This tool filters molecules from a database. These molecules are then used to generate parameters for smirnoff99frosst.
The heart of the tool is dance. It should be used as follows:
- Use GENERATE mode to generate an initial set of trivalent nitrogen molecules from the database. The database must be represented as directories consisting of mol2 files. GENERATE mode ultimately generates an output directory with several files (see Output Directories)
- Use PLOTHIST mode to visualize the Wiberg bond orders from the previous step.
This requires either the
output-tri-n-data.csvfile or theoutput-tri-n-bonds.csvfrom the GENERATE step. Note that if you choose theoutput-tri-n-bonds.csvfile, you will have to change some of the command line arguments, as the defaults are foroutput-tri-n-data.csv. Specifically,hist-min,hist-max, andhist-stepshould be adjusted, most likely to around 0.5, 1.5, and 0.1, respectively. This step ultimately outputs the following file:output-histogram.pdf: a PDF file holding histograms of the bond orders in every output-tri-n-data.csv file you pass in, as well as a histogram of the bond orders in all files combined (put on one plot together)
- Use SELECT mode to separate molecules. This mode creates a directory with SMILES files corresponding to certain molecule bins.
- Use SELECT-ANALYZE mode to provide some statistics about the output of SELECT mode, as well as a bar graph of the counts of molecules in each bin.
- Use SELECT-FINAL mode to select the smallest molecules from each bin created in SELECT mode.
After cloning this repo, run the following command to install DANCE. You may want to set up a virtualenv first. You will also need an Openeye license to be able to use the Openeye toolkits.
pip install --extra-index-url https://pypi.anaconda.org/openeye/simple -e .
The following files are generated whenever DANCE generates an "output directory" of files.
mols.smi: SMILES strings representing the moleculesmols.oeb: an OEB (Openeye Binary) file for raw molecule datatri-n-data.csv: holds data about the trivalent nitrogen in each molecule - the total Wiberg bond order, total bond angle, and total bond length of the bonds surrounding the nitrogentri-n-bonds.csv: holds data about the individual bonds connected to the trivalent nitrogen - the Wiberg bond order, bond length, and element of each bondprops.binary: binary file for storing list of DanceProperties with data about the molecules
During SELECT mode, molecules are separated into bins by two criteria. The first
is the total of the Wiberg bond orders of the bonds around the trivalent
nitrogen in the molecule. The total bond orders are rounded down to the nearest
multiple of the --select-bin-size command line arg. The second is a
"fingerprint", which attempts to describe the environment around the trivalent
nitrogen via several characteristics of each bond:
- atomic number of the atom at the end of the bond - what element the atom is
- connectivity of the atom at the end of the bond - how many other atoms the atom is connected to (including 1 for the trivalent nitrogen)
- rounded Wiberg bond order of the bond
usage: dance [-h] [--mode MODE] [--log LEVEL] [--mol2dirs DIR1,DIR2,...]
[--generate-output-dir DIRNAME] [--wiberg-csvs CSV1,CSV2,...]
[--wiberg-csv-col INT] [--output-histograms FILENAME.pdf]
[--hist-min FLOAT] [--hist-max FLOAT] [--hist-step FLOAT]
[--input-binaries OEB,BINARY,OEB,BINARY,...]
[--select-bin-size FLOAT] [--wiberg-precision FLOAT]
[--select-output-dir DIRNAME] [--select-analyze-dir DIR]
[--select-analyze-output-dir DIR] [--select-final-n N]
[--select-final-dir DIR]
[--select-final-output-file SELECT_FINAL_OUTPUT_FILE]
Performs various functions for selecting molecules from a database. It will do
the following based on the mode. |GENERATE| - Take in directories of mol2
files, generate the initial set of molecules with a single trivalent nitrogen,
and write results to a directory with the following files: mols.smi -
molecules stored in SMILES format, mols.oeb - the same molecules stored in OEB
(Openeye Binary) format, tri_n_data.csv - data about the trivalent nitrogen in
each molecule, tri_n_bonds.csv - data about the bonds around the trivalent
nitrogen in each molecule, props.binary - binary storage of DanceProperties
for the molecules. |PLOTHIST| - Take in data files from the previous step and
use matplotlib to generate histograms of the Wiberg bond orders. |SELECT| -
Separate molecules from the GENERATE step into bins based on their rounded
total Wiberg bond order and "fingerprint". (See README for more info about
bins.) |SELECT-ANALYZE| - Provide statistics and visualizations of the output
from SELECT mode. Writes to the following files: statistics.txt - facts about
the number of molecules in each bin, visualization.pdf - a bar graph of
numbers of molecules in each bin. |SELECT-FINAL| - Selects the smallest
molecules from each bin made in SELECT mode. Writes these molecules to a
SMILES file.
optional arguments:
-h, --help show this help message and exit
Mode Agnostic args:
Arguments which apply to every mode of DANCE
--mode MODE The mode in which to run DANCE - one of GENERATE,
PLOTHIST, or SELECT. See README for more info
(default: GENERATE)
--log LEVEL logging level - one of DEBUG, INFO, WARNING, ERROR,
and CRITICAL - See
https://docs.python.org/3/howto/logging.html for more
information (default: info)
GENERATE args:
--mol2dirs DIR1,DIR2,...
a comma-separated list of directories with mol2 files
to be filtered and saved (default: )
--generate-output-dir DIRNAME
directory for saving the output - refer to beginning
of this msg (default: generate-output)
PLOTHIST args:
--wiberg-csvs CSV1,CSV2,...
a comma-separated list of CSV files with a column
containing wiberg bond orders - these files are likely
generated in the GENERATE step (default: )
--wiberg-csv-col INT Column in the CSV files holding the Wiberg bond orders
(0-indexed) (default: 0)
--output-histograms FILENAME.pdf
location of PDF file for histograms (default: output-
histograms.pdf)
--hist-min FLOAT Minimum bin for histogram (default: 2.0)
--hist-max FLOAT Maximum bin for histogram (default: 3.4)
--hist-step FLOAT Step/bin size for histogram (default: 0.1)
SELECT args:
--input-binaries OEB,BINARY,OEB,BINARY,...
a comma-separated list of pairs of OEB and
DanceProperties binary files - each OEB should
correspond to the binary file next to it (default: )
--select-bin-size FLOAT
bin size for separating molecules by total Wiberg bond
order around the trivalent nitrogen (default: 0.02)
--wiberg-precision FLOAT
value to which to round the Wiberg bond orders in the
fingerprints; e.g. round to the nearest 0.02 (default:
0.05)
--select-output-dir DIRNAME
directory for writing SMILES files with molecules of
each fingerprint (default: select-output)
SELECT-ANALYZE args:
--select-analyze-dir DIR
directory containing output from SELECT mode (default:
select-output)
--select-analyze-output-dir DIR
directory for saving analysis (default: select-
analyze-output)
SELECT-FINAL args:
--select-final-n N how many molecules to select from each bin (default:
1)
--select-final-dir DIR
directory from SELECT mode with smi files of molecules
(default: select-output)
--select-final-output-file SELECT_FINAL_OUTPUT_FILE
output file for final selection of molecules (default:
select-final.smi)
dance --mode GENERATE \
--mol2dirs dir1,dir2,dir3 \
--generate-output-dir my-output \
--log debug
Reads in molecules from dir1, dir2, and dir3, filters out the ones with a single trivalent nitrogen atom, and writes the results to files in a directory called my-output. Prints log messages as low as DEBUG to stderr.
dance --mode PLOTHIST \
--wiberg-csvs data1.csv,data2.csv,data3.csv \
--output-histograms output-histograms.pdf \
--log debug
Reads in Wiberg bond orders from data1.csv, data2.csv, and data3.csv and generates histograms of the bond orders in each file. Also generates a histogram for the bond orders from all files combined together. Writes the histograms to output-histograms.pdf. Prints log messages as low as DEBUG to stderr.
dance --mode SELECT \
--input-binaries mol1.oeb,prop1.binary,mol2.oeb,prop2.binary \
--select-output-dir my-output
Reads in molecules and their properties from mol1.oeb, prop1.binary, mol2.oeb, and prop2.binary, and writes molecules of each bin to files in a directory called my-output.
dance --mode SELECT-ANALYZE \
--select-analyze-dir select-output \
--select-analyze-output-dir select-analyze-output
Looks at SMILES files in the directory select-output and writes analysis to the directory select-analyze-output.
dance --mode SELECT-FINAL \
--select-final-n 2 \
--select-final-dir select-output \
--select-final-output-file select-final.smi
Selects the 2 smallest molecules from each SMILES file in the select-output directory and writes them to the file select-final.smi.
Python's standard logging library is used to write log messages of varying
severity to stderr. The severity level required for a message to be printed can
be adjusted with the --log flag. To capture the messages in a file, you will
have to redirect stderr to a file. For example, the following command will
redirect stderr to a file called status.txt when running dance.
dance --mode GENERATE --mol2dirs dir1,dir2,dir3 2> status.txt
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