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.Resiude(residue)#: all atoms in a given residue