def launch(self):
"""Launches the execution of the Open Babel module."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# check input/output paths and parameters
self.check_data_params(out_log, err_log)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [self.output_path_par, self.output_path_inp, self.output_path_top]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
return 0
# create unique name for temporary folder (created by acpype)
self.unique_name = create_unique_name(6)
# create command line instruction
cmd = self.create_cmd(out_log, err_log)
# execute cmd
fu.log('Running %s, this execution can take a while' % self.acpype_path, out_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log, self.global_log).launch()
# move files to output_path and removes temporary folder
process_output(self.unique_name, self.basename + "." + self.unique_name + ".acpype", self.remove_tmp, self.basename, get_default_value(self.__class__.__name__), self.output_files, out_log)
return returncode
def launch(self) -> int:
"""Execute the :class:`FPocketSelect <fpocket.fpocket_select.FPocketSelect>` fpocket.fpocket_select.FPocketSelect object."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# check input/output paths and parameters
self.check_data_params(out_log, err_log)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [
self.io_dict["out"]["output_pocket_pdb"],
self.io_dict["out"]["output_pocket_pqr"]
]
if fu.check_complete_files(output_file_list):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# create tmp_folder
self.tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % self.tmp_folder, out_log)
# decompress the input_pockets_zip file to tmp_folder
all_pockets = fu.unzip_list(
zip_file=self.io_dict["in"]["input_pockets_zip"],
dest_dir=self.tmp_folder,
out_log=out_log)
pockets_list = [
i for i in all_pockets if ('pocket' + str(self.pocket)) in i
]
for p in pockets_list:
if PurePath(p).suffix == '.pdb':
fu.log(
'Saving %s file' %
self.io_dict["out"]["output_pocket_pdb"], out_log)
shutil.copy(p, self.io_dict["out"]["output_pocket_pdb"])
else:
fu.log(
'Saving %s file' %
self.io_dict["out"]["output_pocket_pqr"], out_log)
shutil.copy(p, self.io_dict["out"]["output_pocket_pqr"])
if self.remove_tmp:
# remove temporary folder
fu.rm(self.tmp_folder)
fu.log('Removed temporary folder: %s' % self.tmp_folder, out_log)
return 0
def launch(self) -> int:
"""Execute the :class:`FPocket <fpocket.fpocket.FPocket>` fpocket.fpocket.FPocket object."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# check input/output paths and parameters
self.check_data_params(out_log, err_log)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [self.io_dict["out"]["output_pockets_zip"],self.io_dict["out"]["output_summary"]]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
return 0
# create tmp_folder
self.tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % self.tmp_folder, out_log)
tmp_input = str(PurePath(self.tmp_folder).joinpath('input.pdb'))
# copy input_pdb_path to tmp_folder
shutil.copy(self.io_dict["in"]["input_pdb_path"], tmp_input)
# create cmd
cmd = [self.fpocket_path,
'-f', tmp_input]
# adding extra properties
if self.min_radius:
cmd.extend(['-m', str(self.min_radius)])
if self.max_radius:
cmd.extend(['-M', str(self.max_radius)])
if self.num_spheres:
cmd.extend(['-i', str(self.num_spheres)])
fu.log('Executing fpocket', out_log, self.global_log)
cmd = fu.create_cmd_line(cmd, out_log=out_log, global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log, self.global_log).launch()
process_output_fpocket(self.tmp_folder,
self.io_dict["out"]["output_pockets_zip"],
self.io_dict["out"]["output_summary"],
self.sort_by,
self.remove_tmp,
out_log,
self.__class__.__name__)
return returncode
def launch(self) -> int:
"""Execute the :class:`ExtractModelPDBQT <utils.extract_model_pdbqt.ExtractModelPDBQT>` utils.extract_model_pdbqt.ExtractModelPDBQT object."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# check input/output paths and parameters
self.check_data_params(out_log, err_log)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [self.io_dict["out"]["output_pdbqt_path"]]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
return 0
structure_name = PurePath(self.io_dict["in"]["input_pdbqt_path"]).name
parser = Bio.PDB.PDBParser(QUIET = True)
structPDB = parser.get_structure(structure_name, self.io_dict["in"]["input_pdbqt_path"])
models = []
for model in structPDB.get_models():
models.append(model.id + 1)
if not self.model in models:
fu.log(self.__class__.__name__ + ': Selected model %d not found in %s structure.' % (self.model, self.io_dict["in"]["input_pdbqt_path"]), out_log)
raise SystemExit(self.__class__.__name__ + ': Selected model %d not found in %s structure.' % (self.model, self.io_dict["in"]["input_pdbqt_path"]))
save = False
lines = 0
with open(self.io_dict["in"]["input_pdbqt_path"], "r") as input_pdb, open(self.io_dict["out"]["output_pdbqt_path"], "w") as output_pdb:
for line in input_pdb:
if line.startswith('MODEL') and line.split()[1] == str(self.model):
save = True
if line.startswith('ENDMDL'):
save = False
if save and not line.startswith('MODEL'):
lines = lines + 1
output_pdb.write(line)
fu.log('Saving model %d to %s' % (self.model, self.io_dict["out"]["output_pdbqt_path"]), out_log)
return 0
def launch(self):
"""Launches the execution of the Open Babel module."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [self.output_path]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
return 0
# create command line instruction
cmd = self.create_cmd(out_log, err_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log, self.global_log).launch()
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS solvate module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# Unzip topology to topology_out
top_file = fu.unzip_top(zip_file=self.input_top_zip_path,
out_log=out_log)
top_dir = str(Path(top_file).parent)
tmp_files.append(top_dir)
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
if self.container_path:
shutil.copytree(
top_dir,
str(
Path(container_io_dict.get("unique_dir")).joinpath(
Path(top_dir).name)))
top_file = str(
Path(self.container_volume_path).joinpath(
Path(top_dir).name,
Path(top_file).name))
cmd = [
self.gmx_path, 'solvate', '-cp',
container_io_dict["in"]["input_solute_gro_path"], '-cs',
self.input_solvent_gro_path, '-o',
container_io_dict["out"]["output_gro_path"], '-p', top_file
]
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
if self.container_path:
top_file = str(
Path(container_io_dict.get("unique_dir")).joinpath(
Path(top_dir).name,
Path(top_file).name))
# zip topology
fu.log(
'Compressing topology to: %s' %
container_io_dict["out"]["output_top_zip_path"], out_log,
self.global_log)
fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"],
top_file=top_file,
out_log=out_log)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS editconf module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Restart if needed
if self.restart:
output_file_list = [self.io_dict['out'].get("output_top_zip_path")]
if fu.check_complete_files(output_file_list):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# Unzip topology
top_file = fu.unzip_top(
zip_file=self.io_dict['in'].get("input_top_zip_path"),
out_log=out_log)
top_dir = str(Path(top_file).parent)
tmp_files.append(top_dir)
itp_name = str(Path(self.io_dict['in'].get("input_itp_path")).name)
with open(top_file) as top_f:
top_lines = top_f.readlines()
top_f.close()
fu.rm(top_file)
forcefield_pattern = r'#include.*forcefield.itp\"'
for index, line in enumerate(top_lines):
if re.search(forcefield_pattern, line):
break
top_lines.insert(index + 1, '\n')
top_lines.insert(index + 2, '; Including ligand ITP\n')
top_lines.insert(index + 3, '#include "' + itp_name + '"\n')
top_lines.insert(index + 4, '\n')
if self.io_dict['in'].get("input_posres_itp_path"):
top_lines.insert(index + 5, '; Ligand position restraints' + '\n')
top_lines.insert(index + 6, '#ifdef ' + self.posres_name + '\n')
top_lines.insert(
index + 7, '#include "' + str(
Path(self.io_dict['in'].get("input_posres_itp_path")).name)
+ '"\n')
top_lines.insert(index + 8, '#endif' + '\n')
top_lines.insert(index + 9, '\n')
inside_moleculetype_section = False
with open(self.io_dict['in'].get("input_itp_path")) as itp_file:
moleculetype_pattern = r'\[ moleculetype \]'
for line in itp_file:
if re.search(moleculetype_pattern, line):
inside_moleculetype_section = True
continue
if inside_moleculetype_section and not line.startswith(';'):
moleculetype = line.strip().split()[0].strip()
break
molecules_pattern = r'\[ molecules \]'
inside_molecules_section = False
index_molecule = None
molecule_string = moleculetype + (20 -
len(moleculetype)) * ' ' + '1' + '\n'
for index, line in enumerate(top_lines):
if re.search(molecules_pattern, line):
inside_molecules_section = True
continue
if inside_molecules_section and not line.startswith(
';') and line.upper().startswith('PROTEIN'):
index_molecule = index
if index_molecule:
top_lines.insert(index_molecule + 1, molecule_string)
else:
top_lines.append(molecule_string)
new_top = fu.create_name(path=top_dir,
prefix=self.prefix,
step=self.step,
name='ligand.top')
with open(new_top, 'w') as new_top_f:
new_top_f.write("".join(top_lines))
shutil.copy2(self.io_dict['in'].get("input_itp_path"), top_dir)
if self.io_dict['in'].get("input_posres_itp_path"):
shutil.copy2(self.io_dict['in'].get("input_posres_itp_path"),
top_dir)
# zip topology
fu.log(
'Compressing topology to: %s' %
self.io_dict['out'].get("output_top_zip_path"), out_log,
self.global_log)
fu.zip_top(zip_file=self.io_dict['out'].get("output_top_zip_path"),
top_file=new_top,
out_log=out_log)
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return 0
def launch(self) -> int:
"""Execute the :class:`Box <utils.box.Box>` utils.box.Box object."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# check input/output paths and parameters
self.check_data_params(out_log, err_log)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [self.io_dict["out"]["output_pdb_path"]]
if fu.check_complete_files(output_file_list):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# check if cavity (pdb) or pocket (pqr)
input_type = PurePath(
self.io_dict["in"]["input_pdb_path"]).suffix.lstrip('.')
if input_type == 'pdb':
fu.log(
'Loading residue PDB selection from %s' %
(self.io_dict["in"]["input_pdb_path"]), out_log,
self.global_log)
else:
fu.log(
'Loading pocket PQR selection from %s' %
(self.io_dict["in"]["input_pdb_path"]), out_log,
self.global_log)
# get input_pdb_path atoms coordinates
selection_atoms_num = 0
x_coordslist = []
y_coordslist = []
z_coordslist = []
with open(self.io_dict["in"]["input_pdb_path"]) as infile:
for line in infile:
if line.startswith("HETATM") or line.startswith("ATOM"):
x_coordslist.append(float(line[31:38].strip()))
y_coordslist.append(float(line[39:46].strip()))
z_coordslist.append(float(line[47:54].strip()))
selection_atoms_num = selection_atoms_num + 1
## Compute binding site box size
# compute box center
selection_box_center = [
np.average(x_coordslist),
np.average(y_coordslist),
np.average(z_coordslist)
]
fu.log(
'Binding site center (Angstroms): %10.3f%10.3f%10.3f' %
(selection_box_center[0], selection_box_center[1],
selection_box_center[2]), out_log, self.global_log)
# compute box size
selection_coords_max = np.amax(
[x_coordslist, y_coordslist, z_coordslist], axis=1)
selection_box_size = selection_coords_max - selection_box_center
if self.offset:
fu.log('Adding %.1f Angstroms offset' % (self.offset), out_log,
self.global_log)
selection_box_size = [c + self.offset for c in selection_box_size]
fu.log(
'Binding site size (Angstroms): %10.3f%10.3f%10.3f' %
(selection_box_size[0], selection_box_size[1],
selection_box_size[2]), out_log, self.global_log)
# compute volume
vol = np.prod(selection_box_size) * 2**3
fu.log('Volume (cubic Angstroms): %.0f' % (vol), out_log,
self.global_log)
# add box details as PDB remarks
remarks = "REMARK BOX CENTER:%10.3f%10.3f%10.3f" % (
selection_box_center[0], selection_box_center[1],
selection_box_center[2])
remarks += " SIZE:%10.3f%10.3f%10.3f" % (selection_box_size[0],
selection_box_size[1],
selection_box_size[2])
selection_box_coords_txt = ""
# add (optional) box coordinates as 8 ATOM records
if self.box_coordinates:
fu.log('Adding box coordinates', out_log, self.global_log)
selection_box_coords_txt = get_box_coordinates(
selection_box_center, selection_box_size)
with open(self.io_dict["out"]["output_pdb_path"], 'w') as f:
f.seek(0, 0)
f.write(remarks.rstrip('\r\n') + '\n' + selection_box_coords_txt)
fu.log(
'Saving output PDB file (with box setting annotations): %s' %
(self.io_dict["out"]["output_pdb_path"]), out_log, self.global_log)
return 0
def launch(self) -> int:
"""Launches the execution of the GROMACS make_ndx module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
cmd = [
'echo', '-e', '\'' + self.selection + '\\nq' + '\'', '|',
self.gmx_path, 'make_ndx', '-f',
container_io_dict["in"]["input_structure_path"], '-o',
container_io_dict["out"]["output_ndx_path"]
]
if container_io_dict["in"].get("input_ndx_path")\
and Path(container_io_dict["in"].get("input_ndx_path")).exists():
cmd.append('-n')
cmd.append(container_io_dict["in"].get("input_ndx_path"))
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS pdb2gmx module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
output_top_path = fu.create_name(prefix=self.prefix,
step=self.step,
name=self.output_top_path)
output_itp_path = fu.create_name(prefix=self.prefix,
step=self.step,
name=self.output_itp_path)
cmd = [
self.gmx_path, "pdb2gmx", "-f",
container_io_dict["in"]["input_pdb_path"], "-o",
container_io_dict["out"]["output_gro_path"], "-p", output_top_path,
"-water", self.water_type, "-ff", self.force_field, "-i",
output_itp_path
]
if self.his:
cmd.append("-his")
cmd = ['echo', self.his, '|'] + cmd
if self.ignh:
cmd.append("-ignh")
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
if self.container_path:
output_top_path = os.path.join(container_io_dict.get("unique_dir"),
output_top_path)
# zip topology
fu.log(
'Compressing topology to: %s' %
container_io_dict["out"]["output_top_zip_path"], out_log,
self.global_log)
fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"],
top_file=output_top_path,
out_log=out_log)
tmp_files.append(self.output_top_path)
tmp_files.append(self.output_itp_path)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launch the topology generation."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Restart if needed
if self.restart:
output_file_list = [self.io_dict['out'].get("output_top_zip_path")]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
return 0
top_file = fu.unzip_top(zip_file=self.io_dict['in'].get("input_top_zip_path"), out_log=out_log)
# Create index list of index file :)
index_dic = {}
lines = open(self.io_dict['in'].get("input_ndx_path")).read().splitlines()
for index, line in enumerate(lines):
if line.startswith('['):
index_dic[line] = index,
label = line
if index > 0:
index_dic[label] = index_dic[label][0], index
index_dic[label] = index_dic[label][0], index
fu.log('Index_dic: '+str(index_dic), out_log, self.global_log)
self.ref_rest_chain_triplet_list = [tuple(elem.strip(' ()').replace(' ', '').split(',')) for elem in self.ref_rest_chain_triplet_list.split('),')]
fu.log('ref_rest_chain_triplet_list: ' + str(self.ref_rest_chain_triplet_list), out_log, self.global_log)
for reference_group, restrain_group, chain in self.ref_rest_chain_triplet_list:
fu.log('Reference group: '+reference_group, out_log, self.global_log)
fu.log('Restrain group: '+restrain_group, out_log, self.global_log)
fu.log('Chain: '+chain, out_log, self.global_log)
self.io_dict['out']["output_itp_path"] = fu.create_name(path=str(Path(top_file).parent), prefix=self.prefix, step=self.step, name=restrain_group+'.itp')
# Mapping atoms from absolute enumeration to Chain relative enumeration
fu.log('reference_group_index: start_closed:'+str(index_dic['[ '+reference_group+' ]'][0]+1)+' stop_open: '+str(index_dic['[ '+reference_group+' ]'][1]), out_log, self.global_log)
reference_group_list = [int(elem) for line in lines[index_dic['[ '+reference_group+' ]'][0]+1: index_dic['[ '+reference_group+' ]'][1]] for elem in line.split()]
fu.log('restrain_group_index: start_closed:'+str(index_dic['[ '+restrain_group+' ]'][0]+1)+' stop_open: '+str(index_dic['[ '+restrain_group+' ]'][1]), out_log, self.global_log)
restrain_group_list = [int(elem) for line in lines[index_dic['[ '+restrain_group+' ]'][0]+1: index_dic['[ '+restrain_group+' ]'][1]] for elem in line.split()]
selected_list = [reference_group_list.index(atom)+1 for atom in restrain_group_list]
# Creating new ITP with restrictions
with open(self.io_dict['out'].get("output_itp_path"), 'w') as f:
fu.log('Creating: '+str(f)+' and adding the selected atoms force constants', out_log, self.global_log)
f.write('[ position_restraints ]\n')
f.write('; atom type fx fy fz\n')
for atom in selected_list:
f.write(str(atom)+' 1 '+self.force_constants+'\n')
# Including new ITP in the corresponding ITP-chain file
for file_dir in Path(top_file).parent.iterdir():
if not file_dir.name.startswith("posre") and not file_dir.name.endswith("_pr.itp"):
if fnmatch.fnmatch(str(file_dir), "*_chain_"+chain+".itp"):
with open(str(file_dir), 'a') as f:
fu.log('Opening: '+str(f)+' and adding the ifdef include statement', out_log, self.global_log)
f.write('\n')
f.write('; Include Position restraint file\n')
f.write('#ifdef CUSTOM_POSRES\n')
f.write('#include "'+str(Path(self.io_dict['out'].get("output_itp_path")).name)+'"\n')
f.write('#endif\n')
# zip topology
fu.zip_top(zip_file=self.io_dict['out'].get("output_top_zip_path"), top_file=top_file, out_log=out_log)
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return 0
def launch(self):
"""Launches the execution of the template_container module."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check the properties
fu.check_properties(self, self.properties)
# Restart
if self.restart:
# 4. Include here all output file paths
output_file_list = [self.io_dict['out']['output_file_path']]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
return 0
# 5. Copy inputs to container
container_io_dict = fu.copy_to_container(self.container_path, self.container_volume_path, self.io_dict)
# 6. Prepare the command line parameters as instructions list
instructions = ['-j']
if self.boolean_property:
instructions.append('-v')
fu.log('Appending optional boolean property', out_log, self.global_log)
# 7. Build the actual command line as a list of items (elements order will be maintained)
cmd = [self.executable_binary_property,
' '.join(instructions),
container_io_dict['out']['output_file_path'],
container_io_dict['in']['input_file_path1']]
fu.log('Creating command line with instructions and required arguments', out_log, self.global_log)
# 8. Repeat for optional input files if provided
if container_io_dict['in']['input_file_path2']:
# Append optional input_file_path2 to cmd
cmd.append(container_io_dict['in']['input_file_path2'])
fu.log('Appending optional argument to command line', out_log, self.global_log)
# 9. Uncomment to check the command line
# print(' '.join(cmd))
# 10. Create cmd with specdific syntax according to the required container
cmd = fu.create_cmd_line(cmd, container_path=self.container_path,
host_volume=container_io_dict.get('unique_dir'),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_image=self.container_image,
container_shell_path=self.container_shell_path,
out_log=out_log, global_log=self.global_log)
# Launch execution
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log, self.global_log).launch()
# Copy output(s) to output(s) path(s) in case of container execution
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
# Remove temporary file(s)
if self.remove_tmp and container_io_dict.get('unique_dir'):
fu.rm(container_io_dict.get('unique_dir'))
fu.log('Removed: %s' % str(container_io_dict.get('unique_dir')), out_log)
return returncode
def launch(self) -> int:
"""Execute the :class:`BindingSite <utils.bindingsite.BindingSite>` utils.bindingsite.BindingSite object."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# check input/output paths and parameters
self.check_data_params(out_log, err_log)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [self.io_dict["out"]["output_pdb_path"]]
if fu.check_complete_files(output_file_list):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# Parse structure
fu.log(
'Loading input PDB structure %s' %
(self.io_dict["in"]["input_pdb_path"]), out_log, self.global_log)
structure_name = PurePath(self.io_dict["in"]["input_pdb_path"]).name
parser = Bio.PDB.PDBParser(QUIET=True)
structPDB = parser.get_structure(structure_name,
self.io_dict["in"]["input_pdb_path"])
if len(structPDB):
structPDB = structPDB[0]
# Use only one chain
n_chains = structPDB.get_list()
if len(n_chains) != 1:
fu.log(
'More than one chain found in the input PDB structure. Using only the first chain to find the binding site',
out_log, self.global_log)
# get first chain in case there is more than one chain
for struct_chain in structPDB.get_chains():
structPDB = struct_chain
# Get AA sequence
structPDB_seq = get_pdb_sequence(structPDB)
if len(structPDB_seq) == 0:
fu.log(
self.__class__.__name__ +
': Cannot extract AA sequence from the input PDB structure %s. Wrong format?'
% self.io_dict["in"]["input_pdb_path"], out_log)
raise SystemExit(
self.__class__.__name__ +
': Cannot extract AA sequence from the input PDB structure %s. Wrong format?'
% self.io_dict["in"]["input_pdb_path"])
else:
fu.log(
'Found %s residues in %s' %
(len(structPDB_seq), self.io_dict["in"]["input_pdb_path"]),
out_log)
# create temporary folder for decompressing the input_clusters_zip file
unique_dir = PurePath(fu.create_unique_dir())
fu.log('Creating %s temporary folder' % unique_dir, out_log,
self.global_log)
# decompress the input_clusters_zip file
cluster_list = fu.unzip_list(
zip_file=self.io_dict["in"]["input_clusters_zip"],
dest_dir=unique_dir,
out_log=out_log)
clusterPDB_ligands_aligned = []
clusterPDB_ligands_num = 0
fu.log('Iterating on all clusters:', out_log)
for idx, cluster_path in enumerate(cluster_list):
cluster_name = PurePath(cluster_path).stem
fu.log(' ', out_log)
fu.log('------------ Iteration #%s --------------' % (idx + 1),
out_log)
fu.log('Cluster member: %s' % cluster_name, out_log)
# Load and Parse PDB
clusterPDB = {}
clusterPDB = parser.get_structure(cluster_name, cluster_path)[0]
# Use only the first chain
for cluster_chain in clusterPDB.get_chains():
clusterPDB = cluster_chain
# Looking for ligands
clusterPDB_ligands = get_ligand_residues(clusterPDB)
if (len(clusterPDB_ligands)) == 0:
fu.log(
'No ligands found that could guide the binding site search. Ignoring this member: %s'
% cluster_name, out_log)
continue
# Selecting the largest ligand, if more than one
lig_atoms_num = 0
clusterPDB_ligand = {}
if self.ligand:
if self.ligand in [
x.get_resname() for x in clusterPDB_ligands
]:
for lig in clusterPDB_ligands:
if lig.get_resname() == self.ligand:
clusterPDB_ligand = lig
lig_atoms_num = len(lig.get_list())
fu.log(
'Ligand found: %s (%s atoms)' %
(lig.get_resname(), lig_atoms_num), out_log)
else:
fu.log(
'Ligand %s not found in %s cluster member, skipping this cluster'
% (self.ligand, cluster_name), out_log)
continue
else:
if len(clusterPDB_ligands) > 1:
for lig_res in clusterPDB_ligands:
lig_res_atoms_num = len(lig_res.get_list())
fu.log(
'Ligand found: %s (%s atoms)' %
(lig_res.get_resname(), lig_res_atoms_num),
out_log)
if lig_res_atoms_num > lig_atoms_num:
clusterPDB_ligand = lig_res
lig_atoms_num = lig_res_atoms_num
else:
clusterPDB_ligand = clusterPDB_ligands[0]
lig_atoms_num = len(clusterPDB_ligands[0].get_list())
fu.log(
'Member accepted. Valid ligand found: %s (%s atoms)' %
(clusterPDB_ligand.get_resname(), lig_atoms_num), out_log)
## Mapping residues by sequence alignment to match structPDB-clusterPDB paired residues
# Get AA sequence
clusterPDB_seq = get_pdb_sequence(clusterPDB)
# Pairwise align
aln, residue_map = align_sequences(structPDB_seq, clusterPDB_seq,
self.matrix_name, self.gap_open,
self.gap_extend)
fu.log(
'Matching residues to input PDB structure. Alignment is:\n%s' %
(aln[1]), out_log)
# Calculate (gapless) sequence identity
seq_identity, gap_seq_identity = calculate_alignment_identity(
aln[0], aln[1])
fu.log('Sequence identity (%%): %s' % (seq_identity), out_log)
fu.log('Gap less identity (%%): %s' % (gap_seq_identity), out_log)
## Selecting aligned CA atoms from first model, first chain
struct_atoms = []
cluster_atoms = []
for struct_res in residue_map:
try:
cluster_atoms.append(
clusterPDB[residue_map[struct_res]]['CA'])
struct_atoms.append(
get_residue_by_id(structPDB, struct_res)['CA'])
except KeyError:
fu.log(
'Cannot find CA atom for residue %s (input PDB %s)' %
(get_residue_by_id(
structPDB, struct_res).get_resname(), struct_res),
out_log)
pass
if len(cluster_atoms) == 0:
fu.log(
self.__class__.__name__ +
': Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member.'
% (cluster_name, structure_name), out_log)
raise SystemExit(
self.__class__.__name__ +
': Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member.'
% (cluster_name, structure_name))
else:
fu.log(
'Superimposing %s aligned protein residues' %
(len(cluster_atoms)), out_log)
## Align against input structure
si = Bio.PDB.Superimposer()
si.set_atoms(struct_atoms, cluster_atoms)
si.apply(clusterPDB.get_atoms())
fu.log('RMSD: %s' % (si.rms), out_log)
# Save transformed structure (and ligand)
clusterPDB_ligand_aligned = clusterPDB[clusterPDB_ligand.get_id()]
fu.log('Saving transformed ligand coordinates', out_log)
clusterPDB_ligands_aligned.append(clusterPDB_ligand_aligned)
## Stop after n accepted cluster members
clusterPDB_ligands_num += 1
if clusterPDB_ligands_num > self.max_num_ligands:
break
fu.log(' ', out_log)
fu.log('----------------------------------------', out_log)
fu.log(
'All transformed ligand coordinates saved, getting binding site residues',
out_log)
## Select binding site atoms as those around cluster superimposed ligands
fu.log(
'Defining binding site residues as those %sÅ around the %s cluster superimposed ligands'
% (self.radius, clusterPDB_ligands_num), out_log)
# select Atoms from aligned ligands
clusterPDB_ligands_aligned2 = [
res for res in clusterPDB_ligands_aligned
]
clusterPDB_ligands_aligned_atoms = Bio.PDB.Selection.unfold_entities(
clusterPDB_ligands_aligned2, 'A')
# select Atoms from input PDB structure
structPDB_atoms = [atom for atom in structPDB.get_atoms()]
# compute neighbors for aligned ligands in the input PDB structure
structPDB_bs_residues_raw = {}
structPDB_neighbors = Bio.PDB.NeighborSearch(structPDB_atoms)
for ligand_atom in clusterPDB_ligands_aligned_atoms:
# look for PDB atoms 5A around each ligand atom
k_l = structPDB_neighbors.search(ligand_atom.coord, self.radius,
'R')
for k in k_l:
structPDB_bs_residues_raw[k.get_id()] = k.get_full_id()
## Save binding site to PDB
io = Bio.PDB.PDBIO()
fu.log(
'Writing binding site residues into %s' %
(self.io_dict["out"]["output_pdb_path"]), out_log)
# unselect input PDB atoms not in binding site
structPDB_bs_atoms = 0
p = re.compile('H_|W_|W')
residue_ids_to_remove = []
for res in structPDB.get_residues():
if res.id not in structPDB_bs_residues_raw.keys():
# add residue to residue_ids_to_remove list
residue_ids_to_remove.append(res.id)
elif p.match(res.resname):
# add residue to residue_ids_to_remove list
residue_ids_to_remove.append(res.id)
else:
# this residue will be preserved
structPDB_bs_atoms += len(res.get_list())
# unselect input PDB atoms not in binding site
for chain in structPDB:
for idr in residue_ids_to_remove:
chain.detach_child(idr)
# write PDB file
io.set_structure(structPDB)
io.save(self.io_dict["out"]["output_pdb_path"])
if self.remove_tmp:
# remove temporary folder
fu.rm(unique_dir)
fu.log(' ', out_log)
fu.log('----------------------------------------', out_log)
fu.log('Removed temporary folder: %s' % unique_dir, out_log)
return 0
def launch(self) -> int:
"""Launches the execution of the GROMACS mdrun module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if (not self.mpi_bin) and (not self.container_path):
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
cmd = [
self.gmx_path, 'mdrun', '-s',
container_io_dict["in"]["input_tpr_path"], '-o',
container_io_dict["out"]["output_trr_path"], '-c',
container_io_dict["out"]["output_gro_path"], '-e',
container_io_dict["out"]["output_edr_path"], '-g',
container_io_dict["out"]["output_log_path"], '-nt',
self.num_threads
]
if self.use_gpu:
cmd += ["-nb", "gpu", "-pme", "gpu"]
if self.mpi_bin:
mpi_cmd = [self.mpi_bin]
if self.mpi_np:
mpi_cmd.append('-np')
mpi_cmd.append(str(self.mpi_np))
if self.mpi_hostlist:
mpi_cmd.append('-hostfile')
mpi_cmd.append(self.mpi_hostlist)
cmd = mpi_cmd + cmd
if container_io_dict["out"].get("output_xtc_path"):
cmd.append('-x')
cmd.append(container_io_dict["out"]["output_xtc_path"])
if container_io_dict["out"].get("output_cpt_path"):
cmd.append('-cpo')
cmd.append(container_io_dict["out"]["output_cpt_path"])
if container_io_dict["out"].get("output_dhdl_path"):
cmd.append('-dhdl')
cmd.append(container_io_dict["out"]["output_dhdl_path"])
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Execute the :class:`FPocketFilter <fpocket.fpocket_filter.FPocketFilter>` fpocket.fpocket_filter.FPocketFilter object."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# check input/output paths and parameters
self.check_data_params(out_log, err_log)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [self.io_dict["out"]["output_filter_pockets_zip"]]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
return 0
# load input_summary into a dictionary
with open(self.io_dict["in"]["input_summary"]) as json_file:
data = json.load(json_file)
# build search_list
search_list = []
ranges = {}
if self.score:
check_range('score', self.score, [0,1], out_log, self.__class__.__name__)
search_list.append(self.score_matcher(self.score))
ranges['score'] = self.score
if self.druggability_score:
check_range('druggability_score', self.druggability_score, [0,1], out_log, self.__class__.__name__)
search_list.append(self.druggability_score_matcher(self.druggability_score))
ranges['druggability_score'] = self.druggability_score
if self.volume:
check_range('volume', self.volume, [0,10000], out_log, self.__class__.__name__)
search_list.append(self.volume_matcher(self.volume))
ranges['volume'] = self.volume
fu.log('Performing a search under the next parameters: %s' % (', '.join(['{0}: {1}'.format(k, v) for k,v in ranges.items()])), out_log)
# perform search
search = [ x for x in data if all([f(data[x]) for f in search_list]) ]
if len(search) == 0:
fu.log('No matches found', out_log)
return 0
str_out = '';
for s in search:
str_out = str_out + ('\n**********\n%s\n**********\nscore: %s\ndruggability_score: %s\nvolume: %s\n' % (s, data[s]["score"], data[s]["druggability_score"], data[s]["volume"]))
fu.log('Found %d matches:%s' % (len(search), str_out), out_log)
# create tmp_folder
self.tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % self.tmp_folder, out_log)
process_output_fpocket_filter(search,
self.tmp_folder,
self.io_dict["in"]["input_pockets_zip"],
self.io_dict["out"]["output_filter_pockets_zip"],
self.remove_tmp,
out_log)
return 0
def launch(self) -> int:
"""Launches the execution of the GROMACS select module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
cmd = [
self.gmx_path, 'select', '-s',
container_io_dict["in"]["input_structure_path"], '-on',
container_io_dict["out"]["output_ndx_path"]
]
if container_io_dict["in"].get("input_ndx_path") and pl.Path(
container_io_dict["in"].get("input_ndx_path")).exists():
cmd.append('-n')
cmd.append(container_io_dict["in"].get("input_ndx_path"))
cmd.append('-select')
cmd.append("\'" + self.selection + "\'")
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
if self.container_path:
if self.container_path.endswith('singularity'):
fu.log('Using Singularity image %s' % self.container_image,
out_log, self.global_log)
cmd = [
self.container_path, 'exec', '--bind',
container_io_dict.get("unique_dir") + ':' +
self.container_volume_path, self.container_image,
" ".join(cmd)
]
elif self.container_path.endswith('docker'):
fu.log('Using Docker image %s' % self.container_image, out_log,
self.global_log)
docker_cmd = [
self.container_path,
'run',
]
if self.container_working_dir:
docker_cmd.append('-w')
docker_cmd.append(self.container_working_dir)
if self.container_volume_path:
docker_cmd.append('-v')
docker_cmd.append(
container_io_dict.get("unique_dir") + ':' +
self.container_volume_path)
if self.container_user_id:
docker_cmd.append('--user')
docker_cmd.append(self.container_user_id)
docker_cmd.append(self.container_image)
docker_cmd.append(" ".join(cmd))
cmd = docker_cmd
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS grompp module.
Examples:
This is a use example of how to use the Grommpp module from Python
>>> from biobb_md.gromacs.grompp import Grompp
>>> prop = { 'mdp':{ 'type': 'minimization', 'emtol':'500', 'nsteps':'5000'}}
>>> Grompp(input_gro_path='/path/to/myStructure.gro', input_top_zip_path='/path/to/myTopology.zip', output_tpr_path='/path/to/NewCompiledBin.tpr', properties=prop).launch()
"""
tmp_files = []
mdout = 'mdout.mdp'
tmp_files.append(mdout)
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# Unzip topology to topology_out
top_file = fu.unzip_top(zip_file=self.input_top_zip_path,
out_log=out_log)
top_dir = str(Path(top_file).parent)
tmp_files.append(top_dir)
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
if self.input_mdp_path:
self.output_mdp_path = self.input_mdp_path
else:
mdp_dir = fu.create_unique_dir()
tmp_files.append(mdp_dir)
self.output_mdp_path = self.create_mdp(
path=str(Path(mdp_dir).joinpath(self.output_mdp_path)))
md = self.mdp.get('type', 'minimization')
if md not in ('index', 'free'):
fu.log('Will run a %s md of %s steps' % (md, self.nsteps), out_log,
self.global_log)
elif md == 'index':
fu.log('Will create a TPR to be used as structure file')
else:
fu.log(
'Will run a %s md of %s' %
(md, fu.human_readable_time(
int(self.nsteps) * float(self.dt))), out_log,
self.global_log)
if self.container_path:
fu.log('Container execution enabled', out_log)
shutil.copy2(self.output_mdp_path,
container_io_dict.get("unique_dir"))
self.output_mdp_path = str(
Path(self.container_volume_path).joinpath(
Path(self.output_mdp_path).name))
shutil.copytree(
top_dir,
str(
Path(container_io_dict.get("unique_dir")).joinpath(
Path(top_dir).name)))
top_file = str(
Path(self.container_volume_path).joinpath(
Path(top_dir).name,
Path(top_file).name))
cmd = [
self.gmx_path, 'grompp', '-f', self.output_mdp_path, '-c',
container_io_dict["in"]["input_gro_path"], '-r',
container_io_dict["in"]["input_gro_path"], '-p', top_file, '-o',
container_io_dict["out"]["output_tpr_path"], '-po', mdout,
'-maxwarn', self.maxwarn
]
if container_io_dict["in"].get("input_cpt_path") and Path(
container_io_dict["in"]["input_cpt_path"]).exists():
cmd.append('-t')
if self.container_path:
shutil.copy2(container_io_dict["in"]["input_cpt_path"],
container_io_dict.get("unique_dir"))
cmd.append(
str(
Path(self.container_volume_path).joinpath(
Path(container_io_dict["in"]
["input_cpt_path"]).name)))
else:
cmd.append(container_io_dict["in"]["input_cpt_path"])
if container_io_dict["in"].get("input_ndx_path") and Path(
container_io_dict["in"]["input_ndx_path"]).exists():
cmd.append('-n')
if self.container_path:
shutil.copy2(container_io_dict["in"]["input_ndx_path"],
container_io_dict.get("unique_dir"))
cmd.append(
Path(self.container_volume_path).joinpath(
Path(container_io_dict["in"]["input_ndx_path"]).name))
else:
cmd.append(container_io_dict["in"]["input_ndx_path"])
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS editconf module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
cmd = [
self.gmx_path, 'editconf', '-f',
container_io_dict["in"]["input_gro_path"], '-o',
container_io_dict["out"]["output_gro_path"], '-d',
str(self.distance_to_molecule), '-bt', self.box_type
]
if self.center_molecule:
cmd.append('-c')
fu.log('Centering molecule in the box.', out_log, self.global_log)
fu.log(
"Distance of the box to molecule: %6.2f" %
self.distance_to_molecule, out_log, self.global_log)
fu.log("Box type: %s" % self.box_type, out_log, self.global_log)
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Execute the :class:`BoxResidues <utils.box_residues.BoxResidues>` utils.box_residues.BoxResidues object."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# check input/output paths and parameters
self.check_data_params(out_log, err_log)
# Check the properties
fu.check_properties(self, self.properties)
if self.restart:
output_file_list = [self.io_dict["out"]["output_pdb_path"]]
if fu.check_complete_files(output_file_list):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# Parse structure
fu.log(
'Loading input PDB structure %s' %
(self.io_dict["in"]["input_pdb_path"]), out_log, self.global_log)
structure_name = PurePath(self.io_dict["in"]["input_pdb_path"]).name
parser = Bio.PDB.PDBParser(QUIET=True)
structPDB = parser.get_structure(structure_name,
self.io_dict["in"]["input_pdb_path"])
if len(structPDB):
structPDB = structPDB[0]
## Mapping residue structure into input structure
fu.log('Mapping residue structure into input structure', out_log,
self.global_log)
# Listing residues to be selected from the residue structure
residPDB_res_list = []
for residPDB_res in self.resid_list:
if self.residue_offset:
residPDB_res_list.append(
(' ', residPDB_res + self.residue_offset, ' '))
else:
residPDB_res_list.append((' ', residPDB_res, ' '))
selection_res_list = []
selection_atoms_num = 0
for struct_chain in structPDB:
for struct_res in struct_chain:
if struct_res.get_id() in residPDB_res_list:
selection_res_list.append(struct_res)
selection_atoms_num += len(struct_res.get_list())
if len(selection_res_list) == 0:
fu.log(
self.__class__.__name__ +
': Cannot match any of the residues listed in [%s] into %s' %
(', '.join(str(v) for v in self.resid_list),
self.io_dict["in"]["input_pdb_path"]), out_log)
raise SystemExit(
self.__class__.__name__ +
': Cannot match any of the residues listed in [%s] into %s' %
(', '.join(str(v) for v in self.resid_list),
self.io_dict["in"]["input_pdb_path"]))
elif len(selection_res_list) != len(residPDB_res_list):
fu.log(
'Cannot match all the residues listed in %s into %s. Found %s out of %s'
% (', '.join(str(v) for v in self.resid_list),
self.io_dict["in"]["input_pdb_path"],
len(selection_res_list), len(residPDB_res_list)), out_log)
else:
fu.log('Selection of residues successfully matched', out_log,
self.global_log)
## Compute binding site box size
# compute box center
selection_box_center = sum(
atom.coord for res in selection_res_list
for atom in res.get_atoms()) / selection_atoms_num
fu.log(
'Binding site center (Angstroms): %10.3f%10.3f%10.3f' %
(selection_box_center[0], selection_box_center[1],
selection_box_center[2]), out_log, self.global_log)
# compute box size
selection_coords_max = np.amax([
atom.coord for res in selection_res_list
for atom in res.get_atoms()
],
axis=0)
selection_box_size = selection_coords_max - selection_box_center
if self.offset:
selection_box_size = [c + self.offset for c in selection_box_size]
fu.log(
'Binding site size (Angstroms): %10.3f%10.3f%10.3f' %
(selection_box_size[0], selection_box_size[1],
selection_box_size[2]), out_log, self.global_log)
# compute volume
vol = np.prod(selection_box_size) * 2**3
fu.log('Volume (cubic Angstroms): %.0f' % (vol), out_log,
self.global_log)
# add box details as PDB remarks
remarks = "REMARK BOX CENTER:%10.3f%10.3f%10.3f" % (
selection_box_center[0], selection_box_center[1],
selection_box_center[2])
remarks += " SIZE:%10.3f%10.3f%10.3f" % (selection_box_size[0],
selection_box_size[1],
selection_box_size[2])
selection_box_coords_txt = ""
# add (optional) box coordinates as 8 ATOM records
if self.box_coordinates:
fu.log('Adding box coordinates', out_log, self.global_log)
selection_box_coords_txt = get_box_coordinates(
selection_box_center, selection_box_size)
with open(self.io_dict["out"]["output_pdb_path"], 'w') as f:
f.seek(0, 0)
f.write(remarks.rstrip('\r\n') + '\n' + selection_box_coords_txt)
fu.log(
'Saving output PDB file (with box setting annotations): %s' %
(self.io_dict["out"]["output_pdb_path"]), out_log, self.global_log)
return 0
def launch(self):
"""Launches the execution of the template module."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check the properties
fu.check_properties(self, self.properties)
# Restart
if self.restart:
# 4. Include here all output file paths
output_file_list = [self.io_dict['out']['output_file_path']]
if fu.check_complete_files(output_file_list):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# Creating temporary folder
self.tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % self.tmp_folder, out_log)
# 5. Include here all mandatory input files
# Copy input_file_path1 to temporary folder
shutil.copy(self.io_dict['in']['input_file_path1'], self.tmp_folder)
# 6. Prepare the command line parameters as instructions list
instructions = ['-j']
if self.boolean_property:
instructions.append('-v')
fu.log('Appending optional boolean property', out_log,
self.global_log)
# 7. Build the actual command line as a list of items (elements order will be maintained)
cmd = [
self.executable_binary_property, ' '.join(instructions),
self.io_dict['out']['output_file_path'],
str(
PurePath(self.tmp_folder).joinpath(
PurePath(self.io_dict['in']['input_file_path1']).name))
]
fu.log(
'Creating command line with instructions and required arguments',
out_log, self.global_log)
# 8. Repeat for optional input files if provided
if self.io_dict['in']['input_file_path2']:
# Copy input_file_path2 to temporary folder
shutil.copy(self.io_dict['in']['input_file_path2'],
self.tmp_folder)
# Append optional input_file_path2 to cmd
cmd.append(
str(
PurePath(self.tmp_folder).joinpath(
PurePath(
self.io_dict['in']['input_file_path2']).name)))
fu.log('Appending optional argument to command line', out_log,
self.global_log)
# 9. Uncomment to check the command line
# print(' '.join(cmd))
# Launch execution
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log).launch()
# Remove temporary file(s)
if self.remove_tmp:
fu.rm(self.tmp_folder)
fu.log('Removed: %s' % str(self.tmp_folder), out_log)
return returncode
