Dear all, following suggestions from James and Michal, I implemented some functionality to add constraints to UFF and MMFF force-fields. The new functionality is exposed in both C++ and Python APIs, and is available in the current GitHub version.
Details: - support for fixed atoms was already there, but could be accessed only from C++. I exposed it in Python through the AddFixedPoint() method - Python support for distance constraints was already there through the AddDistanceConstraint() method. However, now there are two more functions, namely UFFAddDistanceConstraint() and MMFFAddDistanceConstraint(), which compared to AddDistanceConstraint() accept one more boolean parameter (i.e., relative). If relative is True, then minLen and maxLen values are intended as deltas relative to the current value - Similarly, now there are UFFAddAngleConstraint(), MMFFAddAngleConstraint(), UFFAddTorsionConstraint(), MMFFAddTorsionConstraint() methods to constrain angles and dihedrals - To harmonically restrain individual atoms to their original positions, there are UFFAddPositionConstraint() and MMFFAddPositionConstraint() All constraints are implemented as flat-bottomed potentials, which are effective only when the target property is below min (distance, angle and dihedral constraints) or above max (distance, angle, dihedral and position constraints). Examples of use: C++: check Code/ForceField/UFF/testUFFForceField.cpp and Code/ForceField/MMFF/testMMFFForceField.cpp Python: check Code/ForceField/Wrap/testConstraints.py Regards, Paolo -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: [email protected] http://open3dqsar.org | http://open3dalign.org ========================================================== ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
