schrodinger.application.matsci.packmol module

Utilities for working with packmol.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.packmol.PDBdata(pdbname, pdbres, resnum, chain_name, order)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

chain_name

Alias for field number 3

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

order

Alias for field number 4

pdbname

Alias for field number 0

pdbres

Alias for field number 1

resnum

Alias for field number 2

class schrodinger.application.matsci.packmol.SurfactantInfo(st, name, packing_pct, number, layer, hydrophilic_idxs, hydrophobic_idxs, cion_st, cion_name)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

cion_name

Alias for field number 8

cion_st

Alias for field number 7

count(value, /)

Return number of occurrences of value.

hydrophilic_idxs

Alias for field number 5

hydrophobic_idxs

Alias for field number 6

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

layer

Alias for field number 4

name

Alias for field number 1

number

Alias for field number 3

packing_pct

Alias for field number 2

st

Alias for field number 0

class schrodinger.application.matsci.packmol.SolventInfo(st, name, packing_pct, number, layer)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

layer

Alias for field number 4

name

Alias for field number 1

number

Alias for field number 3

packing_pct

Alias for field number 2

st

Alias for field number 0

class schrodinger.application.matsci.packmol.PackmolKw(value)

Bases: schrodinger.StrEnum

Enum to hold packmol keywords.

OUTPUT = 'output'
FILETYPE = 'filetype'
COMMENT = '#'
STRUCTURE = 'structure'
NUMBER = 'number'
END = 'end'
ATOMS = 'atoms'
RADIUS = 'radius'
INSIDE = 'inside'
BOX = 'box'
FIXED = 'fixed'
SIDEMAX = 'sidemax'
schrodinger.application.matsci.packmol.get_idxs(idxs_str)

Return integer indices from the given string of indices.

Parameters

idxs_str (str) – the string of indices

Return type

tuple

Returns

the integer indices

schrodinger.application.matsci.packmol.get_class_map()

Return the class map.

Return type

dict

Returns

the class map

schrodinger.application.matsci.packmol.get_pdb_data(pdbname, pdbres, resnum=None, chain_name=None, order=None)

Return a PDBdata.

Parameters
  • pdbname (str) – the PDB atom name

  • pdbres (str) – the PDB residue name

  • resnum (int or None) – the PDB residue number if needed

  • chain_name (str or None) – the PDB chain name if needed

  • order (int or None) – a bond order to be used when bonding to the atom corresponding to this object

Return type

PDBdata

Returns

the PDB data

schrodinger.application.matsci.packmol.get_cg_radii_lines(st)

Return the coarse-grained radii body.

Parameters

st (schrodinger.structure.Structure) – the structure

Return type

list[str]

Returns

list of the coarse-grain radii body lines

class schrodinger.application.matsci.packmol.Job(*args, **kwargs)

Bases: schrodinger.job.queue.SubprocessJob

__init__(*args, **kwargs)

See parent class for documentation.

doCommand(*args, **kwargs)

See parent class for documentation.

postCommand()

See parent class for documentation.

addFinalizer(function: Callable[[schrodinger.job.queue.BaseJob], None], run_dir: Optional[str] = None)

Add a function to be invoked when the job completes successfully.

See also the add_multi_job_finalizer function.

addGroupPrereq(job: schrodinger.job.queue.BaseJob)

Make all jobs connected to job prerequisites of all jobs connected to this Job.

addPrereq(job: schrodinger.job.queue.BaseJob)

Add a job that is an immediate prerequisite for this one.

cancel()

Send termination request to subprocess managed job. This method will eventually deprecate SubprocessJob.kill

finalize()

Clean up after a job successfully runs.

genAllJobs(seen: Optional[Set[schrodinger.job.queue.BaseJob]] = None) Generator[schrodinger.job.queue.BaseJob, None, None]

A generator that yields all jobs connected to this one.

genAllPrereqs(seen=None) Generator[schrodinger.job.queue.BaseJob, None, None]

A generator that yields all jobs that are prerequisites on this one.

getCommand() List[str]

Return the command used to run this job.

getCommandDir() str

Return the launch/command directory name. If None is returned, the job will be launched in the current directory.

getDuration() Optional[int]

Return the CPU time of the job in seconds.

If the job is still running, returns None.

getJobDJ() schrodinger.job.queue.JobDJ

Return the JobDJ instance that this job has been added to.

getPrereqs()

Return a set of all immediate prerequisites for this job.

getStatusStrings() Tuple[str, str, str]

Return a tuple of status strings for printing by JobDJ.

The strings returned are (status, jobid, host).

hasExited() bool

Returns True if this job finished, successfully or not.

hasStarted() bool

Returns True if this job has started (not waiting)

init_count = 0
isComplete() bool

Returns True if this job finished successfully

kill()

Send termination request to subprocess managed job.

maxFailuresReached(msg: str)

This is a method that will be called after the job has failed and the maximum number of failures per JobDJ run has been reached. After invoking this method, JobDJ will raise a RuntimeError and the process will exit.

preCommand()

A method to make pre-command changes, like cd’ing to the correct directory to run the command in.

run(*args, **kwargs)

Run the job.

The steps taken are as follows:
  1. Execute the preCommand method for things like changing the working directory.

  2. Call the doCommand to do the actual work of computation or job launching.

  3. Call the postCommand method to undo the changes from the preCommand that need to be undone.

runsLocally() bool

Return True if the job runs on the JobDJ control host, False if not. Jobs that run locally don’t need hosts.

There is no limit on the number of locally run jobs.

setup()

A method to do initial setup; executed after preCommand, just before doCommand.

property state: schrodinger.job.queue.JobState

Return the current state of the job.

Note that this method can be overridden by subclasses that wish to provide for restartability at a higher level than unpickling BaseJob instances. For example, by examining some external condition (e.g. presence of output files) the state JobState.DONE could be returned immediately and the job would not run.

update()

Update the current job status and set state.

schrodinger.application.matsci.packmol.run(input_files, max_failures=None)

Run.

Parameters
  • input_files (list) – packmol input files

  • max_failures (int) – Total number of allowed subjob failures before JobDJ exits. See schrodinger.job.queue.py::JobDJ for more docs.

Return type

dict

Returns

keys are input files, values are structure output files

class schrodinger.application.matsci.packmol.PDBWriter(filename, reorder_by_sequence=False, first_occ=False, translate_pdb_resnames=True)

Bases: schrodinger.structure._io.PDBWriter

write(ct)

See parent class for documentation.

__init__(filename, reorder_by_sequence=False, first_occ=False, translate_pdb_resnames=True)

Initialize needed mmlibs and open the file ‘filename’.

Note that the file will not be completely written until it is explicitly closed or the object is garbage collected.

Parameters
  • filename (str) – The filename to write to.

  • reorder_by_sequence (bool) – Whether to re-order the residues by sequence before writing the PDB file.

  • first_occ (bool) – If True and there are alternate occupancy sites, only the first occupancy site will be included in the output PDB file. Otherwise, all occupancy sites will be included.

  • translate_pdb_resnames (bool) – If True, the pdb residue names get converted to a standard set. If False, the translation is turned off.

NOTE: Any existing file will be overwritten when the class instance is created.

append(ct)

Alias to the write() method (for consistency with the other Writer classes).

close()

Does nothing. Added for consistency with other Writer classes.

setOption(option, value)

Set a single option for this writer. This method is meant for options that may not be supported for all writer formats. See the StructureWriter class documentation for details on the available options.

Raises an OptionError subclass (either UnsupportedOption or UnsupportedOptionValue) if unsuccessful.

Parameters
  • option (str) – The name of the option to set.

  • value – The value for the option. The data type of this parameter depends on the option being set.

schrodinger.application.matsci.packmol.set_unique_pdb_atom_names(st)

Set unique PDB atom names on the given structure.

Parameters

st (schrodinger.structure.Structure) – the structure

schrodinger.application.matsci.packmol.has_imperfect_packing(log_fn)

Return True if the given packmol log file name indicates a solution with imperfect packing.

Parameters

log_fn (str) – the packmol log file name

Return type

bool

Returns

True if there is imperfect packing

schrodinger.application.matsci.packmol.set_pbc(st, a_len, b_len, c_len, log_fn=None, pbc_buffer=2, logger=None)

Set the PBC on the given structure.

Parameters
  • st (schrodinger.structure.Structure) – the structure on which to set the PBC

  • a_len (float) – the PBC length of the a-vector in Ang.

  • b_len (float) – the PBC length of the b-vector in Ang.

  • c_len (float) – the PBC length of the c-vector in Ang.

  • log_fn (str or None) – the packmol log file name to check if the given PBC can be used if there is one

  • pbc_buffer (float) – if the given PBC can not be used then determine it from the given structure and then add this buffer length

  • logger (logging.Logger or None) – output logger or None if there isn’t one

schrodinger.application.matsci.packmol.add_atom_properties(pdb_st, mae_structs, props=('b_matsci_hydrophilic', 'b_matsci_hydrophobic', 'b_matsci_polymer_head_atom', 'b_matsci_polymer_tail_atom'))

Transfer the given properties from the mae structures to the structure created from pdb

Parameters
schrodinger.application.matsci.packmol.get_cells(input_files, sts, logger=None)

Return cells.

Parameters
  • input_files (dict) – keys are packmol input files, values are tuples of the 3 box lengths (Angstrom) defining the PBC

  • sts (dict) – keys are file names (referenced in the given packmol input files), values are schrodinger.structure.Structure

  • logger (logging.Logger or None) – output logger or None if there isn’t one

Raises

RuntimeError – if there is a problem with the input

Return type

dict

Returns

keys are input files, values are schrodinger.structure.Structure

schrodinger.application.matsci.packmol.write_desmond_cells(input_files, sts, force_field=None, water_force_field='SPC', cg_ff_loc_type='local', logger=None)

Write Desmond cells.

Parameters
  • input_files (dict) – keys are packmol input files, values are tuples of the 3 box lengths (Angstrom) defining the PBC

  • sts (dict) – keys are file names (referenced in the given packmol input files), values are schrodinger.structure.Structure

  • force_field (str) – name of FF to apply

  • water_force_field (str) – name of the water force field to apply, options are available in desmondutils

  • cg_ff_loc_type (str) – specifies the location to which to look for coarse-grained force field files, one of parserutils.INSTALLED_CG_FF_LOCATION_TYPE or parserutils.LOCAL_CG_FF_LOCATION_TYPE

  • logger (logging.Logger or None) – output logger or None if there isn’t one

Raises

RuntimeError – if there is a problem with the input

Return type

dict

Returns

keys are input files, values are names of written Desmond *cms files

schrodinger.application.matsci.packmol.set_unique_pdb_res_names(st)

Set unique PDB residue names on the given structure.

Raises

RuntimeError – if there is a problem with the input

Parameters

st (schrodinger.structure.Structure) – the structure

schrodinger.application.matsci.packmol.unset_unique_pdb_res_names(st)

Unset unique PDB residue names on the given structure.

Parameters

st (schrodinger.structure.Structure) – the structure

schrodinger.application.matsci.packmol.group_infos_by_layer(infos)

Group the given information objects into a dictionary keyed by layer.

Parameters

infos (list[SurfactantInfo] or list[SolventInfo]) – contains surfactant or solvent infos

Return type

dict

Returns

the information objects keyed by layer

schrodinger.application.matsci.packmol.get_max_distance_btw_groups(st, idxs, jdxs)

Return the maximum distance (Angstrom) between the given groups of atom indices.

Parameters
Return type

float

Returns

the maximum distance in Angstrom

exception schrodinger.application.matsci.packmol.PackmolInputFileException

Bases: Exception

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.packmol.PackmolInputFile(tolerance=2, filetype='pdb', output_base_name='packmol', comment='', general_body='')

Bases: object

Manage a packmol input file.

IN_EXT = '.inp'
__init__(tolerance=2, filetype='pdb', output_base_name='packmol', comment='', general_body='')

Create an instance.

Parameters
  • tolerance (float) – the distance tolerance in Angstrom

  • filetype (str) – the file type to use for all structure files, pdb, tinker, xyz, or moldy

  • output_base_name (str) – the base name to use for the packmol output structure file

  • comment (str) – a comment placed at the top of the the packmol input file, include preceeding ‘#’

  • general_body (str) – the general body, should contain newlines, this is for any additional top level parameters that do not have to do with structures

addStructureBody(base_name, body)

Add a structure body to the input file.

Parameters
  • base_name (str) – the base name of the input structure file

  • body (str) – the body, should contain indentation and newlines

addStructureBodies()

Add structure bodies to the input file.

Raises

PackmolInputFileException – if there is an issue with the input

write(input_base_name='packmol')

Write the packmol input file.

Parameters

input_base_name (str) – the base name to use for the packmol input file

Raises

PackmolInputFileException – if there is an issue with the input

Return type

str

Returns

the packmol input file name

class schrodinger.application.matsci.packmol.StructuredLiquidInputFile(*args, **kwargs)

Bases: schrodinger.application.matsci.packmol.PackmolInputFile

Manage a structured liquid input file.

__init__(*args, **kwargs)

See parent class for documentation.

check()

Check cell lengths.

Raises

PackmolInputFileException – if there is an issue with the input

prepare(cell_lengths, surfactant_infos, solvent_infos, layer_sep=1, packing_f=0.8, min_constraint_window_surfactant_idxs=25)

Prepare.

Parameters
  • cell_lengths (tuple) – the cell lengths of the output structure file

  • surfactant_infos (list) – contains SurfactantInfo

  • solvent_infos (list) – contains SolventInfo

  • layer_sep (float) – the layer separation in Angstrom

  • packing_f (float) – a packing efficiency factor used to control the density of surfactant and solvent molecules

  • min_constraint_window_surfactant_idxs (float) – this is the minimum window length for constraining surfactant hydrophilic and hydrophobic indices as a percentage of the surfactant length, should be in (0, 50)

Raises

PackmolInputFileException – if there is an issue with the input

getMaxDists(all_infos)

Return a dictionary of maximum distances (Ang.) among the structures in each layer of the given all_infos.

Parameters

all_infos (dict) – keys are layers, values are lists containing either SurfactantInfo or SolventInfo

Return type

dict

Returns

keys are layers, values are maximum distances

getBoxSliceVol(cmin, cmax)

Return the box slice volume.

Parameters
  • cmin (float) – the lower bound on the layer in Angstrom

  • cmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the box slice volume in Ang.^3

getSphereSliceVol(rmin, rmax)

Return the sphere slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the sphere slice volume in Ang.^3

getOutsideSphereVol(radius)

Return the box volume less the sphere volume.

Parameters

radius (float) – the radius of the sphere in Angstrom

Return type

float

Returns

the box volume less the sphere volume in Ang.^3

getCylinderSliceVol(rmin, rmax, length)

Return the cylinder slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the cylinder slice volume in Ang.^3

getOutsideCylinderVol(radius, length)

Return the box volume less the cylinder volume.

Parameters
  • radius (float) – the radius of the cylinder in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the box volume less the cylinder volume in Ang.^3

getEllipsoidSliceVol(rmin, rmax)

Return the ellipsoid slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the ellipsoid slice volume in Ang.^3

getOutsideEllipsoidVol(radius)

Return the box volume less the ellipsoid volume.

Parameters

radius (float) – the radius of the ellipsoid in Angstrom, this is half the length of the minor axis

Return type

float

Returns

the box volume less the ellipsoid volume in Ang.^3

getNumber(info, amin, amax)

Return the number of surfactant or solvent molecules to add for the given info.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

Return type

int

Returns

the number of molecules

getLayerVolume(amin, amax, buffer_len=0)

Return the volume of this layer.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • buffer_len (float) – a buffer length in Angstrom

Return type

int

Returns

the volume in Ang.^3

addLayer(info, amin, amax, hydrophilic_at_max=False, number=None, add_cion=False)

Add a layer.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • hydrophilic_at_max (bool) – if info is SurfactantInfo whether the hydrophilic atoms are to be located at the maximum

  • number (int or None) – the number of molecules to add, if None it will be determined

  • add_cion (bool) – if info is SurfactantInfo whether the layer is for the counter-ion

getTotalSurfactantThickness(layers_are_bilayers=True)

Return the total surfactant thickness in Angstrom.

Parameters

layers_are_bilayers (bool) – whether layers are bilayers

Return type

float

Returns

the total surfactant thickness in Angstrom

getTotalCIonThickness()

Return the total counter-ion thickness in Angstrom.

Return type

float

Returns

the total counter-ion thickness in Angstrom

getTotalNonSurfactantThickness()

Return the total non-surfactant thickness in Angstrom.

Return type

float

Returns

the total non-surfactant thickness in Angstrom

addSurfactantBodies(start_dist, start_hydrophilic_at_max=False, layers=None, layers_are_bilayers=True)

Add surfactant bodies to the input file.

Parameters
  • start_dist (float) – start adding surfactants at this distance in Angstrom

  • start_hydrophilic_at_max (bool) – specifies whether the hydrophilic atoms for the starting layer are to be located at the maximum

  • layers (list or None) – the surfactant layers to add, if None then all will be added

  • layers_are_bilayers (bool) – whether layers are bilayers

Return type

float, bool

Returns

surfactants stopped being added at this distance in Angstrom, whether the hydrophilic atoms for the final layer are located at the maximum

addCIonBodies(start_dist, stop_dist, layers=None, factor=1)

Add counter-ion bodies to the input file.

Parameters
  • start_dist (float) – start adding counter-ions at this distance in Angstrom

  • stop_dist (float) – stop adding counter-ions at this distance in Angstrom

  • layers (list or None) – the counter-ion layers to add, if None then all will be added

  • factor (float) – multiplies the corresponding number of surfactant molecules to set the number of counter-ions in the given region

addSolventBodies(start_dist, stop_dist, layers=None, layer_sep=None)

Add solvent bodies to the input file.

Parameters
  • start_dist (float) – start adding solvents at this distance in Angstrom

  • stop_dist (float) – stop adding solvents at this distance in Angstrom

  • layers (list or None) – the solvent layers to add, if None then all will be added

  • layer_sep (float) – the layer separation in Angstrom

getSurfactantLayers()

Return a list of surfactant layers.

Return type

list

Returns

the surfactant layers

getSolventLayers()

Return a list of solvent layers.

Return type

list

Returns

the solvent layers

getConstraintType(parameter)

Return the constraint type.

Parameters

parameter (float) – the parameter in Angstrom

Return type

str

Returns

the constraint type

IN_EXT = '.inp'
addStructureBodies()

Add structure bodies to the input file.

Raises

PackmolInputFileException – if there is an issue with the input

addStructureBody(base_name, body)

Add a structure body to the input file.

Parameters
  • base_name (str) – the base name of the input structure file

  • body (str) – the body, should contain indentation and newlines

write(input_base_name='packmol')

Write the packmol input file.

Parameters

input_base_name (str) – the base name to use for the packmol input file

Raises

PackmolInputFileException – if there is an issue with the input

Return type

str

Returns

the packmol input file name

class schrodinger.application.matsci.packmol.MonolayerInputFile(*args, **kwargs)

Bases: schrodinger.application.matsci.packmol.StructuredLiquidInputFile

Manage a monolayer input file.

SURFACTANT_TOP_ATOM_CONSTRAINT = 'over'
SURFACTANT_BOTTOM_ATOM_CONSTRAINT = 'below'
CONSTRAINT_TYPE = 'plane 0 0 1 {parameter}'
getMinCellLengths()

Return the minimum cell lengths.

Return type

tuple

Returns

a triple containing float and/or None, float is a minimum cell length in Angstrom, None indicates that there is no minimum

check()

Check cell lengths.

Raises

PackmolInputFileException – if there is an issue with the input

getVol(amin, amax)

Return the volume.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the volume in Ang.^3

getSurfactantConstraints(amin, amax)

Return the surfactant constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the surfactant constraints

getSolventConstraints(amin, amax)

Return the solvent constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the solvent constraints

addStructureBodies()

See parent class for documentation.

IN_EXT = '.inp'
__init__(*args, **kwargs)

See parent class for documentation.

addCIonBodies(start_dist, stop_dist, layers=None, factor=1)

Add counter-ion bodies to the input file.

Parameters
  • start_dist (float) – start adding counter-ions at this distance in Angstrom

  • stop_dist (float) – stop adding counter-ions at this distance in Angstrom

  • layers (list or None) – the counter-ion layers to add, if None then all will be added

  • factor (float) – multiplies the corresponding number of surfactant molecules to set the number of counter-ions in the given region

addLayer(info, amin, amax, hydrophilic_at_max=False, number=None, add_cion=False)

Add a layer.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • hydrophilic_at_max (bool) – if info is SurfactantInfo whether the hydrophilic atoms are to be located at the maximum

  • number (int or None) – the number of molecules to add, if None it will be determined

  • add_cion (bool) – if info is SurfactantInfo whether the layer is for the counter-ion

addSolventBodies(start_dist, stop_dist, layers=None, layer_sep=None)

Add solvent bodies to the input file.

Parameters
  • start_dist (float) – start adding solvents at this distance in Angstrom

  • stop_dist (float) – stop adding solvents at this distance in Angstrom

  • layers (list or None) – the solvent layers to add, if None then all will be added

  • layer_sep (float) – the layer separation in Angstrom

addStructureBody(base_name, body)

Add a structure body to the input file.

Parameters
  • base_name (str) – the base name of the input structure file

  • body (str) – the body, should contain indentation and newlines

addSurfactantBodies(start_dist, start_hydrophilic_at_max=False, layers=None, layers_are_bilayers=True)

Add surfactant bodies to the input file.

Parameters
  • start_dist (float) – start adding surfactants at this distance in Angstrom

  • start_hydrophilic_at_max (bool) – specifies whether the hydrophilic atoms for the starting layer are to be located at the maximum

  • layers (list or None) – the surfactant layers to add, if None then all will be added

  • layers_are_bilayers (bool) – whether layers are bilayers

Return type

float, bool

Returns

surfactants stopped being added at this distance in Angstrom, whether the hydrophilic atoms for the final layer are located at the maximum

getBoxSliceVol(cmin, cmax)

Return the box slice volume.

Parameters
  • cmin (float) – the lower bound on the layer in Angstrom

  • cmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the box slice volume in Ang.^3

getConstraintType(parameter)

Return the constraint type.

Parameters

parameter (float) – the parameter in Angstrom

Return type

str

Returns

the constraint type

getCylinderSliceVol(rmin, rmax, length)

Return the cylinder slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the cylinder slice volume in Ang.^3

getEllipsoidSliceVol(rmin, rmax)

Return the ellipsoid slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the ellipsoid slice volume in Ang.^3

getLayerVolume(amin, amax, buffer_len=0)

Return the volume of this layer.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • buffer_len (float) – a buffer length in Angstrom

Return type

int

Returns

the volume in Ang.^3

getMaxDists(all_infos)

Return a dictionary of maximum distances (Ang.) among the structures in each layer of the given all_infos.

Parameters

all_infos (dict) – keys are layers, values are lists containing either SurfactantInfo or SolventInfo

Return type

dict

Returns

keys are layers, values are maximum distances

getNumber(info, amin, amax)

Return the number of surfactant or solvent molecules to add for the given info.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

Return type

int

Returns

the number of molecules

getOutsideCylinderVol(radius, length)

Return the box volume less the cylinder volume.

Parameters
  • radius (float) – the radius of the cylinder in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the box volume less the cylinder volume in Ang.^3

getOutsideEllipsoidVol(radius)

Return the box volume less the ellipsoid volume.

Parameters

radius (float) – the radius of the ellipsoid in Angstrom, this is half the length of the minor axis

Return type

float

Returns

the box volume less the ellipsoid volume in Ang.^3

getOutsideSphereVol(radius)

Return the box volume less the sphere volume.

Parameters

radius (float) – the radius of the sphere in Angstrom

Return type

float

Returns

the box volume less the sphere volume in Ang.^3

getSolventLayers()

Return a list of solvent layers.

Return type

list

Returns

the solvent layers

getSphereSliceVol(rmin, rmax)

Return the sphere slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the sphere slice volume in Ang.^3

getSurfactantLayers()

Return a list of surfactant layers.

Return type

list

Returns

the surfactant layers

getTotalCIonThickness()

Return the total counter-ion thickness in Angstrom.

Return type

float

Returns

the total counter-ion thickness in Angstrom

getTotalNonSurfactantThickness()

Return the total non-surfactant thickness in Angstrom.

Return type

float

Returns

the total non-surfactant thickness in Angstrom

getTotalSurfactantThickness(layers_are_bilayers=True)

Return the total surfactant thickness in Angstrom.

Parameters

layers_are_bilayers (bool) – whether layers are bilayers

Return type

float

Returns

the total surfactant thickness in Angstrom

prepare(cell_lengths, surfactant_infos, solvent_infos, layer_sep=1, packing_f=0.8, min_constraint_window_surfactant_idxs=25)

Prepare.

Parameters
  • cell_lengths (tuple) – the cell lengths of the output structure file

  • surfactant_infos (list) – contains SurfactantInfo

  • solvent_infos (list) – contains SolventInfo

  • layer_sep (float) – the layer separation in Angstrom

  • packing_f (float) – a packing efficiency factor used to control the density of surfactant and solvent molecules

  • min_constraint_window_surfactant_idxs (float) – this is the minimum window length for constraining surfactant hydrophilic and hydrophobic indices as a percentage of the surfactant length, should be in (0, 50)

Raises

PackmolInputFileException – if there is an issue with the input

write(input_base_name='packmol')

Write the packmol input file.

Parameters

input_base_name (str) – the base name to use for the packmol input file

Raises

PackmolInputFileException – if there is an issue with the input

Return type

str

Returns

the packmol input file name

class schrodinger.application.matsci.packmol.BilayerInputFile(*args, **kwargs)

Bases: schrodinger.application.matsci.packmol.MonolayerInputFile

Manage a bilayer input file.

getMinCellLengths()

Return the minimum cell lengths.

Return type

tuple

Returns

a triple containing float and/or None, float is a minimum cell length in Angstrom, None indicates that there is no minimum

check()

Check cell lengths.

Raises

PackmolInputFileException – if there is an issue with the input

addStructureBodies()

See parent class for documentation.

CONSTRAINT_TYPE = 'plane 0 0 1 {parameter}'
IN_EXT = '.inp'
SURFACTANT_BOTTOM_ATOM_CONSTRAINT = 'below'
SURFACTANT_TOP_ATOM_CONSTRAINT = 'over'
__init__(*args, **kwargs)

See parent class for documentation.

addCIonBodies(start_dist, stop_dist, layers=None, factor=1)

Add counter-ion bodies to the input file.

Parameters
  • start_dist (float) – start adding counter-ions at this distance in Angstrom

  • stop_dist (float) – stop adding counter-ions at this distance in Angstrom

  • layers (list or None) – the counter-ion layers to add, if None then all will be added

  • factor (float) – multiplies the corresponding number of surfactant molecules to set the number of counter-ions in the given region

addLayer(info, amin, amax, hydrophilic_at_max=False, number=None, add_cion=False)

Add a layer.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • hydrophilic_at_max (bool) – if info is SurfactantInfo whether the hydrophilic atoms are to be located at the maximum

  • number (int or None) – the number of molecules to add, if None it will be determined

  • add_cion (bool) – if info is SurfactantInfo whether the layer is for the counter-ion

addSolventBodies(start_dist, stop_dist, layers=None, layer_sep=None)

Add solvent bodies to the input file.

Parameters
  • start_dist (float) – start adding solvents at this distance in Angstrom

  • stop_dist (float) – stop adding solvents at this distance in Angstrom

  • layers (list or None) – the solvent layers to add, if None then all will be added

  • layer_sep (float) – the layer separation in Angstrom

addStructureBody(base_name, body)

Add a structure body to the input file.

Parameters
  • base_name (str) – the base name of the input structure file

  • body (str) – the body, should contain indentation and newlines

addSurfactantBodies(start_dist, start_hydrophilic_at_max=False, layers=None, layers_are_bilayers=True)

Add surfactant bodies to the input file.

Parameters
  • start_dist (float) – start adding surfactants at this distance in Angstrom

  • start_hydrophilic_at_max (bool) – specifies whether the hydrophilic atoms for the starting layer are to be located at the maximum

  • layers (list or None) – the surfactant layers to add, if None then all will be added

  • layers_are_bilayers (bool) – whether layers are bilayers

Return type

float, bool

Returns

surfactants stopped being added at this distance in Angstrom, whether the hydrophilic atoms for the final layer are located at the maximum

getBoxSliceVol(cmin, cmax)

Return the box slice volume.

Parameters
  • cmin (float) – the lower bound on the layer in Angstrom

  • cmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the box slice volume in Ang.^3

getConstraintType(parameter)

Return the constraint type.

Parameters

parameter (float) – the parameter in Angstrom

Return type

str

Returns

the constraint type

getCylinderSliceVol(rmin, rmax, length)

Return the cylinder slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the cylinder slice volume in Ang.^3

getEllipsoidSliceVol(rmin, rmax)

Return the ellipsoid slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the ellipsoid slice volume in Ang.^3

getLayerVolume(amin, amax, buffer_len=0)

Return the volume of this layer.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • buffer_len (float) – a buffer length in Angstrom

Return type

int

Returns

the volume in Ang.^3

getMaxDists(all_infos)

Return a dictionary of maximum distances (Ang.) among the structures in each layer of the given all_infos.

Parameters

all_infos (dict) – keys are layers, values are lists containing either SurfactantInfo or SolventInfo

Return type

dict

Returns

keys are layers, values are maximum distances

getNumber(info, amin, amax)

Return the number of surfactant or solvent molecules to add for the given info.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

Return type

int

Returns

the number of molecules

getOutsideCylinderVol(radius, length)

Return the box volume less the cylinder volume.

Parameters
  • radius (float) – the radius of the cylinder in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the box volume less the cylinder volume in Ang.^3

getOutsideEllipsoidVol(radius)

Return the box volume less the ellipsoid volume.

Parameters

radius (float) – the radius of the ellipsoid in Angstrom, this is half the length of the minor axis

Return type

float

Returns

the box volume less the ellipsoid volume in Ang.^3

getOutsideSphereVol(radius)

Return the box volume less the sphere volume.

Parameters

radius (float) – the radius of the sphere in Angstrom

Return type

float

Returns

the box volume less the sphere volume in Ang.^3

getSolventConstraints(amin, amax)

Return the solvent constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the solvent constraints

getSolventLayers()

Return a list of solvent layers.

Return type

list

Returns

the solvent layers

getSphereSliceVol(rmin, rmax)

Return the sphere slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the sphere slice volume in Ang.^3

getSurfactantConstraints(amin, amax)

Return the surfactant constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the surfactant constraints

getSurfactantLayers()

Return a list of surfactant layers.

Return type

list

Returns

the surfactant layers

getTotalCIonThickness()

Return the total counter-ion thickness in Angstrom.

Return type

float

Returns

the total counter-ion thickness in Angstrom

getTotalNonSurfactantThickness()

Return the total non-surfactant thickness in Angstrom.

Return type

float

Returns

the total non-surfactant thickness in Angstrom

getTotalSurfactantThickness(layers_are_bilayers=True)

Return the total surfactant thickness in Angstrom.

Parameters

layers_are_bilayers (bool) – whether layers are bilayers

Return type

float

Returns

the total surfactant thickness in Angstrom

getVol(amin, amax)

Return the volume.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the volume in Ang.^3

prepare(cell_lengths, surfactant_infos, solvent_infos, layer_sep=1, packing_f=0.8, min_constraint_window_surfactant_idxs=25)

Prepare.

Parameters
  • cell_lengths (tuple) – the cell lengths of the output structure file

  • surfactant_infos (list) – contains SurfactantInfo

  • solvent_infos (list) – contains SolventInfo

  • layer_sep (float) – the layer separation in Angstrom

  • packing_f (float) – a packing efficiency factor used to control the density of surfactant and solvent molecules

  • min_constraint_window_surfactant_idxs (float) – this is the minimum window length for constraining surfactant hydrophilic and hydrophobic indices as a percentage of the surfactant length, should be in (0, 50)

Raises

PackmolInputFileException – if there is an issue with the input

write(input_base_name='packmol')

Write the packmol input file.

Parameters

input_base_name (str) – the base name to use for the packmol input file

Raises

PackmolInputFileException – if there is an issue with the input

Return type

str

Returns

the packmol input file name

class schrodinger.application.matsci.packmol.MicelleInputFile(*args, **kwargs)

Bases: schrodinger.application.matsci.packmol.StructuredLiquidInputFile

Manage a micelle input file.

SURFACTANT_TOP_ATOM_CONSTRAINT = 'outside'
SURFACTANT_BOTTOM_ATOM_CONSTRAINT = 'inside'
CONSTRAINT_TYPE = 'sphere 0 0 0 {parameter}'
getMinCellLengths()

Return the minimum cell lengths.

Return type

tuple

Returns

a triple containing float and/or None, float is a minimum cell length in Angstrom, None indicates that there is no minimum

check()

Check cell lengths.

Raises

PackmolInputFileException – if there is an issue with the input

getRadius()

Return the radius.

Return type

float

Returns

the radius in Ang.

getVol(amin, amax)

Return the volume.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the volume in Ang.^3

getOutsideVol()

Return the outside volume.

Return type

float

Returns

the outside volume in Ang.^3

getSurfactantConstraints(amin, amax)

Return the surfactant constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the surfactant constraints

getSolventConstraints(amin, amax)

Return the solvent constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the solvent constraints

addStructureBodies()

See parent class for documentation.

IN_EXT = '.inp'
__init__(*args, **kwargs)

See parent class for documentation.

addCIonBodies(start_dist, stop_dist, layers=None, factor=1)

Add counter-ion bodies to the input file.

Parameters
  • start_dist (float) – start adding counter-ions at this distance in Angstrom

  • stop_dist (float) – stop adding counter-ions at this distance in Angstrom

  • layers (list or None) – the counter-ion layers to add, if None then all will be added

  • factor (float) – multiplies the corresponding number of surfactant molecules to set the number of counter-ions in the given region

addLayer(info, amin, amax, hydrophilic_at_max=False, number=None, add_cion=False)

Add a layer.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • hydrophilic_at_max (bool) – if info is SurfactantInfo whether the hydrophilic atoms are to be located at the maximum

  • number (int or None) – the number of molecules to add, if None it will be determined

  • add_cion (bool) – if info is SurfactantInfo whether the layer is for the counter-ion

addSolventBodies(start_dist, stop_dist, layers=None, layer_sep=None)

Add solvent bodies to the input file.

Parameters
  • start_dist (float) – start adding solvents at this distance in Angstrom

  • stop_dist (float) – stop adding solvents at this distance in Angstrom

  • layers (list or None) – the solvent layers to add, if None then all will be added

  • layer_sep (float) – the layer separation in Angstrom

addStructureBody(base_name, body)

Add a structure body to the input file.

Parameters
  • base_name (str) – the base name of the input structure file

  • body (str) – the body, should contain indentation and newlines

addSurfactantBodies(start_dist, start_hydrophilic_at_max=False, layers=None, layers_are_bilayers=True)

Add surfactant bodies to the input file.

Parameters
  • start_dist (float) – start adding surfactants at this distance in Angstrom

  • start_hydrophilic_at_max (bool) – specifies whether the hydrophilic atoms for the starting layer are to be located at the maximum

  • layers (list or None) – the surfactant layers to add, if None then all will be added

  • layers_are_bilayers (bool) – whether layers are bilayers

Return type

float, bool

Returns

surfactants stopped being added at this distance in Angstrom, whether the hydrophilic atoms for the final layer are located at the maximum

getBoxSliceVol(cmin, cmax)

Return the box slice volume.

Parameters
  • cmin (float) – the lower bound on the layer in Angstrom

  • cmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the box slice volume in Ang.^3

getConstraintType(parameter)

Return the constraint type.

Parameters

parameter (float) – the parameter in Angstrom

Return type

str

Returns

the constraint type

getCylinderSliceVol(rmin, rmax, length)

Return the cylinder slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the cylinder slice volume in Ang.^3

getEllipsoidSliceVol(rmin, rmax)

Return the ellipsoid slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the ellipsoid slice volume in Ang.^3

getLayerVolume(amin, amax, buffer_len=0)

Return the volume of this layer.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • buffer_len (float) – a buffer length in Angstrom

Return type

int

Returns

the volume in Ang.^3

getMaxDists(all_infos)

Return a dictionary of maximum distances (Ang.) among the structures in each layer of the given all_infos.

Parameters

all_infos (dict) – keys are layers, values are lists containing either SurfactantInfo or SolventInfo

Return type

dict

Returns

keys are layers, values are maximum distances

getNumber(info, amin, amax)

Return the number of surfactant or solvent molecules to add for the given info.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

Return type

int

Returns

the number of molecules

getOutsideCylinderVol(radius, length)

Return the box volume less the cylinder volume.

Parameters
  • radius (float) – the radius of the cylinder in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the box volume less the cylinder volume in Ang.^3

getOutsideEllipsoidVol(radius)

Return the box volume less the ellipsoid volume.

Parameters

radius (float) – the radius of the ellipsoid in Angstrom, this is half the length of the minor axis

Return type

float

Returns

the box volume less the ellipsoid volume in Ang.^3

getOutsideSphereVol(radius)

Return the box volume less the sphere volume.

Parameters

radius (float) – the radius of the sphere in Angstrom

Return type

float

Returns

the box volume less the sphere volume in Ang.^3

getSolventLayers()

Return a list of solvent layers.

Return type

list

Returns

the solvent layers

getSphereSliceVol(rmin, rmax)

Return the sphere slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the sphere slice volume in Ang.^3

getSurfactantLayers()

Return a list of surfactant layers.

Return type

list

Returns

the surfactant layers

getTotalCIonThickness()

Return the total counter-ion thickness in Angstrom.

Return type

float

Returns

the total counter-ion thickness in Angstrom

getTotalNonSurfactantThickness()

Return the total non-surfactant thickness in Angstrom.

Return type

float

Returns

the total non-surfactant thickness in Angstrom

getTotalSurfactantThickness(layers_are_bilayers=True)

Return the total surfactant thickness in Angstrom.

Parameters

layers_are_bilayers (bool) – whether layers are bilayers

Return type

float

Returns

the total surfactant thickness in Angstrom

prepare(cell_lengths, surfactant_infos, solvent_infos, layer_sep=1, packing_f=0.8, min_constraint_window_surfactant_idxs=25)

Prepare.

Parameters
  • cell_lengths (tuple) – the cell lengths of the output structure file

  • surfactant_infos (list) – contains SurfactantInfo

  • solvent_infos (list) – contains SolventInfo

  • layer_sep (float) – the layer separation in Angstrom

  • packing_f (float) – a packing efficiency factor used to control the density of surfactant and solvent molecules

  • min_constraint_window_surfactant_idxs (float) – this is the minimum window length for constraining surfactant hydrophilic and hydrophobic indices as a percentage of the surfactant length, should be in (0, 50)

Raises

PackmolInputFileException – if there is an issue with the input

write(input_base_name='packmol')

Write the packmol input file.

Parameters

input_base_name (str) – the base name to use for the packmol input file

Raises

PackmolInputFileException – if there is an issue with the input

Return type

str

Returns

the packmol input file name

class schrodinger.application.matsci.packmol.LiposomeInputFile(*args, **kwargs)

Bases: schrodinger.application.matsci.packmol.MicelleInputFile

Manage a liposome input file.

prepare(*args, **kwargs)

See parent class for documentation.

Parameters

radius (float) – the radius of the liposome in Ang.

getMinRadius()

Return the minimum radius.

Return type

float

Returns

the minimum radius in Angstrom

check()

Check cell lengths.

Raises

PackmolInputFileException – if there is an issue with the input

getRadius()

Return the radius.

Return type

float

Returns

the radius in Ang.

getInnerRadius()

Return the inner radius.

Return type

float

Returns

the inner radius in Ang.

getSolventConstraints(amin, amax)

Return the solvent constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

Return type

str

Returns

the constraints

addStructureBodies()

See parent class for documentation.

CONSTRAINT_TYPE = 'sphere 0 0 0 {parameter}'
IN_EXT = '.inp'
SURFACTANT_BOTTOM_ATOM_CONSTRAINT = 'inside'
SURFACTANT_TOP_ATOM_CONSTRAINT = 'outside'
__init__(*args, **kwargs)

See parent class for documentation.

addCIonBodies(start_dist, stop_dist, layers=None, factor=1)

Add counter-ion bodies to the input file.

Parameters
  • start_dist (float) – start adding counter-ions at this distance in Angstrom

  • stop_dist (float) – stop adding counter-ions at this distance in Angstrom

  • layers (list or None) – the counter-ion layers to add, if None then all will be added

  • factor (float) – multiplies the corresponding number of surfactant molecules to set the number of counter-ions in the given region

addLayer(info, amin, amax, hydrophilic_at_max=False, number=None, add_cion=False)

Add a layer.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • hydrophilic_at_max (bool) – if info is SurfactantInfo whether the hydrophilic atoms are to be located at the maximum

  • number (int or None) – the number of molecules to add, if None it will be determined

  • add_cion (bool) – if info is SurfactantInfo whether the layer is for the counter-ion

addSolventBodies(start_dist, stop_dist, layers=None, layer_sep=None)

Add solvent bodies to the input file.

Parameters
  • start_dist (float) – start adding solvents at this distance in Angstrom

  • stop_dist (float) – stop adding solvents at this distance in Angstrom

  • layers (list or None) – the solvent layers to add, if None then all will be added

  • layer_sep (float) – the layer separation in Angstrom

addStructureBody(base_name, body)

Add a structure body to the input file.

Parameters
  • base_name (str) – the base name of the input structure file

  • body (str) – the body, should contain indentation and newlines

addSurfactantBodies(start_dist, start_hydrophilic_at_max=False, layers=None, layers_are_bilayers=True)

Add surfactant bodies to the input file.

Parameters
  • start_dist (float) – start adding surfactants at this distance in Angstrom

  • start_hydrophilic_at_max (bool) – specifies whether the hydrophilic atoms for the starting layer are to be located at the maximum

  • layers (list or None) – the surfactant layers to add, if None then all will be added

  • layers_are_bilayers (bool) – whether layers are bilayers

Return type

float, bool

Returns

surfactants stopped being added at this distance in Angstrom, whether the hydrophilic atoms for the final layer are located at the maximum

getBoxSliceVol(cmin, cmax)

Return the box slice volume.

Parameters
  • cmin (float) – the lower bound on the layer in Angstrom

  • cmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the box slice volume in Ang.^3

getConstraintType(parameter)

Return the constraint type.

Parameters

parameter (float) – the parameter in Angstrom

Return type

str

Returns

the constraint type

getCylinderSliceVol(rmin, rmax, length)

Return the cylinder slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the cylinder slice volume in Ang.^3

getEllipsoidSliceVol(rmin, rmax)

Return the ellipsoid slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the ellipsoid slice volume in Ang.^3

getLayerVolume(amin, amax, buffer_len=0)

Return the volume of this layer.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • buffer_len (float) – a buffer length in Angstrom

Return type

int

Returns

the volume in Ang.^3

getMaxDists(all_infos)

Return a dictionary of maximum distances (Ang.) among the structures in each layer of the given all_infos.

Parameters

all_infos (dict) – keys are layers, values are lists containing either SurfactantInfo or SolventInfo

Return type

dict

Returns

keys are layers, values are maximum distances

getMinCellLengths()

Return the minimum cell lengths.

Return type

tuple

Returns

a triple containing float and/or None, float is a minimum cell length in Angstrom, None indicates that there is no minimum

getNumber(info, amin, amax)

Return the number of surfactant or solvent molecules to add for the given info.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

Return type

int

Returns

the number of molecules

getOutsideCylinderVol(radius, length)

Return the box volume less the cylinder volume.

Parameters
  • radius (float) – the radius of the cylinder in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the box volume less the cylinder volume in Ang.^3

getOutsideEllipsoidVol(radius)

Return the box volume less the ellipsoid volume.

Parameters

radius (float) – the radius of the ellipsoid in Angstrom, this is half the length of the minor axis

Return type

float

Returns

the box volume less the ellipsoid volume in Ang.^3

getOutsideSphereVol(radius)

Return the box volume less the sphere volume.

Parameters

radius (float) – the radius of the sphere in Angstrom

Return type

float

Returns

the box volume less the sphere volume in Ang.^3

getOutsideVol()

Return the outside volume.

Return type

float

Returns

the outside volume in Ang.^3

getSolventLayers()

Return a list of solvent layers.

Return type

list

Returns

the solvent layers

getSphereSliceVol(rmin, rmax)

Return the sphere slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the sphere slice volume in Ang.^3

getSurfactantConstraints(amin, amax)

Return the surfactant constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the surfactant constraints

getSurfactantLayers()

Return a list of surfactant layers.

Return type

list

Returns

the surfactant layers

getTotalCIonThickness()

Return the total counter-ion thickness in Angstrom.

Return type

float

Returns

the total counter-ion thickness in Angstrom

getTotalNonSurfactantThickness()

Return the total non-surfactant thickness in Angstrom.

Return type

float

Returns

the total non-surfactant thickness in Angstrom

getTotalSurfactantThickness(layers_are_bilayers=True)

Return the total surfactant thickness in Angstrom.

Parameters

layers_are_bilayers (bool) – whether layers are bilayers

Return type

float

Returns

the total surfactant thickness in Angstrom

getVol(amin, amax)

Return the volume.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the volume in Ang.^3

write(input_base_name='packmol')

Write the packmol input file.

Parameters

input_base_name (str) – the base name to use for the packmol input file

Raises

PackmolInputFileException – if there is an issue with the input

Return type

str

Returns

the packmol input file name

class schrodinger.application.matsci.packmol.WormlikeMicelleInputFile(*args, **kwargs)

Bases: schrodinger.application.matsci.packmol.MicelleInputFile

Manage a wormlike micelle input file.

CONSTRAINT_TYPE = 'cylinder 0 0 {bottom} 0 0 1 {parameter} {length}'
getMinCellLengths()

Return the minimum cell lengths.

Return type

tuple

Returns

a triple containing float and/or None, float is a minimum cell length in Angstrom, None indicates that there is no minimum

getVol(amin, amax)

Return the volume.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the volume in Ang.^3

getOutsideVol()

Return the outside volume.

Return type

float

Returns

the outside volume in Ang.^3

getConstraintType(parameter)

Return the constraint type.

Parameters

parameter (float) – the parameter in Angstrom

Return type

str

Returns

the constraint type

IN_EXT = '.inp'
SURFACTANT_BOTTOM_ATOM_CONSTRAINT = 'inside'
SURFACTANT_TOP_ATOM_CONSTRAINT = 'outside'
__init__(*args, **kwargs)

See parent class for documentation.

addCIonBodies(start_dist, stop_dist, layers=None, factor=1)

Add counter-ion bodies to the input file.

Parameters
  • start_dist (float) – start adding counter-ions at this distance in Angstrom

  • stop_dist (float) – stop adding counter-ions at this distance in Angstrom

  • layers (list or None) – the counter-ion layers to add, if None then all will be added

  • factor (float) – multiplies the corresponding number of surfactant molecules to set the number of counter-ions in the given region

addLayer(info, amin, amax, hydrophilic_at_max=False, number=None, add_cion=False)

Add a layer.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • hydrophilic_at_max (bool) – if info is SurfactantInfo whether the hydrophilic atoms are to be located at the maximum

  • number (int or None) – the number of molecules to add, if None it will be determined

  • add_cion (bool) – if info is SurfactantInfo whether the layer is for the counter-ion

addSolventBodies(start_dist, stop_dist, layers=None, layer_sep=None)

Add solvent bodies to the input file.

Parameters
  • start_dist (float) – start adding solvents at this distance in Angstrom

  • stop_dist (float) – stop adding solvents at this distance in Angstrom

  • layers (list or None) – the solvent layers to add, if None then all will be added

  • layer_sep (float) – the layer separation in Angstrom

addStructureBodies()

See parent class for documentation.

addStructureBody(base_name, body)

Add a structure body to the input file.

Parameters
  • base_name (str) – the base name of the input structure file

  • body (str) – the body, should contain indentation and newlines

addSurfactantBodies(start_dist, start_hydrophilic_at_max=False, layers=None, layers_are_bilayers=True)

Add surfactant bodies to the input file.

Parameters
  • start_dist (float) – start adding surfactants at this distance in Angstrom

  • start_hydrophilic_at_max (bool) – specifies whether the hydrophilic atoms for the starting layer are to be located at the maximum

  • layers (list or None) – the surfactant layers to add, if None then all will be added

  • layers_are_bilayers (bool) – whether layers are bilayers

Return type

float, bool

Returns

surfactants stopped being added at this distance in Angstrom, whether the hydrophilic atoms for the final layer are located at the maximum

check()

Check cell lengths.

Raises

PackmolInputFileException – if there is an issue with the input

getBoxSliceVol(cmin, cmax)

Return the box slice volume.

Parameters
  • cmin (float) – the lower bound on the layer in Angstrom

  • cmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the box slice volume in Ang.^3

getCylinderSliceVol(rmin, rmax, length)

Return the cylinder slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the cylinder slice volume in Ang.^3

getEllipsoidSliceVol(rmin, rmax)

Return the ellipsoid slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the ellipsoid slice volume in Ang.^3

getLayerVolume(amin, amax, buffer_len=0)

Return the volume of this layer.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • buffer_len (float) – a buffer length in Angstrom

Return type

int

Returns

the volume in Ang.^3

getMaxDists(all_infos)

Return a dictionary of maximum distances (Ang.) among the structures in each layer of the given all_infos.

Parameters

all_infos (dict) – keys are layers, values are lists containing either SurfactantInfo or SolventInfo

Return type

dict

Returns

keys are layers, values are maximum distances

getNumber(info, amin, amax)

Return the number of surfactant or solvent molecules to add for the given info.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

Return type

int

Returns

the number of molecules

getOutsideCylinderVol(radius, length)

Return the box volume less the cylinder volume.

Parameters
  • radius (float) – the radius of the cylinder in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the box volume less the cylinder volume in Ang.^3

getOutsideEllipsoidVol(radius)

Return the box volume less the ellipsoid volume.

Parameters

radius (float) – the radius of the ellipsoid in Angstrom, this is half the length of the minor axis

Return type

float

Returns

the box volume less the ellipsoid volume in Ang.^3

getOutsideSphereVol(radius)

Return the box volume less the sphere volume.

Parameters

radius (float) – the radius of the sphere in Angstrom

Return type

float

Returns

the box volume less the sphere volume in Ang.^3

getRadius()

Return the radius.

Return type

float

Returns

the radius in Ang.

getSolventConstraints(amin, amax)

Return the solvent constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the solvent constraints

getSolventLayers()

Return a list of solvent layers.

Return type

list

Returns

the solvent layers

getSphereSliceVol(rmin, rmax)

Return the sphere slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the sphere slice volume in Ang.^3

getSurfactantConstraints(amin, amax)

Return the surfactant constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the surfactant constraints

getSurfactantLayers()

Return a list of surfactant layers.

Return type

list

Returns

the surfactant layers

getTotalCIonThickness()

Return the total counter-ion thickness in Angstrom.

Return type

float

Returns

the total counter-ion thickness in Angstrom

getTotalNonSurfactantThickness()

Return the total non-surfactant thickness in Angstrom.

Return type

float

Returns

the total non-surfactant thickness in Angstrom

getTotalSurfactantThickness(layers_are_bilayers=True)

Return the total surfactant thickness in Angstrom.

Parameters

layers_are_bilayers (bool) – whether layers are bilayers

Return type

float

Returns

the total surfactant thickness in Angstrom

prepare(cell_lengths, surfactant_infos, solvent_infos, layer_sep=1, packing_f=0.8, min_constraint_window_surfactant_idxs=25)

Prepare.

Parameters
  • cell_lengths (tuple) – the cell lengths of the output structure file

  • surfactant_infos (list) – contains SurfactantInfo

  • solvent_infos (list) – contains SolventInfo

  • layer_sep (float) – the layer separation in Angstrom

  • packing_f (float) – a packing efficiency factor used to control the density of surfactant and solvent molecules

  • min_constraint_window_surfactant_idxs (float) – this is the minimum window length for constraining surfactant hydrophilic and hydrophobic indices as a percentage of the surfactant length, should be in (0, 50)

Raises

PackmolInputFileException – if there is an issue with the input

write(input_base_name='packmol')

Write the packmol input file.

Parameters

input_base_name (str) – the base name to use for the packmol input file

Raises

PackmolInputFileException – if there is an issue with the input

Return type

str

Returns

the packmol input file name

class schrodinger.application.matsci.packmol.ElongatedMicelleInputFile(*args, **kwargs)

Bases: schrodinger.application.matsci.packmol.MicelleInputFile

Manage an elongated micelle input file.

CONSTRAINT_TYPE = 'ellipsoid 0 0 0 {parameter} {parameter} {parameter_p} 1'
prepare(*args, **kwargs)

See parent class for documentation.

Parameters

factor (float) – the scale factor for the principal axis

getMinCellLengths()

Return the minimum cell lengths.

Return type

tuple

Returns

a triple containing float and/or None, float is a minimum cell length in Angstrom, None indicates that there is no minimum

getMajorRadius()

Return the major radius.

Return type

float

Returns

the major radius in Ang.

getVol(amin, amax)

Return the volume.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the volume in Ang.^3

getOutsideVol()

Return the outside volume.

Return type

float

Returns

the outside volume in Ang.^3

getConstraintType(parameter)

Return the constraint type.

Parameters

parameter (float) – the parameter in Angstrom

Return type

str

Returns

the constraint type

IN_EXT = '.inp'
SURFACTANT_BOTTOM_ATOM_CONSTRAINT = 'inside'
SURFACTANT_TOP_ATOM_CONSTRAINT = 'outside'
__init__(*args, **kwargs)

See parent class for documentation.

addCIonBodies(start_dist, stop_dist, layers=None, factor=1)

Add counter-ion bodies to the input file.

Parameters
  • start_dist (float) – start adding counter-ions at this distance in Angstrom

  • stop_dist (float) – stop adding counter-ions at this distance in Angstrom

  • layers (list or None) – the counter-ion layers to add, if None then all will be added

  • factor (float) – multiplies the corresponding number of surfactant molecules to set the number of counter-ions in the given region

addLayer(info, amin, amax, hydrophilic_at_max=False, number=None, add_cion=False)

Add a layer.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • hydrophilic_at_max (bool) – if info is SurfactantInfo whether the hydrophilic atoms are to be located at the maximum

  • number (int or None) – the number of molecules to add, if None it will be determined

  • add_cion (bool) – if info is SurfactantInfo whether the layer is for the counter-ion

addSolventBodies(start_dist, stop_dist, layers=None, layer_sep=None)

Add solvent bodies to the input file.

Parameters
  • start_dist (float) – start adding solvents at this distance in Angstrom

  • stop_dist (float) – stop adding solvents at this distance in Angstrom

  • layers (list or None) – the solvent layers to add, if None then all will be added

  • layer_sep (float) – the layer separation in Angstrom

addStructureBodies()

See parent class for documentation.

addStructureBody(base_name, body)

Add a structure body to the input file.

Parameters
  • base_name (str) – the base name of the input structure file

  • body (str) – the body, should contain indentation and newlines

addSurfactantBodies(start_dist, start_hydrophilic_at_max=False, layers=None, layers_are_bilayers=True)

Add surfactant bodies to the input file.

Parameters
  • start_dist (float) – start adding surfactants at this distance in Angstrom

  • start_hydrophilic_at_max (bool) – specifies whether the hydrophilic atoms for the starting layer are to be located at the maximum

  • layers (list or None) – the surfactant layers to add, if None then all will be added

  • layers_are_bilayers (bool) – whether layers are bilayers

Return type

float, bool

Returns

surfactants stopped being added at this distance in Angstrom, whether the hydrophilic atoms for the final layer are located at the maximum

check()

Check cell lengths.

Raises

PackmolInputFileException – if there is an issue with the input

getBoxSliceVol(cmin, cmax)

Return the box slice volume.

Parameters
  • cmin (float) – the lower bound on the layer in Angstrom

  • cmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the box slice volume in Ang.^3

getCylinderSliceVol(rmin, rmax, length)

Return the cylinder slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the cylinder slice volume in Ang.^3

getEllipsoidSliceVol(rmin, rmax)

Return the ellipsoid slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the ellipsoid slice volume in Ang.^3

getLayerVolume(amin, amax, buffer_len=0)

Return the volume of this layer.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

  • buffer_len (float) – a buffer length in Angstrom

Return type

int

Returns

the volume in Ang.^3

getMaxDists(all_infos)

Return a dictionary of maximum distances (Ang.) among the structures in each layer of the given all_infos.

Parameters

all_infos (dict) – keys are layers, values are lists containing either SurfactantInfo or SolventInfo

Return type

dict

Returns

keys are layers, values are maximum distances

getNumber(info, amin, amax)

Return the number of surfactant or solvent molecules to add for the given info.

Parameters
  • info (SurfactantInfo or SolventInfo) – the info object for this layer

  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float or None) – the upper bound on the layer in Angstrom or None if there isn’t one in which case the remaining outermost space of the cell will be used

Return type

int

Returns

the number of molecules

getOutsideCylinderVol(radius, length)

Return the box volume less the cylinder volume.

Parameters
  • radius (float) – the radius of the cylinder in Angstrom

  • length (float) – the length of the cylinder in Angstrom

Return type

float

Returns

the box volume less the cylinder volume in Ang.^3

getOutsideEllipsoidVol(radius)

Return the box volume less the ellipsoid volume.

Parameters

radius (float) – the radius of the ellipsoid in Angstrom, this is half the length of the minor axis

Return type

float

Returns

the box volume less the ellipsoid volume in Ang.^3

getOutsideSphereVol(radius)

Return the box volume less the sphere volume.

Parameters

radius (float) – the radius of the sphere in Angstrom

Return type

float

Returns

the box volume less the sphere volume in Ang.^3

getRadius()

Return the radius.

Return type

float

Returns

the radius in Ang.

getSolventConstraints(amin, amax)

Return the solvent constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the solvent constraints

getSolventLayers()

Return a list of solvent layers.

Return type

list

Returns

the solvent layers

getSphereSliceVol(rmin, rmax)

Return the sphere slice volume.

Parameters
  • rmin (float) – the lower bound on the layer in Angstrom

  • rmax (float) – the upper bound on the layer in Angstrom

Return type

float

Returns

the sphere slice volume in Ang.^3

getSurfactantConstraints(amin, amax)

Return the surfactant constraints.

Parameters
  • amin (float) – the lower bound on the layer in Angstrom

  • amax (float) – the upper bound on the layer in Angstrom

Return type

str

Returns

the surfactant constraints

getSurfactantLayers()

Return a list of surfactant layers.

Return type

list

Returns

the surfactant layers

getTotalCIonThickness()

Return the total counter-ion thickness in Angstrom.

Return type

float

Returns

the total counter-ion thickness in Angstrom

getTotalNonSurfactantThickness()

Return the total non-surfactant thickness in Angstrom.

Return type

float

Returns

the total non-surfactant thickness in Angstrom

getTotalSurfactantThickness(layers_are_bilayers=True)

Return the total surfactant thickness in Angstrom.

Parameters

layers_are_bilayers (bool) – whether layers are bilayers

Return type

float

Returns

the total surfactant thickness in Angstrom

write(input_base_name='packmol')

Write the packmol input file.

Parameters

input_base_name (str) – the base name to use for the packmol input file

Raises

PackmolInputFileException – if there is an issue with the input

Return type

str

Returns

the packmol input file name

schrodinger.application.matsci.packmol.get_writer(surfactant_infos, solvent_infos, base_name, seed, n_loop, cell_lengths, packing_f, model_type, **kwargs)

Get the writer.

Parameters
  • surfactant_infos (list[SurfactantInfo]) – contains surfactant infos

  • solvent_infos (list[SolventInfo]) – contains solvent infos

  • base_name (str) – base name used for output file naming

  • seed (int) – seed for random

  • n_loop (int) – the number of packmol loops

  • cell_lengths (tuple[float]) – the cell lengths in Angstrom

  • packing_f (float) – the packing factor

  • model_type (str) – the model type, a key in the class map

Return type

StructuredLiquidInputFile

Returns

the writer

schrodinger.application.matsci.packmol.get_parser(description, packmol_input=True)

Get the command line argument parser.

Parameters
  • description (str) – the description

  • packmol_input (bool) – whether the input is a packmol input file

Return type

parserutils.DriverParser

Returns

command line argument parser

schrodinger.application.matsci.packmol.get_job_spec_from_args(argv, description, program_name='Structured Liquid', default_job_name='structured_liquid', packmol_input=True)

Return a JobSpecification.

Parameters
  • argv (list) – command line arguments including the script name at [0]

  • description (str) – the description

  • program_name (str) – the program name

  • default_job_name (str) – the default job name

  • packmol_input (bool) – whether the input is a packmol input file

Return type

schrodinger.job.launchapi.JobSpecification

Returns

the JobSpecification

schrodinger.application.matsci.packmol.main(description, *args, default_job_name='structured_liquid')

Main function used by drivers to run packmol.

Parameters
  • description (str) – the parser description

  • default_job_name (str) – the default job name

schrodinger.application.matsci.packmol.get_surfactant_infos(slb_dict)

Return surfactant information from the given dictionary of structured liquid builder options. Maestro files referenced within must exist in the current working directory.

Parameters

slb_dict (dict) – contains structured liquid builder options

Raises

RuntimeError – if there is an issue

Return type

list[SurfactantInfo], list[str]

Returns

the surfactant information objects and any extra structure file flags

schrodinger.application.matsci.packmol.get_solvent_infos(slb_dict)

Return solvent information from the given dictionary of structured liquid builder options. Maestro files referenced within must exist in the current working directory.

Parameters

slb_dict (dict) – contains structured liquid builder options

Raises

RuntimeError – if there is an issue

Return type

list[SolventInfo]

Returns

the solvent information objects

schrodinger.application.matsci.packmol.write_packmol_input_file(slb_dict, box_lengths)

Write the packmol input file from the given dictionary of structured liquid builder options.

Parameters
  • slb_dict (dict) – contains structured liquid builder options

  • box_lengths (tuple[float]) – the cell lengths in Angstrom

Raises

RuntimeError – if there is an issue

Return type

str, list[str]

Returns

the packmol input file name and any extra structure file flags