schrodinger.application.desmond.mdkey module

Functions for initializing, reading, and writing Desmond parameters.

This is also where global variables that are shared among different tabs are defined.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.mdkey.AtomGroup(name)

Bases: object

class schrodinger.application.desmond.mdkey.CfgAtom(s)

Bases: object

This class represents the “atomic” parameters in a config file. Atomic parameters do not contain further sub-elements. For example, ‘force.type’ is an atomic parameter, whereas ‘force’ is not because it has sub-elements like ‘type’, ‘gibbs’, etc.

Public attributes:

• validate - None by default. This attribute can be set to be a callable object that assesses whether a given value is legal or not for this ‘CfgAtom’ object. The callable object should be able to take one argument – the value subject to its assessment and returns

  either True (if the value is OK) or False (if the value is illegal).

Properties:

• val - This is a read-write property for accessing the value of this ‘CfgAtom’ object.

backup()

Internally makes a copy of the current value. This internal copy can be used later on to recover the value if the value was changed unwantedly.

clearUmarker(umarker)

expand_macro(macro_dict)

This method will replace all occurences (in the value) of each key (in ‘macro_dict’) to the corresponding value. It has effect only for string type of values.

For example, if the value is '$JOBNAME on $DATE', then with a ‘macro_dict’ of {'$JOBNAME' : 'my_jobname', '$DATE' : 'Oct. 10, 2007'}, this method will change the value to 'my_jobname on Oct. 10, 2007'.

Parameters:macro_dict – Should be dictionary, e.g., {'$JOBNAME' : 'my_jobname', '$DATE' : 'Oct. 10, 2007'}.

isChanged()

Compares the value with the internal copy, and returns True if there is difference or False otherwise.

recover_macro()

This is usually called after an expand_macro call and recovers the value to the original macro-containing form.

For example, if the value is changed (by expand_macro) from '$JOBNAME on $DATE' to 'my_jobname on Oct. 10, 2007', then a call to this function will restore the value to '$JOBNAME on $DATE'.

rollback()

Recovers the value to the internal copy of the value. The internal copy of the value was made by the last call to the ‘backup’ function.

update(val, umarker=None)

Updates the value with ‘val’, which is exactly the same as setting the value via the ‘val’ property.

If the public attribute ‘validate’ is not None, then after the conversion the value will be sent to the callable object as pointed by the ‘validate’ attribute for assessment. If the assessment returns True, the value will be set; otherwise it is discarded.

Parameters:val – Can be any object as long as it can be converted to the internal type of the value via the _convert method. If ‘val’ cannot be converted, it is ignored.

val

Readwrite. When read, this returns the current value.

work_val(macro_dict)

class schrodinger.application.desmond.mdkey.FepSchedule(n_win, fep_type)

Bases: object

get_lambda()

class schrodinger.application.desmond.mdkey.GuiMap

BAROSTAT_MAP = {'None': 'MTK_NPT', 'V_NVE': 'None', 'Langevin': 'L_NPT', 'L_NVT': 'None', 'L_NPT': 'Langevin', 'Berendsen': 'Ber_NPT', 'Ber_NPT': 'Berendsen', 'NH_NVT': 'None', 'Ber_NVT': 'None', 'MTK_NPT': 'Martyna-Tobias-Klein', 'Martyna-Tobias-Klein': 'MTK_NPT'}

THERMOSTAT_MAP = {'None': 'NH_NVT', 'Langevin': 'L_NVT', 'L_NVT': 'Langevin', 'L_NPT': 'Langevin', 'V_NVE': 'None', 'Ber_NPT': 'Berendsen', 'Nose-Hoover': 'NH_NVT', 'Berendsen': 'Ber_NVT', 'Ber_NVT': 'Berendsen', 'MTK_NPT': 'Nose-Hoover', 'NH_NVT': 'Nose-Hoover'}

class schrodinger.application.desmond.mdkey.Key(cfg='{nDesmond = {n config_version = 2n}nglobal_cell = {n reference_time = 0.0n topology = periodicn n_replica = 1n partition = [2 2 2]n r_clone = 5.903366n clone_policy = roundedn #est_pdens = 0.1n est_n_atom_per_voxel = 1.0n}nremd = {n # Parameters that are absent in 'mdsim'.n first = 120.0n interval = 12.0n type = 0 # exchange strategy; 0=neighbors, 1=randomn seed = 2008 # random number seedn #cfg = ["" "" "" "" "" "" "" ""]nn title = "Desmond Replica Exchange Simulation"n last_time = 1200.0 # In psn #n plugins = [status randomize_velocities eneseq trajectory maeff_output maeff_snapshot simbox_output]n #n status.first = 0.0n status.interval = 0.3n #n eneseq.name = "system.ene"n eneseq.first = 0.0n eneseq.interval = 1.2n #n trajectory.name = "trj"n trajectory.write_velocity = truen trajectory.first = 0.0n trajectory.interval = 4.8n trajectory.periodicfix = truen trajectory.frames_per_file= 250n #n checkpt.name = "checkpt.cpt"n checkpt.first = 0.0n checkpt.interval = 240.0n checkpt.write_last_step = truen #n maeff_output = {n first = 0.0n interval = 120.0n name = ""n write_last_step = truen periodicfix = truen precision = 8n full_system_only = falsen trjdir = ""n }n #n maeff_snapshot = {n name = ""n first = 0.0n interval = 1.2n }n #n randomize_velocities = {n first = 0.0n interval = infn seed = 2007n temperature = 300.0n remove_com_motion = truen }n #n simbox_output = {n name = ""n first = 0.0n interval = 1.2n }n energy_groups = {n name = ""n first = 0.0n interval = 1.2n }n}nmdsim = {n title = "Desmond Simulation"n #first_step = 0 # Probably ignored by Desmondn last_time = 1200.0 # In psn #n plugins = [status randomize_velocities eneseq trajectory maeff_output maeff_snapshot simbox_output]n #n anneal = {n first = 0.0n interval = 0.03n schedule = {n time = [0.0 30.0 60.0 90.0 600.0]n value = [0.0 300.0 600.0 900.0 300.0]n }n }n #n status.first = 0.0n status.interval = 0.3n #n eneseq.name = "system.ene"n eneseq.first = 0.0n eneseq.interval = 1.2n #n trajectory.name = "trj"n trajectory.write_velocity = truen trajectory.first = 0.0n trajectory.interval = 4.8n trajectory.periodicfix = truen trajectory.frames_per_file= 250n #n checkpt.name = "checkpt.cpt"n checkpt.first = 0.0n checkpt.interval = 240.0n checkpt.write_last_step = truen #n maeff_output = {n first = 0.0n interval = 120.0n name = ""n write_last_step = truen periodicfix = truen precision = 8n full_system_only = falsen trjdir = ""n }n #n maeff_snapshot = {n name = ""n first = 0.0n interval = 1.2n }n #n randomize_velocities = {n first = 0.0n interval = infn seed = 2007n temperature = 300.0n remove_com_motion = truen }n #n simbox_output = {n name = ""n first = 0.0n interval = 1.2n }n energy_groups = {n name = ""n first = 0.0n interval = 1.2n }n}nconstraint = {n type = mshake # mshake | nonen tol = 1e-08n maxit = 8n}nforce = {n type = desmond # desmond | gibbsn #bonded_terms = [stretch angle dihedral improper pair cmap posre]n nonbonded = {n type = vdw-elec # nonen r_lazy = 11.807732n r_cut = 9.0n r_tap = 9.0n n_zone = 1024n taper = nonen #average_dispersion = 69.5 # In kcal/mol A^6. If not set, it will be caculated by Desmond.n far = {n type = pme # none | pme | gsen sigma = 2.791856n sigma_s = 0.85n r_spread = 4.0n n_k = [16 16 16]n order = [4 4 4]n }n }n gibbs = {n fec_type = none # none | alchemical | ligand_bindingn alpha_vdw = 0.5n i_window = -1n n_windows = 12n lambda = {n vdw = [0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0 1.0 1.0 1.0]n vdwA = [0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0 1.0 1.0 1.0]n vdwB = [0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0 1.0 1.0 1.0]n coulomb = [0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 0.0 0.0 0.0 0.0]n chargeA = [1.0 0.67 0.33 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0]n chargeB = [0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.33 0.67 1.0]n bonded = [0.0 0.125 0.25 0.375 0.5 0.5 0.5 0.5 0.625 0.75 0.875 1.0]n bondedA = [0.0 0.125 0.25 0.375 0.5 0.5 0.5 0.5 0.625 0.75 0.875 1.0]n bondedB = [0.0 0.125 0.25 0.375 0.5 0.5 0.5 0.5 0.625 0.75 0.875 1.0]n }n output = {n name = "fep.dE"n first = 0.0n interval = 0.1n }n }n}nintegrator = {n type = MTK_NPT # Ber_NPT | Ber_NVT | MTK_NPT | NH_NVT | V_NVE | L_NVT | L_NPTn dt = 0.002n temperature = [{T_ref = 300.0 groups = [0]}]n freeze = truen center_frozen_group = truen remove_com_motion = falsen migrate.first = 0.0n migrate.interval = 0.012n respa = {n bonded_interval = 1n nonbonded_near_interval = 1n nonbonded_far_interval = 3n }n pressure = {n isotropy = isotropic # anisotropic constant_area isotropic semi_isotropicn max_margin_contraction = 0.9n #compressibility = [4.5e-05 0.0 0.0 0.0 4.5e-05 0.0 0.0 0.0 4.5e-05]n #p_ref = [1.01325 0.0 0.0 0.0 1.01325 0.0 0.0 0.0 1.01325]n p_ref = 1.01325n }n anneal = {n type = Ber_NVTn MTK_NPT = {n barostat = {n tau = 2.0n T_ref = 300.0n thermostat = {n mts = 2n tau = [1.0 1.0 1.0 ]n }n }n thermostat = [n { mts = 2n tau = [1.0 1.0 1.0 ] }n ]n }n NH_NVT = {n thermostat = [n { mts = 2n tau = [1.0 1.0 1.0 ] }n ]n }n Ber_NPT = {n tau = [1.0]n min_velocity_scaling = 0.85n max_velocity_scaling = 1.2n barostat = {n tau = 2.0n kappa = 4.5e-05n min_contraction_per_step = 0.95n max_expansion_per_step = 1.1n }n }n Ber_NVT = {n tau = [1.0]n min_velocity_scaling = 0.85n max_velocity_scaling = 1.2n }n L_NVT = {n thermostat = {n tau = 0.016129 # Gamma = 1/tau = 62 is default.n seed = 2007n }n }n L_NPT = {n thermostat = {n tau = 0.016129 # Gamma = 1/tau = 62 is default.n seed = 2007n }n barostat = {n tau = 1.0n T_ref = 300.0n thermostat = {n tau = 0.016129n seed = 2007n }n }n }n Piston_NPH = {n barostat = {n tau = 1.0n T_ref = 300.0n }n }n V_NVE = {}n }n MTK_NPT = {n barostat = {n tau = 2.0n T_ref = 300.0n thermostat = {n mts = 2n tau = [1.0 1.0 1.0 ]n }n }n thermostat = [n { mts = 2n tau = [1.0 1.0 1.0 ] }n ]n }n NH_NVT = {n thermostat = [n { mts = 2n tau = [1.0 1.0 1.0 ] }n ]n }n Ber_NPT = {n tau = [1.0]n min_velocity_scaling = 0.85n max_velocity_scaling = 1.2n barostat = {n tau = 2.0n kappa = 4.5e-05n min_contraction_per_step = 0.95n max_expansion_per_step = 1.1n }n }n Ber_NVT = {n tau = [1.0]n min_velocity_scaling = 0.85n max_velocity_scaling = 1.2n }n L_NVT = {n thermostat = {n tau = 0.016129 # Gamma = 1/tau = 62 is default.n seed = 2007n }n }n L_NPT = {n thermostat = {n tau = 0.016129 # Gamma = 1/tau = 62 is default.n seed = 2007n }n barostat = {n tau = 1.0n T_ref = 300.0n thermostat = {n tau = 0.016129n seed = 2007n }n }n }n Piston_NPH = {n barostat = {n tau = 1.0n T_ref = 300.0n }n }n V_NVE = {}n}nn#nboot.file = ""nn# For minimizationnminimize = {n m = 3 # Number of L-BFGS vectors to usen maxsteps = 200 # Max number of iterationsn tol = 1.0 # Converging criteria for gradient norm (kcal/mol)n stepsize = 0.005 # Norm of first stepn switch = 25.0 # Minimal gradient norm before switching to LBFGS (kcal/mol)n sdsteps = 10 # Min number of initial SD stepsn #n plugins = [maeff_output]n #n #status.first = 0.0n #status.interval = 1.0n #n eneseq.name = "system.ene"n eneseq.first = 0.0n eneseq.interval = 1.2n #n trajectory.name = "trj"n trajectory.write_velocity = falsen trajectory.first = 0.0n trajectory.interval = 10.0n trajectory.frames_per_file= 250n #n checkpt.name = "checkpt.cpt"n checkpt.first = 0.0n checkpt.interval = 60.0n #n maeff_output = {n first = infn interval = infn name = ""n write_last_step = truen periodicfix = truen precision = 8n full_system_only = falsen trjdir = ""n }n #n maeff_snapshot = {n name = ""n first = 0.0n interval = 1.0n }n}nn# For GUI onlyngui = {n sim_task = "Molecular dynamics"n integrator = "RESPA"n remd.temperature = [300.0 350.0 400.0 450.0 500.0 600.0 700.0 800.0]n remd.scheme = 2 # 2 = quadratic, 1 = linear, 0 = manually setn selected_lambda_win = [0 1 2 3 4 5 6 7 8 9 10 11]n should_autoset_fep = truen should_selall_fep = truen should_autoset_respa = truen should_autoset_coeff = truen should_relax = truen should_glue = truen relax_prot_file = ""n max_cutoff = 30.0n ewald_tol = 1E-9n thermostat = Nose-Hoover # Berendsen | Nose-Hoover | Langevin | Nonen barostat = Martyna-Tobias-Klein # Berendsen | Martyna-Tobias-Klein | Langevin | Nonen tension_ref = 4E3n box = [64.0 0.0 0.0 0.0 64.0 0.0 0.0 0.0 64.0] # Ignored by the Desmond; overwritten by data in .cms.n JOBNAME = ""n}nn# Macrosndesmond_macro = {n force.gibbs.output.name = "$JOBNAME.$LAMBDA.dE"n remd = {n title = "Desmond Replica Exchange Simulation - $JOBNAME"n eneseq.name = "$JOBNAME_replica$REPLICA.ene"n trajectory.name = "$JOBNAME_replica$REPLICA_trj"n checkpt.name = "$JOBNAME.cpt"n maeff_output.name = "$JOBNAME_replica$REPLICA-out.cms"n maeff_output.trjdir = "$JOBNAME_replica$REPLICA_trj"n maeff_snapshot.name = "$JOBNAME_replica$REPLICA_mon.maegz"n simbox_output.name = "$JOBNAME_replica$REPLICA_simbox.dat"n energy_groups.name = "$JOBNAME_replica$REPLICA_enegrp.dat"n }n mdsim = {n title = "Desmond Simulation - $JOBNAME"n eneseq.name = "$JOBNAME.ene"n trajectory.name = "$JOBNAME_trj"n checkpt.name = "$JOBNAME.cpt"n maeff_output.name = "$JOBNAME-out.cms"n maeff_output.trjdir = "$JOBNAME_trj"n maeff_snapshot.name = "$JOBNAME_mon.maegz"n simbox_output.name = "$JOBNAME_simbox.dat"n energy_groups.name = "$JOBNAME_enegrp.dat"n }n minimize = {n eneseq.name = "$JOBNAME.ene"n trajectory.name = "$JOBNAME_trj"n checkpt.name = "$JOBNAME.cpt"n maeff_output.name = "$JOBNAME-out.cms"n maeff_snapshot.name = "$JOBNAME_mon.maegz"n #maeff_output.trjdir = "$JOBNAME_trj"n }n}nn}')

Bases: object

INDEX_PATTERN = <_sre.SRE_Pattern object>

KEYMAP_CFG2MY = {'lambda': 'lambda_'}

KEYMAP_MY2CFG = {'lambda_': 'lambda'}

addKey(key, val)

backup()

clearUmarker(umarker=None)

clone(orig)

delKey(key)

expand_macro(macro_dict)

getKey(key_str)

inject_macro()

isChanged()

param(umarker=None)

recover_macro()

rollback()

update(cfg=None, file=None, umarker=None)

class schrodinger.application.desmond.mdkey.List(*arg, **kwarg)

Bases: list

clearUmarker(umarker)

schrodinger.application.desmond.mdkey.add_plugin(key, plugin_name, position=None)

schrodinger.application.desmond.mdkey.check_key(key, valid=<schrodinger.application.desmond.mdkey.Key object>, ev=None, prefix='')

schrodinger.application.desmond.mdkey.check_key2(key, valid)

schrodinger.application.desmond.mdkey.clean_struc(struc)

For each ‘Structure’ ojbect in ‘struct’, this function removes the ‘_ffh’ attribute of the member object and frees the memory as held by ‘_ffh’. This “cleaning up” may be necessary for the ‘Structure’ objects to be garbage-collected.

Parameters:struc – A list of schrodinger.structure.Structure objects.

schrodinger.application.desmond.mdkey.compare_atom_group(grp1, grp2, group_selector=<function _default_group_selector>)

Compares two given atom groups ‘grp1’ and ‘grp2’, and returns True if they are the same or False if they are not.

Both ‘grp1’ and ‘grp2’ should be lists of AtomGroup objects.

Note that empty groups are ignored in the comparison.

schrodinger.application.desmond.mdkey.compare_restr_grp(grp1, grp2)

Compares two given restraint groups ‘grp1’ and ‘grp2’, and returns True if they are the same or False if they are not.

Both ‘grp1’ and ‘grp2’ should be lists of ‘AtomGroup’ objects. Note that each ‘AtomGroup’ object’s ‘name’ attribute should be the restraint force constant of the ‘float’ type.

Note that any group with a force constant of 0.0 will be ignored as it does not have any effects on the actual simulation. This means if the atom sets of two groups are different but their force constants are 0.0, then this is not considered as a real difference. Also note that empty groups are ignored in the comparison.

schrodinger.application.desmond.mdkey.condense_atom_group(grp, group_selector)

schrodinger.application.desmond.mdkey.crossprod(v, u)

Returns the cross product of two 3-D vectors.

schrodinger.application.desmond.mdkey.del_all_atom_grp(struc)

schrodinger.application.desmond.mdkey.diff(x, reference)

schrodinger.application.desmond.mdkey.dotprod(v, u)

Returns the dot product of two 3-D vectors.

schrodinger.application.desmond.mdkey.fep_schedule(n_win, fep_type='alchemical')

Returns a FEP schedule, which is calculated for the given FEP type (‘fep_type’).

Parameters:fep_type – Can take the following values: “alchemical”, “ligand_binding”.

schrodinger.application.desmond.mdkey.gen_key(file=None, raise_exception=False)

Returns a Key object that is constructed based on ‘DEFAULT_CONFIG’ (see above) and the default config file that is saved in the directory as given by ‘DEFAULT_CONFIG_FILE’ (see above).

If the default config file is found, the values there will be used to update those as in ‘DEFAULT_CONFIG’.

schrodinger.application.desmond.mdkey.get_asl(raw_grp)

Returns an ASL string for a given group of atoms (‘raw_grp’).

Parameters:raw_grp – Must be an iterable of 2-element tuples. The first element of the tuple is the entry ID, the second is the atom ID within the entry.

schrodinger.application.desmond.mdkey.get_atom_grp(struc)

schrodinger.application.desmond.mdkey.get_box(struc)

Given a list of CTs, return None if something is wrong, or a tuple of (size_x, size_y, size_z, (9-element list for box matrix)).

This function will check the consistency of the simulation-box data through all CTs.

Parameters:struc – A list of schrodinger.structure.Structure objects.

schrodinger.application.desmond.mdkey.get_boxsize(box)

Given a simulation box in the form of a 3x3 matrix, this function returns the size of the box.

schrodinger.application.desmond.mdkey.get_boxvolume(box)

schrodinger.application.desmond.mdkey.get_clone_xyz(r_clone, homebox_volume, homebox_size)

schrodinger.application.desmond.mdkey.get_homebox(box, cpu_top)

schrodinger.application.desmond.mdkey.get_model_system_type(struc)

Returns 1 if the CTs in ‘struc’ have a fepio_fep block. Returns 2 if the CTs in ‘struc’ have a non-empty ligand atom group and do not have an fepio_fep block. Returns 0 otherwise.

Parameters:struc – A list of schrodinger.structure.Structure objects.

schrodinger.application.desmond.mdkey.get_restr(struc)

schrodinger.application.desmond.mdkey.get_restr2(struc)

• This differs from ‘get_restr’ in that this one get the complete restraint information whereas ‘get_restr’ does not get the atom coordinates and assumes that the force constants are the same for x, y, and z directions.

schrodinger.application.desmond.mdkey.has_fepio(struc)

Returns True if any of the Structures in ‘struc’ have a fepio_fep block, or False if they do not.

Parameters:struc – A list of schrodinger.structure.Structure objects.

schrodinger.application.desmond.mdkey.has_mmffio(ct)

Returns 1 if ‘ct’ has an mmffio block, or 0 if it does not.

schrodinger.application.desmond.mdkey.has_plugin(key, plugin_name)

schrodinger.application.desmond.mdkey.inject_atom_grp(struc, atom_grp)

schrodinger.application.desmond.mdkey.inject_restr(struc, restr_grp)

schrodinger.application.desmond.mdkey.is_powerof2(x)

Returns True if ‘x’ is a power of 2, or False otherwise.

schrodinger.application.desmond.mdkey.is_triclinic_box(box)

schrodinger.application.desmond.mdkey.merge_restr2(ct, restr, k, atom_list)

schrodinger.application.desmond.mdkey.norm(v)

Returns the norm of the 3-D vector ‘v’.

schrodinger.application.desmond.mdkey.optimize_key(key, n_k=None, should_retry=True, num_atom=None, grid=1.2)

Optimizes the simulation parameters in ‘key’, where ‘key’ must represent a complete config file.

schrodinger.application.desmond.mdkey.prep_struc(struc)

This function does the following mutations to each element of ‘struc’:

1. It adds a pointer to the the ffio block. This pointer is saved

   into the ‘Structure’ object as the ‘_ffh’ attribute.

2. Second, it removes the ffio block from the CT. This treatment is

   necessary for use of a few functions below (specifically, calc_average_vdw_coeff, inject_restr, set_restr_block).

Parameters:struc – A list of schrodinger.structure.Structure objects.

schrodinger.application.desmond.mdkey.reg_xcheck(name, func)

schrodinger.application.desmond.mdkey.remove_plugin(key, plugin_name)

schrodinger.application.desmond.mdkey.resize_restr_block(ffh, size)

Resizes the “ffio_restraints” block, i.e., changes the number of entries of the block.

What will happen?

• If the new size is the same as the existing size, nothing changes.
• If the new size is smaller, the entries at the end of the block will be deleted.
• If the new size is larger, new entries will be appended. These new entries will have undetermined values.

Parameters:

• ffh – The handle of the ffio block.
• size – The wanted size of the restraint block.

schrodinger.application.desmond.mdkey.restr_grp_selector(grp)

schrodinger.application.desmond.mdkey.set_farterm(key)

Optimizes the parameters of the far term of the Coulombic potential.

schrodinger.application.desmond.mdkey.set_restr(ffh, i, k, i_atom, x, y, z)

schrodinger.application.desmond.mdkey.set_restr2(struc, restr)

schrodinger.application.desmond.mdkey.set_restr_block(ct, restr)