Package schrodinger :: Package application :: Package desmond :: Module struc
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Module struc

A collection of miscellaneous molecular-structure-related functions.

Copyright Schrodinger, LLC. All rights reserved.

Functions [hide private]
 
get_sidechain_att_atom(residue)
Given an amino acide residue 'residue' (must be a schrodinger.structure._Residue object), this function returns a tuple that is composed of two atoms (instances of the schrodinger.structure._StructureAtom class) that are the attachment atoms of the sidechain to the backbone of the given residue.
 
get_residue_sitename(residue)
Given a schrodinger.structure._Residue object ('residue'), this function returns a string that represents the name of the residue site.
 
delete_ct_property(struc, prop_name)
Deletes a property from a set of CTs, and returns the list of mutated CTs.
 
delete_atom_property(struc, prop_name)
Similar to the delete_ct_property, but this function deletes atom properties for all atoms.
 
rename_atom_property(struc, prop_name, new_name)
 
read_all_ct(fname)
 
read_fep_cms(cms_fname)
Reads a .cms file 'cms_fname' and returns a 4-tuple.
 
read_anni_fep_cms(cms_fname)
Reads a .cms file 'cms_fname' and returns a 3-tuple.
 
get_fragname(fname)
Variables [hide private]
  BACKBONE_ATOM_NAME = ["H", "HN", "HA", "N", "CA", "C", "O",]
Function Details [hide private]

get_sidechain_att_atom(residue)

 

Given an amino acide residue 'residue' (must be a schrodinger.structure._Residue object), this function returns a tuple that is composed of two atoms (instances of the schrodinger.structure._StructureAtom class) that are the attachment atoms of the sidechain to the backbone of the given residue.

The first element of the returned tuple is the atom at the backbone, and the 2nd one is the atom at the sidechain.

If the attachment atoms cannot be identified, None is returned.

get_residue_sitename(residue)

 

Given a schrodinger.structure._Residue object ('residue'), this function returns a string that represents the name of the residue site.

The string is in the format C:RESXX[I] where C is the chain name, RES is the residue type name, XX is the residue number in the chain, and I is the insertion code. For example, a string could be "A:Tyr45[B]".

If there is no insertion code, the string will be reduced to C:RESXX, e.g. "A:Tyr45".

delete_ct_property(struc, prop_name)

 

Deletes a property from a set of CTs, and returns the list of mutated CTs.

The CTs are given via the 'struc' argument, which is a list of schrodinger.structure.Structure objects.

Parameters:
  • prop_name (string or list of strings) - The property name or names to be deleted. If a list of names is provided, all of them will be deleted.

read_fep_cms(cms_fname)

 

Reads a .cms file 'cms_fname' and returns a 4-tuple.

The return tuple has the following elements:

  • The first element is the 'full_system' CT or None if the 'full_system' not found in the .cms file.
  • The second element is a list of environment CTs (i.e. CTs without the CT-level property 's_fep_fragname').
  • The third element is a list of reference CTs (i.e., CTs whose 's_fep_fragname' property is 'none'). Normally there is only CT in this list.
  • The fourth element is a list of mutant CTs (i.e., CTs whose 's_fep_fragname' property is NOT 'none'). Normally there is only CT in this list.

read_anni_fep_cms(cms_fname)

 

Reads a .cms file 'cms_fname' and returns a 3-tuple.

The return tuple has the following elements:

  • The first element is the 'full_system' CT or None if the 'full_system' not found in the .cms file.
  • The second element is a list of environment CTs (i.e. CTs without the atom property 'i_ffio_grp_ligand' (or the property value is 0))).
  • The third element is a list of mutant CTs (i.e., CTs whose atom property 'i_ffio_grp_ligand' is nonzero). Normally there is only CT in this list.