Re: [Rdkit-discuss] Building RDKit on Windows for pgAdmin (Postgres)
Hi Charmaine, my suggestion is to build starting from a conda environment. That will significantly simplify your dependencies, since most packages are available pre-built. You can look into .azure-pipelines\vs_build_dll.yml for how to set up your conda environment and for the cmake flags to use. For Postgres, these are the cmake flags that I use to configure the PostgreSQL DLL build: -D RDK_BUILD_PGSQL=ON ^ -D RDK_PGSQL_STATIC=OFF ^ -D PostgreSQL_INCLUDE_DIR="C:/Program Files/PostgreSQL/14/include" ^ -D PostgreSQL_TYPE_INCLUDE_DIR="C:/Program Files/PostgreSQL/14/include/server" ^ -D PostgreSQL_LIBRARY="C:/Program Files/PostgreSQL/14/lib/postgres.lib" ^ .. Note that this is to build against Postgres installed using the Windows installer from the PostgreSQL website, not the version provided by conda. Cheers, p. On Thu, Apr 14, 2022 at 11:36 AM Charmaine Siu Man Chu < charmaine@liverpoolchirochem.com> wrote: > Hello, > > > > I’ve been trying to build RDKit on Windows so that I can get the RDKit > extension in pgAdmin (Postgres) but I’ve been unsuccessful. > > I’ve tried to follow the instruction on > https://www.rdkit.org/docs/Install.html to build RDKit and encountered > several problems. > > Some of them I manage to resolve myself but can someone help on this? > > > > Here is what I’ve tried: > > > > To start off, I’m using the Windows 11 64-bit OS and Postgres 14 was > installed. > > I then went to install the following: > > Python 3.10 along with numpy and Pillow > > Visual Studio 2022 with Visual Studio Community 2022, Visual Studio Build > Tools 2022 > > Cmake 3.23.0 > > Boost_1_78_0 using the .exe installer > > And downloaded and extracted the rdkit-Release_2022_03_1 > > > > After install the above, I ran the below in Comand Prompt > > cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 > -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON > -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" > -G"Visual Studio 17 2022" .. > > came back with error: > > The following variants have been tried and rejected: > > > > * boost_python310-vc143-mt-gd-x64-1_78.lib (shared, default on Windows is > > static, set Boost_USE_STATIC_LIBS=OFF to override) > > > > * boost_python310-vc143-mt-x64-1_78.lib (shared, default on Windows is > > static, set Boost_USE_STATIC_LIBS=OFF to override) > > > > I then edit the command line to > > cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 > -DBoost_USE_STATIC_LIBS=OFF -DRDK_BUILD_INCHI_SUPPORT=ON > -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON > -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 > 2022" .. > > and this time following error occured > > Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) > (Required is at least version "2.91.0") > > CMake Error at C:/Program > Files/CMake/share/cmake-3.23/Modules/ExternalProject.cmake:2540 (message): > > error: could not find git for clone of Eigen > > > > So I went to download and extracted eigen 3.4.0 and edit the command line > to > > cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 > -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0" > -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON > -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" > -G"Visual Studio 17 2022" .. > > which gave the following error > > CMake Error at C:/Program > Files/CMake/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230 > (message): > > Could NOT find Freetype (missing: FREETYPE_LIBRARY FREETYPE_INCLUDE_DIRS) > > > > So again I went to obtain freetype-2.12.0 and build it following the > instructions on > https://bobhowto.wordpress.com/2020/11/10/build-freetype-on-windows-10-using-visual-studio-2017/, > using VS 2022 instead, and edit the command line to > > cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/local/boost_1_78_0 > -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON > -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0" > -DFREETYPE_INCLUDE_DIRS="C:/freetype-2.12.0/include" > -DFREETYPE_LIBRARY="C:/freetype-2.12.0/objs/freetype.lib" > -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" > -G"Visual Studio 17 2022" .. > > and it managed to compile > > However, when running > > "C:\Program Files\Microsoft Visual > Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" /m:4 > /p:Configuration=Release INSTALL.vcxproj > > Gave the following error with 47 other warnings > > "C:\rdkit-Release_2022_03_1\build\INSTALL.vcxproj" (default target) (1) -> > >"C:\rdkit-Release_2022_03_1\build\ALL_BUILD.vcxproj" (default > target) (3) -> > > > "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\Deprotect\Wrap\rdDeprotect.vcxproj" > (default target) (20) -> > > > "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\ChemReactions\ChemReactions.vcxproj" > (default target) (48) -> > >
Re: [Rdkit-discuss] how to report SDF records for which Chem.ForwardSDMolSupplier returns None?
Thank you Ivan, that's great!
It does exactly what I wanted.
OK, I cannot read the properties for wrong records, but one could argue when
the molecule is wrong there is no point reading the properties.
I only adjusted a couple of details (made sure that the file is read as text,
not binary, otherwise no valid record is found; included the handling of
gzipped files; added a writer to store the wrong records as they are read).
Something like this:
import gzip
import rdkit
from rdkit import Chem
import pickle
def read_record(fh):
lines = []
for line in fh:
lines.append(line)
if line.rstrip() == '':
return ''.join(lines)
def read_records(fh):
while True:
rec = read_record(fh)
if rec is None:
return
yield rec
sup = Chem.SDMolSupplier()
d = dict()
mols_pickled = []
i = 0
with gzip.open('x.sdf.gz', 'rt') as fh, gzip.open('x_wrong.sdf.gz', 'wt') as
fh_wrong:
for rec in read_records(fh):
sup.SetData(rec)
mol = next(sup)
if mol is None:
fh_wrong.write(rec)
else:
d[i] = mol.GetPropsAsDict()
mols_pickled.append(pickle.dumps(mol))
i += 1
After running this, there is a file with the wrong records (if any), the
correct molecules are pickled and stored in a list, and their data are in a
dictionary of dictionaries that can be converted for instance to a DataFrame.
I take your point of caution regarding whether it is safe or not to split
records by detecting a line exactly equal to string ''.
Not sure how much of a practical problem it really is.
I can report that I've just ran the above script on an SDF with 1.5 M molecules
coming from several sources, and it completed in 5 minutes without stumbling.
But yes, if someone is dead set on making this go wrong, it is possible, by
just defining a property with exact value '' and writing it out to an SDF.
I've yet to come across such an occurrence, after several years of working with
SDF's. So I'm not overly worried.
Thanks again for your input!
Giovanni
From: Ivan Tubert-Brohman
Sent: 14 April 2022 12:58
To: Giovanni Tricarico
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] how to report SDF records for which
Chem.ForwardSDMolSupplier returns None?
You don't often get email from
ivan.tubert-broh...@schrodinger.com.
Learn why this is important
How about splitting the file on lines consisting of "", and then parsing
each record? If the parsing fails, you can write out the bad record for future
inspection. (This addresses the basic use case, but not the "even better" one.)
Here's a proof of concept:
from rdkit import Chem
def read_record(fh):
lines = []
for line in fh:
lines.append(line)
if line.rstrip() == '':
return ''.join(lines)
def read_records(fh):
while True:
rec = read_record(fh)
if rec is None:
return
yield rec
sup = Chem.SDMolSupplier()
with open('x.sdf') as fh:
for rec in read_records(fh):
sup.SetData(rec)
mol = next(sup)
if mol is None:
print("Bad record:\n", rec)
continue
print(mol.GetPropsAsDict())
I worry that this is not strictly correct, because what if the value of a
property happens to be ""? But apparently RDKit's own SDMolSupplier is also
confused by this (or maybe such values are forbidden by the file format and/or
there's some escape mechanism? I haven't checked), so I don't feel nearly as
bad about that.
Ivan
On Wed, Apr 13, 2022 at 4:29 PM Giovanni Tricarico
mailto:giovanni.tricar...@glpg.com>> wrote:
Hello,
I am using rdkit to read data from SD files.
My goal is to extract both the molecules and their associated properties (which
for our purposes are separate entities) from the SDF.
[For 100% clarity: by 'properties' I don't mean calculated properties or atom
or bond properties, but the text properties that were saved in the SDF with
each molecule, i.e. those that you get when you do mol.GetPropsAsDict() ].
After several tests I found that Chem.ForwardSDMolSupplier does what I need.
But there is an issue.
When Chem.ForwardSDMolSupplier decides that a molecule is not OK, i.e. when it
says it is None, the SDF record is lost:
I cannot access its Props; I cannot save the failed SDF record for later
inspection.
[Or at least, I don't know how to do it, hence this question].
At most I can collect the indices of the records that fail.
> Would anyone be able to suggest how to save to a text file (which an SDF
> essentially already is) the SDF records for which Chem.ForwardSDMolSupplier
> returns a None?
> Even better, could the properties associated to the failed molecules be read
> independently? In theory the properties are in a separate part of the CTAB,
> so even when the atoms, bonds, etc.
Re: [Rdkit-discuss] how to report SDF records for which Chem.ForwardSDMolSupplier returns None?
On Apr 14, 2022, at 12:57, Ivan Tubert-Brohman wrote: > How about splitting the file on lines consisting of "", and then parsing > each record? If the parsing fails, you can write out the bad record for > future inspection. (This addresses the basic use case, but not the "even > better" one.) Yes, if you know your data is "clean", then you can do that. I wrote an essay at http://www.dalkescientific.com/writings/diary/archive/2020/09/18/handling_the_sdf_record_delimiter.html about some of the ways that can cause problems. They do occur in real-world data sets. And they do cause problems in some processing pipelines. Public data sets like PubChem, ChEMBL, etc. don't have these problems. They are mostly in in-house data sets. Though it's not common to have a problem. > def read_record(fh): > lines = [] > for line in fh: > lines.append(line) > if line.rstrip() == '': > return ''.join(lines) See also https://baoilleach.blogspot.com/2020/05/python-patterns-for-processing-large.html . The reasons I think there should be a low-level library for this sort of work are: 1) the edge cases are tricky to handle, 2) the simple readers like this are slow 3) I believe good error reporting needs things like the starting line number and/or starting byte position for the record. Implementing that is a bit tricky (and boring), and tracking that information in a compiled extension has a much lower overhead than doing it in Python. Cheers, Andrew da...@dalkescientific.com ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] how to report SDF records for which Chem.ForwardSDMolSupplier returns None?
How about splitting the file on lines consisting of "", and then
parsing each record? If the parsing fails, you can write out the bad record
for future inspection. (This addresses the basic use case, but not the
"even better" one.)
Here's a proof of concept:
from rdkit import Chem
def read_record(fh):
lines = []
for line in fh:
lines.append(line)
if line.rstrip() == '':
return ''.join(lines)
def read_records(fh):
while True:
rec = read_record(fh)
if rec is None:
return
yield rec
sup = Chem.SDMolSupplier()
with open('x.sdf') as fh:
for rec in read_records(fh):
sup.SetData(rec)
mol = next(sup)
if mol is None:
print("Bad record:\n", rec)
continue
print(mol.GetPropsAsDict())
I worry that this is not strictly correct, because what if the value of a
property happens to be ""? But apparently RDKit's own SDMolSupplier is
also confused by this (or maybe such values are forbidden by the file
format and/or there's some escape mechanism? I haven't checked), so I don't
feel nearly as bad about that.
Ivan
On Wed, Apr 13, 2022 at 4:29 PM Giovanni Tricarico <
giovanni.tricar...@glpg.com> wrote:
> Hello,
>
> I am using rdkit to read data from SD files.
>
>
>
> My goal is to extract both the molecules and their associated properties
> (which for our purposes are separate entities) from the SDF.
>
> [For 100% clarity: by ‘properties’ I don’t mean calculated properties or
> atom or bond properties, but the text properties that were saved in the SDF
> with each molecule, i.e. those that you get when you do
> mol.GetPropsAsDict() ].
>
>
>
> After several tests I found that Chem.ForwardSDMolSupplier does what I
> need.
>
>
>
> But there is an issue.
>
> When Chem.ForwardSDMolSupplier decides that a molecule is not OK, i.e.
> when it says it is None, the SDF record is lost:
>
> I cannot access its Props; I cannot save the failed SDF record for later
> inspection.
>
> [Or at least, I don’t know how to do it, hence this question].
>
> At most I can collect the indices of the records that fail.
>
>
>
> > Would anyone be able to suggest how to save to a text file (which an SDF
> essentially already is) the SDF records for which
> Chem.ForwardSDMolSupplier returns a None?
>
> > Even better, could the properties associated to the failed molecules be
> read independently? In theory the properties are in a separate part of the
> CTAB, so even when the atoms, bonds, etc. have a problem, the properties
> might still be OK.
>
>
>
> (Note: PandasTools.LoadSDF gives the same issue, it does not even store
> in the DataFrame the records for which the molecule is None, and in any
> case it cannot be used with the kind of SDF’s I am handling, as it uses an
> enormous amount of memory for the molecules – hence the decision to use
> Chem.ForwardSDMolSupplier and pickle the molecules as soon as they are
> read).
>
>
>
> Thanks
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Re: [Rdkit-discuss] how to report SDF records for which Chem.ForwardSDMolSupplier returns None?
On Apr 14, 2022, at 09:16, Gyro Funch wrote:
> I don't know the sdf format well, so please excuse my ignorance, but instead
> of a custom parser, would it be possible to write a preprocessor to eliminate
> the offending information? Perhaps something using regular expressions in
> python, perl, sed, or awk?
The SDF format is too complicated to be parsed with a regular expression[1],
and the failure modes often cannot be detected at the syntax level[2]. I
suggest people may consider using chemfp for this [3].
[1] For example, in a V2000-formatted record, the number of atom records and
the number of bond records are given by a repeat count. A traditional/formal
regular expression does not support counts where the count from the pattern
matching.
Most regular expression engines have more powerful capabilities than formal
regular expression, such as matches to back-reference captured groups. However,
few support using a backreference as a repeat count.
I wrote one that did, which would let you specify
(?P...)(?P...) and so on)
(?P(?P.{10})(?P.{10}) and so on){atom_count}
(?P(?P.{3})(?P.{3}) and so on){bond_count}
but in practice, defining the grammar through a regular expression grammar was
decidedly not easy!
I've wanted to experiment with using WUFFS to make a low-level SDF parser
library, see
https://github.com/google/wuffs
[2] For example, RDKit by default rejects atoms where the valence is too high.
Detecting this in filter code calls for reverse-engineering what RDKit already
does.
[3] Chemfp is best known as a fingerprint generation and search program.
However, there are a few use cases where I wanted to have access to the input
record (eg, to detect toolkit failures, or to add fingerprint data to the input
record rather than round-tripping the SDF through a toolkit.) I did this by
writing my own SDF record reader (in the "text_toolkit"), and writing a wrapper
to the RDKit toolkit (in the "rdkit_toolkit"), and using a error handler which
can decide how to handle errors (ignore, report, raise an exception, log,
etc.). That error handler has access to location information, which includes
the record number, the record text, the line number of the start of the record,
and more.
Here's what it looks like for Giovanni's use case:
from chemfp import rdkit_toolkit as T
from chemfp import text_toolkit
filename = "/Users/dalke/databases/ChEBI_complete_3star.sdf.gz"
class ErrorHandler:
def __init__(self):
self.error_ids = []
def error(self, msg, location, extra=None):
record = location.record
chebi_id = text_toolkit.get_sdf_tag(location.record, "ChEBI ID")
print(f"!!! Error reading record {location.recno} with ID:
{chebi_id!r}")
print(f"at {location.where()}")
self.error_ids.append(chebi_id)
errors = ErrorHandler()
count = 0
num_atoms = 0
for mol in T.read_molecules(filename, errors=errors):
count += 1
num_atoms += mol.GetNumAtoms() # This is a RDMol.
print(f"Parsed {count} records ({num_atoms} atoms), skipped
{len(errors.error_ids)}.")
This functionality is available in the pre-compiled version of chemfp for
Linux-base OSes, available from https://chemfp.com/download/ . The default
license agreement (that is, you can use it without a license key) lets you use
it for any internal purpose.
If anyone is interested in working on a stand-alone SDF parsing library under a
free software license, I can provide some pointers and feedback, and will
contribute chemfp's SDF parser under the MIT license.
Andrew
da...@dalkescientific.com
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[Rdkit-discuss] Building RDKit on Windows for pgAdmin (Postgres)
Hello, I've been trying to build RDKit on Windows so that I can get the RDKit extension in pgAdmin (Postgres) but I've been unsuccessful. I've tried to follow the instruction on https://www.rdkit.org/docs/Install.html to build RDKit and encountered several problems. Some of them I manage to resolve myself but can someone help on this? Here is what I've tried: To start off, I'm using the Windows 11 64-bit OS and Postgres 14 was installed. I then went to install the following: Python 3.10 along with numpy and Pillow Visual Studio 2022 with Visual Studio Community 2022, Visual Studio Build Tools 2022 Cmake 3.23.0 Boost_1_78_0 using the .exe installer And downloaded and extracted the rdkit-Release_2022_03_1 After install the above, I ran the below in Comand Prompt cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 2022" .. came back with error: The following variants have been tried and rejected: * boost_python310-vc143-mt-gd-x64-1_78.lib (shared, default on Windows is static, set Boost_USE_STATIC_LIBS=OFF to override) * boost_python310-vc143-mt-x64-1_78.lib (shared, default on Windows is static, set Boost_USE_STATIC_LIBS=OFF to override) I then edit the command line to cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 -DBoost_USE_STATIC_LIBS=OFF -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 2022" .. and this time following error occured Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0") CMake Error at C:/Program Files/CMake/share/cmake-3.23/Modules/ExternalProject.cmake:2540 (message): error: could not find git for clone of Eigen So I went to download and extracted eigen 3.4.0 and edit the command line to cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0 -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0" -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 2022" .. which gave the following error CMake Error at C:/Program Files/CMake/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find Freetype (missing: FREETYPE_LIBRARY FREETYPE_INCLUDE_DIRS) So again I went to obtain freetype-2.12.0 and build it following the instructions on https://bobhowto.wordpress.com/2020/11/10/build-freetype-on-windows-10-using-visual-studio-2017/, using VS 2022 instead, and edit the command line to cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/local/boost_1_78_0 -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0" -DFREETYPE_INCLUDE_DIRS="C:/freetype-2.12.0/include" -DFREETYPE_LIBRARY="C:/freetype-2.12.0/objs/freetype.lib" -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17 2022" .. and it managed to compile However, when running "C:\Program Files\Microsoft Visual Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" /m:4 /p:Configuration=Release INSTALL.vcxproj Gave the following error with 47 other warnings "C:\rdkit-Release_2022_03_1\build\INSTALL.vcxproj" (default target) (1) -> "C:\rdkit-Release_2022_03_1\build\ALL_BUILD.vcxproj" (default target) (3) -> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\Deprotect\Wrap\rdDeprotect.vcxproj" (default target) (20) -> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\ChemReactions\ChemReactions.vcxproj" (default target) (48) -> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\Descriptors\Descriptors.vcxproj" (default target) (55) -> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\FileParsers\FileParsers.vcxproj" (default target) (56) -> (ClCompile target) -> C:\rdkit-Release_2022_03_1\Code\GraphMol\FileParsers\PNGParser.cpp(25,10): fatal error C1083: Cannot open incl ude file: 'zlib.h': No such file or directory [C:\rdkit-Release_2022_03_1\build\Code\GraphMol\FileParsers\FilePa rsers.vcxproj] So I went to obtain zlib 1.2.12 and build it via cmake -G"Visual Studio 17 2022" .. "C:\Program Files\Microsoft Visual Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" zlib.sln copy /Y zconf.h .. and compiled the boost libraries via b2 --prefix=C:\local\boost_1_78_0 -sZLIB_SOURCE="C:/zlib-1.2.12" -sZLIB_INCLUDE="C:/zlib-1.2.12" -sZLIB_LIBPATH="C:/zlib-1.2.12/build/Release" -sZLIB_BINARY="C:/zlib-1.2.12/build/Release/zlib.lib" --debug-configuration -d0 address-model=64 link=shared install and changed the PATH in the environment variables to C:\local\boost_1_78_0\lib but running the build code and the INSTALL.vcxproj gave the same error
Re: [Rdkit-discuss] how to report SDF records for which Chem.ForwardSDMolSupplier returns None?
On 2022-04-14 08:12 AM, Giovanni Tricarico wrote: Thank you Nils. In fact I do want the sanitize + parse to happen, and I do some further checks on the molecules, too (ChEMBL pipeline etc). The issue is that whatever does not pass the initial steps just completely disappears and cannot be reported or inspected in any way. Indeed, making a custom SDF parser would be one option, as an SDF is just text, and rigidly 'structured' by its very definition; only, I was hoping someone had already written such a parser :) For now I will just output the indices of the failed records; the user will then have to read them in another application for inspection. Thanks Giovanni -Original Message- From: Nils Weskamp Sent: 13 April 2022 22:55 To: Giovanni Tricarico ; rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] how to report SDF records for which Chem.ForwardSDMolSupplier returns None? [You don't often get email from nils.wesk...@gmail.com. Learn why this is important at http://aka.ms/LearnAboutSenderIdentification.] Hello Giovanni, have you tried using the ForwardSDMolSupplier with sanitize = False and / or strictParsing = False ? This should at least reduce the number of cases where molecules are not accepted. You would then have to sanitize the structures yourself afterwards and handle possible errors explicitly. If that doesn't solve your problem, I would consider to write my own parser that just ignores everything looking like a CTAB. Hope this helps, Nils Am 13.04.2022 um 18:15 schrieb Giovanni Tricarico: Hello, I am using rdkit to read data from SD files. My goal is to extract both the molecules and their associated properties (which for our purposes are separate entities) from the SDF. [For 100% clarity: by 'properties' I don't mean calculated properties or atom or bond properties, but the text properties that were saved in the SDF with each molecule, i.e. those that you get when you do mol.GetPropsAsDict() ]. After several tests I found that Chem.ForwardSDMolSupplier does what I need. But there is an issue. When Chem.ForwardSDMolSupplier decides that a molecule is not OK, i.e. when it says it is None, the SDF record is lost: I cannot access its Props; I cannot save the failed SDF record for later inspection. [Or at least, I don't know how to do it, hence this question]. At most I can collect the indices of the records that fail. > Would anyone be able to suggest how to save to a text file (which an SDF essentially already is) the SDF records for which Chem.ForwardSDMolSupplier returns a None? > Even better, could the properties associated to the failed molecules be read independently? In theory the properties are in a separate part of the CTAB, so even when the atoms, bonds, etc. have a problem, the properties might still be OK. (Note: PandasTools.LoadSDF gives the same issue, it does not even store in the DataFrame the records for which the molecule is None, and in any case it cannot be used with the kind of SDF's I am handling, as it uses an enormous amount of memory for the molecules - hence the decision to use Chem.ForwardSDMolSupplier and pickle the molecules as soon as they are read). Thanks I don't know the sdf format well, so please excuse my ignorance, but instead of a custom parser, would it be possible to write a preprocessor to eliminate the offending information? Perhaps something using regular expressions in python, perl, sed, or awk? Kind regards, gyro ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
