afmEmulator

#!/usr/bin/env python

import io,struct,sys,time,random
from os.path import splitext,isfile
from math import pi,log,sqrt,exp
from operator import itemgetter
from datetime import datetime
from threading import Thread

import numpy as np

import AFM
import yaml
import argparse

import matplotlib
matplotlib.use('Agg')

import matplotlib.pyplot as plt
import copy

# Initial Set up

dpi = plt.gcf().dpi

_DEFAULT_EXCL_DOMAIN_DISTANCE_         = 20.0
_DEFAULT_CONSECUTIVE_RESIDUE_DISTANCE_ = 3.78
_DEFAULT_CONSECUTIVE_RESIDUE_AMIN_     = 100.0
_DEFAULT_CONSECUTIVE_RESIDUE_AMAX_     = 140.0
_DEFAULT_INTRA_RESIDUE_DISTANCE_       = 2.5
_DEFAULT_EXCL_RESIDUE_DISTANCE_        = 10.0

RESTR_TYPES = {};
RESTR_NAME = [{'NAME': 'RESIDUE_CONNECTION'},
              {'NAME': 'RESIDUE_TRIPLET'},
              {'NAME': 'RESIDUE_QUARTET'},
              {'NAME': 'RESIDUE_INTERNAL'},
              {'NAME': 'RESIDUE_EXCL'},
              {'NAME': 'DOMAIN_PAIR'},
              {'NAME': 'DOMAIN_EXCL'}]
for i in range(len(RESTR_NAME)): RESTR_TYPES[i] = RESTR_NAME[i]

# Parse arguments

parser = argparse.ArgumentParser(description='Emulate AFM Image')
parser.add_argument("-f","--file",dest="projectFile",help="input options",metavar="FILE",
                    default="emu.yaml")
parser.add_argument("-s","--seed",dest="seed",help="random seed",metavar="SEED",
                    default=100,type=int)
interactiveSession=False
try:
  __file__
except NameError:
  interactiveSession=True

if interactiveSession:
  args = parser.parse_args("-f emu.yaml".split())
else:
  args = parser.parse_args()

if isfile(args.projectFile):
  print("Reading project options from projectFile %s" % args.projectFile)
  with open(args.projectFile, 'r') as stream:
    try:
      opt = yaml.load(stream)
    except yaml.YAMLError as exc:
      print(exc)
else:  
  raise Exception("Input Project File %s not found" % args.projectFile)

if 'SEED' in opt: 
  seed = opt['SEED']
else: 
  seed = args.seed
  opt['SEED'] = seed

# Set-up options

gopt = AFM.OptionAFM()
nerr = gopt.reset_options(opt)
if nerr > 0: sys.exit()

# Initialize a project

project = AFM.Project(gopt)

# Read Input and set representation
project.set_input(asis=False,set_representation=True)
if opt['INPUTFILE']['FORMAT'] == 'pdb':
  p0 = AFM.Project(gopt) # For calculation of transformation
  p0.set_input(asis=True,set_representation=False)
  shift = np.array([opt['MESH']['BUFFER']['X'],opt['MESH']['BUFFER']['Y'],opt['MESH']['BUFFER']['Z']])
  translation = shift - p0.pdb.objMin
  project.write_pdb()  

# Set Image property
project.set_resolutions()
project.set_image_property()

# Set up ellipsoid representation
project.representation.SetupMesh(filename=opt['OUTPUTFILE']["IMGFILE"],dpi=project.opt['DPI'])
project.representation.dumpMeshGMM(filename=opt['OUTPUTFILE']["GMMFILE"])
project.representation.dumpMeshVRML(filename=opt['OUTPUTFILE']["VRMLFILE"])
if opt['INPUTFILE']['FORMAT'] == 'pdb':
  print("Translation applied to coordinate: %.8f %.8f %.8f" % (translation[0],translation[1],translation[2]))