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)
* mol_file * - MOL 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)
* sasa * - set this to 1 to turn on solvent accessible surface area calculation (currently only works across whole trajectory)
* 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__ = "06.2018"
def __init__(self,topology,trajectory,mol_file,ligand,offset,cutoff,start_frame,end_frame,skip,analysis_cutoff,sasa,diagram_type,output_name,cfg):
"""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 = []
if mol_file!=None:
self.mol_file = os.path.abspath(mol_file)
else:
self.mol_file = mol_file
self.ligand = ligand
self.offset = offset
self.cutoff = cutoff
if cfg==False:
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))]
else:
self.start = start_frame
self.end = end_frame
self.skip = skip
self.analysis_cutoff = analysis_cutoff
self.sasa = sasa
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 mol 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.mol_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.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):
"""
The classes and function that deal with protein-ligand interaction analysis.
"""
self.hbonds = HBonds(self.topol_data,self.trajectory,self.start,self.end,self.skip,self.analysis_cutoff,distance=3)
self.pistacking = PiStacking(self.topol_data,self.trajectory,self.start,self.end,self.skip, self.analysis_cutoff)
if self.sasa==1:
self.sasa = SASA(self.topol_data,self.trajectory)
self.lig_descr = LigDescr(self.topol_data)
if self.trajectory!=[]:
self.rmsf = RMSF_measurements(self.topol_data,self.topology,self.trajectory,self.ligand,self.start,self.end,self.skip)
self.salt_bridges = SaltBridges(self.topol_data,self.trajectory,self.lig_descr,self.start,self.end,self.skip,self.analysis_cutoff)
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,data_for_color=None, data_for_size=None, data_for_clouds=None, rot_bonds=None, color_for_clouds="Blues", color_type_color="viridis"):
"""
Draws molecule through Molecule() and then puts the final figure together with
Figure().
"""
self.molecule = Molecule(self.topol_data)
self.draw = Draw(self.topol_data,self.molecule,self.hbonds,self.pistacking,self.salt_bridges,self.lig_descr)
self.draw.draw_molecule(data_for_color, data_for_size, data_for_clouds, rot_bonds, color_for_clouds, color_type_color)
self.figure = Figure(self.molecule,self.topol_data,self.draw)
self.figure.add_bigger_box()
self.figure.manage_the_plots()
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."""
while True:
try:
os.mkdir(self.output_name)
except Exception as e:
self.output_name = raw_input("This directory already exists - please enter a new name:")
else:
break
self.workdir = os.getcwd()
os.chdir(self.workdir+"/"+self.output_name)
def write_config_file(self, cfg):
if cfg!=None:
#copy the config file to results directory
shutil.copy("../"+cfg, "lintools.config")
else:
#If there was no config file, write one
cfg_dir = {'input':{
'topology':self.topology,
'trajectory':self.trajectory,
'mol file':self.mol_file,
'ligand':self.ligand,
'traj start':self.start,
'traj end':self.end,
'traj skip': self.skip,
'offset': self.offset,
'distance cutoff': self.cutoff,
'analysis cutoff': self.analysis_cutoff,
'sasa': self.sasa,
'diagram type': self.diagram_type,
'output name': self.output_name},
'representation':{
'data to show in color':None,
'data to show as size':None,
'data to show as cloud':None,
'rotatable bonds':None,
'cloud color scheme':'Blues',
'atom color scheme':'viridis',
'clock color scheme':'summer'}
}
with open("lintools.config","wb") as ymlfile:
yaml.dump(cfg_dir,ymlfile,default_flow_style=False)
def remove_files(self):
"""Removes intermediate files."""
file_list = ["molecule.svg","lig.pdb","HIS.pdb","PHE.pdb","TRP.pdb","TYR.pdb","lig.mol","test.xtc"]
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)
class Lintools(object):
def __init__(self, topology, trajectory, ligand_name, offset, cutoff,
analysis_cutoff, diagram_type, domain_file, HB_flag,
RMSF_flag, debug_flag, resinfo_flag, mol2_file, output_name):
self.topology = os.path.abspath(topology)
try:
self.trajectory = []
for traj in trajectory:
self.trajectory.append(os.path.abspath(traj))
except Exception:
self.trajectory = trajectory
self.ligand_name = ligand_name
self.offset = offset
self.cutoff = cutoff
self.analysis_cutoff = analysis_cutoff
self.diagram_type = diagram_type
try:
self.domain_file = os.path.abspath(domain_file)
except Exception:
self.domain_file = domain_file
self.HB_flag = HB_flag
self.RMSF_flag = RMSF_flag
self.debug_flag = debug_flag
self.resinfo_flag = resinfo_flag
try:
self.mol2_file = os.path.abspath(mol2_file)
except Exception:
self.mol2_file = mol2_file
self.output_name = output_name
self.rmsf = None
self.hbonds = None
def get_info_about_input_and_analyse(self):
"""This function loads all input files and decides which residues to plot"""
self.topol_data = Topol_Data(self.topology, self.trajectory,
self.ligand_name, self.offset,
self.mol2_file)
self.topol_data.define_ligand(self.ligand_name, self.mol2_file)
if self.trajectory == None:
self.topol_data.find_res_to_plot(self.cutoff)
else:
self.occurrence = Occurrence_analysis(self.topology,
self.trajectory,
self.ligand_name,
self.cutoff, self.offset,
self.topol_data)
self.occurrence.get_closest_residues(self.analysis_cutoff)
if self.HB_flag != True:
self.hbonds = HBonds(self.topol_data, self.topology,
self.trajectory, self.ligand_name,
self.offset, self.analysis_cutoff)
self.topol_data.get_closest_ligand_atoms(self.hbonds)
else:
self.topol_data.get_closest_ligand_atoms()
if self.RMSF_flag == True:
self.rmsf = RMSF_measurements(self.topol_data, self.topology,
self.trajectory, self.ligand_name,
self.offset, self.output_name)
def plot_residues(self):
self.plots = Plots(self.topol_data)
if self.diagram_type == "amino":
self.plots.define_amino_acids()
self.plots.plot_amino_diagramms()
if self.diagram_type == "domains":
assert len(self.domain_file) > 0, "Provide a file defining domains"
self.plots.define_domains(self.domain_file, self.offset)
self.plots.plot_domains_diagramms()
if self.diagram_type == "clock":
self.plots.plot_clock_diagramms()
def draw_molecule_and_figure(self, tests=False):
self.molecule = Molecule(self.topol_data, self.rmsf)
self.figure = Figure(self.molecule, self.diagram_type, self.topol_data,
self.hbonds, self.plots, self.rmsf, tests)
if self.HB_flag != True:
self.figure.draw_hbonds_in_graph(self.diagram_type)
self.figure.draw_white_circles_at_atoms(self.diagram_type)
if self.debug_flag == True:
self.figure.draw_lines_in_graph(
) #a function for debugging purposes
self.figure.put_everything_together()
self.figure.write_final_draw_file(self.output_name)
if self.trajectory != None and self.resinfo_flag != True:
self.res_info = Residue_Info(self.topol_data, self.occurrence,
self.figure)
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):
file_list = [
"molecule.svg", "LIG.pdb", "test.xtc", "rmsf_colorbar.svg"
]
for residue in self.topol_data.dict_of_plotted_res.keys():
file_list.append(str(residue[3:]) + ".svg")
for f in file_list:
if os.path.isfile(f) == True:
os.remove(f)
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)
* mol_file * - MOL 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, mol_file, ligand, offset, cutoff,
start_frame, end_frame, skip, analysis_cutoff, diagram_type,
output_name, cfg):
"""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 = []
if mol_file != None:
self.mol_file = os.path.abspath(mol_file)
else:
self.mol_file = mol_file
self.ligand = ligand
self.offset = offset
self.cutoff = cutoff
if cfg == False:
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))
]
else:
self.start = start_frame
self.end = end_frame
self.skip = skip
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 mol 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.mol_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.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):
"""
The classes and function that deal with protein-ligand interaction analysis.
"""
self.hbonds = HBonds(self.topol_data,
self.trajectory,
self.start,
self.end,
self.skip,
self.analysis_cutoff,
distance=3)
self.pistacking = PiStacking(self.topol_data, self.trajectory,
self.start, self.end, self.skip,
self.analysis_cutoff)
self.sasa = SASA(self.topol_data, self.trajectory)
self.lig_descr = LigDescr(self.topol_data)
if self.trajectory != []:
self.rmsf = RMSF_measurements(self.topol_data, self.topology,
self.trajectory, self.ligand,
self.start, self.end, self.skip)
self.salt_bridges = SaltBridges(self.topol_data, self.trajectory,
self.lig_descr, self.start, self.end,
self.skip, self.analysis_cutoff)
def plot_residues(self, colormap):
"""
Calls Plot() that plots the residues with the required diagram_type.
"""
self.plots = Plots(self.topol_data, self.diagram_type, colormap)
def draw_figure(self,
data_for_color=None,
data_for_size=None,
data_for_clouds=None,
rot_bonds=None,
color_for_clouds="Blues",
color_type_color="viridis"):
"""
Draws molecule through Molecule() and then puts the final figure together with
Figure().
"""
self.molecule = Molecule(self.topol_data)
self.draw = Draw(self.topol_data, self.molecule, self.hbonds,
self.pistacking, self.salt_bridges, self.lig_descr)
self.draw.draw_molecule(data_for_color, data_for_size, data_for_clouds,
rot_bonds, color_for_clouds, color_type_color)
self.figure = Figure(self.molecule, self.topol_data, self.draw)
self.figure.add_bigger_box()
self.figure.manage_the_plots()
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."""
while True:
try:
os.mkdir(self.output_name)
except Exception as e:
self.output_name = raw_input(
"This directory already exists - please enter a new name:")
else:
break
self.workdir = os.getcwd()
os.chdir(self.workdir + "/" + self.output_name)
def write_config_file(self, cfg):
if cfg != None:
#copy the config file to results directory
shutil.copy("../" + cfg, "lintools.config")
else:
#If there was no config file, write one
cfg_dir = {
'input': {
'topology': self.topology,
'trajectory': self.trajectory,
'mol file': self.mol_file,
'ligand': self.ligand,
'traj start': self.start,
'traj end': self.end,
'traj skip': self.skip,
'offset': self.offset,
'distance cutoff': self.cutoff,
'analysis cutoff': self.analysis_cutoff,
'diagram type': self.diagram_type,
'output name': self.output_name
},
'representation': {
'data to show in color': None,
'data to show as size': None,
'data to show as cloud': None,
'rotatable bonds': None,
'cloud color scheme': 'Blues',
'atom color scheme': 'viridis',
'clock color scheme': 'summer'
}
}
with open("lintools.config", "wb") as ymlfile:
yaml.dump(cfg_dir, ymlfile, default_flow_style=False)
def remove_files(self):
"""Removes intermediate files."""
file_list = [
"molecule.svg", "lig.pdb", "HIS.pdb", "PHE.pdb", "TRP.pdb",
"TYR.pdb", "lig.mol", "test.xtc"
]
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)
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)