Returns the structure encoded in input using the Chem::VASP::Chgcar file format. Arguments are forwarded to Chem::VASP::Chgcar::Reader.open.

Returns the structure encoded in input using the Chem::Cube file format. Arguments are forwarded to Chem::Cube::Reader.open.

Returns the structure encoded in input using the Chem::Gen file format. Arguments are forwarded to Chem::Gen::Reader.open.

Returns the structure encoded in input using the Chem::JDFTx file format. Arguments are forwarded to Chem::JDFTx::Reader.open.

Returns the structure encoded in input using the Chem::VASP::Locpot file format. Arguments are forwarded to Chem::VASP::Locpot::Reader.open.

Returns the structure encoded in input using the Chem::Mol file format. Arguments are forwarded to Chem::Mol::Reader.open.

Returns the structure encoded in input using the Chem::Mol2 file format. Arguments are forwarded to Chem::Mol2::Reader.open.

If input contains multiple entries, this method returns the first one only. Use Array#from_mol2 or Chem::Mol2::Reader#each to get multiple entries instead.

Returns the structure encoded in input using the Chem::PDB file format. Arguments are forwarded to Chem::PDB::Reader.open.

If input contains multiple entries, this method returns the first one only. Use Array#from_pdb or Chem::PDB::Reader#each to get multiple entries instead.

Returns the structure encoded in input using the Chem::VASP::Poscar file format. Arguments are forwarded to Chem::VASP::Poscar::Reader.open.

Returns the structure encoded in input using the Chem::PSF file format. Arguments are forwarded to Chem::PSF::Reader.open.

Returns the structure encoded in input using the Chem::SDF file format. Arguments are forwarded to Chem::SDF::Reader.open.

If input contains multiple entries, this method returns the first one only. Use Array#from_sdf or Chem::SDF::Reader#each to get multiple entries instead.

Returns the structure encoded in input using the Chem::XYZ file format. Arguments are forwarded to Chem::XYZ::Reader.open.

If input contains multiple entries, this method returns the first one only. Use Array#from_xyz or Chem::XYZ::Reader#each to get multiple entries instead.

Returns the structure encoded in the specified file using format. Raises ArgumentError if format has required arguments or cannot read Chem::Structure.

If input contains multiple entries, this method returns the first one only. Use Array.read or Chem::FormatReader::MultiEntry#each (reader can be obtained via Chem::Format.reader) to get multiple entries instead.

The supported file formats are Chem::Cube, Chem::Gen, Chem::JDFTx, Chem::Mol2, Chem::Mol, Chem::PDB, Chem::PSF, Chem::SDF, Chem::VASP::Chgcar, Chem::VASP::Locpot, Chem::VASP::Poscar, Chem::XYZ. Use the .from_* methods to customize how the object is decoded in the corresponding file format if possible.

Returns the structure encoded in 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.

If the file contains multiple entries, this method returns the first one only. Use Array.read to get multiple entries instead.

The supported file formats are the following:

• Chem::Gen (.gen)
• Chem::JDFTx (.ionpos, .lattice)
• Chem::Mol (.mol)
• Chem::Mol2 (.mol2)
• Chem::PDB (.ent, .pdb)
• Chem::PSF (.psf)
• Chem::SDF (.sdf)
• Chem::XYZ (.xyz)
• Chem::VASP::Poscar (.poscar, POSCAR, CONTCAR)
• Chem::Cube (.cube)
• Chem::VASP::Chgcar (CHGCAR)
• Chem::VASP::Locpot (LOCPOT)

Use the .from_* methods to customize how the object is decoded in the corresponding file format if possible.

Returns the element of an atom based on its name. Raises Error if the element could not be determined. Refer to .guess_element? for details.

TODO Move to Chem namespace

Returns the element of an atom based on its name if possible, else nil.

This is a naive approach, where the first letter of atom_name is tested first to get the element, then the name with trailing digits stripped.

TODO Move to Chem namespace

Returns the angles in the topology. See Angle for definition.

Angles in the topology. See Angle for definition.

Assign bonds, formal charges, and residue's type from known residue types.

Returns the bonds between all atoms.

Returns the unit cell. Raises Spatial::NotPeriodicError if cell is nil.

Returns a deep copy of self, that is, every chain/residue/atom is copied.

Unlike array-like classes in the language, #dup (shallow copy) is not possible.

structure = Structure.new "/path/to/file.pdb"
other = structure.clone
other == structure     # => true
other.same?(structure) # => false

structure.dig('A', 23, "OG").partial_charge         # => 0.0
other.dig('A', 23, "OG").partial_charge             # => 0.0
structure.dig('A', 23, "OG").partial_charge = 0.635 # => 0.635
other.dig('A', 23, "OG").partial_charge             # => 0.0

Returns the dihedral angles in the topology. See Dihedral for definition.

Dihedral angles in the topology. See Dihedral for definition.

Returns a new structure containing the selected atoms by the given block.

Structure properties such as biases, unit cell, title, etc. are copied only if copy_properties is true.

TODO implement compound accessors in a global module

Determines the angles based on connectivity. See Angle for definition.

NOTE It deletes existing angles.

Determines the bonds from connectivity and geometry.

Bonds are added when the pairwise distances are within the corresponding covalent distances (see PeriodicTable.covalent_distance). Bonds are added until the atoms' valences are fulfilled. If extraneous bonds are found (beyond the maximum number of bonds, see Element#max_bonds), the longest ones will be removed.

Bonds to atoms that could potential be as cations (K, Na, etc.) are disfavored such that they won't be added if the neighbor is over-valence or the bond can be substituted by increasing the bond order of another bond of the neighbor (e.g., C-O + K is preferred over C-O-K since C-O can be converted to C=O).

Bond orders are assigned based on the following procedure. First, atom hybridization is guessed from the geometry. Then, the bond orders are determined such that both atoms must have the same hybridization to assign a double (sp2) or triple (sp) bond. Bond order is only changed if the bonded atoms have missing valence. If multiple bonded atoms fulfill the requirements for increasing the bond order, the atom with the most missing valence or that is closest to the current atom is selected first. This procedure is loosely based on OpenBabel's PerceiveBondOrders function.

Determines the dihedral angles based on connectivity. See Dihedral for definition.

NOTE It deletes existing dihedral angles.

Sets the formal charges based on the existing bonds.

For most cases, the formal charge is calculated as

Nele - Tele + V

where Nele is the number of valence electrons, Tele is the number of electrons in the full valence shell, and V is the effective valence, which is equivalent to the sum of the bond orders. Tele is usually 8 following the octet rule, but there are some exceptions (see Element#target_electrons).

If an atom has no bonds, it is considered as a monoatomic ion, where the formal charge is set according to the following rule: if the valence electrons < 4 (cation, e.g., Na+, Mg2+), the formal charge is equal to the number of valence electrons, else (anions, e.g., Cl-) it is equal to Nele - Tele.

WARNING Elements that have no valence determined such as transition metals are ignored.

Determines the improper dihedral angles based on connectivity. See Improper for definition.

Improper dihedral angles are often used to constraint the planarity of certain functional groups of molecules in molecular mechanics simulations, and so not every possible improper dihedral angle is required. This method lists every possible improper dihedral angle following the formal definition, which will probably generate extraneous angles.

NOTE It deletes existing improper dihedral angles.

Detects and assigns topology names from known residue templates based on bond information.

The method creates chains and residues according to the detected fragments and residue matches. The procedure is as follows. First, atoms are split into fragments, where each fragment is scanned for matches to known residue templates. Then, fragments are divided into polymer (e.g., peptide) and non-polymer (e.g., water) fragments based on the number of residues per fragment. Non-polymer residues are grouped together by their type (i.e., ion, solvent, etc.). Finally, every polymer fragment and group of non-polymer fragments are assigned to a unique chain and residues are created for each match.

NOTE Fragments are assigned to a unique chain unless the chain limit (62) is reached, otherwise all residues are assigned to the same chain.

WARNING Existing chains and residues are invalid after calling this method so do not cache them.

Determines the type of unknown residues based on their neighbors.

Returns the improper dihedral angles in the topology. See Improper for definition.

Improper dihedral angles in the topology. See Improper for definition.

Appends a String representation of this object which includes its class name, its object address and the values of all instance variables.

class Person
  def initialize(@name : String, @age : Int32)
  end
end

Person.new("John", 32).inspect # => #<Person:0x10fd31f20 @name="John", @age=32>

Hash-like container that stores the structure's properties as key (string)-value pairs. A property's value can be any of the primitive types (string, integer, float, or bool), and so it's internally stored as Metadata::Any. Use the cast methods (#as_*) to convert to the desired type.

structure.metadata["foo"] = 123
structure.metadata["foo"]      # => Metadata::Any(123)
structure.metadata["foo"].as_i # => 123
structure.metadata["foo"].as_f # => 123.0
structure.metadata["foo"].as_s # raises TypeCastError

Sets the atom coordinates and cell.

Sets the atom coordinates.

Renumber residues per chain based on the order by the output value of the block.

NOTE This won't change the order of the existing chains.

Renumber chain and residues based on bond information.

Residue fragments are assigned to unique chains unless split_chains is false, which keeps existing chains intact. Residue ordering is computed based on the link bond if available.

NOTE existing chains are reused to re-arrange the residues among them, so avoid caching them before calling this.

Deletes all bonds and resets formal charges to zero.

Returns a string representation of the structure using the Chem::Gen file format. Arguments are forwarded to Chem::Gen::Writer.open.

Writes the structure to output using the Chem::Gen file format. Arguments are forwarded to Chem::Gen::Writer.open.

Returns a string representation of the structure using the Chem::JDFTx file format. Arguments are forwarded to Chem::JDFTx::Writer.open.

Writes the structure to output using the Chem::JDFTx file format. Arguments are forwarded to Chem::JDFTx::Writer.open.

Returns a string representation of the structure using the Chem::Mol file format. Arguments are forwarded to Chem::Mol::Writer.open.

Writes the structure to output using the Chem::Mol file format. Arguments are forwarded to Chem::Mol::Writer.open.

Writes the structure to output using the Chem::Mol2 file format. Arguments are forwarded to Chem::Mol2::Writer.open.

Returns a string representation of the structure using the Chem::Mol2 file format. Arguments are forwarded to Chem::Mol2::Writer.open.

Returns a string representation of the structure using the Chem::PDB file format. Arguments are forwarded to Chem::PDB::Writer.open.

Writes the structure to output using the Chem::PDB file format. Arguments are forwarded to Chem::PDB::Writer.open.

Returns a string representation of the structure using the Chem::VASP::Poscar file format. Arguments are forwarded to Chem::VASP::Poscar::Writer.open.

Writes the structure to output using the Chem::VASP::Poscar file format. Arguments are forwarded to Chem::VASP::Poscar::Writer.open.

Writes the structure to output using the Chem::PyMOL file format. Arguments are forwarded to Chem::PyMOL::Writer.open.

Returns a string representation of the structure using the Chem::PyMOL file format. Arguments are forwarded to Chem::PyMOL::Writer.open.

Appends a short String representation of this object which includes its class name and its object address.

class Person
  def initialize(@name : String, @age : Int32)
  end
end

Person.new("John", 32).to_s # => #<Person:0x10a199f20>

Returns a string representation of the structure using the Chem::SDF file format. Arguments are forwarded to Chem::SDF::Writer.open.

Writes the structure to output using the Chem::SDF file format. Arguments are forwarded to Chem::SDF::Writer.open.

Writes the structure to output using the Chem::Protein::Stride file format. Arguments are forwarded to Chem::Protein::Stride::Writer.open.

Returns a string representation of the structure using the Chem::Protein::Stride file format. Arguments are forwarded to Chem::Protein::Stride::Writer.open.

Writes the structure to output using the Chem::VMD file format. Arguments are forwarded to Chem::VMD::Writer.open.

Returns a string representation of the structure using the Chem::VMD file format. Arguments are forwarded to Chem::VMD::Writer.open.

Returns a string representation of the structure using the Chem::XYZ file format. Arguments are forwarded to Chem::XYZ::Writer.open.

Writes the structure to output using the Chem::XYZ file format. Arguments are forwarded to Chem::XYZ::Writer.open.

Writes the structure to output using format. Raises ArgumentError if format has required arguments or cannot write Chem::Structure.

The supported file formats are Chem::Gen, Chem::JDFTx, Chem::Mol2, Chem::Mol, Chem::PDB, Chem::Protein::Stride, Chem::PyMOL, Chem::SDF, Chem::VASP::Poscar, Chem::VMD, Chem::XYZ. Use the #to_* methods to customize how the object is written in the corresponding file format if possible.

Writes the structure 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::JDFTx (.ionpos, .lattice)
• Chem::Mol (.mol)
• Chem::Mol2 (.mol2)
• Chem::PDB (.ent, .pdb)
• Chem::PyMOL (.pml)
• Chem::SDF (.sdf)
• Chem::VMD (.vmd)
• Chem::XYZ (.xyz)
• Chem::Protein::Stride (.stride)
• Chem::VASP::Poscar (.poscar, POSCAR, CONTCAR)

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