# Chemoinformatics Module (cheminfo)

## Tutorial

## API Documentation

<h3><font color=#b8860s><b>class</b></font> Atom()</h3>

<h3><font color=#b8860s><b>class</b></font> Bond()</h3>

<h3><font color=#b8860s><b>class</b></font> Molecule()</h3>

`Molecule` property and method list, generated by AI.

| Method Name                        | Description                                   |  
|------------------------------------|-----------------------------------------------|  
| `__init__`                         | Constructor method                            |  
| `__dir__`                          | Built-in method for dir()                     |  
| `__getattr__`                      | Fallback attribute getter                     |  
| `__repr__`                         | String representation                         |  
| `__add__`                          | Addition operator overloading                 |  
| `__copy__`                         | Object copy                                   |  
| `_hided_bonds`                     | (Likely internal, name suggests hidden bonds) |  
| `copy`                             | Copy molecule                                 |  
| `crystal`                          | Related to crystals?                          |  
| `create_crystal`                   | Create a crystal                              |  
| `setattr`                          | Custom setattr (not dunder)                   |  
| `read_one`                         | Read one record/item?                         |  
| `hydrogens`                        | Hydrogen operations                           |  
| `sum_explicit_hydrogens`           | Sum explicit hydrogens                        |  
| `sum_implicit_hydrogens`           | Sum implicit hydrogens                        |  
| `has_hydrogens`                    | Check hydrogens                               |  
| `calc_mol_default_charge`          | Calculate default molecule charge             |  
| `_after_hide_metal_ligand_bonds`   | Internal, likely after hiding specific bonds  |  
| `_retrieve_torsions`               | Internal torsion retrieval                    |  
| `simple_paths`                     | Calculate simple paths                        |  
| `_set_coordinates`                 | Set coordinates (internal)                    |  
| `_update_atom_neighbours_bonds`    | Update atom neighbors and bonds               |  
| `_update_graph`                    | Update graph representation                   |  
| `_add_atom`                        | Internal atom addition                        |  
| `_add_bond`                        | Internal bond addition                        |  
| `add_atom`                         | Add atom                                      |  
| `_replace_atom`                    | Internal atom replacement                     |  
| `build_all_pair_links`             | Build pairwise links                          |  
| `auto_pair_metal`                  | Automate pairing with metals                  |  
| `replace_atom`                     | Replace atom                                  |  
| `add_bond`                         | Add bond                                      |  
| `add_bonds`                        | Add multiple bonds                            |  
| `add_component`                    | Add a molecular component                     |  
| `add_hydrogens`                    | Add hydrogens                                 |  
| `cid`                              | PubChem CID                                   |  
| `name`                             | Get/set name                                  |  
| `cas`                              | CAS number operations                         |  
| `get_thermo`                       | Get thermodynamic properties                  |  
| `clear_constraints`                | Clear constraints                             |  
| `clear_metal_ligand_bonds`         | Clear metal-ligand bonds                      |  
| `clear_hided_covalent_bonds`       | Clear hidden covalent bonds                   |  
| `clear_hided_bonds`                | Clear hidden bonds                            |  
| `recover_hided_metal_ligand_bonds` | Recover hidden metal-ligand bonds             |  
| `recover_hided_covalent_bonds`     | Recover hidden covalent bonds                 |  
| `atom_pairs`                       | Atom pairs operations                         |  
| `angles`                           | Geometric angles                              |  
| `torsions`                         | Torsion angles                                |  
| `assign_aromatic`                  | Assign aromaticity                            |  
| `assign_bond_order`                | Assign bond order                             |  
| `atom_attr_matrix`                 | Atom attribute matrix                         |  
| `atoms`                            | Atom access                                   |  
| `c_bonds`                          | Likely covalent bonds?                        |  
| `bonds`                            | Bonds access                                  |  
| `bond`                             | Access a bond                                 |  
| `build3d`                          | Build 3D structure                            |  
| `update_mol_charge`                | Update molecule charge                        |  
| `sum_atoms_charge`                 | Sum all charges                               |  
| `default_unpaired_electrons`       | Default unpaired electrons                    |  
| `default_spin_mult`                | Default spin multiplicity                     |  
| `determine_rings_aromatic`         | Determine aromatic rings                      |  
| `conformers`                       | Conformers retrieval                          |  
| `conformer_load`                   | Load conformer                                |  
| `conformers_number`                | Number of conformers                          |  
| `conformer_add`                    | Add conformer                                 |  
| `conformer_clear`                  | Clear conformers                              |  
| `conformer_get`                    | Get specific conformer                        |  
| `optimize`                         | Optimize geometry                             |  
| `optimize_complexes`               | Optimize complexes                            |  
| `complexes_build_optimize_`        | Build & optimize complexes                    |  
| `calc_atom_valence`                | Calculate atomic valence                      |  
| `calc_implicit_hydrogens`          | Calculate implicit hydrogens                  |  
| `components`                       | Access components                             |  
| `constraint_bonds_angles`          | Constraint bonds/angles                       |  
| `coordinates`                      | Get coordinates                               |
| `_create_atom_from_array`          | Internal: create atom from array              |  
| `_create_atom`                     | Internal: create atom                         |  
| `create_atom`                      | Create atom                                   |  
| `atom_pairwise_index`              | Atom pairwise index                           |  
| `get_partial_charge`               | Get partial charge                            |  
| `assign_partial_charge`            | Assign partial charge                         |  
| `pair_dist`                        | Pairwise distances                            |  
| `dist_matrix`                      | Distance matrix                               |  
| `element_counts`                   | Count elements                                |  
| `simple_graph`                     | Simple graph representation                   |  
| `_node_with_attrs`                 | Internal: Node with attributes                |  
| `_edge_with_attrs`                 | Internal: Edge with attributes                |  
| `_hide_bond`                       | Internal: Hide bond                           |  
| `hide_bonds`                       | Hide bonds                                    |  
| `hide_metal_ligand_bonds`          | Hide metal-ligand bonds                       |  
| `graph`                            | Graph object                                  |  
| `atom_bond_graph`                  | Atom-bond graph                               |  
| `graph_spectral`                   | Graph spectral analysis                       |  
| `formula`                          | Molecular formula                             |  
| `is_disorder`                      | Check disorder                                |  
| `has_3d`                           | 3D structure check                            |  
| `has_metal`                        | Metal presence check                          |  
| `has_bond_ring_intersection`       | Check bond-ring intersection                  |  
| `intersection_bonds_rings`         | Bonds/rings intersection                      |  
| `heavy_atoms`                      | Heavy atom operations                         |  
| `is_organic`                       | Organic molecule check                        |  
| `is_full_halogenated`              | Full halogenation check                       |  
| `link_atoms`                       | Link atoms                                    |  
| `link_matrix`                      | Linkage matrix                                |  
| `metals`                           | Metals access                                 |  
| `refresh_atom_id`                  | Refresh atom ID                               |  
| `atom_id_dict`                     | Atom ID dictionary                            |  
| `bond_id_dict`                     | Bond ID dictionary                            |  
| `_rm_atom`                         | Internal: remove atom                         |  
| `_rm_atoms`                        | Internal: remove multiple atoms               |  
| `remove_atom`                      | Remove atom                                   |  
| `remove_atoms`                     | Remove atoms                                  |  
| `_rm_bond`                         | Internal: remove bond                         |  
| `_rm_bonds`                        | Internal: remove multiple bonds               |  
| `remove_bond`                      | Remove bond                                   |  
| `remove_bonds`                     | Remove bonds                                  |  
| `force_remove_polar_hydrogens`     | Force remove polar hydrogens                  |  
| `remove_hydrogens`                 | Remove hydrogens                              |  
| `remove_metals`                    | Remove metals                                 |  
| `set_default_valence`              | Set default valence                           |  
| `similarity`                       | Similarity metric                             |  
| `_longest_path`                    | Internal: longest path                        |  
| `longest_path`                     | Longest path                                  |  
| `canonical_tree`                   | Canonical tree                                |  
| `super_acyclic_graph`              | Super acyclic graph                           |  
| `InChi`                            | InChI string                                  |  
| `shortest_path_index`              | Shortest path index                           |  
| `shortest_path`                    | Shortest path                                 |  
| `shortest_paths_indices`           | Indices for shortest paths                    |  
| `smiles`                           | SMILES string                                 |  
| `kekulize_smiles`                  | Kekulize SMILES                               |  
| `rings`                            | Rings operations                              |  
| `aromatic_joint_rings`             | Joint aromatic rings                          |  
| `rings_small`                      | Small rings                                   |  
| `ligand_rings`                     | Ligand rings                                  |  
| `to_obmol`                         | Convert to OBMol                              |  
| `to_rdmol`                         | Convert to RDMol                              |  
| `to_pybel_mol`                     | Convert to Pybel mol                          |  
| `translation`                      | Translation operation                         |  
| `update_atoms_attrs_from_id_dict`  | Update atom attributes                        |  
| `update_bonds_attrs_from_id_dict`  | Update bond attributes                        |  
| `update_angles`                    | Update angles                                 |  
| `update_torsions`                  | Update torsions                               |  
| `weight`                           | Molecular weight                              |  
| `write`                            | Write/serialize molecule                      |  

- Properties:

  > atoms
  > bonds
  > hydrogens

<h3><font color=#b8860s><b>class</b></font> Conformer()</h3>

<h3><font color=#b8860s><b>class</b></font> Crystal()</h3>