schrodinger.trajectory.analyze_trajectories.

Class _KeywordProcessor

This class processes ARK keywords coming from a .st2 input file, it turns the keywords into Analysis objects to be used by the backend. st2 files are generated by sim_event_analysis.py

Instance Methods

[hide private]

__init__(self, csim, trj_directory=None, cfgfn=None)

str(self, ark_obj)
return string value of an ark obj.

_get_idx(self, params, count)
Returns atom lists of FIS atoms from ark_kw

_get_atoms(self, params, count)
Returns atom lists of FIS atoms from ark_kw

process_ark(self, ark_kw)
Picks the correct function to process the keyword type

_process_interaction_energy(self, ark_kw)
Get an analysis object for interaction energies (non bonbded)

_setup_energy_groups_by_molecules(self, cmsstr)

_process_bulk(self, ark_kw)
calculate buld properties, usually for material-science type...

_process_energy(self, ark_kw)
Get an analysis object for energies

_process_rog(self, ark_kw)
Get analysis object for radius of gyration For these, we calculate for all solute atoms (incl hydrogens)

_process_mol_surface_area(self, ark_kw)
Get analysis object for molecular surface area

_process_sa_surface_area(self, ark_kw)
Get analysis object for solvent accessible surface area

_process_sa_surface_area_by_residue(self, ark_kw)
get analysis object for solvent accessible surface area by residue

_process_polar_surface_area(self, ark_kw)
Get analysis object for polar surface area

_process_secstructure(self, ark_kw)
Get analysis object for desired Secondary Structure

_process_distance(self, ark_kw)
Get analysis object for desired distance

_process_angle(self, ark_kw)
Get analysis object for desired angle

_process_torsion(self, ark_kw)
Get analysis object for desired torsion

_process_planar_angle(self, ark_kw)
Get analysis object for desired planar angle

_process_jcoupling(self, ark_kw)
Get analysis object for jcoupling

_process_membrane_thick(self, ark_kw)
Calculate thikness of the bilayer

_process_area_per_lipid(self, ark_kw)
Calculate area per lipid in the membrane bilayer

_process_salt_bridge(self, ark_kw)
Generate a salt bridge analysis object

_process_hphobe_interact(self, ark_kw)
Generate a hydrophobe interaction analysis object

_process_hbonds(self, ark_kw)
Generate an hbond analisys object

_process_rmsd(self, ark_kw)

_process_rmsf(self, ark_kw)

_process_pl_interact(self, ark_kw)

Static Methods

[hide private]

requires_energy(ark_kws)

_get_type(ark_kw)
The ark_kw passed is a sea.Map, whose single key is the kw type

_process_bulk(self, ark_kw)


calculate buld properties, usually for material-science type
systems
- volume
- density
- delta -- mixing energy
- intermolecular energy
- intermolecular vdW energy
- intermolecular Electrostatic energy
- heat of vaporization
- specific heat

_process_energy(self, ark_kw)

Get an analysis object for energies

If selection is None, the solute is used as the main selection.

_process_salt_bridge(self, ark_kw)

Generate a salt bridge analysis object

This will be an SaltBridgeFinder object, which will then be processed. Note, only potential salt bridge atoms are checked.

_process_hbonds(self, ark_kw)

Generate an hbond analisys object

This will be an HydrogenBondFinder object, which will then be processed. Note, only potential hbonding atoms are checked.