schrodinger.application.matsci.desmondutils module¶

Utilities for working with Desmond.

class schrodinger.application.matsci.desmondutils.ENEGRP_VALUE(time, value)¶

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.

time¶: Alias for field number 0

value¶: Alias for field number 1

class schrodinger.application.matsci.desmondutils.DesmondModel(msys, cms)¶

Bases: tuple

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

cms¶: Alias for field number 1

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.

msys¶: Alias for field number 0

schrodinger.application.matsci.desmondutils.exit_if_incompatible_with_desmond(logger=None)¶

Desmond only runs on certain platforms. Exit if the platform being used is not compatible. If a logger is supplied, it will print an error to the logger.

Parameters: logger (logging.Logger) – The logging object to print an error to if the platform is incompatible. If not supplied, nothing will print.
Raises: SystemExit – If the current platform is not compatible with Desmond

schrodinger.application.matsci.desmondutils.make_chorus_orthorhombic(struct)¶

Zero out all the non-diagonal Chorus box properties. The main use of this function is to remove numerical imprecision in the off-diagonal elements that causes Desmond to consider the box triclinic. The function returns the largest off-diagonal element pre-zeroing so the calling routine can decide what to do (warn user, etc) if the off-diagonals looked large enough to be intentionally non-zero.

Parameters: struct (schrodinger.structure.Structure) – The structure whose Chorus box properties should be modified
Return type: float
Returns: The absolute value of the largest off-diagonal element before zeroing

schrodinger.application.matsci.desmondutils.has_orthorhombic_pbc(struct, tolerance=0.0)¶

Detect if the given structure has a PBC that is orthorhombic (all angles are 90 degrees).

Parameters

struct (schrodinger.structure.Structure) – The structure to check
tolerance (float) – The tolerance for the 90 degree check, in degrees

Return type

bool

Returns

True if a PBC exists and it is orthorhombic

schrodinger.application.matsci.desmondutils.might_be_system(structs)¶

Check if we’re using a Desmond system or system is infinite.

Parameters: structs (iterable) – Each item should be a structure.Structure object
Return type: bool or str
Returns: False if none of the structures are infinite or Desmond systems. An error message is returned if at least one such structure is detected

schrodinger.application.matsci.desmondutils.determine_box_size(struct)¶

Determine the size of a cubic box that encloses the entire structure

Parameters: struct (schrodinger.structure.Structure) – The structure to use in determining the box size.
Return type: float
Returns: The largest span in the X, Y or Z direction

schrodinger.application.matsci.desmondutils.add_cubic_chorus_box_props(struct)¶

Add the Chorus box properties to the structure for a cubic box

Parameters: struct (schrodinger.structure.Structure) – The structure to add the properties to

schrodinger.application.matsci.desmondutils.store_chorus_box_props(struct, ax, ay=0.0, az=0.0, bx=0.0, by=None, bz=0.0, cx=0.0, cy=0.0, cz=None)¶

Add properties to the structure that define the periodic boundary condition in the way Desmond wants it defined.

Parameters

struct (schrodinger.structure.Structure) – The structure to add the properties to
ax (float) – The value of the ax box property
ay (float) – The value of the ay box property. Defaults to 0.
az (float) – The value of the az box property. Defaults to 0.
bx (float) – The value of the bx box property. Defaults to 0.
by (float) – The value of the by box property. If not given, this value is set the same as ax.
bz (float) – The value of the bz box property. Defaults to 0.
cx (float) – The value of the cx box property. Defaults to 0.
cy (float) – The value of the cy box property. Defaults to 0.
cz (float) – The value of the cz box property. If not given, this value is set the same as ax.

schrodinger.application.matsci.desmondutils.has_chorus_box_props(struct)¶

Check if the structure has all the Chorus box properties

Parameters: struct (schrodinger.structure.Structure) – The structure to check for properties
Return type: bool
Returns: Whether the structure has all the chorus box properties

schrodinger.application.matsci.desmondutils.has_space_group_pbc_props(struct)¶

Check if the structure has all the space group PBC properties

Parameters: struct (schrodinger.structure.Structure) – The structure to check for properties
Return type: bool
Returns: Whether the structure has all the space group pbc properties

schrodinger.application.matsci.desmondutils.is_opls3_model(model)¶

Check if the given Cms model was made with OPLS3

Parameters: model (schrodinger.application.desmond.cms.Cms) – The cms model to check
Return type: bool
Returns: True if OPLS3 was detected, False if not

schrodinger.application.matsci.desmondutils.is_opls2005_model(model)¶

Check if the given Cms model was made with OPLS_2005

Parameters: model (schrodinger.application.desmond.cms.Cms) – The cms model to check
Return type: bool
Returns: True if OPLS_2005 was detected, False if not

schrodinger.application.matsci.desmondutils.get_model_ff_name(model)¶

If possible detect what force field the model was created with

Parameters: model (schrodinger.application.desmond.cms.Cms) – The cms model to check
Return type: str
Returns: The name of the detected forcefield or and empty string if no known force field was detected. FF names are the module constants OPLS3 or OPLS2005

schrodinger.application.matsci.desmondutils.copy_atom_properties(struct1, struct2, atom_props)¶

Parameters

struct1 (schrodinger.structure.Structure) – The structure from which atom properties are copied
struct2 (schrodinger.structure.Structure) – The structure to which atom properties are copied
atom_props (list of strings) – Atom properties that are copied

schrodinger.application.matsci.desmondutils.get_npseudos_per_molecule(comp_ct)¶

Get number of pseudo atoms per molecule.

Parameters: comp_ct (FFIOSTructure) – CMS component
Return type: int
Returns: Number of pseudo atoms in the first molecule of the component

schrodinger.application.matsci.desmondutils.get_molecules_pseudos(comp_ct, molecules)¶

Given component and molecules indices return the corresponding pseudo indices.

Parameters

comp_ct (FFIOSTructure) – CMS component
molecules (list) – List of molecules indices

Return type

set[int]

Returns

Set of pseudo atoms indices

schrodinger.application.matsci.desmondutils.extend_comp(comp_ct, struct)¶

Given a component (comp_ct) with possible some pseudo atoms, extend it with struct (must be the same isomers, NUM_COMPONENT == 1 is enforced).

Parameters

comp_ct (FFIOSTructure) – CMS component
npseudos (int) – Number of pseudo atoms in the first molecule of the component
struct (structure.Structure) – Structure to extend the component with

schrodinger.application.matsci.desmondutils.is_traj_gcmc(trj_path, check_all_frames=False)¶

Whether trajectory is generated during Grand-canonical Monte Carlo simulation :param str trj_path: The path to input trajectory

Parameters: check_all_frames (bool) – Whether to check all the frames of a trajectory. In case of false it will only check the first frame
Return type: bool
Returns: Whether passed trajectory is generated during Grand-canonical Monte Carlo simulation

class schrodinger.application.matsci.desmondutils.SystemBuilder(struct, basename, forcefield='OPLS_2005', rezero_system=True, logger=None, copy_output=True, fatal_atom_properties=['i_ffio_grp_ligand', 'i_ffio_grp_energy', 'i_psp_parent', 'f_psp_parent', 's_psp_parent'], check_infinite=True, split_components=False, water_fftype='SPC', set_incorporation=True, wam_type=None, per_structure_wam=False, build_geometry_msj=None, redistribute_hydrogen_mass=False)¶

Bases: object

SOLVATION_RADIUS_KEY = 'solvation_exclusion_radius'¶

__init__(struct, basename, forcefield='OPLS_2005', rezero_system=True, logger=None, copy_output=True, fatal_atom_properties=['i_ffio_grp_ligand', 'i_ffio_grp_energy', 'i_psp_parent', 'f_psp_parent', 's_psp_parent'], check_infinite=True, split_components=False, water_fftype='SPC', set_incorporation=True, wam_type=None, per_structure_wam=False, build_geometry_msj=None, redistribute_hydrogen_mass=False)¶

Parameters

struct (schrodinger.structure.Structure) – The structure to run the system builder on.
basename (str) – The base name of the output file
forcefield (str) – The name of the force field to use. The default is ‘OPLS_2005’. Note that any custom directory needed for OPLS3 is taken care of via the runtime environment as long as the script was launched via launcher with the oplsdir argument.
rezero_system (bool) – Whether to move the center of mass to the origin
logger (logging.Logger) – The logger to use to record non-error messages. If None, the messages are printed.
copy_output (bool) – specifies to copy output files back to the launch directory by adding them to the job control backend
fatal_atom_properties (tuple of strings) – Properties to remove from structure
check_infinite (bool) – request assign is_infinite during FF assignment
split_components (bool) – Whether to split system in components in the system build
water_fftype (str) – the force field type for water solute. Must be a key in the WATER_FFTYPES dictionary.
set_incorporation (bool) – Set the cms as the incorporated structure when set_incorporation=True and copy_output=True
wam_type (int or None) – One of the enums defined in workflow_action_menu.h if the results should have a Workflow Action Menu in Maestro
per_structure_wam (bool) – Whether wam is to be added per structure
build_geoemtry_msj (str or None) – build_geometry stage msj file
redistribute_hydrogen_mass (bool) – whether to perform hydrogen mass repartition

run()¶

Prepare and run the desmond system builder

Raises: FileNotFoundError – If the certain files cannot be found.

cleanAtomProperties()¶: Clean atom properties that cause the system builder to fail

setChorusBoxProps()¶: If the chorus box properties are not set to define the periodic boundary condition, a cubic PBC will be imposed based on the largest span of the X, Y or Z coordinates.

cleanStructProperties()¶: Romove or re-assign the structure-level properties that causes issues.

setForceFieldDir()¶: Set custom OPLS directory, if any

centerStruct()¶: Translate the whole structure so that the centroid is at the origin.

splitComponents()¶: Each list in Component cts contains isomers.

writeMae()¶

Write out the mae file for Desmond forceField assignment input.

Raises: FileNotFoundError – if input files for desmond assign forcefield stage cannot be generated.

writeMsj()¶: Write out the msj file for Desmond forceField assignment input.

static validateBuildGeometryMsj(msj_fn=None, msj_sea=None)¶

Validate MSJ file or Map to have two stages, task and build_geometry.

Return type: (bool, sea.Map) or (bool, str)
Returns: Whether MSJ is valid. If it is, return Map of the MSJ, otherwise error message

prepareBuildGeometryInput(in_mae)¶

Prepare mae input for the structure builder

Parameters: in_mae (str) – Input mae (not modified)
Return str: Mae file with prepared input for build_geometry

setupBuildGeometryMSJ(msj_fn)¶

Write msj with build_geometry stage.

Parameters: msj_fn (str) – MSJ filename to use
Return type: bool or float
Returns: False on error. 0 if no solvation was requested, otherwise solvation radius

runBuildGeometry()¶: Run build_geometry with multisim if requested. self.in_mae may be updated here.

runForceFieldAssignment()¶: Run the desmond assign forcefield stage.

addFilesToBackend()¶: Add intermediate and final files to backend.

postProcessCms()¶

Post process of desmond cms output.

Raises: FileNotFoundError – If the cms cannot be found.

prepareWaterModel(struct)¶

Prepare water component.

Parameters: struct (schrodinger.structure.Structure) – The structure whose atom properties to be modified. Must be one component (all molecules of the same type)

schrodinger.application.matsci.desmondutils.run_system_builder(struct, base, *args, **kwargs)¶

Run the Desmond multisim system builder.

See SystemBuilder for argument documentation.

Parameters

location_type (str) – the location type, either parserutils.INSTALLED_CG_FF_LOCATION_TYPE or parserutils.LOCAL_CG_FF_LOCATION_TYPE
encrypt (bool or None) – whether to encrypt the FF parameters in the written cms, if None and an encrypted CG FF file is used then the cms is automatically encrypted
adapt_ff (bool) – applies structure specific modifications to the FF after its raw application to the given structure
scale (bool) – Scale the lattice vector to get density representative of the force field parameters

Return type

str or None

Returns

The name of the resulting .cms file, or None if the file was not produced successfully

schrodinger.application.matsci.desmondutils.find_forcefield_invalid_structures(structs, ffield_num=None, handle=None)¶

Check structures to see if the specified forcefield is valid for them

Parameters

structs (list) – A list of schrodinger.structure.Structure objects
ffield_num (int or None) – An integer specifying which forcefield to use, if None then handle must be given
handle (int or None) – A forcefield handle, if None then ffield_num must be given

Return type

list

Returns

A list containing all the structures that fail the force field test. The list is empty if all structures are valid for the force field

schrodinger.application.matsci.desmondutils.validate_ff_name_and_get_number(name)¶

Check that the given name is a valid force field name and if so, return the mmffld number associated with that name

Parameters: name (str) – The force field name to check
Return type: (str or None, int)
Returns: The first item is an error message if an error occurred. The second item is the mmffld integer for the given forcefield, or 0 if an error occurred.

schrodinger.application.matsci.desmondutils.read_density_from_eaf(density_eaf, fraction=0.2, logger=None)¶

Reads in a .eaf file generated by an ms_analysis stage of a Desmond MD run and returns density data.

Parameters

density_eaf (str) – EAF file containing density information
fraction (float) – The last fraction of the frames to use in the density averaging
logger (logging.Logger) – The logger to use while logging errors. If not supplied, messages will be printed.

Return type

(None, None), or (float, float)

Returns

(None, None) if the density cannot be read from the file, or tuple of the calculated density and standard deviation.

schrodinger.application.matsci.desmondutils.validate_box_size(model, temp=300.0, simple=True)¶

Validate model or structure box (lattice) size.

Parameters

model (cms.Cms or structure.Structure) – Desmond model or structure. For structure chorus properties must be set
temp (float) – Temperature in K
simple (bool) – If true, run an empirical test based on the lattice constants

Return bool

True if cell is valid for Desmond, False otherwise

schrodinger.application.matsci.desmondutils.get_multisim_command(input_name, output_name, msj_name=None, job_name=None, num_retries=None, for_shell=False, hosts=None, add_license=True, license_host=None, **kwargs)¶

Return a command to run the Desmond multisim utility

Parameters

input_name (str) – The name of the input file
output_name (str) – The name to use for the output CMS file
msj_name (str) – The name of the .msj command file
job_name (str) – The name to use for the job
num_retries (None or int) – Number of retries by multisim. If None, default value is used. Multisim retries are different from job retries. JobDj retries correspond to resubmission of job if it fizzled or died which is not error. Desmond multisim contains its own retries in case desmond job dies. The defined parameter is used for desmond multisim job.
gpu (bool) – Does nothing, left in for backwards compatibility. All calculations run on GPU
procs (int) – Does nothing, left in for backwards compatibility. All calculations run on GPU
for_shell (bool) – True if this will be used directly in a shell, such as when a panel writes a .sh file or used via subprocess. False if the command will be issued via normal Schrodinger job launching. If True, $SCHRORDINGER will be prepended to the command.
hosts (str) – the hosts to run this job in the hostname:nprocs format
add_license (bool) – Whether Desmond GPU license should be added to the command. Should be False when running force field assignment.
license_host (None or str) – Host to be used to generate license. It will NOT appear in the returned cmd. To keep the host pass it in hosts. This option cannot be used together with hosts

Return type

list

Returns

The command line command to use

schrodinger.application.matsci.desmondutils.get_default_near_timestep()¶

Return the default near timestep

Returns: Default near timestep in femtoseconds
Return type: float

schrodinger.application.matsci.desmondutils.get_default_far_timestep()¶

Return the default far timestep

Returns: Default far timestep in femtoseconds
Return type: float

schrodinger.application.matsci.desmondutils.prepare_cms_properties_for_writing(model)¶

Deletes several properties that should be removed before writing a CMS. Notably, this function removes the trajectory property.

Parameters: model (cms.Cms) – System to update

schrodinger.application.matsci.desmondutils.delete_molecules_from_comps(model, comp_data)¶

Delete molecules from specific components of a model system

Parameters

model (cms.Cms) – Desmond model/system to update
comp_data (dict) – keys - components ids, values list of molecules ids

Return set

Set of empty (removed) component names

schrodinger.application.matsci.desmondutils.delete_molecules_from_model(model, mol_indices, cg_ff_path=None)¶

Delete molecules from a Desmond system

Parameters

model (cms.Cms) – Model to update
mol_indices (list(int)) – A list of integers containing the indices of the molecules that should be removed. These indices should correspond with the model.molecule indices.
cg_ff_path (str) – The path to the force field file for the coarse-grain system. Used to reassign the forcefield for coarse-grained systems after delete molecules.

Return type

schrodinger.application.desmond.cms.Cms

Returns

A copy of the input model with the molecules removed

Raises

TypeError – When a coarse-grain model is given, but no cg_ff_path argument is given.

schrodinger.application.matsci.desmondutils.delete_molecules_from_cg_model(model, mol_indices, ff_path)¶

Delete molecules from a coarse-grained Desmond system

Parameters

model (cms.Cms) – Model to update
mol_indices (list(int)) – A list of integers containing the indices of the molecules that should be removed. These indices should correspond with the model.molecule indices.
ff_path (str) – The path to the force field file

Return type

schrodinger.application.desmond.cms.Cms

Returns

A copy of the input model with the molecules removed

schrodinger.application.matsci.desmondutils.delete_molecules_from_aa_model(model, mol_indices)¶

Delete molecules from an all-atom system

Parameters

model (cms.Cms) – Model to update
mol_indices (list(int)) – A list of integers containing the indices of the molecules that should be removed. These indices should correspond with the model.molecule indices.

Return type

set

Returns

Set of empty (removed) components names

schrodinger.application.matsci.desmondutils.parse_ene_file(filename=None, fileobj=None, prop=None, gcmc=False)¶

Parse data from a Desmond .ene file. All the data from the file can be returned in a dictionary, or just the data from a single property can be returned in a list.

Parameters

filename (str) – The name of the .ene file to read
fileobj (file or io.BufferedReader) – The open file object for the .ene file. Only one of filename or fileobj should be supplied. If both are given, filename will take precedence. io.BufferedReader objects come from tarfile.extractfile, for instance. Note - in Python 3, open file objects are io.TextIOWrapper
prop (str) – If given, should match one of the properties in the ene file header (such as ‘V’). The return value will be a list of values for this property only
gcmc (bool) – Whether to parse GMCM or a standard MD file

Return type

dict, dict, or list, list or dict or list

Returns

If prop is not specified, the return value is a dict if gcmc is False, otherwise two dicts. Keys are property names from the ene header (without units, such as ‘V’) and values are lists of floating point values for that property in the order obtained from the .ene file. If prop is specified, the return value is a list if gcmc is False, otherwise two lists of those property values in the order found in the .ene file.

Raises

ValueError – If a line of unknown format is found while reading the file, or if neither filename or fileobj is specified.
TypeError – If prop is supplied but does not match a property in the header line

schrodinger.application.matsci.desmondutils.get_density_from_ene(ene_file, struct, fraction=0.2)¶

Parse the volume from the ene file and compute the density from it. The density is averaged over the last fraction of frames.

Parameters

ene_file (str) – The name of the file to read in.
struct (schrodinger.structure.Structure) – The structure to compute the density for
fraction (float) – The fraction of frames to average the density over. For instance, use 0.20 to compute the density over the final 20% of frames. Use the special value 0 to just use the final density. With fraction=0, the returned standard deviation is 0.

Return type

(float, float)

Returns

The mean density and standard deviation of the density.

Raises

IOError – If unable to read the volumes from the ene file (from get_prop_from_ene method)

schrodinger.application.matsci.desmondutils.get_prop_from_ene(ene_file, prop, fraction=0.2, reciprocal=False, include_first=False, average=True)¶

Parse the ene file and compute mean and std for a specific property. The property is averaged over the last fraction of frames.

Parameters

ene_file (str) – The name of the file to read in.
prop (str) – The name of the property to read in
fraction (float) – The fraction of frames to average the density over. For instance, use 0.20 to compute the prop over the final 20% of frames. Use the special value 0 to just use the final density. With fraction=0, the returned standard deviation is 0.
reciprocal (bool) – If True, the mean and std will be done on the reciprocal of the property values.
include_first (bool) – If true, the first entry of the ene file will be included in averaging.
average (bool) – If true, the average and std of the property will be returned. If false, then a list of the values will be returned.

Return type

(float, float) or list

Returns

The mean property and standard deviation of the property or the list of values if average=False. (or the reciprocal ones if reciprocal=True)

Raises

IOError – If unable to read the volumes from the ene file
ValueError – If data have zeros, and the reciprocal of them are requested.

schrodinger.application.matsci.desmondutils.update_pdb_pbc(icms_obj=None, icms_file=None, ocms_file=None)¶

Update the PDB PBC properties given a cms-type input.

Parameters

icms_obj (cms.Cms or None) – input cms.Cms object or None if icms_file is given instead
icms_file (str or None) – input .cms file name or None if icms_obj is given instead
ocms_file (str or None) – if provided the updated cms.Cms will be written to this file, if None then no file will be written

Raises

RuntimeError – if there is a problem with the input

Return type

cms.Cms

Returns

the updated cms.Cms

schrodinger.application.matsci.desmondutils.get_desmond_trj_frames(cms_path=None, traj_dir=None, traj_frames=None)¶

Yield a desmond trajectory frame by frame. The memory taken by the previous frame is released before yielding the next one.

Parameters

cms_path (str or None) – path to the CMS file
traj_dir (str or None) – path to trajectory dir
traj_frames (An iterable of trajectory frames) – trajectory to yield

Raises

RuntimeError – if there is a problem with the input

Return type

iterator(schrodinger.application.desmond.packages.traj.frame)

Returns

an iterator for a trajectory frame

schrodinger.application.matsci.desmondutils.get_desmond_frames_in_range(traj_dir, trj_min, trj_max, trj_step=None)¶

Get desmond frames from trajectory within the selected range (top and bottom included).

Parameters

traj_dir (str) – Path to the trajectory directory.
trj_min (int or None) – Index of frame in trajectory to start with. If None it will start from the begining of the trajectory,
trj_max (int or None) – Index of frame in trajectory to end at. If None it will end at the ending of the trajectory
trj_step (int or None) – The step for the trajectory

Return type

list

Returns

list of trajectory frames selected

Raises

ValueError – Will raise if no frames are selected.

schrodinger.application.matsci.desmondutils.get_desmond_frames_from_options(options)¶

Convenience function to get desmond frames in the range specified by the user from commandline options

Parameters: options (parserutils.SubscriptableNameSpace) – Parsed commandline options
Return list: List of trajectory frames

schrodinger.application.matsci.desmondutils.get_cutoff(length, percent)¶

Get cutoff given length and percent.

Parameters

length (int) – Length
percent (float) – Percent for the cutoff

Return int

Cutoff (minimum 1)

schrodinger.application.matsci.desmondutils.parse_enegrp_file(enegrp_fn, props=('en', 'E_p', 'E_k', 'E_x', 'P', 'V', 'Dispersion_Correction', 'Self_Energy_Correction', 'Net_Charge_Correction', 'Global_Force_Sum', 'Kinetic', 'pair_elec', 'pair_vdw', 'stretch', 'angle', 'dihedral', 'far_exclusion', 'nonbonded_elec', 'nonbonded_vdw', 'far_terms', 'Total', 'Virial', 'K.E.tensor', 'Pressure_Tensor', 'Simulation_Box'))¶

Parse data from a Desmond *enegrp.dat file. All the data from the file can be returned in a dictionary where key is the property name and values are dict, key is the time and values are the property value at that time.

Parameters: enegrp_fn (str) – name of enegrp file to read
Props list props: list of properties to parse. Check ALL_ENEGRP_PROPS for the list of supported properties.
Return type: dict
Returns: dictionary where key is the property name and values are namedtuple. The namedtuple has two fields, time and value. The value is the value for the property at that timestep. Value at the timestep can be a float or a list depending on the property.

schrodinger.application.matsci.desmondutils.get_ptensor_from_enegrp(enegrp_fn, percent_to_avg, log=None)¶

Extract and calculate average pressure from an energy group file.

Parameters

enegrp_fn (str) – Energy group filename
percent_to_avg (float) – Percent to use when averaging pressure tensor
log (method) – Log method

Return type

numpy.array()

Returns

Averaged pressure tensor

schrodinger.application.matsci.desmondutils.get_lattice_param_from_enegrp(enegrp_fn, percent_to_avg)¶

Extract and calculate average lattice parameter from an energy group file.

Parameters

enegrp_fn (str) – Energy group filename
percent_to_avg (float) – Percent to use when averaging lattice parameter

Raises

IOError – fail in reading enegrp file

Return type

numpy.ndarray

Returns

Averaged lattice parameters matrix

schrodinger.application.matsci.desmondutils.get_ptensor_from_trj(trj, percent_to_avg, log=None)¶

Extract and calculate average pressure from trajectory. Trajectory must be in the DTR format trajectory.write_velocity should be True.

Parameters

trj (str or iterable) – Trajectory directory or iterable trajectory
percent_to_avg (float) – Percent to use when averaging pressure tensor
log (method) – Log method

Return type

numpy.array

Returns

Averaged pressure tensor

schrodinger.application.matsci.desmondutils.get_ptensor_from_plugin(ptensor_fn, percent_to_avg, print_volume=False, log=None)¶

Extract and calculate average pressure from pressure tensor plugin.

Parameters

ptensor_fn (str) – Output file of ptensor plugin
percent_to_avg (float) – Percent to use when averaging pressure tensor
log (method or None) – Log method. If None, print will be used

Return type

numpy.array

Returns

Averaged pressure tensor

schrodinger.application.matsci.desmondutils.deform_cms_model(model, box, remap=True)¶

Deform the CMS box using values from box, and atom coordinates in the model are scaled proportionally to fit the new box if remap=True.

Parameters

model (cms.Cms) – model to modify
box (list[float]) – Values (9) of the new box
remap (bool) – Whether to strain atom coordinates besides lattice

schrodinger.application.matsci.desmondutils.is_infinite(model)¶

Return a boolean indicating whether the given desmond model has components that are infinitely bonded, meaning that it has bonds that cross the periodic boundary which can not be eliminated by means of molecule contraction.

Parameters: model (cms.Cms) – model to check
Return type: bool
Returns: True if infinite, False otherwise

schrodinger.application.matsci.desmondutils.set_physical_properties(model)¶

Set cell formula, volume and density to model.

Type: cms.Cms
Param: Model to set

schrodinger.application.matsci.desmondutils.cms_writer(cms_fn_in, cms_fn_out=None)¶

Context manager to modify desmond CMS model.

with desmondutils.cms_writer(cms_in) as model:: model.set_cts_property(‘r_matsci_real_property’, 11.2)

Parameters

cms_fn_in (str) – Input CMS filename
cms_fn_in – Output CMS filename. If None, cms_fn_in will be used

Yield

cms.Cms

schrodinger.application.matsci.desmondutils.assign_lipid_ff(model)¶

Assign the lipid forcefield to the given model.

Parameters: model (cms.Cms) – the model containing the lipid
Raises: ValueError – if there is no known lipid present

schrodinger.application.matsci.desmondutils.combine_trajectories(trj_path, trj_dirs, trj_int, backend)¶

Combine multiple trajectories into a single one

Parameters

trj_path (str) – The path to the final trj directory
trj_dirs (list) – List of trajectory directory paths
trj_int (float) – Trajectory recording interval in ps
backend (schrodinger.job._Backend or None) – Backend handle, or None if not running under job control

Return type

None or str

Returns

The path to the combined trj file, or None if the operation failed

schrodinger.application.matsci.desmondutils.use_monomer_charges(struct, ff_name)¶

Add charges to the structure based on the charges computed by monomer. To compute monomer charges we create a fragment for each residue that includes the residue and all attached residues or atoms. Whether attached residues or attached atoms are used depends on the size of the created fragment.

The partial_charge property of atoms in the structure will be modified with the computed charges and also the property ‘r_ffio_custom_charge’ will be added to each atom in the structure to indicate that these charges should be used by the force field

Parameters

struct (schrodinger.structure.Structure) – The structure to compute charges for.
ff_name (str) – The name of the OPLS forcefield

schrodinger.application.matsci.desmondutils.balance_charge(struct)¶

Ensure that the total of the partial charges on the molecule equals the total of the formal charges.

Parameters: struct (schrodinger.structure.Structure) – The structure to modify

schrodinger.application.matsci.desmondutils.partial_to_custom_charges(struct)¶

Set the current partial charges as custom FF charges

Parameters: struct (schrodinger.structure.Structure) – The structure to modify

class schrodinger.application.matsci.desmondutils.AnalysisDriverMixin¶

Bases: object

Class containing methods that are shared by most trajectory analysis drivers.

setDefaultAnalysisParams(opts, static_allowed=False)¶

Set default class variables that all trajectory analysis drivers use.

Parameters

opts (parserutils.SubscriptableNameSpace) – options for running the driver
static_allowed (bool) – whether static frames are allowed

trjFrames()¶

Yield the trajectory frame by frame. The memory taken by the previous frame is released before yielding the next one.

Return type: iterator(schrodinger.application.desmond.packages.traj.frame)
Returns: an iterator for trajectory frames

getOutfileName(extension, add_to_backend=True)¶

Get an outfile name by appending the extension to the job name

Parameters: add_to_backend (bool) – Whether the outfile should be added to backend
Return str: The outfile name

writeOutputCmsAndData(wam_type, per_structure_wam=False)¶

Write the modified cms_model and set it as output structure. If a data file is generated (data_filename) if will be added to the backend.

Parameters

wam_type (int) – One of the enums defined in workflow_action_menu.h
per_structure_wam (bool) – Whether the WAM should be set on the cms model instead of file-level

getFirstCellPositions(frame)¶

Get all the positions from the frame and then translate to first unit cell

Parameters: frame ('schrodinger.application.desmond.packages.traj.Frame') – current frame
Return ‘numpy.ndarray’: numpy array containing translated positional coordinates

exportStructuresForDebugging()¶: Export the full system structure at each frame for debugging

schrodinger.application.matsci.desmondutils.validate_ff_and_water_model(ffld, model)¶

Verify that the chosen water model is compatible with the chosen forcefield

Parameters

ffld (str) – The name of the forcefield
model (str) – The name of the water model. From water combobox use currentData method.

Return type

True or (False, str)

Returns

The return type is compatible with AF2 validators. Either True if everything is OK, or False with an error message if not.

schrodinger.application.matsci.desmondutils.struct_has_ffio_ct_type(st)¶

Return True if the given structure has the ‘s_ffio_ct_type’ property defined.

Parameters: st (schrodinger.structure.Structure) – structure to check
Return type: bool
Returns: True if defined

schrodinger.application.matsci.desmondutils.get_cms_and_trj_path_from_st(struct)¶

Get trajectory and cms path for the passed structure in maestro: using structure property

Parameters

schrodinger.structure.Structure (struct) – Structure to get associated cms and trajectory of
str (source_path) – Path to source cms and trj folder

Return str,str

Path to the cms file trajectory frames if both are found.

schrodinger.application.matsci.desmondutils.make_pos_restraints(model, asl, force_const=500.0)¶

Create kwargs that can be used in MD MSJ stringers to restrain atoms

Parameters

model (cms.Cms) – the Desmond system that you want to restrain
asl (str) – the atom-specification-language string used to identify the atoms in the system that should be restrained
force_const (float) – the force constant of the restraints that you want imposed on the specified atoms, in units of kcal/mol/Ang^2

Return type

dict(str=str)

Returns

key-word arguments that can be passed to MDMSJStringer to restrain the atoms

schrodinger.application.matsci.desmondutils.has_atom_vel(struct)¶

Check whether structure (or CMS model) has atoms with FFIO velocity set.

Parameters: struct (structure.Structure or cms.Cms) – Structure or CMS model
Return type: bool
Returns: Whether at least one atom has velocity set

schrodinger.application.matsci.desmondutils.add_energy_atom_groups(cms, asl, overwrite=False)¶

Add an energy atom group to the CMS.

Parameters

cms (cms.Cms) – cms object where atom group will be added
asl (string) – ASL string to select atom
overwrite (bool) – overwrite energy group if True. If not true and energy group already exists in model, raise error

schrodinger.application.matsci.desmondutils.register_md_outfiles(save_files, cms_fname, trj_dirname)¶

Add cms and trj to backend based on the value of parserutils.SAVE_FLAG

Parameters

save_files (str) – One of parserutils.SAVE_NONE, parserutils.SAVE_CMS or parserutils.SAVE_TRJ
cms_fname (str) – Cms file name
trj_dirname (str) – Trj directory name