Displaying pharmacophores from Pharao in Avogadro

Following on from the equivalent post for Pharmer, here is an extended Avogadro plugin that works for both Pharmer and Pharao generated pharmacophores.

The plugin allows the user to click through all of the pharmacophores defined in a file and display them one by one. See install instructions in the previous post. The code is kinda rough-and-ready so be prepared to hack around if you need to sort something out:

	import os
	from PyQt4.Qt import *
	import Avogadro as avo
	from numpy import array
	# Get JSON from my own Python installation
	import sys
	sys.path.append("C:\\Python26\\Lib\\site-packages")
	sys.path.append("C:\\Python26\\lib")
	import json
	colorlookup = {
	'Hydrophobic': [0, 139, 69],
	'HydrogenAcceptor': [255, 165, 0],
	'HydrogenDonor': [211, 211, 211],
	'Aromatic': [205, 0, 205],
	'PositiveIon': [0, 0, 238],
	'NegativeIon': [255, 0, 0],
	'HybridAromLipo': [205./2., 139/2., (69+205.)/2.]
	}
	pharaolookup = {
	"HYBL": "HybridAromLipo",
	"HDON": "HydrogenDonor",
	"HACC": "HydrogenAcceptor",
	"NEGC": "NegativeIon",
	"POSC": "PositiveIon",
	"LIPO": "Hydrophobic",
	"AROM": "Aromatic",
	"HYBH": "HyrogenAcceptor"
	}
	def debug(text):
	return
	filename = os.path.join("C:\\", "Users", "Noel", "Desktop", "tmp.txt")
	output = open(filename, "a")
	print >> output, text
	output.close()
	def readpharmacophore(filename):
	NONE, PHARAO, PHARMER = range(3)
	software = NONE
	pharmas = []
	# Detect whether Pharmer or Pharao
	with open(filename) as f:
	line = f.next()
	if line[0] == "{":
	software = PHARMER
	else:
	software = PHARAO
	with open(filename) as f:
	if software == PHARMER:
	query = json.load(f)
	pharmas.append(("No title", [x for x in query['points'] if x['enabled']]))
	else:
	for line in f:
	pharma = []
	title = line
	line = f.next()
	while line.rstrip() != "$$$$":
	broken = line.rstrip().split()
	data = {}
	data["name"] = pharaolookup[broken[0]]
	for a, b in zip(["x", "y", "z"], broken[1:4]):
	data[a] = float(b)
	data["radius"] = float(broken[4])
	if broken[5] == "1":
	tmp = {}
	for a, b in zip(["x", "y", "z"], broken[6:9]):
	tmp[a] = (float(b) - data[a])*2.5 + data[a] # Increase length
	data["vector"] = tmp
	data["vector_on"] = True
	pharma.append(data)
	line = f.next()
	pharmas.append((title, pharma))
	if software == PHARMER:
	pharma = pharmas[0]
	if len(pharma) > 0:
	x = y = z =0
	for p in pharma:
	x += p['x']
	y += p['y']
	z += p['z']
	x /= len(pharma)
	y /= len(pharma)
	z /= len(pharma)
	for p in pharma:
	p['x'] -= x
	p['y'] -= y
	p['z'] -= z
	return pharmas
	class Engine(QObject):
	# declare the changed() signal
	__pyqtSignals__ = ("changed()",)
	# constructor
	def __init__(self):
	QObject.__init__(self)
	self.widget = None
	self.textbox = None
	self.filename = ""
	self.pharmas = []
	def name(self):
	return "Pharmacophore"
	def flags(self):
	return avo.EngineFlags.NoFlags
	@pyqtSignature("")
	def browse(self):
	self.filename = str(QFileDialog.getOpenFileName())
	if not self.filename:
	return
	self.textbox.setText(self.filename)
	self.pharmas = readpharmacophore(self.filename)
	self.allpharmas.setRowCount(len(self.pharmas))
	for i, pharma in enumerate(self.pharmas):
	newItem = QTableWidgetItem(pharma[0])
	self.allpharmas.setItem(0, i, newItem)
	self.chosenpharma = 0
	self.allpharmas.setCurrentCell(0, self.chosenpharma, QItemSelectionModel.ClearAndSelect)
	self.emit(SIGNAL("changed()"))
	@pyqtSignature("")
	def clear(self):
	self.filename = ""
	self.textbox.setText(self.filename)
	self.pharmas = []
	self.emit(SIGNAL("changed()"))
	@pyqtSignature("")
	def myupdate(self):
	self.pharmas = readpharmacophore(self.filename)
	self.allpharmas.setRowCount(len(self.pharmas))
	for i, pharma in enumerate(self.pharmas):
	newItem = QTableWidgetItem(pharma[0])
	self.allpharmas.setItem(0, i, newItem)
	if self.chosenphara > len(self.pharmas):
	self.chosenpharma = len(self.pharmas) - 1
	self.emit(SIGNAL("changed()"))
	@pyqtSignature("int, int, int, int")
	def myotherupdate(self, x, y, a, b):
	debug("value: %d" % self.allpharmas.currentRow())
	debug("values: %d %d %d %d" % (x, y, a, b))
	self.chosenpharma = self.allpharmas.currentRow()
	debug("chosenpharma: %d N pharmas: %d" % (self.chosenpharma, len(self.pharmas)))
	if self.chosenpharma > len(self.pharmas):
	self.chosenpharma = len(self.pharmas) - 1
	self.emit(SIGNAL("changed()"))
	def settingsWidget(self):
	self.widget = QWidget()
	layout = QVBoxLayout(self.widget)
	self.textbox = QLineEdit(self.filename)
	self.textbox.setReadOnly(True)
	layout.addWidget(self.textbox)
	self.allpharmas = QTableWidget(self.widget)
	self.allpharmas.setAlternatingRowColors(True)
	self.allpharmas.setSelectionMode(QAbstractItemView.SingleSelection)
	layout.addWidget(self.allpharmas)
	self.allpharmas.clear()
	self.allpharmas.setRowCount(1)
	self.allpharmas.setColumnCount(1)
	self.allpharmas.horizontalHeader().setResizeMode(QHeaderView.Stretch)
	self.allpharmas.setHorizontalHeaderLabels(["Pharmacophore Title"])
	buttons = QHBoxLayout(self.widget)
	layout.addLayout(buttons)
	self.browsebtn = QPushButton("Browse")
	self.updatebtn = QPushButton("Reload")
	self.clearbtn = QPushButton("Clear")
	buttons.addWidget(self.browsebtn)
	buttons.addWidget(self.updatebtn)
	buttons.addWidget(self.clearbtn)
	QObject.connect(self.browsebtn,SIGNAL("clicked()"),self, SLOT("browse()"))
	QObject.connect(self.clearbtn, SIGNAL("clicked()"),self, SLOT("clear()"))
	QObject.connect(self.updatebtn,SIGNAL("clicked()"),self, SLOT("myupdate()"))
	QObject.connect(self.allpharmas,
	SIGNAL("currentCellChanged(int, int, int, int)"),
	self, SLOT("myotherupdate(int,int,int,int)"))
	debug("End of widget 2")
	return self.widget
	def renderOpaque(self, pd):
	if len(self.pharmas) == 0:
	return
	# Painter
	painter = pd.painter
	# Molecule
	molecule = pd.molecule
	# Color
	color = pd.colorMap
	for point in self.pharmas[self.chosenpharma][1]:
	if point['name'] in colorlookup:
	colvals = [float(x) / 255. for x in colorlookup[point['name']]] + [1.0]
	color.setFromRgba(*colvals)
	else:
	color.setFromRgba(0.3, 0.6, 1.0, 1.0)
	painter.setColor(color)
	r = point['radius']
	x, y, z = point['x'], point['y'], point['z']
	painter.drawSphere(array([x, y, z]), r)
	if "vector" in point and point.get("vector_on") != False:
	v = point['vector']
	a, b, c = v['x'], v['y'], v['z']
	painter.drawCylinder(array([x, y, z]), array([a, b, c]), 0.2)
	painter.drawCone(array([a, b, c]),
	array([(a-x)*0.1+a,(b-y)*0.1+b,(c-z)*0.1+c]), 0.3)

view raw pharamcophore.py hosted with ❤ by GitHub