inspector.py

# -*- mode:python;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-

import sys,os,inspect
newpath = os.path.dirname(inspect.getfile(inspect.currentframe())) # script directory
if not newpath in sys.path:
		sys.path.append(newpath)
import string, math, re, gzip, itertools, glob, sets
# from random import randrange
from math import sqrt
import xyzMath as xyz
from xyzMath import Ux,Uy,Uz,Imat
from functools import partial
import cProfile


def setup_matdes(inspector):
	cmd.select("comp1","chain A+C+E")
	cmd.select("comp2","chain B+H+L")
	cmd.select("ocompA1","chain I+G")
	cmd.select("ocompA2","chain J+F")
	cmd.select("ocompB1","chain K+M")
	cmd.select("ocompB2","chain D+N")
	cmd.select("iface","byres ((comp1 within 8 of comp2) or (comp2 within 8 of comp1) or (comp1 within 8 of ocompA1) or (ocompA1 within 8 of comp1) or (comp2 within 8 of ocompA2) or (ocompA2 within 8 of comp2))")
	util.cbc()
	util.cnc()
	cmd.show('car')
	cmd.orient()
	cmd.zoom('iface')
	cmd.show('sti','iface')
	cmd.hide('ev','hydro')
	cmd.select('None')
	v = cmd.get_view()
	inspector.nat1 = inspector.current[ 0: 9]
	inspector.nat2 = inspector.current[10:19]
	print inspector.nat1, inspector.nat2
	cmd.load("/work/sheffler/data/jacob_"+inspector.nat1[:2]+"/"+inspector.nat1+".pdb.gz")
	cmd.load("/work/sheffler/data/jacob_"+inspector.nat2[:2]+"/"+inspector.nat2+".pdb.gz")
	cmd.super(inspector.nat1,inspector.current+" and chain C")
	cmd.super(inspector.nat2,inspector.current+" and chain A")
	cmd.color("white","(%s or %s) and elem C"%(inspector.nat1,inspector.nat2))
	cmd.hide("ev","(%s or %s)"%(inspector.nat1,inspector.nat2))
	cmd.show("lines","(%s or %s)"%(inspector.nat1,inspector.nat2))
	cmd.set_view(v)

def setup_splice(inspector):
	# hide ev
	# remove not name n+ca+c+oxt+3h
	# show rib
	# show sph, name oxt+3H
	# util.cbc
	cmd.hide()
	cmd.remove("not name n+ca+c+oxt+3h")
	cmd.show('rib')
	cmd.show('sph','name oxt+3h')
	util.cbc()
	util.cnc()
	cmd.zoom()


class PymolInspector(object):
	"""docstring for PymolInspector"""
	def __init__(self, l="/Users/sheffler/tmp/ariel10_p6_32_reverted/list",tgt="/Users/sheffler/tmp/ariel10_p6_32_reverted/pymol_picks/", setup_func=setup_matdes):
		super(PymolInspector, self).__init__()
		self.pdblist = list()
		with open(l) as infile:
			for pdb in infile.readlines():
				self.pdblist.append(pdb.strip())
		print "PymolInspector pdb list:"
		for p in self.pdblist: print " ",p
		self.setup_func = setup_func
		self.index = 0
		self.tgt = tgt+"/"
		self.current = None
		self.nat1 = None
		self.nat2 = None
		if not os.path.exists(self.tgt):
			os.mkdir(self.tgt)
		if not os.path.exists(self.tgt+"seenit.list"):
			self.seenit = []
		else:
			with open(self.tgt+"seenit.list") as infile:
				self.seenit = [x.strip() for x in infile.readlines()]

	def write_seenit(self):
		with open(self.tgt+"seenit.list","w") as outfile:
			for x in self.seenit: outfile.write(x+"\n")

	def next(self):
		if self.current:
			if self.current: cmd.delete(self.current)
			if self.nat1: cmd.delete(self.nat1)
			if self.nat2: cmd.delete(self.nat2)
			cmd.delete("all")
			self.seenit.append(self.pdblist[self.index])
			self.write_seenit()

		while self.pdblist[self.index] in self.seenit:
			self.index += 1
			if self.index >= len(self.pdblist):
				print "out of structures!"
				return

		cmd.load(self.pdblist[self.index])
		self.current = cmd.get_object_list()[-1]

		print "============================================================================================================================="
		print "inspecting",self.current
		print self.setup_func(self)

	def keep(self):
		if self.current:
			os.system("cp "+self.pdblist[self.index] + " " + self.tgt)

# examples:
# inspect = PymolInspector("/Users/sheffler/Dropbox/project/tca_fusions/results/list","/Users/sheffler/Dropbox/project/tca_fusions/results/picks",setup_func=setup_splice)


def yes():
	global inspect
	inspect.keep()
	inspect.next()
def no():
	global inspect
	inspect.next()

cmd.extend("yes",yes)
cmd.extend("no",no)