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foldx Buildmodel mutation interfact - convenience interface #374

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foldx Buildmodel mutation interfact - convenience interface #374

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e391079
foldx
Feb 23, 2022
947a230
foldx with docs
Feb 23, 2022
2c67100
updade pdbqt->pdb
Feb 23, 2022
80886c3
add hydrogens
Feb 24, 2022
a8c1762
add hydrogens
Feb 24, 2022
127dc35
go around the ligand loading in pdbqt
Mar 24, 2022
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81 changes: 47 additions & 34 deletions src/biotite/application/autodock/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,14 +63,15 @@ class VinaApp(LocalApp):
... )
"""
def __init__(self, ligand, receptor, center, size, flexible=None,
bin_path="vina"):
bin_path="vina", custom_ligand_loc = None):
super().__init__(bin_path)

if ligand.bonds is None:
raise ValueError("The ligand has no associated BondList")
if receptor.bonds is None:
raise ValueError("The receptor has no associated BondList")

self._custom_ligand_loc = custom_ligand_loc
self._ligand = ligand.copy()
self._receptor = receptor.copy()
self._center = copy.deepcopy(center)
Expand All @@ -86,7 +87,7 @@ def __init__(self, ligand, receptor, center, size, flexible=None,
self._flex_res_starts = np.unique(get_residue_starts_for(
receptor, flexible_indices
))

self._ligand_file = NamedTemporaryFile(
"w", suffix=".pdbqt", delete=False
)
Expand All @@ -99,7 +100,7 @@ def __init__(self, ligand, receptor, center, size, flexible=None,
self._out_file = NamedTemporaryFile(
"r", suffix=".pdbqt", delete=False
)

@requires_state(AppState.CREATED)
def set_seed(self, seed):
"""
Expand All @@ -114,7 +115,7 @@ def set_seed(self, seed):
The seed for the random number generator.
"""
self._seed = seed

@requires_state(AppState.CREATED)
def set_exhaustiveness(self, exhaustiveness):
"""
Expand All @@ -131,7 +132,7 @@ def set_exhaustiveness(self, exhaustiveness):
Must be greater than 0.
"""
self._exhaustiveness = exhaustiveness

@requires_state(AppState.CREATED)
def set_max_number_of_models(self, number):
"""
Expand All @@ -147,7 +148,7 @@ def set_max_number_of_models(self, number):
The maximum number of generated modes/models.
"""
self._number = number

@requires_state(AppState.CREATED)
def set_energy_range(self, energy_range):
"""
Expand Down Expand Up @@ -178,20 +179,20 @@ def run(self):
))

ligand_file = PDBQTFile()
# Contains 'true' entries for all atoms that have not been
# Contains 'true' entries for all atoms that have not been
# removed from ligand
self._ligand_mask = ligand_file.set_structure(
self._ligand,
rotatable_bonds="all"
)
ligand_file.write(self._ligand_file)
self._ligand_file.flush()

if self._is_flexible:
self._rigid_mask = np.ones(
self._receptor.array_length(), dtype=bool
)
# Contains 'true' entries for all atoms that have not been
# Contains 'true' entries for all atoms that have not been
# removed from receptor in flexible side chains
self._receptor_mask = np.zeros(
self._receptor.array_length(), dtype=bool
Expand Down Expand Up @@ -234,18 +235,30 @@ def run(self):
)
receptor_file.write(self._receptor_file)
self._receptor_file.flush()

arguments = [
"--ligand", self._ligand_file.name,
"--receptor", self._receptor_file.name,
"--out", self._out_file.name,
"--center_x", f"{self._center[0]:.3f}",
"--center_y", f"{self._center[1]:.3f}",
"--center_z", f"{self._center[2]:.3f}",
"--size_x", f"{self._size[0]:.3f}",
"--size_y", f"{self._size[1]:.3f}",
"--size_z", f"{self._size[2]:.3f}",
]
if self._custom_ligand_loc is None:
arguments = [
"--ligand", self._ligand_file.name,
"--receptor", self._receptor_file.name,
"--out", self._out_file.name,
"--center_x", f"{self._center[0]:.3f}",
"--center_y", f"{self._center[1]:.3f}",
"--center_z", f"{self._center[2]:.3f}",
"--size_x", f"{self._size[0]:.3f}",
"--size_y", f"{self._size[1]:.3f}",
"--size_z", f"{self._size[2]:.3f}",
]
else:
arguments = [
"--ligand", self._custom_ligand_loc,
"--receptor", self._receptor_file.name,
"--out", self._out_file.name,
"--center_x", f"{self._center[0]:.3f}",
"--center_y", f"{self._center[1]:.3f}",
"--center_z", f"{self._center[2]:.3f}",
"--size_x", f"{self._size[0]:.3f}",
"--size_y", f"{self._size[1]:.3f}",
"--size_z", f"{self._size[2]:.3f}",
]
if self._seed is not None:
arguments.extend(["--seed", str(self._seed)])
if self._exhaustiveness is not None:
Expand All @@ -259,32 +272,32 @@ def run(self):

self.set_arguments(arguments)
super().run()

def evaluate(self):
super().evaluate()
out_file = PDBQTFile.read(self._out_file)

models = out_file.get_structure()

n_ligand_atoms = np.count_nonzero(self._ligand_mask)
self._ligand_models = models[..., :n_ligand_atoms]
self._flex_models = models[..., n_ligand_atoms:]
self._n_models = models.stack_depth()

remarks = out_file.get_remarks()
self._energies = np.array(
# VINA RESULT: -5.8 0.000 0.000
# ^
[float(remark[12:].split()[0]) for remark in remarks]
)

def clean_up(self):
super().clean_up()
cleanup_tempfile(self._ligand_file)
cleanup_tempfile(self._receptor_file)
cleanup_tempfile(self._receptor_flex_file)
cleanup_tempfile(self._out_file)

@requires_state(AppState.JOINED)
def get_energies(self):
"""
Expand All @@ -302,7 +315,7 @@ def get_energies(self):
@requires_state(AppState.JOINED)
def get_ligand_models(self):
"""
Get the ligand structure with the conformations for each
Get the ligand structure with the conformations for each
generated binding mode.

Returns
Expand All @@ -312,7 +325,7 @@ def get_ligand_models(self):
Each model corresponds to one binding mode.
The models are sorted from best to worst predicted binding
affinity.

Notes
-----
The returned structure may contain less atoms than the input
Expand Down Expand Up @@ -343,7 +356,7 @@ def get_ligand_coord(self):
)
coord[:, self._ligand_mask] = self._ligand_models.coord
return coord

@requires_state(AppState.JOINED)
def get_flexible_residue_models(self):
"""
Expand All @@ -360,7 +373,7 @@ def get_flexible_residue_models(self):
Each model corresponds to one binding mode.
The models are sorted from best to worst predicted binding
affinity.

Notes
-----
The returned structure may contain less atoms than the input
Expand All @@ -385,7 +398,7 @@ def get_receptor_coord(self):
affinity.
Missing coordinates due to the removed nonpolar hydrogen
atoms from flexible side chains are set to *NaN*.

Notes
-----
The output is only meaningful, if flexible side chains were
Expand Down Expand Up @@ -433,7 +446,7 @@ def _get_flexible_residue(self, residue_start):
flex_mask = np.zeros(self._receptor.array_length(), dtype=bool)
rigid_mask = np.ones(self._receptor.array_length(), dtype=bool)
return flex_mask, rigid_mask, root_index

# Remove the root bond from the bond list
# to find the atoms involved in the flexible part
bonds = self._receptor.bonds.copy()
Expand All @@ -442,7 +455,7 @@ def _get_flexible_residue(self, residue_start):
if root_index in flexible_indices:
raise BadStructureError(
"There are multiple connections between the flexible and "
"rigid part, maybe a cyclic residue like proline was selected"
"rigid part, maybe a cyclic residue like proline was selected"
)

flex_mask = np.zeros(self._receptor.array_length(), dtype=bool)
Expand All @@ -452,7 +465,7 @@ def _get_flexible_residue(self, residue_start):
flex_mask[root_index] = True

return flex_mask, rigid_mask, root_index


@staticmethod
def dock(ligand, receptor, center, size, flexible=None, bin_path="vina"):
Expand Down
12 changes: 12 additions & 0 deletions src/biotite/application/foldx/__init__.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
# This source code is part of the Biotite package and is distributed
# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
# information.

"""
A subpackage for static ligand docking with *FoldX*.
"""

__name__ = "biotite.application.foldX"
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Suggested change
__name__ = "biotite.application.foldX"
__name__ = "biotite.application.foldx"

__author__ = "Mojmir Mutny"

from .app import *
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