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epmvGui.py
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"""
Copyright (C) <2010> Autin L.
This file ePMV_git/epmvGui.py is part of ePMV.
ePMV is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
ePMV is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with ePMV. If not, see <http://www.gnu.org/licenses/gpl-3.0.html>.
"""
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 13 08:38:56 2010
@author: Ludovic Autin - [email protected]
"""
# import DejaVu
# DejaVu.enableVertexArray = False
# TODO change all windows size
import os, sys
import upy
# uiadaptor = upy.getUIClass()
from upy import uiadaptor
from ePMV import comput_util as C
import ePMV
from MolKit.molecule import AtomSet
from MolKit.protein import ResidueSetSelector, Chain, Protein, Residue
from ePMV import comput_util as util
# need to check python version...
if sys.version_info < (2, 8):
import ePMV.pmv_dev.APBSCommands_2x as APBS
else:
import ePMV.pmv_dev.APBSCommands as APBS
APBSgui = APBS.APBSgui
from ePMV.pmv_dev.buildDNAGui import BuildDNAGui
from ePMV.register_epmv import Register_User_ePMV_ui
from time import time
class BindGeomToMol(uiadaptor):
# savedialog dont work
def setup(self, epmv, id=None):
self.subdialog = True
self.block = True
self.epmv = epmv
self.title = "Bind Polygon to Mol" # +self.mol.name
self.SetTitle(self.title)
witdh = 350
self.h = 130
self.w = 300
if id is not None:
id = id
else:
id = self.bid
self.id = id
# define the widget here too
self.BTN = {}
# need a filename + browse button
self.BTN["bind"] = self._addElemt(label="Polygon Name",
width=40, height=10)
self._polyname = self.addVariable("str", "")
self.NAME = self._addElemt(name="polyname", action=None, width=100,
value="", type="inputStr", variable=self._polyname)
self.BTN["ok"] = self._addElemt(name="Ok", width=40, height=10,
action=self.bind, type="button")
self.BTN["cancel"] = self._addElemt(name="Cancel", width=40, height=10,
action=self.close, type="button")
self.LABEL = self._addElemt(label="Bind Polygon to current molecule", width=100)
self.setupLayout()
def setupLayout(self):
# form layout for each SS types ?
self._layout = []
self._layout.append([self.LABEL, ])
self._layout.append([self.BTN["bind"], self.NAME])
self._layout.append([self.BTN["ok"], self.BTN["cancel"]])
def bind(self, *args):
# get the object name
name = self.getString(self.NAME)
self.bind_cb(name)
self.epmv.gui.updateCGeomList()
self.drawMessage(message=name + " binded to " + self.mol.name + "!\n")
self.close()
def bind_cb(self, name, ):
self.mol = self.epmv.gui.current_mol
# get the object name
# name = self.getString(self.NAME)
# rule for binded geometry name: b_name
obj = self.epmv.helper.getObject(name)
# check if already exist in geomContainer.
if name in list(self.mol.geomContainer.geoms.keys()):
g = self.mol.geomContainer.geoms["b_" + name]
else:
# create the indexed polygon
from DejaVu.IndexedPolygons import IndexedPolygons
g = IndexedPolygons(name="b_" + name)
# update g
mesh = obj # self.epmv.helper.getMesh(obj)
g.Set(vertices=self.epmv.helper.getMeshVertices(mesh),
faces=self.epmv.helper.getMeshFaces(mesh))
# do the binding
self.epmv.mv.bindGeomToMolecularFragment(g, self.mol.allAtoms)
self.epmv._addObjToGeom([obj, ], g)
# add it to the main combo_box if not already there
def CreateLayout(self):
self._createLayout()
# self.restorePreferences()
return True
def Command(self, *args):
# print args
self._command(args)
return True
class ParameterModeller(uiadaptor):
def setup(self, epmv, id=1005):
self.subdialog = True
self.block = True # special type for blender
self.title = "Modeller"
self.SetTitle(self.title)
self.epmv = epmv
witdh = 200
self.h = 350
self.w = 300
if id is not None:
id = id
else:
id = self.bid
self.id = id
self.LABEL_ID = {}
self.NUMBERS = {
"miniIterMax": self._addElemt(name="Max iteration", width=50, height=10,
action=None, type="inputInt",
icon=None,
value=1000,
variable=self.addVariable("int", 1000),
mini=0, maxi=100000, step=1),
"mdIterMax": self._addElemt(name="Max iteration", width=50, height=10,
action=None, type="inputInt",
icon=None,
value=1000,
variable=self.addVariable("int", 1000),
mini=0, maxi=100000, step=1),
"mdTemp": self._addElemt(name="Temperature", width=50, height=10,
action=None, type="inputInt",
icon=None,
value=300,
variable=self.addVariable("int", 300),
mini=-100, maxi=1000, step=1),
"rtstep": self._addElemt(name="number of steps", width=50, height=10,
action=self.setRealTimeStep,
type="inputInt",
icon=None,
value=2,
variable=self.addVariable("int", 2),
mini=0, maxi=100, step=1)
}
self.LABEL_ID["miniIterMax"] = self._addElemt(
label=self.NUMBERS["miniIterMax"]["name"],
width=80)
self.LABEL_ID["mdIterMax"] = self._addElemt(
label=self.NUMBERS["mdIterMax"]["name"],
width=80)
self.LABEL_ID["mdTemp"] = self._addElemt(
label=self.NUMBERS["mdTemp"]["name"],
width=80)
self.LABEL_ID["rtstep"] = self._addElemt(
label=self.NUMBERS["rtstep"]["name"],
width=80)
self.BTN = {
"mini": self._addElemt(name="Minimize", width=50, height=10,
label='Minimize options',
action=self.epmv.gui.modellerOptimize, type="button"),
"md": self._addElemt(name="run MD", width=50, height=10,
label='Molecular Dynamic options',
action=self.epmv.gui.modellerMD, type="button"),
"cancel": self._addElemt(name="Close", width=50, height=10,
action=self.cancel, type="button"),
"update coordinate": self._addElemt(name="Update coordinates", width=100, height=10,
action=self.updateCoord, type="button")
}
self.LABEL_ID["mini"] = self._addElemt(
label=self.BTN["mini"]["label"],
width=80)
self.LABEL_ID["md"] = self._addElemt(
label=self.BTN["md"]["label"],
width=80)
self.CHECKBOXS = {
"store": self._addElemt(name="store", width=100, height=10,
action=self.setStoring, type="checkbox", icon=None,
variable=self.addVariable("int", 0)),
"real-time": self._addElemt(name="real-time", width=100, height=10,
action=self.setRealTime, type="checkbox", icon=None,
variable=self.addVariable("int", 0)),
'moddisplay': self._addElemt(name="moddisplay", width=100, height=10,
action=None, type="checkbox", icon=None,
variable=self.addVariable("int", 0))
}
self.rtType = ["mini", "md"]
self.sObject = ["cpk", "lines", "bones", "spline"]
self.COMB_BOX = {"sobject": self._addElemt(name="Object",
value=self.sObject,
width=60, height=10, action=self.setObjectSynchrone,
variable=self.addVariable("int", 0),
type="pullMenu", ),
"rtType": self._addElemt(name="rtType",
value=self.rtType,
width=60, height=10, action=self.setRToptimzeType,
variable=self.addVariable("int", 0),
type="pullMenu", )}
self.setupLayout()
return True
def setupLayout(self):
self._layout = []
# Miniisation
elemFrame = []
elemFrame.append([self.LABEL_ID["miniIterMax"], self.NUMBERS["miniIterMax"]])
elemFrame.append([self.BTN["mini"], ])
frame = self._addLayout(name="Minimization", elems=elemFrame, collapse=False)
self._layout.append(frame)
# MD
elemFrame = []
elemFrame.append([self.LABEL_ID["mdIterMax"], self.NUMBERS["mdIterMax"]])
elemFrame.append([self.LABEL_ID["mdTemp"], self.NUMBERS["mdTemp"]])
elemFrame.append([self.BTN["md"], ])
frame = self._addLayout(name="Molecular Dynamics", elems=elemFrame, collapse=False)
self._layout.append(frame)
# RealTime
elemFrame = []
elemFrame.append([self.CHECKBOXS["real-time"], self.COMB_BOX["rtType"]])
elemFrame.append([self.LABEL_ID["rtstep"], self.NUMBERS["rtstep"]])
elemFrame.append([self.BTN["update coordinate"], self.COMB_BOX["sobject"]])
frame = self._addLayout(name="Real-Time", elems=elemFrame, collapse=False)
self._layout.append(frame)
# general options
self._layout.append([self.CHECKBOXS["store"], self.CHECKBOXS["moddisplay"]])
# self._layout.append([self.CHECKBOXS["real-time"],self.COMB_BOX["rtType"]])
# self._layout.append([self.LABEL_ID["rtstep"],self.NUMBERS["rtstep"]])
# self._layout.append([self.BTN["update coordinate"],self.COMB_BOX["sobject"]])
# self._layout.append([self.LABEL_ID["mini"],])
# self._layout.append([self.LABEL_ID["miniIterMax"],self.NUMBERS["miniIterMax"]])
# self._layout.append([self.BTN["mini"],])
# self._layout.append([self.LABEL_ID["md"],])
# self._layout.append([self.LABEL_ID["mdIterMax"],self.NUMBERS["mdIterMax"]])
# self._layout.append([self.LABEL_ID["mdTemp"],self.NUMBERS["mdTemp"]])
# self._layout.append([self.BTN["md"],])
self._layout.append([self.BTN["cancel"], ])
# return True
def CreateLayout(self):
self._createLayout()
# self.restorePreferences()
return True
# overwrite RT checkbox action
def setRealTime(self, *args):
if hasattr(self.epmv.gui, 'current_mol'):
mol = self.epmv.gui.current_mol
mol.pmvaction.temp = self.getLong(self.NUMBERS["mdTemp"])
mol.pmvaction.realtime = self.getBool(self.CHECKBOXS['real-time'])
def setRealTimeStep(self, *args):
if hasattr(self.epmv.gui, 'current_mol'):
mol = self.epmv.gui.current_mol
mol.pmvaction.mdstep = self.getLong(self.NUMBERS['rtstep'])
def setStoring(self, *args):
if hasattr(self.epmv.gui, 'current_mol'):
mol = self.epmv.gui.current_mol
mol.pmvaction.store = self.getBool(self.CHECKBOXS['store'])
def setObjectSynchrone(self, *args):
if hasattr(self.epmv.gui, 'current_mol'):
mol = self.epmv.gui.current_mol
mol.pmvaction.sObject = self.sObject[self.getLong(self.COMB_BOX["sobject"])]
def setRToptimzeType(self, *args):
if hasattr(self.epmv.gui, 'current_mol'):
mol = self.epmv.gui.current_mol
rtype = self.rtType[self.getLong(self.COMB_BOX["rtType"])]
if mol.pmvaction.rtType != rtype:
mol.pmvaction.rtType = rtype
# need to update the optimizer ie delete and create a new one
mol.pmvaction.resetOptimizer()
def updateCoord(self, *args):
if hasattr(self.epmv, 'gui'):
mol = self.epmv.gui.current_mol
if hasattr(mol, 'pmvaction'):
self.epmv.updateMolAtomCoord(mol, mol.pmvaction.idConf, types=mol.pmvaction.sObject)
mol.pmvaction.updateModellerCoord(mol.pmvaction.idConf, mol.mdl)
def doIt(self, *args):
# print args
pass
def cancel(self, *args):
self.close()
def Command(self, *args):
# print args
self._command(args)
return True
class ParameterScoringGui(uiadaptor):
_scorer = 'ad3Score'
_display = False
label = None
def setup(self, epmv, id=1005):
self.subdialog = True
self.block = True # special type for blender
self.title = "PyAutodock"
self.SetTitle(self.title)
self.epmv = epmv
self.h = 320
self.w = 220
witdh = 350
if id is not None:
id = id
else:
id = self.bid
self.BTN = {"rec": self._addElemt(id=id, name="Browse", width=50, height=10,
action=None, type="button"),
"lig": self._addElemt(id=id + 1, name="Browse", width=50, height=10,
action=None, type="button"),
"ok": self._addElemt(id=id + 2, name="Add Scorer", width=100, height=10,
action=self.setupScoring, type="button"),
"gScore": self._addElemt(id=id + 3, name="Get Score", width=100, height=10,
action=self.getScore, type="button"),
"cancel": self._addElemt(id=id + 4, name="Close", width=100, height=10,
action=self.cancel, type="button")
}
id = id + len(self.BTN)
self.LABEL_ID = {"rec": self._addElemt(id=id, label="Receptor", width=100, height=10),
"lig": self._addElemt(id=id + 1, label="Ligand", width=100, height=10),
"score": self._addElemt(id=id + 2, label="Type of score", width=100, height=10),
"scorer": self._addElemt(id=id + 2, label="Available scorer", width=100, height=10),
}
id = id + len(self.LABEL_ID)
# txt input
self.TXT = {"rec": self._addElemt(id=id, name="Receptor", action=None, width=100,
value="hsg1:::;", type="inputStr",
variable=self.addVariable("str", "hsg1:::;")),
"lig": self._addElemt(id=id + 1, name="Ligand", action=None, width=100,
value="ind:::;", type="inputStr",
variable=self.addVariable("str", "ind:::;"))
}
id = id + len(self.TXT)
self.scorertype = ['PyPairWise', 'ad3Score', 'ad4Score']
if C.cAD: # cAutodock is available
self.scorertype.append('c_ad3Score')
self.scorertype.append('PairWise')
self.scoreravailable = self.getScorerAvailable()
self.COMB_BOX = {"score": self._addElemt(id=id, name="Type of score",
value=self.scorertype,
width=60, height=10, action=self.setScorer,
variable=self.addVariable("int", 0),
type="pullMenu", ),
"scorer": self._addElemt(id=id + 1, name="Available scorer",
value=self.scoreravailable,
width=60, height=10, action=self.setCurrentScorer,
variable=self.addVariable("int", 0),
type="pullMenu", ),
}
id = id + len(self.COMB_BOX)
self.CHECKBOXS = {"store": self._addElemt(id=id, name="Store",
width=100, height=10,
action=None, type="checkbox", icon=None,
variable=self.addVariable("int", 0)),
"displayLabel": self._addElemt(id=id + 1, name="Display Label",
width=100, height=10,
action=self.toggleDisplay, type="checkbox", icon=None,
variable=self.addVariable("int", 0)),
"colorRec": self._addElemt(id=id + 2, name="Color Rec",
width=100, height=10,
action=self.toggleColor, type="checkbox", icon=None,
variable=self.addVariable("int", 0)),
"colorLig": self._addElemt(id=id + 3, name="Color Lig",
width=100, height=10,
action=self.toggleColor, type="checkbox", icon=None,
variable=self.addVariable("int", 0)),
"realtime": self._addElemt(id=id + 4, name="Real time", width=100, height=10,
action=self.setRealtime, type="checkbox", icon=None,
variable=self.addVariable("int", 0)),
}
id = id + len(self.CHECKBOXS)
self.setupLayout()
return True
def setupLayout(self):
self._layout = []
# setup
self._layout.append([self.LABEL_ID["rec"], self.TXT["rec"]])
self._layout.append([self.LABEL_ID["lig"], self.TXT["lig"]])
self._layout.append([self.LABEL_ID["score"], self.COMB_BOX["score"]])
self._layout.append([self.BTN["ok"], ])
# current scorer if any
self._layout.append([self.LABEL_ID["scorer"], self.COMB_BOX["scorer"]])
# option for the current score
for butk in list(self.CHECKBOXS.keys()):
self._layout.append([self.CHECKBOXS[butk], ])
self._layout.append([self.BTN["gScore"], ])
self._layout.append([self.BTN["cancel"], ])
def CreateLayout(self):
self._createLayout()
return True
def setRealtime(self, *args):
if hasattr(self.epmv.mv, 'energy'):
self.epmv.mv.energy.realTime = self.getBool(self.CHECKBOXS['realtime'])
def toggleDisplay(self, *args):
if hasattr(self.epmv.mv, 'energy'):
display = self.getBool(self.CHECKBOXS['displayLabel'])
if display:
if self.label is None:
self.initDisplay()
self.epmv._toggleDisplay(self.label, display)
if not hasattr(self.epmv.mv.energy, 'label'):
setattr(self.epmv.mv.energy, 'label', display)
else:
self.epmv.mv.energy.label = display
def toggleStore(self, *args):
store = self.getBool(self.CHECKBOXS['store'])
def toggleColor(self, *args):
if hasattr(self.epmv.mv, 'energy'):
r = self.getBool(self.CHECKBOXS['colorRec'])
l = self.getBool(self.CHECKBOXS['colorLig'])
if hasattr(self.epmv.mv, 'energy'):
if not hasattr(self.epmv.mv.energy, 'color'):
setattr(self.epmv.mv.energy, 'color', [r, l])
else:
self.epmv.mv.energy.color = [r, l]
def getScore(self, *args):
if hasattr(self.epmv.mv, 'energy'):
self.epmv.get_nrg_score(self.epmv.mv.energy)
def setRec(self):
pass
def setLig(self):
pass
def getScorerAvailable(self, *args):
if hasattr(self.epmv.mv, 'energy'):
return list(self.epmv.mv.energy.data.keys())
else:
return []
def setCurrentScorer(self, *args):
self.scoreravailable = self.getScorerAvailable()
if self.scoreravailable:
name = self.scoreravailable[self.getLong(self.COMB_BOX["scorer"])]
self.epmv.mv.energy.current_scorer = self.epmv.mv.energy.data[name]
def setScorer(self, *args):
self._scorer = self.scorertype[self.getLong(self.COMB_BOX["score"])]
def setupScoring(self, *args):
# get Rec
rname = self.getString(self.TXT['rec'])
# get Lig
print(rname)
lname = self.getString(self.TXT['lig'])
print(lname)
# is this can be selection ? yep
# recSet=self.mv.select(rname,negate=False, only=True, xor=False,
# log=0, intersect=False)
recSet = self.epmv.mv.expandNodes(rname)
rec = recSet[0].top
# =self.epmv.mv.getMolFromName(rname)
ligSet = self.epmv.mv.expandNodes(lname)
lig = ligSet[0].top
# test lig and rec
scorer_name = rec.name + '-' + lig.name + '-' + self._scorer
if rec is not None and lig is not None:
if not hasattr(self.epmv.mv, 'energy'):
self.epmv.mv.energy = C.EnergyHandler(self.epmv.mv)
self.getScorerAvailable()
self.epmv.mv.energy.add(recSet, ligSet, score_type=self._scorer)
self.addItemToPMenu(self.COMB_BOX["scorer"], scorer_name)
confNum = 1
for mol in [rec, lig]:
# check number of conformations available
current_confNum = len(mol.allAtoms[0]._coords) - 1
mol.allAtoms.addConformation(mol.allAtoms.coords)
mol.cconformationIndex = len(mol.allAtoms[0]._coords) - 1
self.toggleDisplay()
self.toggleColor()
self.setRealtime()
def initDisplay(self):
scene = self.epmv.helper.getCurrentScene()
# label
self.label = label = self.epmv.helper.newEmpty("label")
self.epmv.helper.addObjectToScene(scene, label)
self.epmv.helper.constraintLookAt(label)
listeName = ["score", "el", "hb", "vw", "so"]
y = 0.0
self.listeO = []
for i, name in enumerate(listeName):
o = self.epmv.helper.Text(name, string=name + " : 0.00", pos=[0., y, 0.],
parent=label)
self.listeO.append(o)
y += 5.0
self.epmv.mv.energy.labels = self.listeO
# constraint the label to be oriented toward the persp camera
self.epmv.mv.energy.display = True
self.epmv.mv.energy.label = True
def cancel(self, *args):
self.close()
def Command(self, *args):
# print args
self._command(args)
return True
class Parameter_beadRibbons(uiadaptor):
def setup(self, epmv, id=None):
self.subdialog = True
self.block = True
self.title = "beadRibbons"
self.SetTitle(self.title)
self.epmv = epmv
witdh = 350
self.h = 250
self.w = 200
if id is not None:
id = id
else:
id = self.bid
# default value and parameters type
self.tapertypes = ["sin", "linear", "cos"]
self.paramstype = {'quality': {"type": "inputInt", "value": 12},
'taperLength': {"type": "inputInt", "value": 6},
'taperType': {"type": "pullMenu", "value": self.tapertypes},
'helixBeaded': {"type": "checkbox", "value": 1},
# 'helixCylinder':{"type":"checkbox","value":0},
'helixWidth': {"type": "inputFloat", "value": 1.6},
'helixThick': {"type": "checkbox", "value": 1},
'helixThickness': {"type": "inputFloat", "value": 0.20},
'helixBeadRadius': {"type": "inputFloat", "value": 0.32},
'helixColor1': {"type": "color", "value": (1, 1, 1)},
'helixColor2': {"type": "color", "value": (1, 0, 1)},
'helixBeadColor1': {"type": "color", "value": (1, 1, 1)},
'helixBeadColor2': {"type": "color", "value": (1, 1, 1)},
'helixSideColor': {"type": "color", "value": (1, 1, 1)},
'coilRadius': {"type": "inputFloat", "value": 0.1},
'coilColor': {"type": "color", "value": (1, 1, 1)},
'turnRadius': {"type": "inputFloat", "value": 0.1},
'turnColor': {"type": "color", "value": (0, 0, 1)},
'sheetBeaded': {"type": "checkbox", "value": 1},
'sheetWidth': {"type": "inputFloat", "value": 1.6},
'sheetBodyStartScale': {"type": "inputFloat", "value": 0.4},
'sheetThick': {"type": "checkbox", "value": 1},
'sheetThickness': {"type": "inputFloat", "value": 0.20},
'sheetBeadRadius': {"type": "inputFloat", "value": 0.32},
'sheetColor1': {"type": "color", "value": (1, 1, 0)},
'sheetColor2': {"type": "color", "value": (0, 1, 1)},
'sheetBeadColor1': {"type": "color", "value": (1, 1, 1)},
'sheetBeadColor2': {"type": "color", "value": (1, 1, 1)},
'sheetSideColor': {"type": "color", "value": (1, 1, 1)},
'sheetArrowhead': {"type": "checkbox", "value": 1},
'sheetArrowheadWidth': {"type": "inputFloat", "value": 2.0},
'sheetArrowHeadLength': {"type": "inputInt", "value": 8},
}
# create the widget
# size order ???
self.PARAMS = {}
self.LABELS = {}
for key in self.paramstype:
self.PARAMS[key] = self._addElemt(name=key,
width=40, height=10,
action=self.SetPreferences, type=self.paramstype[key]["type"],
icon=None,
value=self.paramstype[key]["value"],
variable=self.addVar(self.paramstype[key]["type"],
self.paramstype[key]["value"]))
self.LABELS[key] = self._addElemt(label=key, width=100)
self.BTN = {}
self.BTN["ok"] = self._addElemt(name="Update Bead", action=self.SetPreferences, width=50,
type="button")
self.BTN["reset"] = self._addElemt(name="Reset to default", action=self.restorePreferences, width=50,
type="button")
self.BTN["close"] = self._addElemt(name="Close", action=self.close, width=50,
type="button")
self.setupLayout()
return True
def setupLayout(self):
# form layout for each SS types ?
self._layout = []
ordered = list(self.PARAMS.keys())
ordered.sort()
# frame=[]
i = 0
if self.host != "blender24":
label = ["helix", "sheet", "coil", "turn", "general"]
frame = {}
elemframe = {}
for l in label:
elemframe[l] = []
for key in ordered:
found = False
for l in label:
if key.find(l) != -1:
elemframe[l].append([self.LABELS[key], self.PARAMS[key], ])
found = True
break
if not found:
elemframe["general"].append([self.LABELS[key], self.PARAMS[key], ])
for l in label:
frame = self._addLayout(name=l, elems=elemframe[l], collapse=True)
self._layout.append(frame)
else:
while i < len(ordered) - 3: # in range(len(ordered)/2):
self._layout.append([self.LABELS[ordered[i]], self.PARAMS[ordered[i]],
self.LABELS[ordered[i + 1]], self.PARAMS[ordered[i + 1]],
self.LABELS[ordered[i + 2]], self.PARAMS[ordered[i + 2]]])
i = i + 3
# for key in ordered:
# self._layout.append([self.LABELS[key],self.PARAMS[key],])
# elemFrame=[]
# elemFrame.append([self.LOAD_BTN,self.LABEL_ID[0],self.LABEL_ID[1]])
# elemFrame.append([self.EDIT_TEXT,self.FETCH_BTN,self.COMB_BOX["pdbtype"]])
## elemFrame.append([self.LABEL_ID[2],self.COMB_BOX["mol"]])
#
# frame = self._addLayout(id=196,name="Get a Molecule",elems=elemFrame,collapse=False)
# self._layout.append(frame)
#
self._layout.append([self.BTN["reset"], ])
self._layout.append([self.BTN["ok"], self.BTN["close"]])
def CreateLayout(self):
self._createLayout()
# self.restorePreferences()
return True
def SetPreferences_cb(self, param):
if hasattr(self.epmv.gui, 'current_mol'):
mol = self.epmv.gui.current_mol
self.epmv.storeLastUsed(mol.name, "bead", param)
if self.epmv.uniq_ss:
self.epmv.mv.beadedRibbonsUniq(mol, redraw=0, createEvents=False, **param)
else:
self.epmv.mv.beadedRibbons(mol, redraw=0, createEvents=False, **param)
def SetPreferences(self, *args):
# get the value
# could use a general getCommand on the elem
param = {}
for key in self.PARAMS:
param[key] = self.getVal(self.PARAMS[key])
self.SetPreferences_cb(param)
def restorePreferences(self, *args):
for key in self.paramstype:
# print (key,self.PARAMS[key],self.paramstype[key]["value"])
try:
self.setVal(self.PARAMS[key], self.paramstype[key]["value"])
except:
print(("problem with ", key, self.paramstype[key]["value"]))
def Command(self, *args):
# print args
self._command(args)
return True
from Pmv.pmvPalettes import AtomElements
from Pmv.pmvPalettes import DavidGoodsell, DavidGoodsellSortedKeys
from Pmv.pmvPalettes import RasmolAmino, RasmolAminoSortedKeys
from Pmv.pmvPalettes import Shapely
from Pmv.pmvPalettes import SecondaryStructureType
from Pmv.colorPalette import ColorPaletteNG, ColorPaletteFunctionNG
class Parameter_pmvPalette(uiadaptor):
def setup(self, epmv, id=None):
self.subdialog = True
self.block = True
self.title = "pmv Palette"
self.SetTitle(self.title)
self.epmv = epmv
# self.witdh=200
self.w = 200
self.h = 300
from mglutil.util.defaultPalettes import MolColors, Rainbow, RainbowSortedKey
c = 'Color palette chain number'
self.epmv.mv.colorByChains.palette = ColorPaletteFunctionNG(
'MolColors', MolColors, readonly=0, info=c,
lookupFunction=lambda x, length=len(RainbowSortedKey): \
x.number % length, sortedkeys=RainbowSortedKey)
chainPalette = {}
chainPaletteDefault = {}
for i, label in enumerate(self.epmv.mv.colorByChains.palette.labels):
chainPaletteDefault[label] = chainPalette[label] = self.epmv.mv.colorByChains.palette.ramp[i]
if id is not None:
id = id
else:
id = self.bid
self.defaultColor = {
"atoms": AtomElements.copy(),
"atomsDG": DavidGoodsell.copy(),
"amino": self.epmv.RasmolAminocorrected.copy(),
"aminoS": Shapely.copy(),
"ss": SecondaryStructureType.copy(),
"chain": chainPaletteDefault
}
self.listPalettes = {
"atoms": ["atoms type", AtomElements],
"atomsDG": ["atoms polarity type", DavidGoodsell],
"amino": ["residue type", self.epmv.RasmolAminocorrected],
"aminoS": ["residue shape type", Shapely],
"ss": ["secondary structure", SecondaryStructureType],
"chain": ["chains", chainPalette]
}
self.group = {}
for key in self.listPalettes:
self.group[key] = {}
palette = self.listPalettes[key][1]
self.group[key]["title"] = self._addElemt(label=self.listPalettes[key][0], width=100)
self.group[key]["widget"] = {}
for name in palette:
pname = name
if key == "chain":
name = "ch" + name
widget = self._addElemt(name=name,
width=40, height=10,
action=self.SetColors, type="color",
icon=None,
value=palette[pname],
variable=self.addVar("color", palette[pname]))
label = self._addElemt(label=name, width=100)
self.group[key]["widget"][name] = [label, widget]
self.BTN = {}
self.BTN["ok"] = self._addElemt(name="Set Color", action=self.SetColors, width=50,
type="button")
self.BTN["reset"] = self._addElemt(name="Reset to default", action=self.restoreColors, width=50,
type="button")
self.BTN["close"] = self._addElemt(name="Close", action=self.close, width=50,
type="button")
self.setupLayout()
return True
def setupLayout(self):
# form layout for each SS types ?
self._layout = []
ordered = ["atoms", "atomsDG", "amino", "aminoS", "ss", "chain"]
# if self.host != "blender":
frame = {}
elemframe = {}
for l in ordered:
elemframe[l] = []
for key in ordered:
for name in self.group[key]["widget"]:
wi = self.group[key]["widget"][name][1]
la = self.group[key]["widget"][name][0]
elemframe[key].append([wi, la, ])
frame = self._addLayout(name=self.listPalettes[key][0],
elems=elemframe[key], collapse=True, )
# type = "tab")
self._layout.append(frame)
# else:
# for key in ordered:
# title = self.group[key]["title"]
# self._layout.append([title,])
# for name in self.group[key]["widget"]:
# print key,name,name in self.group[key]["widget"]
# w = self.group[key]["widget"][name][1]
# l = self.group[key]["widget"][name][0]
# self._layout.append([l,w])
self._layout.append([self.BTN["reset"], ])
self._layout.append([self.BTN["ok"], self.BTN["close"]])
def CreateLayout(self):
self._createLayout()
if self.host != "maya" and self.host != "blender25":
# print "restore"
self.restorePreferences()
return True
def SetColors(self, *args):
# get the value
# could use a general getCommand on the elem
ordered = ["atoms", "atomsDG", "amino", "aminoS", "ss", "chain"]
fcolors = [self.epmv.mv.colorByAtomType,
self.epmv.mv.colorAtomsUsingDG,
self.epmv.mv.colorByResidueType,
self.epmv.mv.colorResiduesUsingShapely,
self.epmv.mv.colorBySecondaryStructure,
self.epmv.mv.colorByChains] # ,
# self.epmv.mv.color,
# self.epmv.mv.colorByProperty]
for i, key in enumerate(ordered):
palette = self.listPalettes[key][1]
for name in palette:
wname = name
if key == "chain":
wname = "ch" + name
w = self.group[key]["widget"][wname][1]
color = self.getVal(w)
self.listPalettes[key][1][name] = color
lfction = None
lmenber = fcolors[i].palette.lookupMember
colorClass = ColorPaletteNG
if hasattr(fcolors[i].palette, "lookupFunction"):
lfction = fcolors[i].palette.lookupFunction
colorClass = ColorPaletteFunctionNG
fcolors[i].palette = colorClass(
self.listPalettes[key][0], self.listPalettes[key][1], readonly=0,
lookupFunction=lfction)
else:
fcolors[i].palette = colorClass(
self.listPalettes[key][0], self.listPalettes[key][1], readonly=0,
lookupMember=lmenber)
# need to update the palette attached to the MV commands
def restoreColors(self, *args):
for key in self.defaultColor:
palette = self.defaultColor[key]
for name in palette:
pname = name
if key == "chain":
name = "ch" + name
w = self.group[key]["widget"][name][1]
self.setVal(w, palette[pname])
self.listPalettes[key][1][name] = palette[name]
def restorePreferences(self, *args):
for key in self.listPalettes:
# self.group[key] = {}
palette = self.listPalettes[key][1]
for name in palette:
pname = name
if key == "chain":
name = "ch" + name
if key in self.group and "widget" in self.group[key]:
w = self.group[key]["widget"][name][1]
self.setVal(w, palette[pname])
self.listPalettes[key][1][name] = palette[name]
def Command(self, *args):
# print args
self._command(args)
return True
class SavePanel(uiadaptor):
# savedialog dont work
def setup(self, epmv, id=None):
self.subdialog = True
self.block = True
self.epmv = epmv
self.title = "Save Current Molecule" # +self.mol.name
self.SetTitle(self.title)
self.w = 250
self.h = 200
witdh = 350
if id is not None:
id = id
else:
id = self.bid
self.id = id
# define the widget here too
self.BTN = {}
# need a filename + browse button
self.filename = None
self._filename = self.addVariable("str", "")
self.FILE = self._addElemt(name="file", action=None, width=100,
value="", type="inputStr", variable=self._filename)
self.BTN["browse"] = self._addElemt(name="Browse", width=40, height=10,
action=self.browse, type="button") # self.buttonBrowse
# need a check box for transfrm + pullDown menu of possible transformation node ie spline bones..
self.BTN["transf"] = self._addElemt(name="Apply Transformation from ", width=120, height=10,
action=None, type="checkbox", icon=None,
variable=self.addVariable("int", 0))
self.sObject = ["cpk", "lines", "bones", "spline"]
self.COMB_BOX = self._addElemt(name="Object",
value=self.sObject,
width=60, height=10, action=None,
variable=self.addVariable("int", 0),
type="pullMenu", )
self.BTN["save"] = self._addElemt(name="Save", width=40, height=10,
action=self.save, type="button")
self.BTN["cancel"] = self._addElemt(name="Cancel", width=40, height=10,
action=self.close, type="button")
self.setupLayout()
def setupLayout(self):
# form layout for each SS types ?
self._layout = []
self._layout.append([self.FILE, ]) # self.BTN["browse"]])
self._layout.append([self.BTN["transf"], self.COMB_BOX])
self._layout.append([self.BTN["save"], self.BTN["cancel"]])
def browse_cb(self, filename):
self.setVal(self.FILE, filename)
self.filename = filename
def browse(self, *args):
self.saveDialog(label="choose a file", callback=self.browse_cb)
def save(self, *args):
self.mol = self.epmv.gui.current_mol
# get the filename
filename = self.getVal(self.FILE)
if not filename:
filename = self.filename
# get if transform and the mode of transform
transform = self.getVal(self.BTN["transf"])
if transform:
mode = self.sObject[self.getLong(self.COMB_BOX)]
# do the transform
self.epmv.updateMolAtomCoord(self.mol, 0, types=mode)
self.epmv.mv.writePDB(self.mol, filename=filename)
self.drawMessage(message=self.mol.name + " saved to :\n" + filename)
self.close()
def CreateLayout(self):
self._createLayout()
# self.restorePreferences()
return True
def Command(self, *args):
# print args
self._command(args)
return True
class ApplyTransformationPanel(uiadaptor):
# savedialog dont work
def setup(self, epmv, id=None):
self.subdialog = True
self.block = True
self.epmv = epmv
self.title = "Apply Coordinates" # +self.mol.name
self.SetTitle(self.title)
witdh = 350
self.h = 130
self.w = 300
if id is not None:
id = id
else:
id = self.bid
self.id = id
# define the widget here too
self.BTN = {}
# need a filename + browse button