Index

_

__call__() (molmod.graphs.Anything method) (molmod.graphs.CritAnd method) (molmod.graphs.CritNot method) (molmod.graphs.CritOr method) (molmod.graphs.CritXor method) (molmod.graphs.GraphSearch method) (molmod.minimizer.ConvergenceCondition method) (molmod.minimizer.GoldenLineSearch method) (molmod.minimizer.LineSearch method) (molmod.minimizer.NewtonLineSearch method) (molmod.minimizer.Preconditioner method) (molmod.minimizer.StopLossCondition method) (molmod.molecular_graphs.BondLongerThan method) (molmod.molecular_graphs.HasAtomNumber method) (molmod.molecular_graphs.HasNeighborNumbers method) (molmod.molecular_graphs.HasNeighbors method) (molmod.molecular_graphs.HasNumNeighbors method) (molmod.toyff.ToyFF method)

A

about_axis() (molmod.transformations.Complete class method) active (molmod.unit_cells.UnitCell attribute) active_inactive (molmod.unit_cells.UnitCell attribute) add_cell_vector() (molmod.unit_cells.UnitCell method) add_hydrogens() (molmod.molecular_graphs.MolecularGraph method) add_item() (molmod.clusters.Cluster method) add_molecular_graph() (molmod.io.psf.PSFFile method) add_molecule() (molmod.io.psf.PSFFile method) add_related() (molmod.clusters.ClusterFactory method) add_relation() (molmod.graphs.OneToOne method) add_relations() (molmod.graphs.OneToOne method)

alignment_a (molmod.unit_cells.UnitCell attribute) alignment_c (molmod.unit_cells.UnitCell attribute) Ame2003 (class in molmod.isotopes) Anything (class in molmod.graphs) append() (molmod.io.cp2k.CP2KSection method) apply_to() (molmod.transformations.Complete method) (molmod.transformations.Rotation method) (molmod.transformations.Translation method) atom_criteria() (in module molmod.molecular_graphs) AtomInfo (class in molmod.periodic) ATRJFrame (class in molmod.io.atrj) ATRJReader (class in molmod.io.atrj)

B

bend_angle() (in module molmod.ic) bend_cos() (in module molmod.ic) BendingAnglePattern (class in molmod.molecular_graphs) blob (molmod.molecular_graphs.MolecularGraph attribute) bond_length() (in module molmod.ic)

bond_tolerance (molmod.bonds.BondData attribute) BondData (class in molmod.bonds) bonded() (molmod.bonds.BondData method) BondLongerThan (class in molmod.molecular_graphs) BondPattern (class in molmod.molecular_graphs)

C

cached (class in molmod.utils) canonical_order (molmod.graphs.Graph attribute) cast() (molmod.transformations.Complete class method) central_vertex (molmod.graphs.Graph attribute) central_vertices (molmod.graphs.Graph attribute) check_anagrad() (in module molmod.minimizer) check_delta() (in module molmod.minimizer) check_next_match() (molmod.graphs.CustomPattern method) (molmod.graphs.Pattern method) (molmod.graphs.RingPattern method) (molmod.molecular_graphs.NRingPattern method) check_symmetry() (molmod.graphs.Pattern method) chemical_formula (molmod.molecules.Molecule attribute) clear() (molmod.io.psf.PSFFile method) Cluster (class in molmod.clusters) ClusterFactory (class in molmod.clusters) com (molmod.molecules.Molecule attribute) compare() (molmod.graphs.EqualPattern method) (molmod.graphs.Pattern method) (molmod.transformations.Complete method) (molmod.transformations.Rotation method) (molmod.transformations.Translation method) Complete (class in molmod.transformations) complete() (molmod.graphs.CustomPattern method) (molmod.graphs.Pattern method) (molmod.graphs.RingPattern method) (molmod.molecular_graphs.NRingPattern method)

compute_fd_hessian() (in module molmod.minimizer) compute_rotsym() (in module molmod.symmetry) (molmod.molecules.Molecule method) ConjugateGradient (class in molmod.minimizer) Constraints (class in molmod.minimizer) ConvergenceCondition (class in molmod.minimizer) coordinates (molmod.molecules.Molecule attribute) copy() (molmod.ic.Scalar method) (molmod.ic.Vector3 method) (molmod.io.cube.Cube method) copy_with() (molmod.utils.ReadOnly method) copy_with_new_relations() (molmod.graphs.Match method) CP2KInputFile (class in molmod.io.cp2k) CP2KKeyword (class in molmod.io.cp2k) CP2KSection (class in molmod.io.cp2k) CPMDTrajectoryReader (class in molmod.io.cpmd) CritAnd (class in molmod.graphs) CriteriaSet (class in molmod.graphs) CritNot (class in molmod.graphs) CritOr (class in molmod.graphs) CritXor (class in molmod.graphs) cross() (in module molmod.ic) Cube (class in molmod.io.cube) CubeReader (class in molmod.io.cube) CustomPattern (class in molmod.graphs)

D

DiagonalPreconditioner (class in molmod.minimizer) dihed_angle() (in module molmod.ic) dihed_cos() (in module molmod.ic) DihedralAnglePattern (class in molmod.molecular_graphs) distance_matrix (molmod.molecules.Molecule attribute) distances (molmod.graphs.Graph attribute) DLPolyHistoryReader (class in molmod.io.dlpoly) DLPolyOutputReader (class in molmod.io.dlpoly) do() (molmod.minimizer.DiagonalPreconditioner method) (molmod.minimizer.FullPreconditioner method) (molmod.minimizer.Preconditioner method)

dot() (in module molmod.ic) dump() (molmod.io.cp2k.CP2KInputFile method) (molmod.io.cp2k.CP2KKeyword method) (molmod.io.cp2k.CP2KSection method) (molmod.io.number_state.NumberState method) (molmod.io.psf.PSFFile method) (molmod.io.xyz.XYZWriter method) dump_children() (molmod.io.cp2k.CP2KSection method) dump_cml() (in module molmod.io.cml) dump_pdb() (in module molmod.io.pdb)

E

edge_index (molmod.graphs.Graph attribute) edges (molmod.graphs.Graph attribute) (molmod.molecular_graphs.MolecularGraph attribute)

eps (molmod.unit_cells.UnitCell attribute) EqualPattern (class in molmod.graphs) equivalent_vertices (molmod.graphs.Graph attribute)

F

FCHKFile (class in molmod.io.fchk) FileFormatError fingerprint (molmod.graphs.Graph attribute) fit_rmsd() (in module molmod.transformations) free_shake() (molmod.minimizer.Constraints method) from_blob() (molmod.molecular_graphs.MolecularGraph class method) from_file() (molmod.io.cube.Cube class method) (molmod.molecules.Molecule class method) from_first_relation() (molmod.graphs.Match class method)

from_geometry() (molmod.molecular_graphs.MolecularGraph class method) from_matrix() (molmod.transformations.Complete class method) (molmod.transformations.Rotation class method) (molmod.transformations.Translation class method) from_parameters3() (molmod.unit_cells.UnitCell class method) from_properties() (molmod.transformations.Complete class method) (molmod.transformations.Rotation class method) full_match() (molmod.graphs.Graph method) FullPreconditioner (class in molmod.minimizer)

G

get() (molmod.io.number_state.NumberState method) get_angle() (molmod.toyff.SpecialAngles method) get_clusters() (molmod.clusters.ClusterFactory method) get_cube_points() (in module molmod.io.cube) get_destination() (molmod.graphs.OneToOne method) get_edge_string() (molmod.graphs.Graph method) (molmod.molecular_graphs.MolecularGraph method) get_final() (molmod.minimizer.Minimizer method) get_first_molecule() (molmod.io.xyz.XYZReader method) get_graph() (molmod.io.psf.PSFFile method) get_groups() (molmod.io.psf.PSFFile method) get_halfs() (molmod.graphs.Graph method) get_halfs_double() (molmod.graphs.Graph method) get_header() (molmod.minimizer.ConvergenceCondition method) get_hessian() (molmod.io.fchk.FCHKFile method) get_length() (molmod.bonds.BondData method) get_molecular_graph() (molmod.io.psf.PSFFile method) get_molecule() (molmod.io.xyz.XYZFile method) get_name() (molmod.io.cp2k.CP2KKeyword method) (molmod.io.cp2k.CP2KSection method) get_new_edges() (molmod.graphs.CustomPattern method) (molmod.graphs.Match method) (molmod.graphs.Pattern method) (molmod.graphs.RingPattern method) get_optimization_coordinates() (molmod.io.fchk.FCHKFile method)

get_optimization_energies() (molmod.io.fchk.FCHKFile method) get_optimization_gradients() (molmod.io.fchk.FCHKFile method) get_optimization_lowest_index() (molmod.io.fchk.FCHKFile method) get_optimized_energy() (molmod.io.fchk.FCHKFile method) get_optimized_gradient() (molmod.io.fchk.FCHKFile method) get_optimized_molecule() (molmod.io.fchk.FCHKFile method) get_part() (molmod.graphs.Graph method) get_points() (molmod.io.cube.Cube method) get_radius_indexes() (molmod.unit_cells.UnitCell method) get_radius_ranges() (molmod.unit_cells.UnitCell method) get_source() (molmod.graphs.OneToOne method) get_subgraph() (molmod.graphs.Graph method) (molmod.molecular_graphs.MolecularGraph method) get_unit() (molmod.io.cp2k.CP2KKeyword method) get_value() (molmod.io.cp2k.CP2KKeyword method) get_vertex_fingerprints() (molmod.graphs.Graph method) get_vertex_string() (molmod.graphs.Graph method) (molmod.molecular_graphs.MolecularGraph method) GoldenLineSearch (class in molmod.minimizer) goto_next_frame() (molmod.io.dlpoly.DLPolyOutputReader method) Graph (class in molmod.graphs) graph (molmod.molecules.Molecule attribute) GraphError GraphSearch (class in molmod.graphs) GroReader (class in molmod.io.gromacs) guess_geometry() (in module molmod.toyff)

H

HasAtomNumber (class in molmod.molecular_graphs) HasNeighborNumbers (class in molmod.molecular_graphs)

HasNeighbors (class in molmod.molecular_graphs) HasNumNeighbors (class in molmod.molecular_graphs)

I

identity() (molmod.transformations.Complete class method) (molmod.transformations.Rotation class method) (molmod.transformations.Translation class method) in_destinations() (molmod.graphs.OneToOne method) in_sources() (molmod.graphs.OneToOne method) independent_vertices (molmod.graphs.Graph attribute) inertia_tensor (molmod.molecules.Molecule attribute) initialize() (molmod.minimizer.Minimizer method) insert() (molmod.io.cp2k.CP2KSection method) inv (molmod.transformations.Complete attribute) (molmod.transformations.Rotation attribute) (molmod.transformations.Translation attribute) inv() (molmod.ic.Scalar method) inverse() (molmod.graphs.OneToOne method)

is_sd() (molmod.minimizer.ConjugateGradient method) (molmod.minimizer.QuasiNewton method) (molmod.minimizer.SearchDirection method) (molmod.minimizer.SteepestDescent method) iter_breadth_first() (molmod.graphs.Graph method) iter_breadth_first_edges() (molmod.graphs.Graph method) iter_final_matches() (molmod.graphs.CustomPattern method) (molmod.graphs.Pattern method) iter_initial_relations() (molmod.graphs.CustomPattern method) (molmod.graphs.EqualPattern method) (molmod.graphs.Pattern method) (molmod.graphs.RingPattern method) iter_numbers() (molmod.periodic.PeriodicData method) iter_shortest_paths() (molmod.graphs.Graph method)

L

LAMMPSDumpReader (class in molmod.io.lammps) limit_step() (molmod.minimizer.LineSearch method) LineSearch (class in molmod.minimizer) load() (molmod.io.cp2k.CP2KKeyword method) (molmod.io.cp2k.CP2KSection method) (molmod.io.number_state.NumberState method)

load_children() (molmod.io.cp2k.CP2KSection method) load_cml() (in module molmod.io.cml) load_pdb() (in module molmod.io.pdb)

M

mass (molmod.molecules.Molecule attribute) masses (molmod.molecules.Molecule attribute) Match (class in molmod.graphs) MatchClass (molmod.graphs.EqualPattern attribute) (molmod.graphs.Pattern attribute) matrix (molmod.transformations.Complete attribute) (molmod.transformations.Rotation attribute) (molmod.transformations.Translation attribute) (molmod.unit_cells.UnitCell attribute) max_distance (molmod.graphs.Graph attribute) Minimizer (class in molmod.minimizer) MolecularGraph (class in molmod.molecular_graphs) Molecule (class in molmod.molecules) molmod.binning (module) molmod.bonds (module) molmod.clusters (module) molmod.constants (module) molmod.graphs (module) molmod.ic (module) molmod.io (module) molmod.io.atrj (module) molmod.io.cml (module) molmod.io.common (module)

molmod.io.cp2k (module) molmod.io.cpmd (module) molmod.io.cube (module) molmod.io.dlpoly (module) molmod.io.fchk (module) molmod.io.gamess (module) molmod.io.gromacs (module) molmod.io.lammps (module) molmod.io.number_state (module) molmod.io.pdb (module) molmod.io.psf (module) molmod.io.sdf (module) molmod.io.xyz (module) molmod.isotopes (module) molmod.minimizer (module) molmod.molecular_graphs (module) molmod.molecules (module) molmod.periodic (module) molmod.symmetry (module) molmod.toyff (module) molmod.transformations (module) molmod.unit_cells (module) molmod.units (module) molmod.utils (module)

N

name (molmod.io.cp2k.CP2KKeyword attribute) (molmod.io.cp2k.CP2KSection attribute) neighbors (molmod.graphs.Graph attribute) NewtonLineSearch (class in molmod.minimizer) norm() (molmod.ic.Vector3 method) NRingPattern (class in molmod.molecular_graphs)

NubTab03 (class in molmod.isotopes) num_edges (molmod.graphs.Graph attribute) num_vertices (molmod.graphs.Graph attribute) (molmod.molecular_graphs.MolecularGraph attribute) numbers (molmod.molecular_graphs.MolecularGraph attribute) (molmod.molecules.Molecule attribute) NumberState (class in molmod.io.number_state)

O

OneToOne (class in molmod.graphs) opbend_angle() (in module molmod.ic) opbend_cos() (in module molmod.ic) opbend_dist() (in module molmod.ic)

opbend_mangle() (in module molmod.ic) opbend_mcos() (in module molmod.ic) ordered (molmod.unit_cells.UnitCell attribute) orders (molmod.molecular_graphs.MolecularGraph attribute) OutOfPlanePattern (class in molmod.molecular_graphs)

P

pair_distance() (in module molmod.ic) PairSearchInter (class in molmod.binning) PairSearchIntra (class in molmod.binning) parameters (molmod.unit_cells.UnitCell attribute) parse_unit() (in module molmod.units) Pattern (class in molmod.graphs) PeriodicData (class in molmod.periodic)

Preconditioner (class in molmod.minimizer) print_debug() (molmod.graphs.GraphSearch method) project() (molmod.minimizer.Constraints method) propagate() (molmod.minimizer.Minimizer method) properties (molmod.transformations.Complete attribute) (molmod.transformations.Rotation attribute) PSFFile (class in molmod.io.psf) PunchFile (class in molmod.io.gamess)

Q

QuasiNewton (class in molmod.minimizer)

R

r (molmod.transformations.Complete attribute) (molmod.transformations.Rotation attribute) random() (molmod.transformations.Rotation class method) read_from_file() (molmod.io.cp2k.CP2KInputFile static method) (molmod.io.psf.PSFFile method) read_size() (molmod.io.xyz.XYZReader method) readline() (molmod.io.cp2k.CP2KSection method) ReadOnly (class in molmod.utils) reciprocal (molmod.unit_cells.UnitCell attribute)

reset() (molmod.minimizer.ConjugateGradient method) (molmod.minimizer.QuasiNewton method) (molmod.minimizer.SearchDirection method) (molmod.minimizer.SteepestDescent method) (molmod.minimizer.StopLossCondition method) results() (molmod.ic.Scalar method) RingPattern (class in molmod.graphs) rmsd() (molmod.molecules.Molecule method) Rotation (class in molmod.transformations) RuleCluster (class in molmod.clusters)

S

safe_shake() (molmod.minimizer.Constraints method) Scalar (class in molmod.ic) SDFReader (class in molmod.io.sdf) SearchDirection (class in molmod.minimizer) set() (molmod.io.number_state.NumberState method) set_default_graph() (molmod.molecules.Molecule method) set_default_masses() (molmod.molecules.Molecule method) set_default_symbols() (molmod.molecules.Molecule method) set_value() (molmod.io.cp2k.CP2KKeyword method) shortest_vector() (molmod.unit_cells.UnitCell method) size (molmod.molecules.Molecule attribute) slice_match() (in module molmod.io.common)

SlicedReader (class in molmod.io.common) spacings (molmod.unit_cells.UnitCell attribute) SpecialAngles (class in molmod.toyff) SteepestDescent (class in molmod.minimizer) StopLossCondition (class in molmod.minimizer) sub (molmod.graphs.EqualPattern attribute) (molmod.graphs.Pattern attribute) superpose() (in module molmod.transformations) symbols (molmod.molecular_graphs.MolecularGraph attribute) (molmod.molecules.Molecule attribute) symmetries (molmod.graphs.Graph attribute) symmetry_cycles (molmod.graphs.Graph attribute)

T

t (molmod.transformations.Complete attribute) (molmod.transformations.Translation attribute) test_match() (molmod.graphs.CriteriaSet method) TetraPattern (class in molmod.molecular_graphs) title (molmod.molecules.Molecule attribute)

to_cartesian() (molmod.unit_cells.UnitCell method) to_fractional() (molmod.unit_cells.UnitCell method) ToyFF (class in molmod.toyff) Translation (class in molmod.transformations) tune_geometry() (in module molmod.toyff)

U

undo() (molmod.minimizer.DiagonalPreconditioner method) (molmod.minimizer.FullPreconditioner method) (molmod.minimizer.Preconditioner method) unit (molmod.io.cp2k.CP2KKeyword attribute) unit_cell (molmod.molecules.Molecule attribute) UnitCell (class in molmod.unit_cells) update() (molmod.clusters.Cluster method) (molmod.clusters.RuleCluster method) (molmod.minimizer.ConjugateGradient method) (molmod.minimizer.DiagonalPreconditioner method) (molmod.minimizer.FullPreconditioner method) (molmod.minimizer.Preconditioner method) (molmod.minimizer.QuasiNewton method) (molmod.minimizer.SearchDirection method) (molmod.minimizer.SteepestDescent method)

V

value (molmod.io.cp2k.CP2KKeyword attribute) Vector3 (class in molmod.ic)

vertex_fingerprints (molmod.graphs.Graph attribute) volume (molmod.unit_cells.UnitCell attribute)

W

write_to_file() (molmod.io.cp2k.CP2KInputFile method) (molmod.io.cube.Cube method) (molmod.io.psf.PSFFile method) (molmod.io.xyz.XYZFile method) (molmod.molecules.Molecule method)

X

XYZFile (class in molmod.io.xyz)

XYZReader (class in molmod.io.xyz) XYZWriter (class in molmod.io.xyz)