#!/usr/bin/env python

"""phipsi: compute the phi and psi angles in a protein.
Supported input format is currently only PDB.
Supported output format is residue-angle list or phi-psi-count histogram."""

import logging

def main():
	import sys, getopt, os.path
	import pdb

	# Set up default values
	try:
		logging.basicConfig(format=os.path.basename(sys.argv[0])
					+ ": %(levelname)s: %(message)s")
	except TypeError:
		logging.basicConfig()
	try:
		opts, args = getopt.getopt(sys.argv[1:], "dv")
	except getopt.GetoptError as e:
		logging.error(e)
		raise SystemExit(1)
	surfaceType = "SES"

	# Process command line flags
	for opt, val in opts:
		if opt == "-d":
			logging.getLogger().setLevel(logging.DEBUG)
		elif opt == "-v":
			logging.getLogger().setLevel(logging.INFO)

	# Identify input and output streams
	Stdin = "<standard input>"
	Stdout = "<standard output>"
	if len(args) == 2:
		inFilename = args[0]
		outFilename = args[1]
	elif len(args) == 1:
		inFilename = args[0]
		outFilename = "<standard output>"
	elif len(args) == 0:
		inFilename = "<standard input>"
		outFilename = "<standard output>"
	else:
		logging.error("Usage: %s [-dv] [ input_PDB [ output ]]"
				% sys.argv[0])
		raise SystemExit(1)

	# Read in data
	logging.info("Reading from %s" % inFilename)
	if inFilename is Stdin:
		inFile = sys.stdin
	else:
		try:
			inFile = open(inFilename, "r")
		except IOError as e:
			logging.error(e)
			raise SystemExit(1)
	import protein
	try:
		p = protein.read(inFile, inFilename)
	except IOError as msg:
		logging.error("%s: %s", inFilename, msg)
		raise SystemExit(1)
	inFile.close()

	# Convert atoms into protein and compute phi-psi values
	protein.computePhiPsi(p)
	for c in protein.chains(p):
		logging.debug("%d amino acids in chain",
				len(protein.aminoAcids(c)))

	# Write out data
	logging.info("Writing to %s" % outFilename)
	if outFilename is Stdout:
		outFile = sys.stdout
	else:
		try:
			outFile = open(outFilename, "w")
		except IOError as e:
			logging.error(e)
			raise SystemExit(1)
	import output
	try:
		output.write(outFile, outFilename, p)
	except IOError as msg:
		logging.error("%s: %s", outFilename, msg)
		raise SystemExit(1)
	outFile.close()
	raise SystemExit(0)

if __name__ == "__main__":
	main()