# bni-tools Copyright Notice
# =====================================
#
# The bni-tools source code is copyrighted, but you can freely
# use and copy it as long as you don't change or remove any of the
# Copyright notices. bni-tools is made available under the
# following open-source license terms:
# ----------------------------------------------------------------------
# bni-tools is Copyright (C) 2008-2016 Georg Steinkellner / Schrodinger LLC
# All Rights Reserved
# Permission to use, copy, modify, distribute, and distribute modified
# versions of this software and its built-in documentation for any
# purpose and without fee is hereby granted, provided that the above
# copyright notice appears in all copies and that both the copyright
# notice and this permission notice appear in supporting documentation,
# and that the names of the authors not be
# used in advertising or publicity pertaining to distribution of the
# software without specific, written prior permission.
# The authors DISCLAIM ALL WARRANTIES WITH
# REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHORS BE
# LIABLE FOR ANY SPECIAL, INDIRECT OR
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
# PERFORMANCE OF THIS SOFTWARE.
# ----------------------------------------------------------------------
# for plugin description begin
'''The BNI (Beyond Normal Interaction)- Tools is a
plug in for the PyMOL molecular visualization
system which adds additional functionalities and
presets to the PyMOL GUI.
'''
from __future__ import print_function
# for plugin description end
from pymol import cmd
from pymol import util
from pymol import preset
from pymol import stored
from pymol import menu
from chempy import cpv
import os
import base64
import zlib
import sys
if sys.version_info[0] < 3:
from Tkinter import *
import Tkinter
import tkSimpleDialog
import tkFileDialog
else:
from tkinter import *
import tkinter as Tkinter
from tkinter import simpledialog as tkSimpleDialog
from tkinter import filedialog as tkFileDialog
__version__ = "0.39"
__bni_year__ = "2016"
__copyright__ = "(c) %s" % __bni_year__
__pymol_version__ = cmd.get_version()[1]
# Look for integrated BNI Tools in menu.py by checking preset settings
show_bni = 1
menu_list = [1 for i in menu.presets(cmd, "None") if "track main chain" in i]
if menu_list:
show_bni = 0
#
# Pymol Tools v.039
#
# AUTHOR: Georg Steinkellner
#
#.
sidebar_stdwidth = int(cmd.get("internal_gui_width"))
# set keys
if __pymol_version__: #<= 1.41:
try:
#cmd.set_key('CTRL-X',cmd.create,(None,"sele",-1,-1,0))
cmd.set_key('CTRL-A', cmd.select, ("sele", "visible", 1))
except:
pass
####################
# ICON and IMAGE GENERATION START
###################
#DATA BEGIN
bni_gif = b'''
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'''
about_gif = b'''
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Z08pgPY/nQHJmIGiSBMiDkKtQAdErT/lCi8V052pAk2h9dyN6zrwfNalT+Qa8PEogJCWf5mvqu06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'''
# DATA END
def getpic(picture, decode=0):
if decode == 1:
pic = zlib.decompress(base64.decodestring(picture))
else:
pic = base64.encodestring(
zlib.decompress(base64.decodestring(picture)))
return pic
bni_image = getpic(bni_gif)
try:
bni_image = Tkinter.PhotoImage(data=bni_image)
except:
bni_image = ""
def do_nothing():
pass
####################
# ICON and IMAGE GENERATION END
###################
###################
# ABOUT SECTION BEGIN
###################
######################################################
bni_info = '''The BNI (Beyond Normal Interaction)- Tools is a
plug in for the PyMOL molecular visualization
system which adds additional functionalities and
presets to the PyMOL GUI.
Version: %s (%s)
Please cite BNI-Tools if you find the following
additional features useful.
# BNI tools dropdown menu
[+]Load Files->
[-]modeller files
* load multiple modeller files and sort by
* objective function energy
* and add energy to object title
[-]autodock files
* load autodock .dlg or .dlg.pdb file into
* different states with energy in object
* title
[-]amber minimization
* load amber minimization file with energy in
* title if the .info file is present in same
* directory and has the same name as the pdb file.
[-]delphi phi,dx map
* load delphi map and corresponding pdb file
* simultaneously and show surface colored by
* PHI or DX map. (show the surface to see the
* effect)
[-]casox map
* load casox map (cavity calculation) and
* show ligsite accessibility
* value maps. (7 closed cavity to 1 open)
[-]multiple files into states
* load multiple pdb files (e.g. MD simulation
* snapshots) into one state. (object is named
* by first object loaded)
[+]Fetch->
[-]Density View (EDS)
* load density and pdb file from EDS
* (Electron Density Server)
* if available, and show density with density
* wizard
[-]RCSB Biol. Assembly
* load biological assembly from RCSB
* protein database
[-]2FoFc map(s)
* load (multiple) 2FoFc maps
* from EDS density server
* if available
[-]FoFc maps(s)
* load (multiple) FoFc maps
* from EDS density server
* if available
[+]Edit->
[-]HIS --> HID,HIE,HIP
* change histidine residues to HID,HIE,HIP
* depending on hydrogens on histidine
[-]HID,HIE,HIP --> HIS
* change altered histidine residues
* back to HIS
[-]Poly-Alanine Chain
* create a poly alanine chain (GLY and ALA)
* for molecular replacement
[-]MSE --> MET
* change selenomethionine to methionine
[-]del alternates
* delete alternates in selection
[-]Unbond- >
* unbond atoms in selection
[+]Images->
* create ray traced images depending on
* x size and resolution (dpi)
[+]Create->
* create compiled graphics objects (CGO)
* these objects can be altered in color or
* transparency, and they can be dragged
* and rotated in space by the
* "action->drag" command and using
* "shift" and mouse buttons.
[-]Plane
* create a plane (with certain cushion)
* using a selection of three atoms
[-]Box
* create a box around selection
* the whole box can be altered as group
* or by side planes separately
[-]Triangle
* create a triangle using a selection of three
* atoms
[+]pseudo center atom
* create pseudo atom at the center of atoms
* in selection
* move atoms with editing->"shift"
* and middle mouse button
# BNI tools integrated in PyMOL sidebar
[+]Action on "all"
[-]delete enabled
* delete all enabled objects or
* selections
[-]invert enabled/disabled
* disable currently enabled objects
[-]combine selections
* combine all enabled or disabled
* selections to selection (sele)
[+]action
[-]sequence
* show sequence in different formats
* of selection
* copy and paste to text file for later use
[.]fasta
* show sequence of selection
* in fasta format
[.]pir
* show sequence of selection
* in pir format
[.]modeller
* show sequence of selection
* in modeller pir format
[.]list
* create residue or atom lists
* of selection
[+]preset
[-]track main chain
* create a new object which tracks the
* main chain atoms and shows main chain
* and side chain polar contacts
[-]symmetry surface
* create a symmetry view of the selected
* atoms showing the contact surface as well
* as a selection entry of the atoms in
* contact with symmetry mates
* (only includes atoms of the initial selection).
[-]hydrophobic residues
* show hydrophobic residues
* depending on hydrophobic residue scales
* by KandD (Kyte & Doolittle
* J Mol Biol 157:105, 1982)
* Rose (Rose et al.
* Science, 229, 834-838,1985)
* GES (Engelman Engelman et al.
* Annu Rev Biophys Biophys Chem,
* 15, 321-353(1986)
* (no window selection; just raw categories
* are colored by: blue-hydrophile
* green-neutral
* red-hydrophobe )
[-]surface inspection
* create selections for surface
* inspections
# BNI tools additional settings in PyMOL sidebar
[+]color
[-]by ss
* color helix,sheet and loop separately
[.]Helix
[.]Sheet
[.]Loop
[-]surface
* color surface separately from atoms
[.]by atom
* set surface color to standard
[.]by map
* if a map or ramp is loaded
* color surface by ramp/map
[.]my color
* color surface by own defined color
[-]mesh
* color mesh separately from atoms
[.]by atom
* set mesh color to standard
[.]by map
* if a map or ramp is loaded
* color mesh by ramp/map
[.]my color
* color mesh by own defined color
[-]label
* color labels separately
[.]by atom
* set label color by atom
[.]my color
* color labels by own defined color
[-]stick
* color sticks separately
[.]standard
* set stick color to standard
[.]my color
* color sticks by own defined color
[-]my colors
* use/append own defined colors
* own colors can be defined by
* Setting->Colors..->New
* to keep color settings for
* other pymol sessions
* you have to set the colors
* in .pymolrc or similar
* pymol setting file
* like
* set_color mycolor,[ 1.00, 1.00, 1.00]
[+]show/hide
[-]surface flag
* set surface flag of atoms to show hide
* or ignore fro surface calculation
[-]transparency
* set different transparency types
* on selections or atoms
''' % (__version__, __bni_year__)
class AboutGui:
def __init__(self, parent):
self.buttons = ['Ok', 'Cite', 'Thanks', 'Info', 'Exit']
self.lastinterior = None
self.txtcolors = (("Green", ("#")),
("DarkBlue", ("[+]",
)),
("Blue", ("[-]", "[.]"
)),
("Purple", ("*",
)),
("Red", ("ACKNOWLEDGEMENTS",
)),
)
about_image = getpic(about_gif)
try:
self.about_image = Tkinter.PhotoImage(data=about_image)
except:
self.about_image = ""
self.dialog = Pmw.Dialog(parent,
title='BNI-Tools (c) SCHRODINGER',
buttons=self.buttons,
defaultbutton=self.buttons[0],
command=self.execute,
)
self.defaultwindow()
def write_info(self, bni_info):
listone = bni_info.split("\n")
if self.txt:
for line in listone:
style = self.check_syntax(str(line), use=1, case=1)
self.txt.insert('end', str(line) + "\n", style)
def get_info(self, bni_info, joinit=0):
a = []
s = ""
if joinit:
a.extend(b.strip() for b in bni_info.split("\n"))
if joinit == 1:
sign = " "
else:
sign = "\n"
s = sign.join(a)
if joinit == 0:
return "%s" % bni_info
else:
return "%s" % s
def check_syntax(self, line, use=1, case=1):
'''Check syntax highlighting.
line: str:line to check for syntax
use:0: just return empty string.
case:1: case sensitive
'''
syntax = [""]
if use == 0:
return tuple(syntax)
if case == 1:
low = str.lower
else:
low = lambda x: x
for color, tags in self.txtcolors:
for tag in tags:
if low(tag) in low(line):
syntax.append(color)
return tuple(syntax)
def tag_list(self, txt_parent):
'''Tag list for tags to color log output.
'''
for color, filter in self.txtcolors:
txt_parent.tag_configure(color, foreground=color)
def destroylast(self):
if self.lastinterior is not None:
self.lastinterior.destroy()
def defaultwindow(self):
self.destroylast()
self.w = Tkinter.Label(self.dialog.interior(),
text='Beyond Normal Interaction - Tools',
background='white',
foreground='black',
image=self.about_image,
pady=20)
self.w.pack(expand=1, fill='both', padx=4, pady=4)
self.lastinterior = self.w
def message(self, parent, text="", hull_width=400, hull_height=90):
fixedFont = Pmw.logicalfont('Fixed')
self.txt = Pmw.ScrolledText(parent,
labelpos=None,
columnheader=0,
rowheader=0,
rowcolumnheader=0,
usehullsize=1,
hull_width=hull_width,
hull_height=hull_height,
text_wrap='word',
text_font=fixedFont,
text_padx=4,
text_pady=4,
)
self.txt.pack(padx=0, pady=0, fill='both', expand=1)
self.tag_list(self.txt)
self.txt.appendtext(text)
def showcite(self, text="", label_text="", hull_width=400, hull_height=300, vertflex="expand", horizflex="expand"):
self.destroylast()
self.sf = Pmw.ScrolledFrame(self.dialog.interior(),
labelpos='n',
label_text=label_text,
usehullsize=1,
hull_width=hull_width,
hull_height=hull_height,
vertflex=vertflex,
horizflex=horizflex,
)
pixelperchar = 12
hull_width = int(len(text) / 3) * pixelperchar
hull_height = int(3 * pixelperchar)
self.message(
self.sf.interior(), text=text, hull_width=hull_width, hull_height=hull_height)
self.sf.pack(padx=5, pady=5, fill='both', expand=1)
self.lastinterior = self.sf
def execute(self, action):
if action not in self.buttons:
self.dialog.destroy()
elif action == self.buttons[0]:
self.defaultwindow()
elif action == self.buttons[-1]:
self.dialog.destroy()
elif action == self.buttons[1]:
citetext = "Steinkellner, G.(%s). BNI-Tools (Version %s)[Computer software]. Schrodinger, LLC." % (
__bni_year__, __version__)
self.showcite(label_text="How to cite BNI - Tools...",
hull_width=400,
hull_height=120,
horizflex="elastic",
text=citetext)
print(citetext)
elif action == self.buttons[2]:
namelist = ["Schrodinger LLC",
"J. Vertrees",
"T. Holder",
"K. Gruber",
"M. Uhl",
"G. Oberdorfer",
"A. Lyskowski",
"C. C. Gruber",
"the strubi group"]
text = "Thanks to ...\n%s" % "\n".join(namelist)
self.showcite(label_text="Thanks for contributing, support and testing...",
hull_width=400,
hull_height=120,
horizflex="elastic",
text=text)
#print(text)
elif action == self.buttons[3]:
self.showcite(label_text="Info about BNI-Tools",
hull_width=570,
hull_height=120,
horizflex="elastic",
text='')
self.write_info(bni_info)
#pass
###################
# ABOUT SECTION END
###################
def bni_toggleHelp(a):
print('Toggle value:', a.bni_toggleHelp.get())
####################
# system variable settings
####################
def get_env(variable="BNI_SHOW"):
'''Get the environment variable if set.
variable: variable name
'''
try:
value = os.environ.get(variable)
except:
value=""
return value
show_bni_env = get_env("BNI_SHOW")
if show_bni_env and show_bni == 0:
show_bni = show_bni_env
def __init__(self):
self.__class__._gui = self
seletext = "act on selection (sele)"
self.menuBar.addcascademenu('Plugin', 'bni-tools', 'BNI Tools',
label='BNI Tools', tearoff=True)
self.menuBar.addmenuitem('bni-tools', 'separator', '')
self.menuBar.addmenuitem('bni-tools',
'command',
'BNIInfo',
'BNI info',
background="lightblue",
activebackground="lightblue",
foreground="darkblue",
activeforeground="darkblue",
label='BNI Tools v. %s %s' % (
__version__, __copyright__),
image=bni_image,
command=do_nothing)
self.menuBar.addmenuitem('bni-tools',
'command',
'BNIInfo2',
'BNI info2',
background="lightblue",
activebackground="lightblue",
foreground="blue",
activeforeground="blue",
label='v. %s %s' % (__version__, __copyright__),
command=do_nothing)
self.bni_toggleHelp = Tkinter.IntVar(self.root)
# Initialise the checkbutton to 0:
self.bni_toggleHelp.set(0)
self.menuBar.addmenuitem('bni-tools', 'separator', '')
self.menuBar.addmenuitem('bni-tools',
'command',
'About',
'AboutHelpCite',
background="lightblue",
activebackground="blue",
foreground="darkblue",
activeforeground="white",
label='About / How to cite',
#image=bni_image,
command=lambda s=self: AboutGui(s.root))
# Pseudo menue for clicking if clicking stucks
# Symmetry BEGIN
#import info
if show_bni:
self.menuBar.addmenuitem('bni-tools', 'separator', '')
self.menuBar.addcascademenu('bni-tools', 'symmetry', statusHelp='Symmetry settings',
traverseSpec=None,
label='Symmetry ->'
)
self.menuBar.addmenuitem('symmetry', 'command', background="lightblue", activebackground="lightblue",
foreground="blue", activeforeground="blue", label=seletext, command=do_nothing)
self.menuBar.addmenuitem('symmetry', 'separator', '')
self.menuBar.addcascademenu('symmetry', 'symview', 'Create Symmetry',
label='Create Symmetry View ->'
)
self.distances = ["set", 3.0, 3.5, 4.0, 4.5, 5.0, 10.0]
for item in self.distances:
self.menuBar.addmenuitem('symview', 'command',
'Distance %s' % item,
label='%s' % item,
command=lambda a=item, b=self: fast_sym(cutoff=a, app=b, selection="sele"))
self.menuBar.addmenuitem('symview', 'separator', '')
self.menuBar.addcascademenu(
'symview', 'colorsym', 'Color surface', label="Surface Patch Color ->")
self.menuBar.addmenuitem('colorsym', 'command',
'Set Surface to Symetry representation',
label='by symetry mates',
command=lambda a="symmetry": set_surface(mode=a))
self.menuBar.addmenuitem('colorsym', 'command',
'Set Surface to standard representation',
label='standard coloring',
command=lambda a="standard": set_surface(mode=a))
# Symmetry END
# Settings BEGIN
# PyMOL integration into Setting menu
# Side Bar settings
self.menuBar.addcascademenu('Setting', 'SideBar',
'SideBar settings',
label='Side Bar ->', tearoff=True)
self.menuBar.addcascademenu('SideBar', 'width',
'SideBar settings ->',
label='width', tearoff=True)
self.sidebar_lenght = ["set", 100, 200, 250, 350, 450]
for item in self.sidebar_lenght:
self.menuBar.addmenuitem('width', 'command',
'Width %s' % item,
label='%s' % item,
command=lambda a=item, b=self: runsidebar(set="width", value=a, app=b))
self.menuBar.addmenuitem('SideBar', 'command',
'fit sidebar to names',
label='fit to name',
command=lambda a="fit1": sidebar(set="width", value=a))
self.menuBar.addmenuitem('SideBar', 'command',
'fit sidebar to titles',
label='fit to title',
command=lambda a="fit2": sidebar(set="width", value=a))
self.menuBar.addmenuitem('SideBar', 'command',
'sidebar off',
label='off',
command=lambda a="fit2": sidebar(set="off", value=a))
self.menuBar.addmenuitem('SideBar', 'command',
'sidebar on',
label='on',
command=lambda a="fit2": sidebar(set="on", value=a))
self.menuBar.addcascademenu('SideBar', 'overlay',
'Overlay settings ->',
label='overlay')
self.menuBar.addmenuitem('overlay', 'command',
'set sidebar overlay on',
label='on',
command=lambda a="": sidebar(set="overlayon", value=a))
self.menuBar.addmenuitem('overlay', 'command',
'set sidebar overlay off',
label='off',
command=lambda a="": sidebar(set="overlayoff", value=a))
# Settings END
self.menuBar.addmenuitem('bni-tools', 'separator', '')
# Presets BEGIN
if show_bni:
self.menuBar.addcascademenu('bni-tools', 'presets', 'Preset Views',
label='Preset Views ->', tearoff=True
)
self.menuBar.addmenuitem('presets', 'command', background="lightblue", activebackground="lightblue",
foreground="blue", activeforeground="blue", label=seletext, command=do_nothing)
self.menuBar.addmenuitem('presets', 'separator', '')
self.menuBar.addmenuitem('presets', 'command',
'Track Mainchain',
label='Track MainChain',
command=lambda a="track_mainchain": new_views(preset=a))
self.menuBar.addcascademenu('presets', 'HPvalue',
'Hydrophobic Values',
label='Hydrophobic Values ->'
)
#
self.HPvalues = ["KandD", "Rose", "GES"]
for item in self.HPvalues:
self.menuBar.addmenuitem('HPvalue', 'command',
'HPvalues %s' % item,
label='%s' % item,
command=lambda a=item: select_hp(hp_value=a))
#
self.menuBar.addmenuitem('presets', 'command',
'Surface Atoms',
label='Atoms for Surface Inspection',
command=lambda a="surf_rel_res": new_views(preset=a))
# Presets END
self.menuBar.addmenuitem('bni-tools', 'separator', '')
# Load Begin
self.menuBar.addcascademenu('bni-tools', 'Load Files', 'Load Files',
label='Load Files ->',
tearoff=True)
if show_bni:
self.menuBar.addmenuitem('Load Files', 'command',
'Multiple Files',
label='Multiple Files',
command=lambda b=self: multi_pdb(b).fetchFileName())
self.menuBar.addmenuitem('Load Files', 'command',
'Modeller Files',
label='Modeller Files',
command=lambda b=self: multi_pdb(b).fetchFileName(ext="modeller"))
self.menuBar.addmenuitem('Load Files', 'command',
'AutoDock Files',
label='AutoDock Files',
command=lambda b=self: multi_pdb(b).fetchFileName(ext="autodock"))
self.menuBar.addmenuitem('Load Files', 'command',
'Amber mimimization',
label='Amber minimization',
command=lambda b=self: multi_pdb(b).fetchFileName(ext="ambermin"))
self.menuBar.addmenuitem('Load Files', 'command',
'Delphi Map Files',
label='Delphi PHI,DX Map',
command=lambda b=self: multi_pdb(b).fetchFileName(ext="delphi"))
self.menuBar.addmenuitem('Load Files', 'command',
'Casox Map',
label='Casox Map',
command=lambda b=self: multi_pdb(b).fetchFileName(ext="casox"))
self.menuBar.addmenuitem('Load Files', 'command',
'One Object',
label='Multiple Files into states',
command=lambda b=self: multi_pdb(b).fetchFileName(ext="oneobject"))
self.menuBar.addcascademenu('bni-tools',
'FetchPdb',
label='Fetch ->',
tearoff=True)
fetch_types = ["pdb", "pdb 2fofc fofc", "pdb1", "2fofc", "fofc"]
fetch_types_names = [
"PDB Codes(s)", "Density View (EDS)", "RCSB Biol. Assembly", "2FoFc map(s)", "FoFc map(s)"]
for typ, typn in zip(fetch_types, fetch_types_names):
self.menuBar.addmenuitem('FetchPdb',
'command',
'Fetch %s' % (typn.strip()),
label='%s' % (typn.strip()),
command=lambda b=self, a=typ: bni_fetch(parent=b, typ=a))
#Load End
self.menuBar.addmenuitem('bni-tools', 'separator', '')
# Edit BEGIN
self.menuBar.addcascademenu('bni-tools',
'EditAtom',
'Edit Atoms',
label='Edit ->',
tearoff=True)
self.menuBar.addmenuitem('EditAtom', 'command', background="lightblue", activebackground="lightblue",
foreground="blue", activeforeground="blue", label=seletext, command=do_nothing)
self.menuBar.addmenuitem('EditAtom', 'separator', '')
self.menuBar.addmenuitem('EditAtom',
'command',
'His2',
label="HIS --> HID,HIE,HIP",
command=lambda b="his2hid": his_handle(b))
self.menuBar.addmenuitem('EditAtom',
'command',
'Hid2',
label="HID,HIE,HIP --> HIS",
command=lambda b="hid2his": his_handle(b))
self.menuBar.addmenuitem('EditAtom',
'command',
'polyalanine',
label="Poly-Alanine Chain",
command=lambda: polyala("sele", name="polyala"))
self.menuBar.addmenuitem('EditAtom',
'command',
'MSE->MET',
label="MSE-->MET",
command=lambda: altermse("sele"))
self.menuBar.addmenuitem('EditAtom',
'command',
'delalt',
label="del alternates",
command=lambda: delalternate("sele"))
self.menuBar.addcascademenu('EditAtom',
'UnbondAtoms',
'Unbond Atoms',
label='Unbond ->',
tearoff=True)
self.menuBar.addmenuitem('UnbondAtoms',
'command',
'unbondatom',
label="atoms",
command=lambda: unbondatom(selection1="sele",
selection2="all",
selection="sele"))
self.menuBar.addmenuitem('UnbondAtoms',
'command',
'unbondallmetals',
label="metals",
command=lambda: unbondatom(selection1="metals",
selection2="all",
selection="sele"))
self.menuBar.addmenuitem('UnbondAtoms',
'command',
'unbondallhetatoms',
label="het atoms",
command=lambda: unbondatom(selection1="hetatm and not r. MES and not solvent",
selection2="!hetatm",
selection="sele"))
# Edit END
# Create BEGIN
self.menuBar.addmenuitem('bni-tools', 'separator', '')
self.menuBar.addcascademenu('bni-tools',
'Image',
'Create Image',
label='Images ->',
tearoff=True)
#Ray BEGIN
self.ray_settings = [
"set", "standard", "journal single", "journal double", "poster", "hires"]
ray_settings_menu = ["set (x mm/cm/inch y dpi)", "standard (10 cm 200 dpi) ", "single column (86 mm 400 dpi)",
"double column (178 mm 400 dpi)", "poster (30 cm 300 dpi)", "hires (12 cm 1200 dpi)"]
for item, item_names in zip(self.ray_settings, ray_settings_menu):
self.menuBar.addmenuitem('Image', 'command',
'Ray %s' % item,
label='%s' % item_names,
command=lambda a=item, b=self: _set_bni_ray(setting=a, app=b))#fast_sym(cutoff=item))
#self.menuBar.addmenuitem('Ray',
# 'command',
# 'His2',
# label="HIS --> HID,HIE,HIP",
# command= lambda b="his2hid": his_handle(b))
#Ray End
#Plane begin
self.menuBar.addcascademenu('bni-tools',
'Create',
'Create',
label='Create ->',
tearoff=True)
self.menuBar.addmenuitem('Create', 'command', background="lightblue", activebackground="lightblue",
foreground="blue", activeforeground="blue", label=seletext, command=do_nothing)
self.menuBar.addmenuitem('Create', 'separator', '')
self.menuBar.addcascademenu(
'Create', 'GetPlane', 'Get Plane', label='Plane ->', tearoff=True)
triangle_txt = "3 atoms in (sele)"
self.menuBar.addmenuitem('GetPlane', 'command', background="lightblue", activebackground="lightblue",
foreground="blue", activeforeground="blue", label=triangle_txt, command=do_nothing)
self.menuBar.addmenuitem('GetPlane', 'separator', '')
self.plane_settings = ["set", "small", "medium", "large"]
self.plane_settings_names = [
"set plane size", "small (size 5.0 %s)" % "Ang", "medium (size 10.0 %s)" % "Ang", "large (size 20.0 %s)" % "Ang"]
for item, itemnames in zip(self.plane_settings, self.plane_settings_names):
self.menuBar.addmenuitem('GetPlane', 'command',
'Plane %s' % item,
label='%s' % itemnames,
command=lambda a=item, b=self: get_plane_handler(action=a, app=b))
#Plane end
#Box begin
self.menuBar.addcascademenu('Create', 'GetBox', 'Get Box',
label='Box ->', tearoff=True
)
self.box_settings = ["set", "small", "medium", "large"]
self.box_settings_names = [
"set box cushion", "small (cushion 1.0 %s)" % "Ang", "medium (cushion 2.0 %s)" % "Ang", "large (cushion 3.0 %s)" % "Ang"]
for item, itemname in zip(self.box_settings, self.box_settings_names):
self.menuBar.addmenuitem('GetBox', 'command',
'Box %s' % item,
label='%s' % itemname,
command=lambda a=item, b=self: get_box_handler(action=a, app=b))
#Box End
#Triangle BEGIN
self.menuBar.addcascademenu('Create', 'Triangle',
'Triangle',
label='Triangle ->',
tearoff=True)
triangle_txt = "3 atoms in (sele)"
self.menuBar.addmenuitem('Triangle', 'command', background="lightblue", activebackground="lightblue",
foreground="blue", activeforeground="blue", label=triangle_txt, command=do_nothing)
self.menuBar.addmenuitem('Triangle', 'separator', '')
self.menuBar.addmenuitem('Triangle', 'command',
'create',
label='create ..',
command=lambda a="sele": get_triangle(selection=a, invert=0))
#Triangle END
if show_bni:
#Set Surface BEGIN
self.menuBar.addcascademenu('Create', 'SetSurface', 'Set surface',
label='Surface ->', tearoff=True
)
self.surf_settings = [
"Methionine", "Include", "Exclude", "Hide", "Show"]
for item in self.surf_settings:
self.menuBar.addmenuitem('SetSurface', 'command',
'Surface %s' % item,
label='%s' % item,
command=lambda a=item, b=self: get_surface_handler(action=a, app=b))
#Set Surface End
# Create END
# Show selection on BNI Tools or in PyMOL directly
if show_bni:
selemenu = "bni-tools"
self.menuBar.addmenuitem(selemenu, 'separator', '')
# Delete BEGIN
self.menuBar.addcascademenu(selemenu, 'delete',
'Delete all',
label='Delete enabled',
tearoff=True)
self.menuBar.addmenuitem('delete', 'command',
'enabled',
label='all',
command=lambda: del_enabled('all'))
self.menuBar.addmenuitem('delete', 'command',
'objects',
label='objects',
command=lambda: del_enabled('obj'))
self.menuBar.addmenuitem('delete', 'command',
'selections',
label='selections',
command=lambda: del_enabled('selections'))
self.menuBar.addcascademenu(selemenu, 'invert',
'invert all',
label='Invert enabled/disabled',
tearoff=True)
self.menuBar.addmenuitem('invert', 'command',
'all',
label='all',
command=lambda: inv_enabled('all'))
self.menuBar.addmenuitem('invert', 'command',
'objects',
label='objects',
command=lambda: inv_enabled('obj'))
self.menuBar.addmenuitem('invert', 'command',
'selections',
label='selection',
command=lambda: inv_enabled('selections'))
#combine BEGIN
self.menuBar.addcascademenu(selemenu, 'Combine', 'Combine selections',
label='Combine sele..', tearoff=True
)
self.combine_sele = ["all", "enabled", "disabled"]
for item in self.combine_sele:
self.menuBar.addmenuitem('Combine', 'command',
'combine %s' % item,
label='%s' % item,
command=lambda a=item: combine_sele(check=a))
#combine END
# Delete END
self.menuBar.addmenuitem('bni-tools', 'separator', '')
# Create Pseudo Atom for centers
self.menuBar.addmenuitem('bni-tools', 'command',
'Create PseudoCenter Atom',
label='PseudoCenter Atom',
command=lambda: get_center_atom(selection='(sele)', enabled="1", onlysele="1"))
# Get sequence
if show_bni:
self.menuBar.addmenuitem('bni-tools', 'separator', '')
self.menuBar.addcascademenu('bni-tools', 'Sequences',
'get sequence',
label='Sequences',
tearoff=True)
self.menuBar.addmenuitem('Sequences', 'command', background="lightblue", activebackground="lightblue",
foreground="blue", activeforeground="blue", label=seletext, command=do_nothing)
self.menuBar.addmenuitem('Sequences', 'separator', '')
self.menuBar.addmenuitem('Sequences', 'command', 'Fasta', label='fasta', command=lambda: get_sequence(
selection='(sele)', format="fasta"))
self.menuBar.addmenuitem('Sequences', 'command',
'pir',
label='pir',
command=lambda: get_sequence(selection='(sele)', format="pir"))
self.menuBar.addmenuitem('Sequences', 'command',
'modeller',
label='modeller',
command=lambda: get_sequence(selection='(sele)', format="modeller"))
self.menuBar.addcascademenu('Sequences', 'Normal',
'get normal sequence',
label='List ->',
tearoff=True)
self.menuBar.addmenuitem('Normal', 'command',
'Residue',
label='residues',
command=lambda: get_sequence(selection='(sele)', format="normal"))
self.menuBar.addcascademenu(
'Normal', 'bfac', 'bfac per res', label='bfac per res ->')
calc_fac_name = ['all', 'mainchain', 'sidechain']
calc_fac = ['all', 'main', 'side']
for item, itemname in zip(calc_fac, calc_fac_name):
self.menuBar.addmenuitem('bfac', 'command',
'bfac %s atoms' % itemname,
label='%s atoms' % itemname,
command=lambda a=item: get_sequence(selection='(sele)', format="normalb_%s" % a))
self.menuBar.addcascademenu(
'Normal', 'occ', 'occ per res', label='occ per res ->')
for item, itemname in zip(calc_fac, calc_fac_name):
self.menuBar.addmenuitem('occ', 'command',
'occ %s atoms' % itemname,
label='%s atoms' % itemname,
command=lambda a=item: get_sequence(selection='(sele)', format="normalq_%s" % a))
self.menuBar.addmenuitem('Normal', 'command',
'Residue',
label='all atoms',
command=lambda: get_sequence(selection='(sele)', selecting='atom', format="normal"))
# Print PDB line
self.menuBar.addmenuitem("Sequences", 'command',
'Get PDB lines',
label='PDB Format',
command=lambda: get_pdb_lines(selection='(sele)', state="0", enabled="1"))
cmd.extend('bni_fast_sym', fast_sym)
cmd.extend('bni_del_enabled', del_enabled)
cmd.extend('bni_del_sym', del_sym)
cmd.extend('bni_new_views', new_views)
cmd.extend('bni_new_name', rename_object)
cmd.extend('bni_get_pdb_lines', get_pdb_lines)
cmd.extend('bni_mse', mse)
cmd.extend('bni_get_box', get_box)
cmd.extend('bni_get_axes', get_axes)
cmd.extend('bni_get_point', get_point)
cmd.extend('bni_get_atom', get_atom)
cmd.extend('bni_get_center', getCenter)
cmd.extend('bni_get_center_atom', get_center_atom)
cmd.extend('bni_check_names', check_names)
cmd.extend('bni_sidebar', sidebar)
cmd.extend("bni_get_plane", get_plane)
cmd.extend("bni_get_polyala", polyala)
cmd.extend("bni_his_handle", his_handle)
cmd.extend("bni_get_sequence", get_sequence)
cmd.extend("bni_ray", bni_ray)
cmd.extend("bni_combine_sele", combine_sele)
cmd.extend("bni_unbondatom", unbondatom)
def bni_fetch(parent, typ="pdb"):
'''Fetch PDB codes or maps.
USAGE: bni_fetch(window,typ='pdb')
window: parent
typ: 'pdb'
'pdb 2fofc fofc'
'pdb1'
'2fofc'
'fofc'
'''
print("# -------------------#")
print("# BNI-Tools v. %s" % __version__)
print("# -------------------#")
PDBcode = tkSimpleDialog.askstring('BNI Fetch',
'Please enter 4-digit\npdb codes (space separated):',
parent=parent.root)
if PDBcode:
PDBcode = PDBcode.lower()
PDBcode = PDBcode.strip().split()
failed = 0
typ = typ.lower()
if typ == "pdb 2fofc fofc":
if len(PDBcode) > 1:
code = PDBcode[0]
print(
"# Density Wizard only for one map at once. Multiple PDB codes are given.")
print("# First PDB code (%s) will be used." % code)
else:
code = PDBcode[0]
typ = typ.strip().split()
names_uplow = cmd.get_names()
names = [nam.lower() for nam in names_uplow]
if code in names:
code_index = names.index(code)
code = names_uplow[code_index]
typ = ["2fofc", "fofc"]
for source in typ:
print("# Fetch %s of %s" % (source, code))
cmd.fetch(code, type=source)
if __pymol_version__ < 1.4:
print("# Pymol < 1.4 detected.(v. %s)" % __pymol_version__)
print("# Maps are mixed up. FoFc is 2FoFc and FoFc is 2FoFc.")
map1 = ["w1_", 0, "%s_%s" %
(code, "fofc"), 1.0, "slate"]
map2 = ["w2_", 1, "%s_%s" %
(code, "2fofc"), -3.0, "tv_red"]
map3 = ["w3_", 2, "%s_%s" %
(code, "2fofc"), 3.0, "tv_green"]
else:
map1 = ["w1_", 0, "%s_%s" %
(code, "2fofc"), 1.0, "slate"]
map2 = ["w2_", 1, "%s_%s" %
(code, "fofc"), -3.0, "tv_red"]
map3 = ["w3_", 2, "%s_%s" %
(code, "fofc"), 3.0, "tv_green"]
names = [nam.lower() for nam in cmd.get_names()]
if map1[2].lower() not in names or map2[2].lower() not in names:
print(map1[2], map2[2], names)
print(
"# Some maps could not be loaded. Density Wizard closed.")
return
try:
cmd.wizard("density")
cmd.refresh_wizard()
cmd.delete(map1[0] + map1[2])
cmd.delete(map2[0] + map2[2])
cmd.delete(map3[0] + map3[2])
cmd.get_wizard().set_map(0, "")
cmd.get_wizard().set_map(1, "")
cmd.get_wizard().set_map(2, "")
cmd.get_wizard().set_track(1)
maps = [map1, map2, map3]
group_name = code.upper() + "_maps_g"
try:
cmd.group(group_name, map1[2])
cmd.group(group_name, map2[2])
except:
pass
for map in maps:
cmd.get_wizard().set_map(map[1], map[2])
cmd.get_wizard().set_level(map[1], map[3])
cmd.color(map[4], map[0] + map[2])
try:
cmd.group(group_name, map[0] + map[2])
except: #no group command available
pass
cmd.get_wizard().update_maps()
except:
print(
"# Density Wizard could not be loaded with current settings.")
return
else:
typ = typ.strip().split()
for code in PDBcode:
for source in typ:
print("# Fetch %s of %s" % (source, code))
cmd.fetch(code, type=source)
if source == "pdb1":
cmd.split_states(code)
cmd.delete(code)
def unbondatom(selection1="sele", selection2="all", selection="all"):
'''Unbond atoms.
USAGE: unbondatom(selection1="sele",selection2="all",selection="sele")
PYMOL USAGE: bni_unbondatom selection1,selection2,selection
selection1="sele",
"metals", metals in selection (sele)
selection2="all"
selection="sele" overall selection1 restriction ("all" for no restiction)
unbonds selection1 (with restriction 'selection') from selection2
'''
selection = _remove_brakets(selection, brakets=0)
selection1 = _remove_brakets(selection1, brakets=0)
selection2 = _remove_brakets(selection2, brakets=0)
metals = ["mg", "zn", "ca", "fe", "mn", "cd", "cu", "co", "ni"]
info = []
info.append("# BNI-Tools v. %s" % __version__)
if selection1 == "metals":
metal = "+".join(metals)
selection1 = "symbol %s and (%s)" % (metal, selection)
try:
info.append("# Metals:")
for metal in metals:
cmd.select("_bni_metal_sele_%s" %
metal, "symbol %s and (%s)" % (metal, selection))
metalcount = cmd.count_atoms("_bni_metal_sele_%s" % metal)
if metalcount > 0:
info.append("# %s%s:%s metal ions found in selection (%s)." % (
metal[0].upper(), metal[1].lower(), metalcount, selection))
cmd.select("_bni_selection1", selection1)
atoms1 = cmd.count_atoms("_bni_selection1")
if atoms1 == 0:
info.append("# No Metals found in selection (%s)." % selection)
info.append("# %d Metals selected." % atoms1)
except:
info.append("# No atoms selected in (%s)" % selection)
print("\n".join(info))
return
try:
cmd.select("_bni_selection1", selection1)
atoms1 = cmd.count_atoms("_bni_selection1")
if atoms1 == 0:
info.append("# No atoms in selection. (%s)" % selection)
info.append("# Unbond %d atoms" % atoms1)
cmd.unbond(selection1, selection2)
except:
info.append("# No atoms selected in (%s)" % selection)
print("\n".join(info))
return
print("\n".join(info))
def combine_sele(selections=None, check="enabled", name="sele"):
'''Combine selections.
USAGE: combine_sele(selections=None,check="enabled",name="sele")
selections: "sele1 sele2 sele3": add additinal selections
check: "enabled": add only enabled selections
"all": add all selections
"disabled": add only disabled selectins
-1: do not look for selections
name: sele: specify name of combined selection
PYMOL: bni_combine_sele selections=None,check=-1,name="sele"
'''
selections = _remove_brakets(selections)
enabled = str(_remove_brakets(check))
name = str(_remove_brakets(name))
if enabled == "enabled":# combine enabled selections
sele_names = set(cmd.get_names("public_selections", enabled_only=1))
elif enabled == "all":# combine all selections
sele_names = set(cmd.get_names("public_selections", enabled_only=0))
elif enabled == "disabled":# combine not enabled selections
sele1 = set(cmd.get_names("public_selections", enabled_only=1))
sele2 = set(cmd.get_names("public_selections", enabled_only=0))
sele_names = sele2 - sele1
elif enabled == "-1":# do not check only use selections input
sele_names = []
sele_names = list(sele_names)
if selections:
addsele = selections.split()
for item in addsele:
sele_names.append(item)
if sele_names:
cmd.select(name, selection="(" + " or ".join(sele_names) + ")")
#cmd.set_name("_bni"+name,name)
else:
cmd.select(name, selection=None)
#cmd.set_name("_bni"+name,name)
print("# BNI - Tools v. %s" % __version__)
print("# Combined selections: %s" % sele_names)
print("# to (%s)" % name)
def _set_bni_ray(setting="set", app=None, async_=1):
'''Run sidebar input
'''
width = 100
dpi = 200
width_unit = "mm"
if setting == "set" and app:
value = tkSimpleDialog.askstring('Width mm/cm/inch/dots resolution dpi',
'Please specify width of image and resolution',
parent=app.root)
value = _remove_brakets(value)
if value:
value = value.split()
else:
return
if len(value) == 1:
width = value[0]
elif len(value) == 2:# width / dpi
width = value[0]
dpi = value[1]
elif len(value) >= 3:#width width_unit
width = value[0]
width_unit = value[1]
dpi = value[2]
else:
print("# Wrong input. Set at least the width.")
return
try:
float(width)
except ValueError:
print("# Width has to be a number.")
return
units = ["cm", "mm", "inch", "dots"]
if not width_unit.lower().strip() in units:
print("# Unit has to be either %s " % (" or ".join(units)))
return
try:
int(dpi)
except ValueError:
print("# DPI has to be an integer number.")
return
elif setting == "poster":
print("# POSTER SETTING")
width = 30
width_unit = "cm"
dpi = 300
print("# width: %s %s" % (width, width_unit))
print("# resolution: %s dpi" % dpi)
elif setting == "journal single":
print("# JOURNAL SETTING single column")
width = 86
width_unit = "mm"
dpi = 400
print("# width: %s %s" % (width, width_unit))
print("# resolution: %sdpi" % dpi)
elif setting == "journal double":
print("# JOURNAL SETTING double column")
width = 178
width_unit = "mm"
dpi = 400
print("# width: %s %s" % (width, width_unit))
print("# resolution: %s dpi" % dpi)
elif setting == "presentation":
print("# PRESENTATION SETTING")
width = 150
width_unit = "mm"
dpi = 150
print("# width: %s %s" % (width, width_unit))
print("# resolution: %s dpi" % dpi)
elif setting == "hires":
print("# HIRES SETTING")
width = 120
width_unit = "mm"
dpi = 1200
print("# width: %s %s" % (width, width_unit))
print("# resolution: %s dpi" % dpi)
if async_ == 1:
print("# Ray is working in the background")
bni_ray(width, width_unit=width_unit, dpi=dpi, **{'async': async_})
def bni_ray(width, name_png=None, dpi="300", width_unit="cm", **arg):
'''Ray specified with dpi and width.
USAGE: bni_ray(width,dpi="300",width_unit="cm",name_png=None,**arg)
width: width of ray picture in defined units
name_png: ./name.png: write png file with ./name.png
: : do not write png just do ray
width_unit: : unit of width
cm: centimeter
inch: inch
mm: millimeter
dots: (normal behaviour of ray)
dpi: 300: dots per inch (resolution)
**arg: additinal arguments for ray
height: integer :{default: 0 (current)}
antialias: integer :{default: -1 (use antialias setting)}
angle: float :y-axis rotation for stereo image generation
{default: 0.0}
shift: float : x-axis translation for stereo image generation
{default: 0.0}
renderer: -1 :respectively
0 :default
1 :built-in
2 :pov-ray, or dry-run {default: 0}
async: 0 : do not run in background thread
1 : background thread
PYMOL: bni_ray width,name_png=./my.png,dpi="300",width_unit="cm",**arg e.g. angle=3.0
'''
width = float(_remove_brakets(width))
width_unit = _remove_brakets(width_unit)
dpi = int(_remove_brakets(dpi))
if width_unit == "cm":
calc_res = round(width * dpi / 2.54)
elif width_unit == "mm":
calc_res = round(width * dpi / 25.4)
elif width_unit == "inch":
calc_res = round(width * dpi)
elif width_unit == "dots":
calc_res = int(width)
else:
print("Unit not recognized: %s" % width_unit)
return
print("# BNI - Tools v. %s" % __version__)
print("# %d (dots in x direction)" % (calc_res))
print("# Size(x): %s %s, resolution: %sdpi" % (width, width_unit, dpi))
print("# [Size(y): calculated automatically.]")
cmd.ray(width=calc_res, **arg)
if name_png is not None:
name_png = _remove_brakets(name_png)
name = os.path.abspath(os.path.normpath(name_png))
cmd.png(name, dpi=dpi)
print("# saved as: %s " % name)
def his_handle(fromto="his2hid", selection="(sele)", hisH_dic=None):
'''Alter HIS.
fromto:"his2hid": HIS to HIP HID HIE
:"hid2his": HIS HIP HIE to HIS
hisH_dic: dictionary of his hydrogen naming convention
e.g. {"HID":["HD1","H0X"],
"HIE":["HE2","H01"]}
selection: (sele):
'''
selection = _remove_brakets(selection, brakets=0)
fromto = _remove_brakets(fromto)
try:
cmd.count_atoms(selection)
except:
print("Please select at least one residue in (sele)")
return
if fromto == "his2hid":
print("# BNI - Tools v. %s" % __version__)
print("# ---------------------")
print("# Rename HIS to HID HIE HIP")
print("# Hydrogens have to be added accordingly")
print("# at the HIS residues ")
print("# HD1 ? --> HID")
print("# HE2 ? --> HIE")
print("# HD1 and HE2 ? --> HIP")
print("# ---------------------")
allhis = cmd.count_atoms("(r. HIS) and n. CA")
#hisH_dic naming convention [reduce,pymol]
if not hisH_dic:
hisH_dic = {"HID": ["HD1"],
"HIE": ["HE2", "H01"]}
cmd.select("HIP", "(byres ((n. %s) and r. HIS) and byres ((n. %s) and r. HIS))" % (
",".join(hisH_dic.get("HID")), ",".join(hisH_dic.get("HIE"))))
cmd.alter("(HIP)", "resn='HIP'")
cmd.sort()
cmd.select("HID", "(byres ((n. %s) and r. HIS))" %
(",".join(hisH_dic.get("HID"))))
cmd.alter("(HID)", "resn='HID'")
cmd.sort()
cmd.select("HIE", "(byres ((n. %s) and r. HIS))" %
(",".join(hisH_dic.get("HIE"))))
cmd.alter("(HIE)", "resn='HIE'")
cmd.sort()
print("# %s HIS residues" % allhis)
print("# -------------------------------")
print("# %s HID" % cmd.count_atoms("(r. HID and n. CA)"))
print("# %s HIE" % cmd.count_atoms("(r. HIE and n. CA)"))
print("# %s HIP" % cmd.count_atoms("(r. HIP and n. CA)"))
print("# -------------------------------")
print("# %s HIS residues altered" %
cmd.count_atoms("((r. HID,HIE,HIP) and n. CA)"))
print("# -------------------------------")
elif fromto == "hid2his":
print("# BNI - Tools v. %s" % __version__)
print("# --------------------")
print("# Rename HID HIE HIP to HIS")
print("# --------------------")
allhidhiehis = cmd.count_atoms("((r. HID,HIE,HIP) and n. CA)")
print("# %s HID" % cmd.count_atoms("(r. HID and n. CA)"))
print("# %s HIE" % cmd.count_atoms("(r. HIE and n. CA)"))
print("# %s HIP" % cmd.count_atoms("(r. HIP and n. CA)"))
cmd.select("HIS", "(byres (r. HIE,HIP,HID))")
cmd.alter("(HIS)", "resn='HIS'")
cmd.sort()
allhis = cmd.count_atoms("(r. HIS) and n. CA")
print("# %s HIS residues" % allhis)
print("# -------------------------------")
print("# %s HID,HIE,HIP residues altered" % allhidhiehis)
cmd.sort()
def polyala(selection="(sele)", name=None):
'''Get poly alanine chain of selected residues.
USAGE: polyala(selection=None,name=None)
selection: selection of residues
name: name of created polyalanine
if no name is given the original input
will be altered to polyalanine
PYMOL: bni_get_polyala (selection),[name]
selection: selection of residues
name: name of created polyalanine
if no name is given the original input
will be altered to polyalanine
ADDITIONAL: if "name" is specified the structure looks wired because of the
lack of bonds between the altered alanine residues.
If you want to see the bonds you can save and reopen the struture.
(Pymol recognize the new bonds after loading)
'''
if selection is None:
print("# Please select at least one residue.")
return
tmpname2 = "_polyala2"
tmpname3 = "_polyala3"
selection = _remove_brakets(selection)
try:
cmd.count_atoms(selection)
except:
print("# Empty selection. Select at least one atom.")
return
if name != None:
if name in cmd.get_names():
cmd.delete(name)
cmd.select(tmpname2, "((byobj %s) and not (byres %s))" %
(selection, selection))
cmd.create(
tmpname3, "((byres %s) and (n. CB,O,CA,N,C) and not hetatm and not solvent)" % (selection))
cmd.alter(("%s and not r. GLY") % tmpname3, "resn='ALA'")
cmd.sort()
cmd.create(name, ("(%s or %s)" % (tmpname3, tmpname2)))
cmd.delete(tmpname2)
cmd.delete(tmpname3)
else:
cmd.remove(
"((byres %s) and not (n. CB,O,CA,N,C) and not hetatm and not solvent)" % selection)
cmd.select(
tmpname3, "((byres %s) and (n. CB,O,CA,N,C) and not hetatm and not solvent)" % (selection))
cmd.alter(("%s and not r. GLY") % tmpname3, "resn='ALA'")
cmd.sort()
cmd.delete(tmpname3)
def cgo_point(p):
cgo = cgo_dic()
COLOR = cgo["COLOR"]
SPHERE = cgo["SPHERE"]
x, y, z = p
return [SPHERE, float(x), float(y), float(z), 0.2]
def get_triangle(selection, name="tri", invert=1, sphere=0):
'''Get a triangle from 3 atom selection.
USAGE: get_triangle(selection,name="tri",size=100,invert=0,sphere=1)
name : :name of the triangle
selection: :selection containing three atoms
invert : int : 2: invert normal for lightning
1: do not invert normal
0: do not create normal
sphere : int : 1: draw spheres on edges of the plane
: 0: do not draw spheres
PYMOL: bni_get_triangle selection,name,invert,sphere
'''
name = _remove_brakets(name)
selection = _remove_brakets(selection, brakets=0)
invert = _remove_brakets(invert)
invert = int(invert)
coordinates = []
try:
mol = cmd.get_model(selection)
mol.sort()
except:
print("# Empty selection %s" % selection)
return
else:
if len(mol.atom) != 3:
print("# Please select exactly three atoms.")
return
for a in mol.atom:
coordinates.append(a.coord)
tri = get_triangle_coord(
points=coordinates, invert=invert, sphere=sphere)
triName = check_names(name)
cmd.load_cgo(tri, triName)
cmd.show("cgo", triName)
def get_triangle_coord(points=((0, 0, 0), (0, 1, 0), (1, 0, 0)), invert=0, sphere=1):
'''Get coords for triangle polygon.
Currently only 3 points are supported.
'''
#invert=0
cgo = cgo_dic()
END = cgo["END"]
obj = []
rounds = len(points) - 1
centre = getCenterCoord(points)
# create triangles from midpoint of points (useful for later versions with
# more points)
point_index = [0, 1, 2]
for i in range(rounds):
#cpv.normalize(cpv.sub(points[i], centre))
vector1 = cpv.normalize(cpv.sub(centre, points[i]))
#cpv.normalize(cpv.sub(points[i+1], centre))
vector2 = cpv.normalize(cpv.sub(centre, points[i + 1]))
#vector3 = cpv.normalize(cpv.sub(points[i], points[i+1]))
#if normal_indication==1:
#normal = cpv.normalize(cpv.cross_product(vector1, vector2))
normal = cpv.cross_product(vector2, vector1)
#
obj_new = triangle([centre, points[i], points[i + 1]], norm=normal,
invert=invert, sphere=sphere, point_index=point_index, finishobj=0)
obj.extend(obj_new)
if rounds > 1:
vector1 = cpv.normalize(cpv.sub(centre, points[-1]))
vector2 = cpv.normalize(cpv.sub(centre, points[0]))
normal = cpv.cross_product(vector2, vector1)
obj_new = triangle([centre, points[-1], points[0]], norm=normal,
invert=invert, sphere=sphere, point_index=point_index, finishobj=0)
obj.extend(obj_new)
obj.append(END)
return obj
def triangle(points=[(0, 0, 0), (1, 1, 0), (1, 0, 0), (0, 1, 0)], norm=None, invert=0, sphere=1, point_index=[0, 1, 2, 0, 2, 3], finishobj=1):
'''Get triangles.
points: unique list of points for triangles in same plane.
norm: normal of triangles in plane
invert: 0,1 : invert normal
sphere: 0,1 :show additional spheres on edges
point_index: list of point indices to create triangles
finishobj: 0,1 : add END to object or not
'''
cgo = cgo_dic()
BEGIN = cgo["BEGIN"]
COLOR = cgo["COLOR"]
TRIANGLE_STRIP = cgo["TRIANGLE_STRIP"]
TRIANGLES = cgo["TRIANGLES"]
NORMAL = cgo["NORMAL"]
VERTEX = cgo["VERTEX"]
END = cgo["END"]
obj = []
if sphere == 1:
for p in points:
obj.extend(cgo_point(p))
obj.extend([BEGIN, TRIANGLES])
corners = []
for indexes in point_index:
corners.append(points[indexes])
if invert == 2 and norm is not None:
normal = norm
elif invert == 1 and norm is not None:
normal = [i * (-1) for i in norm]
else:
for corner in corners:
obj.append(VERTEX)
obj.extend(corner)
if finishobj == 1:
obj.append(END)
return obj
for corner in corners:
obj.append(NORMAL)
obj.extend(normal)
obj.append(VERTEX)
obj.extend(corner)
if finishobj == 1:
obj.append(END)
return obj
def get_plane_coord(p1, p2, p3, cushion, invert=0, sphere=1):
'''Get coords of plane.
'''
vector1 = cpv.normalize(cpv.sub(p2, p1))
vector2 = cpv.normalize(cpv.sub(p3, p1))
normal = cpv.cross_product(vector1, vector2)
centre = getCenterCoord([p1, p2, p3])
vector2 = cpv.cross_product(normal, vector1)
x = cpv.scale(vector1, cushion)
y = cpv.scale(vector2, cushion)
c1 = cpv.add(cpv.add(centre, x), y)
c2 = cpv.sub(cpv.add(centre, x), y)
c3 = cpv.sub(cpv.sub(centre, x), y)
c4 = cpv.add(cpv.sub(centre, x), y)
return triangle([c1, c2, c3, c4], norm=normal, invert=invert, sphere=sphere, point_index=[0, 1, 2, 0, 2, 3])
def get_plane_handler(selection="(sele)", app=None, action="set", name="plane", size=100, invert=2, sphere=0):
'''Get a plane using get_plane GUI.
'''
action = _remove_brakets(action)
name = check_names(name)
size = size
invert = str(invert)
sphere = str(sphere)
if action == "set" and app:
value = tkSimpleDialog.askstring('Plane settings',
'Specify [size %s] [invert 2/1/0] [sphere 1/0]' % "A",
parent=app.root)
value = _remove_brakets(value)
if value:
value = value.split()
else:
return
if len(value) == 1:
size = value[0]
elif len(value) == 2:
size = value[0]
invert = str(value[1])
elif len(value) >= 3:
size = value[0]
invert = str(value[1])
sphere = str(value[2])
else:
print("# Wrong input. Set at least the size.")
return
try:
float(size)
except ValueError:
print("# Size has to be a number.")
return
units = ["0", "1", "2"]
if not invert.lower().strip() in units:
print("# Invert has to be either %s " % (" or ".join(units)))
return
units = ["1", "0"]
if not sphere.lower().strip() in units:
print("# Sphere has to be either %s " % (" or ".join(units)))
return
elif action == "small":
size = 5
invert = 1
sphere = 0
elif action == "medium":
size = 10
invert = 1
sphere = 0
elif action == "large":
size = 20
invert = 1
sphere = 0
get_plane(selection, name=name, size=size, invert=invert, sphere=sphere)
def get_plane(selection, name="plane", size=100, invert=0, sphere=1):
'''Get a plane from 3 atom selection.
USAGE: get_plane(selection,name="plane",size=100,invert=0,sphere=1)
name : :name of the plane
selection: :selection containing three atoms
size : int :cushion size of the plane around selection
invert : int : 2: invert normal for lightning
1: do not invert normal
0: do not create normal
sphere : int : 1: draw spheres on edges of the plane
: 0: do not draw spheres
PYMOL: bni_get_plane selection,name,size,invert,sphere
'''
name = _remove_brakets(name)
selection = _remove_brakets(selection, brakets=0)
size = _remove_brakets(size)
invert = _remove_brakets(invert)
size = int(size)
invert = int(invert)
coordinates = []
try:
mol = cmd.get_model(selection)
except:
print("# Empty selection %s" % selection)
return
else:
if len(mol.atom) != 3:
print("# Please select exactly three atoms.")
return
for a in mol.atom:
coordinates.append(a.coord)
p1 = coordinates[0]
p2 = coordinates[1]
p3 = coordinates[2]
plane = get_plane_coord(p1, p2, p3, int(size), invert, sphere)
planeName = name
cmd.load_cgo(plane, planeName)
cmd.show("cgo", planeName)
def _get_list(input, message="Error"):
'''Remove brakets and return list.
Returns a list from input,
else a error massage is printed
'''
input = _remove_brakets(input)
if type(input) is str:
try:
input = map(int, input.split(","))
except TypeError:
print("# %s:\n%s" % (message, mobile))
return
except ValueError:
input = input.split(",")
return list(input)
def _maxnamelenght(types):
'''Get max lenght of names.
types: 1 : get name lenght
2 : get name and title lenght
'''
stdwidth = sidebar_stdwidth
multipl = 12.0
addpixel = 1 * multipl
if __pymol_version__ > 1.4:
addpixel = 6 * multipl
names = cmd.get_names("public_selections")
names.extend(cmd.get_names("public_objects"))
if types == 1:
try:
maxlenght = max([len(i) for i in names])
except ValueError:
return stdwidth
try:
namelenght = int(
round(float(maxlenght * multipl + addpixel + 0.5)))
except ValueError:
return stdwidth
if namelenght < stdwidth:
namelenght = stdwidth
return namelenght
elif types == 2:
titles = []
for tit in names:
try:
title = cmd.get_title(tit, cmd.get_state())
if title == None:
title = ""
except AttributeError:
titles.append("")
titles.append(title)
if len(names) != len(titles):
print("# WARNING: name and title mismatch/nnames:%s/ntitles:%s" %
(names, titles))
else:
try:
maxlenght = max([len(u) + len(v)
for u, v in zip(names, titles)])
#maxlenght=maxlenght+2*multipl
except ValueError:
return stdwidth
try:
namelenght = int(
round(float(maxlenght * multipl + addpixel + 0.5)))
except ValueError:
return stdwidth
if namelenght < stdwidth:
namelenght = stdwidth
return namelenght
def runsidebar(set="", value=None, app=None):
'''Run sidebar input
'''
if value == "set" and app:
value = tkSimpleDialog.askstring('Input Sidebar Value',
'Please specify a Value e.g 250',
parent=app.root)
sidebar(set="width", value=value)
def sidebar(set="", value=None):
'''Sidebar Settings.
USAGE: sidebar(set,value)
set:
"on" : set sidebar on
"off" : set sidebar off
"width": set sidebar to value
"size" : set hight of each sidebar entry
"overlayon": sidebar overlay on
"overlayoff": sidebar overlay off
value:
value : int : value of sidebar
'''
valuedic = {}
if set == "on":
cmd.set("internal_gui", "on")
elif set == "off":
cmd.set("internal_gui", "off")
elif set == "overlayon":
try:
if __pymol_version__ < 1.2:
cmd.set("internal_gui_mode", 1)
else:
cmd.set("internal_gui_mode", 2)
except:
pass
elif set == "overlayoff":
try:
cmd.set("internal_gui_mode", 0)
except:
pass
elif set == "width":
if type(value) != type(None):
if value == "fit1":#fit to names
fit = _maxnamelenght(1)
valuedic.update({"width": fit})
elif value == "fit2":#fit to names and titles
fit = _maxnamelenght(2)
valuedic.update({"width": fit})
else:
try:
value = int(float(value))
valuedic.update({"width": value})
except:
print("# Wrong value:", value)
return
else:
return
try:
cmd.set("internal_gui_width", valuedic.get("width", 250))
print("# Set sidebar to %s" % valuedic.get("width", 250))
except:
return
elif set == "size":
cmd.set("internal_gui_control_size", valuedic.get("size", 18))
def _check_selection(selection="(sele)"):
'''Check if selection contains atoms.
'''
try:
return cmd.count_atoms(selection)
except:
return 0
def get_surface_handler(selection="(sele)", action="mse", app=None):
'''Surface representation GUI using mse.
'''
selection = _remove_brakets(selection)
action = _remove_brakets(action)
len_atoms = _check_selection(selection)
if action == "Standard":
mse(sele=selection + " and (hetatm or solvent)",
stype="-1", ssurface="0")
mse(sele=selection + " and ! (hetatm or solvent)",
stype="-1", ssurface="1")
print("# BIN - Tools v. %s" % __version__)
print("# surface representation flags are set to standard values")
print("# for ( %s ). (current present objects only)." % (selection))
print("# show the surface to see the effect")
return
if action == "Reset":
mse(sele="(hetatm or solvent)", stype="-1", ssurface="0")
mse(sele="!(hetatm and solvent)", stype="-1", ssurface="1")
print("# BIN - Tools v. %s" % __version__)
print("# all surface representation flags are set to standard values")
print("# (current present objects only)." % (selection))
print("# show the surface to see the effect")
return
if action == "Methionine" or action == "mse":
mse(sele=selection + " and r. MSE", stype="-1", ssurface="1")
print("# BIN - Tools v. %s" % __version__)
print("# Methionine surface representation is set to on")
print("# for ( %s ). (current present objects only)." % (selection))
print("# show the surface to see the effect")
return
if len_atoms == 0:
print("# No atoms in selection %s. Select at least one atom." %
selection)
return
elif action == "Include":
mse(sele=selection, stype="-1", ssurface="1")
print("# BIN - Tools v. %s" % __version__)
print("# Included %s atom(s) to surface calculation." % len_atoms)
print("# show the surface to see the effect")
elif action == "Exclude":
mse(sele=selection, stype="-1", ssurface="0")
print("# BIN - Tools v. %s" % __version__)
print("# Excluded %s atom(s) from surface calculation." % len_atoms)
print("# show the surface to see the effect")
elif action == "Show":
mse(sele=selection, stype="-1", ssurface="1")
print("# BIN - Tools v. %s" % __version__)
print("# Show surface for %s atom(s)." % len_atoms)
print("# show the surface to see the effect")
elif action == "Hide":
mse(sele=selection, stype="-1", ssurface="2")
print("# BIN - Tools v. %s" % __version__)
print("# Hide surface for %s atom(s)." % len_atoms)
print("# show the surface to see the effect")
def delalternate(sele="sele"):
'''Delete alternates.
'''
sele = _remove_brakets(sele, brakets=0)
selection = "(" + sele + " and not (alt '' or alt A))"
try:
len_atoms = cmd.count_atoms(selection)
len_residues = cmd.count_atoms(
"(byres " + selection + ") and n. CA and not e. CA and (alt '' or alt A)")
except:
print("# No residues in selection to delete.")
return
cmd.remove(selection)
cmd.sort()
print("# BIN - Tools v. %s" % __version__)
print("# Deleted %d alternate atoms in %d residues." %
(len_atoms, len_residues))
def altermse(sele="(sele)"):
'''Edit MSE to MET permanantly.
'''
sele = _remove_brakets(sele, brakets=0)
try:
cmd.count_atoms(sele)
except:
print("# No atoms in selection %s" % sele)
return
selection = "(" + sele + " and r. MSE and n. SE)"
cmd.alter(selection=selection, expression="name='SD'", quiet=1, space=None)
cmd.sort()
selection = "(" + sele + " and r. MSE and n. SD)"
cmd.alter(selection=selection, expression="elem='S'", quiet=1, space=None)
cmd.sort()
cmd.flag(25, "(" + sele + " and r. MSE)", "clear")
cmd.sort()
selection = "(" + sele + " and r. MSE)"
mses = cmd.count_atoms(selection + " and n. CA and not e. CA")
cmd.alter(
selection=selection, expression="type='ATOM'", quiet=1, space=None)
cmd.sort()
cmd.alter(
selection=selection, expression="resn='MET'", quiet=1, space=None)
print("# BIN - Tools v. %s" % __version__)
print("# Changed %d MSE residues to MET." % mses)
cmd.sort()
def mse(sele="r. MSE", stype="-1", ssurface="1"):
'''Handle MSE atom surface representation (Seleno- Methionine).
USAGE: bni_mse sele="r. MSE" stype=-1 ssurface=1
sele: selection : standard is "r. MSE"
stype: 1: set MSE type from HETATM to ATOM
0: set MSE type from ATOM to HETATM
-1: do nothing (standard)
ssurface: 1: set surface representation to 1 for MSE (create surface) (standard)
2: set surface representation to 2 for MSE (dont show but include)
0: set surface representation to 0 for MSE (exclude from surface)
this is standard within pymol
-1: do nothing
'''
sele = _remove_brakets(sele, brakets=0)
if stype == "1":
cmd.alter("%s" % sele, 'type="ATOM"')
elif stype == "0":
cmd.alter("%s" % sele, 'type="HETATM"')
else:
pass
if ssurface == "1":
cmd.flag(25, sele, "clear")
cmd.flag(24, sele, "clear")
elif ssurface == "2":
cmd.flag(25, sele, "clear")
cmd.flag(24, sele, "set")
elif ssurface == "0":
cmd.flag(25, sele, "set")
cmd.flag(24, sele, "clear")
else:
pass
cmd.sort()
def _redirect_alter(selection, property, addprint=1, command="alter"):
'''redirect standart out temporarily to get cmd.alter command variables.
selection:
property: index
addprint:1: additional print to stdout
command:"alter": use the cmd.alter command
"iterate": use the cmd.iterate command (v.1.2r1 also needs print redirection!)
'''
if command == "alter":
command = cmd.alter
elif command == "iterate":
command = cmd.iterate
values = []
class MyRedirect:
def __init__(self, stdout):
self.stdout = stdout
def write(self, s):
if s.strip():
values.append(s)
if addprint == 1:
self.stdout.write(s)
old_stdout = sys.stdout
sys.stdout = MyRedirect(sys.stdout)
# index of the atoms is now in a list(values) as string
command(selection, property)
sys.stdout = old_stdout
return values
def _seq_format(selection="sele", wrap=60, format="fasta", gap=1, gap_sign="-"):
'''sequence output.
format: pir
modeller
fasta
wrap: sequence chars in one line
gap: 1:
0:
gap_sign: -:
.:
_:
lower:gap AA are written in lower case
returns (fromated sequences,gap_residues)
'''
output_format = "'%s;%s'%(resn,resi)"
chains = cmd.get_chains(selection)
allnu = []
try:
names = cmd.get_names("public_objects")
except:
names = cmd.get_names()
exc = HP()
nr_out = []
for obj in names:
for chain in chains:
if chain == '':
chain = "''"
select_new = "%s and " % obj + selection + " and c. %s" % chain
u = _redirect_alter(
select_new, output_format, addprint=0, command="alter")
#print select_new
if not u:
continue
u = [((_remove_brakets(i.split(";")[0]), _remove_brakets(i.split(";")[1])))
for i in u if type(i) is type("string")]
lenght = len(u)
aa = [a[0] for a in u]
nr = [a[1] for a in u]
aa = exc.three2one(aa)
if not len(aa) == len(nr):
print("# WARNING: AA and NR do not have the same lenght.")
print(
"# WARNING: output in line 2 of pir format may be incorrect.")
nu = "".join(aa)
if chain == '':
chain = "."
#compare with whole chain to insert gaps as "-"
if gap == 1:
select_gap = "(bychain " + select_new + \
") and n. CA and not e. CA and (alt '' or alt A)"
u_gap = _redirect_alter(select_gap, output_format, addprint=0)
u_gap = [((_remove_brakets(i.split(";")[0]), _remove_brakets(
i.split(";")[1]))) for i in u_gap if type(i) is type("string")]
lenght_gap = len(u_gap)
aa_gap = [a_gap[0] for a_gap in u_gap]
nr_gap = [a_gap[1] for a_gap in u_gap]
aa_gap = exc.three2one(aa_gap)
if not len(aa_gap) == len(nr_gap):
print(
"# WARNING: AA_gap and NR_gap do not have the same lenght.")
print("# WARNING: output may be incorrect.")
#nu_gap="".join(aa_gap)
#compare and create new seq with gaps
new_seq = []
#print nr_gap,aa_gap
#print nr,aa
nr_out.append("# Residue from - to")
nr_out.append("# for %s:%s:%d (out of %d)" %
(obj, chain, lenght, len(nr_gap)))
contains_gap = 0
new_nr = []
for number, amino in zip(nr_gap, aa_gap):
if number in nr:
new_seq.append(amino)
new_nr.append((number, amino))
else:
if new_nr:
nr_out.append("%1s %4s - %1s %4s : (%3d AA)" % (new_nr[0][1], new_nr[0][
0], new_nr[-1][1], new_nr[-1][0], len(new_nr)))
contains_gap = 1
new_nr = []
if gap_sign == "lower":
new_seq.append(amino.lower())
else:
new_seq.append(gap_sign)
if contains_gap == 0:# no gaps
nr_out.append("%1s %4s - %1s %4s : (%3d AA)" %
(aa_gap[0], nr_gap[0], aa_gap[-1], nr_gap[-1], len(nr_gap)))
elif new_nr:
nr_out.append("%1s %4s - %1s %4s : (%3d AA)" % (new_nr[0][1], new_nr[0][
0], new_nr[-1][1], new_nr[-1][0], len(new_nr)))
new_nr = []
if gap_sign == "lower":
new_seq.append(amino.lower())
else:
new_seq.append(gap_sign)
nu = "".join(new_seq)
if format == "modeller":
allnu.append(">P1;%s" % (obj))
label = "structureX"
source = "source"
rfac = -1.0
resolution = -1.0
if gap != 1:
allnu.append("%s:%s:%s:%d:%s:%d:SeqLenght %d:%s:%.2f:%.2f" % (
label, obj, chain, int(nr[0]), chain, int(nr[-1]), lenght, source, rfac, resolution))
else:
allnu.append("%s:%s:%s:%d:%s:%d:SeqLenght %d:%s:%.2f:%.2f" % (label, obj, chain, int(
nr_gap[0]), chain, int(nr_gap[-1]), lenght, source, rfac, resolution))
#every "wrap" res return
nu = _seq_wrap(nu, wrap)
nu[-1] += "*"
elif format == "pir":
allnu.append(">P1;%s" % (obj))
allnu.append("")
#every "wrap" res return
nu = _seq_wrap(nu, wrap)
nu[-1] += "*"
elif format == "fasta":
if gap == 1:
allnu.append(">%s:%s:%d out of %d:" %
(obj, chain, lenght, len(nr_gap)))
else:
allnu.append(">%s:%s:%d" % (obj, chain, lenght))
#every "wrap" res return
nu = _seq_wrap(nu, wrap)
allnu.extend(nu)
return allnu, nr_out
def _seq_wrap(seq, wrap=60):
'''Sequence wrapper.
Wraps a sequence into a list.
seq: string input
wrap: 60: chars per list entry
'''
slice_begin = 0
slice_end = wrap
seq_list = []
while 1:
seq_slice = seq[slice_begin:slice_end]
if len(seq_slice) < wrap:
seq_list.append(seq_slice)
break
seq_list.append(seq_slice)
slice_begin = slice_end
slice_end += wrap
return seq_list
def _mw(values=[]):
'''Return MW and variance and len.
'''
sum1 = sum(values)
num = len(values)
try:
mean = float(sum1) / float(num)
std = (sum([(a - mean) ** 2 for a in values]) / (num)) ** 0.5
except ZeroDivisionError:
mean = 0.
std = 0.
return mean, std, num
def get_sequence(selection="sele", selecting="residue", format="normal", name=None, wrap="60", gap="1", gap_sign="-"):
'''Print selected residues.
USAGE: get_sequence(selection="sele",selecting="residue",format="normal",name=None,wrap="60")
selection: sele : selection of residues or atoms.
selecting: residue: get all residues of selection (without alternates)
atom: get all atoms of selection
chain: get all chains of selection
name: None : name of selection for output
format: normal: object: chain: residue-residue number
normalb: calc bfac per residue
normalb_main: calc bfac per residue (only mainchain)
normalb_side: calc bfac per residue (only sidechain)
normalq: calc occ per residue
normalq_main: calc occ per residue (only mainchain)
normalq_side: calc occ per residue (only mainchain)
fasta: amino acid one letter code in fasta format
pir: amino acid one letter code in pir format
modeller: amino acid one letter code in Modeller pir format
wrap: 60: for sequence output wrap at 60 residues
gap: 1: add gaps between selected amino acids
0: do not add gaps
gap_sign: - : char of gap
"lower": gap amino acids are written as lower case
PYMOL: bni_get_sequence selection=sele,selecting=residue,format=normal,wrap=60,gap_sign=lower
ADDITIONAL: alternates are not considered! eighter alternate A or alterneta "" are selected
'''
format = _remove_brakets(format)
selecting = _remove_brakets(selecting)
selection = _remove_brakets(selection)
wrap = int(_remove_brakets(wrap))
gap = int(_remove_brakets(gap))
gap_sign = _remove_brakets(gap_sign)
try:
a = cmd.count_atoms(selection)
except:
a = None
if not a:
print("# Select at least one atom.")
return
if name is None:
name = selection
prelist = []
prelist.append("# BNI-Tools v. %s" % __version__)
prelist.append("# ---------------")
prelist.append("# Output for %s" % name)
prelist.append("# ---------------")
if selection == "enabled":
pass
elif selection == "enabled1":
pass
else:
output_format = '"%s:%s: %s-%s"%(model,chain,resn,resi)'
if selecting == "residue":
selection = "(byres " + selection + ")"
selection = "(" + selection + " and (alt '' or alt A))"
if format == "normal" or format[:7] == "normalb" or format[:7] == "normalq":
output_format = '"%s:%s: %s-%s "%(model,chain,resn,resi)'
u = _redirect_alter(selection, output_format, addprint=0)
u = [_remove_brakets(i) for i in u]
resis = []
atoms = []
for resi in u:
r = resi.split(":")
#obj:chain:resn:resi
radd = (r[0], r[1], r[2].split("-")[0], r[2].split("-")[1])
if radd not in resis:
atoms.append(resi)
resis.append(radd)
u = atoms[:]
if format[:7] == "normalb" or format[:7] == "normalq":
if format[:7] == "normalb":
val = "b"
output_format = '"%4.2f"%(b)'
else:
val = "q"
output_format = '"%4.2f"%(q)'
resi = []
val_allatoms=[]
for residue in u:
residue = residue.split(":")
selection = "(" + residue[0] + " and c. " + residue[1] + " and r. " + residue[
2].split("-")[0] + " and i. " + residue[2].split("-")[1] + ")"
selection = "(" + selection + \
" and (alt '' or alt A) and !n. H)"
if format[7:] == "_main":
selection = "(" + selection + " and (n. CA,C,N,O) or (" + \
selection + ") and !polymer and !n. H)"
elif format[7:] == "_side":
selection = "(" + selection + " and (!(n. CA,C,O or (n. N and !r. PRO))) or (" + \
selection + ") and !polymer and !n. H)"
a = _redirect_alter(
selection, output_format, addprint=0)
a = [_remove_brakets(i) for i in a]
val_list = [float(i) for i in a]
val0, val1, val2 = _mw(val_list)
residue.extend(
["%s= %5.2f" % (val, val0), "%s= %5.2f" % ("s", val1), "atoms %2d" % val2])
val_allatoms.extend(val_list)
resi.append(":".join(residue))
# calc mean for all atoms
valall0,valall1,valall2 = _mw(val_allatoms)
u = resi
if format[:7] == "normalb" or format[:7] == "normalq":
prelist.append("# No hydrogens and no alternates are considered in calculation")
if format[7:] == "_main":
prelist.append(
"# Only mainchain atoms are considered in calculation.")
elif format[7:] == "_side":
prelist.append(
"# Only sidechain atoms are considered in calculation.")
prelist.extend(u)
if format[:7] == "normalb" or format[:7] == "normalq":
prelist.append("#----------")
prelist.append("All atoms:%s= %5.2f:%s= %5.2f:atoms %2d" % (val, valall0,"s",valall1,valall2))
print("\n".join(prelist))
return u, []
elif format == "fasta" or format == "pir" or format == "modeller":
selection = "(" + selection + " and n. CA and not e. CA )"
(allnu, nr_gap) = _seq_format(selection=selection,
wrap=wrap,
gap=gap,
gap_sign=gap_sign,
format=format)
if gap == 1:
prelist.extend(nr_gap)
prelist.append("# SEQUENCE FORMAT: %s" % format)
prelist.append("# ---------------------------")
prelist.extend(allnu)
print("\n".join(prelist))
return allnu, nr_gap
else:
output_format = '"%s"%(resn)'
u = _redirect_alter(selection, output_format, addprint=0)
#print u
u = [_remove_brakets(i) for i in u]
print("\n".join(u))
return u, []
elif selecting == "atom":
selection = selection
output_format = '"%s:%s: %s-%s :%s"%(model,chain,resn,resi,name)'
u = _redirect_alter(selection, output_format, addprint=0)
#print u
u = [_remove_brakets(i) for i in u]
print("\n".join(u))
return u, []
elif selecting == "chain":
u = cmd.get_chains(selection)
print("\n".join(u))
return u, []
#cmd.alter(selection,output_format)
class Sym:
def __init__(self):
self.org_cc = []
self.sym_cc = []
self.org_sel = []
self.org_sel_show = []
self.sym_sel = []
self._cutoff = 0.0
self.name_sym_obj = ""
self.picked_selection = ""
self.ngroup = None
def create_group(self, gname="bni_sym"):
'''Create group.
'''
self.ngroup = bni_group(gname)
def groupit(self, names=[]):
'''Try to group names.
'''
if self.ngroup:
try:
cmd.group(self.ngroup, " ".join(names))
except:
pass
def _setcutoff(self, restrict=6.0):
'''Check if cutoff has to be restricted.
'''
if self._cutoff > restrict:
self._cutoff = restrict
def create_sym(self, cutoff=4.0, selection="sele"):
'''Create smmetry mates of selection.
USAGE:
create_sym([cutoff=4.0[,selection="sele"]])
RETURNS:
selection_name(s) of symetry involved atoms of symetry mates
'''
selection = _remove_brakets(selection)
self.picked_selection = selection
self._cutoff = cutoff
self._setcutoff()
try:
self.name_sym_obj = cmd.get_object_list(selection)[0]
except:
self.name_sym_obj = ""
cmd.select("_sym_sele", "(byobj %s)" % selection)
cmd.create("_sym", "_sym_sele")
name_symetry_mate = "s_%s_" % self.name_sym_obj
name_symetry_mate = check_names(name_symetry_mate)
cmd.symexp(name_symetry_mate, "_sym", selection, cutoff=cutoff, segi=1)
cmd.delete("_sym_sele")
cmd.delete("_sym")
select_name = "_sym_%s_%1.1f" % (self.name_sym_obj, self._cutoff)
select_name = check_names(select_name)
#remove
name_symetry_mates = name_symetry_mate + "*"
cmd.select(select_name, "((byobj %s) around %1.1f) and not ((byobj %s) and not %s ) and %s" % (
selection, self._cutoff, selection, selection, name_symetry_mates), enable=0)
cmd.select(select_name[1:], "(%s around %1.1f) and not ((byobj %s) and not %s ) and %s" % (
selection, self._cutoff, selection, selection, name_symetry_mates), enable=0)
symetrys = [r for r in cmd.get_names() if name_symetry_mate in r]
colors = 2
self.create_group()
self.groupit(symetrys)
self.groupit([select_name[1:]])
for item in symetrys:
try:
util.cba(colors, item)
except:
pass
colors += 1
return select_name
def create_org(self, cutoff=4.0, sele=None):
'''Create selection of orig atoms involved within symmetry.
USAGE:
create_org([cutoff=4.0
[,sele="s_*"
]])
'''
if sele is None:
sele = "s_%s*" % self.name_sym_obj
self._cutoff = cutoff
#restrict selection cutoff to a reasonable distance (max. 6.0 A)
self._setcutoff()
cmd.select("_sym", sele)
#restrict selection cutoff to a reasonable distance (max. 6.0 A)
select_name = "_org_%s_%1.1f" % (self.name_sym_obj, self._cutoff)
cmd.select(select_name[1:], "(_sym around %1.1f) and (%s)" % (
self._cutoff, self.picked_selection), enable=0)
cmd.select(select_name, "(_sym around %1.1f)" %
(self._cutoff), enable=0)
cmd.delete("_sym")
self.groupit([select_name[1:]])
return select_name
def show_org(self, select_name, show_name="surface", cutoff=4.0, surf_transparency=0.0):
'''Create different views of symmetry involved selection.
USAGE: show_org(select_name,
[show_name="surface"
[,cutoff=4.0,
[,surface_transparency=0.0,
]])
show_name:"sticks"
"surface"
'''
select_name = _remove_brakets(select_name)
self._cutoff = cutoff
#restrict selection cutoff to a reasonable distance (max. 6.0 A)
self._setcutoff()
cmd.enable(select_name)
cmd.show(show_name, "_org_%s_%1.1f" %
(self.name_sym_obj, self._cutoff))
if show_name == "surface":
cmd.set("transparency", surf_transparency)
cmd.disable("_org_%s_%1.1f" % (self.name_sym_obj, self._cutoff))
def show_sym(self, select_name, show_name="surface", cutoff=4.0, surf_transparency=0.0, object=None):
'''Create different views of symmetry involved selection.
USAGE: show_sym(select_name,
[show_name="surface"
[,cutoff=4.0,
[,surface_transparency=0.0,
[,sele="s_*"]]])
show_name:"sticks"
"surface"
'''
select_name = _remove_brakets(select_name)
self._cutoff = cutoff
#restrict selection cutoff to a reasonable distance (max. 6.0 A)
self._setcutoff()
cmd.enable(select_name)
cmd.show(show_name, "_sym_%s_%1.1f" %
(self.name_sym_obj, self._cutoff))
if object is None:
object = "s_%s*" % (self.name_sym_obj)
if show_name == "surface":
cmd.set("transparency", surf_transparency, object)
cmd.disable("_sym_%s_%1.1f" % (self.name_sym_obj, self._cutoff))
def get_model(self, selection=""):
'''Return Model of selection.
'''
selection = _remove_brakets(selection)
try:
mol = cmd.get_model(selection)
except:
print("# Please specify a selection.")
return 0
return mol
class HP:
def __init__(self):
self.one_letter = {"ALA": ["A"],
"ARG": ["R"],
"ASN": ["N"],
"ASP": ["D"],
"ASX": ["B"],
"CYS": ["C"],
"CYH": ["C"],#protonated cys
"CYX": ["C"],#cystein
"GLN": ["Q"],
"GLU": ["E"],
"GLY": ["G"],
"GLX": ["Z"],
"HIS": ["H"],
"HIP": ["H"],#protonated
"HID": ["H"],#h on delta
"HIE": ["H"],#h on epsilon
"ILE": ["I"],
"LEU": ["L"],
"LYS": ["K"],
"MET": ["M"],
"MSE": ["M"],#Seleno- Methionin
"PHE": ["F"],
"PRO": ["P"],
"SER": ["S"],
"THR": ["T"],
"TRP": ["W"],
"TYR": ["Y"],
"VAL": ["V"],
"UNK": ["X"]}
self.three_letter = {"A": ["ALA"],
"R": ["ARG"],
"N": ["ASN"],
"D": ["ASP"],
"B": ["ASX"],
"C": ["CYS", "CYH", "CYX"],
"Q": ["GLN"],
"E": ["GLU"],
"G": ["GLY"],
"Z": ["GLX"],
"H": ["HIS", "HIE", "HIP", "HID"],
"I": ["ILE"],
"L": ["LEU"],
"K": ["LYS"],
"M": ["MET"],
"MSE": ["MSE"],#selenomethionine
"F": ["PHE"],
"P": ["PRO"],
"S": ["SER"],
"T": ["THR"],
"W": ["TRP"],
"Y": ["TYR"],
"V": ["VAL"],
"X": ["UNK"]}
def one2three(self, aa_list):
'''Get one letter code from AA list.
'''
u = []
tmp_list = [self.three_letter.get(l, ["UNK"]) for l in aa_list]
for item in tmp_list:
u.extend(item)
return u
def three2one(self, aa_list):
'''Get one letter code from AA list.
'''
u = []
tmp_list = [self.one_letter.get(l, ["X"]) for l in aa_list]
for item in tmp_list:
u.extend(item)
return u
def get_HP_set(self, hp_value="GES", output="names"):
'''Get one letter code for hydrophobic,neutral,hydrophilic.
USAGE: get_HP_set(hp_value="GES")
hp_value: "GES"
"KandD"
"Rose"
output: "names" :return AA names and category
"values":return dic of AA names and values
RETURNS: output names: (hydrophobic_AA,neutral_AA,hydrophilic_AA)
output values {'AA',value}
'''
hpvalues = {"GES": {"A": 1.6,
"C": 2,
"D": -9.2,
"E": -8.2,
"F": 3.7,
"G": 1,
"H": -3,
"I": 3.1,
"K": -8.8,
"L": 2.8,
"M": 3.4,
"N": -4.8,
"P": -0.2,
"Q": -4.1,
"R": -12.3,
"S": 0.6,
"T": 1.2,
"V": 2.6,
"W": 1.9,
"Y": -0.7, },
"KandD": {"A": 1.8,
"C": 2.5,
"D": -3.5,
"E": -3.5,
"F": 2.8,
"G": -0.4,
"H": -3.2,
"I": 4.5,
"K": -3.9,
"L": 3.8,
"M": 1.9,
"N": -3.5,
"P": -1.6,
"Q": -3.5,
"R": -4.5,
"S": -0.8,
"T": -0.7,
"V": 4.2,
"W": -0.9,
"Y": -1.3, },
"Rose": {"A": 0.74,
"C": 0.91,
"D": 0.62,
"E": 0.62,
"F": 0.88,
"G": 0.72,
"H": 0.78,
"I": 0.88,
"K": 0.52,
"L": 0.85,
"M": 0.85,
"N": 0.63,
"P": 0.64,
"Q": 0.62,
"R": 0.64,
"S": 0.66,
"T": 0.7,
"V": 0.86,
"W": 0.85,
"Y": 0.76, }}
hydrophobic = {"GES":
["F", "M", "I", "L", "V", "C", "W",
"A", "T", "G", "S", "MSE"],
"KandD":
["A", "C", "I", "L", "M", "F", "V", "MSE"],
"Rose":
["C", "I", "L", "M", "F", "W", "V", "MSE"]
}
hydrophilic = {"GES": ["E", "K", "D", "R"],
"KandD":
["R", "N", "D", "Q", "E", "H", "K"],
"Rose":
["R", "N", "D", "Q", "E", "K", "P", "S"]
}
neutral = {"GES": ["P", "Y", "H", "Q", "N"],
"KandD":
["G", "P", "S", "T", "W", "Y"],
"Rose":
["A", "G", "H", "T", "Y"]
}
if output == "names":
return (self.one2three(hydrophobic.get(hp_value)), self.one2three(neutral.get(hp_value)), self.one2three(hydrophilic.get(hp_value)))
elif output == "values":
return hpvalues.get(hp_values)
class set_views:
def __init__(self):
self.selection = "all"
def mainchain(self, sele="all", obj_name="MC"):
'''Create mainchain track in a Mainchain Object.
mainchain(sele="all")
'''
group_name = obj_name + "_track_g"
group_name = check_names(group_name)
obj_name = obj_name + "_track"
obj_name = check_names(obj_name)
dist1 = check_names(obj_name + "_mcp_cont")
dist2 = check_names(obj_name + "_scp_cont")
self.selection = _remove_brakets(sele)
try:
cmd.create(obj_name, "(%s) and (n. C,N,O,CA)" % (self.selection))
# create polar contacts of mainchain with preset and rename the
# contacts
cmd.dist(dist1, "(%s) and not (solvent or (polymer and not name n,o,h))" % self.selection,
"(%s) and not (solvent or (polymer and not name n,o,h))" % self.selection, quiet=1, mode=2, label=0, reset=1)
cmd.enable(dist1)
try:
cmd.color(8, dist1)#color magenta
except:
pass
cmd.show_as("sticks", obj_name)
cmd.set("stick_radius", 0.35, obj_name)
cmd.set("stick_transparency", 0.5, obj_name)
cmd.dist(dist2, "(%s)" % self.selection, "(%s) and not (polymer and name n,o,h)" %
self.selection, quiet=1, mode=2, label=0, reset=1)
cmd.enable(dist2)
try:
cmd.group(group_name, "%s %s %s" % (obj_name, dist1, dist2))
except:
pass
except:
print("# Can not create track. (no selection ?)")
cmd.color("white", obj_name)
def sidechain(self, sele="all"):
'''Create sidechain.
'''
self.selection = _remove_brakets(sele)
cmd.select("Sidechain", "(%s) and not n. C,N.O" % self.selection)
cmd.show("lines", "Sidechain")
def surface_atoms_preset(self, sele="all"):
'''Get different important atoms.
'''
self.selection = _remove_brakets(sele, brakets=0)
try:
cmd.set("surface_color", -1, self.selection)
cmd.select("HIS", "(%s) and (r. HIS,HIE,HID,HIP)" % self.selection)
cmd.select(
"HIS_ND1NE2", "(%s) and (r. HIS,HIE,HID,HIP) and (n. ND1,NE2)" % self.selection)
cmd.color("gray", "(%s)" % self.selection)
try:
util.cba(29, "HIS_ND1NE2")
except:
pass
cmd.select("ASP", "(%s) and (r. ASP)" % self.selection)
cmd.select(
"ASP_OD12", "(%s) and (r. ASP) and (n. OD1,OD2)" % self.selection)
try:
util.cba(29, "ASP_OD12")
except:
pass
cmd.select("GLU", "(%s) and (r. GLU)" % self.selection)
cmd.select(
"GLU_OE12", "(%s) and (r. GLU) and (n. OE1,OE2)" % self.selection)
try:
util.cba(29, "GLU_OE12")
except:
pass
cmd.select("ARG", "(%s) and (r. ARG)" % self.selection)
cmd.select(
"ARG_NH12", "(%s) and (r. ARG) and (n. NH1,NH2)" % self.selection)
try:
util.cba(29, "ARG_NH12")
except:
pass
cmd.select("LYS", "(%s) and (r. LYS)" % self.selection)
cmd.select("LYS_NZ", "(%s) and (r. LYS) and (n. NZ)" %
self.selection)
try:
util.cba(29, "LYS_NZ")
except:
pass
cmd.select("CYS", "(%s) and (r. CYS,CYH,CYX)" % self.selection)
cmd.select(
"CYS_SG", "(%s) and (r. CYS,CYH,CYX) and (n. SG)" % self.selection)
try:
util.cba(29, "CYS_SG")
except:
pass
except:
print("# Could not create preset. (No Structure enabled?)")
def new_views(preset="track_mainchain", selection='sele'):
'''Create Preset Views.
'''
#look if object is molecule and not a previous track run
#names=[i for i in cmd.get_names("objects",enabled_only=1) if cmd.get_type(i)=="object:molecule"]
selection = _remove_brakets(selection)
if _check_selection(selection) == 0:
print("# No (sele) selection, please select at least one atom.")
return
selectionname = selection
selection = '(byres (%s))' % selection
if preset == "track_mainchain":
#create for all enabled objects
obj_name = check_names(selectionname)
#try:
# names.remove(obj_name)
#except ValueError:
# pass
#selection=_remove_brakets(' or '.join(names))
v = set_views()
v.mainchain(selection, obj_name=obj_name)
if preset == "surf_rel_res":
#selection=_remove_brakets(' or '.join(names))
#selection=_remove_brakets(selection)
v = set_views()
v.surface_atoms_preset(selection)
def set_surface(mode="standard"):
'''Set surface to standard values.
USAGE:
set_surface(mode="standard")
mode: "standard"
"symmetry"
'''
if mode == "standard":
transparency = 0.0
surfmode = -1
selection = "all"
cmd.set("surface_color", surfmode, selection)
cmd.set("transparency", transparency, selection)
elif mode == "symmetry":
surf_transparency = 0.5
selection = "all"
set_surf_color(color="blue", sele="all")
set_surf_color(color="white", sele="s_*")
cmd.set("transparency", surf_transparency, selection)
else:
pass
def inv_enabled(selection='all'):
'''Invert all enabled objects.
USAGE:
inv_enabled selection="obj" # delete all enabled objects
inv_enabled "selections" # delete all enabled selections
inv_enabled "all" # delete all enabled
'''
#invert
selection = _remove_brakets(selection)
print("# invert")
vers = __pymol_version__
if vers >= 1.21 and selection == "obj":
selection = "objects"
set_enabled = set(cmd.get_names(selection, enabled_only=1))
set_all = set(cmd.get_names(selection, enabled_only=0))
enabled = set_enabled
disabled = set_all - set_enabled
#print "disabled",disabled
#cmd.disable(item)
#cmd.enable(item)
try:
cmd.disable(' and '.join(enabled))
except IndexError:
pass
try:
cmd.enable(' and '.join(disabled))
except IndexError:
pass
def del_enabled(selection="obj"):
'''Delete all enabled objects.
USAGE:
del_enabled selection="obj" # delete all enabled objects
del_enabled "selections" # delete all enabled selections
del_enabled "all" # delete all enabled
'''
selection = _remove_brakets(selection)
vers = cmd.get_version()[1]
if vers >= 1.21 and selection == "obj":
selection = "objects"
for item in cmd.get_names(selection, enabled_only=1):
cmd.delete(item)
def rename_object(old_name="sele", new_name="new"):
'''Rename any object without wizard.
(The wizard cannot rename ramps and other stuff.)
'''
old_name = _remove_brakets(old_name)
new_name = _remove_brakets(new_name)
cmd.set_name(old_name, new_name)
def set_surf_color(color="-1", sele="all"):
'''Set surface color idependently from structure.
color: "-1" : default
color: white
"1"
"2"
"3"
.
'''
color = _remove_brakets(color)
sele = _remove_brakets(sele)
try:
color = int(color)
except ValueError:
pass
cmd.set("surface_color", color, sele)
def get_pdb_lines(selection="all", state="0", enabled="0"):
'''Get pdb lines from selection.
USAGE: get_pdb_lines(selection="all",state="0",enabled="0")
PYMOL: get_pdb (select),state
selection: object or selection
state: state
enabled: 1: get only enabled items
0: get all items
'''
selection = _remove_brakets(selection)
if selection != "all":
names = [selection]
else:
names = [i for i in cmd.get_names(selection, enabled_only=int(enabled)) if cmd.get_type(
i) == "object:molecule" or cmd.get_type(i) == "selection"]
cnt = sum([cmd.count_atoms(i) for i in names])
print("REMARK ________-Cut-Here-_________")
print("REMARK Created by BNI Pymol Plugin v.%s" % (__version__))
print("REMARK %s %s ATOMS" % (','.join(names), cnt))
print("REMARK BEGIN PDB LINES FOR : %s" % (','.join(names)))
for item in names:
print(get_pdb(selection=item, state=int(state)))
print("REMARK END PDB LINES FOR : %s" % item)
print("REMARK ________-Cut-END-_________")
def get_pdb(selection="all", state="0"):
'''Get pdb lines from selection.
USAGE: get_pdb(selection="all",state=0)
selection: object or selection
state: state
'''
selection = _remove_brakets(selection)
pdbline = cmd.get_pdbstr(selection=selection, state=int(state))
return pdbline
def del_sym(select_name="s_*"):
'''Delete created symmetry mates.
'''
cmd.delete(select_name)
def select_hp(hp_value="KandD", selection="(sele)"):
'''Select HP and color HP Values.
'''
u = HP()
selection = _remove_brakets(selection)
try:
cmd.count_atoms(selection)
except:
print("# Please select at least one residue. (sele)")
return
(hydrophobic, neutral, hydrophilic) = u.get_HP_set(hp_value=hp_value)
print("HP_Values %s" % hp_value)
print("HP_pos (Hydrophobic) brown")
print('\t' + ', '.join(hydrophobic))
print("HP_ntr (Neutral) green")
print('\t' + ', '.join(neutral))
print("HP_neg (Hydrophilic) blue")
print('\t' + ', '.join(hydrophilic))
HP_pos = check_names("HP_pos")
HP_ntr = check_names("HP_ntr")
HP_neg = check_names("HP_neg")
cmd.select(HP_pos, '%s and r. %s' % (selection, ','.join(hydrophobic)))
cmd.color("brown", "(%s)" % HP_pos)
cmd.select(HP_ntr, '%s and r. %s' % (selection, ','.join(neutral)))
cmd.color("green", "(%s)" % HP_ntr)
cmd.select(HP_neg, '%s and r. %s' % (selection, ','.join(hydrophilic)))
cmd.color("blue", "(%s)" % HP_neg)
try:
HP_group = check_names(hp_value)
members = "%s %s %s" % (HP_pos, HP_ntr, HP_neg)
cmd.group(HP_group, members)
except AttributeError: #no group command
pass
def cgo_dic():
cgo_dic = {
'POINTS': 0.0,
'LINES': 1.0,
'LINE_LOOP': 2.0,
'LINE_STRIP': 3.0,
'TRIANGLES': 4.0,
'TRIANGLE_STRIP': 5.0,
'TRIANGLE_FAN': 6.0,
#QUADS : 7.0
#QUAD_STRIP : 8.0
#POLYGON : 9.0
'STOP': 0.0,
'NULL': 1.0,
'BEGIN': 2.0,
'END': 3.0,
'VERTEX': 4.0,
'NORMAL': 5.0,
'COLOR': 6.0,
'SPHERE': 7.0,
'TRIANGLE': 8.0,
'CYLINDER': 9.0,
'LINEWIDTH': 10.0,
'WIDTHSCALE': 11.0,
'ENABLE': 12.0,
'DISABLE': 13.0,
'SAUSAGE': 14.0,
'CUSTOM_CYLINDER': 15.0,
'SHAPE_VERTEX': 16.0,
'SHAPE_COLOR': 17.0,
'SHAPE_NORMAL': 18.0,
'FONT': 19.0,
'FONT_SCALE': 20.0,
'FONT_VERTEX': 21.0,
'FONT_AXES': 22.0,
'CHAR': 23.0,
'ALPHA': 25.0, #transparency 1.00-0.01
'LIGHTING': float(0x0B50)}
return cgo_dic
def _remove_brakets(string, brakets=1):
'''Remove brakets and quotation marks from string.
brackets: 1: remove also brackets "(" and ")"
'''
if type(string) is not str:
return string
string = string.replace("'", "")
string = string.replace('"', "")
if brakets:
string = string.replace("(", "")
string = string.replace(")", "")
return string
def get_center_atom(selection='all', name="patom", enabled="0", onlysele="0"):
'''Get pseudo center of selection.
USAGE: get_center_atom(selection,[name="center",enabled="0",onlysele=0])
PYMOL: bni_get_center_atom selection,[name=center,enabled=0,onlysele=0])
'''
selection = _remove_brakets(selection)
if selection != "all":
names = [selection]
#enabled="0"
else:
if onlysele == "0":
names = [i for i in cmd.get_names(selection, enabled_only=int(enabled)) if cmd.get_type(
i) == "object:molecule" or cmd.get_type(i) == "selection"]
elif onlysele == "1":
names = [i for i in cmd.get_names(
selection, enabled_only=int(enabled)) if cmd.get_type(i) == "selection"]
cnt = sum([cmd.count_atoms(i) for i in names])
py_name = _remove_brakets(name)
py_name = check_names(py_name)
for item in names:
print(item)
center = getCenter(source=item)
if center:
if not name:
py_name = "c_" + item
py_name = check_names(py_name)
get_atom(name=py_name, coord=center)
else:
print("# No Center to create.")
def getCenterCoord(coordlist):
'''Get center coordinates of a coordinate list.
coordlist=[(x,y,z),(x,y,z), ...]
'''
center = [0., 0., 0.]
num_atom = 0
for a in coordlist:
num_atom = num_atom + 1
center[0] = center[0] + a[0]
center[1] = center[1] + a[1]
center[2] = center[2] + a[2]
if num_atom > 0:
center[0] = center[0] / num_atom
center[1] = center[1] / num_atom
center[2] = center[2] / num_atom
else:
return
return (center[0], center[1], center[2])
def getCenter(source='', logprint=1):
'''
DESCRIPTION:
calculate the coordinate center of a selection
USAGE:
get_center selection
'''
source = _remove_brakets(source)
try:
mol = cmd.get_model(source)
except:
if logprint == 1:
print("# Empty selection.")
print("# create pseudo atom at (0.0,0.0,0.0)")
return (0.0, 0.0, 0.0)
#print getCenter.__doc__
else:
center = [0., 0., 0.]
num_atom = 0
for a in mol.atom:
num_atom = num_atom + 1
center[0] = center[0] + a.coord[0]
center[1] = center[1] + a.coord[1]
center[2] = center[2] + a.coord[2]
if num_atom > 0:
center[0] = center[0] / num_atom
center[1] = center[1] / num_atom
center[2] = center[2] / num_atom
else:
if logprint == 1:
print("# No Atoms in selection.")
return
if logprint == 1:
print("# gridcenter %8.3f %8.3f %8.3f\n" %
(center[0], center[1], center[2]))
return (center[0], center[1], center[2])
def get_atom(name="atom", coord="(0.0,0.0,0.0)"):
'''Create dummy atom on specified coordinate.
USAGE: get_atom(name="atom",coord="(0.0,0.0,0.0)")
PYMOL: get_atom name="atom",coord=(0.0,0.0,0.0)
'''
get_point(name, coord, radius="0.5", atom="1")
def check_names(name=''):
'''Check if name is already in pymol viewer and create new name.
USAGE: check_names(name='')
OUTPUT: new name string: name_01
'''
names = cmd.get_names("all")
if not names:
return name
check = 0
for item in names:
if item.lower() == name.lower():
check = 1
break
if check == 1:
try:
a = cmd.get_unused_name(name + "_")
return a
except AttributeError:
names = cmd.get_names("all")
if not names:
return name
i = 1
name_check = name
check_again = 1
a = 0
while check_again:
if check_again == 0:
break
for item in names:
if item.lower() == name_check.lower():
try:#add additional number
a += 1
counter = int(name.split("_")[-1])
counter += a
name_check = "_".join(
name.split("_")[:-1]) + "_" + str(counter).zfill(2)
check_again = 1
i = 0
break
except (IndexError, ValueError):#add new number
i += 1
name_check = name + "_" + str(i).zfill(2)
a = 0 # set count for additional number to 0
check_again = 1
break
else:
check_again = 0
return name_check
else:
return name
def get_point(name="point", coord="(0.0,0.0,0.0)", radius="0.5", atom="0", state="new"):
'''Create CGO Sphere point.
USAGE: get_point(name="point",
coord="(0.0,0.0,0.0)",
radius="0.5",
atom="0")
PYMOL: get_point name="point", #Name of object
coord="(0.0,0.0,0.0)", #coord of object
radius="0.5", #radius of cgo
atom="0" #1: create dummy atom instead of cgo
state="new" #"new": create unique name if name already exists
'''
radius = float(radius)
if state == "new":
name = check_names(name=name)
if type(coord) is str:
coord = _remove_brakets(coord)
coord = coord.split(",")
coord = tuple(map(float, coord))
print(coord)
else:
print(coord)
if int(atom) == 0:
dic = cgo_dic()
BEGIN = dic['BEGIN']
TRIANGLES = dic['TRIANGLES']
COLOR = dic['COLOR']
SPHERE = dic['SPHERE']
LINES = dic['LINES']
NORMAL = dic['NORMAL']
VERTEX = dic['VERTEX']
END = dic['END']
p = [SPHERE,
coord[0], coord[1], coord[2], radius]
cmd.load_cgo(p, name)
elif int(atom) == 1:
record_name = 'ATOM '
atom_id = 5
atom_name = ' PO '
alternate = ' '
residue_name = "INT"
chain_id = 'P'
residue_id = 1
icode = " "
x = coord[0]
y = coord[1]
z = coord[2]
occ = 0.00
bfac = 100.00
free = 6 * ' '
seqid = "POIN"
symbol = " T"
charge = " "
state = -1
cmd.read_pdbstr('%6s%5d %4s%1s%3s %1s%4d%1s %8.3f%8.3f%8.3f%6.2f%6.2f%6s%4s %2s%2s' %
(record_name,
atom_id,
atom_name,
alternate,
residue_name,
chain_id,
residue_id,
icode,
x,
y,
z,
occ,
bfac,
free,
seqid,
symbol,
charge
), name, state)
try:
cmd.show_as("nb_spheres", name)
except AttributeError:
print(
"# cmd.as() has changed to cmd.show_as() in later and previous versions of PyMOL ")
#cmd.show_as("nb_spheres",name)
def get_axes(name="axes", origin="(0.0,0.0,0.0)", lenght="10.0", linewidth="3.0"):
'''Create Axes.
USAGE: get_axes(name="axes",origin="(0.0,0.0,0.0)",lenght="10.0",linewidth="1.0")
PYMOL: axes name="axes",origin="(0.0,0.0,0.0)",lenght="10.0",linewidth="1.0"
name: name of object
origin: zero coordinates of axes or "box" for origin coordinates of selection min coordinates
lenght: lenght of axes
linewidth: thickness of axes
'''
if origin == "box":
origin, (xmax, ymax, zmax) = cmd.get_extent(selection)
try:
linewidth = float(linewidth)
except ValueError:
print("# Wrong linewidth input 1.0 is used instead.")
linewidth = 1.0
if type(origin) is str:
origin = _remove_brakets(origin)
origin = origin.split(",")
origin = tuple(map(float, origin))
else:
pass
lenght = float(lenght)
dic = cgo_dic()
BEGIN = dic['BEGIN']
TRIANGLES = dic['TRIANGLES']
COLOR = dic['COLOR']
SPHERE = dic['SPHERE']
LINES = dic['LINES']
NORMAL = dic['NORMAL']
VERTEX = dic['VERTEX']
END = dic['END']
LINEWIDTH = dic['LINEWIDTH']
a = [LINEWIDTH, linewidth,
BEGIN,
LINES,
COLOR, 0.0, 1.0, 0.0,
VERTEX,
0.0 + origin[0], 0.0 + origin[1], 0.0 + origin[2],
VERTEX,
0.0 + origin[0], lenght + origin[1], 0.0 + origin[2],
COLOR, 1.0, 0.0, 0.0,
VERTEX,
0.0 + origin[0], 0.0 + origin[1], 0.0 + origin[2],
VERTEX,
lenght + origin[0], 0.0 + origin[1], 0.0 + origin[2],
COLOR, 0.0, 0.0, 1.0,
VERTEX,
0.0 + origin[0], 0.0 + origin[1], 0.0 + origin[2],
VERTEX,
0.0 + origin[0], 0.0 + origin[1], lenght + origin[2],
END,
COLOR, 1.0, 0.0, 0.0,
SPHERE,
0.0 + origin[0], 0.0 + origin[1], 0.0 + origin[2], 0.2]
print("# Axes\n-----\n\tX :red\n\tY :green\n\tZ :blue")
cmd.load_cgo(a, name)
def get_box_handler(selection="(sele)", app=None, action="medium", name="box", cushion="1.5", draw="full", coord="None", linewidth="3.0"):
'''Get a box using get_box GUI.
'''
action = _remove_brakets(action)
name = check_names(name)
cushion = cushion
draw = str(draw)
linewidth = str(linewidth)
if action == "set" and app:
value = tkSimpleDialog.askstring('Box settings',
'Specify [cushion] [draw full/lines] [linewidth]',
parent=app.root)
value = _remove_brakets(value)
if value:
value = value.split()
else:
return
if len(value) == 1:
cushion = value[0]
elif len(value) == 2:# width / dpi
cushion = value[0]
draw = str(value[1])
elif len(value) >= 3:#width width_unit
cushion = value[0]
draw = str(value[1])
linewidth = str(value[2])
else:
print("# Wrong input. Set at least size.")
return
try:
float(cushion)
except ValueError:
print("# Cushion has to be a number.")
return
units = ["full", "lines"]
if not draw.lower().strip() in units:
print("# Draw has to be either %s " % (" or ".join(units)))
return
try:
float(linewidth)
except ValueError:
print("# Linewidth has to be a number.")
return
elif action == "small":
cushion = 1
draw = "full"
linewidth = 3
elif action == "medium":
cushion = 2
draw = "full"
linewidth = 3
elif action == "large":
cushion = 5
draw = "full"
linewidth = 3
get_box(selection=selection, name=name,
cushion=cushion, draw=draw, linewidth=linewidth)
def bni_group(group_name="TEST_Group"):
'''Check if group is present if so add new group.
'''
#try:
name = check_names(group_name)
try:
cmd.group(name)
except:
return
return name
def get_box(name="box", selection="all", cushion="1.5", draw="full", coord="None", linewidth="3.0"):
'''Create a box.
USAGE: get_box(name="box",
selection="all",
cushion=0.0,
draw="full",
coord="None" or "(xmin,ymin,zmin,xmax,ymax,zmax)",
linewidth="1.0"
)
PYMOL: get_box name=box,selection=all,cushion=2.0,draw=full,coord=None,linewidth=1.0
name: name of the cgo box
selection: selection for min and max of box calculation
cushion : extend box with cushion in Angstroms each side
or each side separately by "(xcmin,ycmin,zcmin,xcmax,ycmax,zcmax)"
draw: lines: draw a box with lines
full: draw a full box with each side separated
to hide box walls separately
coord : if coord is given as "(xmin,ymin,zmin,xmax,ymax,zmax)"
selection will be ignored
linewidth: 1.0 : in case of box with lines define linewidth
'''
draw = _remove_brakets(draw)
name = _remove_brakets(name)
gn = bni_group("BNI-box")
dic = cgo_dic()
try:
cushion = float(cushion)
cushion = (cushion, cushion, cushion, cushion, cushion, cushion)
except ValueError:
try:
cushion = _remove_brakets(cushion)
cushion = cushion.split(",")
cushion = tuple(map(float, cushion))
except ValueError:
pass
if len(cushion) == 6:
pass
else:
cushion = (0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
linewidth = float(linewidth)
if coord == "None":
(xmin, ymin, zmin), (xmax, ymax, zmax) = cmd.get_extent(selection)
(xmin, ymin, zmin), (xmax, ymax, zmax) = (xmin - cushion[0], ymin - cushion[
1], zmin - cushion[2]), (xmax + cushion[3], ymax + cushion[4], zmax + cushion[5])
else:
if type(coord) is str:
coord = _remove_brakets(coord)
coord = coord.split(",")
coord = tuple(map(float, coord))
else:
pass
xmin, ymin, zmin, xmax, ymax, zmax = coord
xmin, ymin, zmin, xmax, ymax, zmax = xmin - cushion[0], ymin - cushion[
1], zmin - cushion[2], xmax + cushion[3], ymax + cushion[4], zmax + cushion[5]
edge01 = (xmax, ymax, zmax)
edge02 = (xmin, ymax, zmax)
edge03 = (xmin, ymax, zmin)
edge04 = (xmax, ymax, zmin)
edge05 = (xmax, ymin, zmin)
edge06 = (xmax, ymin, zmax)
edge07 = (xmin, ymin, zmax)
edge08 = (xmin, ymin, zmin)
normx = (-1.0, 0.0, 0.0)
normx1 = (1.0, 0.0, 0.0)
normy = (0.0, -1.0, 0.0)
normy1 = (0.0, 1.0, 0.0)
normz = (0.0, 0.0, -1.0)
normz1 = (0.0, 0.0, 1.0)
if draw == "lines":
BEGIN = dic['BEGIN']
LINES = dic['LINES']
LINEWIDTH = dic['LINEWIDTH']
VERTEX = dic['VERTEX']
END = dic['END']
box = [
LINEWIDTH, linewidth,
BEGIN,
LINES,
VERTEX, edge01[0], edge01[1], edge01[2],
VERTEX, edge02[0], edge02[1], edge02[2],
VERTEX, edge02[0], edge02[1], edge02[2],
VERTEX, edge03[0], edge03[1], edge03[2],
VERTEX, edge03[0], edge03[1], edge03[2],
VERTEX, edge04[0], edge04[1], edge04[2],
VERTEX, edge04[0], edge04[1], edge04[2],
VERTEX, edge01[0], edge01[1], edge01[2],
VERTEX, edge04[0], edge04[1], edge04[2],
VERTEX, edge05[0], edge05[1], edge05[2],
VERTEX, edge01[0], edge01[1], edge01[2],
VERTEX, edge06[0], edge06[1], edge06[2],
VERTEX, edge04[0], edge04[1], edge04[2],
VERTEX, edge05[0], edge05[1], edge05[2],
VERTEX, edge02[0], edge02[1], edge02[2],
VERTEX, edge07[0], edge07[1], edge07[2],
VERTEX, edge03[0], edge03[1], edge03[2],
VERTEX, edge08[0], edge08[1], edge08[2],
VERTEX, edge05[0], edge05[1], edge05[2],
VERTEX, edge06[0], edge06[1], edge06[2],
VERTEX, edge06[0], edge06[1], edge06[2],
VERTEX, edge07[0], edge07[1], edge07[2],
VERTEX, edge07[0], edge07[1], edge07[2],
VERTEX, edge08[0], edge08[1], edge08[2],
VERTEX, edge08[0], edge08[1], edge08[2],
VERTEX, edge05[0], edge05[1], edge05[2],
END
]
name = check_names(name)
cmd.load_cgo(box, name)
try:
#name=name+"_%d"%(i+1)
#name=check_names(name)
cmd.group(gn, name)
except:
pass
elif draw == "full":
box = []
BEGIN = dic['BEGIN']
TRIANGLES = dic['TRIANGLES']
COLOR = dic['COLOR']
SPHERE = dic['SPHERE']
LINES = dic['LINES']
NORMAL = dic['NORMAL']
VERTEX = dic['VERTEX']
END = dic['END']
a = [
BEGIN, TRIANGLES,
NORMAL, normy[0], normy[1], normy[2],
VERTEX, edge01[0], edge01[1], edge01[2],
NORMAL, normy[0], normy[1], normy[2],
VERTEX, edge02[0], edge02[1], edge02[2],
NORMAL, normy[0], normy[1], normy[2],
VERTEX, edge04[0], edge04[1], edge04[2],
NORMAL, normy[0], normy[1], normy[2],
VERTEX, edge02[0], edge02[1], edge02[2],
NORMAL, normy[0], normy[1], normy[2],
VERTEX, edge03[0], edge03[1], edge03[2],
NORMAL, normy[0], normy[1], normy[2],
VERTEX, edge04[0], edge04[1], edge04[2],
END
]
box.append(a)
a = [
BEGIN, TRIANGLES,
NORMAL, normx[0], normx[1], normx[2],
VERTEX, edge04[0], edge04[1], edge04[2],
NORMAL, normx[0], normx[1], normx[2],
VERTEX, edge05[0], edge05[1], edge05[2],
NORMAL, normx[0], normx[1], normx[2],
VERTEX, edge06[0], edge06[1], edge06[2],
NORMAL, normx[0], normx[1], normx[2],
VERTEX, edge01[0], edge01[1], edge01[2],
NORMAL, normx[0], normx[1], normx[2],
VERTEX, edge04[0], edge04[1], edge04[2],
NORMAL, normx[0], normx[1], normx[2],
VERTEX, edge06[0], edge06[1], edge06[2],
END
]
box.append(a)
a = [
BEGIN, TRIANGLES,
NORMAL, normz1[0], normz1[1], normz1[2],
VERTEX, edge03[0], edge03[1], edge03[2],
NORMAL, normz1[0], normz1[1], normz1[2],
VERTEX, edge08[0], edge08[1], edge08[2],
NORMAL, normz1[0], normz1[1], normz1[2],
VERTEX, edge05[0], edge05[1], edge05[2],
NORMAL, normz1[0], normz1[1], normz1[2],
VERTEX, edge03[0], edge03[1], edge03[2],
NORMAL, normz1[0], normz1[1], normz1[2],
VERTEX, edge05[0], edge05[1], edge05[2],
NORMAL, normz1[0], normz1[1], normz1[2],
VERTEX, edge04[0], edge04[1], edge04[2],
END
]
box.append(a)
a = [
BEGIN, TRIANGLES,
NORMAL, normx1[0], normx1[1], normx1[2],
VERTEX, edge03[0], edge03[1], edge03[2],
NORMAL, normx1[0], normx1[1], normx1[2],
VERTEX, edge02[0], edge02[1], edge02[2],
NORMAL, normx1[0], normx1[1], normx1[2],
VERTEX, edge07[0], edge07[1], edge07[2],
NORMAL, normx1[0], normx1[1], normx1[2],
VERTEX, edge03[0], edge03[1], edge03[2],
NORMAL, normx1[0], normx1[1], normx1[2],
VERTEX, edge07[0], edge07[1], edge07[2],
NORMAL, normx1[0], normx1[1], normx1[2],
VERTEX, edge08[0], edge08[1], edge08[2],
END
]
box.append(a)
a = [
BEGIN, TRIANGLES,
NORMAL, normz[0], normz[1], normz[2],
VERTEX, edge02[0], edge02[1], edge02[2],
NORMAL, normz[0], normz[1], normz[2],
VERTEX, edge01[0], edge01[1], edge01[2],
NORMAL, normz[0], normz[1], normz[2],
VERTEX, edge06[0], edge06[1], edge06[2],
NORMAL, normz[0], normz[1], normz[2],
VERTEX, edge07[0], edge07[1], edge07[2],
NORMAL, normz[0], normz[1], normz[2],
VERTEX, edge02[0], edge02[1], edge02[2],
NORMAL, normz[0], normz[1], normz[2],
VERTEX, edge06[0], edge06[1], edge06[2],
END
]
box.append(a)
a = [
BEGIN, TRIANGLES,
NORMAL, normy1[0], normy1[1], normy1[2],
VERTEX, edge07[0], edge07[1], edge07[2],
NORMAL, normy1[0], normy1[1], normy1[2],
VERTEX, edge06[0], edge06[1], edge06[2],
NORMAL, normy1[0], normy1[1], normy1[2],
VERTEX, edge05[0], edge05[1], edge05[2],
NORMAL, normy1[0], normy1[1], normy1[2],
VERTEX, edge05[0], edge05[1], edge05[2],
NORMAL, normy1[0], normy1[1], normy1[2],
VERTEX, edge08[0], edge08[1], edge08[2],
NORMAL, normy1[0], normy1[1], normy1[2],
VERTEX, edge07[0], edge07[1], edge07[2],
END
]
box.append(a)
color = ["wheat",
"lightpink",
"palecyan",
"darksalmon",
"gray90",
"palegreen"]
for i, (item, color) in enumerate(zip(box, color)):
n = name + "-%s" % str(i + 1).zfill(2)
n = check_names(n)
cmd.load_cgo(item, n)
cmd.color(color, n)
try:
cmd.group(gn, n)
except:
pass
#print("Cannot group %s"%group_name)
def fast_sym(selection='', cutoff=4.0, delete_sym=1, use=1, app=None):
'''Create a view of symmetry involved interactions.
USAGE: fast_sym selection,cutoff=4.0,delete_sym=1
selection: object for symmetry calculation
cutoff: distance cutoff
delete_sym: delete previous sym files ("s_*")
'''
selection = _remove_brakets(selection)
if cutoff == "set" and app:
cutoff = tkSimpleDialog.askstring('Input Symetry Distance',
'Please specify a Distance e.g 4.25',
parent=app.root)
if cutoff:
try:
cutoff = float(cutoff)
use = int(use)
delete_sym = int(delete_sym)
except:
print("# Wrong input")
print(fast_sym.__doc__)
else:
cryst = Sym()
if delete_sym == 1:#delete previous symetry objects
print(delete_sym)
del_sym()
if selection:
if cmd.get_object_list(selection) is None:
print(
"# No structure in selection (sele). Select at least one atom")
print("# in a structure.")
return
if len(cmd.get_object_list(selection)) > 1:
print("# WARNING: more than one object in selection.")
print(
"# WARNING: first object will be used for calculation")
try:
selection = selection + " and " + \
cmd.get_object_list(selection)[0]#just use first hit
except IndexError:
print("# no object enabled")
print("# enable an object")
selection = ''
return
elif selection == '':#get first object
names = cmd.get_names(enabled_only=1)
#selection=' or '.join(names)
if len(names) > 1:
print("# WARNING: more than one object is enabled")
print("# WARNING: first object is used")
elif len(names) == 0:
print("# load a structure into PyMOL first.")
return
try:
selection = names[0]#just use first hit
except IndexError:
print("# no object enabled")
print("# enable an object")
selection = ''
else:
print("# load a structure into pymol. No structure selected")
return
mol = cryst.get_model(selection)
if mol:
if len(mol.atom) == 0:
print("# no atoms in selection")
elif use == 1:
original = selection
cmd.hide("surface")
sym_select = cryst.create_sym(
cutoff=cutoff, selection=selection)
set_surface(mode="symmetry")
org_select = cryst.create_org(cutoff=cutoff, sele="s_*")
cryst.show_org(
select_name=org_select, show_name="surface", cutoff=cutoff, surf_transparency=0.5)
cryst.show_org(
select_name=org_select, show_name="stick", cutoff=cutoff, surf_transparency=0.5)
cryst.show_sym(select_name=sym_select, show_name="surface",
cutoff=cutoff, surf_transparency=0.5, object="s_*")
cryst.show_sym(select_name=sym_select, show_name="stick",
cutoff=cutoff, surf_transparency=0.5, object="s_*")
cmd.delete("tmp_org")
import Pmw
class multi_pdb:
'''Multiple input load.
'''
filedir = '.'
def __init__(self, app, case=1, message=None):
self._message = message
try:
self._app = app.root
except:
self._app = app
self.filedir = self.__class__.filedir
self.filename = []
self.filetypes = [('PDB File', '.pdb'),
('PDB File', '.ent'),
('Modeller PDB File', '.B9999*.pdb'),
('Modeller PDB File', '.B9999*_fit.pdb'),
('Delphi PHI File', '.phi'),
('all', '*'),
]
def _map(self, filenamelist):
'''load Electon density map.
'''
pass
def _casox_map(self, filenamelist, repr="mesh"):
'''Load a CaSoX map (xplor format) and generate different level views.
USAGE: _casox_map(filenamelist,repr="mesh")
repr: "mesh" :show levels in mesh format
"surf" :show levels in surf format
ADDITIONAL: this will create a map and different mesh representations
in different colors depending on casox ligsite values
level 0 --> "white" --> casox ligsite level 1
level 1 --> "bluewhite" --> casox ligsite level 2
level 2 --> "palecyan" --> casox ligsite level 3
level 3 --> "lightteal" --> casox ligsite level 4
level 4 --> "lightorange" --> casox ligsite level 5
level 5 --> "orange" --> casox ligsite level 6
level 6 --> "red" --> casox ligsite level 7 (complete closed cavity)
level-1 --> "blue" --> casox protein level 0 grid hull
'''
if len(filenamelist) != 1:
print("# please select just one CASoX map.")
file_path = norm_path(filenamelist[0])
self.__class__.filedir = file_path.dirname
return
else:
file_path = norm_path(filenamelist[0])
objcasox = file_path.splitname + "_map"
self.open_filename(file_path.all, obj=objcasox, format="xplor")
self.__class__.filedir = file_path.dirname
if cmd.get_type(objcasox) == "object:map":
levels = [-1, 6, 5, 4, 3, 2, 1, 0]
colors = ["blue", "red", "orange", "lightorange",
"lightteal", "palecyan", "bluewhite", "white"]
print("# CaSoX Map")
print("# --------------")
print("# Loaded by BNI-Tools v.%s" % __version__)
print("# Map: %s " % (objcasox))
print("# Levels for Ligsite 1 - 7(closed cavity)")
cmd.feedback("disable", "cmd", "everything")
try:
for level, color in zip(levels, colors):
objmesh = file_path.splitname + "_%d" % (level + 1)
if repr == "mesh":
cmd.isomesh(objmesh, objcasox, 1.0)
elif repr == "surf":
cmd.isosurface(objmesh, objcasox, 1.0)
cmd.hide("surface", objmesh)
cmd.isolevel(objmesh, float(level))
cmd.color(color, objmesh)
print("%15s : %15s" % (objmesh, color))
except:
print("# casox map could not be recognized")
print("# loading of casox map failed.")
print("# --------------")
cmd.feedback("enable", "cmd", "everything")
def _delphi(self, filenamelist):
'''Load phi and pdb file to create a delphi surface.
'''
if len(filenamelist) > 2:
print("# Select .phi or .dx map and corresponding .pdb file.")
file_path = norm_path(filenamelist[0])
self.__class__.filedir = file_path.dirname
return
else:
objphi = "e_lvl"
map = 0
for item in filenamelist:
file_path = norm_path(item)
if file_path.splitext.lower() == ".phi" or file_path.splitext.lower() == ".dx":
objmap = file_path.splitname + "_map"
objmapext = file_path.splitext.lower()
objphi = file_path.splitname
self.open_filename(item, obj=objmap)
map = 1
else:
objpdb = file_path.splitname
self.open_filename(item, obj=objpdb)
self.__class__.filedir = file_path.dirname
if map == 1 and cmd.get_type(objmap) == "object:map":
objramp = objphi + "_ramp"
cmd.ramp_new(objramp, objmap, (-15, 0, +15))
if objmapext == ".phi":
print("# DELPHI PHI Map")
elif objmapext == ".dx":
print("# DX Map")
print("# --------------")
print("# Loaded by BNI-Tools v.%s" % __version__)
print("# Map : %s" % objmap)
print("# Ramp : %s" % objramp)
if len(filenamelist) == 2:
cmd.set("surface_color", objramp, objpdb)
print("# File : %s" % objpdb)
else:
print("# load pdb file as object into pymol and")
print("# set surface_color,%s,(object)" % objramp)
print("#--------------")
print(
"# to change ramp values use str+mid mouse button on ramp")
print("# or use")
print("# ramp_new %s,%s,(min,mid,max)" % (objramp, objmap))
print("# to set ramp values.")
else:
print("# No Map loaded ... (extention has to be .phi or .dx)")
def _modeller(self, filenamelist):
'''Load multiple modeller files into Pymol.
'''
filenamelist = list(filenamelist)
filenamelist.sort()
filenamelist = tuple(filenamelist)
self.filename = []
for item in filenamelist:
file_path = norm_path(item)
self.filename.append(file_path.basename)
self.__class__.filedir = file_path.dirname
objfunc = []
seqid = []
modvers = []
filelist = []
object = []
for files in self.filename:
file_path = norm_path(self.__class__.filedir, files)
filelist.append(file_path.all)
obj = file_path.splitname
if ".B9999" in obj:
obj = obj.split(".B9999")
obj1 = obj[0]
try:
obj2 = obj[1]
except IndexError:
obj2 = ""
obj = obj1
try:
obj2 = int(obj2)
except ValueError:
pass
obj = obj1 + '_' + "M" + str(obj2)
elif ".BL" in obj:
obj = obj.split(".BL")
obj1 = obj[0]
try:
obj2 = obj[1][:-4]
except IndexError:
obj2 = ""
obj = obj1
try:
obj2 = int(obj2)
except ValueError:
pass
obj = obj1 + '_' + 'L' + str(obj2)
object.append(obj)
try:
fileobj = open(file_path.all, "r")
except IOError:
print("# cannot read modeller file %s " % file_path.basename)
object.pop()
continue
else:
sid = 0.0
objf = 0.0
while 1:
a = fileobj.readline()
if not a:
break
if "ATOM" in a[:4] or "HETATM" in a[:6]:
break
if "EXPDTA" in a[:6] and "MODELLER" in a:
continue
elif "REMARK" in a[:6] and "MODELLER OBJECTIVE FUNCTION" in a:
try:
objf = float(a.split()[-1])
except (IndexError, ValueError):
print(
"# Cannot parse objective funktion for %s" % file_path.basename)
pass
elif "REMARK" in a[:6] and "MODELLER BEST TEMPLATE" in a:
try:
sid = float(a.split()[-1])
except (IndexError, ValueError):
print("# cannot parse SEQ ID for %s" %
file_path.basename)
pass
objfunc.append(objf)
seqid.append(sid)
s = list(zip(objfunc, filelist, object, seqid))
s.sort()
print("# Modeller Files")
print("# --------------")
print("# Loaded by BNI-Tools v.%s" % __version__)
print("# Sorted by Modeller Objective Function")
print("# Name ;Objective Function; Seq-ID")
for objfunc, item, obj, seqid in s:
if "%.2f" % objfunc == "0.00":
self.open_filename(item, obj=obj)
else:
self.open_filename(item, obj=obj, title="%.2f" % objfunc)
print("%-15s ; %.2f ; %.2f%%" % (obj, objfunc, seqid))
print("# --------------")
def _amber(self, filenamelist):
'''Load multiple amber pdb files with info file and energy.
'''
filenamelist = list(filenamelist)
filenamelist.sort()
filenamelist = tuple(filenamelist)
for item in filenamelist:
file_path = norm_path(item)
self.filename.append(file_path.basename)
self.__class__.filedir = file_path.dirname
filelist = []
print("# Amber Files")
print("# --------------")
print("# Loaded by BNI-Tools v.%s" % __version__)
info_file_ext = ".info"
print("_" * 60)
print("%-40s:%-20s" % ("Name", "Energy"))
print("-" * 60)
for files in self.filename:
file_path = norm_path(self.__class__.filedir, files)
filelist.append(file_path.all)
obj = file_path.splitname
try:
self.open_filename(file_path.all, obj=obj)
except IOError:
print("# cannot open file %s" % file_path.basename)
continue
try:
info_file = norm_path(
file_path.dirname, file_path.splitname + info_file_ext)
if os.path.isfile(info_file.all):
fileobj = open(info_file.all, "r")
#try to find info file if not same name as pdb file
elif "_min." in file_path.basename:
info_name = file_path.splitname.split("_min")[0]
info_file = norm_path(
file_path.dirname, info_name + info_file_ext)
fileobj = open(info_file.all, "r")
else:
print("# %s has no amber .info file in same directory." %
(file_path.basename))
print("# therefore no energy could be read in.")
continue
except IOError:
print("# cannot read amber file %s " % file_path.basename)
continue
else:
energy = 0.0
energy_sign = "NSTEP"
remark_text = []
begin_read = 0
begin_energy = 0
while 1:
a = fileobj.readline()
if not a:
break
if begin_energy == 1:
try:
energy = float(a.split()[1])
except (IndexError, ValueError):
energy = 0.0
begin_energy = 0
if energy_sign in a:
begin_read = 1
begin_energy = 1
remark_text.append(a)
fileobj.close()
print("%-40s:%-20.3f" % (obj, energy))
try:
cmd.set_title(obj, -1, "%-5.1f" % (energy))
except:
pass
print("-" * 60)
def _autodock(self, filenamelist):
'''Load multiple autodock MODEL files.
'''
filenamelist = list(filenamelist)
filenamelist.sort()
filenamelist = tuple(filenamelist)
for item in filenamelist:
file_path = norm_path(item)
self.filename.append(file_path.basename)
self.__class__.filedir = file_path.dirname
filelist = []
print("# AutoDock Files")
print("# --------------")
print("# Loaded by BNI-Tools v.%s" % __version__)
print("_" * 60)
print("%-30s:%-30s" % ("Name", "Nr. of Models"))
print("-" * 60)
for files in self.filename:
file_path = norm_path(self.__class__.filedir, files)
filelist.append(file_path.all)
obj = file_path.splitname
try:
self.open_filename(file_path.all, obj=obj)
except IOError:
print("# cannot open file %s" % file_path.basename)
continue
try:
fileobj = open(file_path.all, "r")
except IOError:
print("# cannot read autodock file %s " % file_path.basename)
continue
else:
cluster = []
cluster_sign = "Number of conformations in this cluster"
cluster_split = "="
energy = []
energy_sign = "Estimated Free Energy of Binding"
energy_split = "="
remarks = []
remark_text = []
model_state = []
model_state_id = 0
model_id = []
begin_read = 0
while 1:
a = fileobj.readline()
if not a:
break
if "ENDMDL" in a[:6] and begin_read == 1:
begin_read = 0
remarks.append(remark_text)
remark_text = []
continue
if "REMARK" in a[:6] or "USER" in a[:4] and begin_read == 1:
try:
remark_text.append(a.split()[1])
except IndexError:
remark_text.append(" ")
if cluster_sign in a:
try:
cluster.append(
int(a.split(cluster_split)[1].split()[0]))
except IndexError:
cluster.append(0)
if energy_sign in a:
try:
energy.append(
float(a.split(energy_split)[1].split()[0]))
except IndexError:
energy.append(0.0)
continue
if "MODEL" in a[:5]:
try:
model_id.append(int(a.split()[-1]))
except IndexError:
model_id.append(0)
model_state_id += 1
model_state.append(model_state_id)
begin_read = 1
fileobj.close()
print("%-26s:%-30d" % (obj, len(model_state)))
print("-" * 60)
print("%-5s%-4s:%-4s:%-10s :%-10s" %
(" ", "Nr", "Id", "Energy", "Cluster"))
for item in zip(model_state, model_id, energy, cluster):
#
print(" %-4d:%-4d:%10.3f : %-3s %s" %
(item + ("*" * int(item[-1]),)))
try:
cmd.set_title(
obj, item[0], "%5.2f [%2d]" % (item[2], item[3]))
except:
pass
print("-" * 60)
if file_path.splitext == ".dlg":
print(
"# DLG File loaded (best docking mode in cluster is shown.)")
# additional read all docked models
#s=zip(objfunc,filelist,object,seqid)
#s.sort()
def _oneobject(self, filenamelist, sorting=1):
'''Load multiple files into one object.
Object is named by first filename.
If yasara table (.tbl) is present in selection try to read energies.
sorting: 1: sort by filename
'''
filenamelist = list(filenamelist)
if sorting == 1:
filenamelist.sort()
tablename = None
try:
table_index = [
filenamelist.index(a) for a in filenamelist if "tab" in norm_path(a).splitext]
if table_index:
for tab_index in table_index:
tablename = filenamelist.pop(tab_index)
tablename = norm_path(tablename)
except IndexError:
pass
try:
object_name = norm_path(filenamelist[0]).splitname
except IndexError:
object_name = "obj1"
filenamelist = tuple(filenamelist)
for item in filenamelist:
file_path = norm_path(item)
self.filename.append(file_path.basename)
self.__class__.filedir = file_path.dirname
for files in self.filename:
file = norm_path(self.__class__.filedir, files).all
self.open_filename(file, obj=object_name)
if tablename:
try:
fileobj = open(tablename.all, "r")
except IOError:
print("# cannot read table file %s " % tablename.basename)
else:
begin_read = 0
energy = []
while 1:
a = fileobj.readline()
if not a:
break
if begin_read == 1:
energy.append(a.strip().split())
if "snapshot" in a.strip().lower():
print("Sanapshot Energy")
print("------------------")
begin_read = 1
continue
fileobj.close()
energy = [e for e in energy if len(e) == 2]
for i, (snap, value) in enumerate(energy):
print("%-5s:%-30s" % (snap, value))
try:
cmd.set_title(
object_name, i + 1, "%s:%s" % (snap, value))
except:
pass
print("-" * 60)
def _all(self, filenamelist):
'''Load multiple files.
'''
filenamelist = list(filenamelist)
filenamelist.sort()
filenamelist = tuple(filenamelist)
for item in filenamelist:
file_path = norm_path(item)
self.filename.append(file_path.basename)
self.__class__.filedir = file_path.dirname
for files in self.filename:
file = norm_path(self.__class__.filedir, files).all
self.open_filename(file, obj="None")
def fetchFileName(self, ext="None"):
'''Get multiple filenmes loaded into Pymol with special filename handling.
USAGE: fetchFileName(ext="None")
ext: "None" :load files with filename extention
"modeller" :load modeller files sorted
by modeller objective function
and rename filenames .B9999000X to _X
"autodock" :load autodock pdb files (docked MODELs)
with energy and cluster in title
"ambermin" :load amber minimization pdb with energy
in .info files
"delphi" :load delphi map (*.phi) and pdb file for surface representation
or abps map (*.dx) and pdb file for surface representation
"casox" :load CaSoX Map (xplor like Soft Ligsite Cavity Explorer)
'''
title = 'Open File(s)'
if ext == "None":
filetypes = self.filetypes
elif ext == "oneobject":
filetypes = self.filetypes
elif ext == "modeller":
title = 'Select Modeller PDB file (.B9999*.pdb)'
filetypes = [('Modeller PDB File', '.B9999*.pdb'), ('all', '*')]
elif ext == "autodock":
title = 'Select Autodock .dlg file or .dlg.pdb (old) file and receptor pdb.'
filetypes = [('AutoDock DLG file', '.dlg'), ('AutoDock docked PDB', '.pdb'), (
'AutoDock DLG file', '.pdb'), ('AutoDock docked PDB', '.dlg.pdb'), ('all', '*')]
elif ext == "ambermin":
title = 'Select amber minimization pdb file (.info file in same directory displays energies).'
filetypes = [('Amber minimization', '.pdb'), ('all', '*')]
elif ext == "delphi":
title = 'Select map and also the corresponding .pdb file'
filetypes = [('DelPhi PHI Map', '.phi'), ('DelPhi PHI Map', '.pdb'),
('ABPS dx Map', '.pdb'), ('ABPS dx Map', '.dx'), ('all', '*')]
elif ext == "casox":
title = 'Select CASoX Map'
filetypes = [
('CASoX Map', '.omap'), ('CASoX Map', '.map'), ('all', '*')]
filenamelist = tkFileDialog.askopenfilenames(title=title,
initialdir=self.__class__.filedir,
filetypes=filetypes,
)
self.filename = []
self.filedir = self.__class__.filedir
if __pymol_version__ > 1.3:
try:
filenamelist = self._app.splitlist(filenamelist)
except:
print(
"# cannot create workaround for python askopenfielanmes bug.")
if filenamelist:
if ext == "None":
self._all(filenamelist)
elif ext == "modeller":
self._modeller(filenamelist)
elif ext == "autodock":
self._autodock(filenamelist)
elif ext == "ambermin":
self._amber(filenamelist)
elif ext == "delphi":
self._delphi(filenamelist)
elif ext == "casox":
self._casox_map(filenamelist)
elif ext == "oneobject":
self._oneobject(filenamelist)
def open_filename(self, file, obj="None", state="None", format="None", finish="None", discrete="None", title="None", allinone="0"):
'''Open file in pymol.
USAGE: open_filename(file,
obj="None",
state="None", # not implemented
format="None", # specify format
finish="None", # not implemented
discrete="None", # not implemented
title="None" # write title
allinone="0") # all in one object (first object name) with different states
'''
if obj == "None":
obj = norm_path(file).splitname
else:
pass
if state == "None":
state = -1
if format == "None":
cmd.load(file, object=obj, state=state)
else:
cmd.load(file, object=obj, state=state, format=format)
#print "loaded",file,obj,format,state
if title == "None":
title = ""
else:
cmd.set_title(obj, state, title)
def norm_path(pathname, *join, **abs):
'''Create normalized path and join path items.
USAGE: norm_path(pathname
[,*join] # join "join" strings to path
[,**abs=1] # 1: create absolute path
0: use relative path
)
RETURNS: Object with obj.all
.dirname
.basename
.splitname
.splitext
ADDITIONAL: e.g. 'C:/user/something\\new/'
.all 'C:\\user\\something\\new'
.dirname 'C:\\user\\something'
.basename 'new'
.splitname 'new'
.splitext ''
'C:/user/something\\new/file.txt'
.all 'C:\\user\\something\\new\\file.txt'
.dirname 'C:\\user\\something\\new'
.basename 'file.txt'
.splitname 'file'
.splitext '.txt'
'''
if abs.get('abs', 1) == 1:
whole = os.path.normpath(
os.path.abspath(os.path.join(pathname, *join)))
else:
whole = os.path.normpath(os.path.join(pathname, *join))
path = os.path.dirname(whole)
file_name = os.path.basename(whole)
pref, ext = os.path.splitext(file_name)
class NormPath:
def __init__(self):
self.all = whole
self.dirname = path
self.basename = file_name
self.splitname = pref
self.splitext = ext
output = NormPath()
return output
def bni_ramp_surf(sele, mapp, command='surface'):
'''Color Surface by ramp.
'''
if command == 'mesh':
surfname = 'mesh'
surfcommand = 'mesh_color'
else:
surfname = 'surface'
surfcommand = 'surface_color'
print("# Color %s by map" % surfname)
print("# --------------------")
print("# BNI-Tools v.%s" % __version__)
if cmd.get_type(mapp) == "object:map":
rampname = check_names(mapp + '_ramp')
cmd.ramp_new(rampname, mapp)
print("# Map : %s" % mapp)
else:
rampname = mapp
mapp = rampname.split("_ramp")[0]
# if len(filenamelist)==2:
# cmd.set("surface_color",objramp,objpdb)
# print "File : %s"%objpdb
# else:
# print "Load Pdb file as object into pymol and"
# print "set surface_color,%s,(object)"%objramp
# else:
# print "No Map loaded ... (extention has to be .phi or .dx)"
print("# Ramp : %s" % rampname)
print("# %7s: %s" % (surfname, sele))
print("--------------")
print("To change ramp values use ctr+mid mouse button on ramp")
print("or use")
print("ramp_new %s,%s,[min,mid,max],[red,white,blue]" % (rampname, mapp))
print("to set ramp values.")
print("# %s of %s colored by" % (surfname, sele))
print("# Ramp: %s" % rampname)
cmd.set(surfcommand, rampname, sele)
class Bni_func_pymol:
'''Class for passing BNI-functions in plug-in for PyMOL sidebar calls and actions.
'''
def __init__(self):
self.new_views = new_views
self.select_hp = select_hp
self.get_surface_handler = get_surface_handler
self.fast_sym = fast_sym
self.set_surface = set_surface
self.bni_ramp_surf = bni_ramp_surf
self.del_enabled = del_enabled
self.inv_enabled = inv_enabled
self.combine_sele = combine_sele
self.get_sequence = get_sequence
self.get_pdb_lines = get_pdb_lines
def test(self):
print("Bni sidebar actions")
stored.bni_func = Bni_func_pymol()
#
# GUI TWEAK - CHANGES TO SIDEBAR MENU for bni-tools
#
from pymol import menu
dummy = lambda *args,**kwargs: []
# MENU DECORATOR
def menuappend(f):
'''Decorator for overloading menu functions by appending to them'''
orig = getattr(menu, f.__name__, dummy)
wrapped = lambda *args,**kwargs: orig(*args,**kwargs) + f(*args,**kwargs)
setattr(menu, f.__name__, wrapped)
return wrapped
# BNIADD
@menuappend
def mol_show(self_cmd, sele):
return [
#BNI-Tools Transparency and Surface
[ 0, '' , '' ],
[ 1, 'transparency' , bni_transparency_all(self_cmd,sele) ],
[ 1, 'surface flag' , bni_surface(self_cmd,sele) ]]
def bni_transparency_all(self_cmd,sele):
result=[[2,'transp:','']]
transitems_obj=["surface","sphere","cgo","nonbonded","space","stick","ribbon","cartoon","cartoon_ring","ellipsoid"]
transitems=transitems_obj
if sele in [a.lower() for a in self_cmd.get_names('objects')]:
transitems=transitems_obj
for transitem in transitems:
if transitem=="space":
result.append([0,'',''])
else:
result.append([1,transitem,bni_transparency(self_cmd,sele,object=transitem)])
return result
def bni_transparency(self_cmd,sele,object="cgo",label="%:"):
result= [[2,label,'']]
if object=="surface":
object=""
else:
object=object+"_"
transproc=[0,10,20,30,40,50,60,70,80,90]
for proc in transproc:
result.append([1,str(proc)+'%','cmd.set("%stransparency",%s,"'%(object,(proc/100.0))+sele+'")'])
return result
#BNI-Transparency END
#BNI-Surface BEGIN
def bni_surface(self_cmd,sele):
result= [[2,"alter surface",''],
[1,"back to standard",'stored.bni_func.get_surface_handler("'+sele+'","Standard")'],
[0,'' ,'' ],
]
surf_settings=["Methionine","Exclude","Hide","separator","Include","Show"]
surf_settings_name=['include seleno-methionine',"exclude for atom(s)","hide for atom(s)","separator","include for atom(s)","show for atom(s)"]
for setting_name,setting in zip(surf_settings_name,surf_settings):
if setting_name=="separator":
result.append([ 0, '' , '' ])
continue
result.append([1,str(setting_name).lower(),'stored.bni_func.get_surface_handler("'+sele+'","'+setting+'")'])
return result
@menuappend
def cgo_show(self_cmd, sele):
return [
#BNI-Tools transparency add to cgo
[ 1, 'transp' , bni_transparency(self_cmd,sele,object="cgo") ]
]
#BNI Tools surf colors,lable colors
if not hasattr(menu,"by_rep"):
@menuappend
def by_surf(self_cmd, sele,command='cmd.set("surface_color",'):
return [[2,'Color','' ],
[ 1, 'by atom','%s-1,selection="'%command+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'by map',bni_surf_map(self_cmd,sele) ]
] + all_surf_colors(self_cmd,sele,command)
@menuappend
def by_mesh(self_cmd, sele,command='cmd.set("mesh_color",'):
return [[2,'Color','' ],
[ 1, 'by atom','%s-1,selection="'%command+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'by map',bni_surf_map(self_cmd,sele,command='mesh') ]
] + all_surf_colors(self_cmd,sele,command)
@menuappend
def by_label(self_cmd, sele,command='cmd.set("label_color",'):
return [[2,'Color','' ],
[ 1, 'by atom','%s"default",selection="'%command+sele+'")' ],
[ 0, '' , '' ]
] + all_surf_colors(self_cmd,sele,command)
@menuappend
def by_stick(self_cmd, sele,command='cmd.set_bond("stick_color",',selekey="selection1"):
self_cmd.set("stick_ball_color","atom")
return [[2,'Color','' ],
[ 1, 'by atom','%s"'%'cmd.unset_bond("stick_color",'+sele+'")' ],
[ 0, '' , '' ]
] + all_surf_colors(self_cmd,sele,command,selekey)
else:
@menuappend
def by_rep_sub(self_cmd, rep, setting, sele):
r = [[ 0, '' , '' ],
[ 1, 'my colors',owncolors_surf(self_cmd,sele,command='cmd.color(')]]
return r
@menuappend
def by_helix(self_cmd, sele,command='cmd.color('):
sele="(ss H and ("+sele+"))"
return [[2,'Color','' ],
] + all_surf_colors(self_cmd,sele,command)
@menuappend
def by_sheet(self_cmd, sele,command='cmd.color('):
sele="(ss S and ("+sele+"))"
return [[2,'Color','' ],
] + all_surf_colors(self_cmd,sele,command)
@menuappend
def by_loop(self_cmd, sele,command='cmd.color('):
sele="((not (ss S+H)) and ("+sele+"))"
return [[2,'Color','' ],
] + all_surf_colors(self_cmd,sele,command)
def bni_surf_map(self_cmd,sele,command='surface'):
result=[[2,'Map','' ]]
list = self_cmd.get_names("public_objects")[0:25] # keep this practical
list = [x for x in list if (self_cmd.get_type(x)=="object:map" or self_cmd.get_type(x)=="object:")]
for mapp in list:
if mapp != sele:
result.append([1,mapp,'stored.bni_func.bni_ramp_surf("'+sele+'","'+mapp+'","'+command+'")'])
if len(result) == 1:
result.append([1,"no map",''])
return result
def all_surf_colors(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 1, '\\900reds' ,reds_surf(self_cmd, sele, command,selekey) ],
[ 1, '\\090greens' ,greens_surf(self_cmd, sele, command,selekey) ],
[ 1, '\\009blues' ,blues_surf(self_cmd, sele, command,selekey) ],
[ 1, '\\990yellows' ,yellows_surf(self_cmd, sele, command,selekey) ],
[ 1, '\\909magentas' , magentas_surf(self_cmd, sele, command,selekey) ],
[ 1, '\\099cyans' , cyans_surf(self_cmd, sele, command,selekey) ],
[ 1, '\\950oranges' , oranges_surf(self_cmd, sele, command,selekey) ],
[ 1, '\\978tints' ,tints_surf(self_cmd, sele, command,selekey) ],
[ 1, '\\666grays' ,grays_surf(self_cmd, sele, command,selekey) ],
[ 0, '', ''],
[ 1, '\\999my colors' ,owncolors_surf(self_cmd, sele, command,selekey) ],
]
def reds_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 2, 'Reds' ,'' ],
[1,'\\900red','%s4,%s="'%(command,selekey)+sele+'")'],
[1,'\\922tv_red','%s32,%s="'%(command,selekey)+sele+'")'],
[1,'\\634raspberry','%s5268,%s="'%(command,selekey)+sele+'")'],
[1,'\\755darksalmon','%s5280,%s="'%(command,selekey)+sele+'")'],
[1,'\\955salmon','%s9,%s="'%(command,selekey)+sele+'")'],
[1,'\\944deepsalmon','%s5258,%s="'%(command,selekey)+sele+'")'],
[1,'\\824warmpink','%s5279,%s="'%(command,selekey)+sele+'")'],
[1,'\\611firebrick','%s49,%s="'%(command,selekey)+sele+'")'],
[1,'\\522ruby','%s21,%s="'%(command,selekey)+sele+'")'],
[1,'\\521chocolate','%s50,%s="'%(command,selekey)+sele+'")'],
[1,'\\632brown','%s51,%s="'%(command,selekey)+sele+'")'],
]
def greens_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 2, 'Greens' ,'' ],
[1,'\\090green','%s3,%s="'%(command,selekey)+sele+'")'],
[1,'\\292tv_green','%s33,%s="'%(command,selekey)+sele+'")'],
[1,'\\490chartreuse','%s14,%s="'%(command,selekey)+sele+'")'],
[1,'\\570splitpea','%s5267,%s="'%(command,selekey)+sele+'")'],
[1,'\\564smudge','%s5270,%s="'%(command,selekey)+sele+'")'],
[1,'\\686palegreen','%s5259,%s="'%(command,selekey)+sele+'")'],
[1,'\\094limegreen','%s15,%s="'%(command,selekey)+sele+'")'],
[1,'\\494lime','%s10,%s="'%(command,selekey)+sele+'")'],
[1,'\\792limon','%s5276,%s="'%(command,selekey)+sele+'")'],
[1,'\\252forest','%s22,%s="'%(command,selekey)+sele+'")'],
]
def blues_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 2, 'Blues' ,'' ],
[1,'\\009blue','%s2,%s="'%(command,selekey)+sele+'")'],
[1,'\\339tv_blue','%s34,%s="'%(command,selekey)+sele+'")'],
[1,'\\049marine','%s17,%s="'%(command,selekey)+sele+'")'],
[1,'\\449slate','%s11,%s="'%(command,selekey)+sele+'")'],
[1,'\\779lightblue','%s5263,%s="'%(command,selekey)+sele+'")'],
[1,'\\247skyblue','%s5277,%s="'%(command,selekey)+sele+'")'],
[1,'\\409purpleblue','%s16,%s="'%(command,selekey)+sele+'")'],
[1,'\\226deepblue','%s23,%s="'%(command,selekey)+sele+'")'],
[1,'\\115density','%s4155,%s="'%(command,selekey)+sele+'")'],
]
def yellows_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 2, 'Yellows' ,'' ],
[1,'\\990yellow','%s6,%s="'%(command,selekey)+sele+'")'],
[1,'\\992tv_yellow','%s35,%s="'%(command,selekey)+sele+'")'],
[1,'\\994paleyellow','%s5256,%s="'%(command,selekey)+sele+'")'],
[1,'\\983yelloworange','%s36,%s="'%(command,selekey)+sele+'")'],
[1,'\\792limon','%s5276,%s="'%(command,selekey)+sele+'")'],
[1,'\\976wheat','%s52,%s="'%(command,selekey)+sele+'")'],
[1,'\\653sand','%s5269,%s="'%(command,selekey)+sele+'")'],
]
def magentas_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 2, 'Magentas' ,'' ],
[1,'\\909magenta','%s8,%s="'%(command,selekey)+sele+'")'],
[1,'\\927lightmagenta','%s154,%s="'%(command,selekey)+sele+'")'],
[1,'\\904hotpink','%s12,%s="'%(command,selekey)+sele+'")'],
[1,'\\968pink','%s48,%s="'%(command,selekey)+sele+'")'],
[1,'\\978lightpink','%s5274,%s="'%(command,selekey)+sele+'")'],
[1,'\\644dirtyviolet','%s5272,%s="'%(command,selekey)+sele+'")'],
[1,'\\949violet','%s53,%s="'%(command,selekey)+sele+'")'],
[1,'\\525violetpurple','%s5271,%s="'%(command,selekey)+sele+'")'],
[1,'\\707purple','%s19,%s="'%(command,selekey)+sele+'")'],
[1,'\\515deeppurple','%s5261,%s="'%(command,selekey)+sele+'")'],
]
def cyans_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 2, 'Cyans' ,'' ],
[1,'\\099cyan','%s5,%s="'%(command,selekey)+sele+'")'],
[1,'\\799palecyan','%s5265,%s="'%(command,selekey)+sele+'")'],
[1,'\\499aquamarine','%s5257,%s="'%(command,selekey)+sele+'")'],
[1,'\\297greencyan','%s5275,%s="'%(command,selekey)+sele+'")'],
[1,'\\077teal','%s20,%s="'%(command,selekey)+sele+'")'],
[1,'\\155deepteal','%s5262,%s="'%(command,selekey)+sele+'")'],
[1,'\\466lightteal','%s5266,%s="'%(command,selekey)+sele+'")'],
]
def oranges_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 2, 'Oranges' ,'' ],
[1,'\\950orange','%s13,%s="'%(command,selekey)+sele+'")'],
[1,'\\951tv_orange','%s37,%s="'%(command,selekey)+sele+'")'],
[1,'\\962brightorange','%s30,%s="'%(command,selekey)+sele+'")'],
[1,'\\985lightorange','%s5264,%s="'%(command,selekey)+sele+'")'],
[1,'\\983yelloworange','%s36,%s="'%(command,selekey)+sele+'")'],
[1,'\\760olive','%s18,%s="'%(command,selekey)+sele+'")'],
[1,'\\551deepolive','%s5260,%s="'%(command,selekey)+sele+'")'],
]
def tints_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 2, 'Tints' ,'' ],
[1,'\\976wheat','%s52,%s="'%(command,selekey)+sele+'")'],
[1,'\\686palegreen','%s5259,%s="'%(command,selekey)+sele+'")'],
[1,'\\779lightblue','%s5263,%s="'%(command,selekey)+sele+'")'],
[1,'\\994paleyellow','%s5256,%s="'%(command,selekey)+sele+'")'],
[1,'\\978lightpink','%s5274,%s="'%(command,selekey)+sele+'")'],
[1,'\\799palecyan','%s5265,%s="'%(command,selekey)+sele+'")'],
[1,'\\985lightorange','%s5264,%s="'%(command,selekey)+sele+'")'],
[1,'\\889bluewhite','%s5278,%s="'%(command,selekey)+sele+'")'],
]
def grays_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
return [
[ 2, 'Grays' ,'' ],
[ 1, '\\999white ', '%s"white",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\999gray90 ', '%s"grey90",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\888gray80 ', '%s"grey80",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\777gray70 ', '%s"grey70",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\666gray60 ', '%s"grey60",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\555gray50 ', '%s"grey50",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\444gray40 ', '%s"grey40",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\333gray30 ', '%s"grey30",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\222gray20 ', '%s"grey20",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\222gray10 ', '%s"grey10",%s="'%(command,selekey)+sele+'")' ],
[ 1, '\\222black ', '%s"black",%s="'%(command,selekey)+sele+'")' ],
]
def owncolors_surf(self_cmd, sele,command='cmd.set("surface_color",',selekey="selection"):
owncolors=[(colname,colnumber) for (colname,colnumber) in self_cmd.get_color_indices() if int(colnumber)>=(5387)]
result=[[ 2, 'My Colors' ,'' ]]
for (colname,colnumber) in owncolors:
result.append([ 1, '\\999%s '%colname, '%s%s,%s="'%(command,colnumber,selekey)+sele+'")' ])
return result
@menuappend
def by_ss(self_cmd, sele):
return [
#BNI-Tools color
[ 0, '' , '' ],
[ 1, '\\900H\\950e\\990l\\090i\\099x' , by_helix(self_cmd, sele)],
[ 1, '\\900S\\950c\\990h\\090e\\099e\\059t', by_sheet(self_cmd, sele)],
[ 1, '\\900L\\950o\\990o\\090p' , by_loop(self_cmd, sele) ]
]
#BNI-Surface END
@menuappend
def spectrum(self_cmd, sele):
r = [
#BNI-Tools color by occupancy
[ 0, '' , '' ],
[ 1, 'occupancy' , 'cmd.spectrum("q",selection=("'+sele+'"),quiet=0)' ],
[ 1, 'occupancy(*/ca)' , 'cmd.spectrum("q",selection="(('+sele+')&*/ca)",quiet=0)' ],
]
return r
# check for older menu versions of PyMOL
# check if by_rep is present
if hasattr(menu,"menucontext") and hasattr(menu,"by_rep"):
@menuappend
def mol_color(self_cmd, sele):
with menu.menucontext(self_cmd, sele):
return (
[[ 0, '' , '' ],
[ 1, 'my colors',owncolors_surf(self_cmd,sele,command='cmd.color(')],])
elif hasattr(menu,"menucontext"):
@menuappend
def mol_color(self_cmd, sele):
with menu.menucontext(self_cmd, sele):
return (
[[ 0, '' , '' ],
[ 1, 'my colors',owncolors_surf(self_cmd,sele,command='cmd.color(')],
[ 0, '' , '' ],
[ 1, 'surface' ,by_surf(self_cmd, sele) ],
[ 1, 'mesh' ,by_mesh(self_cmd, sele) ],
[ 1, 'label' ,by_label(self_cmd,sele) ],
[ 1, 'stick' ,by_stick(self_cmd,sele) ],
[ 0, '' , '' ],
] )
else:
@menuappend
def mol_color(self_cmd, sele):
return (
[[ 0, '' , '' ],
[ 1, 'my colors',owncolors_surf(self_cmd,sele,command='cmd.color(')],
[ 0, '' , '' ],
[ 1, 'surface' ,by_surf(self_cmd, sele) ],
[ 1, 'mesh' ,by_mesh(self_cmd, sele) ],
[ 1, 'label' ,by_label(self_cmd,sele) ],
[ 1, 'stick' ,by_stick(self_cmd,sele) ],
[ 0, '' , '' ],
] )
def bni_preset_hp(self_cmd,sele):
return [[ 2, 'HP values:', ''],
[ 1, 'KandD' , 'stored.bni_func.select_hp("KandD","'+sele+'")' ],
[ 1, 'Rose' , 'stored.bni_func.select_hp("Rose","'+sele+'")' ],
[ 1, 'GES' , 'stored.bni_func.select_hp("GES","'+sele+'")' ],
]
def bni_preset_sym(self_cmd,sele):
result=[[ 2, 'A', '']]
distances=[2.0,2.5,3.0,3.5,4.0,4.5,5.0,5.5,6.0,6.5]
for dist in distances:
result.append([ 1, str(dist) , 'stored.bni_func.fast_sym(cutoff="'+str(dist)+'",selection="'+sele+'")'])
return result
def bni_preset_symops(self_cmd,sele):
return [[ 2, 'show symmetry patch within',''],
[ 1, 'set distance',bni_preset_sym(self_cmd,sele)],
[ 1, 'set surface patch color',bni_preset_sym_color(self_cmd,sele)]]
def bni_preset_sym_color(self_cmd,sele):
return [[ 2, 'surface patch color',''],
[ 1, 'to symmetry representation','stored.bni_func.set_surface(mode="symmetry")'],
[ 1, 'to standard representation','stored.bni_func.set_surface(mode="standard")']]
#BNI Presets end
@menuappend
def presets(self_cmd, sele):
return [
#BNI-Tools 0.3 BEGIN
[ 0, '' ,'' ],
[ 1, 'track main chain' ,'stored.bni_func.new_views("track_mainchain","'+sele+'")'],
[ 1, 'symmetry surface' ,bni_preset_symops(self_cmd,sele)],
[ 1, 'hydrophobic residues' , bni_preset_hp(self_cmd,sele) ],
[ 1, 'surface inspection' , 'stored.bni_func.new_views("surf_rel_res","'+sele+'")'],
]
@menuappend
def sele_action(self_cmd, sele):
return [
#BNI-Tools sequence begin
[ 0, '' ,'' ],
[ 1, 'sequences', bni_sequence(self_cmd,sele)],
[ 0, '' ,'' ],
#BNI Tools sequence end
]
@menuappend
def group_action(self_cmd, sele):
return [
#BNI-Tools sequence begin
[ 0, '' ,'' ],
[ 1, 'sequences', bni_sequence(self_cmd,sele)],
[ 0, '' ,'' ],
#BNI-Tools sequence end
]
@menuappend
def mol_action(self_cmd, sele):
return [
#BNI-Tools sequence begin
[ 0, '' ,'' ],
[ 1, 'sequences', bni_sequence(self_cmd,sele)],
[ 0, '' ,'' ],
#BNI-Tools sequence end
]
@menuappend
def all_action(self_cmd, sele):
return [
#BNI-Tools BEGIN
[ 0, '' ,'' ],
[ 1, 'delete enabled', bni_selection_del(self_cmd,sele)],
[ 1, 'invert enabled/disabled', bni_selection_switch(self_cmd,sele)],
[ 1, 'combine selections',bni_selection_combine(self_cmd,sele)],
[ 0, '' ,'' ],
]
#BNI-Selection BEGIN
def bni_sequence(self_cmd,sele):
return [[2,'Format',''],
[1,'fasta','stored.bni_func.get_sequence(selection="'+sele+'",format="fasta")'],
[1,'pir','stored.bni_func.get_sequence(selection="'+sele+'",format="pir")'],
[1,'modeller','stored.bni_func.get_sequence(selection="'+sele+'",format="modeller")'],
[1,'list',bni_sequence_list(self_cmd,sele)],
[1,'pdb','stored.bni_func.get_pdb_lines(selection="'+sele+'",state="0",enabled="1")']]
def bni_sequence_list(self_cmd,sele):
return [[ 2, 'List',''],
[ 1, 'residues','stored.bni_func.get_sequence(selection="'+sele+'",format="normal")'],
[ 1, 'bfac per res',bni_sequence_all(self_cmd,sele,format="normalb")],
[ 1, 'occ per res',bni_sequence_all(self_cmd,sele,format="normalq")],
[ 1, 'all atoms','stored.bni_func.get_sequence(selection="'+sele+'",selecting="atom",format="normal")']]
def bni_sequence_all(self_cmd,sele,format):
return [[ 2,'include',''],
[ 1,'all atoms','stored.bni_func.get_sequence(selection="'+sele+'",format="%s_all")'%format],
[ 1,'mainchain','stored.bni_func.get_sequence(selection="'+sele+'",format="%s_main")'%format],
[ 1,'sidechain','stored.bni_func.get_sequence(selection="'+sele+'",format="%s_side")'%format]]
def bni_selection_switch(self_cmd,sele):
return [[2,'Invert',''],
[1,'all','stored.bni_func.inv_enabled("all")'],
[1,'objects','stored.bni_func.inv_enabled("obj")'],
[1,'selecions','stored.bni_func.inv_enabled("selections")']]
def bni_selection_combine(self_cmd,sele):
return [[2,'Combine to (sele)',''],
[1,'all','stored.bni_func.combine_sele(check="all")'],
[1,'enabled','stored.bni_func.combine_sele(check="enabled")'],
[1,'disabled','stored.bni_func.combine_sele(check="disabled")']]
def bni_selection_del(self_cmd,sele):
return [[2,'Delete Enabled',''],
[1,'all','stored.bni_func.del_enabled("all")'],
[1,'objects','stored.bni_func.del_enabled("obj")'],
[1,'selecions','stored.bni_func.del_enabled("selections")']]
#BNI-Selection END
# BNIADDEND