![]() Returns new Atoms object containing atoms within region. Update AtomsTopologyMixin class attributes. Return Atom or Atoms from selection command. Rezero position vector components with absolute value less than epsilon. Set values with absolute value less than epsilon to zero. Reset the RingAtomsMixin class attributes. These values could be boolean (is this a protein atom), numeric (as in the atom index or atomic mass), or string (the atom name). It is based around the assumption that every atom has a set of associated with it values which can be accessed through keywords. Reset the POAVAtomsMixin class attributes. 7 VMD Atom Selection Language VMD has a rather powerful atom selection language available. Reset the POAVAtomsMixin class attributes, then call parent class reset_attrs method. Query atom tree for nearest neighbors distances and indices.įind all Atoms within distance r of point(s) pts.įind all pairs of Atoms whose distance is at more r.įind all pairs of points within a distance r. Set/update atom attribute from another atom attribute with dict. Get a VMD selection string for the VMD keyword. Return list of POAVAtom POAV1 POAV2 or POAVR attribute. Return new Atoms filtered by vmd_indices. Return new Atoms object filtered by atom_ids.įiltered_vmd_indices(vmd_indices) Return new list of Atoms filtered by condition. Return True if periodic along the z axis.Īdd atom type for each atom in atoms to TypeAtom.typemap dictionary.Īlign principal_axes` along vector.Īnalyze_network()Īssign unique IDAtom.id to each IDAtom in IDAtoms.Īssign unique TypeAtom.types to each TypeAtom in TypeAtoms from an existing unique atom attribute.Ĭenter atoms on center-of-mass coordinates.Ĭlip_bounds(region)Ĭount how many nearby neighbor pairs can be formed.Ĭount number of neighbor pairs for each atom in self.įilter_vmd_indices(vmd_indices)įilter Atoms by VMDAtomsAdapterMixin.vmd_indices. VMD has a rather powerful atom selection language available. Return True if periodic along the y axis. Return True if periodic along the x axis. Return the total net charge of ChargedAtoms. Return principal axes of rotation computed from the inertia tensor. Return boolean array of periodic boundaries set along x,y,z axes. Return nearest-neighbor adjacency matrix. Return True if neighbors have been analyzed. Return array of nearest-neighbor atoms for each KDTAtom. Return the LatticeAtom.lattice of the first atom in self. Max number of nearest-neighbors to return from kd-tree search. StructureAtoms ( *args, **kwargs ) ¶īases: .AtomsAdapterMixin, .AtomsTopologyMixin, .AtomsTransformationsMixin, .BoundingRegionsMixin, .POAVAtomsMixin, .RingAtomsMixin, _atoms.NeighborAtoms, _atoms.ImageAtoms, _atoms.LatticeAtoms, _atoms.XYZAtoms, _atoms.ChargedAtoms, _atoms.TypeAtoms, _atoms.IDAtomsĪn Atoms sub-class for structure analysis.īool setting for returning angles in degrees.
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