inspector.py

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

import sys
import os
import inspect
newpath = os.path.dirname(inspect.getfile(inspect.currentframe()))  # script directory
if not newpath in sys.path:
   sys.path.append(newpath)
import string
import math
import re
import gzip
import itertools
import glob
import 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()
   next(inspect)

def no():
   global inspect
   next(inspect)

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