LoadMolecule¶
-
libra_py.LoadMolecule.Load_Molecule(univ, syst, mol_file, format, verbosity=0)[source]¶ Load molecular system from various formats
Specify format manually (this gives flexibility) of format recognizable by program
- Parameters
univ (Universe object) – Contains the basic information about chemical elements
syst (System) – The Chemobjects object that represents molecular system - this is what we construct
mol_file (string) – The name of the file containing the molecular structure
format (string) –
The name of the format according to which the file “mol_file” is assumed to be formatted Available options are:
pdb
pdb_1
true_pdb
true_pdb2
xyz
iqmol_pdb
- Returns
but the syst object is modified to add the atoms and bonds, and to group atoms together
- Return type
Note
We assume that the coordinates in the files read are given in Angsrom.
However, the syst stores this data in the atomic units (Borh), so conversion happens