Conformer Filtration (confilter) a package for similar molecules filtration for the data preparation of Machine Learning
Xiang Zhong and Orlando Acevedo*, University of Miami
git clone git://github.com/orlandoacevedo/confilter.git
pip[3] install confilter
Or using source codes
python[3] setup.py install
For helpful information, use
confilter
Or
confilter -h
Or, for sub-command
confilter plot -h
usage:
confilter [-h] [-v] [-f file [file ...]] [-d file [file ...]] [--static] [--separat]
[--vndx VNDX] [--borandom] [--seed SEED] [-btol BTOL] [-atol ATOL]
[-bcon B1 B2, B1-B2 [B1 B2, B1-B2 ..]] [-acon A1 A2 A3, A1-A2-A3 [A1 A2 A3, A1-A2-A3 ...]]
[-g G [G ...]] [--no-oball] [-obpar] [--no-oaall] [-oapar] [-nc] [--features] [-p] [-nu]
[-o FNAME] [-ft FTYPE]
{plot} ...
Conformation Filtration
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-f file [file ...], --datafilelist file [file ...]
Data files, separate by space or comma
-d file [file ...], --indexfilelist file [file ...]
Index files, as the filtration reference
--static turn on static mode calculation, default is in dynamic/all mode
--separate valid in dynamic mode, change to dynamic/separate mode
--vndx VNDX valid in static mode, set filtration index value
--borandom valid in static mode, rather than by lowest-bit, filtering out molecules randomly
--seed SEED random seed, (optional, highest priority)
-btol BTOL, --btol BTOL
bonds tolerance, any changes in bcon smaller than it will be filtered out
-atol ATOL, --atol ATOL
angles tolerance, any changes in acon smaller than it will be filtered out
-bcon B1 B2, B1-B2 [B1 B2, B1-B2 ...]
Bond connections, in pairs, separate by comma
-acon A1 A2 A3, A1-A2-A3 [A1 A2 A3, A1-A2-A3 ...]
Angle connections, in pairs, separate by comma
-g G [G ...], --fragments G [G ...]
fragments, separate by comma
--no-oball turn off bonds probability overall calculation, Boolean
-obpar, --obpar turn on bonds probability parameters calculation, Boolean
--no-oaall turn off angles probability overall calculation, Boolean
-oapar, --oapar turn on angles probability parameters calculation, Boolean
-nc, --no-force-double-check
turn off double check prompt info before execution
--features show development features
-p, --file-format-explanations
show input system file format explanations
-nu, --no-userinputs specify the indexes of input connections start at 0
-o FNAME, --fname FNAME
output system file name
-ft FTYPE, --ftype FTYPE
output system file type, [txt, xsf, xyz]
continuous subcommand:
{plot}
plot plot cross comparsions based on different chosen samples
usage: confilter plot [-h] [-bf B [B ...]] [-nl n [n ...]] [-ns n] [-sn n] [-en n] [-inc n] [-nr n]
optional arguments:
-h, --help show this help message and exit
-bf B [B ...], --probdatafilelist B [B ...]
bulk process probability files
-nl n [n ...], --nmlist n [n ...]
highest priority, select number of samples for plot, (optional)
-ns n, --nmsamples n choose number of samples for plot, default is 5
-sn n, --startndx n start index for the inputs, (optional)
-en n, --endndx n end index for the inputs, (optional)
-inc n, --incndx n increments for choose, (optional)
-nr n, --nmranges n random ranges for increments, (optional)
Please refer to doc/ for more information.
Contributing Authors: Xiang Zhong and Orlando Acevedo*
Software License: Conformer Filtration (confilter) software package. Copyright (C) 2021 Orlando Acevedo