35.1 OEChem 1.6.1

35.1.1 OEChem

RegisterMolParameters renamed to OERegisterMolParameters. However, the function is now automatically called at link time alleviating the user from having to call this function in order to use molecules with OEInterfaces.
OEReadXYZFile uses the "Unichem" numeric convention for elements that don't have a one or two-character IUPAC symbol.
Adding const string& variants of OEParseSmiles and OESmilesAtomCount functions to the OEChem API.

OEPerceiveBondOrders() function is improved by:
1. distinguishing unsaturated allene (C=C=C) from propyne (C#CC)
2. assigning the double bond to a shorter of the bonds to a terminal oxygen in functional groups such as *C(=O)O or *C(=O)[O-]

Hydrogen bond lengths for As, Ge, Se and Te elements are added to improve the 3D coordinates assigned for explicit hydrogens by OESet3DHydrogenGeom function.
Optimization of OEDBMol compression.
Memory leak was fixed in OERMSD.
Bug was fixed in the binary write routine of OEGraphMol and OEMol parameters, that caused problems during a multiprocessor run.
Memory problem that occurred when reading molecules with large number of conformations was fixed by allocating memory from the heap rather than stack in such cases.
Using OEMol::operator= (const OEMolBase &) on itself will no longer crash.

New constructor added to the OEInterface class, that takes the interface data along with argc and argv arguments of main(). Using this constructor, an OEInterface object is configured, parses the command line, and prints the help message if requested.

The direction of rotation matrix given by OEGeom3DEulerToRotMatrix and OEGeom3DQuaternionToRotMatrix functions is now consistent with the other geometry handling routines.
Memory leak, that could occur in multi-threaded environment (such as Java), was fixed.

				OEChem - Java Theory Manual

				OEChem - Java Theory Manual