, FILLMOL)
• asl (str) - the asl

Returns: str

the modified asl with the modifier prepended to it

Get the surfaces associated with entry_id entry

Parameters:

• entry (str) - The entry_id of the entry of interest

Returns: iterable

iterable object containing surfaces associated with this entry

Get the structures in the workspace referred to by a given toggle table entry

Parameters:

• owner (ToggleTableObject) - the object to retrieve entries from

Returns: list

a list of all ToggleTableEntries referred to by owner

Display atoms and bonds with the given style, and turn off ribbons and surfaces

Parameters:

• asl (str) - the asl this action will apply to
• atoms (str) - atom display style
• bonds (str) - bond display style
• owner (ToggleTableObject) - the object this command will operate on - used to see if the atoms should be made visible or not

Display atoms and bonds with the given style, leaving ribbons as is

Parameters:

• asl (str) - the asl this action will apply to
• atoms (str) - atom display style
• bonds (str) - bond display style
• owner (ToggleTableObject) - the object this command will operate on - used to see if the atoms should be made visible or not

Show ribbons

Parameters:

• asl (str) - the asl this action will apply to
• style (str) - the ribbon style
• hideatoms (bool) - True if atoms (i.e. the non-ribbon representation) should be hidden, False if not
• scheme (str) - the ribbon scheme
• owner (ToggleTableObject) - the object this command will operate on - used to see if the atoms should be made visible or not

Rotate the workspace back and forth smoothly by small degree increments over a span of degrees range. If called when rocking is currently occuring, will stop the rocking.

Parameters:

• interval (int) - in units of ~1/20 second, the frequency at which the rocking movement should be made
• amount (int) - The number of degrees the workspace should be rotated each rocking movement
• span (int) - The amount to rotate in one direction (past 0) before reversing

Tries to display the image file in the default image viewer

Parameters:

• image_file (str) - The path to the image to be displayed

Ensure that filename ends with the proper extension

Parameters:

• filename (str) - the filename to check
• extensions (str or list) - a list of valid extensions or a single extension. Extensions should include the '.'

Returns: str or None

either

• filename if filename has a valid extension
• filename + ext if filename has no extension, ext is the value of, or the first item in extensions,
• None if filename has an extension not given by extensions

Create a surface

Parameters:

• entry (str) - The entry id to create the surface for
• asl (str) - The ASL defining the atoms to create the surface for
• name (str) - The name given to the created surface
• style (str or None) - One of the following values
  • 'solid' (default)
  • 'mesh'
  • 'dots'
• quality (int) - The quality of the displayed surface.
  • 1 is medium quality (default)
  • 2 is high quality
• transparancy (int) - transparancy % of the surface. Default is 0 (solid), max is 100.
• viewasl (str) - The ASL that defines the portion of the surface to view - default is to view the entire surface
• viewdistance (str) - A string representation of a number that defines how close the suface needs to be to the set of viewasl atoms to be shown. Default is 3 Angstroms.
• scheme (str) - The coloring scheme for the surface (default is Atom Color)
• owner (ToggleTableEntry) - The object this command will operate on. This is used to decide if the surface will be shown or not. Default is to show the surface

Parameters:

• menu (QMenu) - the QMenu that owns this action
• owner (ToggleTableObject) - the object this Menu will operate on

Parameters:

• menu (QMenu) - the QMenu that owns this action
• owner (ToggleTableObject) - the object this Menu will operate on

Parameters:

• menu (QMenu) - the QMenu that owns this action
• owner (ToggleTableObject) - the object this Menu will operate on

Find all the entries specified by the given owner or asl

Parameters:

• owner (ToggleTableObject) - The ToggleTableObject this function applies to, if None and asl is None,(the default), then all included entry id's are returned
• asl (str) - The asl to find entries for

Returns: list

list of entry ID's the asl spans

Finds the x,y,z coordinates of the center of the atoms

Parameters:

• struct (schrodinger.Structure object) - structure containing the atoms

Returns: list

[x, y, z] specifying the center of the atoms

Finds all polar contacts (hydrogen bonds) between asl1 and asl2.

Parameters:

• asl1 (str) - ASL defining one set of atoms to find H-bonds between. If asl2 is defined, then H-bonds are found between the two sets, but not within. If asl2 is not defined, then H-bonds are found within asl1.
• asl2 (str) - ASL defining one set of atoms to find H-bonds between. If asl2 is defined, then H-bonds are found between asl1 and asl2, but not within. If asl2 is not defined, then H-bonds are found within asl1.

Parameters:

• menu (QMenu) - the QMenu that owns this action
• owner (ToggleTableObject) - the object this Menu will operate on

Hide the atoms given by asl

Parameters:

• asl (str) - the asl this action will apply to. Must be given if owner is None
• owner (ToggleTableObject) - the object this action will apply to. Must be given if asl is None

Hide ribbons

Parameters:

• asl (str) - the asl this action will apply to. If None, then owner must be given, and all atoms specified by owner will be hidden.
• owner (ToggleTableObject) - The object to hide ribbons in. If given and the entry is currently invisible, the ribbons will be appropriately updated. If not given, no invisible atoms will be hidden

Hide a surface

Parameters:

• entry_id (str) - the entry_id this action will apply to
• owner (ToggleTableObject) - The object to hide surfaces from. Used to determine if an entry is invisible. If not given, no invisible atoms will be hidden
• asl (str) - The ASL describing atoms to hide the surface of. If this ASL is given and does not contain any protein atoms, then the no surfaces will be hidden. Otherwise, all surfaces of the specified entry will be hidden.

Hide the labels

Parameters:

• asl (str) - The ASL defining the atoms whose labels will be hidden. If not given, the asl from owner will be used
• owner (ToggleTableObject) - If asl is None, the object containing the labels to be hidden

Hide atoms, ribbons and surfaces

Parameters:

• asl (str) - the asl this action will apply to
• entry_id (str) - the entry_id this action will apply to
• owner (ToggleTableObject)

Create the Hide menu

Parameters:

• menu (QMenu) - the QMenu that owns this action
• owner (ToggleTableObject) - the object this Menu will operate on

Get a user-specified color from the list of known Maestro colors

Returns: tuple

(Maestro color name, (R, G, B, Alpha)) or (None, None) if the user cancels the window.

Colors the specified atoms with the given color

Parameters:

• color_name (str) - a Maestro-recognized color name, found in mmshare/data/colors.res
• asl (str) - The ASL specifying the atoms to color

Colors the specified atoms with the given RGB colors

Parameters:

• red (int) - integer between 0 and 255
• green (int) - integer between 0 and 255
• blue (int) - integer between 0 and 255
• asl (str) - The ASL specifying the atoms to color

Form an ASL that restricts the given ASL to those atoms of a specific element

Parameters:

• asl (str) - The general asl to make element specific
• element (str) - an atomic symbol to restrict the ASL to

Returns: str

Color H, C, N, O and S by colors

Parameters:

• base_asl (str) - asl defining the group of atoms to color
• hydrogen (str) - the Maestro color string defining the color for H atoms
• carbon (str) - the Maestro color string defining the color for C atoms
• nitrogen (str) - the Maestro color string defining the color for N atoms
• oxygen (str) - the Maestro color string defining the color for O atoms
• sulfur (str) - the Maestro color string defining the color for S atoms

The user has selected a new (or re-selected an existing custom set) - add it to the list of custom sets (or move it to the end) so it ends up at the top of the menu

Parameters:

• color_name (str) - the Maestro color name of the color to save
• rgba (4-tuple or None) - tuple of (red, blue, green, alpha) if this is a new color, or None if this is already an existing color
• mytype (str) - the type of color this is (HYDROGEN_COLOR, CARBON_COLOR, OBJECT_COLOR)

Maestro doesn't like blank chain names in ASL without quotes so add the quotes if necessary

Parameters:

• cname (str) - the chain name

Returns: str

cname if cname is not blank, otherwise a double-quoted space

Returns the atom B-factor

Parameters:

• atom (schrodinger._Atom) - atom object to return the B-factor for
• zeros (bool) - True if atoms with No B-factor should return 0.0, False if it should return None

Returns: float or None

the B-factor of the given atom

Divide atoms up into bins based on their B-factor (temperature factor). The groups are determined to span equal ranges of b-factor (some groups may therefore contain no atoms).

Parameters:

• atoms (list) - list of atom indexes to bin
• groups (int) - The number of bins to create
• struct (schrodinger.structure.Structure)

Returns: list

List of binned atom indexes - each item of the list is a list containing the atom indexes for that bin. Item 0 are the lowest B-Factors.

Color all the atoms (and sometimes the ribbons) as chainbows

Parameters:

• asl (str) - the asl this action will apply to
• ribbons (str) - The type of ribbons to create with these colorings. The default is not to create ribbons.

  Color each chain like a rainbow! Each group of atoms within a chain gets different colors. Groups are created to (roughly) equal number of atoms in each group, and all the atoms in a residue are given the same color (if the residue != UNK).

Parameters:

• menu (QMenu) - the QMenu that owns this action
• owner (ToggleTableObject) - the object this Menu will operate on
• c_menu (QMenu) - Submenu for recent custom carbon colors
• h_menu (QMenu) - Submenu for recent custom hydrogen colors

Adds items common to many context menus

Parameters:

• menu (PMLMenu) - the menu to add items to
• select (bool) - True if Select is on the menu, False if not

PROT_AND_DNA_SELE

Value:

'(res. ALA,CYS,CYX,ASP,GLU,PHE,GLY,HIS,HID,HIE,HIP,HISE,HISD,HISP,ILE, LYS,LEU,MET,MSE,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR,A,C,T,G,U)'

SOLVENT_AND_IONS

Value:

'(water) OR atom.ele Ca, Hg, K, Na, Zn, Mg, Cl'

MAESTRO_TO_STRUCT_STYLE

Value:

{None: 0, 'ballnstick': 3, 'cpk': 2, 'none': 0, 'tube': 2, 'wire': 1}

MMCT_TO_MAESTRO_RIBBON_STYLE

Value:

{0: 'none', 1: 'cartoon', 2: 'ribbon', 3: 'tube', 4: 'thintube', 5: 'curvedline', 6: 'calphaline', 7: 'calphatube'}

MAESTRO_TO_MMCT_RIBBON_STYLE

Value:

{'calphaline': 6, 'calphatube': 7, 'cartoon': 1, 'curvedline': 5, 'none': 0, 'ribbon': 2, 'thintube': 4, 'tube': 3}

ATOM_RAINBOW_COLORS

Value:

['user27', 'blue9', 'userM', 'user19', 'user3', 'green', 'olive', 'user16', ...

RIBBON_RAINBOW_COLORS

Value:

['blue', 'lightblue', 'turquoise', 'springgreen', 'darkgreen', 'green', 'yellowgreen', 'yellow', ...

PYMOL_COLOR_CYCLE

Value:

['green', 'user4', 'purple', 'user16', 'pink', 'white', 'blue14', 'orange', ...

RT_COLOR_LABEL_START

Value:

'<span style="background-color:black;font-size:16px">'

RT_TO_MAESTRO_COLORS

Value:

{'cyan': 'user4', 'lime': 'green', 'magenta': 'purple', 'pink': 'pink', 'red': 'red', 'yellow': 'user16'}

mmshare_data

Value:

'/scr/buildbot/savedbuilds/2017-2/NB/build-142/mmshare-v3.8/data'

colorpath

Value:

'/scr/buildbot/savedbuilds/2017-2/NB/build-142/mmshare-v3.8/data/color s.res'

color_dict

Value:

OrderedDict([((191, 0, 191), 'userQ'), ((225, 30, 225), 'purple'), ((2 34, 173, 234), 'plum'), ((216, 191, 216), 'thistle'), ((191, 159, 255) , 'userH'), ((180, 0, 255), 'user62'), ((95, 63, 255), 'userR'), ((120 , 0, 255), 'user61'), ((90, 0, 255), 'user32'), ((75, 0, 255), 'user31 '), ((60, 0, 255), 'user30'), ((45, 0, 255), 'user29'), ((30, 0, 255), 'user28'), ((15, 0, 255), 'user27'), ((0, 0, 38), 'user63'), ((0, 0, 128), 'user2'), ((30, 30, 225), 'blue'), ((247, 247, 255), 'blue31'), ((239, 239, 255), 'blue30'), ((231, 231, 255), 'blue29'), ((223, 223, ...

custom_color_dicts

Value:

{'carbon': OrderedDict(), 'hydrogen': OrderedDict(), 'object': OrderedDict()}