Saving a molecule

You save molecules using the sire.save() function;

>>> sr.save(mol, "cholesterol.pdb")
['/path/to/cholesterol.pdb']

sire will automatically try to guess the file format from the file extension. In this case, the molecule is saved in PDB format.

You can specify the format using the format argument.

>>> sr.save(mol, "cholesterol", format="mol2")
['/path/to/cholesterol.mol2']

Note how the file format extension has been added automatically, and that the full path to the file that was written is returned.

You can specify multiple file formats, and thus write to multiple files, e.g.

>>> sr.save(mol, "cholesterol", format=["mol2", "pdb"])
['/path/to/cholesterol.mol2', '/path/to/cholesterol.pdb']

or you can specify the filenames directly, e.g.

>>> sr.save(mol, ["chol.pdb", "chol.mol2"])
['/path/to/chol.pdb', '/path/to/chol.mol2']

Saving to strings

You can also save a molecule to memory using the sire.save_to_string() function. This saves the molecules to memory, returning the lines of the file as a Python list.

You need to specify the format you want to use, e.g. pdb for PDB, gro for Gro87 etc.

>>> sr.save_to_string(mols, format="pdb")
['MODEL     1',
 'ATOM      1  C   MOL     1      -0.019   1.525   0.010  1.00  0.00           C',
 'ATOM      2  C   MOL     1       0.002  -0.004   0.002  1.00  0.00           C',
 'ATOM      3  C   MOL     1       0.658  -0.518   1.285  1.00  0.00           C',
 'ATOM      4  C   MOL     1       1.418   2.055  -0.000  1.00  0.00           C',
 'ATOM      5  C   MOL     1       2.164   1.442   1.173  1.00  0.00           C',
 ...
 'ATOM     72  H   MOL     1       3.900  -0.359   0.167  1.00  0.00           H',
 'ATOM     73  H   MOL     1       2.811  -1.766   0.235  1.00  0.00           H',
 'ATOM     74  H   MOL     1      -0.762   2.962  -1.208  1.00  0.00           H',
 'ENDMDL',
 'END']

>>> sr.save_to_string(mols, format="gro")
'cholesterol',
 '   74',
 '    1MOL      C    1  -0.001870   0.152540   0.001040',
 '    1MOL      C    2   0.000210  -0.000410   0.000200',
 '    1MOL      C    3   0.065850  -0.051780   0.128510',
 '    1MOL      C    4   0.141830   0.205520  -0.000040',
 '    1MOL      C    5   0.216410   0.144230   0.117300',
 '    1MOL      C    6   0.280940   0.223720   0.197530',
...
 '    1MOL      H   72   0.389970  -0.035920   0.016740',
 '    1MOL      H   73   0.281060  -0.176550   0.023460',
 '    1MOL      H   74  -0.076160   0.296250  -0.120770',
 '   0.00000   0.00000   0.00000']