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¶

Bases: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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