IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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nonspecific methods used across all shared function objects. More...
nonspecific methods used across all shared function objects.
Rules:
Definition at line 125 of file shared_functions.py.
Public Member Functions | |
def | do_md_protein_statistics |
updates statistics for md simulation: target temp, kinetic energy, kinetic temperature, writes coordinates and increments counter. More... | |
def | find_atom |
scans the prot hierarchy and tries to find atom = (resno, name) assumes that resno follows the same numbering as the sequence. More... | |
def | get_pdb |
returns a string corresponding to the pdb structure of hierarchy prot. More... | |
def | init_model_ambiguous_NOE_restraint |
Reads an ambiguous NOE restraint. More... | |
def | init_model_base |
moves to wd and creates model More... | |
def | init_model_charmm_protein_and_ff |
creates a CHARMM protein representation. More... | |
def | init_model_conjugate_kappa |
given a list of scales, returns a RestraintSet('prior') with weight 1.0 that contains a list of vonMisesKappaConjugateRestraint on each scale. More... | |
def | init_model_HBonds_marginal |
read TBL file and store lognormal restraints, using the marginal of the lognormal with one sigma and gamma=1, for the whole dataset. More... | |
def | init_model_jeffreys |
given a list of scales, returns a RestraintSet('prior') with weight 1.0 that contains a list of JeffreysRestraint on each scale. More... | |
def | init_model_jeffreys_kappa |
given a list of scales, returns a RestraintSet('prior') with weight 1.0 that contains a list of vonMisesKappaJeffreysRestraint on each scale. More... | |
def | init_model_NOE_restraint |
Sets up a lognormal distance restraint using the given sigma and gamma. More... | |
def | init_model_NOEs |
read TBL file and store NOE restraints, using one sigma and one gamma for the whole dataset. More... | |
def | init_model_NOEs_marginal |
read TBL file and store NOE restraints, using the marginal of the lognormal with one sigma and one gamma, for the whole dataset. More... | |
def | init_model_setup_scale |
sets up a Scale particle to the initial default value. More... | |
def | init_model_standard_SAXS_restraint |
read experimental SAXS profile and apply restraint the standard way (like foxs) Returns: a restraintset and the experimental profile More... | |
def | init_model_TALOS |
read TALOS dihedral angle data, and create restraints for phi/psi torsion angles, along with the prior for kappa, which is a scale for the whole dataset, compare to 1/sigma**2 in the NOE case. More... | |
def | init_model_vonMises_restraint_full |
Sets up a vonMises torsion angle restraint using the given kappa particle as concentration parameter. More... | |
def | init_model_vonMises_restraint_mean |
Sets up a vonMises torsion angle restraint using the given kappa particle as concentration parameter. More... | |
def | init_simulation_setup_nuisance_mc |
sets up monte carlo on nuisance, at a certain target temperature, optionally using a certain set of restraints only. More... | |
def | init_simulation_setup_protein_hmc_hopper |
setup hybrid monte-carlo on protein. More... | |
def | init_simulation_setup_protein_hmc_nve |
setup hybrid monte-carlo on protein. More... | |
def | init_stats_add_hmc_category |
shortcut for a frequent series of operations on HMC simulations' statistics. More... | |
def | init_stats_add_mc_category |
shortcut for a frequent series of operations on MC simulations' statistics. More... | |
def | init_stats_add_md_category |
shortcut for a frequent series of operations on MD simulations' statistics. More... | |
def | m |
wrapper to call methods of m More... | |
def | rescale_velocities |
rescale the velocities of a bunch of particles having vx vy and vz floatkeys More... | |
def IMP.isd.shared_functions.sfo_common.do_md_protein_statistics | ( | self, | |
md_key, | |||
nsteps, | |||
md_instance, | |||
temperature = 300.0 , |
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prot_coordinates = None |
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) |
updates statistics for md simulation: target temp, kinetic energy, kinetic temperature, writes coordinates and increments counter.
Definition at line 942 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.find_atom | ( | self, | |
atom, | |||
prot | |||
) |
scans the prot hierarchy and tries to find atom = (resno, name) assumes that resno follows the same numbering as the sequence.
Stores already found atoms for increased speed.
Definition at line 371 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.get_pdb | ( | self, | |
prot | |||
) |
returns a string corresponding to the pdb structure of hierarchy prot.
Definition at line 931 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_ambiguous_NOE_restraint | ( | self, | |
prot, | |||
contributions, | |||
distance, | |||
sigma, | |||
gamma | |||
) |
Reads an ambiguous NOE restraint.
contributions is a list of (atom1, atom2) pairs, where atom1 is (resno, atomname). Sets up a lognormal distance restraint using the given sigma and gamma. Returns the restraint.
Definition at line 434 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_base | ( | self, | |
wd | |||
) |
moves to wd and creates model
Definition at line 156 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_charmm_protein_and_ff | ( | self, | |
initpdb, | |||
top, | |||
par, | |||
selector, | |||
pairscore, | |||
ff_temp = 300.0 , |
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disulfides = None , |
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representation = 'custom' |
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) |
creates a CHARMM protein representation.
creates the charmm force field, bonded and nonbonded.
Definition at line 189 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_conjugate_kappa | ( | self, | |
scales, | |||
c, | |||
R, | |||
prior_rs = None |
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) |
given a list of scales, returns a RestraintSet('prior') with weight 1.0 that contains a list of vonMisesKappaConjugateRestraint on each scale.
If argument prior_rs is used, add them to that RestraintSet instead.
Definition at line 356 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_HBonds_marginal | ( | self, | |
prot, | |||
seqfile, | |||
tblfile, | |||
name = 'NOE' , |
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verbose = True |
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) |
read TBL file and store lognormal restraints, using the marginal of the lognormal with one sigma and gamma=1, for the whole dataset.
Definition at line 544 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_jeffreys | ( | self, | |
scales, | |||
prior_rs = None |
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) |
given a list of scales, returns a RestraintSet('prior') with weight 1.0 that contains a list of JeffreysRestraint on each scale.
If argument prior_rs is used, add them to that RestraintSet instead.
Definition at line 344 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_jeffreys_kappa | ( | self, | |
scales, | |||
prior_rs = None |
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) |
given a list of scales, returns a RestraintSet('prior') with weight 1.0 that contains a list of vonMisesKappaJeffreysRestraint on each scale.
If argument prior_rs is used, add them to that RestraintSet instead.
Definition at line 331 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_NOE_restraint | ( | self, | |
prot, | |||
atoms, | |||
distance, | |||
sigma, | |||
gamma | |||
) |
Sets up a lognormal distance restraint using the given sigma and gamma.
Returns the restraint. assumes atoms = (atom1, atom2) where atom1 is (resno, atomname) and resno is the residue sequence number.
Definition at line 413 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_NOEs | ( | self, | |
prot, | |||
seqfile, | |||
tblfile, | |||
name = 'NOE' , |
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prior_rs = None , |
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bounds_sigma = (1.0, 0.1 , |
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bounds_gamma = (1.0, 0.1 , |
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verbose = True , |
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sequence_match = (1, 1 |
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) |
read TBL file and store NOE restraints, using one sigma and one gamma for the whole dataset.
Creates the necessary uninformative priors.
Definition at line 451 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_NOEs_marginal | ( | self, | |
prot, | |||
seqfile, | |||
tblfile, | |||
name = 'NOE' , |
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verbose = True , |
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sequence_match = (1, 1 |
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) |
read TBL file and store NOE restraints, using the marginal of the lognormal with one sigma and one gamma, for the whole dataset.
Definition at line 505 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_setup_scale | ( | self, | |
default, | |||
lower = None , |
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upper = None |
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) |
sets up a Scale particle to the initial default value.
It can optionally be constrained between two positive bounds, or else its range is 0 to infinity.
Definition at line 318 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_standard_SAXS_restraint | ( | self, | |
prot, | |||
profilefile, | |||
name = 'SAXS' , |
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ff_type = IMP.saxs.HEAVY_ATOMS |
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) |
read experimental SAXS profile and apply restraint the standard way (like foxs) Returns: a restraintset and the experimental profile
Definition at line 683 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_TALOS | ( | self, | |
prot, | |||
seqfile, | |||
talos_data, | |||
fulldata = True , |
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sequence_match = (1, 1 , |
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name = 'TALOS' , |
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prior_rs = None , |
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bounds_kappa = (1.0, 0.1 , |
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verbose = True , |
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prior = 'jeffreys' , |
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keep_all = False |
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) |
read TALOS dihedral angle data, and create restraints for phi/psi torsion angles, along with the prior for kappa, which is a scale for the whole dataset, compare to 1/sigma**2 in the NOE case.
Definition at line 580 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_vonMises_restraint_full | ( | self, | |
atoms, | |||
data, | |||
kappa | |||
) |
Sets up a vonMises torsion angle restraint using the given kappa particle as concentration parameter.
Returns the restraint. data is a list of observations.
Definition at line 397 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_vonMises_restraint_mean | ( | self, | |
prot, | |||
atoms, | |||
data, | |||
kappa | |||
) |
Sets up a vonMises torsion angle restraint using the given kappa particle as concentration parameter.
Returns the restraint. data is (mean, standard deviation).
Definition at line 405 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_simulation_setup_nuisance_mc | ( | self, | |
nuis, | |||
temperature = 300.0 , |
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mc_restraints = None , |
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nm_stepsize = 0.1 |
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) |
sets up monte carlo on nuisance, at a certain target temperature, optionally using a certain set of restraints only.
Definition at line 864 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_simulation_setup_protein_hmc_hopper | ( | self, | |
prot, | |||
temperature = 300.0 , |
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gamma = 0.01 , |
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n_md_steps = 10 , |
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md_restraints = None , |
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mc_restraints = None , |
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timestep = 1.0 , |
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sd_threshold = 0.0 , |
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sd_stepsize = 0.01 , |
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sd_maxsteps = 100 |
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) |
setup hybrid monte-carlo on protein.
Uses basin hopping with steepest descent minimization.
Definition at line 788 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_simulation_setup_protein_hmc_nve | ( | self, | |
prot, | |||
temperature = 300.0 , |
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n_md_steps = 100 , |
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md_restraints = None , |
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mc_restraints = None , |
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timestep = 1.0 |
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) |
setup hybrid monte-carlo on protein.
Uses NVE MD and tries the full
Definition at line 824 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_stats_add_hmc_category | ( | self, | |
stat, | |||
name = 'hmc' , |
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coord = 'protein' |
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) |
shortcut for a frequent series of operations on HMC simulations' statistics.
Adds acceptance, number of MD steps and a trajectory for a protein.
Definition at line 996 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_stats_add_mc_category | ( | self, | |
stat, | |||
name = 'mc' , |
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coord = 'particle' |
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) |
shortcut for a frequent series of operations on MC simulations' statistics.
Creates an entry for acceptance, stepsize and one coordinate set printed in the statistics file.
Definition at line 961 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_stats_add_md_category | ( | self, | |
stat, | |||
name = 'md' , |
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coord = 'protein' |
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) |
shortcut for a frequent series of operations on MD simulations' statistics.
Creates an entry for target temp, instantaneous temp, kinetic energy, and one set of coordinates called 'protein' by default.
Definition at line 978 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.m | ( | self, | |
name, | |||
args, | |||
kw | |||
) |
wrapper to call methods of m
Definition at line 151 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.rescale_velocities | ( | self, | |
particles, | |||
factor | |||
) |
rescale the velocities of a bunch of particles having vx vy and vz floatkeys
Definition at line 1014 of file shared_functions.py.