Ligand: Ligand Class

In TJGorrie/localXCR: Shiny GUI to annotate Fragalysis/XChem Experiments

Description

Ligand Class

Ligand Class

Details

Describes a single Ligand from fragalysis-api

Public fields

name

Name of the ligand

crystal

Name of the crystal the ligand belongs to

aligned_loc

path of the aligned folder

metadata_filepath

path to the metadata file

crys_loc

path of the crystallographic folder

Active bindings

apo_pdb_file

file path where apo.pdb should exist

mol_file

file path where .mol should exist

twofofc_file

file path where _2fofc.map should exist

fofc_file

file path where _fofc.map should exist

smiles_file

file path where _smiles.txt should exist

smiles_string

The contents of _smiles.txt

event_map_paths

file paths where event maps should reside

first_event_map

returns the first eventmap

metadata

the contents of the metadata

review_file

file path where _review.txt should exist

review

Contents of the review file

status

What is the review status

crys_pdb_file

file path where crystallographic pdb should exist

crys_event_maps

file path where crystallographic event exist

crys_first_event_map

file path of 1st event map

crys_2fofc_map

filepath of 2fofc map

crys_fofc_map

filepath of fofc map

Methods

Public methods

• Ligand$new()

• Ligand$clone()

---

Method new()

Create a new ligand

Usage

Ligand$new(name, base)

Arguments

name

Name of Ligand

base

Directory path containing ligandy goodness

Returns

ligand class!

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Ligand$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## Not run: 
l <- Ligand$new(name = 'Prot-x1234', base = './')

## End(Not run)

TJGorrie/localXCR documentation built on Dec. 18, 2021, 4:01 p.m.