`SDRecord`#

class biotite.structure.io.mol.SDRecord(header=None, ctab=None, metadata=None)[source]#

Bases: object

A record in a SD file.

Parameters:

headerHeader, optional: The header of the record. By default, an empty header is created.
ctabstr, optional: The connection table (atoms and bonds) in the record. By default, an empty structure is created.
metadataMetadata, Mapping or str, optional: The metadata of the record. Can be given as dictionary mapping Metadata.Key.name to the respective metadata value. By default, no metadata is appended to the record.

Attributes:

header, ctab, metadata: The same as the parameters.

Examples

>>> atoms = residue("ALA")
>>> record = SDRecord(header=Header(mol_name="ALA", dimensions="3D"))
>>> record.set_structure(atoms)
>>> print(record.get_structure())
            0             N        -0.966    0.493    1.500
            0             C         0.257    0.418    0.692
            0             C        -0.094    0.017   -0.716
            0             O        -1.056   -0.682   -0.923
            0             C         1.204   -0.620    1.296
            0             O         0.661    0.439   -1.742
            0             H        -1.383   -0.425    1.482
            0             H        -0.676    0.661    2.452
            0             H         0.746    1.392    0.682
            0             H         1.459   -0.330    2.316
            0             H         0.715   -1.594    1.307
            0             H         2.113   -0.676    0.697
            0             H         0.435    0.182   -2.647
>>> # Add the record to an SD file
>>> file = SDFile()
>>> file["ALA"] = record
>>> print(file)
ALA
                    3D

 13 12  0     0  0  0  0  0  0  1 V2000
   -0.9660    0.4930    1.5000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2570    0.4180    0.6920 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0940    0.0170   -0.7160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0560   -0.6820   -0.9230 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2040   -0.6200    1.2960 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6610    0.4390   -1.7420 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3830   -0.4250    1.4820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6760    0.6610    2.4520 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7460    1.3920    0.6820 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4590   -0.3300    2.3160 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7150   -1.5940    1.3070 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1130   -0.6760    0.6970 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4350    0.1820   -2.6470 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  2  9  1  0  0  0  0
  3  4  2  0  0  0  0
  3  6  1  0  0  0  0
  5 10  1  0  0  0  0
  5 11  1  0  0  0  0
  5 12  1  0  0  0  0
  6 13  1  0  0  0  0
M  END
$$$$

static deserialize(text)#

Create an SDRecord by deserializing the given text content.

Parameters:

textstr: The content to be deserialized.

Returns:

recordSDRecord: The parsed record.

get_structure()#

Parse the structural data in the SD record.

Returns:

arrayAtomArray: This AtomArray contains the optional charge annotation and has an associated BondList. All other annotation categories, except element are empty.

serialize()#

Convert this object into text content.

Returns:

contentstr: The serialized content.

set_structure(atoms, default_bond_type=BondType.ANY, version=None)#

Set the structural data in the SD record.

Parameters:

atomsAtomArray: The array to be saved into this file. Must have an associated BondList.
default_bond_typeBondType, optional: Bond type fallback for the Bond block, if a BondType has no CTAB counterpart. By default, each such bond is treated as BondType.ANY.
version{“V2000”, “V3000”}, optional: The version of the CTAB format. "V2000" uses the Atom and Bond block, while "V3000" uses the Properties block. By default, "V2000" is used, unless the number of atoms or bonds exceeds 999, in which case "V3000" is used.

SDRecord#

`SDRecord`#