schrodinger.application.matsci.packmol module¶

Utilities for working with packmol.

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

Bases: tuple

chain_name¶: Alias for field number 3

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

cion_name¶: Alias for field number 8

cion_st¶: Alias for field number 7

hydrophilic_idxs¶: Alias for field number 5

hydrophobic_idxs¶: Alias for field number 6

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

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, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶

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'¶

FSCALE = 'fscale'¶

SHORT_RADIUS = 'short_radius'¶

SHORT_RADIUS_SCALE = 'short_radius_scale'¶

schrodinger.application.matsci.packmol.get_cuboid_vol(st)¶

Return the cuboid volume of the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: float
Returns: the cuboid volume in Ang.^3

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

schrodinger.application.matsci.packmol.get_atom_radii_lines(st, allow_ring_spears=False, penalty_factor_ring_spears=10, radius_factor_ring_spears=1, tolerance=2, batch_size=5)¶

Return the atom radii body.

Parameters

st (schrodinger.structure.Structure) – the structure
allow_ring_spears (bool) – if True then allow ring-spears
penalty_factor_ring_spears (float) – the penalty factor for ring-spears
radius_factor_ring_spears (float) – the radius factor for ring-spears
tolerance (float) – the distance tolerance in Angstrom
batch_size (int) – the number of atom indices per atom block

Return type

list[str]

Returns

list of the atom radii body lines

class schrodinger.application.matsci.packmol.StdInJob(cmd, subdir=None, log_name=None)¶

Bases: schrodinger.application.matsci.jobutils.LoggingSubprocessJob

Manage a subprocess job with stdin and that sends stdout to a log file.

doCommand(*args, **kwargs)¶: See parent class for documentation.

postCommand()¶: See parent class for documentation.

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.

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, expand_pbc=False, 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.
expand_pbc (bool) – if True then expand the PBC due to packmol imperfect packing
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

pdb_st (schrodinger.structure.Structure) – the structure created from the pdb file
mae_structs (list(schrodinger.structure.Structure)) – the structures created from the mae files
props (list(str)) – the properties to transfer

schrodinger.application.matsci.packmol.check_ring_spears(sts, logger=None)¶

Check for ring-spears.

Parameters

sts (dict) – keys are 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

Return type

dict, dict

Returns

the first and second are w/o and w/ ring-spears, respectively, keys are input files, values are schrodinger.structure.Structure

schrodinger.application.matsci.packmol.add_ring_spear_dummies(st, logger=None)¶

Return a copy of the given structure with dummy atoms added to the rings for the purposes of preventing ring-spears.

Parameters

st (schrodinger.structure.Structure) – the structure
logger (logging.Logger or None) – output logger or None if there isn’t one

Return type

schrodinger.structure.Structure

Returns

the structure with the dummy atoms added

schrodinger.application.matsci.packmol.remove_ring_spear_dummies(st)¶

Return a copy of the given structure with ring-spear dummy atoms removed from the rings.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: schrodinger.structure.Structure
Returns: the structure with the dummy atoms removed

schrodinger.application.matsci.packmol.get_cells(input_files, sts, allow_ring_spears=False, 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
allow_ring_spears (bool) – if True then allow ring-spears
logger (logging.Logger or None) – output logger or None if there isn’t one

Raises

RuntimeError – if there is a problem

Return type

dict, dict

Returns

the first and second are all (good and bad) and just bad cells, respectively, 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', allow_ring_spears=False, 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
allow_ring_spears (bool) – if True then allow ring-spears
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, dict

Returns

the first and second are all (good and bad) and just bad output files, respectively, 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

st (schrodinger.structure.Structure) – the structure
idxs (tuple) – first group of atom indices
jdxs (tuple) – second group of atom indices

Return type

float

Returns

the maximum distance in Angstrom

exception schrodinger.application.matsci.packmol.PackmolInputFileException¶: Bases: Exception

class schrodinger.application.matsci.packmol.PackmolInputFile(tolerance=2, filetype='pdb', output_base_name='packmol', comment='', general_body='', allow_ring_spears=False, penalty_factor_ring_spears=10, radius_factor_ring_spears=1)¶

Bases: object

Manage a packmol input file.

IN_EXT = '.inp'¶

__init__(tolerance=2, filetype='pdb', output_base_name='packmol', comment='', general_body='', allow_ring_spears=False, penalty_factor_ring_spears=10, radius_factor_ring_spears=1)¶

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
allow_ring_spears (bool) – if True then allow ring-spears
penalty_factor_ring_spears (float) – the penalty factor for ring-spears
radius_factor_ring_spears (float) – the radius factor for ring-spears

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

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.

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.

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.

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.

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

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

schrodinger.application.matsci.packmol.get_writer(surfactant_infos, solvent_infos, base_name, seed, n_loop, cell_lengths, packing_f, model_type, allow_ring_spears, penalty_factor_ring_spears, radius_factor_ring_spears, **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
allow_ring_spears (bool) – if True then allow ring-spears
penalty_factor_ring_spears (float) – the penalty factor for ring-spears
radius_factor_ring_spears (float) – the radius factor for ring-spears

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, allow_ring_spears=False, penalty_factor_ring_spears=10, radius_factor_ring_spears=1)¶

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
allow_ring_spears (bool) – if True then allow ring-spears
penalty_factor_ring_spears (float) – the penalty factor for ring-spears
radius_factor_ring_spears (float) – the radius factor for ring-spears

Raises

RuntimeError – if there is an issue

Return type

str, list[str]

Returns

the packmol input file name and any extra structure file flags