class Lintools(object):
"""This class controls the behaviour of all other classes (Data,Plots,Molecule,Figure)
of lintools and inherits and transfers them resulting in a final SVG file that contains
the protein-ligand interactions.
It also controls the analysis (Residence_time and HBonds classes).
Takes:
* topology * - topology file
* trajectory * - trajectory file(s)
* mol2_file * - MOL2 file of the ligand
* ligand * - MDAnalysis atomgroup of ligand that is going to be analysed
* offset * - residue offset which determines by how many numbers the protein residue numbering
should be offset (e.g. with offset = 30 the first residue will be changed from 1 to 30, 2 - 31, etc.)
* cutoff * - cutoff distance in angstroms that defines the native contacts (default - 3.5A)
* start_frame * - start frame(s) for trajectory analysis (can be different for each trajectory)
* end_frame * - end frame(s) for trajectory analysis (can be different for each trajectory)
* skip * - number of frames to skip (can be different for each trajectory)
* analysis_cutoff * - a fraction of time a residue has to fullfil the analysis parameters for (default - 0.3)
* diagram_type * - string of the selected diagram type (e.g. "amino" or "clocks")
* output_name * - name of the folder with results and the final SVG file
"""
__version__ = "09.2016"
def __init__(self, topology, trajectory, mol2_file, ligand, offset, cutoff,
start_frame, end_frame, skip, analysis_cutoff, diagram_type,
output_name):
"""Defines the input variables."""
self.topology = os.path.abspath(topology)
try:
self.trajectory = []
for traj in trajectory:
self.trajectory.append(os.path.abspath(traj))
except Exception:
self.trajectory = []
self.mol2_file = os.path.abspath(mol2_file)
self.ligand = ligand
self.offset = offset
self.cutoff = cutoff
self.start = [
None if start_frame == [None] else int(start_frame[i])
for i in range(len(trajectory))
]
self.end = [
None if end_frame == [None] else int(end_frame[i])
for i in range(len(trajectory))
]
self.skip = [
None if skip == [None] else int(skip[i])
for i in range(len(trajectory))
]
self.analysis_cutoff = analysis_cutoff
self.diagram_type = diagram_type
self.output_name = output_name
def data_input_and_res_time_analysis(self):
"""
Loads the data into Data() - renumbers the residues, imports mol2 file in rdkit.
If there are trajectories to analyse, the residues that will be plotted are determined
from Residence_time() analysis.
"""
self.topol_data = Data()
self.topol_data.load_data(self.topology, self.mol2_file, self.ligand,
self.offset)
if len(self.trajectory) == 0:
self.topol_data.analyse_topology(self.topology, self.cutoff)
else:
self.res_time = Residence_time(self.topol_data, self.trajectory,
self.start, self.end, self.skip,
self.topology, self.mol2_file,
self.ligand, self.offset)
self.res_time.measure_residence_time(self.cutoff)
self.res_time.define_residues_for_plotting_traj(
self.analysis_cutoff)
self.topol_data.find_the_closest_atoms(self.topology)
def analysis_of_prot_lig_interactions(self, hydr_bonds):
"""
The classes and function that deal with protein-ligand interaction analysis.
"""
if hydr_bonds != True:
self.hbonds = HBonds(self.topol_data,
self.trajectory,
self.start,
self.end,
self.skip,
self.analysis_cutoff,
distance=3)
else:
self.hbonds = None
def plot_residues(self):
"""
Calls Plot() that plots the residues with the required diagram_type.
"""
self.plots = Plots(self.topol_data, self.diagram_type)
def draw_figure(self):
"""
Draws molecule through Molecule() and then puts the final figure together with
Figure().
"""
self.molecule = Molecule(self.topol_data)
self.figure = Figure(self.molecule, self.topol_data, self.hbonds)
self.figure.add_bigger_box()
self.figure.manage_the_plots()
self.figure.draw_hydrogen_bonds()
self.figure.draw_white_circles()
self.figure.put_everything_together()
self.figure.write_final_draw_file(self.output_name)
def save_files(self):
"""Saves all output from LINTools run in a single directory named after the output name."""
os.system("mkdir " + self.output_name)
self.workdir = os.getcwd()
os.chdir(self.workdir + "/" + self.output_name)
def remove_files(self):
"""Removes intermediate files."""
file_list = ["molecule.svg", "LIG.pdb"]
for residue in self.topol_data.dict_of_plotted_res.keys():
file_list.append(residue[1] + residue[2] + ".svg")
for f in file_list:
if os.path.isfile(f) == True:
os.remove(f)
