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add newlines for code blocks + typo (#3475)

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This commit is contained in:
Cédric Bouysset
2020-10-13 05:09:34 +02:00
committed by GitHub
parent 240fe4e524
commit 04a2be149f
1 changed files with 11 additions and 6 deletions
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17
Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp
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@@ -59,7 +59,7 @@ const char *CachedMolHolderDoc =
"Holds molecules in their binary representation.\n"
"This allows more molecules to be held in memory at a time\n"
" AddMol(mol) -> adds a molecule to the molecule holder, returns index of "
"molecule\n"
"molecule\n\n"
" AddBinary(data) -> adds a picked molecule molecule to the molecule "
"holder, returns index of molecule\n"
" The data is stored as-is, no checking is done for "
@@ -70,7 +70,7 @@ const char *CachedSmilesMolHolderDoc =
"Holds molecules as smiles string\n"
"This allows more molecules to be held in memory at a time\n"
" AddMol(mol) -> adds a molecule to the molecule holder, returns index of "
"molecule\n"
"molecule\n\n"
" AddSmiles(smiles) -> adds a smiles string to the molecule holder, "
"returns index of molecule\n"
" The smiles is stored as-is, no checking is done "
@@ -81,11 +81,11 @@ const char *CachedTrustedSmilesMolHolderDoc =
"Holds molecules as trusted smiles string\n"
"This allows more molecules to be held in memory at a time and avoids "
"RDKit sanitization\n"
"overhead\n"
"overhead.\n"
"See: "
"http://rdkit.blogspot.com/2016/09/avoiding-unnecessary-work-and.html\n"
" AddMol(mol) -> adds a molecule to the molecule holder, returns index of "
"molecule\n"
"molecule\n\n"
" AddSmiles(smiles) -> adds a smiles string to the molecule holder, "
"returns index of molecule\n"
" The smiles is stored as-is, no checking is done "
@@ -102,6 +102,7 @@ const char *SubstructLibraryDoc =
"The SubstructLibrary takes full advantage of available threads during the "
"search operation.\n"
"Basic operation is simple\n"
"\n"
">>> from __future__ import print_function\n"
">>> import os\n"
">>> from rdkit import Chem, RDConfig\n"
@@ -115,8 +116,8 @@ const char *SubstructLibraryDoc =
">>> len(indices)\n"
"11\n"
"\n"
"\n"
"Substructure matching options can be sent into GetMatches:\n"
"\n"
">>> indices = library.GetMatches(core, useChirality=False) \n"
">>> len(indices)\n"
"11\n"
@@ -124,6 +125,7 @@ const char *SubstructLibraryDoc =
"Controlling the number of threads or the maximum number of matches "
"returned:\n"
"is also available (the default is to run on all cores)\n"
"\n"
">>> indices = library.GetMatches(core, numThreads=2, maxResults=10) \n"
">>> len(indices)\n"
"10\n"
@@ -134,7 +136,9 @@ const char *SubstructLibraryDoc =
"kept in memory.\n"
"To assist this we supply three other molecule holders:\n"
" CachedMolHolder - stores molecules as their pickled representation\n"
"\n"
" CachedSmilesMolHolder - stores molecules internally as smiles strings\n"
"\n"
" CachedTrustedSmilesMolHolder = excepts (and stores) molecules as "
"trusted smiles strings\n"
"\n"
@@ -162,6 +166,7 @@ const char *SubstructLibraryDoc =
"This (obviously) takes longer to initialize. However, both the molecule "
"and pattern\n"
"holders can be populated with raw data, a simple example is below:\n"
"\n"
">>> import csv\n"
">>> molholder = rdSubstructLibrary.CachedSmilesMolHolder()\n"
">>> pattern_holder = rdSubstructLibrary.PatternHolder()\n"
@@ -234,7 +239,7 @@ struct substructlibrary_wrapper {
python::no_init)
.def("__len__", &MolHolderBase::size)
.def("AddMol", &MolHolderBase::addMol,
"Adds molecle to the molecule holder")
"Adds molecule to the molecule holder")
.def("GetMol", &MolHolderBase::getMol,
"Returns a particular molecule in the molecule holder\n\n"
" ARGUMENTS:\n"