usage: averageBuriedVolume.py [-h] [-if {log,out,dat}] [-o output destination]
[-l TARGETS] [-e EXCLUDE_ATOMS] [-c CENTER]
[-r RADIUS] [-vdw {bondi,umn}] [-s SCALE]
[-t TEMPERATURE] [-f] [-w0 W0] [-v]
[-m {MC,Lebedev}] [-rp {20,32,64,75,99,127}]
[-ap {110,194,302,590,974,1454,2030,2702,5810}]
[-i ITERATIONS]
input files [input files ...]
calculate Boltzmann-weighted percent buried volume parameters
positional arguments:
input files file containing coordinates and energy
optional arguments:
-h, --help show this help message and exit
-if {log,out,dat}, --input-format {log,out,dat}
file format of input
-o output destination, --output output destination
output destination
Default: stdout
-l TARGETS, --ligand-atoms TARGETS
atoms to consider in calculation
Default: use all atoms except the center
-e EXCLUDE_ATOMS, --exclude-atoms EXCLUDE_ATOMS
atoms to exclude from the calculation
Default: exclude no ligand atoms
-c CENTER, --center CENTER
atom the sphere is centered on
Default: detect metal center (centroid of all metals if multiple are present)
-r RADIUS, --radius RADIUS
radius around center
Default: 3.5 Ångström
-vdw {bondi,umn}, --vdw-radii {bondi,umn}
VDW radii to use in calculation
umn: main group vdw radii from J. Phys. Chem. A 2009, 113, 19, 5806–5812
(DOI: 10.1021/jp8111556)
transition metals are crystal radii from Batsanov, S.S. Van der Waals
Radii of Elements. Inorganic Materials 37, 871–885 (2001).
(DOI: 10.1023/A:1011625728803)
bondi: radii from J. Phys. Chem. 1964, 68, 3, 441–451 (DOI: 10.1021/j100785a001)
Default: bondi
-s SCALE, --scale SCALE
scale VDW radii by this amount
Default: 1.17
-t TEMPERATURE, --temperature TEMPERATURE
temperature in K
Default: 298.15
-f, --frequency input files are frequency job output files
additional average values will be calculated for ZPE, H, G, etc.
-w0 W0, --frequency-cutoff W0
cutoff frequency for quasi free energy corrections (1/cm)
Default: 100 cm^-1
-v, --verbose also print population
-m {MC,Lebedev}, --method {MC,Lebedev}
integration method - Monte-Carlo (MC) or Lebedev quadrature (Lebedev)
Default: Lebedev
Lebedev integration options:
-rp {20,32,64,75,99,127}, --radial-points {20,32,64,75,99,127}
number of radial shells for Gauss-Legendre integration
of the radial component
lower values are faster, but at the cost of accuracy
Default: 20
-ap {110,194,302,590,974,1454,2030,2702,5810}, --angular-points {110,194,302,590,974,1454,2030,2702,5810}
number of angular points for Lebedev integration
lower values are faster, but at the cost of accuracy
Default: 1454
Monte-Carlo integration options:
-i ITERATIONS, --minimum-iterations ITERATIONS
minimum iterations - each is a batch of 3000 points
MC will continue after this until convergence criteria are met
Default: 25