elbow.become_expert

Switches e-LBOW to expert mode. This provides more options which are more advanced. A complete list of the expert options.

elbow.become_novice

Switches e-LBOW to novice mode which is the default. This removes the more complicated options. A complete list of novice options.

elbow.compare_two_molecules

Attempt to align two molecules from two files and provide a comparison of bond lengths and bond angles.

elbow.convert

A simple utility that takes any of the available inputs for e-LBOW that contains cartesian coordinates and outputs either a PDB or XYZ file. To convert a XYZ to PDB format:

elbow.convert filename.xyz pdb

results in a file filename.xyz.pdb.

To convert a CIF file to XYZ format and specify the filename:

elbow.convert filename.cif filename.xyz

results in a XYZ file named filename.xyz.

For PDB files which have multiple residues, a residue can be specified by the three letter code:

elbow.convert filename.pdb xyz --residue <residue>

Data can also be piped:

cat filename.pdb | elbow.convert --pipe xyz

elbow.doc

Searches for a browser and loads the e-LBOW documentation.

elbow.get_pdb

Several SMILES strings and PDB files are packaged with e-LBOW for testing. A listing of the available PDB files is obtained by running elbow.get_pdb and a PDB file is returned by:

elbow.get_pdb atp

elbow.get_smiles

Several SMILES strings and PDB files are packaged with e-LBOW for testing. A listing of the available SMILES strings is obtained by running elbow.get_smiles and SMILES string is return by:

elbow.get_smiles atp

The SMILES strings can used with elbow.builder thus:

elbow.builder --key atp

elbow.view

Attempts to find a chemical viewing program and display the molecule:

elbow.view filename.pdb

Additionally, a residue in a PDB file can be selected:

elbow.view filename.pdb --residue ATP

Piping is facilitated via:

cat filename.pdb | elbow.view --pipe