Finders¶

finders are used by Geometry.find to locate atoms in a more general way

AaronTools.finders.get_class(name)¶: returns the finder class with the given name

class AaronTools.finders.BondsFrom(central_atom, number_of_bonds, avoid=None)¶: exact number of bonds from specified atom avoid: bonding path cannot pass through these atoms

class AaronTools.finders.WithinBondsOf(central_atom, number_of_bonds, **kwargs)¶: within a specified number of bonds from the atom

class AaronTools.finders.BondedTo(atom)¶: returns all atoms that are bonded to the specified atom

class AaronTools.finders.WithinRadiusFromPoint(point, radius)¶: within a specified radius of a point

class AaronTools.finders.WithinRadiusFromAtom(atom, radius)¶: within a specified radius of a point

class AaronTools.finders.NotAny(*critera, **kwargs)¶: atoms not matching specifiers/Finders

class AaronTools.finders.AnyTransitionMetal¶: any atoms that are transition metals

class AaronTools.finders.AnyNonTransitionMetal(*a, **kw)¶: any atoms that are not transition metals

class AaronTools.finders.HasAttribute(attribute_name)¶: all atoms with the specified attribute

class AaronTools.finders.VSEPR(vsepr, cutoff=0.5)¶

atoms with the specified VSEPR geometry

see Atom.get_shape for a list of valid vsepr strings

class AaronTools.finders.BondedElements(*args, match_exact=True, **kwargs)¶

atoms bonded to the specified neighboring elements

if match_exact=True (default), elements must match exactly

e.g. BondedElements(‘C’) will find atoms bonded to only one carbon and nothing else

class AaronTools.finders.NumberOfBonds(num_bonds)¶: atoms with the specified number of bonds

class AaronTools.finders.ChiralCentres(RS_only=False)¶

chiral centers

atoms with a non-planar VSEPR geometry with all bonded groups being distinct

for rings, looks for a set of unique canonical ranks for atoms that are all the same number of bonds away from one atom

class AaronTools.finders.CloserTo(atom1, atom2, include_ties=False)¶: atoms closer to atom1 than atom2 (based on bonds, not actual distance)

class AaronTools.finders.IsElement(element)¶: all atoms of the specified element

class AaronTools.finders.OfType(atomtype, ignore_metals=True)¶

all atoms of the specified GAFF atom type

if ignore_metals = True (default), bonding with metals will not count towards VSEPR shapes

class AaronTools.finders.ONIOMLayer(layers='')¶: all atoms in a given ONIOM layer or list of ONIOM layers

class AaronTools.finders.AmideCarbon¶

amide carbons

trigonal planar carbons bonded to a linear oxygen and a nitrogen with 3 bonds

class AaronTools.finders.Bridgehead(ring_sizes=None, match_exact=False)¶

bridgehead atoms

can specify ring sizes that the atoms bridge

class AaronTools.finders.SpiroCenters(ring_sizes=None, match_exact=False)¶: atom in two different rings with no other common atoms

class AaronTools.finders.Residue(residue)¶: all atoms in a given residue