schrodinger.application.desmond.fep_struc module¶
Defines a `Struc’ class as a generic represention of molecular structure
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class
schrodinger.application.desmond.fep_struc.
Struc
¶ Bases:
object
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__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
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id
()¶ Returns the ID of this structure.
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set_id
(id)¶ Sets the ID for this structure.
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copy
()¶
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extract
(indices)¶ Return a new structure object which contains the atoms of the current structure that appear in the specified list.
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title
()¶
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set_title
(new_title)¶
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heavy_atoms
()¶ Returns a list of indices of heavy atoms (viz non-hydrogen atoms).
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is_chiral_atom
(atom_index)¶ Returns true if the atom indicated by
atom_index
is chiral; otherwise, false.- Parameters
atom_index (
int
) – Atom index
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chiral_atoms
()¶ Returns the indices of the chiral atoms.
- Return type
list
ofint
- Returns
A list of atom indices
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ring_atoms
()¶ Returns a set of ring atoms.
- Return type
set
ofint
- Returns
A set of atom indices
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bonded_atoms
(atom_index)¶ Returns a list of atom indices of atoms bonded to the indicated atom.
- Parameters
atom_index (
int
) – A single index or a list of indices of the atoms to be deleted- Return type
list
ofint
- Returns
A list of atom indices of atoms bonded to the indicated atom
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total_charge
()¶ Returns the total charge of the structure.
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delete_atom
(atom_index)¶ Deletes a atom.
- Parameters
atom_index (
int
orlist
ofint
) – A single index or a list of indices of the atoms to be deleted
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smarts
()¶ Returns a SMARTS string of this structure.
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smiles
()¶ Returns a SMILES string of this structure.
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write
(format, mode='a')¶ Writes this structure into a file in the designated format.
- Parameters
mode (
char
, ‘a’ | ‘w’) – When a file of the same name exists, this determines whether to overwrite (‘w’) or append (‘a’) to the file.
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class
schrodinger.application.desmond.fep_struc.
SchrodStruc
(struc)¶ Bases:
schrodinger.application.desmond.fep_struc.Struc
A `Struc’ subclass based on Schrodinger’s infrastructure
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copy
()¶ Returns a copy of this structure.
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extract
(indices)¶ Return a new structure object which contains the atoms of the current structure that appear in the specified list.
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title
()¶ Returns the title of this structure. (Normally title’s a user-friendly description)
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set_title
(new_title)¶ Sets a new title to this structure.
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heavy_atoms
()¶ Returns a list of indices of heavy atoms (viz non-hydrogen atoms).
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is_chiral_atom
(atom_index)¶ Returns true if the atom indicated by
atom_index
is chiral; otherwise, false.- Parameters
atom_index (
int
) – Atom index
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chiral_atoms
()¶ Returns the indices of the chiral atoms.
- Return type
list
ofint
- Returns
A list of atom indices
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ring_atoms
(aromaticity=0, group=False)¶ Returns ring atoms.
- Parameters
aromaticity (
int
-1, 0, 1) – -1 = non-aromatic, 0 = all, 1 = aromatic. Make the function return the specified type of ring atoms.group (
bool
) – If true, returns a list ofset
objects, each of which is a set of indices of atoms in the same ring; otherwise, returns a single set containing indices of all selected ring atoms.
:rtype :
set
ofint
or alist
ofset
ofint
:return : A set or a list of sets of atom indices
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bonded_atoms
(atom_index)¶ Returns a list of atom indices of atoms bonded to the indicated atom.
- Parameters
atom_index (
int
) – A single index or a list of indices of the atoms to be deleted- Return type
list
ofint
- Returns
A list of atom indices of atoms bonded to the indicated atom
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molecules
()¶ Returns a list of atom lists. Each element list is a list of atoms of a molecule in the structure. The first element in the returned list belongs to the biggest molecule.
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total_charge
()¶ Returns the formal charge of the structure
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add_hydrogens
()¶ Adds hydrogen atoms to this molecule.
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delete_atom
(atom_index)¶ Deletes a atom.
- Parameters
atom_index (
int
orlist
ofint
) – A single index or a list of indices of the atoms to be deleted
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smarts
(atoms=None)¶ Returns a SMARTS string for this structure.
- Parameters
atoms (
list
ofint
) – A list of atom indices
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smiles
()¶ Returns a SMILES string for this structure.
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write
(filename, format=None, mode='a', cil=False)¶ Writes this structure into a file in the designated format.
- Parameters
format (
str
orNone
) – If its value isNone
, the file format is determined from the filename suffix. If specified, it must be one of the following case-sensitive strings: “pdb”, “mol2”, “sd”, “maestro”, “smiles”, and “smilescsv”.
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id
()¶ Returns the ID of this structure.
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set_id
(id)¶ Sets the ID for this structure.
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