to_pdb(bonds : Chem::PDB::Writer::BondOptions = Chem::PDB::Writer::BondOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : String

Returns a string representation of the atom collection using the Chem::PDB file format. Arguments are fowarded to Chem::PDB::Writer.open.

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to_pdb(output : IO | Path | String, bonds : Chem::PDB::Writer::BondOptions = Chem::PDB::Writer::BondOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : Nil

Writes the atom collection to output using the Chem::PDB file format. Arguments are fowarded to Chem::PDB::Writer.open.

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to_xyz(extended : Bool = false, fields : Array(String) = [] of String) : String

Returns a string representation of the atom collection using the Chem::XYZ file format. Arguments are fowarded to Chem::XYZ::Writer.open.

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to_xyz(output : IO | Path | String, extended : Bool = false, fields : Array(String) = [] of String) : Nil

Writes the atom collection to output using the Chem::XYZ file format. Arguments are fowarded to Chem::XYZ::Writer.open.

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write(output : IO | Path | String, format : Chem::Format | String) : Nil

Writes the atom collection to output using format. Raises ArgumentError if format has required arguments or cannot write Chem::AtomCollection.

The supported file formats are Chem::Gen, Chem::Mol2, Chem::PDB, Chem::XYZ. Use the #to_* methods to customize how the object is written in the corresponding file format if possible.

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write(path : Path | String) : Nil

Writes the atom collection to the specified file. The file format is chosen based on the filename (see Chem::Format#from_filename). Raises ArgumentError if the file format cannot be determined.

The supported file formats are the following:

Chem::Gen (.gen)
Chem::Mol2 (.mol2)
Chem::PDB (.ent, .pdb)
Chem::XYZ (.xyz)

Use the #to_* methods to customize how the object is written in the corresponding file format if possible.

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