schrodinger.application.matsci.desconfig module¶
MSJ configuration tools for working with Desmond.
Copyright Schrodinger, LLC. All rights reserved.
- class schrodinger.application.matsci.desconfig.BarrierInfo(rcut, prefac, direction, exponent, coord, asl, buffer, asl_group, reciprocal)¶
Bases:
schrodinger.application.matsci.desconfig.BarrierInfo
Tuple to store barrier info.
- classmethod create(asl_group, rcut, prefac, direction, exponent, coord=None, asl=None, buffer=None, struct=None, reciprocal=False)¶
Prefer this over the constructor, since validation is implemented here.
- Parameters
asl_group (str) – ASL for impermeable atoms. If ‘all’, wall is impermeable. Otherwise wall is semipermeable.
rcut (float) – R cutoff
prefac (float) – Prefactor
direction (int) – 0 or 1 or 2 axis
exponent (int) – Exponent
coord (float) – Coordinate of the wall (if ASL is not defined)
asl (str) – ASL if coord is not provided
buffer (float) – Buffer to use with ASL
struct (structure.Structure) – Structure to use with ASL
reciprocal (bool) – add coordinate in reciprocal space
- static getPosition(struct, asl, direction, buffer)¶
Get barrier position along the
direction
.- Parameters
struct (structure.Structure) – Structure to run
asl
onasl (str) – ASL
direction (int) – One of the directions 0 or 1 or 2
float – Buffer
- Return type
bool, str or float
- Returns
True and position if no error. Otherwise False and the error message
- anyAtomsTooClose(struct, decimals=3)¶
Check if structure has any atoms too close to the wall.
- class schrodinger.application.matsci.desconfig.BarrierHeader(model=None, barriers=None)¶
Bases:
object
Get header for the barrier based on the model property
- __init__(model=None, barriers=None)¶
Instantiate the class to get for the barrier based on the model property
- Parameters
model (cms.Cms) – model containing barrier information. Barrier information must be present in _raw_fsys_ct to be accessed.
barriers (list[BarrierInfo]) – List of barriers. Either this or model must be passed, not both.
- static extractBarriers(struct)¶
Extract barrier information from the structure.
- Parameters
struct (structure.Structure) – Structure to extract properties from.
- Return type
list[BarrierInfo]
- Returns
List of barriers. On error, return empty list
- addBarrier(barrier)¶
Add a barrier.
- Parameters
barrier (BarrierInfo) – Barrier to add
- Raises
ValueError – If barrier is not of the BarrierInfo type
- static getReciprocalVal(barriers)¶
Get reciprocal values for the barriers
- Parameters
barriers (list[BarrierInfo]) – List of barriers
- Return type
bool
- Returns
return True if wall coordinates are defined in reciprocal space else False
- writeBarriersToStructure(struct)¶
Write list of barriers to the structure property.
- Parameters
struct (structure.Structure) – Structure to be modified
list[BarrierInfo] – List of barriers
- static validateBarriers(barriers)¶
Check if all the barriers are either in reciprocal coordinates or in real coordinates. if not, raise RuntimeError.
- Parameters
barriers (list[BarrierInfo]) – List of barriers
- Raises
RuntimeError – If the barriers coordinate definition are not consistent
- schrodinger.application.matsci.desconfig.create_msj(stringers, filename=None, task_stage=True, extra_task_text='', check_cg=None, check_infinite=None, msj_string_header='', remove_com_motion=None)¶
Write a Desmond .msj file based on the supplied stringers
- Parameters
filename (str) – If given, write the msj string to this path
stringers (list of
MSJStringer
objects) – Each item of the list is the MSJStringer for a single stage. The stages will be written in list ordertask_stage (bool) – Whether the traditional desmond auto task stage should be written before the stages in stringers
extra_task_text (str) – Additional text to place in the task stage. Ignored if task_stage=False.
check_cg (
schrodinger.structure.Structure
) – Check the given structure to see if it is coarse-grained. If it is, add the typical headers for the appropriate coarse-grained structure type. Note that the interplay between extra_task_test and the headers used for coarse-grained structures is uncertain and left to the caller to determine if the results are acceptable if both are used. Ignored if task_stage=False.check_infinite (
schrodinger.structure.Structure
) – Check the given structure to see if it is infinite. If it is, add the typical headers for the infinite systems. Ignored if task_stage=False.msj_string_header (when extra_task_text is empty, use this string as the header of the output msj) – str
remove_com_motion (bool) – None - default behavior, add remove_com_motion only to infinite atomic systems, if True add plugin to msj regardless. If False don’t add remove_com_plugin
- Return type
str
- Returns
The string that was written to the file
- class schrodinger.application.matsci.desconfig.MSJStringer(stype, last=False, use_base=True, **kwargs)¶
Bases:
object
A base class for setting up the information and generating a string describing that information for a stage in a Desmond MSJ file.
- DOT = '_dot_'¶
- MAX_STEPS = 'max_steps'¶
- TIME = 'time'¶
- TEMP = 'temperature'¶
- SEED = 'randomize_velocity.seed'¶
- PRESSURE = 'pressure'¶
- ENSEMBLE = 'ensemble'¶
- ENSEMBLE_CLASS = 'ensemble.class'¶
- ENSEMBLE_METHOD = 'ensemble.method'¶
- TIMESTEP = 'timestep'¶
- JOBNAME = 'jobname'¶
- CHECKPOINT = 'checkpt'¶
- DIR = 'dir'¶
- COMPRESS = 'compress'¶
- INTERVAL = 'trajectory_dot_interval'¶
- ENE_INTERVAL = 'eneseq_dot_interval'¶
- ANALYSIS_TYPE = 'analysis_type'¶
- OTHERS = 'othertag'¶
- TRJ_WRITE_VEL = 'trajectory_dot_write_velocity'¶
- RANDOMIZE_VEL = 'randomize_velocity_dot_first'¶
- ISOTROPY = 'backend_dot_integrator_dot_pressure_dot_isotropy'¶
- MSJ_BASE = {'checkpt': 'no', 'jobname': '"$MASTERJOBNAME"'}¶
- MSJ_LAST = {'compress': '""', 'dir': '"."'}¶
- LINE_ORDER = ['max_steps', 'analysis_type', 'time', 'timestep', 'ensemble', 'ensemble.class', 'ensemble.method', 'temperature', 'pressure', 'trajectory_dot_interval', 'randomize_velocity.seed', 'othertag', 'jobname', 'dir', 'compress', 'checkpt']¶
- KNOWN_LINES = {'analysis_type', 'checkpt', 'compress', 'dir', 'ensemble', 'ensemble.class', 'ensemble.method', 'jobname', 'max_steps', 'othertag', 'pressure', 'randomize_velocity.seed', 'temperature', 'time', 'timestep', 'trajectory_dot_interval'}¶
- SIMULATE = 'simulate'¶
- ANALYSIS = 'matsci_analysis'¶
- SYSBUILD = 'assign_forcefield'¶
- AVE_CELL = 'average_cell'¶
- EN_ANALYSIS = 'analysis'¶
- CONCATENATE = 'concatenate'¶
- FROZEN_PHONON_CORR = 'frozen_phonon_correction'¶
- SETTINGS = {'analysis': None, 'assign_forcefield': None, 'average_cell': None, 'concatenate': None, 'frozen_phonon_correction': None, 'matsci_analysis': None, 'simulate': <schrodinger.utils.sea.sea.Map object>}¶
- PADDING = ' '¶
- INDENT = ' '¶
- __init__(stype, last=False, use_base=True, **kwargs)¶
Create a MSJStringer object
- Parameters
stype (str) – The type of stage this is. Should be one of the class constants MINIMIZE, SIMULATE, SYSBUILD, ANALYSIS, or AVE_CELL
last (bool) – Whether the msj lines typically associated with the last stage (dir, compress) should be included
use_base (bool) – Whether the base msj lines (jobname, checkpoint) that are common to almost all stages should be included.
All other keyword arguments are turned into lines in the .msj file. Keys that have a ‘.’ in them should have that . replaced with the class constant string DOT (_dot_). For instance to include a line setting trajectory.write_velocity to true, use the keyword argument trajectory_dot_write_velocity=’true’
- createString(concatenate=False)¶
Create and return the string that represents this stage in the .msj file
- Parameters
concatenate (bool) – If True enable concatenate mode. In this mode, stage type is not printed
- Return type
str
- Returns
The msj string representing this stage
- formLine(key, value)¶
Create the line that should go in the .msj file for this key.
Subclasses should use this function to create custom strings for specific key values
- Parameters
key (str) – Typically, the string before the key = value pair on an msj line.
value (str) – Typically, the string after the key = value pair on an msj line.
- Return type
str
- Returns
The line (or lines) to put in the .msj file for this key/value pair
- getTitle()¶
This function returns a title for the stage describing the main parameters. The default implementation has no title.
- Return type
str
- Returns
The title for this stage
- class schrodinger.application.matsci.desconfig.AveCellMSJStringer(**kwargs)¶
Bases:
schrodinger.application.matsci.desconfig.MSJStringer
An MSJStringer class for post average cell stage.
- PERCENT_TO_AVG = 'percent_to_avg'¶
- __init__(**kwargs)¶
Create a MSJStringer object
- Parameters
stype (str) – The type of stage this is. Should be one of the class constants MINIMIZE, SIMULATE, SYSBUILD, ANALYSIS, or AVE_CELL
last (bool) – Whether the msj lines typically associated with the last stage (dir, compress) should be included
use_base (bool) – Whether the base msj lines (jobname, checkpoint) that are common to almost all stages should be included.
All other keyword arguments are turned into lines in the .msj file. Keys that have a ‘.’ in them should have that . replaced with the class constant string DOT (_dot_). For instance to include a line setting trajectory.write_velocity to true, use the keyword argument trajectory_dot_write_velocity=’true’
- getTitle()¶
This function returns a title for the stage describing the main parameters. The default implementation has no title.
- Return type
str
- Returns
The title for this stage
- class schrodinger.application.matsci.desconfig.AnalysisMSJStringer(**kwargs)¶
Bases:
schrodinger.application.matsci.desconfig.MSJStringer
An MSJStringer class for the analysis stage.
- __init__(**kwargs)¶
Create a MSJStringer object
- Parameters
stype (str) – The type of stage this is. Should be one of the class constants MINIMIZE, SIMULATE, SYSBUILD, ANALYSIS, or AVE_CELL
last (bool) – Whether the msj lines typically associated with the last stage (dir, compress) should be included
use_base (bool) – Whether the base msj lines (jobname, checkpoint) that are common to almost all stages should be included.
All other keyword arguments are turned into lines in the .msj file. Keys that have a ‘.’ in them should have that . replaced with the class constant string DOT (_dot_). For instance to include a line setting trajectory.write_velocity to true, use the keyword argument trajectory_dot_write_velocity=’true’
- class schrodinger.application.matsci.desconfig.FrozenPhononStringer(**kwargs)¶
Bases:
schrodinger.application.matsci.desconfig.MSJStringer
An MSJStringer class for the Frozen phonon correction stage.
- __init__(**kwargs)¶
Create a MSJStringer object
- Parameters
stype (str) – The type of stage this is. Should be one of the class constants MINIMIZE, SIMULATE, SYSBUILD, ANALYSIS, or AVE_CELL
last (bool) – Whether the msj lines typically associated with the last stage (dir, compress) should be included
use_base (bool) – Whether the base msj lines (jobname, checkpoint) that are common to almost all stages should be included.
All other keyword arguments are turned into lines in the .msj file. Keys that have a ‘.’ in them should have that . replaced with the class constant string DOT (_dot_). For instance to include a line setting trajectory.write_velocity to true, use the keyword argument trajectory_dot_write_velocity=’true’
- class schrodinger.application.matsci.desconfig.MDMSJStringer(time=None, temp=None, pressure=None, random_seed=None, ensemble='NPT', method=None, timestep=None, last=False, **kwargs)¶
Bases:
schrodinger.application.matsci.desconfig.MSJStringer
An MSJStringer class for Molecular Dynamics stages
- __init__(time=None, temp=None, pressure=None, random_seed=None, ensemble='NPT', method=None, timestep=None, last=False, **kwargs)¶
Create a MDMSJStringer object
Any keyword that does not have a value supplied will use the default Desmond value for MD simulations.
- Parameters
time (float) – Time in picoseconds
temp (float) – Temperature in Kelvin
pressure (float) – The pressure in bar
random_seed (int) – The seed for the random number generator
ensemble (str) – Valid Desmond ensemble such as NPT, NVT
method (str) – Valid Desmond ensemble method such as NH, Berendson, Langevin
timestep (int or float or str or list) – The timestep in picoseconds. If a string, will be treated as a float if it converts to float without error, otherwise it is used directly so must be in the proper [ x y z ] format used in .msj and .cfg files. If float or int, a string of the following format will be generated [ timestep timestep timestep * 3. ] If a list, the items will be converted to a string list of [ x y z ]
last (bool) – Whether the msj lines typically associated with the last stage (dir, compress) should be included
All other keyword arguments are turned into lines in the .msj file. See parent class for additional information.
- getTitle()¶
Return a title for the stage describing the main parameters.
- Return type
str
- Returns
The title for this stage
- class schrodinger.application.matsci.desconfig.MSAnalysisMSJStringer(analysis_type=None, **kwargs)¶
Bases:
schrodinger.application.matsci.desconfig.MSJStringer
An MSJStringer class for MS MD Analysis stages
- __init__(analysis_type=None, **kwargs)¶
Create a MSAnalysisMSJStringer object
Any keyword that does not have a value supplied will use the default Desmond value for MD simulations.
- Parameters
analysis_type (str) – A string in the form of [ property property ] that lists the properties to be computed in the analysis.
All other keyword arguments are turned into lines in the .msj file. See parent class for additional information.
- getTitle()¶
Return a title for the stage describing the main parameters.
- Return type
str
- Returns
The title for this stage
- class schrodinger.application.matsci.desconfig.BrownieMSJStringer(time=100.0, temp=10.0, ensemble='NVT', timestep='[ 0.001 0.001 0.003 ]', delta_max=0.1, btau=None, ttau=None, **kwargs)¶
Bases:
schrodinger.application.matsci.desconfig.MDMSJStringer
An MSJStringer class for Brownie stages
- __init__(time=100.0, temp=10.0, ensemble='NVT', timestep='[ 0.001 0.001 0.003 ]', delta_max=0.1, btau=None, ttau=None, **kwargs)¶
Create a BrownieMSJStringer object
Desmond config does not have a specific set of defaults for Brownie stages, so the defaults are supplied here for all keywords.
- Parameters
delta_max (float) – The value of delta_max
btau (float) – The value of the barostat tau
ttau (float) – The value of the thermostat tau
See parent class for additional information.
- getTitle()¶
Return a title for the stage describing the main parameters.
- Return type
str
- Returns
The title for this stage
- class schrodinger.application.matsci.desconfig.SysbuildMSJStringer(forcefield='OPLS_2005', compress='""', **kwargs)¶
Bases:
schrodinger.application.matsci.desconfig.MSJStringer
An MSJStringer class for building systems
- __init__(forcefield='OPLS_2005', compress='""', **kwargs)¶
Create a SysbuildMSJStringer object
- Parameters
forcefield (str) – The forcefield to use
All other keyword arguments are turned into lines in the .msj file. See parent class for additional information.
- class schrodinger.application.matsci.desconfig.ConcatMSJStringer(**kwargs)¶
Bases:
schrodinger.application.matsci.desconfig.MSJStringer
An MSJStringer class for the concatenate stage.
- STAGES = 'stages'¶
- __init__(**kwargs)¶
Create a MSJStringer object
- Parameters
stype (str) – The type of stage this is. Should be one of the class constants MINIMIZE, SIMULATE, SYSBUILD, ANALYSIS, or AVE_CELL
last (bool) – Whether the msj lines typically associated with the last stage (dir, compress) should be included
use_base (bool) – Whether the base msj lines (jobname, checkpoint) that are common to almost all stages should be included.
All other keyword arguments are turned into lines in the .msj file. Keys that have a ‘.’ in them should have that . replaced with the class constant string DOT (_dot_). For instance to include a line setting trajectory.write_velocity to true, use the keyword argument trajectory_dot_write_velocity=’true’
- formLine(key, value)¶
Create the line that should go in the .msj file for the ‘stages’ key. Parent function creates strings for all other keys.
- Parameters
key (str) – Typically, the string before the key = value pair on an msj line.
value (str) – Typically, the string after the key = value pair on an msj line.
- Return type
str
- Returns
The line (or lines) to put in the .msj file for this key/value pair
- schrodinger.application.matsci.desconfig.get_materials_relaxation_stringers(temp=300.0, compress_last=True, pressure_isotropy='anisotropic')¶
Get a list of Stringer objects that reproduce the Materials Relaxation protocol
- Parameters
temp (float) – The temperature for the last of the three stages
compress_last (bool) – If true, compress the last stage - the trajectory will not be available except as part of the tgz file. If False, the last stage will not be compressed and the trajectory will be available.
pressure_isotropy (str) – Barostat coupling between x, y, and z.
- Return type
list
- Returns
Each item of the list is a stage in the Materials Relaxation protocol
- schrodinger.application.matsci.desconfig.get_semicrystalline_relaxation1_stringers(temp=300.0, compress_last=True, pressure_isotropy='anisotropic')¶
Get a list of Stringer objects that reproduce first Semi-Crystalline protocol
- Parameters
temp (float) – The temperature for the last of the three stages
compress_last (bool) – If true, compress the last stage - the trajectory will not be available except as part of the tgz file. If False, the last stage will not be compressed and the trajectory will be available.
pressure_isotropy (str) – Barostat coupling between x, y, and z.
- Return type
list
- Returns
Each item of the list is a stage in the first Semi-Crysatlline relaxation protocol
- schrodinger.application.matsci.desconfig.get_semicrystalline_relaxation2_stringers(temp=300.0, compress_last=True, pressure_isotropy='anisotropic')¶
Get a list of Stringer objects that reproduce second Semi-Crystalline Relaxation protocol
- Parameters
temp (float) – The temperature for the last of the three stages
compress_last (bool) – If true, compress the last stage - the trajectory will not be available except as part of the tgz file. If False, the last stage will not be compressed and the trajectory will be available.
pressure_isotropy (str) – Barostat coupling between x, y, and z.
- Return type
list
- Returns
Each item of the list is a stage in the second Semi-Crysatlline relaxation protocol
- schrodinger.application.matsci.desconfig.get_compressive_relaxation_stringers(temp=300.0, compress_last=True, pressure_isotropy='anisotropic')¶
Get a list of Stringer objects that reproduce the compressive relaxation protocol
- Parameters
temp (float) – The temperature for the last of the three stages
compress_last (bool) – If true, compress the last stage - the trajectory will not be available except as part of the tgz file. If False, the last stage will not be compressed and the trajectory will be available.
pressure_isotropy (str) – Barostat coupling between x, y, and z.
- Return type
list
- Returns
Each item of the list is a stage in the compressive Relaxation protocol
- schrodinger.application.matsci.desconfig.get_ladder_polymer_relaxation_stringers(pressure=1.01325, timestep=0.001)¶
Get a list of Stringer objects that reproduce the ladder polymer relaxation protocol (larsen relaxation protocol).
- Parameters
pressure (float) – maximum value of pressue
timestep (int or float or str or list) – The timestep in picoseconds.
- Return type
list
- Returns
Each item of the list is a stage in the Larsen Relaxation protocol
- schrodinger.application.matsci.desconfig.has_concatenated_stage(msjdata)¶
Check if the MSJData contains at least one concatenated stage.
- Parameters
msjdata (sea.Map) – The MSJData object to be checked
- Return type
bool
- Returns
True if the MSJData object contains concatenated stages, else False
- schrodinger.application.matsci.desconfig.expand_concatenated_stages(msjdata)¶
Remove concatenation from the MSJData. Search for concatenated simulation stages in the MSJData object and expand them.
- schrodinger.application.matsci.desconfig.get_cfg_names_from_msj_data(data)¶
An iterator that yields the index, stage map and cfg file name for each stage in the given data that has a cfg file associated with it
- Parameters
data (schrodinger.utils.sea.Map) – The data for all stages.
- Raises
ValueError – If the data contains concatenated stages.
- Return type
int,
schrodinger.utils.sea.Map
, str- Returns
(The stage index, the Map containing the stage data, and the name of the CFG file for that stage)
- schrodinger.application.matsci.desconfig.get_cfg_names_from_msj_file(path)¶
An iterator that yields the index, stage map and cfg file name for each stage in the given a msj that has a cfg file associated with it
- Parameters
path (str) – The path to the msj file.
- Return type
int,
schrodinger.utils.sea.Map
, str- Returns
(The stage index, the Map containing the stage data, and the name of the CFG file for that stage)
- schrodinger.application.matsci.desconfig.verify_cfg_files_exist(path)¶
Verify that the cfg files referenced in an msj file are present
- Parameters
path (str) – The path to the msj file. cfg files will be searched for in the same directory.
- Return type
list
- Returns
Each item of the list is a name of a required cfg file
- Raises
FileNotFoundError – If any of the cfg files do not exist in the same directory
- schrodinger.application.matsci.desconfig.copy_msj_and_cfg(path, destination_dir='.')¶
Copy the specified msj file and any associated cfg files into the given directory
- Parameters
path (str) – The path to the msj file
destination_dir (str) – The directory to copy the files to
- Return type
list
- Returns
Each item of the list is the name (not path) of a file that was copied, including the msj and any cfg files
- Raises
FileNotFoundError – If any of the files are not found
- schrodinger.application.matsci.desconfig.get_plane_trans_cart_to_frac(coord, direction, a_vec, b_vec, c_vec, rec=False)¶
Transform a plane defined by (coord, direction) from Cartesian ( reciprocal) to reciprocal(cartesian) coordinates.
- Parameters
coord (float) – a float number defining the position of the plane in the direction vector
direction (float) – a float number defining the direction of the plane. 0, 1, 2 corresponds to x, y, z respectively
a_vec (list of 3 floats) – ‘a’ lattice vector
b_vec (list of 3 floats) – ‘b’ lattice vector
c_vec (list of 3 floats) – ‘c’ lattice vector
rec (bool) – If True, work in reciprocal space
- schrodinger.application.matsci.desconfig.add_barrier_to_msj(struct, msj_str)¶
Add barrier information to MSJ task stage
- Parameters
struct (schrodinger.structure.Structure) – The structure object
msj_str (str) – The string representation of the MSJ stages
- Return type
str
- Returns
The update msj string with barrier information