Package schrodinger :: Package application :: Package combiglide :: Package packages :: Module chutils

Module chutils

Classes

ChUtils
Utilities generally useful in core-hopping

MakeRLinkerUtils
Utility functions for use with make_r_linker_sqlite().

BitArray
Minimal bit-array class

_ParseRulesFile
Utility functions (no objects) to read and parse joining-rules files and to write new such files with proper syntax.

JoiningRules
Store joining rules read from a file and provide access methods.

ApplyJoiningRules
APIs to determine what adduct rule matches are required for each substrate attachment point and what rule matches are exhibited for each adduct attachment point.

Substrate
An instance stores required information about a substrate molecule and supplies APIs for later retrieval.

Adduct
An instance stores required information about an adduct molecule and supplies APIs for later retrieval.

Attachment
Store information about an attachment point, which is a heavy atom on a structure.

AdductAttachment

SubstrateAttachment

Join
An object is an allowed join between an attachment atom on a Substrate object and an attachment atom on an Adduct object.

Functions

[hide private]

make_r_linker_sqlite(template_st, template_from_tos, linker_sqlite_fname, r_linker_fname_prefix, verbose=False)
Create an r_linker sqlite file given a template structure, a list of its From-To pairs, and a linker sqlite file.

Function Details

[hide private]

make_r_linker_sqlite(template_st, template_from_tos, linker_sqlite_fname, r_linker_fname_prefix, verbose=False)

Create an r_linker sqlite file given a template structure, a list of its From-To pairs, and a linker sqlite file. When verbose is set to True, copious information is emitted to stdout.