schrodinger.application.desmond.fep_struc module¶
Defines a Struc
class as a generic represention of molecular structure
- class schrodinger.application.desmond.fep_struc.Struc¶
Bases:
object
- __init__()¶
- id()¶
Returns the ID of this structure.
- set_id(id)¶
Sets the ID for this structure.
- copy()¶
- extract(indices)¶
Return a new structure object which contains the atoms of the current structure that appear in the specified list.
- title()¶
- set_title(new_title)¶
- heavy_atoms()¶
Returns a list of indices of heavy atoms (viz non-hydrogen atoms).
- is_chiral_atom(atom_index)¶
Returns true if the atom indicated by
atom_index
is chiral; otherwise, false.- Parameters
atom_index (
int
) – Atom index
- chiral_atoms()¶
Returns the indices of the chiral atoms.
- Return type
list
ofint
- Returns
A list of atom indices
- ring_atoms()¶
Returns a set of ring atoms.
- Return type
set
ofint
- Returns
A set of atom indices
- 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
- total_charge()¶
Returns the total charge of the structure.
- 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
- smarts()¶
Returns a SMARTS string of this structure.
- smiles()¶
Returns a SMILES string of this structure.
- 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.
- class schrodinger.application.desmond.fep_struc.SchrodStruc(struc)¶
Bases:
schrodinger.application.desmond.fep_struc.Struc
A
Struc
subclass based on Schrodinger’s infrastructure- __init__(struc)¶
struc
should be aschrodinger.structure.Structure
object.
- copy()¶
Returns a copy of this structure.
- extract(indices)¶
Return a new structure object which contains the atoms of the current structure that appear in the specified list.
- title()¶
Returns the title of this structure. (Normally title’s a user-friendly description)
- set_title(new_title)¶
Sets a new title to this structure.
- heavy_atoms()¶
Returns a list of indices of heavy atoms (viz non-hydrogen atoms).
- is_chiral_atom(atom_index)¶
Returns true if the atom indicated by
atom_index
is chiral; otherwise, false.- Parameters
atom_index (
int
) – Atom index
- chiral_atoms()¶
Returns the indices of the chiral atoms.
- Return type
list
ofint
- Returns
A list of atom indices
- 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.
- Return type
set
ofint
or alist
ofset
ofint
- Returns
A set or a list of sets of atom indices
- 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
- 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.
- total_charge()¶
Returns the formal charge of the structure
- add_hydrogens()¶
Adds hydrogen atoms to this molecule.
- 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
- smarts(atoms=None)¶
Returns a SMARTS string for this structure.
- Parameters
atoms (
list
ofint
) – A list of atom indices
- smiles()¶
Returns a SMILES string for this structure.
- 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”.