schrodinger.application.desmond.fep_fragment

Class FragmentGroup

Groups of mutating fragments, that attach to at least one common core atom

Instance Methods

__init__(self)

addAttachmentPoint(self, attachment_point)
add one pair of attachment points ((sa, sb), (da, db))...

addAttachmentPoints(self, attachment_points)
add a bunch of attachmentpoints attachment_points: list of attachment_point

addSourceAtoms(self, source_atoms)
add source fragment source_atoms: set of source atom indices

addDestAtoms(self, dest_atoms)
add dest fragment dest_atoms: set of dest atom indices

addAttpointToSourceFragment(self, s_frag_id, att_point)
populate the attachment point dictionary for source fragment,...

addAttpointToDestFragment(self, d_frag_id, att_point)
populate the attachment point dictionary for dest fragment,...

getSourceFragmentAttpoints(self, s_frag_id)
get attachment points for source fragment, s_frag_id s_frag_id: index into source fragment list return: list of attachment points

getDestFragmentAttpoints(self, d_frag_id)
get attachment points for dest fragment, d_frag_id d_frag_id: index into dest fragment list return: list of attachment points

getAttachmentPoints(self)
get all attachmentpoints as a list of tuple, ((sa, sb), (da, db))

getSourceAtoms(self)
return list of source fragment atoms

getNumSourceFrags(self)
return: number of fragments in reactant

getDestAtoms(self)
return list of dest fragment atoms

getNumDestFrags(self)
return: number of fragments in product

getSourceAttachmentPoints(self)
get attachment points for all source fragments

getDestAttachmentPoints(self)
get attachment points for all dest fragments

addAttachmentPoint(self, attachment_point)


add one pair of attachment points ((sa, sb), (da, db))
attachment_point: two-element tuple for both source and dest structures,
                  (core_atom_idx, bridgeatom_idx)

addAttpointToSourceFragment(self, s_frag_id, att_point)


populate the attachment point dictionary for source fragment,
         s_frag_id
s_frag_id: index of fragment in the source fragment list
att_point: attachment point in the form of (sa, sb)
           sa is the core atom where the fragment is connected;
           sb is the dummy atom in the fragment that is connected
              to sa

addAttpointToDestFragment(self, d_frag_id, att_point)


populate the attachment point dictionary for dest fragment,
         d_frag_id
d_frag_id: index of fragment in the source fragment list
att_point: attachment point in the form of (da, db)
           da is the core atom where the fragment is connected;
           db is the dummy atom in the fragment that is connected
              to da