# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved.  This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use.  This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: __init__.py 39545 2014-02-12 22:22:16Z pett $

def readSDF(fileName, identifyAs=None):
	from OpenSave import osOpen
	from chimera import UserError, Molecule, Element, openModels, replyobj
	from chimera import Coord
	state = "init"
	try:
		errFileName = unicode(fileName)
	except UnicodeDecodeError:
		errFileName = str(fileName).decode('utf-8', 'replace')
	f = osOpen(fileName)
	mols = []
	nonblank = False
	for l in f:
		line = l.strip()
		nonblank = nonblank or line
		if state == "init":
			state = "post header 1"
			molName = line
		elif state == "post header 1":
			state = "post header 2"
		elif state == "post header 2":
			state = "counts"
		elif state == "counts":
			if not line:
				break
			state = "atoms"
			serial = 1
			anums = {}
			atoms = []
			try:
				numAtoms = int(l[:3].strip())
				numBonds = int(l[3:6].strip())
			except ValueError:
				raise UserError(u"Atom/bond counts line of"
					" MOL/SDF file '%s' is botched: '%s'"
					% (errFileName, l))
			m = Molecule()
			mols.append(m)
			if identifyAs:
				m.name = identifyAs
			else:
				from chimera.misc import isInformativeName
				mn = molName.strip()
				if isInformativeName(mn):
					m.name = mn
				else:
					import os.path
					m.name = os.path.split(fileName)[-1]
			r = m.newResidue("UNK", " ", 1, " ")
		elif state == "atoms":
			numAtoms -= 1
			if numAtoms == 0:
				if numBonds:
					state = "bonds"
				else:
					state = "properties"
			try:
				x = float(l[:10].strip())
				y = float(l[10:20].strip())
				z = float(l[21:30].strip())
				elem = l[31:34].strip()
			except ValueError:
				raise UserError(u"Atom line of MOL/SDF file"
					" '%s' is not x y z element...: '%s'"
					% (errFileName, l))
			element = Element(elem)
			if element.number == 0:
				# lone pair or somesuch
				atoms.append(None)
				continue
			anum = anums.get(element.name, 0) + 1
			anums[element.name] = anum
			a = m.newAtom("%s%d" % (element.name, anum), element)
			atoms.append(a)
			r.addAtom(a)
			a.setCoord(Coord(x, y, z))
			a.serialNumber = serial
			serial += 1
		elif state == "bonds":
			numBonds -= 1
			if numBonds == 0:
				state = "properties"
			try:
				a1index = int(l[:3].strip())
				a2index = int(l[3:6].strip())
				order = int(l[6:9].strip())
			except ValueError:
				raise UserError(u"Bond line of MOL/SDF file"
					" '%s' is not a1 a2 order...: '%s'"
					% (errFileName, l))
			a1 = atoms[a1index-1]
			a2 = atoms[a2index-1]
			if not a1 or not a2:
				continue
			m.newBond(a1, a2).order = order
		elif state == "properties":
			if not m.atoms:
				raise UserError(u"No atoms found for compound"
						" '%s' in MOL/SDF file '%s'"
						% (m.name, errFileName))
			if line.split() == ["M", "END"]:
				state = "data"
				readingData = None
		elif state == "data":
			if line == "$$$$":
				nonblank = False
				state = "init"
			elif readingData:
					dataItem = line.strip()
					if dataItem:
						try:
							data.append(float(dataItem))
						except ValueError:
							try:
								index, charge = dataItem.split()
								index = int(index) - 1
								charge = float(charge)
							except ValueError:
								raise UserError("Charge data (%s) in %s data is"
									" not either a floating-point number or an"
									" atom idex and a floating-point number"
									% (dataItem, origDataName))
							else:
								if not indexedCharges:
									# for indexed charges, first thing is a count
									data.pop()
									indexedCharges = True
								data.append((index, charge))
					else:
						if not indexedCharges and len(atoms) != len(data):
							raise UserError("Number of charges (%d) in %s data"
								" not equal to number of atoms (%d)" % (
								len(data), origDataName, len(atoms)))
						if indexedCharges:
							for a in atoms:
								a.charge = 0.0
							for index, charge in data:
								atoms[index].charge = charge
						else:
							for a, charge in zip(atoms, data):
								a.charge = charge
						if "mmff94" in dataName:
							m.chargeModel = "MMFF94"
						readingData = None
			elif line.startswith('>'):
				try:
					lp = line.index('<')
					rp = line[lp+1:].index('>') + lp + 1
				except (IndexError, ValueError):
					continue
				origDataName = line[lp+1:rp]
				dataName = origDataName.lower()
				if dataName.endswith("charges") and "partial" in dataName:
					readingData = "charges"
					indexedCharges = False
					data = []
	f.close()
	if nonblank and state not in ["data", "init"]:
		if mols:
			replyobj.warning(u"Extraneous text after final $$$$"
				" in MOL/SDF file '%s'" % errFileName)
		else:
			raise UserError(u"Unexpected end of file (parser state:"
				" %s) in MOL/SDF file '%s'" % (state, errFileName))
	return mols