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"""CML file handler for Python.
This module provides an xml handler for CML file.
Exported classes:
CMLHandler - CML file handler.
"""
import sys
import xml.sax.handler
class CMLHandler(xml.sax.handler.ContentHandler):
"""Class for receiving logical CML content events.
It supports CML entities as defined by the 2.0 version. For more details,
see http://www.xml-cml.org/
The order of event in this class mirrors the order of the information in
the document.
"""
def __init__(self):
"""Creates an instance of the CMLHandler class.
Set the object attributes with default values.
"""
self.id = ""
self.formula = ""
self.inchi = "InChI="
self.smiles = ""
self.name = ""
self.inName = False
self.weight = ""
self.inWeight = False
self.monoisotopic_weight = ""
self.inMonoisotopicWeight = False
self.mp = ""
self.mpSet = False
self.inMp = False
self.bp = ""
self.inBp = False
self.bpSet = False
def startElement(self, name, attributes):
"""Signals the start of an element.
The function set a variable depending on the element and the
attributes.
Parameters:
name - contains the raw CML name of the element type as a string.
attributes - contains an instance of the Attributes class.
"""
if name == "molecule":
self.id = attributes["id"]
if name == "formula":
self.formula = attributes["concise"]
if name == "identifier":
self.inIdentifier = True
if attributes["convention"] == "iupac:inchi":
self.inchi += attributes["value"]
if name == "name":
self.inName = True
if name == "scalar":
if attributes["dictRef"] == "cml:molwt":
self.inWeight = True
elif attributes["dictRef"] == "cml:monoisotopicwt":
self.inMonoisotopicWeight = True
elif attributes["dictRef"] == "cml:mp":
self.inMp = True
elif attributes["dictRef"] == "cml:bp":
self.inBp = True
def characters(self, data):
"""Receives notification of character data.
The parser will call this method to report each chunk of character
data.
Parameters:
data - contains the chunk of character data.
"""
if self.inName:
self.name += data
if self.inWeight:
self.weight += data
if self.inMonoisotopicWeight:
self.monoisotopic_weight += data
if self.inMp:
self.mp += data
if self.inBp:
self.bp += data
def endElement(self,name):
"""Signals the end of an element.
Parameters:
name - contains the name of the element type.
"""
if name == "name":
self.inName = False
if name == "scalar":
if self.inWeight:
self.inWeight = False
elif self.inMonoisotopicWeight:
self.inMonoisotopicWeight = False
elif self.inMp:
self.inMp = False
self.mp = self.mp.strip()
if self.mp:
self.mpSet = True
elif self.inBp:
self.inBp = False
self.bp = self.bp.strip()
if self.bp:
self.bpSet = True
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