IMP
2.0.0
The Integrative Modeling Platform
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nonspecific methods used across all shared function objects. More...
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 | |
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 | |
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_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_simulation_setup_scale_mc |
sets up monte carlo on scale, at a certain target temperature, optionnally using a certain set of restraints only. 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 | |
def | rescale_velocities |
rescale the velocities of a bunch of particles having vx vy and vz floatkeys | |
Rules:
Definition at line 16 of file shared_functions.py.
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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) |
Definition at line 253 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.find_atom | ( | self, | |
atom, | |||
prot | |||
) |
Stores already found atoms for increased speed.
Definition at line 87 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.get_pdb | ( | self, | |
prot | |||
) |
Definition at line 242 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_ambiguous_NOE_restraint | ( | self, | |
prot, | |||
contributions, | |||
distance, | |||
sigma, | |||
gamma | |||
) |
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 114 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 the charmm force field, bonded and nonbonded.
Definition at line 56 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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) |
If argument prior_rs is used, add them to that RestraintSet instead.
Definition at line 81 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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) |
Definition at line 153 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_jeffreys | ( | self, | |
scales, | |||
prior_rs = None |
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) |
If argument prior_rs is used, add them to that RestraintSet instead.
Definition at line 74 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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) |
If argument prior_rs is used, add them to that RestraintSet instead.
Definition at line 68 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_NOE_restraint | ( | self, | |
prot, | |||
atoms, | |||
distance, | |||
sigma, | |||
gamma | |||
) |
Returns the restraint. assumes atoms = (atom1, atom2) where atom1 is (resno, atomname) and resno is the residue sequence number.
Definition at line 107 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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) |
Creates the necessary uninformative priors.
Definition at line 130 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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) |
Definition at line 142 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_setup_scale | ( | self, | |
default, | |||
lower = -1 , |
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upper = -1 |
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) |
It can optionnally be constrained between two positive bounds, or else its range is 0 to infinity.
Definition at line 62 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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) |
Definition at line 181 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_vonMises_restraint_full | ( | self, | |
atoms, | |||
data, | |||
kappa | |||
) |
Returns the restraint. data is a list of observations.
Definition at line 93 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_model_vonMises_restraint_mean | ( | self, | |
prot, | |||
atoms, | |||
data, | |||
kappa | |||
) |
Returns the restraint. data is (mean, standard deviation).
Definition at line 99 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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) |
Uses basin hopping with steepest descent minimization.
Definition at line 206 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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) |
Uses NVE MD and tries the full
Definition at line 225 of file shared_functions.py.
def IMP.isd.shared_functions.sfo_common.init_simulation_setup_scale_mc | ( | self, | |
scale, | |||
temperature = 300.0 , |
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mc_restraints = None , |
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floatkey = IMP.FloatKey('scale') , |
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nm_stepsize = 0.1 |
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) |
Definition at line 237 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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) |
Adds acceptance, number of MD steps and a trajectory for a protein.
Definition at line 272 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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) |
Creates an entry for acceptance, stepsize and one coordinate set printed in the statistics file.
Definition at line 259 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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) |
Creates an entry for target temp, instantaneous temp, kinetic energy, and one set of coordinates called 'protein' by default.
Definition at line 266 of file shared_functions.py.