spectrum_align Command Help

Command: $SCHRODINGER/utilities/spectrum_align

usage: spectrum_align [-h]
                             [-alignment_algorithm {Needleman-Wunsch,Scaling}]
                             [-boltz_dist BOLTZ_DIST [BOLTZ_DIST ...]]
                             [-delimiter DELIMITER]
                             [-exp_baseline EXP_BASELINE]
                             [-theory_baseline THEORY_BASELINE]
                             [-lo_bound LO_BOUND] [-hi_bound HI_BOUND]
                             [-manual_peak_pos MANUAL_PEAK_POS [MANUAL_PEAK_POS ...]]
                             [-allow_upwards] [-param_lo PARAM_LO]
                             [-param_hi PARAM_HI] [-param_step PARAM_STEP]
                             [-set_param SET_PARAM] [-use_robust_modes]
                             exp_spectrum theor_spectra [theor_spectra ...]

positional arguments:
  exp_spectrum          Experimental spectrum, in 'delimiter'-separated
                        format. Each line contains peak position and intensity
                        in that order.
  theor_spectra         Theoretical spectra of confomers of a single
                        enantiomer

options:
  -h, --help            show this help message and exit
  -alignment_algorithm {Needleman-Wunsch,Scaling}
                        Alignment algorithm to apply to
                        experimental/theoretical spectra. Needleman-Wunsch
                        follows the implementation of Riniker et al
                        (doi.org/10.1021/acs.jcim.8b00789).Scaling simply
                        scales the theoretical spectra by various scalars and
                        assesses the fit. Both algorithms scan a parameter
                        whose range can be controlled through the
                        param_lo/param_hi/param_step/set_param args. Default:
                        'Needleman-Wunsch'
  -boltz_dist BOLTZ_DIST [BOLTZ_DIST ...]
                        Boltzmann distribution of conformer spectra. If not
                        provided, equal weights given to all conformers
  -delimiter DELIMITER  Delimiter used to separate peak position/intensity in
                        experimental spectra. For tab-separated use ' '.
                        Default: ','
  -exp_baseline EXP_BASELINE
                        Baseline magnitude used to ignore small peaks in peak
                        detection in experimental spectrum. Relative to
                        experimental amplitudes. Default: 0.0
  -theory_baseline THEORY_BASELINE
                        Baseline magnitude used to ignore small peaks in a
                        normalized Boltzmann-averaged theoretical spectrum.
                        Default: 0.02
  -lo_bound LO_BOUND    Lower bound of experimental spectra peaks to match.
                        Default: 0.0
  -hi_bound HI_BOUND    Upper bound of experimental spectra peaks to match.
                        Default: 4000
  -manual_peak_pos MANUAL_PEAK_POS [MANUAL_PEAK_POS ...]
                        Set to provide a manual list of peak positions for
                        experimental spectrum.
  -allow_upwards        Set to allow upward shifts of theoretical peaks in
                        Needleman-Wunsch algorithm. Default is to disallow
                        this, as theory generally places peaks higher than
                        experiment
  -param_lo PARAM_LO    Lower bound for parameter used in
                        'alignment_algorithm'. Defaults- Needleman-Wunsch:
                        0.97, Scaling: 0.96
  -param_hi PARAM_HI    Upper bound for parameter used in
                        'alignment_algorithm'.Defaults- Needleman-Wunsch:
                        1.03, Scaling: 1.02
  -param_step PARAM_STEP
                        Step size used for parameter in
                        'alignment_algorithm'.Starts from param_lo and goes to
                        <= param_hi. Default: 0.01 for both alignment
                        algorithms
  -set_param SET_PARAM  If set, runs 'alignment_algorithm' with the single
                        provided parameter. Overrides
                        param_lo/param_hi/param_step args. Must be greater
                        than 0.
  -use_robust_modes     Set to extract only 'robust' modes/peaks from
                        theoretical spectra, identified via EDTM/MDTM info in
                        provided mae files.