Index

_

__init__() (autofragment.BatchPartitioner method) (autofragment.MolecularPartitioner method)

A

autofragment.algorithms module autofragment.algorithms.clustering module autofragment.algorithms.geometric module autofragment.algorithms.graph_partition module autofragment.algorithms.hungarian module autofragment.algorithms.ml_interface module autofragment.algorithms.optimizer module autofragment.algorithms.scoring module autofragment.algorithms.seeding module autofragment.chemistry module autofragment.chemistry.ph module autofragment.core module autofragment.core.atom module autofragment.core.bonds module autofragment.core.chemistry module autofragment.core.geometry module autofragment.core.graph module autofragment.core.lattice module autofragment.core.periodic module autofragment.core.types module autofragment.data module autofragment.data.amino_acids module autofragment.data.materials module autofragment.data.nucleotides module autofragment.data.pka_values module autofragment.io module autofragment.io.mmcif module autofragment.io.output module autofragment.io.readers module autofragment.io.readers.base module autofragment.io.readers.cif module autofragment.io.readers.mol2 module autofragment.io.readers.pdb module autofragment.io.readers.qc_inputs module autofragment.io.readers.qcschema module autofragment.io.readers.sdf module autofragment.io.readers.vasp module

autofragment.io.writers module autofragment.io.writers.cfour module autofragment.io.writers.gamess module autofragment.io.writers.molpro module autofragment.io.writers.nwchem module autofragment.io.writers.orca module autofragment.io.writers.pdb_writer module autofragment.io.writers.psi4 module autofragment.io.writers.qchem module autofragment.io.writers.qcschema_writer module autofragment.io.writers.registry module autofragment.io.writers.turbomole module autofragment.io.writers.xyz_writer module autofragment.io.xyz module autofragment.multilevel module autofragment.multilevel.assignment module autofragment.multilevel.layers module autofragment.multilevel.link_atoms module autofragment.multilevel.oniom module autofragment.multilevel.point_charges module autofragment.partitioners module autofragment.partitioners.base module autofragment.partitioners.batch module autofragment.partitioners.bio module autofragment.partitioners.geometric module autofragment.partitioners.matsci module autofragment.partitioners.molecular module autofragment.partitioners.nucleic module autofragment.partitioners.qmmm module autofragment.partitioners.spectral module autofragment.partitioners.topology module autofragment.rules module autofragment.rules.base module autofragment.rules.biological module autofragment.rules.common module autofragment.rules.matsci module

B

BatchPartitioner (class in autofragment)

M

module autofragment.algorithms autofragment.algorithms.clustering autofragment.algorithms.geometric autofragment.algorithms.graph_partition autofragment.algorithms.hungarian autofragment.algorithms.ml_interface autofragment.algorithms.optimizer autofragment.algorithms.scoring autofragment.algorithms.seeding autofragment.chemistry autofragment.chemistry.ph autofragment.core autofragment.core.atom autofragment.core.bonds autofragment.core.chemistry autofragment.core.geometry autofragment.core.graph autofragment.core.lattice autofragment.core.periodic autofragment.core.types autofragment.data autofragment.data.amino_acids autofragment.data.materials autofragment.data.nucleotides autofragment.data.pka_values autofragment.io autofragment.io.mmcif autofragment.io.output autofragment.io.readers autofragment.io.readers.base autofragment.io.readers.cif autofragment.io.readers.mol2 autofragment.io.readers.pdb autofragment.io.readers.qc_inputs autofragment.io.readers.qcschema autofragment.io.readers.sdf autofragment.io.readers.vasp autofragment.io.writers autofragment.io.writers.cfour autofragment.io.writers.gamess autofragment.io.writers.molpro autofragment.io.writers.nwchem autofragment.io.writers.orca autofragment.io.writers.pdb_writer autofragment.io.writers.psi4 autofragment.io.writers.qchem autofragment.io.writers.qcschema_writer autofragment.io.writers.registry autofragment.io.writers.turbomole autofragment.io.writers.xyz_writer autofragment.io.xyz autofragment.multilevel autofragment.multilevel.assignment autofragment.multilevel.layers autofragment.multilevel.link_atoms autofragment.multilevel.oniom autofragment.multilevel.point_charges autofragment.partitioners autofragment.partitioners.base autofragment.partitioners.batch autofragment.partitioners.bio autofragment.partitioners.geometric autofragment.partitioners.matsci autofragment.partitioners.molecular autofragment.partitioners.nucleic autofragment.partitioners.qmmm autofragment.partitioners.spectral autofragment.partitioners.topology autofragment.rules autofragment.rules.base autofragment.rules.biological autofragment.rules.common autofragment.rules.matsci

MolecularPartitioner (class in autofragment)

P

partition_xyz() (in module autofragment)