def load_mem_pose(filename, opm_filename, params_paths=None):
with pymol2.PyMOL() as pymol:
# pymol.cmd.load('SLC38A3_phyre.pdb', 'S38A3')
pymol.cmd.load(filename, 'S38A3')
# pymol.cmd.remove('resi 1-68 or resi 245-282 or resi 494-504')
# pymol.cmd.remove('resi 138-207 or resi 318-392')
map_pdbblock = pymol.cmd.get_pdbstr()
pymol.cmd.load(opm_filename, 'OPM')
pymol.cmd.align('S38A3', 'OPM')
pymol.cmd.remove('resn MEM') # make sure its not there!
pymol.cmd.delete('OPM')
holo_pdbblock = pymol.cmd.get_pdbstr('polymer')
lig_pdbblock = pymol.cmd.get_pdbstr('not polymer')
# pymol.cmd.save('test.pdb')
pose = pyrosetta.Pose()
if params_paths:
pyrosetta.generate_nonstandard_residue_set(pose, params_paths)
# pyrosetta.rosetta.core.import_pose.pose_from_file(pose, 'phyre.gln_Na.PO4.loop_r.pdb')
pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(pose, holo_pdbblock)
addmem = pyrosetta.rosetta.protocols.membrane.AddMembraneMover(
'from_structure')
addmem.apply(pose)
pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder().apply(pose)
ligpose = pyrosetta.Pose()
pyrosetta.generate_nonstandard_residue_set(ligpose, params_paths)
# pyrosetta.rosetta.core.import_pose.pose_from_file(pose, 'phyre.gln_Na.PO4.loop_r.pdb')
pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(
ligpose, lig_pdbblock)
pose.append_pose_by_jump(ligpose, pose.total_residue())
return pose
def score_ligand_alone(self):
pose = pyrosetta.Pose()
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend(
[f'{self.work_path}/{self.name}/{self.name}.params'])
pyrosetta.generate_nonstandard_residue_set(pose, params_paths)
pyrosetta.rosetta.core.import_pose.pose_from_file(
pose, f'{self.work_path}/{self.name}/{self.name}.pdb')
return pyrosetta.get_fa_scorefxn()(pose)
def make_pose(self, pdbblock) -> pyrosetta.Pose:
pose = pyrosetta.Pose()
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend(
[f"{self.work_path}/{self.name}/{self.name}.params"])
pyrosetta.generate_nonstandard_residue_set(pose, params_paths)
pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(pose, pdbblock)
# fix protonation of HIS41.
r = pose.pdb_info().pdb2pose(res=41, chain='A')
MutateResidue = pyrosetta.rosetta.protocols.simple_moves.MutateResidue
MutateResidue(target=r, new_res='HIS_D').apply(pose)
MutateResidue(target=r, new_res='HIS').apply(pose)
return pose
def _load_pose_from_file(cls, filename: str, params_filenames: Optional[List[str]] = None) -> pyrosetta.Pose:
"""
Loads a pose from filename with the params in the params_folder
:param filename:
:param params_filenames:
:return:
"""
pose = pyrosetta.Pose()
if params_filenames:
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend(params_filenames)
pyrosetta.generate_nonstandard_residue_set(pose, params_paths)
pyrosetta.rosetta.core.import_pose.pose_from_file(pose, filename)
return pose
def from_pdbblock(cls,
pdbblock: str,
params_file: str,
constraint_file: str,
ligand_residue: Union[str, int, Tuple[int, str], pyrosetta.Vector1] = 'LIG',
key_residues: Union[None, Sequence[Union[int, str, Tuple[int, str]]], pyrosetta.Vector1] = None):
pose = pyrosetta.Pose()
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend([params_file])
pyrosetta.generate_nonstandard_residue_set(pose, params_paths)
pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(pose, pdbblock)
return cls(pose, constraint_file, ligand_residue, key_residues)
def params_to_pose(paramsfile: str, name: str) -> pyrosetta.Pose:
"""
Staticmethod to get a pose from a params file.
:param paramsfile: params file.
:param name: 3-letter residue name.
:return:
"""
pose = pyrosetta.rosetta.core.pose.Pose()
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend([paramsfile])
resiset = pyrosetta.generate_nonstandard_residue_set(
pose, params_paths)
## This is the most convoluted way of getting it. But I don't known any otherway.
v = pyrosetta.rosetta.core.chemical.ResidueTypeFinder(
resiset).get_all_possible_residue_types()
ligtype = [vv for vv in v if vv.name3() == name][0]
lig = pyrosetta.rosetta.core.conformation.ResidueFactory.create_residue(
ligtype)
pose.append_residue_by_jump(lig, 1)
cycles = 15
scorefxn = pyrosetta.get_fa_scorefxn()
relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, cycles)
relax.apply(pose)
return pose
def from_pdbfile(cls,
pdbfile: str,
params_file: str,
constraint_file: str,
ligand_residue: Union[str, int, Tuple[int, str], pyrosetta.Vector1] = 'LIG',
key_residues: Union[None, Sequence[Union[int, str, Tuple[int, str]]], pyrosetta.Vector1] = None):
"""
Given a PDB with the ligand load it.
:param pdbfile: pdb file
:param params_file: params file
:param constraint_file: filename
:param ligand_residue: ligand -see class docstring
:param key_residues: multiple entries -see class docstring
:return:
"""
pose = pyrosetta.Pose()
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend([params_file])
pyrosetta.generate_nonstandard_residue_set(pose, params_paths)
pyrosetta.rosetta.core.import_pose.pose_from_file(pose, pdbfile)
return cls(pose, constraint_file, ligand_residue, key_residues)
def pose_from_file(pdb_filename: str,
params_filenames: Optional[Union[pyrosetta.rosetta.utility.vector1_string, List[str]]] = None) \
-> pyrosetta.Pose:
"""
Return a pose like pose_from_file but with params.
:param pdb_filename:
:param params_filenames:
:return:
"""
pose = pyrosetta.Pose()
if params_filenames and isinstance(
params_filenames, pyrosetta.rosetta.utility.vector1_string):
pyrosetta.generate_nonstandard_residue_set(pose, params_filenames)
if params_filenames and isinstance(params_filenames, list):
params_filenames2 = pyrosetta.rosetta.utility.vector1_string()
params_filenames2.extend(params_filenames)
pyrosetta.generate_nonstandard_residue_set(pose, params_filenames2)
else:
pass
pyrosetta.rosetta.core.import_pose.pose_from_file(pose, pdb_filename)
return pose
def replace_to_pose(self,
probe_name: str,
probe_smiles: str,
probe_resn: str = 'MMX') -> pyrosetta.Pose:
pdb = self.replace(probe_smiles=probe_smiles,
probe_resn=probe_resn,
probe_name=probe_name)
# pyrosetta.init(f'-extra_res_fa {probe_name}.params -mute all')
pose = pyrosetta.Pose()
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend([f"{probe_name}.params"])
nonstandard_residue_set = pyrosetta.generate_nonstandard_residue_set(
pose, params_paths)
pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(pose, pdb)
return pose
def params_to_pose(paramsfile: str, name: str) -> pyrosetta.Pose:
"""
Staticmethod to get a pose from a params file.
:param paramsfile: params file.
:param name: 3-letter residue name.
:return:
"""
pose = pyrosetta.Pose()
params_paths = pyrosetta.rosetta.utility.vector1_string()
params_paths.extend([paramsfile])
resiset = pyrosetta.generate_nonstandard_residue_set(
pose, params_paths)
lig = pyrosetta.rosetta.core.conformation.ResidueFactory.create_residue(
rts.name_map(name))
pose.append_residue_by_jump(lig, 1)
return pose
from sys import argv
fmt = dict(
zip('ANDRCQEGHILKMPFSTWYV', [
'ALA', 'ASN', 'ASP', 'ARG', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE',
'LEU', 'LYS', 'MET', 'PRO', 'PHE', 'SER', 'THR', 'TRP', 'TYR', 'VAL'
]))
with open('input_files/flags') as fn:
flags = fn.read().replace('\n', ' ')
# init PyRosetta
pyrosetta.init(''.join(flags))
ligand_params = pyrosetta.Vector1(['input_files/pNPG.params'])
new_res_set = pyrosetta.generate_nonstandard_residue_set(ligand_params)
p = pyrosetta.Pose()
pyrosetta.pose_from_file(p, new_res_set, 'input_files/bglb.pdb')
scorefxn = pyrosetta.create_score_function('beta_cst')
add_cst = rosetta.protocols.enzdes.AddOrRemoveMatchCsts()
add_cst.cstfile('input_files/pNPG.enzdes.cst')
add_cst.set_cst_action(rosetta.protocols.enzdes.CstAction.ADD_NEW)
add_cst.apply(p)
target = int(mutant_name[1:-1])
new_res = fmt[mutant_name[-1]]
mut = rosetta.protocols.simple_moves.MutateResidue(target, new_res)
mut.apply(p)
from pyrosetta.rosetta.core.pack.task import TaskFactory
from pyrosetta.rosetta.core.pack.task.operation import ReadResfile
from pyrosetta import create_score_function
#from roseasy.standard_params.filters import FilterContainer
def get_workspace(root_dir, step):
return pipeline.DesignWorkspace(root_dir, step)
if __name__=='__main__':
workspace, job_info = big_jobs.initiate()
test_run = job_info.get('test_run', False)
init()
# Create residue typeset
pose = Pose()
typeset = generate_nonstandard_residue_set(pose,
workspace.ligand_params_paths)
# Figure out input pdb and create a pose
pdbpath = workspace.input_path(job_info)
pose_from_file(pose, typeset, pdbpath)
# Create FastDesign object
fd = fastdesign.FastDesign()
fd.pose = pose
# Create task factory and read the resfile
taskfactory = TaskFactory()
readresfile = ReadResfile(workspace.resfile_path)
taskfactory.push_back(readresfile)
fd.task_factory = taskfactory
import rosetta
from sys import argv
fmt = dict( zip( 'ANDRCQEGHILKMPFSTWYV', [
'ALA','ASN','ASP','ARG','CYS','GLN','GLU',
'GLY','HIS','ILE','LEU','LYS','MET','PRO','PHE','SER',
'THR','TRP','TYR','VAL' ] ) )
with open( 'input_files/flags' ) as fn:
flags = fn.read().replace( '\n', ' ' )
# init PyRosetta
pyrosetta.init( ''.join( flags ) )
ligand_params = pyrosetta.Vector1( [ 'input_files/pNPG.params' ] )
new_res_set = pyrosetta.generate_nonstandard_residue_set( ligand_params )
p = pyrosetta.Pose()
pyrosetta.pose_from_file( p, new_res_set, 'input_files/bglb.pdb' )
scorefxn = pyrosetta.create_score_function( 'beta_cst' )
add_cst = rosetta.protocols.enzdes.AddOrRemoveMatchCsts()
add_cst.cstfile( 'input_files/pNPG.enzdes.cst' )
add_cst.set_cst_action( rosetta.protocols.enzdes.CstAction.ADD_NEW )
add_cst.apply( p )
target = int( mutant_name[ 1:-1 ] )
new_res = fmt[ mutant_name[ -1 ] ]
mut = rosetta.protocols.simple_moves.MutateResidue( target, new_res )
mut.apply( p )