Fileio
FileIO(parent_molecule_object)
¶
A class for saving and loading molecular data into a pymolecule.Molecule object
Initializes the pymolecule.io class.
| PARAMETER | DESCRIPTION |
|---|---|
parent_molecule_object
|
The pymolecule.Molecule object associated with this class.
|
parent_molecule = parent_molecule_object
instance-attribute
¶
load_pdb_into(filename, bonds_by_distance=True, serial_reindex=True, resseq_reindex=False)
¶
Loads the molecular data contained in a pdb file into the current pymolecule.Molecule object.
| PARAMETER | DESCRIPTION |
|---|---|
filename
|
A string, the filename of the pdb file.
|
bonds_by_distance
|
An optional boolean, whether or not to determine atomic bonds based on atom proximity. True by default.
DEFAULT:
|
serial_reindex
|
An optional boolean, whether or not to reindex the pdb serial field. True by default.
DEFAULT:
|
resseq_reindex
|
An optional boolean, whether or not to reindex the pdb resseq field. False by default.
DEFAULT:
|
load_pdb_into_using_file_object(file_obj, bonds_by_distance=True, serial_reindex=True, resseq_reindex=False)
¶
Loads molecular data from a python file object (pdb formatted) into the current pymolecule.Molecule object. Note that most users will want to use the load_pdb_into() function instead, which is identical except that it accepts a filename string instead of a python file object.
| PARAMETER | DESCRIPTION |
|---|---|
file_obj
|
A python file object, containing pdb-formatted data.
|
bonds_by_distance
|
An optional boolean, whether or not to determine atomic bonds based on atom proximity. True by default.
DEFAULT:
|
serial_reindex
|
An optional boolean, whether or not to reindex the pdb serial field. True by default.
DEFAULT:
|
resseq_reindex
|
An optional boolean, whether or not to reindex the pdb resseq field. False by default.
DEFAULT:
|
load_pym_into(filename)
¶
Loads the molecular data contained in a pym file into the current pymolecule.Molecule object.
| PARAMETER | DESCRIPTION |
|---|---|
filename
|
A string, the filename of the pym file.
|
resseq_reindex()
¶
Reindexes the resseq field of the atoms in the molecule, starting with 1
save_pdb(filename='', serial_reindex=True, resseq_reindex=False, return_text=False)
¶
Saves the molecular data contained in a pymolecule.Molecule object to a pdb file.
| PARAMETER | DESCRIPTION |
|---|---|
filename
|
An string, the filename to use for saving.
DEFAULT:
|
serial_reindex
|
An optional boolean, whether or not to reindex the pdb serial field. True by default.
DEFAULT:
|
resseq_reindex
|
An optional boolean, whether or not to reindex the pdb resseq field. False by default.
DEFAULT:
|
return_text
|
An optional boolean, whether or not to return text instead of writing to a file. If True, the filename variable is ignored.
DEFAULT:
|
| RETURNS | DESCRIPTION |
|---|---|
|
If return_text is True, a PDB-formatted string. Otherwise, returns nothing. |
save_pym(filename, save_bonds=False, save_filename=False, save_remarks=False, save_hierarchy=False, save_coordinates_undo_point=False)
¶
Saves the molecular data contained in a pymolecule.Molecule object to a pym file.
| PARAMETER | DESCRIPTION |
|---|---|
filename
|
An string, the filename to use for saving. (Note that this is actually a directory, not a file.)
|
save_bonds
|
An optional boolean, whether or not to save information about atomic bonds. False by default.
DEFAULT:
|
save_filename
|
An optional boolean, whether or not to save the original (pdb) filename. False by default.
DEFAULT:
|
save_remarks
|
An optional boolean, whether or not to save remarks associated with the molecule. False by default.
DEFAULT:
|
save_hierarchy
|
An optional boolean, whether or not to save information about spheres the bound (encompass) the whole molecule, the chains, and the residues. False by default.
DEFAULT:
|
save_coordinates_undo_point
|
An optional boolean, whether or not to save the last coordinate undo point. False by default.
DEFAULT:
|
serial_reindex()
¶
Reindexes the serial field of the atoms in the molecule, starting with 1