Package schrodinger :: Package application :: Package mcpro :: Module perturbations

Module perturbations

Classes

PertReorder
Storage class for perturbation reordering

PertID
Storage class for perturbation identification

Perturbations
Class to read, create, and manipulate the graph of perturbations from which user-specified list of fragments will be converted to a list of FEPs to be run

Functions

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find_pert_db(pert_db_type='ring')
Method to return perturbation database path

import_perturbations(file)
Method reads the perturbation database which includes a list of perturbation ids and the structural reordering lists/dummy additions.

gen_reordered_ct(mode, ct, reorder_obj)
Method to convert input ct for use in Model System creation for FEP mode = 1 convert ct for use as starting struture mode = 2 convert ct for use as ending structure

modify_ct(startCt, endCt)
Method to set bond lengths/angles/torsions for dummy atoms found in start/end Cts

set_dummy_geometry(ct, refct, tmp)
Set dummy atom geometries in ct bond, angle, and torsions are set off first bond/angle/torsion found in refct that doesn't correspond to a newly added dummy atom.

adjustDum(ct, value, atom1, atom2, atom3=None, atom4=None)
Adjust a distance, angle or dihedral angle.

convert_to_pos_dihedral(inDih)

Variables

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__doc__ = ...

perturbation_databases = {"ring": "ring_pert.db", "functional_...

Function Details

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import_perturbations(file)

Method reads the perturbation database which includes a list of perturbation ids and the structural reordering lists/dummy additions. Data in perturb_ids[] is directional, i.e. fragA->fragB

gen_reordered_ct(mode, ct, reorder_obj)

Method to convert input ct for use in Model System creation for FEP mode = 1 convert ct for use as starting struture mode = 2 convert ct for use as ending structure

Take input structure, add any necessary dummy atoms, create new reorder list, reorder molecule.

set_dummy_geometry(ct, refct, tmp)

Set dummy atom geometries in ct bond, angle, and torsions are set off first bond/angle/torsion found in refct that doesn't correspond to a newly added dummy atom. *datom*-batom-aatom,tatom

adjustDum(ct, value, atom1, atom2, atom3=None, atom4=None)

Adjust a distance, angle or dihedral angle. If atom3 is None then the distance between atom1 and atom2 will be set to value, atom2 and all atoms attached to that atom will be moved. If atom4 is None then the angle between atom1, atom2 and atom3 will set to value, atom3 and all other atoms attached to that will be moved. If all atoms are specified then the dihedral angle made by atom1, atom2, atom3 and atom4 will be set to value and atom4 and all other atoms attached to that will be moved. All distances are specified in Angstroms, all angles in degrees.

All atom arguments can be integers or _StructureAtom objects. There is no return value for this function.

Variables Details

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doc

Value:

"""
Classes for dealing with graphs for constructing optimal FEP pathways.

Copyright Schrodinger, LLC. All rights reserved.

"""

perturbation_databases

Value:

{"ring": "ring_pert.db", "functional_group": "pert.db", "residue": "re
sidue.db"}