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Feature/attract_minimize_mcop_physical_approach #40
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…ces Region class)
…re added to Ptools module.
…ption. Can now create reduced pdb files in the mcop format.
… and uses the newly created ReadMcoprigidPDB function (and this function uses newly created functions, line_to_region_number and line_to_copy_number).
…rigid(), Mcoprigid(string filename), Mcoprigid(Mcoprigid mcoprigid_to_duplicate)
… load as Mcoprigid instead of Rigidbody
…ass. It initialises loop weights to 1/(number of loops).
… need to create binding interface for McopForceField.
…ceptor() in order to initialize _mcop_E (energies) attribute.
…nd implemented it in attract.py. Bugfix: energy of copies in McopForceField Function()is = 0 when starting a new region.
…n objToMinimize attribute (type ForceField) only if this attribute is of type McopForceField. Added this function to binding interface.
…rceField. Used these attributes in McopForceField's Function() and Derivatives() instead of _weights and _denorm_weights in order to preserve the original weights from before the minimization.
…nd checkRotation() in Mcoprigid and Attractrigidbody. Added all these functions to binding interface.
…tWeights() in attract.py.
…hts(), normalize_weights(), Derivatives()...
…red active_atoms in mcopff for now.
…ered ligand in mcop docking.
… single docking and create a trajectory file. This is like using the -s single option, but uses the original coordinates rather than the rounded coordinates from the pdb file created by startligand.py.
…es call and in cpl pairlist.
… a more physical approach to multicopy docking.
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Branch containing multi-copy docking method