def parameter_antigen_experiment(experiment, dockingGroups, fileNames):
""" Prepare the antigens for use in OptMAVEn
Modify the residue permisson and parameter them
Output all the information to a "Antigen.txt"
"""
# Loop through the docking groups
for dockingGroup in dockingGroups:
# Go through each molecule
for molID in dockingGroup:
# Get that Molecule
molecule = experiment[molID[0]][molID[1]]
# Modify its Residues' permissions so that all Atoms will be output
for residue in molecule:
residue.permission = "FIXED"
#Parameterize the Molecule
ROTAMERS.parameterize(molecule, experiment)
# Get the energy calculation - ready text
contents = format(molecule, "energy")
# Put those contents in a file
#fileName = "Antigen_" + str(molID[0] + str(molID[1]) + ".txt"
fileName = "Antigen.txt"
f = open(fileName, "a")
f.write(contents)
f.close()
# Store that file name so it can be deleted later
fileNames.append(fileName)
def appropriateness(experiment, nonbonded = True):
"""Check for force field and implicit solvation information validity"""
# Make a list of the Molecules
molecules = []
for data in experiment["Molecules"]:
# This shouldn't be the case, but the function is being written so it
# can be used as a generic checker, in which case "Molecules" would just
# be a list of Molecules
if isinstance(data, MOLECULES.Molecule):
molecules.append(data)
# the normal format is a list with the 3rd entry being a Molecule
else:
molecules.append(data[2])
# Add missing Atoms, depending on the Force Field
if experiment["Force Field"] == "CHARMM":
try:
CHARMM.Missing_Atoms(molecules, experiment)
except CHARMM.CHARMM_Error as error:
text = "There was an error when CHARMM was tested:\n" + str(error)
raise ExperimentError(text)
# If the force field isn't supported
else:
text = "The " + str(experiment["Force Field"]) + " is not supported by "
text += "the appropriateness function"
raise ExperimentError(text)
# Try to parameterize the system
if nonbonded:
try:
ROTAMERS.parameterize(molecules, experiment)
except ROTAMERS.RotamerError as error:
text = "There was an error when attempting to assign non-bonded "
text += "energy parameters:\n" + str(error)
raise ExperimentError(text)
# Return the list of Molecule structures
return molecules
def appropriateness(experiment, nonbonded=True, isOptcdr=False):
"""Check for force field and implicit solvation information validity"""
# Make a list of the Molecules
molecules = []
for data in experiment["Molecules"]:
# This shouldn't be the case, but the function is being written so it
# can be used as a generic checker, in which case "Molecules" would just
# be a list of Molecules
if isinstance(data, MOLECULES.Molecule):
molecules.append(data)
# the normal format is a list with the 3rd entry being a Molecule
else:
molecules.append(data[2])
# Repeat the procedure for the framework molecules if the procedure is
# OptCDR
if isOptcdr:
# Make a list of the Molecules
frameworks = []
# Check information for the light and heavy chains
for chain in ['light', 'heavy']:
# Determine if a framework for this chain was specified
if chain in experiment["Optcdr Frameworks"]:
for data in experiment["Optcdr Frameworks"][chain]:
# Check for a list of Molecules
if isinstance(data, MOLECULES.Molecule):
frameworks.append(data)
# Otherwise choose the 3rd element from the list, which is a
# Molecule
else:
frameworks.append(data[2])
# Add the framework Molecules to the existing Molecules
molecules.extend(frameworks)
# Add missing Atoms, depending on the Force Field
if experiment["Force Field"] == "CHARMM":
try:
CHARMM.Missing_Atoms(molecules, experiment)
except CHARMM.CHARMM_Error as error:
text = "There was an error when CHARMM was tested:\n" + str(error)
raise ExperimentError(text)
# If the force field isn't supported
else:
text = "The " + str(
experiment["Force Field"]) + " is not supported by "
text += "the appropriateness function"
raise ExperimentError(text)
# Try to parameterize the system
if nonbonded:
try:
ROTAMERS.parameterize(molecules, experiment)
except ROTAMERS.RotamerError as error:
text = "There was an error when attempting to assign non-bonded "
text += "energy parameters:\n" + str(error)
raise ExperimentError(text)
# Return the list of Molecule structures if this is the standard use of the
# function
if not isOptcdr:
return molecules
# Otherwise return the framework Molecule structures
else:
return frameworks
def create_static_structures(experiment, movingMolecules, fileNames):
"""Create the structures that don't move during docking."""
# First, determine what Design Groups have structures that move during
# docking
designNumbers = []
for molID in movingMolecules:
if molID[0] not in designNumbers:
designNumbers.append(molID[0])
# Assemble the constant portions of each of those complexes
for gn in designNumbers:
# Store the contents of all of the Molecules in this list
contents = ''
# Loop through the Molecules in this Design Group
for molecule in experiment[gn]:
# If this Molecule moves during docking, don't consider it
if [gn, molecule.name] in movingMolecules:
continue
# Set each Residue's permission to FIXED so all atoms are output
for residue in molecule:
residue.permission = "FIXED"
# Parameterize the Molecule
ROTAMERS.parameterize(molecule, experiment)
# Add its contents to contents
contents += format(molecule, "energy")
# Write these contents to a file, even if they're empty
fileName = "constant" + str(gn) + ".txt"
f = open(fileName, "w")
f.write(contents)
f.close()
# Store the file name so it can be deleted later
fileNames.append(fileName)
def create_moving_structures(experiment, dockingGroups, fileNames):
"""Create the structures that move during docking."""
# Start creating the docking_information.txt file's data with this string
information = str(len(dockingGroups)) + "\n"
# Store each molecule that moves during docking in this list
movingMolecules = []
# Loop through the docking groups
for dockingGroup in dockingGroups:
# Inlcude the number of Molecules in this docking group
information += str(len(dockingGroup)) + "\n"
# Go through each molecule
for molID in dockingGroup:
# Get that Molecule
molecule = experiment[molID[0]][molID[1]]
# Modify its Residues' permissions so that all Atoms will be output
for residue in molecule:
residue.permission = "FIXED"
# Parameterize the Molecule
ROTAMERS.parameterize(molecule, experiment)
# Get the energy calculation - ready text
contents = format(molecule, "energy")
# Put those contents in a file
fileName = "docking_" + str(molID[0]) + str(molID[1]) + ".txt"
f = open(fileName, "w")
f.write(contents)
f.close()
# Store that file name so it can be deleted later
fileNames.append(fileName)
# Store this Molecule in the moving Molecules list
movingMolecules.append(molID)
# Update information with data about this Molecule
information += fileName + " " + str(molID[0]) + "\n"
# Return what needs to be returned
return information, movingMolecules
def create_static_structures(experiment, movingMolecules, fileNames):
"""Create the structures that don't move during docking."""
# First, determine what Design Groups have structures that move during
# docking
designNumbers = []
for molID in movingMolecules:
if molID[0] not in designNumbers:
designNumbers.append(molID[0])
# Assemble the constant portions of each of those complexes
for gn in designNumbers:
# Store the contents of all of the Molecules in this list
contents = ''
# Loop through the Molecules in this Design Group
for molecule in experiment[gn]:
# If this Molecule moves during docking, don't consider it
if [gn, molecule.name] in movingMolecules:
continue
# Set each Residue's permission to FIXED so all atoms are output
for residue in molecule:
residue.permission = "FIXED"
# Parameterize the Molecule
ROTAMERS.parameterize(molecule, experiment)
# Add its contents to contents
contents += format(molecule, "energy")
# Write these contents to a file, even if they're empty
fileName = "constant" + str(gn) + ".txt"
f = open(fileName, "w")
f.write(contents)
f.close()
# Store the file name so it can be deleted later
fileNames.append(fileName)
def create_moving_structures(experiment, dockingGroups, fileNames):
"""Create the structures that move during docking."""
# Start creating the docking_information.txt file's data with this string
information = str(len(dockingGroups)) + "\n"
# Store each molecule that moves during docking in this list
movingMolecules = []
# Loop through the docking groups
for dockingGroup in dockingGroups:
# Inlcude the number of Molecules in this docking group
information += str(len(dockingGroup)) + "\n"
# Go through each molecule
for molID in dockingGroup:
# Get that Molecule
molecule = experiment[molID[0]][molID[1]]
# Modify its Residues' permissions so that all Atoms will be output
for residue in molecule:
residue.permission = "FIXED"
# Parameterize the Molecule
ROTAMERS.parameterize(molecule, experiment)
# Get the energy calculation - ready text
contents = format(molecule, "energy")
# Put those contents in a file
fileName = "docking_" + str(molID[0]) + str(molID[1]) + ".txt"
f = open(fileName, "w")
f.write(contents)
f.close()
# Store that file name so it can be deleted later
fileNames.append(fileName)
# Store this Molecule in the moving Molecules list
movingMolecules.append(molID)
# Update information with data about this Molecule
information += fileName + " " + str(molID[0]) + "\n"
# Return what needs to be returned
return information, movingMolecules
def parameter_output_antigen_normal(antigen, outFile="Antigen.txt"):
""" Parameter the antigen molecule and output the antigen to the Antigen.txt """
#Missing_Atoms(antigen)
for residue in antigen:
#residue.permission = "FIXED"
ROTAMERS.parameterize_Residue(residue)
# Get the energy calculation - ready text
contents = format(antigen, "energy")
# Put those contents in a file
#outFile = "Antigen.txt"
f = open(outFile, "w")
f.write(contents)
f.close()
def distance_setting(experiment, group):
"""Modify Residue freedoms and permissions based on distances"""
# Only do this if the packing method is 'Distance'
if experiment["Packing Method"] == "Distance":
# Make a list of the Residue freedoms that are acceptable
freedoms = ["RESTRAINED"]
if experiment["Packing Selection"] == "FREE":
freedoms.append("FREE")
# Get all of the heavy Atoms in the docking selection
atoms = []
for molecule in group:
for residue in molecule:
if residue.freedom in freedoms:
for atom in residue:
if not ROTAMERS.is_hydrogen(atom):
atoms.append(atom)
# Modify permissions in Design Molecules
for molecule in group:
if not molecule.design:
continue
for residue in molecule:
# If the Residue already has settings, skip it
if residue.freedom != "FIXED":
continue
# Determine if it is sufficiently close
close = False
for atom in residue:
# Only consider heavy atoms
if ROTAMERS.is_hydrogen(atom):
continue
for atom2 in atoms:
dis = MOLECULES.calculate_distance(atom, atom2)
if dis <= experiment["Packing Cutoff"]:
close = True
break
if close:
break
# If the Residue is close to the Packing selection, repack it
if close:
residue.freedom = "FREE"
residue.permission = "ISOMER"
def appropriateness(experiment, nonbonded=True):
"""Check for force field and implicit solvation information validity"""
# Make a list of the Molecules
molecules = []
for data in experiment["Molecules"]:
# This shouldn't be the case, but the function is being written so it
# can be used as a generic checker, in which case "Molecules" would just
# be a list of Molecules
if isinstance(data, MOLECULES.Molecule):
molecules.append(data)
# the normal format is a list with the 3rd entry being a Molecule
else:
molecules.append(data[2])
# Add missing Atoms, depending on the Force Field
if experiment["Force Field"] == "CHARMM":
try:
CHARMM.Missing_Atoms(molecules, experiment)
except CHARMM.CHARMM_Error as error:
text = "There was an error when CHARMM was tested:\n" + str(error)
raise ExperimentError(text)
# If the force field isn't supported
else:
text = "The " + str(
experiment["Force Field"]) + " is not supported by "
text += "the appropriateness function"
raise ExperimentError(text)
# Try to parameterize the system
if nonbonded:
try:
ROTAMERS.parameterize(molecules, experiment)
except ROTAMERS.RotamerError as error:
text = "There was an error when attempting to assign non-bonded "
text += "energy parameters:\n" + str(error)
raise ExperimentError(text)
# Return the list of Molecule structures
return molecules
def prepare_MAPs_parts(experiment={}):
"""Get the MAPs parts ready for use in OptMAVEn"""
# Determine which domains to use
domains = []
if "OptMAVEn Domains" not in experiment:
domains.extend(["H", "K", "L"])
else:
if "Heavy" in experiment["OptMAVEn Domains"]:
domains.append("H")
if "Light" in experiment["OptMAVEn Domains"]:
domains.extend(["K", "L"])
# Store the names of the files made by this function
fileNames = []
# Write out the types of domains being designed
text = ''
for d in domains:
text += d + " "
f = open("domains.txt", "w")
f.write(text[:-1])
f.close()
fileNames.append("domains.txt")
# Get file format and force field information
if "Force Field" in experiment:
ff1 = experiment["Force Field"]
else:
ff1 = defaultField
if "File Format" in experiment:
ff2 = experiment["File Format"]
else:
ff2 = defaultFormat
# Go through those domains and the regions of structure
for D in domains:
for R in ["V", "CDR3", "J"]:
# Store the text of the formatted structures here
text = ''
# Access the MAPs parts
path = InstallFolder + "databases/MAPs/" + D + R + "/"
# Loop through possible number options
for i in range(1, 501):
name = path + D + R + "_" + str(i) + ".pdb"
try:
f = open(name, "r")
except IOError:
# If the file couldn't be opened, we're out of parts
break
# Read in the part
lines = f.readlines()
f.close()
# Make a Molecule out of it
part = MOLECULES.Molecule(lines, None, None, D, True, ff1, ff2)
# parameterize the part
ROTAMERS.parameterize(part, experiment)
# Modify its parameters
modify_parameters(part)
# Get the formatted text, listing the rotamer number as i
for residue in part:
text += format(residue, "all - " + str(i))
# Write the formatted text of this file to a folder
f = open(D + R + ".txt", "w")
f.write(text)
f.close()
# Store the file name
fileNames.append(D + R + ".txt")
# Return the names of the files
return fileNames