scopy.ScoFH package


Created on Fri May 15 21:38:08 2020

A module used for sceening frequent hitters related substructure.

You can freely use and distribute it. If you have any problem, you could contact with us timely.

@Author: Zhi-Jiang Yang, Dong-Sheng Cao.

@Institution: CBDD Group, Xiangya School of Pharmaceutical Science, CSU, China.

@Homepage: http://www.scbdd.com

@Mail: kotori@cbdd.me and oriental-cds@163.com


Submodules

scopy.ScoFH.fh_filter module

scopy.ScoFH.fh_filter.Check_Alarm_NMR(mol, detail=False, showSMILES=False)[source]

There are 75 SMARTS in alarm_nmr

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoFH.fh_filter.Check_AlphaScreen_FHs(mol, detail=False, showSMILES=False)[source]

Check molecule under Check_AlphaScreen_FHs Filter, which presents a compound may be alphascreen frequent hitters. There are 6 SMARTS in this endpoint.

Reference:
  1. Schorpp, Kenji. (2014).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoFH.fh_filter.Check_AlphaScreen_GST_FHs(mol, detail=False, showSMILES=False)[source]

Check molecule under Check_AlphaScreen_GST_FHs Filter, which presents a compound may prevent GST/GSH interaction during HTS. There are 34 SMARTS in this endpoint.

References:
  1. Brenke, Jara K. (2016).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoFH.fh_filter.Check_AlphaScreen_HIS_FHs(mol, detail=False, showSMILES=False)[source]

Check molecule under Check_AlphaScreen_HIS_FHs Filter, which presents a compound prevents the binding of the protein His-tag moiety to nickel chelate. There are 19 SMARTS in this endpoint.

Reference:
  1. Schorpp, Kenji. (2014).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoFH.fh_filter.Check_BMS(mol, detail=False, showSMILES=False)[source]

Check molecule under BMS Filter. Pearce has proposed a Functional Group Compound Filters(FG Filters). The FG filters are consisted of two part, Exclusion FG filters and informational filters. Exclusion FG filters are those intended for compound removal from screening decks; Informational filters are useful for compound annotation. There are 176 SMARTS in this endpoint.

Reference:
  1. Pearce, Bradley C (2006).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoFH.fh_filter.Check_Chelating(mol, detail=False, showSMILES=False)[source]

Check molecule under Chelating Filter, which presents a compound may inhibit metalloproteins. Thers are 55 SMARTS in this endpoint

Reference.:
  1. Agrawal, Arpita. (2010).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoFH.fh_filter.Check_Luciferase_Inhibitory(mol, detail=False, showSMILES=False)[source]

There 3 SMARTS in Luciferase_Inhibitory Filter

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoFH.fh_filter.Check_PAINS(mol, detail=False, showSMILES=False)[source]

Check molecule under PAINS Filter, which presents a type of compounds tend to be hitted in HTS. There are 480 SMARTS in this endpoint.

Reference:
  1. Baell, Jonathan B. and Georgina A. Holloway (2010).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

class scopy.ScoFH.fh_filter.Filter(endpoint, detail=False, showSMILES=False)[source]

Bases: object

the tool to check molecule whether matched frequent hitters endpoints.

Parameters
  • endpoint (str) – The name of endpoint for scanning molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

get_pattl()[source]
scan(mol)[source]

scopy.ScoFH.fh_filter_Lib module

class scopy.ScoFH.fh_filter_Lib.FHfilter(mols, n_jobs=1, detail=False, showSMILES=False)[source]

Bases: object

Here, we comdat the whole function from fh_filter for screeing moleclue library

Parameters
  • mols (Iterable object, each element is rdkit.Chem.rdchem.Mol) – the molecule to be scanned.

  • n_jobs (int, optional) – The number of CPUs to use to do the computation, defaults to 1

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Check_Alarm_NMR()[source]

There are 75 SMARTS in alarm_nmr

Returns

a list of dictionary

Return type

list

Check_AlphaScreen_FHs()[source]

Check molecule under Check_AlphaScreen_FHs Filter, which presents a compound may be alphascreen frequent hitters. There are 6 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_AlphaScreen_GST_FHs()[source]

Check molecule under Check_AlphaScreen_GST_FHs Filter, which presents a compound may prevent GST/GSH interaction during HTS. There are 34 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_AlphaScreen_HIS_FHs()[source]

Check molecule under Check_AlphaScreen_HIS_FHs Filter, which presents a compound prevents the binding of the protein His-tag moiety to nickel chelate. There are 19 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_BMS()[source]

Check molecule under BMS Filter. Pearce has proposed a Functional Group Compound Filters(FG Filters). The FG filters are consisted of two part, Exclusion FG filters and informational filters. Exclusion FG filters are those intended for compound removal from screening decks; Informational filters are useful for compound annotation. There are 176 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_Chelating()[source]

Check molecule under Chelating Filter, which presents a compound may inhibit metalloproteins. Thers are 55 SMARTS in this endpoint

Returns

a list of dictionary

Return type

list

Check_Luciferase_Inhibitory()[source]

There 3 SMARTS in Luciferase_Inhibitory Filter

Returns

a list of dictionary

Return type

list

Check_PAINS()[source]

Check molecule under PAINS Filter, which presents a type of compounds tend to be hitted in HTS. There are 480 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Module contents

Created on Fri May 15 21:38:08 2020

@Author: Zhi-Jiang Yang, Dong-Sheng Cao @Institution: CBDD Group, Xiangya School of Pharmaceutical Science, CSU, China @Homepage: http://www.scbdd.com @Mail: yzjkid9@gmail.com; oriental-cds@163.com @Blog: https://blog.iamkotori.com