logger = logging.getLogger(__name__)
-logging.getLogger().setLevel(logging.DEBUG)
def _flattened(list_of_lists: list) -> list:
@@ -140,7 +139,7 @@ Source code for transformato.mutate
for lambda_value in np.linspace(1, 0, nr_of_steps + 1)[1:]:
print("####################")
print(
- f"Perform parameter scaling on cc in step: {intermediate_factory.current_step} with lamb: {lambda_value}"
+ f"Perform paramteter scaling on cc in step: {intermediate_factory.current_step} with lamb: {lambda_value}"
)
print("####################")
intermediate_factory.write_state(
@@ -450,7 +449,7 @@ Source code for transformato.mutate
self.dummy_region_cc2: DummyRegion
self.asfe: bool = False
- # self._check_cgenff_versions()
+ self._check_cgenff_versions()
except:
logger.info(
@@ -745,6 +744,7 @@ Source code for transformato.mutate
for atom in psf.view[f":{tlc}"].atoms:
if atom.name.find("LP") == False:
+ print(f"die Atome {atom}")
if atom.frame_type.atom1.idx in flat_ordered_connected_dummy_regions:
lp_dict_dummy_region[atom.frame_type.atom1.idx].append(atom.idx)
@@ -1820,6 +1820,8 @@ Source code for transformato.mutate
cc_names_struc1.append(ligand1_atom.name)
cc_names_struc2.append(ligand2_atom.name)
+ print(f"CC Struc1: {cc_names_struc1}")
+ print(f"CC Struc2: {cc_names_struc2}")
return match_atom_names_cc1_to_cc2
@@ -1909,20 +1911,6 @@ Source code for transformato.mutate
ligand1_atom.mod_type = mod_type(
modified_epsilon, modified_rmin
)
- # do this only when using GAFF
- if type(psf) == pm.amber.AmberParm:
- assert (
- psf[f":{self.tlc_cc1}@{ligand1_atom.idx+1}"]
- .atoms[0]
- .name
- == ligand1_atom.name
- )
- pm.tools.actions.changeLJSingleType(
- psf,
- f":{self.tlc_cc1}@{ligand1_atom.idx+1}",
- modified_rmin,
- modified_epsilon,
- ).execute()
if not found:
raise RuntimeError("No corresponding atom in cc2 found")
@@ -1992,16 +1980,6 @@ Source code for transformato.mutate
ligand1_bond.mod_type = mod_type(modified_k, modified_req)
logger.debug(ligand1_bond.mod_type)
- # do this only when using GAFF
- if type(psf) == pm.amber.AmberParm:
- pm.tools.actions.setBond(
- psf,
- f":{self.tlc_cc1}@{ligand1_bond.atom1.idx+1}",
- f":{self.tlc_cc1}@{ligand1_bond.atom2.idx+1}",
- modified_k,
- modified_req,
- ).execute()
-
if not found:
logger.critical(ligand1_bond)
raise RuntimeError(
@@ -2076,17 +2054,6 @@ Source code for transformato.mutate
cc1_angle.mod_type = mod_type(modified_k, modified_theteq)
- # do this only when using GAFF
- if type(psf) == pm.amber.AmberParm:
- pm.tools.actions.setAngle(
- psf,
- f":{self.tlc_cc1}@{cc1_angle.atom1.idx+1}",
- f":{self.tlc_cc1}@{cc1_angle.atom2.idx+1}",
- f":{self.tlc_cc1}@{cc1_angle.atom3.idx+1}",
- modified_k,
- modified_theteq,
- ).execute()
-
if not found:
logger.critical(cc1_angle)
raise RuntimeError("No corresponding angle in cc2 found")
@@ -2197,21 +2164,6 @@ Source code for transformato.mutate
original_torsion.mod_type = mod_types
- # do this only when using GAFF
- if type(psf) == pm.amber.AmberParm:
- pm.tools.actions.addDihedral(
- psf,
- f":{self.tlc_cc1}@{original_torsion.atom1.idx+1}",
- f":{self.tlc_cc1}@{original_torsion.atom2.idx+1}",
- f":{self.tlc_cc1}@{original_torsion.atom3.idx+1}",
- f":{self.tlc_cc1}@{original_torsion.atom4.idx+1}",
- modified_phi_k,
- torsion_t.per,
- torsion_t.phase,
- torsion_t.scnb,
- torsion_t.see,
- ).execute()
-
if not found:
logger.critical(original_torsion)
raise RuntimeError("No corresponding torsion in cc2 found")
@@ -2228,11 +2180,8 @@ Source code for transformato.mutate
lambda_value : float
lambda_value
"""
- try:
- assert type(psf) == pm.charmm.CharmmPsfFile
- except AssertionError:
- assert type(psf) == pm.amber.AmberParm
+ assert type(psf) == pm.charmm.CharmmPsfFile
if self.charge_mutation:
logger.info(f" -- Charge parameters from cc1 are transformed to cc2.")
logger.info(f"Lambda value:{lambda_value}")
@@ -2281,10 +2230,8 @@ Source code for transformato.mutate
def _mutate_charge(
self, psf: pm.charmm.CharmmPsfFile, lambda_value: float, offset: int
):
- total_charge = float(
- round(
- sum([atom.initial_charge for atom in psf.view[f":{self.tlc}"].atoms]), 4
- ),
+ total_charge = int(
+ round(sum([atom.initial_charge for atom in psf.view[f":{self.tlc}"].atoms]))
)
# scale the charge of all atoms
print(f"Scaling charge on: {self.atoms_to_be_mutated}")
@@ -2297,16 +2244,6 @@ Source code for transformato.mutate
atom.charge = atom.initial_charge * lambda_value
logger.debug(f"New charge: {atom.charge}")
- # in the end, we save the topology for amber (lig_in_env.parm7) using parmed
- # pm.save_parm(), this requires all changes applied via an action tool
- if type(psf) == pm.amber.AmberParm:
- pm.tools.actions.change(
- psf,
- "CHARGE",
- f":{self.tlc}@{idx+1}",
- atom.initial_charge * lambda_value,
- ).execute()
-
# check to avoid compensating charges when doing asfe
if (
lambda_value != 1
@@ -2315,8 +2252,6 @@ Source code for transformato.mutate
# compensate for the total change in charge the terminal atom
self._compensate_charge(psf, total_charge, offset)
-
-[docs]
def _mutate_vdw(
self,
psf: pm.charmm.CharmmPsfFile,
@@ -2325,9 +2260,6 @@ Source code for transformato.mutate
offset: int,
to_default: bool,
):
- """
- This is used to scale the LJ parameters of the DDD and DDX atoms to zero in phase II and III
- """
if not set(vdw_atom_idx).issubset(set(self.atoms_to_be_mutated)):
raise RuntimeError(
f"Specified atom {vdw_atom_idx} is not in atom_idx list {self.atoms_to_be_mutated}. Aborting."
@@ -2343,24 +2275,13 @@ Source code for transformato.mutate
atom_type_suffix = "DDX"
atom.rmin = 1.5
atom.epsilon = -0.15
- # do this only when using GAFF
- if type(psf) == pm.amber.AmberParm:
- assert psf[f":{self.tlc}@{atom.idx+1}"].atoms[0].name == atom.name
- pm.tools.actions.changeLJSingleType(
- psf,
- f":{self.tlc}@{atom.idx+1}",
- 1.5,
- 0.15, ### ATTENTION: This should be -0.15 but somehow GAFF does not like negative values
- ).execute()
-
else:
logger.info("Mutate to dummy")
atom_type_suffix = f"DDD"
- self._scale_epsilon_and_rmin(atom, lambda_value, psf, self.tlc)
-
+ self._scale_epsilon(atom, lambda_value)
+ self._scale_rmin(atom, lambda_value)
# NOTEthere is always a type change
- self._modify_type(atom, psf, atom_type_suffix, self.tlc)
-
+ self._modify_type(atom, psf, atom_type_suffix)
[docs]
@@ -2466,7 +2387,7 @@ Source code for transformato.mutate
connecting_real_atom_for_this_dummy_region
)
- #### check if rest charge is missing
+ # check if rest charge is missing
new_charge = sum(
[atom.charge for atom in psf.view[f":{self.tlc.upper()}"].atoms]
)
@@ -2477,37 +2398,20 @@ Source code for transformato.mutate
)
-
-[docs]
@staticmethod
- def _scale_epsilon_and_rmin(atom, lambda_value, psf, tlc):
- """
- This scales the LJ interactions (epsilon and rmin) from non-interacting DDD atom (no charge)
- to 'real' dummy atom (no LJ!), typically this is performed in one step, but to be sure
- we offer scalling possibility here as well
- """
+ def _scale_epsilon(atom, lambda_value: float):
logger.debug(atom)
logger.debug(atom.initial_epsilon)
- logger.debug(atom.initial_rmin)
-
atom.epsilon = atom.initial_epsilon * lambda_value
- atom.rmin = atom.initial_rmin * lambda_value
-
- ### do this only when using GAFF
- if type(psf) == pm.amber.AmberParm:
- # Quick check, if selected atom via AMBER mask is the same as the atom
- # we want to modify
- assert psf[f":{tlc}@{atom.idx+1}"].atoms[0].type == atom.type
- pm.tools.actions.addLJType(
- psf,
- f":{tlc}@{atom.idx+1}",
- radius=atom.initial_rmin * lambda_value,
- epsilon=atom.initial_epsilon * lambda_value,
- ).execute()
+ @staticmethod
+ def _scale_rmin(atom, lambda_value: float):
+ logger.debug(atom)
+ logger.debug(atom.initial_rmin)
+ atom.rmin = atom.initial_rmin * lambda_value
@staticmethod
- def _modify_type(atom, psf, atom_type_suffix, tlc):
+ def _modify_type(atom, psf, atom_type_suffix: str):
if hasattr(atom, "initial_type"):
# only change parameters
pass
@@ -2520,15 +2424,7 @@ Source code for transformato.mutate
psf.mutations_to_default += 1
new_type = f"{atom_type_suffix}{psf.mutations_to_default}"
- atom.type = new_type
-
- if type(psf) == pm.amber.AmberParm:
- pm.tools.actions.change(
- psf,
- "AMBER_ATOM_TYPE",
- f":{tlc}@{atom.idx+1}",
- new_type,
- ).execute()
+ atom.type = new_type
diff --git a/_modules/transformato/state.html b/_modules/transformato/state.html
index 18d84a99..0ef1bc28 100644
--- a/_modules/transformato/state.html
+++ b/_modules/transformato/state.html
@@ -178,50 +178,6 @@ Source code for transformato.state
fin.close()
fout.close()
-
-[docs]
- def _write_amber_files(
- self, psf: pm.amber.AmberParm, output_file_base: str, tlc: str, env: str
- ):
- """
- Write a parm7 and rst7 file for each intermediate step, including information about the dummy atoms
- """
- if env == "waterbox":
- psf.write_parm(f"{output_file_base}/lig_in_{env}.parm7")
- psf.write_rst7(f"{output_file_base}/lig_in_{env}.rst7")
- elif env == "vacuum":
- psf[f":{tlc}"].write_parm(f"{output_file_base}/lig_in_{env}.parm7")
- psf[f":{tlc}"].write_rst7(f"{output_file_base}/lig_in_{env}.rst7")
- ### This is only necessary, because we create the parm7 and rst7 by slicing the corresponding waterbox
- ### In this case there is one flag left which tells openmm when reading in the parm7 file, that there is
- ### a box (PBC). For that reason we have to manually set this flag to False (0).
- lines_left = 0
- with open(f"{output_file_base}/lig_in_{env}.parm7", "r") as file:
- with open(
- f"{output_file_base}/lig_in_{env}_temp.parm7", "w"
- ) as tempFile:
- for line in file:
- if line.startswith("%FLAG POINTERS"):
- lines_left = 6
- if lines_left > 0:
- lines_left -= 1
- if lines_left == 1:
- newLine = line[:63] + "0" + line[64:]
- assert (
- line.split()[7] == "1"
- ) # in this position it is usually 1 indicating a box, if we change it to 0, openmm thinks there is no box (see: https://ambermd.org/FileFormats.php#topo.cntrl)
- tempFile.write(newLine)
- else:
- tempFile.write(line)
- else:
- tempFile.write(line)
-
- shutil.move(tempFile.name, file.name)
-
- else:
- logger.critical(f"Environment {env} not supported")
-
-
[docs]
def write_state(
@@ -255,8 +211,7 @@ Source code for transformato.state
for mutation_type in mutation_conf:
if (
common_core_transformation < 1.0
- ): # NOTE: THis is inconsistent -- the mutatino_type is the actual mutation in this case
- # This happens only for one ligand and starts the process of changing cc1 into cc2
+ ): # NOTE: THis is inconsisten -- the mutatino_type is the actual mutation in this case
mutation_type.mutate(
psf=self.system.psfs[env],
lambda_value=common_core_transformation,
@@ -271,6 +226,7 @@ Source code for transformato.state
atoms_to_be_mutated=mutation_type.atoms_to_be_mutated,
dummy_region=mutation_type.dummy_region,
)
+
mutator.mutate(
psf=self.system.psfs[env],
lambda_value_electrostatic=lambda_value_electrostatic,
@@ -278,24 +234,10 @@ Source code for transformato.state
vdw_atom_idx=mutation_type.vdw_atom_idx,
steric_mutation_to_default=mutation_type.steric_mutation_to_default,
)
- if self.system.ff == "amber":
- # needed for each environment
- self._write_amber_files(
- self.system.psfs[env], output_file_base, self.system.tlc, env
- )
- elif self.system.ff == "charmm":
- self._write_psf(self.system.psfs[env], output_file_base, env)
-
- if self.system.ff == "charmm":
- # needed only once per intermediate state
- self._write_rtf_file(
- self.system.psfs[env], output_file_base, self.system.tlc
- )
- self._write_prm_file(
- self.system.psfs[env], output_file_base, self.system.tlc
- )
- self._write_toppar_str(output_file_base)
-
+ self._write_psf(self.system.psfs[env], output_file_base, env)
+ self._write_rtf_file(self.system.psfs[env], output_file_base, self.system.tlc)
+ self._write_prm_file(self.system.psfs[env], output_file_base, self.system.tlc)
+ self._write_toppar_str(output_file_base)
self._copy_files(output_file_base)
# Create run folder for dcd output for each intst state
@@ -323,6 +265,21 @@ Source code for transformato.state
self.current_step += 1
+ def _add_serializer(self, file):
+ # adding serializer functions
+ with open(file, "a") as f:
+ f.write(
+ """
+# mw: adding xml serializer to the simulation script
+file_name = str(args.psffile).replace('.psf', '')
+print(file_name)
+with open(file_name + '_integrator.xml','w') as outfile:
+ outfile.write(XmlSerializer.serialize(integrator))
+with open(file_name + '_system.xml','w') as outfile:
+ outfile.write(XmlSerializer.serialize(system))
+"""
+ )
+
def _get_simulations_parameters(self):
prms = {}
for key in self.configuration["simulation"]["parameters"]:
@@ -500,7 +457,7 @@ Source code for transformato.state
try:
shutil.copyfile(rst_file_source, rst_file_target)
except FileNotFoundError:
- logger.info(
+ logger.warning(
f"No restart file found for {env} -- starting simulation from crd file."
)
@@ -513,11 +470,11 @@ Source code for transformato.state
fout = open(f"{shFile}.tmp", "wt")
with open(f"{shFile}", "r+") as f:
for line in f:
- if line.startswith(f"istep=lig_in_"):
+ if line.startswith(f"input=lig_in_"):
fout.write("for i in {1.." + f"{self.multiple_runs}" + "};\n")
fout.write("do \n")
fout.write(line)
- elif line.startswith("python openmm"):
+ elif line.startswith("python -u openmm"):
line = line.replace("${istep}.dcd", "run_${i}/${istep}.dcd")
fout.write(
line.replace(
@@ -620,9 +577,13 @@ Source code for transformato.state
# copy diverse set of helper functions for openMM
FILES = [
+ "omm_barostat.py",
"omm_readinputs.py",
"omm_readparams.py",
+ "omm_restraints.py",
+ "omm_rewrap.py",
"omm_vfswitch.py",
+ "omm_hmr.py",
]
for f in FILES:
try:
@@ -633,13 +594,31 @@ Source code for transformato.state
logger.critical(f"Could not find file: {f}")
# copy omm simulation script
+ # start with waterbox
omm_simulation_script_source = f"{self.configuration['bin_dir']}/openmm_run.py"
omm_simulation_script_target = f"{intermediate_state_file_path}/openmm_run.py"
shutil.copyfile(omm_simulation_script_source, omm_simulation_script_target)
# add serialization
self._check_hmr(omm_simulation_script_target)
+ self._add_serializer(omm_simulation_script_target)
self._change_platform(omm_simulation_script_target)
- check_switching_function(self.vdw_switch)
+ check_switching_function(self.vdw_switch)
+
+ if (
+ self.configuration["simulation"]["free-energy-type"] == "rsfe"
+ or self.configuration["simulation"]["free-energy-type"] == "asfe"
+ ):
+ # add vacuum scripts
+ omm_simulation_script_source = (
+ f"{self.configuration['bin_dir']}/openmm_run_vacuum.py"
+ )
+ omm_simulation_script_target = (
+ f"{intermediate_state_file_path}/openmm_run_vacuum.py"
+ )
+ shutil.copyfile(omm_simulation_script_source, omm_simulation_script_target)
+ self._check_hmr(omm_simulation_script_target)
+ self._add_serializer(omm_simulation_script_target)
+ self._change_platform(omm_simulation_script_target)
@@ -666,60 +645,34 @@ Source code for transformato.state
f = open(file, "r")
g = open(f"{file}_tmp", "w+")
i = 0 # counting lines
- try:
- if self.configuration["simulation"]["GPU"].upper() == "OPENCL":
- for line in f.readlines():
- if "# Set platform" in line and i == 0:
- i += 1
- g.write(line)
- elif i == 1:
- i += 1
- g.write("platform = Platform.getPlatformByName('OpenCL')\n")
- elif i == 2:
- i += 2
- g.write("prop = dict(UseCpuPme='true')\n")
- else:
- g.write(line)
- elif self.configuration["simulation"]["GPU"].upper() == "CUDA":
- for line in f.readlines():
- if "# Set platform" in line and i == 0:
- i += 1
- g.write(line)
- elif i == 1:
- i += 1
- g.write("platform = Platform.getPlatformByName('CUDA')\n")
- elif i == 2:
- i += 2
- g.write("prop = dict()\n")
- else:
- g.write(line)
- except AttributeError:
- if self.configuration["simulation"]["GPU"] == True:
- for line in f.readlines():
- if "# Set platform" in line and i == 0:
- i += 1
- g.write(line)
- elif i == 1:
- i += 1
- g.write("platform = Platform.getPlatformByName('CUDA')\n")
- elif i == 2:
- i += 2
- g.write("prop = dict()\n")
- else:
- g.write(line)
- else:
- for line in f.readlines():
- if "# Set platform" in line and i == 0:
- i += 1
- g.write(line)
- elif i == 1:
- i += 1
- g.write("platform = Platform.getPlatformByName('CPU')\n")
- elif i == 2:
- i += 2
- g.write("prop = dict()\n")
- else:
- g.write(line)
+
+ if self.configuration["simulation"]["GPU"]:
+ logger.debug("Preparing for CUDA")
+ for line in f.readlines():
+ if "# Set platform" in line and i == 0:
+ i += 1
+ g.write(line)
+ elif i == 1:
+ i += 1
+ g.write("platform = Platform.getPlatformByName('CUDA')\n")
+ elif i == 2:
+ i += 2
+ g.write("prop = dict(CudaPrecision='mixed')\n")
+ else:
+ g.write(line)
+ else:
+ for line in f.readlines():
+ if "# Set platform" in line and i == 0:
+ i += 1
+ g.write(line)
+ elif i == 1:
+ i += 1
+ g.write("platform = Platform.getPlatformByName('CPU')\n")
+ elif i == 2:
+ i += 2
+ g.write("prop = dict()\n")
+ else:
+ g.write(line)
f.close()
g.close()
@@ -780,10 +733,8 @@ Source code for transformato.state
self._copy_ligand_specific_str(basedir, intermediate_state_file_path)
# copy crd file
- try:
- self._copy_crd_file((intermediate_state_file_path))
- except:
- pass
+ self._copy_crd_file((intermediate_state_file_path))
+
# copy openMM and charmm specific scripts
self._copy_omm_files(intermediate_state_file_path)
self._copy_charmm_files(intermediate_state_file_path)
@@ -853,27 +804,21 @@ Source code for transformato.state
)
logger.critical(f"###################")
- try:
- for l in input_simulation_parameter.readlines():
- if l.strip():
- t1, t2_comment = [e.strip() for e in l.split("=")]
- t2, comment = [e.strip() for e in t2_comment.split("#")]
- comment = comment.strip()
- if t1 in overwrite_parameters.keys():
- t2 = overwrite_parameters[t1]
- del overwrite_parameters[t1] # remove from dict
- if t1 == "vdw":
- t2 = t2.capitalize()
- output_simulation_parameter.write(
- f"{t1:<25} = {t2:<25} # {comment:<30}\n"
- )
- else:
- output_simulation_parameter.write("\n")
- except ValueError:
- logger.critical(
- f"The original inp {input_simulation_parameter.name} file contains a line without a comment "
- )
- raise SystemExit
+ for l in input_simulation_parameter.readlines():
+ if l.strip():
+ t1, t2_comment = [e.strip() for e in l.split("=")]
+ t2, comment = [e.strip() for e in t2_comment.split("#")]
+ comment = comment.strip()
+ if t1 in overwrite_parameters.keys():
+ t2 = overwrite_parameters[t1]
+ del overwrite_parameters[t1] # remove from dict
+ if t1 == "vdw":
+ t2 = t2.capitalize()
+ output_simulation_parameter.write(
+ f"{t1:<25} = {t2:<25} # {comment:<30}\n"
+ )
+ else:
+ output_simulation_parameter.write("\n")
# set parameters that have no equivalent in the pregenerated parameter file
for t1 in overwrite_parameters.keys():
diff --git a/_modules/transformato/system.html b/_modules/transformato/system.html
index 229305c9..fcb84e69 100644
--- a/_modules/transformato/system.html
+++ b/_modules/transformato/system.html
@@ -115,20 +115,11 @@ Source code for transformato.system
self.name: str = configuration["system"][structure]["name"]
self.tlc: str = configuration["system"][structure]["tlc"]
self.charmm_gui_base: str = configuration["system"][structure]["charmm_gui_dir"]
+ self.psfs: defaultdict = defaultdict(pm.charmm.CharmmPsfFile)
self.offset: defaultdict = defaultdict(int)
+ self.parameter = self._read_parameters("waterbox")
+ self.cgenff_version: float
self.envs = set()
-
- try:
- self.ff: str = str.lower(configuration["simulation"]["forcefield"])
- self.psfs: defaultdict = defaultdict(pm.amber.AmberParm)
- except KeyError:
- self.ff: str = "charmm"
- self.psfs: defaultdict = defaultdict(pm.charmm.CharmmPsfFile)
- self.parameter = self._read_parameters(
- "waterbox"
- ) # not sure if this is really needed
- self.cgenff_version: float
-
# running a binding-free energy calculation?
if configuration["simulation"]["free-energy-type"] == "rbfe":
self.envs = set(["complex", "waterbox"])
@@ -157,32 +148,17 @@ Source code for transformato.system
):
self.envs = set(["waterbox", "vacuum"])
for env in self.envs:
- if self.ff == "charmm":
- parameter = self._read_parameters(env)
- # set up system
- self.psfs[env] = self._initialize_system(configuration, env)
- # load parameters
- self.psfs[env].load_parameters(parameter)
- self.offset[
- env
- ] = self._determine_offset_and_set_possible_dummy_properties(
- self.psfs[env]
- )
-
- elif self.ff == "amber":
- self.psfs[env] = pm.load_file(
- f"{self.charmm_gui_base}/waterbox/openmm/step3_input.parm7"
- )
- self.psfs[env].load_rst7(
- f"{self.charmm_gui_base}/waterbox/openmm/step3_input.rst7"
- )
- self.offset[
- env
- ] = self._determine_offset_and_set_possible_dummy_properties(
- self.psfs[env]
- )
- # if env == "vacuum":
- # self.psfs["vacuum"] = self.psfs["waterbox"][f":{self.tlc}"]
+ parameter = self._read_parameters(env)
+ # set up system
+ self.psfs[env] = self._initialize_system(configuration, env)
+ # load parameters
+ self.psfs[env].load_parameters(parameter)
+ # get offset
+ self.offset[
+ env
+ ] = self._determine_offset_and_set_possible_dummy_properties(
+ self.psfs[env]
+ )
# generate rdkit mol object of small molecule
self.mol: Chem.Mol = self._generate_rdkit_mol(
@@ -293,7 +269,7 @@ Source code for transformato.system
)
# check cgenff versions
- if parameter_files and self.ff == "charmm":
+ if parameter_files:
with open(parameter_files[0]) as f:
_ = f.readline()
cgenff = f.readline().rstrip()
@@ -416,11 +392,7 @@ Source code for transformato.system
Returns
----------
"""
- if self.ff == "amber":
- assert type(psf) == pm.amber._amberparm.AmberParm
- else:
- assert type(psf) == pm.charmm.CharmmPsfFile
-
+ assert type(psf) == pm.charmm.CharmmPsfFile
if len(psf.view[f":{self.tlc}"].atoms) < 1:
raise RuntimeError(f"No ligand selected for tlc: {self.tlc}")
@@ -490,6 +462,7 @@ Source code for transformato.system
mol: rdkit.Chem.rdchem.Mol
"""
+ assert type(psf) == pm.charmm.CharmmPsfFile
mol = self._return_small_molecule(env)
(
atom_idx_to_atom_name,
@@ -510,12 +483,11 @@ Source code for transformato.system
)
# check if psf and sdf have same indeces
- # if self.ff == "charmm":
- # for a in mol.GetAtoms():
- # if str(psf[a.GetIdx()].element_name) == str(a.GetSymbol()):
- # pass
- # else:
- # raise RuntimeError("PSF to mol conversion did not work! Aborting.")
+ for a in mol.GetAtoms():
+ if str(psf[a.GetIdx()].element_name) == str(a.GetSymbol()):
+ pass
+ else:
+ raise RuntimeError("PSF to mol conversion did not work! Aborting.")
return mol
diff --git a/_sources/autosummary/transformato.utils.rst.txt b/_sources/autosummary/transformato.utils.rst.txt
index f57b8745..c5878af9 100644
--- a/_sources/autosummary/transformato.utils.rst.txt
+++ b/_sources/autosummary/transformato.utils.rst.txt
@@ -28,6 +28,8 @@ Functions
.. automethod:: transformato.utils.get_structure_name
+.. automethod:: transformato.utils.get_test_output_dir
+
.. automethod:: transformato.utils.get_toppar_dir
.. automethod:: transformato.utils.isnotebook
@@ -38,8 +40,6 @@ Functions
.. automethod:: transformato.utils.postprocessing
-.. automethod:: transformato.utils.print_mutations
-
.. automethod:: transformato.utils.psf_correction
.. automethod:: transformato.utils.run_simulation
diff --git a/autosummary/transformato.mutate.html b/autosummary/transformato.mutate.html
index 693f6cfa..9c64fbc8 100644
--- a/autosummary/transformato.mutate.html
+++ b/autosummary/transformato.mutate.html
@@ -331,31 +331,6 @@ Description
-
-_mutate_vdw(psf, lambda_value, vdw_atom_idx, offset, to_default)[source]
-This is used to scale the LJ parameters of the DDD and DDX atoms to zero in phase II and III
-
-- Parameters:
-
-psf (CharmmPsfFile) –
lambda_value (float) –
vdw_atom_idx (List[int]) –
offset (int) –
to_default (bool) –
-
-
--
-static _scale_epsilon_and_rmin(atom, lambda_value, psf, tlc)[source]
-This scales the LJ interactions (epsilon and rmin) from non-interacting DDD atom (no charge)
-to ‘real’ dummy atom (no LJ!), typically this is performed in one step, but to be sure
-we offer scalling possibility here as well
-
-
-
mutate(psf, lambda_value_electrostatic=1.0, lambda_value_vdw=1.0, vdw_atom_idx=[], steric_mutation_to_default=False)[source]
diff --git a/autosummary/transformato.state.html b/autosummary/transformato.state.html
index cd5d6a93..aa7fa755 100644
--- a/autosummary/transformato.state.html
+++ b/autosummary/transformato.state.html
@@ -220,22 +220,6 @@ Description
--
-_write_amber_files(psf, output_file_base, tlc, env)[source]
-Write a parm7 and rst7 file for each intermediate step, including information about the dummy atoms
-
-- Parameters:
-
-psf (AmberParm) –
output_file_base (str) –
tlc (str) –
env (str) –
-
-
-
-
static _write_psf(psf, output_file_base, env)[source]
diff --git a/autosummary/transformato.utils.html b/autosummary/transformato.utils.html
index 63a03353..024d0a7d 100644
--- a/autosummary/transformato.utils.html
+++ b/autosummary/transformato.utils.html
@@ -66,12 +66,12 @@
utils.check_switching_function()utils.get_bin_dir()utils.get_structure_name()utils.get_test_output_dir()utils.get_toppar_dir()utils.isnotebook()utils.load_config_yaml()utils.map_lj_mutations_to_atom_idx()utils.postprocessing()utils.print_mutations()utils.psf_correction()utils.run_simulation()Description
+
+utils.get_test_output_dir()
+
+
-
utils.get_toppar_dir()
@@ -206,16 +211,6 @@ Description
--
-utils.print_mutations()
-
-- Parameters:
-mutation (dict) –
-
-
-
-
utils.psf_correction()
diff --git a/genindex.html b/genindex.html
index e1b5bf49..d8c754ef 100644
--- a/genindex.html
+++ b/genindex.html
@@ -194,12 +194,12 @@ _
_check_for_lp() (transformato.mutate.ProposeMutationRoute method)
+
+
- _copy_charmm_files() (transformato.state.IntermediateStateFactory method)
- _copy_files() (transformato.state.IntermediateStateFactory method)
@@ -233,20 +233,14 @@
_
- _mutate_atoms() (transformato.mutate.CommonCoreTransformation method)
- _mutate_to_common_core() (transformato.mutate.ProposeMutationRoute method)
-
- - _mutate_vdw() (transformato.mutate.Mutation method)
- _overwrite_simulation_script_parameters() (transformato.state.IntermediateStateFactory method)
- _read_parameters() (transformato.system.SystemStructure method)
-
- - _scale_epsilon_and_rmin() (transformato.mutate.Mutation static method)
- _show_common_core() (transformato.mutate.ProposeMutationRoute method)
- _transform_common_core() (transformato.mutate.ProposeMutationRoute method)
-
- - _write_amber_files() (transformato.state.IntermediateStateFactory method)
- _write_psf() (transformato.state.IntermediateStateFactory static method)
@@ -475,6 +469,8 @@ G
- get_idx_of_all_atoms() (transformato.mutate.ProposeMutationRoute method)
- get_structure_name() (transformato.utils method)
+
+ - get_test_output_dir() (transformato.utils method)
- get_toppar_dir() (transformato.utils method)
@@ -671,8 +667,6 @@ P
- perform_mutations() (transformato.mutate method)
- postprocessing() (transformato.utils method)
-
- - print_mutations() (transformato.utils method)
diff --git a/objects.inv b/objects.inv
index d60f403c..f921c70d 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index 6fccbee4..4cfa004f 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["Additional_Settings", "Analysis", "Installation", "Running_Simulation", "System_Setup", "Troubleshooting", "api", "autosummary/transformato.mutate", "autosummary/transformato.restraints", "autosummary/transformato.state", "autosummary/transformato.system", "autosummary/transformato.utils", "index", "whatistransformato"], "filenames": ["Additional_Settings.rst", "Analysis.rst", "Installation.rst", "Running_Simulation.rst", "System_Setup.rst", "Troubleshooting.rst", "api.rst", "autosummary/transformato.mutate.rst", "autosummary/transformato.restraints.rst", "autosummary/transformato.state.rst", "autosummary/transformato.system.rst", "autosummary/transformato.utils.rst", "index.rst", "whatistransformato.rst"], "titles": ["Additional Settings", "Trajectory Analysis", "Installation", "Running Simulations", "System Setup", "Troubleshooting", "API Documentation", "transformato.mutate", "transformato.restraints", "transformato.state", "transformato.system", "transformato.utils", "Welcome to the documentation for transformato!", "Theoretical background"], "terms": {"thi": [0, 1, 2, 3, 4, 5, 7, 8, 11, 13], "section": [0, 4, 8], "onli": [0, 1, 3, 7, 8, 11, 13], "appli": [0, 1, 4, 8], "you": [0, 1, 2, 3, 4, 5, 8, 12], "ar": [0, 1, 2, 3, 4, 5, 7, 8, 9, 11, 12, 13], "run": [0, 1, 2, 4, 5, 8, 9, 12, 13], "your": [0, 1, 2, 3, 4, 5, 8], "simul": [0, 1, 2, 4, 8, 9, 12, 13], "openmm": [0, 1, 2, 3, 4, 8, 9, 11, 12], "should": [0, 1, 3, 4, 5, 7, 8, 9], "us": [0, 1, 2, 3, 7, 8, 9, 11, 12, 13], "charmm": [0, 1, 3, 7, 9, 10, 11, 12], "give": [0, 9], "warn": [0, 3], "about": [0, 4, 9], "texttt": [0, 1, 3, 4, 12, 13], "transformato": [0, 1, 3, 4, 5, 6, 13], "support": [0, 1, 4], "two": [0, 1, 3, 4, 7, 8, 9, 12, 13], "type": [0, 4, 7, 8, 9, 10, 11], "To": [0, 1, 3], "activ": [0, 1, 2, 3], "ligand": [0, 1, 3, 4, 7, 8, 10, 13], "add": [0, 3, 7, 8, 9], "auto": 0, "config": [0, 1, 3, 4, 5, 8, 9], "yaml": [0, 1, 2, 3, 5, 8, 12], "wil": 0, "restrain": 0, "its": [0, 4, 7, 8, 11, 13], "origin": [0, 3, 9], "posit": [0, 4, 8], "harmon": [0, 8], "potenti": [0, 8], "form": [0, 5], "e": [0, 1, 4, 5, 7, 8], "0": [0, 4, 5, 7, 8, 9, 11, 13], "5k": 0, "cdot": 0, "r": [0, 12, 13], "r_0": 0, "\u00b2": 0, "where": [0, 3, 4, 5, 8], "i": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 12, 13], "current": [0, 2, 3, 12], "distanc": [0, 8], "math": [0, 13], "initi": [0, 3, 8], "k": [0, 8], "forc": [0, 8, 13], "constant": [0, 8], "within": [0, 2, 4], "center": [0, 8], "surround": [0, 8], "protein": [0, 4, 13], "structur": [0, 3, 4, 5, 8, 10, 13], "keep": 0, "vagu": 0, "fix": 0, "mai": [0, 2, 3, 4], "specifi": [0, 5, 8, 9], "further": [0, 1, 4, 8, 13], "keyword": 0, "option": [0, 1, 3, 7, 9, 11], "int": [0, 1, 4, 7, 8, 9, 10, 11], "defin": [0, 3, 4, 5, 7, 8, 9], "spring": [0, 8], "calcul": [0, 1, 4, 8, 11, 12, 13], "default": [0, 1, 3, 4, 7, 8, 9, 11, 13], "3": [0, 1, 4, 8, 12, 13], "extrem": [0, 8], "If": [0, 2, 3, 4, 8, 12], "entir": 0, "common": [0, 1, 3, 8, 12], "core": [0, 1, 3, 7, 8, 12], "rather": 0, "look": [0, 3, 4, 7, 12], "These": [0, 3, 4, 8], "carbon": [0, 8], "alpha": [0, 8], "shape": [0, 8], "flatbottom": [0, 8], "energi": [0, 1, 4, 8, 11, 12, 13], "The": [0, 3, 4, 7, 8, 9, 11, 12], "term": 0, "given": [0, 4, 9, 11], "step": [0, 7, 8, 9, 12, 13], "thresh": 0, "function": [0, 1], "return": [0, 7, 8, 10, 11], "until": [0, 8], "threshold": 0, "wellsiz": [0, 8], "ha": [0, 3, 4, 7], "been": [0, 7], "surpass": 0, "after": [0, 1, 3, 4, 8], "which": [0, 1, 4, 7, 8, 9, 13], "1": [0, 1, 3, 5, 7, 9, 12, 13], "As": [0, 1, 4], "flat": [0, 8], "bottom": [0, 3, 8], "essenti": [0, 3], "well": [0, 3, 4, 7, 8, 13], "zero": [0, 7], "note": [0, 3], "act": 0, "like": [0, 1, 3, 4, 12], "radiu": 0, "mean": [0, 4, 5, 13], "extend": [0, 4], "all": [0, 1, 3, 4, 5, 8, 9, 10, 13], "direct": 0, "from": [0, 1, 3, 4, 7, 8, 9, 10, 12, 13], "figur": [0, 4, 13], "differ": [0, 1, 10, 12, 13], "between": [0, 3, 4, 5, 7, 8, 11, 13], "A": [0, 2, 4, 7, 8, 10, 12, 13], "b": [0, 12, 13], "while": [0, 2], "both": [0, 1, 3, 8, 13], "allow": [0, 3], "more": [0, 1, 3, 5], "movement": 0, "closer": 0, "effect": 0, "sampl": [0, 3, 11, 13], "area": 0, "can": [0, 1, 2, 3, 4, 5, 7, 11, 12, 13], "move": [0, 4], "without": [0, 3, 12, 13], "hindranc": 0, "cannot": [0, 8], "leav": 0, "assum": [0, 3], "strong": 0, "enough": 0, "valu": [0, 7, 9], "scale": [0, 3, 7, 13], "present": 0, "linearli": 0, "first": [0, 2, 4, 5, 13], "four": 0, "intermedi": [0, 1, 2, 3, 4, 5, 8, 9, 13], "state": [0, 1, 2, 4, 5, 8, 12, 13], "intst1": [0, 3, 5], "intst2": [0, 3, 8], "25": 0, "intst3": 0, "5": [0, 3, 7, 8, 13], "intst4": 0, "75": 0, "intst5": 0, "float": [0, 7, 8, 9], "take": [0, 1, 2, 3, 4, 8, 12], "nanomet": [0, 8], "nm": 0, "full": [0, 8], "entri": 0, "might": [0, 3, 4], "thu": [0, 13], "10": [0, 2, 7, 13], "Be": [0, 7], "somewhat": [0, 3], "sure": [0, 1, 2, 3, 4, 7], "what": [0, 3], "do": [0, 2, 3, 4, 5, 7], "saniti": 0, "check": [0, 1, 2, 4, 7, 8], "gener": [0, 2, 3, 4, 8, 9, 10, 12, 13], "befor": [0, 1, 3, 5, 7], "product": [0, 4, 9, 12], "an": [0, 1, 2, 3, 4, 8, 9, 12, 13], "arbitrarili": 0, "high": 0, "number": [0, 1, 3, 4, 5, 8, 9, 11, 13], "exterm": 0, "lead": 0, "strang": 0, "result": [0, 1, 4, 13], "It": [0, 3, 4, 7, 12], "small": [0, 3, 10], "file": [0, 2, 3, 5, 7, 8, 9, 10, 11, 12], "call": [0, 1, 2, 3, 4, 5, 7, 8], "creat": [0, 1, 2, 5, 7, 8, 9, 12, 13], "intst": [0, 3, 9], "folder": [0, 1, 3, 4, 9, 10, 13], "have": [0, 1, 3, 4, 5, 7], "follow": [0, 1, 2, 3, 4, 6, 8, 13], "system": [0, 1, 3, 7, 8, 9, 11, 12, 13], "tlc": [0, 4, 7, 9], "lig": [0, 4], "same": [0, 1, 3, 4, 7, 13], "one": [0, 1, 2, 3, 4, 7, 8, 13], "relev": 0, "cc": [0, 1, 7, 12, 13], "repres": [0, 8], "arrai": [0, 7, 8, 13], "upon": 0, "c1": 0, "c2": 0, "h2": 0, "8": [0, 3, 13], "non": [0, 5, 7, 13], "immedi": 0, "switch": [0, 3, 4, 11], "how": [0, 3, 4, 7, 8, 9], "far": 0, "along": [0, 3, 4], "recommend": [0, 1, 3, 4], "edit": 0, "thei": 0, "each": [0, 3, 4, 8, 9, 13], "below": [0, 1, 3, 4], "now": [0, 1, 2, 3, 4], "arbitrari": 0, "mdanalysi": [0, 8, 11, 13], "select": [0, 8, 9, 11, 13], "syntax": 0, "manualrestraint": 0, "restraint1": 0, "group1": 0, "resnam": [0, 4], "c": [0, 2, 3, 8, 13], "group2": 0, "ca": 0, "30": [0, 13], "r0": 0, "2": [0, 1, 3, 5, 7, 11, 12, 13], "41": 0, "mani": [0, 3, 4, 7, 8, 9], "code": [0, 1, 3, 7, 12], "exampl": [0, 3, 4], "multipl": [0, 13], "restraint2": 0, "restraint3": 0, "name": [0, 1, 4, 7, 8, 11], "c14": 0, "sphlayer": [0, 8], "15": 0, "individu": [0, 13], "need": [0, 1, 3, 4, 7, 8, 9, 13], "distinct": 0, "etc": [0, 1, 3, 4], "requir": [0, 2, 3, 4, 5, 12], "simpli": 0, "adher": 0, "freeli": 0, "choos": [0, 1], "here": [0, 1, 3, 7, 8], "provid": [0, 3, 4, 8, 9], "speak": 0, "identif": 0, "later": [0, 3, 4], "see": [0, 1, 2, 3, 4, 8], "detail": [0, 3, 4, 8], "string": [0, 8], "atom": [0, 3, 5, 9, 11, 12], "member": 0, "pleas": [0, 3], "must": [0, 4], "unit": 0, "even": 0, "never": 0, "would": [0, 3, 4, 7], "nonsens": 0, "acceler": 0, "md": [0, 3, 11, 12, 13], "possibl": [0, 3, 4, 7, 10, 11], "reweight": 0, "reduc": 0, "vibrat": 0, "frequenc": [0, 4], "correspond": [0, 4], "heavi": [0, 13], "bond": [0, 7, 8, 13], "when": [0, 1, 4, 5, 8, 13], "con": [0, 4], "hbond": [0, 4], "safe": 0, "increas": 0, "time": [0, 1, 2, 3, 4, 12, 13], "4": [0, 7, 11, 13], "f": [0, 1, 3, 5], "either": [0, 3, 4, 5, 9, 10, 11, 12, 13], "box": [0, 4], "last": [0, 4, 5], "gui": [0, 9, 10, 12], "solut": [0, 4, 13], "builder": [0, 4, 13], "parm": [0, 3, 7, 13], "action": 0, "tool": [0, 12, 13], "also": [0, 1, 3, 4], "avail": [0, 3], "fep": [0, 1, 2, 3, 4, 5], "conda": [0, 1, 2, 3], "environ": [0, 1, 2, 3, 4, 10, 13], "psf": [0, 3, 4, 7, 9, 10, 11], "pm": [0, 7, 10], "charmmpsffil": [0, 7, 10], "step3_input_orig": 0, "hmassrepartit": 0, "execut": [0, 1], "save": 0, "step3_input": [0, 4], "overwrit": [0, 9], "true": [0, 1, 3, 4, 7], "In": [1, 3, 4, 13], "theori": 1, "could": [1, 5], "directli": [1, 4, 7, 8, 12, 13], "submit": [1, 3, 4, 13], "ipynb": [1, 3, 4], "done": [1, 3, 13], "howev": [1, 3, 4, 13], "we": [1, 3, 4, 7, 13], "instead": [1, 13], "least": 1, "rbfe": [1, 3, 4, 5, 12, 13], "put": [1, 5], "separ": 1, "usual": [1, 5, 7, 8, 9, 13], "alias": 1, "shell": 1, "script": [1, 3, 4], "command": [1, 2, 3], "necessari": [1, 2, 3, 4, 7, 13], "analys": [1, 2, 3], "trajetori": 1, "snippet": 1, "jupyt": [1, 3], "notebook": [1, 3], "finish": [1, 3], "termin": [1, 5, 7], "python": [1, 2, 3, 12, 13], "output_dir": [1, 3, 5, 11], "path": [1, 3, 5, 8, 9], "conf": 1, "whether": [1, 3, 4], "properli": [1, 3], "go": [1, 2, 4], "intstx": 1, "directori": [1, 2, 3, 4, 5, 7, 8, 9, 11], "waterbox_out": [1, 3, 5], "log": [1, 3, 5], "complex_out": [1, 3, 5], "rsfe": [1, 3, 4, 12, 13], "vacuum_out": 1, "decent": 1, "amout": 1, "just": [1, 3, 4], "amount": [1, 3, 8], "comput": [1, 12, 13], "resourc": 1, "depend": [1, 3, 4], "therefor": 1, "especi": [1, 13], "import": [1, 2, 3, 4, 7], "load_config_yaml": [1, 3, 5, 10, 11], "util": [1, 3, 5, 8, 10], "postprocess": [1, 3, 5, 11], "sy": 1, "come": 1, "frome": 1, "sh": [1, 3, 9], "standalon": 1, "outsid": 1, "argv": 1, "configur": [1, 3, 7, 8, 9, 10, 11], "input_dir": [1, 3, 5, 11], "structure1": [1, 3, 4, 10], "structure2": [1, 3, 4, 10], "ddg_openmm": [1, 5], "dddg": [1, 5], "f_openmm": [1, 5], "engin": [1, 3, 4, 11, 12, 13], "max_snapshot": [1, 11], "10000": 1, "num_proc": [1, 11], "6": [1, 13], "analyze_traj_with": [1, 11], "mda": 1, "show_summari": [1, 11], "print": [1, 2, 3, 5], "free": [1, 4, 11, 12, 13], "kt": 1, "set": [1, 3, 4, 7, 10, 12], "up": [1, 2, 3, 4, 12], "sever": [1, 3], "thing": 1, "want": [1, 3, 4, 8], "analyz": [1, 4], "enter": 1, "300": [1, 11], "snapshot": [1, 11], "per": [1, 4, 9, 11], "longer": 1, "mdtraj": [1, 11], "program": [1, 12, 13], "main": [1, 8], "multiprocess": [1, 3], "less": 1, "memori": 1, "gpu": [1, 3, 4], "get": [1, 7, 12], "substructur": 1, "g": [1, 4, 5, 7, 8, 12, 13], "delta": [1, 13], "bind": [1, 4, 12, 13], "_": [1, 13], "l1": [1, 13], "rightarrow": [1, 13], "dl_1": [1, 13], "r_": [1, 13], "final": [1, 3, 4, 7, 13], "l2": [1, 13], "substract": 1, "ligand2": [1, 4], "dl_2": [1, 13], "explain": 1, "theoret": [1, 12], "background": [1, 12], "start": [1, 3, 8, 13], "via": [1, 3, 12], "open": [1, 2], "analysis_": [1, 5], "w": 1, "write": [1, 3, 4, 8, 9], "bin": [1, 3, 9, 11], "bash": [1, 3], "n": [1, 8, 12, 13], "sbatch": [1, 3], "gre": [1, 3], "input": [1, 3, 4], "line": [1, 5], "slurm": [1, 3, 4, 5], "p": [1, 3, 4], "lgpu": [1, 3], "d": [1, 3, 12, 13], "afterani": 1, "jobid": 1, "make": [1, 2, 3, 4], "sourc": [1, 3, 7, 8, 9, 10], "miniconda3": 1, "profil": [1, 3], "cd": [1, 2, 3], "wd": [1, 3], "out": [1, 3, 5, 13], "ex": [1, 3], "subprocess": [1, 3], "popen": [1, 3], "ssh": [1, 3], "clusternam": [1, 3], "text": [1, 3], "stdout": [1, 3], "pipe": [1, 3], "output": [1, 2, 3, 4, 5, 9, 10, 12, 13], "read": [1, 3, 8, 10], "variabl": [1, 3, 5], "known": 1, "begin": 1, "manual": [1, 3], "simplifi": 1, "matter": 1, "contain": [1, 3, 4, 5, 10, 13], "case": [1, 3, 4, 7], "addit": [1, 3, 4, 8, 12], "work": [2, 3, 8, 12, 13], "version": 2, "miniconda": 2, "git": 2, "cuda": 2, "capabl": 2, "devic": 2, "local": [2, 3, 5], "node": [2, 7], "machin": [2, 3], "Then": 2, "clone": 2, "repositori": [2, 12, 13], "http": 2, "github": [2, 12], "com": 2, "wiederm": 2, "newli": 2, "found": [2, 3, 8, 9], "devtool": 2, "env": [2, 5, 9, 10], "fep_env": 2, "minut": 2, "For": [2, 3, 5, 8, 11, 12, 13], "nvidia": 2, "packag": [2, 5, 11, 12, 13], "cudatoolkit": 2, "higher": 2, "than": 2, "driver": 2, "smi": 2, "list": [2, 3, 8, 9, 10, 11], "correct": [2, 3, 11], "x": [2, 5], "y": 2, "forg": 2, "setup": [2, 3, 8, 12], "py": [2, 3, 4, 5, 8, 12], "try": 2, "__version__": 2, "congratul": 2, "readi": [2, 13], "unsur": 3, "inspir": 3, "actual": [3, 4, 8], "compris": 3, "dure": [3, 4], "stage": 3, "adjust": [3, 7], "dummi": [3, 5, 7, 9, 13], "region": [3, 5, 7, 13], "conduct": 3, "complex": [3, 4, 9, 10], "waterbox": [3, 4, 9, 10, 11], "trajcetori": 3, "shown": 3, "xxxxxxxxxxxxxxxx": 3, "ipython": 3, "interpret": 3, "vscode": 3, "enabl": [3, 4], "easier": 3, "visual": 3, "load": [3, 8, 11], "part": [3, 4, 13], "modul": [3, 5, 6, 7], "tell": 3, "our": [3, 12], "argument": 3, "find": [3, 5, 7, 8], "respect": [3, 4, 5, 13], "systemstructur": [3, 7, 9, 10], "intermediatestatefactori": [3, 9], "proposemutationrout": [3, 7, 9], "mutat": [3, 4, 9, 11, 13], "perform_mut": [3, 7], "displai": 3, "svg": 3, "run_simul": [3, 11], "filterwarn": 3, "ignor": 3, "24to25": 3, "longrun": 3, "norestraint": 3, "paramet": [3, 4, 5, 7, 8, 9, 10, 11, 13], "user": 3, "store": [3, 4], "intermediat": 3, "rout": 3, "process": 3, "alchem": [3, 12, 13], "connect": [3, 7, 12, 13], "s1": [3, 7], "s2": [3, 7], "s1_to_s2": [3, 7], "propose_common_cor": [3, 7], "suggest": 3, "show_common_core_on_mol1": [3, 7], "show_common_core_on_mol2": [3, 7], "doe": [3, 12], "interfer": 3, "add_idx_to_common_core_of_mol1": [3, 7], "idx1": 3, "idx2": 3, "add_idx_to_common_core_of_mol2": [3, 7], "remov": [3, 7], "remove_idx_to_common_core_of_mol1": 3, "remove_idx_to_common_core_of_mol2": 3, "idx": [3, 7, 8, 11], "graphic": 3, "beforehand": 3, "order": 3, "finish_common_cor": [3, 7], "attempt": 3, "charg": [3, 5, 7], "repeat": 3, "abov": [3, 4], "chang": [3, 4, 7, 9], "made": 3, "mutation_list": [3, 7, 9], "generate_mutations_to_common_core_for_mol1": [3, 7], "endstat": [3, 4, 7, 12, 13], "nr_of_mutation_steps_charg": [3, 7], "With": [3, 7, 13], "written": [3, 9], "error": [3, 12], "proce": 3, "nr_of_mutation_steps_cc": [3, 7], "interpol": [3, 7], "output_fil": [3, 11], "decid": [3, 7], "alreadi": [3, 7], "instal": [3, 4, 12], "oneself": 3, "technic": 3, "lot": 3, "reason": [3, 13], "strongli": [3, 4], "offload": [3, 12], "them": [3, 4, 8], "supercomput": 3, "though": 3, "easili": 3, "locat": [3, 9], "project": 3, "replic": 3, "combinedstructur": [3, 8], "singlestructur": 3, "ll": 3, "simulation_charmm": 3, "unsurprisingli": 3, "respons": 3, "inform": [3, 4, 8, 9, 10, 12, 13], "featur": 3, "modifi": [3, 8, 12], "futur": 3, "some": [3, 5], "wai": [3, 4], "anaconda3": [3, 5], "pwd": 3, "hostnam": 3, "lig_in_complex": [3, 4, 5], "init": 3, "pstep": 3, "istep": 3, "irst": 3, "orst": 3, "lig_in_complex_rst": 3, "u": 3, "openmm_run": [3, 8], "inp": [3, 4], "t": [3, 12], "toppar": [3, 9, 10], "str": [3, 7, 8, 9, 10, 11], "crd": [3, 4], "rst": [3, 4, 5], "odcd": 3, "dcd": 3, "lig_in_waterbox": [3, 4], "lig_in_waterbox_rst": 3, "bit": 3, "debug": [3, 11, 12], "importantli": [3, 4], "so": [3, 11, 12], "absolut": 3, "rel": [3, 4, 12, 13], "intermediatest": [3, 7], "suppli": [3, 4], "run_complex": 3, "charmm_run_complex": 3, "omp_num_thread": 3, "log_complex": 3, "run_waterbox": 3, "charmm_run_waterbox": 3, "log_solv": 3, "esac": 3, "unlik": 3, "statement": [3, 11], "alwai": [3, 4, 7], "autom": 3, "cluster": [3, 12], "There": [3, 11], "method": [3, 4], "advantag": 3, "extra": 3, "being": [3, 13], "facil": 3, "caprici": 3, "variant": 3, "inspect": 3, "submiss": 3, "o": [3, 5, 12], "glob": 3, "getcwd": 3, "recurs": 3, "point": [3, 8], "sort": [3, 7], "replac": [3, 11], "accord": [3, 7, 13], "reliabl": 3, "modif": 3, "instruct": [3, 8], "similar": [3, 8, 13], "prevent": 3, "issu": [3, 11], "prefer": 3, "sbash": 3, "workload": [3, 4, 9], "manag": [3, 4, 5, 8, 9], "back": 3, "next": [3, 5, 7], "loop": 3, "ani": [3, 4], "correctli": [3, 5], "built": 3, "restrict": 3, "certain": 3, "talk": 4, "vacuum": [4, 9, 10, 13], "ga": 4, "phase": [4, 7], "automat": [4, 10], "successfulli": 4, "three": [4, 7, 11], "item": 4, "": [4, 10, 12, 13], "solvat": [4, 12, 13], "onc": 4, "pure": 4, "describ": 4, "standard": [4, 13], "analysi": [4, 12, 13], "cover": 4, "trajectori": [4, 11, 12, 13], "page": [4, 13], "overal": 4, "everyth": [4, 9, 10], "interest": 4, "physic": [4, 7, 12, 13], "encourag": 4, "specif": [4, 7, 9, 10], "pdb": [4, 9], "bound": [4, 13], "sdf": 4, "mol2": [4, 7], "someth": 4, "4842148": 4, "renam": 4, "second": 4, "third": 4, "fourth": 4, "equillibr": 4, "equilibr": [4, 5], "indict": 4, "strucr": 4, "among": 4, "other": [4, 7, 13], "prm": 4, "rtf": [4, 9], "strictli": 4, "build": 4, "yourself": 4, "proper": 4, "cgenff": 4, "length": 4, "restraint": [4, 12], "let": 4, "complet": 4, "vim2_zn148": 4, "dirnam": 4, "psf_file_nam": 4, "crd_file_nam": 4, "rst_file_nam": 4, "step4_equilibr": 4, "simulation_paramet": 4, "step5_product": 4, "filenam": 4, "step3": 4, "vim2_zn222": 4, "nstep": [4, 5], "1250000": 4, "nstdcd": [4, 5], "1000": 4, "nstout": 4, "dt": 4, "004": 4, "vfswitch": [4, 11], "mini_nstep": 4, "steps_for_equilibr": 4, "most": [4, 5, 7], "referenc": [4, 5], "residu": 4, "often": 4, "unk": 4, "refer": [4, 7, 8, 9, 10, 12, 13], "variou": 4, "subfold": 4, "coordin": [4, 10], "none": [4, 5, 7], "constraint": 4, "timestep": 4, "picosecond": 4, "001": 4, "002": 4, "hydrogen": [4, 7, 12, 13], "mass": [4, 8, 12], "repartit": [4, 12], "vdw": [4, 7], "cut": 4, "off": [4, 7, 13], "minim": 4, "fals": [4, 7, 9, 11], "sge": 4, "continu": 4, "worload": 5, "812311": 5, "intstat": [5, 8], "typic": [5, 7], "except": 5, "yamlerror": 5, "exc": 5, "settingsmap": 5, "rais": [5, 7, 8, 9], "keyerror": 5, "els": [5, 9], "unboundlocalerror": 5, "assign": [5, 7], "typo": 5, "rememb": 5, "space": [5, 11], "colon": 5, "data": 5, "runtimeerror": [5, 7, 9], "compens": [5, 7], "fail": 5, "introduc": 5, "integ": [5, 9], "total": 5, "584000000000001": 5, "target": [5, 7], "root": 5, "ensur": [5, 8], "sensibl": 5, "new": [5, 7, 9], "filenotfounderror": 5, "errno": 5, "No": 5, "site": 5, "raid4": 5, "student4": 5, "production_transformato": 5, "tablit_24to25": 5, "run1": 5, "2oj9_tablit_struc24": 5, "2oj9_tablit_struc25": 5, "occur": 5, "restart": 5, "wa": 5, "due": 5, "traceback": 5, "recent": 5, "alex": 5, "taapdb_24to25": 5, "23": 5, "home": 5, "lib": 5, "python3": 5, "9": [5, 12, 13], "129": [5, 13], "gee57388": 5, "py3": 5, "egg": 5, "60": 5, "calculate_dg_to_common_cor": 5, "636": 5, "self": [5, 7], "mbar_result": 5, "_analyse_results_using_mda": 5, "507": 5, "nr_of_stat": 5, "len": [5, 8], "walk": 5, "base_path": 5, "stopiter": 5, "commonli": 5, "consist": 6, "commoncoretransform": 7, "cc1_indici": 7, "cc2_indici": 7, "ligand1_psf": 7, "ligand2_psf": 7, "tlc_cc1": 7, "tlc_cc2": 7, "charge_compensated_ligand2_psf": 7, "charge_mut": 7, "bonded_terms_mut": 7, "bool": [7, 9, 11], "__init__": [7, 8, 9, 10], "insid": 7, "param": [7, 9, 10], "indic": 7, "cc1": 7, "cc2": 7, "copi": [7, 9], "parmaet": 7, "letter": 7, "__weakref__": [7, 8, 9, 10], "weak": [7, 8, 9, 10], "object": [7, 8, 9, 10, 11], "_get_atom_map": 7, "match": 7, "dict": [7, 8, 9, 10, 11], "_mutate_atom": 7, "lambda_valu": 7, "dummyregion": 7, "mol_nam": 7, "match_termin_real_and_dummy_atom": 7, "connected_dummy_region": 7, "lj_default": 7, "__eq__": 7, "__hash__": 7, "__repr__": 7, "repr": 7, "atoms_to_be_mut": 7, "dummy_region": 7, "_compensate_charg": 7, "total_charg": 7, "offset": [7, 10], "real": 7, "group": 7, "_mutate_vdw": 7, "vdw_atom_idx": 7, "to_default": 7, "ddd": 7, "ddx": 7, "ii": 7, "iii": 7, "static": [7, 9], "_scale_epsilon_and_rmin": 7, "epsilon": 7, "rmin": 7, "perform": [7, 9, 11], "offer": 7, "scall": 7, "lambda_value_electrostat": [7, 9], "lambda_value_vdw": [7, 9], "steric_mutation_to_default": 7, "mutationdefinit": 7, "common_cor": 7, "factori": [7, 8], "propos": 7, "base": [7, 9], "mol": [7, 10, 12], "chem": [7, 10, 12, 13], "_calculate_order_of_lj_mut": 7, "match_terminal_atom": 7, "cyclecheck": 7, "ordercycl": 7, "exclude_h": 7, "theses": 7, "helper_funct": 7, "updat": 7, "weight": 7, "cycl": 7, "particip": 7, "ordercheck": 7, "exactli": 7, "preferenti": 7, "neighbourhood": 7, "workflow": 7, "graph": 7, "_check_for_lp": 7, "odered_connected_dummy_regions_cc_with_lp": 7, "help": 7, "ordered_connected_dummy_region": 7, "lonepair": 7, "wheather": 7, "lp": 7, "belong": 7, "accordingli": 7, "_find_mc": 7, "mol1_nam": 7, "mol2_nam": 7, "iterate_over_match": 7, "max_match": 7, "_find_terminal_atom": 7, "cc_idx": 7, "index": [7, 12], "rdkit": [7, 10, 13], "tupl": 7, "_get_common_cor": 7, "helper": 7, "_match_terminal_real_and_dummy_atom": 7, "real_atoms_cc": 7, "dummy_atoms_cc": 7, "kei": [7, 9], "_match_terminal_real_and_dummy_atoms_for_mol1": 7, "_match_terminal_real_and_dummy_atoms_for_mol2": 7, "_mutate_to_common_cor": 7, "_show_common_cor": 7, "highlight": 7, "show_atom_typ": 7, "intern": 7, "show": 7, "_transform_common_cor": 7, "transform": [7, 13], "idx_list": 7, "awar": 7, "ad": 7, "connected_dummy_regions_cc1": 7, "connected_dummy_regions_cc2": 7, "odered_connected_dummy_regions_cc1": 7, "odered_connected_dummy_regions_cc2": 7, "collect": 7, "own": 7, "generate_mutations_to_common_core_for_mol2": 7, "rtype": 7, "get_common_core_idx_mol1": 7, "get_common_core_idx_mol2": 7, "get_idx_of_all_atom": 7, "search": [7, 13], "asf": 7, "mutate_pure_tautom": 7, "system1": 7, "system2": 7, "single_st": 7, "nr_of_bonded_window": 7, "list_of_heavy_atoms_to_be_mut": 7, "nr_of_mutation_steps_lj_of_hydrogen": 7, "nr_of_mutation_steps_lj_of_heavy_atom": 7, "endstate_correct": 7, "dictionari": [7, 9, 10], "instanc": [7, 8], "nr": [7, 9], "topologi": [7, 8, 11, 13], "appropri": 8, "exist": 8, "commensur": 8, "desir": 8, "That": 8, "ist": 8, "unless": 8, "document": 8, "selligand": 8, "selprotein": 8, "05": 8, "kwarg": 8, "univers": [8, 12], "intermediari": [8, 12], "attributeerror": 8, "request": [8, 9], "implement": [8, 11, 12, 13], "formula": 8, "geometri": 8, "onesid": 8, "sharp": 8, "twosid": 8, "size": 8, "side": 8, "catcher": 8, "restraint_arg": 8, "_add_flatbottom_paramet": 8, "care": 8, "customcentroidbondforc": 8, "applyforc": 8, "createforc": 8, "common_core_nam": 8, "dismiss": 8, "molecul": [8, 10, 12], "create_restraints_from_config": 8, "pdbpath": 8, "invok": 8, "safe_load": 8, "generate_extrem": 8, "n_extrem": 8, "sphinner": 8, "sphouter": 8, "furthest": 8, "doc": 8, "algorithm": 8, "oper": 8, "extremity_cor": 8, "pick": 8, "sum": [8, 13], "previou": 8, "greatest": 8, "exce": 8, "end": 8, "valueerror": 8, "invalid": 8, "nest": 8, "vicin": 8, "selection_str": 8, "generate_simple_select": 8, "simpl": 8, "ident": 8, "get3ddist": 8, "pos2": 8, "3d": 8, "pos1": 8, "write_restraints_yaml": 8, "current_step": 8, "multiple_run": [9, 11], "definit": [9, 11], "_check_hmr": 9, "hmr": [9, 12], "_copy_charmm_fil": 9, "intermediate_state_file_path": 9, "_copy_fil": 9, "_copy_omm_fil": 9, "copyi": 9, "_init_base_dir": 9, "central": 9, "dir": [9, 10], "_init_intermediate_state_dir": 9, "_overwrite_simulation_script_paramet": 9, "omm_simulation_parameter_sourc": 9, "omm_simulation_parameter_target": 9, "pair": 9, "_write_amber_fil": 9, "output_file_bas": 9, "parm7": 9, "rst7": 9, "includ": 9, "amberparm": 9, "_write_psf": 9, "_write_rtf_fil": 9, "_write_workload_preambl": 9, "filepath": 9, "prepend": 9, "preambl": 9, "_script_target": 9, "write_st": 9, "mutation_conf": 9, "common_core_transform": 9, "singl": 10, "construct": 10, "obtain": [10, 13], "_determine_offset_and_set_possible_dummy_properti": 10, "determin": 10, "properti": 10, "_generate_rdkit_mol": 10, "rdchem": 10, "_initialize_system": 10, "_read_paramet": 10, "topparamet": 10, "charmmparameterset": 10, "generate_atom_tables_from_psf": 10, "map": [10, 11], "check_switching_funct": 11, "get_bin_dir": 11, "get_structure_nam": 11, "structure_nam": 11, "get_toppar_dir": 11, "isnotebook": 11, "map_lj_mutations_to_atom_idx": 11, "lj_mutat": 11, "lj": [11, 13], "methan": 11, "different_path_for_dcd": 11, "only_single_st": 11, "estim": 11, "mbar": [11, 13], "deposit": 11, "maximum": [11, 13], "lambda": [11, 13], "window": 11, "plot": 11, "accumul": 11, "overlap": 11, "purpos": [11, 13], "print_mut": 11, "psf_correct": 11, "miss": 11, "ngrp": 11, "charmm_openmm": 11, "handl": 11, "correspo": 11, "str_object": 11, "stringio": 11, "only_vacuum": 11, "format": 11, "ool": 12, "un": 12, "tic": 12, "FOR": 12, "m": [12, 13], "ultist": 12, "serial": 12, "ato": 12, "insert": 12, "sai": 12, "approach": 12, "pathwai": [12, 13], "veri": 12, "littl": 12, "design": [12, 13], "head": 12, "over": 12, "interplai": 12, "citat": 12, "licens": 12, "contact": 12, "acknowledg": 12, "prerequisit": 12, "troubleshoot": 12, "messag": 12, "caus": 12, "api": 12, "boresch": [12, 13], "bruckner": [12, 13], "2011": [12, 13], "avoid": [12, 13], "van": [12, 13], "der": [12, 13], "waal": [12, 13], "endpoint": [12, 13], "problem": [12, 13], "j": [12, 13], "32": [12, 13], "2449": [12, 13], "2458": [12, 13], "doi": [12, 13], "wieder": [12, 13], "fleck": [12, 13], "braunsfeld": [12, 13], "2022": [12, 13], "speed": [12, 13], "limit": [12, 13], "framework": [12, 13], "independ": [12, 13], "underli": [12, 13], "molecular": [12, 13], "dynam": [12, 13], "43": [12, 13], "1151": [12, 13], "1160": [12, 13], "karwounopoulo": [12, 13], "front": 12, "biosic": 12, "954638": 12, "maintain": 12, "marku": 12, "depart": 12, "pharmaceut": 12, "scienc": [12, 13], "vienna": 12, "johann": 12, "institut": 12, "biolog": 12, "chemistri": [12, 13], "stefan": 12, "turn": 13, "wise": 13, "electrostat": 13, "contribut": 13, "lennard": 13, "jone": 13, "interact": 13, "basi": 13, "water": 13, "receptor": 13, "plain": 13, "sinc": 13, "close": 13, "togeth": 13, "fe": 13, "nonbond": 13, "coupl": 13, "ideal": 13, "reach": 13, "cancel": 13, "fulli": 13, "releas": 13, "under": 13, "mit": 13, "visit": 13, "apart": 13, "reli": 13, "larg": 13, "numpi": 13, "7": 13, "manipul": 13, "pymbar": 13, "visualis": 13, "shirt": 13, "moblei": 13, "l": 13, "chodera": 13, "2007": 13, "prime": 13, "annual": 13, "report": 13, "vol": 13, "frontier": 13, "gower": 13, "et": 13, "al": 13, "2016": 13, "rapid": 13, "proceed": 13, "confer": 13, "scipi": 13, "michaud": 13, "agraw": 13, "toolkit": 13, "journal": 13, "pp": 13, "2319": 13, "2327": 13, "walt": 13, "colbert": 13, "varoquaux": 13, "effici": 13, "numer": 13, "13": 13, "22": 13, "mr": 13, "jd": 13, "statist": 13, "optim": 13, "equilibrium": 13, "phy": 13, "124105": 13, "2008": 13, "michael": 13, "christoph": 13, "klein": 13, "lesson": 13, "learn": 13, "compar": 13, "sampl5": 13, "dataset": 13, "aid": 13}, "objects": {"transformato": [[7, 0, 0, "module-0", "mutate"], [8, 0, 0, "module-0", "restraints"], [9, 0, 0, "module-0", "state"], [10, 0, 0, "module-0", "system"], [11, 0, 0, "module-0", "utils"]], "transformato.mutate": [[7, 1, 1, "", "CommonCoreTransformation"], [7, 1, 1, "", "DummyRegion"], [7, 1, 1, "", "Mutation"], [7, 1, 1, "", "MutationDefinition"], [7, 1, 1, "", "ProposeMutationRoute"], [7, 2, 1, "", "mutate_pure_tautomers"], [7, 2, 1, "", "perform_mutations"]], "transformato.mutate.CommonCoreTransformation": [[7, 2, 1, "", "__init__"], [7, 3, 1, "", "__weakref__"], [7, 2, 1, "", "_get_atom_mapping"], [7, 2, 1, "", "_mutate_atoms"], [7, 2, 1, "", "mutate"]], "transformato.mutate.DummyRegion": [[7, 2, 1, "", "__eq__"], [7, 3, 1, "", "__hash__"], [7, 2, 1, "", "__init__"], [7, 2, 1, "", "__repr__"], [7, 3, 1, "", "__weakref__"]], "transformato.mutate.Mutation": [[7, 2, 1, "", "__init__"], [7, 3, 1, "", "__weakref__"], [7, 2, 1, "", "_compensate_charge"], [7, 2, 1, "", "_mutate_vdw"], [7, 2, 1, "", "_scale_epsilon_and_rmin"], [7, 2, 1, "", "mutate"]], "transformato.mutate.MutationDefinition": [[7, 2, 1, "", "__eq__"], [7, 3, 1, "", "__hash__"], [7, 2, 1, "", "__init__"], [7, 2, 1, "", "__repr__"], [7, 3, 1, "", "__weakref__"]], "transformato.mutate.ProposeMutationRoute": [[7, 2, 1, "", "__init__"], [7, 3, 1, "", "__weakref__"], [7, 2, 1, "", "_calculate_order_of_LJ_mutations"], [7, 2, 1, "", "_check_for_lp"], [7, 2, 1, "", "_find_mcs"], [7, 2, 1, "", "_find_terminal_atom"], [7, 2, 1, "", "_get_common_core"], [7, 2, 1, "", "_match_terminal_real_and_dummy_atoms"], [7, 2, 1, "", "_match_terminal_real_and_dummy_atoms_for_mol1"], [7, 2, 1, "", "_match_terminal_real_and_dummy_atoms_for_mol2"], [7, 2, 1, "", "_mutate_to_common_core"], [7, 2, 1, "", "_show_common_core"], [7, 2, 1, "", "_transform_common_core"], [7, 2, 1, "", "add_idx_to_common_core_of_mol1"], [7, 2, 1, "", "add_idx_to_common_core_of_mol2"], [7, 2, 1, "", "finish_common_core"], [7, 2, 1, "", "generate_mutations_to_common_core_for_mol1"], [7, 2, 1, "", "generate_mutations_to_common_core_for_mol2"], [7, 2, 1, "", "get_common_core_idx_mol1"], [7, 2, 1, "", "get_common_core_idx_mol2"], [7, 2, 1, "", "get_idx_of_all_atoms"], [7, 2, 1, "", "propose_common_core"], [7, 2, 1, "", "show_common_core_on_mol1"], [7, 2, 1, "", "show_common_core_on_mol2"]], "transformato.restraints": [[8, 1, 1, "", "Restraint"], [8, 2, 1, "", "create_restraints_from_config"], [8, 2, 1, "", "generate_extremities"], [8, 2, 1, "", "generate_simple_selection"], [8, 2, 1, "", "get3DDistance"], [8, 2, 1, "", "write_restraints_yaml"]], "transformato.restraints.Restraint": [[8, 2, 1, "", "__init__"], [8, 3, 1, "", "__weakref__"], [8, 2, 1, "", "_add_flatbottom_parameters"], [8, 2, 1, "", "applyForce"], [8, 2, 1, "", "createForce"]], "transformato.state": [[9, 1, 1, "", "IntermediateStateFactory"]], "transformato.state.IntermediateStateFactory": [[9, 2, 1, "", "__init__"], [9, 3, 1, "", "__weakref__"], [9, 2, 1, "", "_check_hmr"], [9, 2, 1, "", "_copy_charmm_files"], [9, 2, 1, "", "_copy_files"], [9, 2, 1, "", "_copy_omm_files"], [9, 2, 1, "", "_init_base_dir"], [9, 2, 1, "", "_init_intermediate_state_dir"], [9, 2, 1, "", "_overwrite_simulation_script_parameters"], [9, 2, 1, "", "_write_amber_files"], [9, 2, 1, "", "_write_psf"], [9, 2, 1, "", "_write_rtf_file"], [9, 2, 1, "", "_write_workload_preamble"], [9, 2, 1, "", "write_state"]], "transformato.system": [[10, 1, 1, "", "SystemStructure"]], "transformato.system.SystemStructure": [[10, 2, 1, "", "__init__"], [10, 3, 1, "", "__weakref__"], [10, 2, 1, "", "_determine_offset_and_set_possible_dummy_properties"], [10, 2, 1, "", "_generate_rdkit_mol"], [10, 2, 1, "", "_initialize_system"], [10, 2, 1, "", "_read_parameters"], [10, 2, 1, "", "generate_atom_tables_from_psf"]], "transformato.utils": [[11, 2, 1, "", "check_switching_function"], [11, 2, 1, "", "get_bin_dir"], [11, 2, 1, "", "get_structure_name"], [11, 2, 1, "", "get_toppar_dir"], [11, 2, 1, "", "isnotebook"], [11, 2, 1, "", "load_config_yaml"], [11, 2, 1, "", "map_lj_mutations_to_atom_idx"], [11, 2, 1, "", "postprocessing"], [11, 2, 1, "", "print_mutations"], [11, 2, 1, "", "psf_correction"], [11, 2, 1, "", "run_simulation"]], "": [[4, 4, 1, "cmdoption-arg-workload-manager", ""SGE"])"], [4, 4, 1, "cmdoption-arg-free-energy-type", ""rsfe"])"], [4, 4, 1, "cmdoption-arg-switch", ""switch"])"], [4, 4, 1, "cmdoption-arg-GPU", "False])"], [4, 4, 1, "cmdoption-arg-GPU", "GPU:"], [4, 4, 1, "cmdoption-arg-cons", "None]"], [1, 4, 1, "cmdoption-arg-analyze_traj_with", "analyze_traj_with"], [3, 4, 1, "cmdoption-arg-config", "config"], [4, 4, 1, "cmdoption-arg-cons", "cons:"], [1, 4, 1, "cmdoption-arg-engine", "default:"], [4, 4, 1, "cmdoption-arg-dt", "dt:"], [1, 4, 1, "cmdoption-arg-engine", "engine"], [0, 4, 1, "cmdoption-arg-extremities", "extremities"], [4, 4, 1, "cmdoption-arg-free-energy-type", "free-energy-type:"], [0, 4, 1, "cmdoption-arg-group1-group2", "group1,group2"], [3, 4, 1, "cmdoption-arg-input_dir", "input_dir"], [0, 4, 1, "cmdoption-arg-k", "k"], [1, 4, 1, "cmdoption-arg-max_snapshots", "max_snapshots"], [4, 4, 1, "cmdoption-arg-mini_nstep", "mini_nstep:"], [1, 4, 1, "cmdoption-arg-name", "name"], [3, 4, 1, "cmdoption-arg-nr_of_mutation_steps_cc", "nr_of_mutation_steps_cc"], [3, 4, 1, "cmdoption-arg-nr_of_mutation_steps_charge", "nr_of_mutation_steps_charge"], [4, 4, 1, "cmdoption-arg-nstdcd", "nstdcd:"], [4, 4, 1, "cmdoption-arg-nstep", "nstep:"], [4, 4, 1, "cmdoption-arg-nstout", "nstout:"], [4, 4, 1, "cmdoption-arg-other", "other"], [3, 4, 1, "cmdoption-arg-output_dir", "output_dir"], [0, 4, 1, "cmdoption-arg-scaling", "scaling"], [0, 4, 1, "cmdoption-arg-shape", "shape"], [4, 4, 1, "cmdoption-arg-switch", "switch:"], [4, 4, 1, "cmdoption-arg-tlc", "tlc"], [0, 4, 1, "cmdoption-arg-wellsize", "wellsize"], [4, 4, 1, "cmdoption-arg-workload-manager", "workload-manager:"]]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:attribute", "4": "std:cmdoption"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "attribute", "Python attribute"], "4": ["std", "cmdoption", "program option"]}, "titleterms": {"addit": 0, "set": 0, "restraint": [0, 8], "automat": 0, "manual": 0, "hydrogen": 0, "mass": 0, "repartit": 0, "hmr": 0, "trajectori": 1, "analysi": [1, 5], "The": [1, 13], "py": 1, "file": [1, 4], "offload": 1, "cluster": 1, "instal": 2, "prerequisit": 2, "get": [2, 5], "texttt": 2, "transformato": [2, 7, 8, 9, 10, 11, 12], "run": 3, "simul": [3, 5], "step": [3, 4], "3": 3, "creat": [3, 4], "intermediari": 3, "state": [3, 9], "system": [4, 5, 10], "setup": [4, 5], "1": 4, "us": 4, "charmm": [4, 13], "gui": [4, 13], "For": 4, "expert": 4, "user": 4, "onli": 4, "2": 4, "modifi": 4, "yaml": 4, "troubleshoot": 5, "debug": 5, "inform": 5, "error": 5, "messag": 5, "common": [5, 7, 13], "caus": 5, "dure": 5, "api": 6, "document": [6, 12], "mutat": 7, "descript": [7, 8, 9, 10, 11], "class": [7, 8, 9, 10], "bf": 7, "djikstra": 7, "algorithm": 7, "appli": 7, "calcul": 7, "order": 7, "turn": 7, "lj": 7, "interact": 7, "heavi": 7, "atom": [7, 13], "gener": 7, "rout": 7, "fore": 7, "mol1": 7, "iter": 7, "over": 7, "all": 7, "molecul": 7, "save": 7, "them": 7, "list": 7, "function": [7, 8, 11], "basic": 8, "usag": 8, "util": 11, "welcom": 12, "content": 12, "theoret": 13, "background": 13, "interplai": 13, "core": 13, "approach": 13, "serial": 13, "insert": 13, "citat": 13, "licens": 13, "contact": 13, "acknowledg": 13}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx.ext.intersphinx": 1, "sphinx": 60}, "alltitles": {"Additional Settings": [[0, "additional-settings"]], "Restraints": [[0, "restraints"]], "Automatic Restraints": [[0, "automatic-restraints"]], "Manual Restraints": [[0, "manual-restraints"]], "Hydrogen Mass Repartitioning (HMR)": [[0, "hydrogen-mass-repartitioning-hmr"]], "Trajectory Analysis": [[1, "trajectory-analysis"]], "The analysis.py file": [[1, "the-analysis-py-file"]], "Offloading the analysis to a cluster": [[1, "offloading-the-analysis-to-a-cluster"]], "Installation": [[2, "installation"]], "Prerequisites": [[2, "prerequisites"]], "Getting \\texttt{TRANSFORMATO}": [[2, "getting-trafo"]], "Running Simulations": [[3, "running-simulations"]], "Step 3 - Creating intermediary states": [[3, "step-3-creating-intermediary-states"]], "System Setup": [[4, "system-setup"]], "Step 1 \u2013 creating Systems using CHARMM-GUI": [[4, "step-1-creating-systems-using-charmm-gui"]], "For expert users only!": [[4, null]], "Step 2 \u2013 modifying the yaml file": [[4, "step-2-modifying-the-yaml-file"]], "Troubleshooting": [[5, "troubleshooting"]], "Getting debug information": [[5, "getting-debug-information"]], "Error messages and common causes:": [[5, "error-messages-and-common-causes"]], "Errors during system setup:": [[5, "errors-during-system-setup"]], "Errors during simulation:": [[5, "errors-during-simulation"]], "Errors during analysis:": [[5, "errors-during-analysis"]], "API Documentation": [[6, "api-documentation"]], "transformato.mutate": [[7, "transformato-mutate"]], "Description": [[7, "description"], [8, "description"], [9, "description"], [10, "description"], [11, "description"]], "Classes": [[7, "classes"], [8, "classes"], [9, "classes"], [10, "classes"]], "bfs/djikstra-algorithm applied to calculate the ordere for turning of the LJ interactions of the heavy atoms": [[7, "bfs-djikstra-algorithm-applied-to-calculate-the-ordere-for-turning-of-the-lj-interactions-of-the-heavy-atoms"]], "Generates the mutation route to the common fore for mol1.": [[7, "generates-the-mutation-route-to-the-common-fore-for-mol1"]], "Iterates over all atoms of the molecule and saves them as a list": [[7, "iterates-over-all-atoms-of-the-molecule-and-saves-them-as-a-list"]], "Functions": [[7, "functions"], [8, "functions"], [11, "functions"]], "transformato.restraints": [[8, "transformato-restraints"]], "Basic function:": [[8, "basic-function"]], "Usage:": [[8, "usage"]], "transformato.state": [[9, "transformato-state"]], "transformato.system": [[10, "transformato-system"]], "transformato.utils": [[11, "transformato-utils"]], "Welcome to the documentation for transformato!": [[12, "welcome-to-the-documentation-for-transformato"]], "Contents:": [[12, null]], "Theoretical background": [[13, "theoretical-background"]], "Interplay with CHARMM-GUI": [[13, "interplay-with-charmm-gui"]], "The common-core approach": [[13, "the-common-core-approach"]], "Serial-Atom-Insertion approach": [[13, "serial-atom-insertion-approach"]], "Citations, License and Contact": [[13, "citations-license-and-contact"]], "Acknowledgements": [[13, "acknowledgements"]]}, "indexentries": {"command line option": [[0, "cmdoption-arg-0"], [0, "cmdoption-arg-1"], [0, "cmdoption-arg-2"], [0, "cmdoption-arg-extremities"], [0, "cmdoption-arg-group1-group2"], [0, "cmdoption-arg-k"], [0, "cmdoption-arg-scaling"], [0, "cmdoption-arg-shape"], [0, "cmdoption-arg-wellsize"], [1, "cmdoption-arg-analyze_traj_with"], [1, "cmdoption-arg-engine"], [1, "cmdoption-arg-max_snapshots"], [1, "cmdoption-arg-name"], [3, "cmdoption-arg-config"], [3, "cmdoption-arg-input_dir"], [3, "cmdoption-arg-nr_of_mutation_steps_cc"], [3, "cmdoption-arg-nr_of_mutation_steps_charge"], [3, "cmdoption-arg-output_dir"], [4, "cmdoption-arg-GPU"], [4, "cmdoption-arg-cons"], [4, "cmdoption-arg-dt"], [4, "cmdoption-arg-free-energy-type"], [4, "cmdoption-arg-mini_nstep"], [4, "cmdoption-arg-name"], [4, "cmdoption-arg-nstdcd"], [4, "cmdoption-arg-nstep"], [4, "cmdoption-arg-nstout"], [4, "cmdoption-arg-other"], [4, "cmdoption-arg-switch"], [4, "cmdoption-arg-tlc"], [4, "cmdoption-arg-workload-manager"]], "extremities": [[0, "cmdoption-arg-extremities"]], "group1,group2": [[0, "cmdoption-arg-group1-group2"]], "k": [[0, "cmdoption-arg-1"], [0, "cmdoption-arg-k"]], "scaling": [[0, "cmdoption-arg-scaling"]], "shape": [[0, "cmdoption-arg-0"], [0, "cmdoption-arg-shape"]], "wellsize": [[0, "cmdoption-arg-2"], [0, "cmdoption-arg-wellsize"]], "analyze_traj_with": [[1, "cmdoption-arg-analyze_traj_with"]], "default:": [[1, "cmdoption-arg-analyze_traj_with"], [1, "cmdoption-arg-engine"], [1, "cmdoption-arg-max_snapshots"]], "engine": [[1, "cmdoption-arg-engine"]], "max_snapshots": [[1, "cmdoption-arg-max_snapshots"]], "name": [[1, "cmdoption-arg-name"], [4, "cmdoption-arg-name"]], "config": [[3, "cmdoption-arg-config"]], "input_dir": [[3, "cmdoption-arg-input_dir"]], "nr_of_mutation_steps_cc": [[3, "cmdoption-arg-nr_of_mutation_steps_cc"]], "nr_of_mutation_steps_charge": [[3, "cmdoption-arg-nr_of_mutation_steps_charge"]], "output_dir": [[3, "cmdoption-arg-output_dir"]], "\"sge\"])": [[4, "cmdoption-arg-workload-manager"]], "\"rsfe\"])": [[4, "cmdoption-arg-free-energy-type"]], "\"switch\"])": [[4, "cmdoption-arg-switch"]], "false])": [[4, "cmdoption-arg-GPU"]], "gpu:": [[4, "cmdoption-arg-GPU"]], "none]": [[4, "cmdoption-arg-cons"]], "cons:": [[4, "cmdoption-arg-cons"]], "dt:": [[4, "cmdoption-arg-dt"]], "free-energy-type:": [[4, "cmdoption-arg-free-energy-type"]], "mini_nstep:": [[4, "cmdoption-arg-mini_nstep"]], "nstdcd:": [[4, "cmdoption-arg-nstdcd"]], "nstep:": [[4, "cmdoption-arg-nstep"]], "nstout:": [[4, "cmdoption-arg-nstout"]], "other": [[4, "cmdoption-arg-other"]], "switch:": [[4, "cmdoption-arg-switch"]], "tlc": [[4, "cmdoption-arg-tlc"]], "workload-manager:": [[4, "cmdoption-arg-workload-manager"]], "commoncoretransformation (class in transformato.mutate)": [[7, "transformato.mutate.CommonCoreTransformation"]], "dummyregion (class in transformato.mutate)": [[7, "transformato.mutate.DummyRegion"]], "mutation (class in transformato.mutate)": [[7, "transformato.mutate.Mutation"]], "mutationdefinition (class in transformato.mutate)": [[7, "transformato.mutate.MutationDefinition"]], "proposemutationroute (class in transformato.mutate)": [[7, "transformato.mutate.ProposeMutationRoute"]], "__eq__() (transformato.mutate.dummyregion method)": [[7, "transformato.mutate.DummyRegion.__eq__"]], "__eq__() (transformato.mutate.mutationdefinition method)": [[7, "transformato.mutate.MutationDefinition.__eq__"]], "__hash__ (transformato.mutate.dummyregion attribute)": [[7, "transformato.mutate.DummyRegion.__hash__"]], "__hash__ (transformato.mutate.mutationdefinition attribute)": [[7, "transformato.mutate.MutationDefinition.__hash__"]], "__init__() (transformato.mutate.commoncoretransformation method)": [[7, "transformato.mutate.CommonCoreTransformation.__init__"]], "__init__() (transformato.mutate.dummyregion method)": [[7, "transformato.mutate.DummyRegion.__init__"]], "__init__() (transformato.mutate.mutation method)": [[7, "transformato.mutate.Mutation.__init__"]], "__init__() (transformato.mutate.mutationdefinition method)": [[7, "transformato.mutate.MutationDefinition.__init__"]], "__init__() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.__init__"]], "__repr__() (transformato.mutate.dummyregion method)": [[7, "transformato.mutate.DummyRegion.__repr__"]], "__repr__() (transformato.mutate.mutationdefinition method)": [[7, "transformato.mutate.MutationDefinition.__repr__"]], "__weakref__ (transformato.mutate.commoncoretransformation attribute)": [[7, "transformato.mutate.CommonCoreTransformation.__weakref__"]], "__weakref__ (transformato.mutate.dummyregion attribute)": [[7, "transformato.mutate.DummyRegion.__weakref__"]], "__weakref__ (transformato.mutate.mutation attribute)": [[7, "transformato.mutate.Mutation.__weakref__"]], "__weakref__ (transformato.mutate.mutationdefinition attribute)": [[7, "transformato.mutate.MutationDefinition.__weakref__"]], "__weakref__ (transformato.mutate.proposemutationroute attribute)": [[7, "transformato.mutate.ProposeMutationRoute.__weakref__"]], "_calculate_order_of_lj_mutations() (transformato.mutate.proposemutationroute static method)": [[7, "transformato.mutate.ProposeMutationRoute._calculate_order_of_LJ_mutations"]], "_check_for_lp() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._check_for_lp"]], "_compensate_charge() (transformato.mutate.mutation method)": [[7, "transformato.mutate.Mutation._compensate_charge"]], "_find_mcs() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._find_mcs"]], "_find_terminal_atom() (transformato.mutate.proposemutationroute static method)": [[7, "transformato.mutate.ProposeMutationRoute._find_terminal_atom"]], "_get_atom_mapping() (transformato.mutate.commoncoretransformation method)": [[7, "transformato.mutate.CommonCoreTransformation._get_atom_mapping"]], "_get_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._get_common_core"]], "_match_terminal_real_and_dummy_atoms() (transformato.mutate.proposemutationroute static method)": [[7, "transformato.mutate.ProposeMutationRoute._match_terminal_real_and_dummy_atoms"]], "_match_terminal_real_and_dummy_atoms_for_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._match_terminal_real_and_dummy_atoms_for_mol1"]], "_match_terminal_real_and_dummy_atoms_for_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._match_terminal_real_and_dummy_atoms_for_mol2"]], "_mutate_atoms() (transformato.mutate.commoncoretransformation method)": [[7, "transformato.mutate.CommonCoreTransformation._mutate_atoms"]], "_mutate_to_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._mutate_to_common_core"]], "_mutate_vdw() (transformato.mutate.mutation method)": [[7, "transformato.mutate.Mutation._mutate_vdw"]], "_scale_epsilon_and_rmin() (transformato.mutate.mutation static method)": [[7, "transformato.mutate.Mutation._scale_epsilon_and_rmin"]], "_show_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._show_common_core"]], "_transform_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._transform_common_core"]], "add_idx_to_common_core_of_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.add_idx_to_common_core_of_mol1"]], "add_idx_to_common_core_of_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.add_idx_to_common_core_of_mol2"]], "finish_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.finish_common_core"]], "generate_mutations_to_common_core_for_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.generate_mutations_to_common_core_for_mol1"]], "generate_mutations_to_common_core_for_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.generate_mutations_to_common_core_for_mol2"]], "get_common_core_idx_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.get_common_core_idx_mol1"]], "get_common_core_idx_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.get_common_core_idx_mol2"]], "get_idx_of_all_atoms() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.get_idx_of_all_atoms"]], "module": [[7, "module-0"], [7, "module-transformato.mutate"], [8, "module-0"], [8, "module-transformato.restraints"], [9, "module-0"], [9, "module-transformato.state"], [10, "module-0"], [10, "module-transformato.system"], [11, "module-0"], [11, "module-transformato.utils"]], "mutate() (transformato.mutate.commoncoretransformation method)": [[7, "transformato.mutate.CommonCoreTransformation.mutate"]], "mutate() (transformato.mutate.mutation method)": [[7, "transformato.mutate.Mutation.mutate"]], "mutate_pure_tautomers() (transformato.mutate method)": [[7, "transformato.mutate.mutate_pure_tautomers"]], "perform_mutations() (transformato.mutate method)": [[7, "transformato.mutate.perform_mutations"]], "propose_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.propose_common_core"]], "show_common_core_on_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.show_common_core_on_mol1"]], "show_common_core_on_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.show_common_core_on_mol2"]], "transformato.mutate": [[7, "module-0"], [7, "module-transformato.mutate"]], "restraint (class in transformato.restraints)": [[8, "transformato.restraints.Restraint"]], "__init__() (transformato.restraints.restraint method)": [[8, "transformato.restraints.Restraint.__init__"]], "__weakref__ (transformato.restraints.restraint attribute)": [[8, "transformato.restraints.Restraint.__weakref__"]], "_add_flatbottom_parameters() (transformato.restraints.restraint method)": [[8, "transformato.restraints.Restraint._add_flatbottom_parameters"]], "applyforce() (transformato.restraints.restraint method)": [[8, "transformato.restraints.Restraint.applyForce"]], "createforce() (transformato.restraints.restraint method)": [[8, "transformato.restraints.Restraint.createForce"]], "create_restraints_from_config() (transformato.restraints method)": [[8, "transformato.restraints.create_restraints_from_config"]], "generate_extremities() (transformato.restraints method)": [[8, "transformato.restraints.generate_extremities"]], "generate_simple_selection() (transformato.restraints method)": [[8, "transformato.restraints.generate_simple_selection"]], "get3ddistance() (transformato.restraints method)": [[8, "transformato.restraints.get3DDistance"]], "transformato.restraints": [[8, "module-0"], [8, "module-transformato.restraints"]], "write_restraints_yaml() (transformato.restraints method)": [[8, "transformato.restraints.write_restraints_yaml"]], "intermediatestatefactory (class in transformato.state)": [[9, "transformato.state.IntermediateStateFactory"]], "__init__() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory.__init__"]], "__weakref__ (transformato.state.intermediatestatefactory attribute)": [[9, "transformato.state.IntermediateStateFactory.__weakref__"]], "_check_hmr() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._check_hmr"]], "_copy_charmm_files() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._copy_charmm_files"]], "_copy_files() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._copy_files"]], "_copy_omm_files() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._copy_omm_files"]], "_init_base_dir() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._init_base_dir"]], "_init_intermediate_state_dir() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._init_intermediate_state_dir"]], "_overwrite_simulation_script_parameters() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._overwrite_simulation_script_parameters"]], "_write_amber_files() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._write_amber_files"]], "_write_psf() (transformato.state.intermediatestatefactory static method)": [[9, "transformato.state.IntermediateStateFactory._write_psf"]], "_write_rtf_file() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._write_rtf_file"]], "_write_workload_preamble() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._write_workload_preamble"]], "transformato.state": [[9, "module-0"], [9, "module-transformato.state"]], "write_state() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory.write_state"]], "systemstructure (class in transformato.system)": [[10, "transformato.system.SystemStructure"]], "__init__() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure.__init__"]], "__weakref__ (transformato.system.systemstructure attribute)": [[10, "transformato.system.SystemStructure.__weakref__"]], "_determine_offset_and_set_possible_dummy_properties() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure._determine_offset_and_set_possible_dummy_properties"]], "_generate_rdkit_mol() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure._generate_rdkit_mol"]], "_initialize_system() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure._initialize_system"]], "_read_parameters() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure._read_parameters"]], "generate_atom_tables_from_psf() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure.generate_atom_tables_from_psf"]], "transformato.system": [[10, "module-0"], [10, "module-transformato.system"]], "check_switching_function() (transformato.utils method)": [[11, "transformato.utils.check_switching_function"]], "get_bin_dir() (transformato.utils method)": [[11, "transformato.utils.get_bin_dir"]], "get_structure_name() (transformato.utils method)": [[11, "transformato.utils.get_structure_name"]], "get_toppar_dir() (transformato.utils method)": [[11, "transformato.utils.get_toppar_dir"]], "isnotebook() (transformato.utils method)": [[11, "transformato.utils.isnotebook"]], "load_config_yaml() (transformato.utils method)": [[11, "transformato.utils.load_config_yaml"]], "map_lj_mutations_to_atom_idx() (transformato.utils method)": [[11, "transformato.utils.map_lj_mutations_to_atom_idx"]], "postprocessing() (transformato.utils method)": [[11, "transformato.utils.postprocessing"]], "print_mutations() (transformato.utils method)": [[11, "transformato.utils.print_mutations"]], "psf_correction() (transformato.utils method)": [[11, "transformato.utils.psf_correction"]], "run_simulation() (transformato.utils method)": [[11, "transformato.utils.run_simulation"]], "transformato.utils": [[11, "module-0"], [11, "module-transformato.utils"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["Additional_Settings", "Analysis", "Installation", "Running_Simulation", "System_Setup", "Troubleshooting", "api", "autosummary/transformato.mutate", "autosummary/transformato.restraints", "autosummary/transformato.state", "autosummary/transformato.system", "autosummary/transformato.utils", "index", "whatistransformato"], "filenames": ["Additional_Settings.rst", "Analysis.rst", "Installation.rst", "Running_Simulation.rst", "System_Setup.rst", "Troubleshooting.rst", "api.rst", "autosummary/transformato.mutate.rst", "autosummary/transformato.restraints.rst", "autosummary/transformato.state.rst", "autosummary/transformato.system.rst", "autosummary/transformato.utils.rst", "index.rst", "whatistransformato.rst"], "titles": ["Additional Settings", "Trajectory Analysis", "Installation", "Running Simulations", "System Setup", "Troubleshooting", "API Documentation", "transformato.mutate", "transformato.restraints", "transformato.state", "transformato.system", "transformato.utils", "Welcome to the documentation for transformato!", "Theoretical background"], "terms": {"thi": [0, 1, 2, 3, 4, 5, 7, 8, 11, 13], "section": [0, 4, 8], "onli": [0, 1, 3, 7, 8, 11, 13], "appli": [0, 1, 4, 8], "you": [0, 1, 2, 3, 4, 5, 8, 12], "ar": [0, 1, 2, 3, 4, 5, 7, 8, 9, 11, 12, 13], "run": [0, 1, 2, 4, 5, 8, 9, 12, 13], "your": [0, 1, 2, 3, 4, 5, 8], "simul": [0, 1, 2, 4, 8, 9, 12, 13], "openmm": [0, 1, 2, 3, 4, 8, 9, 11, 12], "should": [0, 1, 3, 4, 5, 7, 8, 9], "us": [0, 1, 2, 3, 7, 8, 9, 11, 12, 13], "charmm": [0, 1, 3, 7, 9, 10, 11, 12], "give": [0, 9], "warn": [0, 3], "about": [0, 4], "texttt": [0, 1, 3, 4, 12, 13], "transformato": [0, 1, 3, 4, 5, 6, 13], "support": [0, 1, 4], "two": [0, 1, 3, 4, 7, 8, 9, 12, 13], "type": [0, 4, 7, 8, 9, 10, 11], "To": [0, 1, 3], "activ": [0, 1, 2, 3], "ligand": [0, 1, 3, 4, 7, 8, 10, 13], "add": [0, 3, 7, 8, 9], "auto": 0, "config": [0, 1, 3, 4, 5, 8, 9], "yaml": [0, 1, 2, 3, 5, 8, 12], "wil": 0, "restrain": 0, "its": [0, 4, 7, 8, 11, 13], "origin": [0, 3, 9], "posit": [0, 4, 8], "harmon": [0, 8], "potenti": [0, 8], "form": [0, 5], "e": [0, 1, 4, 5, 7, 8], "0": [0, 4, 5, 7, 8, 9, 11, 13], "5k": 0, "cdot": 0, "r": [0, 12, 13], "r_0": 0, "\u00b2": 0, "where": [0, 3, 4, 5, 8], "i": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 12, 13], "current": [0, 2, 3, 12], "distanc": [0, 8], "math": [0, 13], "initi": [0, 3, 8], "k": [0, 8], "forc": [0, 8, 13], "constant": [0, 8], "within": [0, 2, 4], "center": [0, 8], "surround": [0, 8], "protein": [0, 4, 13], "structur": [0, 3, 4, 5, 8, 10, 13], "keep": 0, "vagu": 0, "fix": 0, "mai": [0, 2, 3, 4], "specifi": [0, 5, 8, 9], "further": [0, 1, 4, 8, 13], "keyword": 0, "option": [0, 1, 3, 7, 9, 11], "int": [0, 1, 4, 7, 8, 9, 10, 11], "defin": [0, 3, 4, 5, 7, 8, 9], "spring": [0, 8], "calcul": [0, 1, 4, 8, 11, 12, 13], "default": [0, 1, 3, 4, 7, 8, 9, 11, 13], "3": [0, 1, 4, 8, 12, 13], "extrem": [0, 8], "If": [0, 2, 3, 4, 8, 12], "entir": 0, "common": [0, 1, 3, 8, 12], "core": [0, 1, 3, 7, 8, 12], "rather": 0, "look": [0, 3, 4, 7, 12], "These": [0, 3, 4, 8], "carbon": [0, 8], "alpha": [0, 8], "shape": [0, 8], "flatbottom": [0, 8], "energi": [0, 1, 4, 8, 11, 12, 13], "The": [0, 3, 4, 7, 8, 9, 11, 12], "term": 0, "given": [0, 4, 9, 11], "step": [0, 7, 8, 12, 13], "thresh": 0, "function": [0, 1], "return": [0, 7, 8, 10, 11], "until": [0, 8], "threshold": 0, "wellsiz": [0, 8], "ha": [0, 3, 4, 7], "been": [0, 7], "surpass": 0, "after": [0, 1, 3, 4, 8], "which": [0, 1, 4, 7, 8, 9, 13], "1": [0, 1, 3, 5, 7, 9, 12, 13], "As": [0, 1, 4], "flat": [0, 8], "bottom": [0, 3, 8], "essenti": [0, 3], "well": [0, 3, 4, 8, 13], "zero": 0, "note": [0, 3], "act": 0, "like": [0, 1, 3, 4, 12], "radiu": 0, "mean": [0, 4, 5, 13], "extend": [0, 4], "all": [0, 1, 3, 4, 5, 8, 9, 10, 13], "direct": 0, "from": [0, 1, 3, 4, 7, 8, 9, 10, 12, 13], "figur": [0, 4, 13], "differ": [0, 1, 10, 12, 13], "between": [0, 3, 4, 5, 7, 8, 11, 13], "A": [0, 2, 4, 7, 8, 10, 12, 13], "b": [0, 12, 13], "while": [0, 2], "both": [0, 1, 3, 8, 13], "allow": [0, 3], "more": [0, 1, 3, 5], "movement": 0, "closer": 0, "effect": 0, "sampl": [0, 3, 11, 13], "area": 0, "can": [0, 1, 2, 3, 4, 5, 7, 11, 12, 13], "move": [0, 4], "without": [0, 3, 12, 13], "hindranc": 0, "cannot": [0, 8], "leav": 0, "assum": [0, 3], "strong": 0, "enough": 0, "valu": [0, 7, 9], "scale": [0, 3, 7, 13], "present": 0, "linearli": 0, "first": [0, 2, 4, 5, 13], "four": 0, "intermedi": [0, 1, 2, 3, 4, 5, 8, 9, 13], "state": [0, 1, 2, 4, 5, 8, 12, 13], "intst1": [0, 3, 5], "intst2": [0, 3, 8], "25": 0, "intst3": 0, "5": [0, 3, 7, 8, 13], "intst4": 0, "75": 0, "intst5": 0, "float": [0, 7, 8, 9], "take": [0, 1, 2, 3, 4, 8, 12], "nanomet": [0, 8], "nm": 0, "full": [0, 8], "entri": 0, "might": [0, 3, 4], "thu": [0, 13], "10": [0, 2, 7, 13], "Be": [0, 7], "somewhat": [0, 3], "sure": [0, 1, 2, 3, 4], "what": [0, 3], "do": [0, 2, 3, 4, 5, 7], "saniti": 0, "check": [0, 1, 2, 4, 7, 8], "gener": [0, 2, 3, 4, 8, 9, 10, 12, 13], "befor": [0, 1, 3, 5, 7], "product": [0, 4, 9, 12], "an": [0, 1, 2, 3, 4, 8, 9, 12, 13], "arbitrarili": 0, "high": 0, "number": [0, 1, 3, 4, 5, 8, 9, 11, 13], "exterm": 0, "lead": 0, "strang": 0, "result": [0, 1, 4, 13], "It": [0, 3, 4, 7, 12], "small": [0, 3, 10], "file": [0, 2, 3, 5, 7, 8, 9, 10, 11, 12], "call": [0, 1, 2, 3, 4, 5, 7, 8], "creat": [0, 1, 2, 5, 7, 8, 9, 12, 13], "intst": [0, 3, 9], "folder": [0, 1, 3, 4, 9, 10, 13], "have": [0, 1, 3, 4, 5, 7], "follow": [0, 1, 2, 3, 4, 6, 8, 13], "system": [0, 1, 3, 7, 8, 9, 11, 12, 13], "tlc": [0, 4, 7, 9], "lig": [0, 4], "same": [0, 1, 3, 4, 7, 13], "one": [0, 1, 2, 3, 4, 8, 13], "relev": 0, "cc": [0, 1, 7, 12, 13], "repres": [0, 8], "arrai": [0, 7, 8, 13], "upon": 0, "c1": 0, "c2": 0, "h2": 0, "8": [0, 3, 13], "non": [0, 5, 13], "immedi": 0, "switch": [0, 3, 4, 11], "how": [0, 3, 4, 7, 8, 9], "far": 0, "along": [0, 3, 4], "recommend": [0, 1, 3, 4], "edit": 0, "thei": 0, "each": [0, 3, 4, 8, 13], "below": [0, 1, 3, 4], "now": [0, 1, 2, 3, 4], "arbitrari": 0, "mdanalysi": [0, 8, 11, 13], "select": [0, 8, 9, 11, 13], "syntax": 0, "manualrestraint": 0, "restraint1": 0, "group1": 0, "resnam": [0, 4], "c": [0, 2, 3, 8, 13], "group2": 0, "ca": 0, "30": [0, 13], "r0": 0, "2": [0, 1, 3, 5, 7, 11, 12, 13], "41": 0, "mani": [0, 3, 4, 7, 8, 9], "code": [0, 1, 3, 7, 12], "exampl": [0, 3, 4], "multipl": [0, 13], "restraint2": 0, "restraint3": 0, "name": [0, 1, 4, 7, 8, 11], "c14": 0, "sphlayer": [0, 8], "15": 0, "individu": [0, 13], "need": [0, 1, 3, 4, 7, 8, 9, 13], "distinct": 0, "etc": [0, 1, 3, 4], "requir": [0, 2, 3, 4, 5, 12], "simpli": 0, "adher": 0, "freeli": 0, "choos": [0, 1], "here": [0, 1, 3, 8], "provid": [0, 3, 4, 8, 9], "speak": 0, "identif": 0, "later": [0, 3, 4], "see": [0, 1, 2, 3, 4, 8], "detail": [0, 3, 4, 8], "string": [0, 8], "atom": [0, 3, 5, 9, 11, 12], "member": 0, "pleas": [0, 3], "must": [0, 4], "unit": 0, "even": 0, "never": 0, "would": [0, 3, 4, 7], "nonsens": 0, "acceler": 0, "md": [0, 3, 11, 12, 13], "possibl": [0, 3, 4, 7, 10, 11], "reweight": 0, "reduc": 0, "vibrat": 0, "frequenc": [0, 4], "correspond": [0, 4], "heavi": [0, 13], "bond": [0, 7, 8, 13], "when": [0, 1, 4, 5, 8, 13], "con": [0, 4], "hbond": [0, 4], "safe": 0, "increas": 0, "time": [0, 1, 2, 3, 4, 12, 13], "4": [0, 7, 11, 13], "f": [0, 1, 3, 5], "either": [0, 3, 4, 5, 9, 10, 11, 12, 13], "box": [0, 4], "last": [0, 4, 5], "gui": [0, 9, 10, 12], "solut": [0, 4, 13], "builder": [0, 4, 13], "parm": [0, 3, 7, 13], "action": 0, "tool": [0, 12, 13], "also": [0, 1, 3, 4], "avail": [0, 3], "fep": [0, 1, 2, 3, 4, 5], "conda": [0, 1, 2, 3], "environ": [0, 1, 2, 3, 4, 10, 13], "psf": [0, 3, 4, 7, 9, 10, 11], "pm": [0, 7, 10], "charmmpsffil": [0, 7, 10], "step3_input_orig": 0, "hmassrepartit": 0, "execut": [0, 1], "save": 0, "step3_input": [0, 4], "overwrit": [0, 9], "true": [0, 1, 3, 4, 7], "In": [1, 3, 4, 13], "theori": 1, "could": [1, 5], "directli": [1, 4, 7, 8, 12, 13], "submit": [1, 3, 4, 13], "ipynb": [1, 3, 4], "done": [1, 3, 13], "howev": [1, 3, 4, 13], "we": [1, 3, 4, 13], "instead": [1, 13], "least": 1, "rbfe": [1, 3, 4, 5, 12, 13], "put": [1, 5], "separ": 1, "usual": [1, 5, 7, 8, 9, 13], "alias": 1, "shell": 1, "script": [1, 3, 4], "command": [1, 2, 3], "necessari": [1, 2, 3, 4, 7, 13], "analys": [1, 2, 3], "trajetori": 1, "snippet": 1, "jupyt": [1, 3], "notebook": [1, 3], "finish": [1, 3], "termin": [1, 5, 7], "python": [1, 2, 3, 12, 13], "output_dir": [1, 3, 5, 11], "path": [1, 3, 5, 8, 9], "conf": 1, "whether": [1, 3, 4], "properli": [1, 3], "go": [1, 2, 4], "intstx": 1, "directori": [1, 2, 3, 4, 5, 7, 8, 9, 11], "waterbox_out": [1, 3, 5], "log": [1, 3, 5], "complex_out": [1, 3, 5], "rsfe": [1, 3, 4, 12, 13], "vacuum_out": 1, "decent": 1, "amout": 1, "just": [1, 3, 4], "amount": [1, 3, 8], "comput": [1, 12, 13], "resourc": 1, "depend": [1, 3, 4], "therefor": 1, "especi": [1, 13], "import": [1, 2, 3, 4, 7], "load_config_yaml": [1, 3, 5, 10, 11], "util": [1, 3, 5, 8, 10], "postprocess": [1, 3, 5, 11], "sy": 1, "come": 1, "frome": 1, "sh": [1, 3, 9], "standalon": 1, "outsid": 1, "argv": 1, "configur": [1, 3, 7, 8, 9, 10, 11], "input_dir": [1, 3, 5, 11], "structure1": [1, 3, 4, 10], "structure2": [1, 3, 4, 10], "ddg_openmm": [1, 5], "dddg": [1, 5], "f_openmm": [1, 5], "engin": [1, 3, 4, 11, 12, 13], "max_snapshot": [1, 11], "10000": 1, "num_proc": [1, 11], "6": [1, 13], "analyze_traj_with": [1, 11], "mda": 1, "show_summari": [1, 11], "print": [1, 2, 3, 5], "free": [1, 4, 11, 12, 13], "kt": 1, "set": [1, 3, 4, 7, 10, 12], "up": [1, 2, 3, 4, 12], "sever": [1, 3], "thing": 1, "want": [1, 3, 4, 8], "analyz": [1, 4], "enter": 1, "300": [1, 11], "snapshot": [1, 11], "per": [1, 4, 9, 11], "longer": 1, "mdtraj": [1, 11], "program": [1, 12, 13], "main": [1, 8], "multiprocess": [1, 3], "less": 1, "memori": 1, "gpu": [1, 3, 4], "get": [1, 7, 12], "substructur": 1, "g": [1, 4, 5, 7, 8, 12, 13], "delta": [1, 13], "bind": [1, 4, 12, 13], "_": [1, 13], "l1": [1, 13], "rightarrow": [1, 13], "dl_1": [1, 13], "r_": [1, 13], "final": [1, 3, 4, 7, 13], "l2": [1, 13], "substract": 1, "ligand2": [1, 4], "dl_2": [1, 13], "explain": 1, "theoret": [1, 12], "background": [1, 12], "start": [1, 3, 8, 13], "via": [1, 3, 12], "open": [1, 2], "analysis_": [1, 5], "w": 1, "write": [1, 3, 4, 8, 9], "bin": [1, 3, 9, 11], "bash": [1, 3], "n": [1, 8, 12, 13], "sbatch": [1, 3], "gre": [1, 3], "input": [1, 3, 4], "line": [1, 5], "slurm": [1, 3, 4, 5], "p": [1, 3, 4], "lgpu": [1, 3], "d": [1, 3, 12, 13], "afterani": 1, "jobid": 1, "make": [1, 2, 3, 4], "sourc": [1, 3, 7, 8, 9, 10], "miniconda3": 1, "profil": [1, 3], "cd": [1, 2, 3], "wd": [1, 3], "out": [1, 3, 5, 13], "ex": [1, 3], "subprocess": [1, 3], "popen": [1, 3], "ssh": [1, 3], "clusternam": [1, 3], "text": [1, 3], "stdout": [1, 3], "pipe": [1, 3], "output": [1, 2, 3, 4, 5, 9, 10, 12, 13], "read": [1, 3, 8, 10], "variabl": [1, 3, 5], "known": 1, "begin": 1, "manual": [1, 3], "simplifi": 1, "matter": 1, "contain": [1, 3, 4, 5, 10, 13], "case": [1, 3, 4, 7], "addit": [1, 3, 4, 8, 12], "work": [2, 3, 8, 12, 13], "version": 2, "miniconda": 2, "git": 2, "cuda": 2, "capabl": 2, "devic": 2, "local": [2, 3, 5], "node": [2, 7], "machin": [2, 3], "Then": 2, "clone": 2, "repositori": [2, 12, 13], "http": 2, "github": [2, 12], "com": 2, "wiederm": 2, "newli": 2, "found": [2, 3, 8, 9], "devtool": 2, "env": [2, 5, 9, 10], "fep_env": 2, "minut": 2, "For": [2, 3, 5, 8, 11, 12, 13], "nvidia": 2, "packag": [2, 5, 11, 12, 13], "cudatoolkit": 2, "higher": 2, "than": 2, "driver": 2, "smi": 2, "list": [2, 3, 8, 9, 10, 11], "correct": [2, 3, 11], "x": [2, 5], "y": 2, "forg": 2, "setup": [2, 3, 8, 12], "py": [2, 3, 4, 5, 8, 12], "try": 2, "__version__": 2, "congratul": 2, "readi": [2, 13], "unsur": 3, "inspir": 3, "actual": [3, 4, 8], "compris": 3, "dure": [3, 4], "stage": 3, "adjust": [3, 7], "dummi": [3, 5, 7, 9, 13], "region": [3, 5, 7, 13], "conduct": 3, "complex": [3, 4, 9, 10], "waterbox": [3, 4, 9, 10, 11], "trajcetori": 3, "shown": 3, "xxxxxxxxxxxxxxxx": 3, "ipython": 3, "interpret": 3, "vscode": 3, "enabl": [3, 4], "easier": 3, "visual": 3, "load": [3, 8, 11], "part": [3, 4, 13], "modul": [3, 5, 6, 7], "tell": 3, "our": [3, 12], "argument": 3, "find": [3, 5, 7, 8], "respect": [3, 4, 5, 13], "systemstructur": [3, 7, 9, 10], "intermediatestatefactori": [3, 9], "proposemutationrout": [3, 7, 9], "mutat": [3, 4, 9, 11, 13], "perform_mut": [3, 7], "displai": 3, "svg": 3, "run_simul": [3, 11], "filterwarn": 3, "ignor": 3, "24to25": 3, "longrun": 3, "norestraint": 3, "paramet": [3, 4, 5, 7, 8, 9, 10, 11, 13], "user": 3, "store": [3, 4], "intermediat": 3, "rout": 3, "process": 3, "alchem": [3, 12, 13], "connect": [3, 7, 12, 13], "s1": [3, 7], "s2": [3, 7], "s1_to_s2": [3, 7], "propose_common_cor": [3, 7], "suggest": 3, "show_common_core_on_mol1": [3, 7], "show_common_core_on_mol2": [3, 7], "doe": [3, 12], "interfer": 3, "add_idx_to_common_core_of_mol1": [3, 7], "idx1": 3, "idx2": 3, "add_idx_to_common_core_of_mol2": [3, 7], "remov": [3, 7], "remove_idx_to_common_core_of_mol1": 3, "remove_idx_to_common_core_of_mol2": 3, "idx": [3, 7, 8, 11], "graphic": 3, "beforehand": 3, "order": 3, "finish_common_cor": [3, 7], "attempt": 3, "charg": [3, 5, 7], "repeat": 3, "abov": [3, 4], "chang": [3, 4, 7, 9], "made": 3, "mutation_list": [3, 7, 9], "generate_mutations_to_common_core_for_mol1": [3, 7], "endstat": [3, 4, 7, 12, 13], "nr_of_mutation_steps_charg": [3, 7], "With": [3, 7, 13], "written": [3, 9], "error": [3, 12], "proce": 3, "nr_of_mutation_steps_cc": [3, 7], "interpol": [3, 7], "output_fil": [3, 11], "decid": [3, 7], "alreadi": [3, 7], "instal": [3, 4, 12], "oneself": 3, "technic": 3, "lot": 3, "reason": [3, 13], "strongli": [3, 4], "offload": [3, 12], "them": [3, 4, 8], "supercomput": 3, "though": 3, "easili": 3, "locat": [3, 9], "project": 3, "replic": 3, "combinedstructur": [3, 8], "singlestructur": 3, "ll": 3, "simulation_charmm": 3, "unsurprisingli": 3, "respons": 3, "inform": [3, 4, 8, 10, 12, 13], "featur": 3, "modifi": [3, 8, 12], "futur": 3, "some": [3, 5], "wai": [3, 4], "anaconda3": [3, 5], "pwd": 3, "hostnam": 3, "lig_in_complex": [3, 4, 5], "init": 3, "pstep": 3, "istep": 3, "irst": 3, "orst": 3, "lig_in_complex_rst": 3, "u": 3, "openmm_run": [3, 8], "inp": [3, 4], "t": [3, 12], "toppar": [3, 9, 10], "str": [3, 7, 8, 9, 10, 11], "crd": [3, 4], "rst": [3, 4, 5], "odcd": 3, "dcd": 3, "lig_in_waterbox": [3, 4], "lig_in_waterbox_rst": 3, "bit": 3, "debug": [3, 11, 12], "importantli": [3, 4], "so": [3, 11, 12], "absolut": 3, "rel": [3, 4, 12, 13], "intermediatest": [3, 7], "suppli": [3, 4], "run_complex": 3, "charmm_run_complex": 3, "omp_num_thread": 3, "log_complex": 3, "run_waterbox": 3, "charmm_run_waterbox": 3, "log_solv": 3, "esac": 3, "unlik": 3, "statement": [3, 11], "alwai": [3, 4, 7], "autom": 3, "cluster": [3, 12], "There": [3, 11], "method": [3, 4], "advantag": 3, "extra": 3, "being": [3, 13], "facil": 3, "caprici": 3, "variant": 3, "inspect": 3, "submiss": 3, "o": [3, 5, 12], "glob": 3, "getcwd": 3, "recurs": 3, "point": [3, 8], "sort": [3, 7], "replac": [3, 11], "accord": [3, 7, 13], "reliabl": 3, "modif": 3, "instruct": [3, 8], "similar": [3, 8, 13], "prevent": 3, "issu": [3, 11], "prefer": 3, "sbash": 3, "workload": [3, 4, 9], "manag": [3, 4, 5, 8, 9], "back": 3, "next": [3, 5, 7], "loop": 3, "ani": [3, 4], "correctli": [3, 5], "built": 3, "restrict": 3, "certain": 3, "talk": 4, "vacuum": [4, 9, 10, 13], "ga": 4, "phase": 4, "automat": [4, 10], "successfulli": 4, "three": [4, 7, 11], "item": 4, "": [4, 10, 12, 13], "solvat": [4, 12, 13], "onc": 4, "pure": 4, "describ": 4, "standard": [4, 13], "analysi": [4, 12, 13], "cover": 4, "trajectori": [4, 11, 12, 13], "page": [4, 13], "overal": 4, "everyth": [4, 9, 10], "interest": 4, "physic": [4, 7, 12, 13], "encourag": 4, "specif": [4, 7, 9, 10], "pdb": [4, 9], "bound": [4, 13], "sdf": 4, "mol2": [4, 7], "someth": 4, "4842148": 4, "renam": 4, "second": 4, "third": 4, "fourth": 4, "equillibr": 4, "equilibr": [4, 5], "indict": 4, "strucr": 4, "among": 4, "other": [4, 7, 13], "prm": 4, "rtf": [4, 9], "strictli": 4, "build": 4, "yourself": 4, "proper": 4, "cgenff": 4, "length": 4, "restraint": [4, 12], "let": 4, "complet": 4, "vim2_zn148": 4, "dirnam": 4, "psf_file_nam": 4, "crd_file_nam": 4, "rst_file_nam": 4, "step4_equilibr": 4, "simulation_paramet": 4, "step5_product": 4, "filenam": 4, "step3": 4, "vim2_zn222": 4, "nstep": [4, 5], "1250000": 4, "nstdcd": [4, 5], "1000": 4, "nstout": 4, "dt": 4, "004": 4, "vfswitch": [4, 11], "mini_nstep": 4, "steps_for_equilibr": 4, "most": [4, 5, 7], "referenc": [4, 5], "residu": 4, "often": 4, "unk": 4, "refer": [4, 7, 8, 9, 10, 12, 13], "variou": 4, "subfold": 4, "coordin": [4, 10], "none": [4, 5, 7], "constraint": 4, "timestep": 4, "picosecond": 4, "001": 4, "002": 4, "hydrogen": [4, 7, 12, 13], "mass": [4, 8, 12], "repartit": [4, 12], "vdw": [4, 7], "cut": 4, "off": [4, 7, 13], "minim": 4, "fals": [4, 7, 9, 11], "sge": 4, "continu": 4, "worload": 5, "812311": 5, "intstat": [5, 8], "typic": 5, "except": 5, "yamlerror": 5, "exc": 5, "settingsmap": 5, "rais": [5, 7, 8, 9], "keyerror": 5, "els": [5, 9], "unboundlocalerror": 5, "assign": [5, 7], "typo": 5, "rememb": 5, "space": [5, 11], "colon": 5, "data": 5, "runtimeerror": [5, 7, 9], "compens": [5, 7], "fail": 5, "introduc": 5, "integ": [5, 9], "total": 5, "584000000000001": 5, "target": [5, 7], "root": 5, "ensur": [5, 8], "sensibl": 5, "new": [5, 7, 9], "filenotfounderror": 5, "errno": 5, "No": 5, "site": 5, "raid4": 5, "student4": 5, "production_transformato": 5, "tablit_24to25": 5, "run1": 5, "2oj9_tablit_struc24": 5, "2oj9_tablit_struc25": 5, "occur": 5, "restart": 5, "wa": 5, "due": 5, "traceback": 5, "recent": 5, "alex": 5, "taapdb_24to25": 5, "23": 5, "home": 5, "lib": 5, "python3": 5, "9": [5, 12, 13], "129": [5, 13], "gee57388": 5, "py3": 5, "egg": 5, "60": 5, "calculate_dg_to_common_cor": 5, "636": 5, "self": [5, 7], "mbar_result": 5, "_analyse_results_using_mda": 5, "507": 5, "nr_of_stat": 5, "len": [5, 8], "walk": 5, "base_path": 5, "stopiter": 5, "commonli": 5, "consist": 6, "commoncoretransform": 7, "cc1_indici": 7, "cc2_indici": 7, "ligand1_psf": 7, "ligand2_psf": 7, "tlc_cc1": 7, "tlc_cc2": 7, "charge_compensated_ligand2_psf": 7, "charge_mut": 7, "bonded_terms_mut": 7, "bool": [7, 9, 11], "__init__": [7, 8, 9, 10], "insid": 7, "param": [7, 9, 10], "indic": 7, "cc1": 7, "cc2": 7, "copi": [7, 9], "parmaet": 7, "letter": 7, "__weakref__": [7, 8, 9, 10], "weak": [7, 8, 9, 10], "object": [7, 8, 9, 10, 11], "_get_atom_map": 7, "match": 7, "dict": [7, 8, 9, 10, 11], "_mutate_atom": 7, "lambda_valu": 7, "dummyregion": 7, "mol_nam": 7, "match_termin_real_and_dummy_atom": 7, "connected_dummy_region": 7, "lj_default": 7, "__eq__": 7, "__hash__": 7, "__repr__": 7, "repr": 7, "atoms_to_be_mut": 7, "dummy_region": 7, "_compensate_charg": 7, "total_charg": 7, "offset": [7, 10], "real": 7, "group": 7, "lambda_value_electrostat": [7, 9], "lambda_value_vdw": [7, 9], "vdw_atom_idx": 7, "steric_mutation_to_default": 7, "perform": [7, 9, 11], "mutationdefinit": 7, "common_cor": 7, "factori": [7, 8], "propos": 7, "base": [7, 9], "mol": [7, 10, 12], "chem": [7, 10, 12, 13], "static": [7, 9], "_calculate_order_of_lj_mut": 7, "match_terminal_atom": 7, "cyclecheck": 7, "ordercycl": 7, "exclude_h": 7, "theses": 7, "helper_funct": 7, "updat": 7, "weight": 7, "cycl": 7, "particip": 7, "ordercheck": 7, "exactli": 7, "preferenti": 7, "neighbourhood": 7, "workflow": 7, "graph": 7, "_check_for_lp": 7, "odered_connected_dummy_regions_cc_with_lp": 7, "help": 7, "ordered_connected_dummy_region": 7, "lonepair": 7, "wheather": 7, "lp": 7, "belong": 7, "accordingli": 7, "_find_mc": 7, "mol1_nam": 7, "mol2_nam": 7, "iterate_over_match": 7, "max_match": 7, "_find_terminal_atom": 7, "cc_idx": 7, "index": [7, 12], "rdkit": [7, 10, 13], "tupl": 7, "_get_common_cor": 7, "helper": 7, "_match_terminal_real_and_dummy_atom": 7, "real_atoms_cc": 7, "dummy_atoms_cc": 7, "kei": [7, 9], "_match_terminal_real_and_dummy_atoms_for_mol1": 7, "_match_terminal_real_and_dummy_atoms_for_mol2": 7, "_mutate_to_common_cor": 7, "_show_common_cor": 7, "highlight": 7, "show_atom_typ": 7, "intern": 7, "show": 7, "_transform_common_cor": 7, "transform": [7, 13], "idx_list": 7, "awar": 7, "ad": 7, "connected_dummy_regions_cc1": 7, "connected_dummy_regions_cc2": 7, "odered_connected_dummy_regions_cc1": 7, "odered_connected_dummy_regions_cc2": 7, "collect": 7, "own": 7, "generate_mutations_to_common_core_for_mol2": 7, "rtype": 7, "get_common_core_idx_mol1": 7, "get_common_core_idx_mol2": 7, "get_idx_of_all_atom": 7, "search": [7, 13], "asf": 7, "mutate_pure_tautom": 7, "system1": 7, "system2": 7, "single_st": 7, "nr_of_bonded_window": 7, "list_of_heavy_atoms_to_be_mut": 7, "nr_of_mutation_steps_lj_of_hydrogen": 7, "nr_of_mutation_steps_lj_of_heavy_atom": 7, "endstate_correct": 7, "dictionari": [7, 9, 10], "instanc": [7, 8], "nr": [7, 9], "topologi": [7, 8, 11, 13], "appropri": 8, "exist": 8, "commensur": 8, "desir": 8, "That": 8, "ist": 8, "unless": 8, "document": 8, "selligand": 8, "selprotein": 8, "05": 8, "kwarg": 8, "univers": [8, 12], "intermediari": [8, 12], "attributeerror": 8, "request": [8, 9], "implement": [8, 11, 12, 13], "formula": 8, "geometri": 8, "onesid": 8, "sharp": 8, "twosid": 8, "size": 8, "side": 8, "catcher": 8, "restraint_arg": 8, "_add_flatbottom_paramet": 8, "care": 8, "customcentroidbondforc": 8, "applyforc": 8, "createforc": 8, "common_core_nam": 8, "dismiss": 8, "molecul": [8, 10, 12], "create_restraints_from_config": 8, "pdbpath": 8, "invok": 8, "safe_load": 8, "generate_extrem": 8, "n_extrem": 8, "sphinner": 8, "sphouter": 8, "furthest": 8, "doc": 8, "algorithm": 8, "oper": 8, "extremity_cor": 8, "pick": 8, "sum": [8, 13], "previou": 8, "greatest": 8, "exce": 8, "end": 8, "valueerror": 8, "invalid": 8, "nest": 8, "vicin": 8, "selection_str": 8, "generate_simple_select": 8, "simpl": 8, "ident": 8, "get3ddist": 8, "pos2": 8, "3d": 8, "pos1": 8, "write_restraints_yaml": 8, "current_step": 8, "multiple_run": [9, 11], "definit": [9, 11], "_check_hmr": 9, "hmr": [9, 12], "_copy_charmm_fil": 9, "intermediate_state_file_path": 9, "_copy_fil": 9, "_copy_omm_fil": 9, "copyi": 9, "_init_base_dir": 9, "central": 9, "dir": [9, 10], "_init_intermediate_state_dir": 9, "_overwrite_simulation_script_paramet": 9, "omm_simulation_parameter_sourc": 9, "omm_simulation_parameter_target": 9, "pair": 9, "_write_psf": 9, "output_file_bas": 9, "_write_rtf_fil": 9, "_write_workload_preambl": 9, "filepath": 9, "prepend": 9, "preambl": 9, "_script_target": 9, "write_st": 9, "mutation_conf": 9, "common_core_transform": 9, "singl": 10, "construct": 10, "obtain": [10, 13], "_determine_offset_and_set_possible_dummy_properti": 10, "determin": 10, "properti": 10, "_generate_rdkit_mol": 10, "rdchem": 10, "_initialize_system": 10, "_read_paramet": 10, "topparamet": 10, "charmmparameterset": 10, "generate_atom_tables_from_psf": 10, "map": [10, 11], "check_switching_funct": 11, "get_bin_dir": 11, "get_structure_nam": 11, "structure_nam": 11, "get_test_output_dir": 11, "get_toppar_dir": 11, "isnotebook": 11, "map_lj_mutations_to_atom_idx": 11, "lj_mutat": 11, "lj": [11, 13], "methan": 11, "different_path_for_dcd": 11, "only_single_st": 11, "estim": 11, "mbar": [11, 13], "deposit": 11, "maximum": [11, 13], "lambda": [11, 13], "window": 11, "plot": 11, "accumul": 11, "overlap": 11, "purpos": [11, 13], "psf_correct": 11, "miss": 11, "ngrp": 11, "charmm_openmm": 11, "handl": 11, "correspo": 11, "str_object": 11, "stringio": 11, "only_vacuum": 11, "format": 11, "ool": 12, "un": 12, "tic": 12, "FOR": 12, "m": [12, 13], "ultist": 12, "serial": 12, "ato": 12, "insert": 12, "sai": 12, "approach": 12, "pathwai": [12, 13], "veri": 12, "littl": 12, "design": [12, 13], "head": 12, "over": 12, "interplai": 12, "citat": 12, "licens": 12, "contact": 12, "acknowledg": 12, "prerequisit": 12, "troubleshoot": 12, "messag": 12, "caus": 12, "api": 12, "boresch": [12, 13], "bruckner": [12, 13], "2011": [12, 13], "avoid": [12, 13], "van": [12, 13], "der": [12, 13], "waal": [12, 13], "endpoint": [12, 13], "problem": [12, 13], "j": [12, 13], "32": [12, 13], "2449": [12, 13], "2458": [12, 13], "doi": [12, 13], "wieder": [12, 13], "fleck": [12, 13], "braunsfeld": [12, 13], "2022": [12, 13], "speed": [12, 13], "limit": [12, 13], "framework": [12, 13], "independ": [12, 13], "underli": [12, 13], "molecular": [12, 13], "dynam": [12, 13], "43": [12, 13], "1151": [12, 13], "1160": [12, 13], "karwounopoulo": [12, 13], "front": 12, "biosic": 12, "954638": 12, "maintain": 12, "marku": 12, "depart": 12, "pharmaceut": 12, "scienc": [12, 13], "vienna": 12, "johann": 12, "institut": 12, "biolog": 12, "chemistri": [12, 13], "stefan": 12, "turn": 13, "wise": 13, "electrostat": 13, "contribut": 13, "lennard": 13, "jone": 13, "interact": 13, "basi": 13, "water": 13, "receptor": 13, "plain": 13, "sinc": 13, "close": 13, "togeth": 13, "fe": 13, "nonbond": 13, "coupl": 13, "ideal": 13, "reach": 13, "cancel": 13, "fulli": 13, "releas": 13, "under": 13, "mit": 13, "visit": 13, "apart": 13, "reli": 13, "larg": 13, "numpi": 13, "7": 13, "manipul": 13, "pymbar": 13, "visualis": 13, "shirt": 13, "moblei": 13, "l": 13, "chodera": 13, "2007": 13, "prime": 13, "annual": 13, "report": 13, "vol": 13, "frontier": 13, "gower": 13, "et": 13, "al": 13, "2016": 13, "rapid": 13, "proceed": 13, "confer": 13, "scipi": 13, "michaud": 13, "agraw": 13, "toolkit": 13, "journal": 13, "pp": 13, "2319": 13, "2327": 13, "walt": 13, "colbert": 13, "varoquaux": 13, "effici": 13, "numer": 13, "13": 13, "22": 13, "mr": 13, "jd": 13, "statist": 13, "optim": 13, "equilibrium": 13, "phy": 13, "124105": 13, "2008": 13, "michael": 13, "christoph": 13, "klein": 13, "lesson": 13, "learn": 13, "compar": 13, "sampl5": 13, "dataset": 13, "aid": 13}, "objects": {"transformato": [[7, 0, 0, "module-0", "mutate"], [8, 0, 0, "module-0", "restraints"], [9, 0, 0, "module-0", "state"], [10, 0, 0, "module-0", "system"], [11, 0, 0, "module-0", "utils"]], "transformato.mutate": [[7, 1, 1, "", "CommonCoreTransformation"], [7, 1, 1, "", "DummyRegion"], [7, 1, 1, "", "Mutation"], [7, 1, 1, "", "MutationDefinition"], [7, 1, 1, "", "ProposeMutationRoute"], [7, 2, 1, "", "mutate_pure_tautomers"], [7, 2, 1, "", "perform_mutations"]], "transformato.mutate.CommonCoreTransformation": [[7, 2, 1, "", "__init__"], [7, 3, 1, "", "__weakref__"], [7, 2, 1, "", "_get_atom_mapping"], [7, 2, 1, "", "_mutate_atoms"], [7, 2, 1, "", "mutate"]], "transformato.mutate.DummyRegion": [[7, 2, 1, "", "__eq__"], [7, 3, 1, "", "__hash__"], [7, 2, 1, "", "__init__"], [7, 2, 1, "", "__repr__"], [7, 3, 1, "", "__weakref__"]], "transformato.mutate.Mutation": [[7, 2, 1, "", "__init__"], [7, 3, 1, "", "__weakref__"], [7, 2, 1, "", "_compensate_charge"], [7, 2, 1, "", "mutate"]], "transformato.mutate.MutationDefinition": [[7, 2, 1, "", "__eq__"], [7, 3, 1, "", "__hash__"], [7, 2, 1, "", "__init__"], [7, 2, 1, "", "__repr__"], [7, 3, 1, "", "__weakref__"]], "transformato.mutate.ProposeMutationRoute": [[7, 2, 1, "", "__init__"], [7, 3, 1, "", "__weakref__"], [7, 2, 1, "", "_calculate_order_of_LJ_mutations"], [7, 2, 1, "", "_check_for_lp"], [7, 2, 1, "", "_find_mcs"], [7, 2, 1, "", "_find_terminal_atom"], [7, 2, 1, "", "_get_common_core"], [7, 2, 1, "", "_match_terminal_real_and_dummy_atoms"], [7, 2, 1, "", "_match_terminal_real_and_dummy_atoms_for_mol1"], [7, 2, 1, "", "_match_terminal_real_and_dummy_atoms_for_mol2"], [7, 2, 1, "", "_mutate_to_common_core"], [7, 2, 1, "", "_show_common_core"], [7, 2, 1, "", "_transform_common_core"], [7, 2, 1, "", "add_idx_to_common_core_of_mol1"], [7, 2, 1, "", "add_idx_to_common_core_of_mol2"], [7, 2, 1, "", "finish_common_core"], [7, 2, 1, "", "generate_mutations_to_common_core_for_mol1"], [7, 2, 1, "", "generate_mutations_to_common_core_for_mol2"], [7, 2, 1, "", "get_common_core_idx_mol1"], [7, 2, 1, "", "get_common_core_idx_mol2"], [7, 2, 1, "", "get_idx_of_all_atoms"], [7, 2, 1, "", "propose_common_core"], [7, 2, 1, "", "show_common_core_on_mol1"], [7, 2, 1, "", "show_common_core_on_mol2"]], "transformato.restraints": [[8, 1, 1, "", "Restraint"], [8, 2, 1, "", "create_restraints_from_config"], [8, 2, 1, "", "generate_extremities"], [8, 2, 1, "", "generate_simple_selection"], [8, 2, 1, "", "get3DDistance"], [8, 2, 1, "", "write_restraints_yaml"]], "transformato.restraints.Restraint": [[8, 2, 1, "", "__init__"], [8, 3, 1, "", "__weakref__"], [8, 2, 1, "", "_add_flatbottom_parameters"], [8, 2, 1, "", "applyForce"], [8, 2, 1, "", "createForce"]], "transformato.state": [[9, 1, 1, "", "IntermediateStateFactory"]], "transformato.state.IntermediateStateFactory": [[9, 2, 1, "", "__init__"], [9, 3, 1, "", "__weakref__"], [9, 2, 1, "", "_check_hmr"], [9, 2, 1, "", "_copy_charmm_files"], [9, 2, 1, "", "_copy_files"], [9, 2, 1, "", "_copy_omm_files"], [9, 2, 1, "", "_init_base_dir"], [9, 2, 1, "", "_init_intermediate_state_dir"], [9, 2, 1, "", "_overwrite_simulation_script_parameters"], [9, 2, 1, "", "_write_psf"], [9, 2, 1, "", "_write_rtf_file"], [9, 2, 1, "", "_write_workload_preamble"], [9, 2, 1, "", "write_state"]], "transformato.system": [[10, 1, 1, "", "SystemStructure"]], "transformato.system.SystemStructure": [[10, 2, 1, "", "__init__"], [10, 3, 1, "", "__weakref__"], [10, 2, 1, "", "_determine_offset_and_set_possible_dummy_properties"], [10, 2, 1, "", "_generate_rdkit_mol"], [10, 2, 1, "", "_initialize_system"], [10, 2, 1, "", "_read_parameters"], [10, 2, 1, "", "generate_atom_tables_from_psf"]], "transformato.utils": [[11, 2, 1, "", "check_switching_function"], [11, 2, 1, "", "get_bin_dir"], [11, 2, 1, "", "get_structure_name"], [11, 2, 1, "", "get_test_output_dir"], [11, 2, 1, "", "get_toppar_dir"], [11, 2, 1, "", "isnotebook"], [11, 2, 1, "", "load_config_yaml"], [11, 2, 1, "", "map_lj_mutations_to_atom_idx"], [11, 2, 1, "", "postprocessing"], [11, 2, 1, "", "psf_correction"], [11, 2, 1, "", "run_simulation"]], "": [[4, 4, 1, "cmdoption-arg-workload-manager", ""SGE"])"], [4, 4, 1, "cmdoption-arg-free-energy-type", ""rsfe"])"], [4, 4, 1, "cmdoption-arg-switch", ""switch"])"], [4, 4, 1, "cmdoption-arg-GPU", "False])"], [4, 4, 1, "cmdoption-arg-GPU", "GPU:"], [4, 4, 1, "cmdoption-arg-cons", "None]"], [1, 4, 1, "cmdoption-arg-analyze_traj_with", "analyze_traj_with"], [3, 4, 1, "cmdoption-arg-config", "config"], [4, 4, 1, "cmdoption-arg-cons", "cons:"], [1, 4, 1, "cmdoption-arg-engine", "default:"], [4, 4, 1, "cmdoption-arg-dt", "dt:"], [1, 4, 1, "cmdoption-arg-engine", "engine"], [0, 4, 1, "cmdoption-arg-extremities", "extremities"], [4, 4, 1, "cmdoption-arg-free-energy-type", "free-energy-type:"], [0, 4, 1, "cmdoption-arg-group1-group2", "group1,group2"], [3, 4, 1, "cmdoption-arg-input_dir", "input_dir"], [0, 4, 1, "cmdoption-arg-k", "k"], [1, 4, 1, "cmdoption-arg-max_snapshots", "max_snapshots"], [4, 4, 1, "cmdoption-arg-mini_nstep", "mini_nstep:"], [1, 4, 1, "cmdoption-arg-name", "name"], [3, 4, 1, "cmdoption-arg-nr_of_mutation_steps_cc", "nr_of_mutation_steps_cc"], [3, 4, 1, "cmdoption-arg-nr_of_mutation_steps_charge", "nr_of_mutation_steps_charge"], [4, 4, 1, "cmdoption-arg-nstdcd", "nstdcd:"], [4, 4, 1, "cmdoption-arg-nstep", "nstep:"], [4, 4, 1, "cmdoption-arg-nstout", "nstout:"], [4, 4, 1, "cmdoption-arg-other", "other"], [3, 4, 1, "cmdoption-arg-output_dir", "output_dir"], [0, 4, 1, "cmdoption-arg-scaling", "scaling"], [0, 4, 1, "cmdoption-arg-shape", "shape"], [4, 4, 1, "cmdoption-arg-switch", "switch:"], [4, 4, 1, "cmdoption-arg-tlc", "tlc"], [0, 4, 1, "cmdoption-arg-wellsize", "wellsize"], [4, 4, 1, "cmdoption-arg-workload-manager", "workload-manager:"]]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:attribute", "4": "std:cmdoption"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "attribute", "Python attribute"], "4": ["std", "cmdoption", "program option"]}, "titleterms": {"addit": 0, "set": 0, "restraint": [0, 8], "automat": 0, "manual": 0, "hydrogen": 0, "mass": 0, "repartit": 0, "hmr": 0, "trajectori": 1, "analysi": [1, 5], "The": [1, 13], "py": 1, "file": [1, 4], "offload": 1, "cluster": 1, "instal": 2, "prerequisit": 2, "get": [2, 5], "texttt": 2, "transformato": [2, 7, 8, 9, 10, 11, 12], "run": 3, "simul": [3, 5], "step": [3, 4], "3": 3, "creat": [3, 4], "intermediari": 3, "state": [3, 9], "system": [4, 5, 10], "setup": [4, 5], "1": 4, "us": 4, "charmm": [4, 13], "gui": [4, 13], "For": 4, "expert": 4, "user": 4, "onli": 4, "2": 4, "modifi": 4, "yaml": 4, "troubleshoot": 5, "debug": 5, "inform": 5, "error": 5, "messag": 5, "common": [5, 7, 13], "caus": 5, "dure": 5, "api": 6, "document": [6, 12], "mutat": 7, "descript": [7, 8, 9, 10, 11], "class": [7, 8, 9, 10], "bf": 7, "djikstra": 7, "algorithm": 7, "appli": 7, "calcul": 7, "order": 7, "turn": 7, "lj": 7, "interact": 7, "heavi": 7, "atom": [7, 13], "gener": 7, "rout": 7, "fore": 7, "mol1": 7, "iter": 7, "over": 7, "all": 7, "molecul": 7, "save": 7, "them": 7, "list": 7, "function": [7, 8, 11], "basic": 8, "usag": 8, "util": 11, "welcom": 12, "content": 12, "theoret": 13, "background": 13, "interplai": 13, "core": 13, "approach": 13, "serial": 13, "insert": 13, "citat": 13, "licens": 13, "contact": 13, "acknowledg": 13}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx.ext.intersphinx": 1, "sphinx": 60}, "alltitles": {"Additional Settings": [[0, "additional-settings"]], "Restraints": [[0, "restraints"]], "Automatic Restraints": [[0, "automatic-restraints"]], "Manual Restraints": [[0, "manual-restraints"]], "Hydrogen Mass Repartitioning (HMR)": [[0, "hydrogen-mass-repartitioning-hmr"]], "Trajectory Analysis": [[1, "trajectory-analysis"]], "The analysis.py file": [[1, "the-analysis-py-file"]], "Offloading the analysis to a cluster": [[1, "offloading-the-analysis-to-a-cluster"]], "Installation": [[2, "installation"]], "Prerequisites": [[2, "prerequisites"]], "Getting \\texttt{TRANSFORMATO}": [[2, "getting-trafo"]], "Running Simulations": [[3, "running-simulations"]], "Step 3 - Creating intermediary states": [[3, "step-3-creating-intermediary-states"]], "System Setup": [[4, "system-setup"]], "Step 1 \u2013 creating Systems using CHARMM-GUI": [[4, "step-1-creating-systems-using-charmm-gui"]], "For expert users only!": [[4, null]], "Step 2 \u2013 modifying the yaml file": [[4, "step-2-modifying-the-yaml-file"]], "Troubleshooting": [[5, "troubleshooting"]], "Getting debug information": [[5, "getting-debug-information"]], "Error messages and common causes:": [[5, "error-messages-and-common-causes"]], "Errors during system setup:": [[5, "errors-during-system-setup"]], "Errors during simulation:": [[5, "errors-during-simulation"]], "Errors during analysis:": [[5, "errors-during-analysis"]], "API Documentation": [[6, "api-documentation"]], "transformato.mutate": [[7, "transformato-mutate"]], "Description": [[7, "description"], [8, "description"], [9, "description"], [10, "description"], [11, "description"]], "Classes": [[7, "classes"], [8, "classes"], [9, "classes"], [10, "classes"]], "bfs/djikstra-algorithm applied to calculate the ordere for turning of the LJ interactions of the heavy atoms": [[7, "bfs-djikstra-algorithm-applied-to-calculate-the-ordere-for-turning-of-the-lj-interactions-of-the-heavy-atoms"]], "Generates the mutation route to the common fore for mol1.": [[7, "generates-the-mutation-route-to-the-common-fore-for-mol1"]], "Iterates over all atoms of the molecule and saves them as a list": [[7, "iterates-over-all-atoms-of-the-molecule-and-saves-them-as-a-list"]], "Functions": [[7, "functions"], [8, "functions"], [11, "functions"]], "transformato.restraints": [[8, "transformato-restraints"]], "Basic function:": [[8, "basic-function"]], "Usage:": [[8, "usage"]], "transformato.state": [[9, "transformato-state"]], "transformato.system": [[10, "transformato-system"]], "transformato.utils": [[11, "transformato-utils"]], "Welcome to the documentation for transformato!": [[12, "welcome-to-the-documentation-for-transformato"]], "Contents:": [[12, null]], "Theoretical background": [[13, "theoretical-background"]], "Interplay with CHARMM-GUI": [[13, "interplay-with-charmm-gui"]], "The common-core approach": [[13, "the-common-core-approach"]], "Serial-Atom-Insertion approach": [[13, "serial-atom-insertion-approach"]], "Citations, License and Contact": [[13, "citations-license-and-contact"]], "Acknowledgements": [[13, "acknowledgements"]]}, "indexentries": {"command line option": [[0, "cmdoption-arg-0"], [0, "cmdoption-arg-1"], [0, "cmdoption-arg-2"], [0, "cmdoption-arg-extremities"], [0, "cmdoption-arg-group1-group2"], [0, "cmdoption-arg-k"], [0, "cmdoption-arg-scaling"], [0, "cmdoption-arg-shape"], [0, "cmdoption-arg-wellsize"], [1, "cmdoption-arg-analyze_traj_with"], [1, "cmdoption-arg-engine"], [1, "cmdoption-arg-max_snapshots"], [1, "cmdoption-arg-name"], [3, "cmdoption-arg-config"], [3, "cmdoption-arg-input_dir"], [3, "cmdoption-arg-nr_of_mutation_steps_cc"], [3, "cmdoption-arg-nr_of_mutation_steps_charge"], [3, "cmdoption-arg-output_dir"], [4, "cmdoption-arg-GPU"], [4, "cmdoption-arg-cons"], [4, "cmdoption-arg-dt"], [4, "cmdoption-arg-free-energy-type"], [4, "cmdoption-arg-mini_nstep"], [4, "cmdoption-arg-name"], [4, "cmdoption-arg-nstdcd"], [4, "cmdoption-arg-nstep"], [4, "cmdoption-arg-nstout"], [4, "cmdoption-arg-other"], [4, "cmdoption-arg-switch"], [4, "cmdoption-arg-tlc"], [4, "cmdoption-arg-workload-manager"]], "extremities": [[0, "cmdoption-arg-extremities"]], "group1,group2": [[0, "cmdoption-arg-group1-group2"]], "k": [[0, "cmdoption-arg-1"], [0, "cmdoption-arg-k"]], "scaling": [[0, "cmdoption-arg-scaling"]], "shape": [[0, "cmdoption-arg-0"], [0, "cmdoption-arg-shape"]], "wellsize": [[0, "cmdoption-arg-2"], [0, "cmdoption-arg-wellsize"]], "analyze_traj_with": [[1, "cmdoption-arg-analyze_traj_with"]], "default:": [[1, "cmdoption-arg-analyze_traj_with"], [1, "cmdoption-arg-engine"], [1, "cmdoption-arg-max_snapshots"]], "engine": [[1, "cmdoption-arg-engine"]], "max_snapshots": [[1, "cmdoption-arg-max_snapshots"]], "name": [[1, "cmdoption-arg-name"], [4, "cmdoption-arg-name"]], "config": [[3, "cmdoption-arg-config"]], "input_dir": [[3, "cmdoption-arg-input_dir"]], "nr_of_mutation_steps_cc": [[3, "cmdoption-arg-nr_of_mutation_steps_cc"]], "nr_of_mutation_steps_charge": [[3, "cmdoption-arg-nr_of_mutation_steps_charge"]], "output_dir": [[3, "cmdoption-arg-output_dir"]], "\"sge\"])": [[4, "cmdoption-arg-workload-manager"]], "\"rsfe\"])": [[4, "cmdoption-arg-free-energy-type"]], "\"switch\"])": [[4, "cmdoption-arg-switch"]], "false])": [[4, "cmdoption-arg-GPU"]], "gpu:": [[4, "cmdoption-arg-GPU"]], "none]": [[4, "cmdoption-arg-cons"]], "cons:": [[4, "cmdoption-arg-cons"]], "dt:": [[4, "cmdoption-arg-dt"]], "free-energy-type:": [[4, "cmdoption-arg-free-energy-type"]], "mini_nstep:": [[4, "cmdoption-arg-mini_nstep"]], "nstdcd:": [[4, "cmdoption-arg-nstdcd"]], "nstep:": [[4, "cmdoption-arg-nstep"]], "nstout:": [[4, "cmdoption-arg-nstout"]], "other": [[4, "cmdoption-arg-other"]], "switch:": [[4, "cmdoption-arg-switch"]], "tlc": [[4, "cmdoption-arg-tlc"]], "workload-manager:": [[4, "cmdoption-arg-workload-manager"]], "commoncoretransformation (class in transformato.mutate)": [[7, "transformato.mutate.CommonCoreTransformation"]], "dummyregion (class in transformato.mutate)": [[7, "transformato.mutate.DummyRegion"]], "mutation (class in transformato.mutate)": [[7, "transformato.mutate.Mutation"]], "mutationdefinition (class in transformato.mutate)": [[7, "transformato.mutate.MutationDefinition"]], "proposemutationroute (class in transformato.mutate)": [[7, "transformato.mutate.ProposeMutationRoute"]], "__eq__() (transformato.mutate.dummyregion method)": [[7, "transformato.mutate.DummyRegion.__eq__"]], "__eq__() (transformato.mutate.mutationdefinition method)": [[7, "transformato.mutate.MutationDefinition.__eq__"]], "__hash__ (transformato.mutate.dummyregion attribute)": [[7, "transformato.mutate.DummyRegion.__hash__"]], "__hash__ (transformato.mutate.mutationdefinition attribute)": [[7, "transformato.mutate.MutationDefinition.__hash__"]], "__init__() (transformato.mutate.commoncoretransformation method)": [[7, "transformato.mutate.CommonCoreTransformation.__init__"]], "__init__() (transformato.mutate.dummyregion method)": [[7, "transformato.mutate.DummyRegion.__init__"]], "__init__() (transformato.mutate.mutation method)": [[7, "transformato.mutate.Mutation.__init__"]], "__init__() (transformato.mutate.mutationdefinition method)": [[7, "transformato.mutate.MutationDefinition.__init__"]], "__init__() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.__init__"]], "__repr__() (transformato.mutate.dummyregion method)": [[7, "transformato.mutate.DummyRegion.__repr__"]], "__repr__() (transformato.mutate.mutationdefinition method)": [[7, "transformato.mutate.MutationDefinition.__repr__"]], "__weakref__ (transformato.mutate.commoncoretransformation attribute)": [[7, "transformato.mutate.CommonCoreTransformation.__weakref__"]], "__weakref__ (transformato.mutate.dummyregion attribute)": [[7, "transformato.mutate.DummyRegion.__weakref__"]], "__weakref__ (transformato.mutate.mutation attribute)": [[7, "transformato.mutate.Mutation.__weakref__"]], "__weakref__ (transformato.mutate.mutationdefinition attribute)": [[7, "transformato.mutate.MutationDefinition.__weakref__"]], "__weakref__ (transformato.mutate.proposemutationroute attribute)": [[7, "transformato.mutate.ProposeMutationRoute.__weakref__"]], "_calculate_order_of_lj_mutations() (transformato.mutate.proposemutationroute static method)": [[7, "transformato.mutate.ProposeMutationRoute._calculate_order_of_LJ_mutations"]], "_check_for_lp() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._check_for_lp"]], "_compensate_charge() (transformato.mutate.mutation method)": [[7, "transformato.mutate.Mutation._compensate_charge"]], "_find_mcs() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._find_mcs"]], "_find_terminal_atom() (transformato.mutate.proposemutationroute static method)": [[7, "transformato.mutate.ProposeMutationRoute._find_terminal_atom"]], "_get_atom_mapping() (transformato.mutate.commoncoretransformation method)": [[7, "transformato.mutate.CommonCoreTransformation._get_atom_mapping"]], "_get_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._get_common_core"]], "_match_terminal_real_and_dummy_atoms() (transformato.mutate.proposemutationroute static method)": [[7, "transformato.mutate.ProposeMutationRoute._match_terminal_real_and_dummy_atoms"]], "_match_terminal_real_and_dummy_atoms_for_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._match_terminal_real_and_dummy_atoms_for_mol1"]], "_match_terminal_real_and_dummy_atoms_for_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._match_terminal_real_and_dummy_atoms_for_mol2"]], "_mutate_atoms() (transformato.mutate.commoncoretransformation method)": [[7, "transformato.mutate.CommonCoreTransformation._mutate_atoms"]], "_mutate_to_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._mutate_to_common_core"]], "_show_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._show_common_core"]], "_transform_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute._transform_common_core"]], "add_idx_to_common_core_of_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.add_idx_to_common_core_of_mol1"]], "add_idx_to_common_core_of_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.add_idx_to_common_core_of_mol2"]], "finish_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.finish_common_core"]], "generate_mutations_to_common_core_for_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.generate_mutations_to_common_core_for_mol1"]], "generate_mutations_to_common_core_for_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.generate_mutations_to_common_core_for_mol2"]], "get_common_core_idx_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.get_common_core_idx_mol1"]], "get_common_core_idx_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.get_common_core_idx_mol2"]], "get_idx_of_all_atoms() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.get_idx_of_all_atoms"]], "module": [[7, "module-0"], [7, "module-transformato.mutate"], [8, "module-0"], [8, "module-transformato.restraints"], [9, "module-0"], [9, "module-transformato.state"], [10, "module-0"], [10, "module-transformato.system"], [11, "module-0"], [11, "module-transformato.utils"]], "mutate() (transformato.mutate.commoncoretransformation method)": [[7, "transformato.mutate.CommonCoreTransformation.mutate"]], "mutate() (transformato.mutate.mutation method)": [[7, "transformato.mutate.Mutation.mutate"]], "mutate_pure_tautomers() (transformato.mutate method)": [[7, "transformato.mutate.mutate_pure_tautomers"]], "perform_mutations() (transformato.mutate method)": [[7, "transformato.mutate.perform_mutations"]], "propose_common_core() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.propose_common_core"]], "show_common_core_on_mol1() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.show_common_core_on_mol1"]], "show_common_core_on_mol2() (transformato.mutate.proposemutationroute method)": [[7, "transformato.mutate.ProposeMutationRoute.show_common_core_on_mol2"]], "transformato.mutate": [[7, "module-0"], [7, "module-transformato.mutate"]], "restraint (class in transformato.restraints)": [[8, "transformato.restraints.Restraint"]], "__init__() (transformato.restraints.restraint method)": [[8, "transformato.restraints.Restraint.__init__"]], "__weakref__ (transformato.restraints.restraint attribute)": [[8, "transformato.restraints.Restraint.__weakref__"]], "_add_flatbottom_parameters() (transformato.restraints.restraint method)": [[8, "transformato.restraints.Restraint._add_flatbottom_parameters"]], "applyforce() (transformato.restraints.restraint method)": [[8, "transformato.restraints.Restraint.applyForce"]], "createforce() (transformato.restraints.restraint method)": [[8, "transformato.restraints.Restraint.createForce"]], "create_restraints_from_config() (transformato.restraints method)": [[8, "transformato.restraints.create_restraints_from_config"]], "generate_extremities() (transformato.restraints method)": [[8, "transformato.restraints.generate_extremities"]], "generate_simple_selection() (transformato.restraints method)": [[8, "transformato.restraints.generate_simple_selection"]], "get3ddistance() (transformato.restraints method)": [[8, "transformato.restraints.get3DDistance"]], "transformato.restraints": [[8, "module-0"], [8, "module-transformato.restraints"]], "write_restraints_yaml() (transformato.restraints method)": [[8, "transformato.restraints.write_restraints_yaml"]], "intermediatestatefactory (class in transformato.state)": [[9, "transformato.state.IntermediateStateFactory"]], "__init__() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory.__init__"]], "__weakref__ (transformato.state.intermediatestatefactory attribute)": [[9, "transformato.state.IntermediateStateFactory.__weakref__"]], "_check_hmr() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._check_hmr"]], "_copy_charmm_files() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._copy_charmm_files"]], "_copy_files() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._copy_files"]], "_copy_omm_files() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._copy_omm_files"]], "_init_base_dir() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._init_base_dir"]], "_init_intermediate_state_dir() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._init_intermediate_state_dir"]], "_overwrite_simulation_script_parameters() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._overwrite_simulation_script_parameters"]], "_write_psf() (transformato.state.intermediatestatefactory static method)": [[9, "transformato.state.IntermediateStateFactory._write_psf"]], "_write_rtf_file() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._write_rtf_file"]], "_write_workload_preamble() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory._write_workload_preamble"]], "transformato.state": [[9, "module-0"], [9, "module-transformato.state"]], "write_state() (transformato.state.intermediatestatefactory method)": [[9, "transformato.state.IntermediateStateFactory.write_state"]], "systemstructure (class in transformato.system)": [[10, "transformato.system.SystemStructure"]], "__init__() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure.__init__"]], "__weakref__ (transformato.system.systemstructure attribute)": [[10, "transformato.system.SystemStructure.__weakref__"]], "_determine_offset_and_set_possible_dummy_properties() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure._determine_offset_and_set_possible_dummy_properties"]], "_generate_rdkit_mol() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure._generate_rdkit_mol"]], "_initialize_system() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure._initialize_system"]], "_read_parameters() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure._read_parameters"]], "generate_atom_tables_from_psf() (transformato.system.systemstructure method)": [[10, "transformato.system.SystemStructure.generate_atom_tables_from_psf"]], "transformato.system": [[10, "module-0"], [10, "module-transformato.system"]], "check_switching_function() (transformato.utils method)": [[11, "transformato.utils.check_switching_function"]], "get_bin_dir() (transformato.utils method)": [[11, "transformato.utils.get_bin_dir"]], "get_structure_name() (transformato.utils method)": [[11, "transformato.utils.get_structure_name"]], "get_test_output_dir() (transformato.utils method)": [[11, "transformato.utils.get_test_output_dir"]], "get_toppar_dir() (transformato.utils method)": [[11, "transformato.utils.get_toppar_dir"]], "isnotebook() (transformato.utils method)": [[11, "transformato.utils.isnotebook"]], "load_config_yaml() (transformato.utils method)": [[11, "transformato.utils.load_config_yaml"]], "map_lj_mutations_to_atom_idx() (transformato.utils method)": [[11, "transformato.utils.map_lj_mutations_to_atom_idx"]], "postprocessing() (transformato.utils method)": [[11, "transformato.utils.postprocessing"]], "psf_correction() (transformato.utils method)": [[11, "transformato.utils.psf_correction"]], "run_simulation() (transformato.utils method)": [[11, "transformato.utils.run_simulation"]], "transformato.utils": [[11, "module-0"], [11, "module-transformato.utils"]]}})
\ No newline at end of file