PyMatGen Structures

Important

This page provides a concise list of available properties and methods, grouped by topic.

Refer to Pymatgen's API docs for detailed descriptions.

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Molecole Loading

• from_dict
• from_file
• from_magnetic_spacegroup
• from_prototype
• from_sites
• from_spacegroup
• from_str

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Molecole Exporting

• as_dataframe
• as_dict
• copy
• to
• to_json

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Key Attributes

• composition
• lattice
• sites
• species
• species_and_occu
• types_of_specie
• types_of_species

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Basic Properties

• site_properties
• atomic_numbers
• cart_coords
• charge
• density
• distance_matrix
• formula
• frac_coords
• is_3d_periodic
• is_ordered
• is_valid
• num_sites
• pbc
• symbol_set
• volume

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Inter-structure Utils

• interpolate
• matches

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Structure Modification

Composition Transforms

• substitute
• replace
• replace_species

Cell Transforms

• apply_operation
• scale_lattice
• apply_strain
• make_supercell

Site Transforms

• merge_sites
• rotate_sites
• translate_sites
• perturb

Charges

• set_charge
• unset_charge
• add_oxidation_state_by_element
• add_oxidation_state_by_guess
• add_oxidation_state_by_site
• add_site_property
• add_spin_by_element
• add_spin_by_site
• remove_oxidation_states
• remove_site_property
• remove_sites
• remove_species
• remove_spin

List-like API

• append
• count
• extend
• index
• insert
• ntypesp
• pop
• remove
• reverse
• sort

Other

• relax

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Analysis Methods

• extract_cluster
• group_by_types
• get_all_neighbors
• get_all_neighbors_old
• get_all_neighbors_py
• get_angle
• get_dihedral
• get_distance
• get_miller_index_from_site_indexes
• get_neighbor_list
• get_neighbors
• get_neighbors_in_shell
• get_neighbors_old
• get_orderings
• get_primitive_structure
• get_reduced_structure
• get_sites_in_sphere
• get_sorted_structure
• get_space_group_info
• get_symmetric_neighbor_list
• indices_from_symbol

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JSON Utils

• unsafe_hash
• validate_monty_v1
• validate_monty_v2

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