MDLCT (Connection Table) Format specification Is there a specification for MDL Connection Table format somewhere. At some places it is mentioned that the format writes the line length as a character then the actual line characters. If I save a structure using ChemDraw, I see no such thing and the lines are separated using CarriageReturn and LineFeed characters. Can someone please point me to the correct format? Is it that the format is different while SAVING TO FILE and while COPYING TO CLIPBOARD?
I know this is an old question but like to provide some detail since this does not seem to be documented officially anywhere.
The MDL connection table format used in MOL files is described in the CT File Formats document referenced in the first answer. This is simple ASCII text with hard linebreaks (LF or CR+LF, depending on platform). 

But there is also a special clipboard format MDL_CT created by ISIS/Draw, Accelrys/Draw etc. on Windows. This is not simply a MOL file put as text onto the clipboard. Instead each line of the molfile data is prefixed by a byte holding the number of characters, followed by the ASCII (one byte) characters of the line. The lines are not terminated by line breaks! This is basically the good old TurboPascal string format.

In addition to a single molecule the MDL_CT clipboard format also supports reactions. In that case the data comes from a RXN file, which is converted to the clipboard format the same way a molfile is: prefix each line with a length byte, remove hard linebreaks.