Package schrodinger :: Package trajectory :: Module analyze_trajectories

Module analyze_trajectories

Classes

FAS
A class for selecting atoms from frames in a given simulation using ASL.

FIS
A class that defines a static set of indices to be selected from all frames.

_KeywordProcessor
This class processes ARK keywords coming from a .st2 input file, it turns the keywords into Analysis objects to be used by the backend.

Functions

[hide private]

get_st_from_file(filename)
Read in a Structure file

read_trj_idx_file(trjfn)
Obtain the trajectory directory from the trj idx file

write_log(msg)
Write to log file

write_error(msg)
Write an error message, cleanup, and exit

write_warning(msg, incl_time=True)
Write a warning message

assemble_interaction_energy_results(energy_type, asl1, asl2, frame_results)

assemble_bulk_results(calc_type, frame_results, temperature=None, nmol=None)

assemble_energy_results(energy_type, component_type, frame_results)

unique(seq, idfun=None)
An funtion to return unique element of a sequence with order preserved.

get_temp_from_cfg(cfgfn)
extract target simulation temperature from the cfg file

get_old2new(st, prop='i_m_original_index')
get dictionary for atom-level property 'prop' as a key, and return it's new atom index (aid)

get_rb_potential(cmsstr, kw)
given a full system, and a torsion of interest (usually applies for a ligand-like molecule).

get_rb_torsions_potential(cmsstr, kw)

main(cmsfn, st2fn, outfn, trjfn=default_trj_fn, cfgfn=default_cfg_fn)

Variables

[hide private]

__doc__ = """analyze_trajectories.py -- analyze a set of Desmo...

_version = '$Revision: 0.0 $'

logger = log.get_output_logger("analyze_trajectories")

ffld_exec_dir = util.hunt("ffld")

sep = '/'

ffld_inst_dir = sep.join(ffld_exec_dir.split(sep) [:-2])

ffld_python_dir = os.path.join(ffld_inst_dir, 'python')

default_cfg_fn = None
hash(x)

default_trj_fn = None
hash(x)

_energy_attr_dict = {'COULOMB': 'elec', 'VDW': 'vdw', 'BOND': ...

_component_list = ['SELF', 'OTHER', 'SOLUTE', 'MEMBRANE', 'SOL...

Function Details

[hide private]

write_error(msg)

Write an error message, cleanup, and exit

An error is output when the program encounters an issue which causes the program to exit. Also see write_warning.

write_warning(msg, incl_time=True)

Write a warning message

A warning is output only for information and does not cause the program to exit. It is written to the error stream. Also see write_err.

get_rb_potential(cmsstr, kw)

given a full system, and a torsion of interest (usually applies for a ligand-like molecule). This routine extracts the small molecule, and gets the potential around the rotatable bond by scanning its conformations

Variables Details

[hide private]

doc

Value:

"""analyze_trajectories.py -- analyze a set of Desmond trajectories

This script will generate data for a series of analyses performed on
set of Desmond trajectories. It needs to be provided with the output
cms file, an input st2 (ark keyword) file, and an output filename.

This script has been rewritten mostly from scratch for the purpose of 
processing
...

_energy_attr_dict

Value:

{'COULOMB': 'elec', 'VDW': 'vdw', 'BOND': 'stretch', 'ANGLE': 'angle',
 'TORSION': 'dihedral', 'TOTAL': 'Total'}

_component_list

Value:

['SELF', 'OTHER', 'SOLUTE', 'MEMBRANE', 'SOLVENT']