Update of RDkit
Clash Royale CLAN TAG#URR8PPP up vote
1
down vote
favorite
I installed RDkit following instructions from the following website using the following line of code,
sudo apt-get install python-rdkit librdkit1 rdkit-data
But when I check the version using the following code (in python), following instructions from this webpage
>>> import rdkit
>>> from rdkit import rdBase
>>> rdBase.rdkitVersion
'2013.09.1'
I don't get the latest version.
How can I update this version, either in ubuntu at the command line or in python?
System details
>>> import sys
>>> print(sys.version)
2.7.6 (default, Nov 23 2017, 15:49:48)
[GCC 4.8.4]
and Ubuntu
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 14.04.5 LTS
Release: 14.04
Codename: trusty
ps If it is of any interest I want to run a piece of python code called, take_elementary_step
updates python
asked Feb 27 at 16:36
user1945827
17611
add a comment |Â
up vote
1
down vote
favorite
I installed RDkit following instructions from the following website using the following line of code,
sudo apt-get install python-rdkit librdkit1 rdkit-data
But when I check the version using the following code (in python), following instructions from this webpage
>>> import rdkit
>>> from rdkit import rdBase
>>> rdBase.rdkitVersion
'2013.09.1'
I don't get the latest version.
How can I update this version, either in ubuntu at the command line or in python?
System details
>>> import sys
>>> print(sys.version)
2.7.6 (default, Nov 23 2017, 15:49:48)
[GCC 4.8.4]
and Ubuntu
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 14.04.5 LTS
Release: 14.04
Codename: trusty
ps If it is of any interest I want to run a piece of python code called, take_elementary_step
updates python
asked Feb 27 at 16:36
user1945827
17611
Ubuntu repositories don't always have the latest version. The version it has is always the most compatible. That means it should work with the version of Ubuntu you have.
– user68186
Feb 27 at 17:21
It works with my Ubuntu but not with the code I'm trying to run. The author tells me (twitter exchange) that the rdkit version is too low.
– user1945827
Feb 27 at 19:13
add a comment |Â
up vote
1
down vote
favorite
up vote
1
down vote
favorite
I installed RDkit following instructions from the following website using the following line of code,
sudo apt-get install python-rdkit librdkit1 rdkit-data
But when I check the version using the following code (in python), following instructions from this webpage
>>> import rdkit
>>> from rdkit import rdBase
>>> rdBase.rdkitVersion
'2013.09.1'
I don't get the latest version.
How can I update this version, either in ubuntu at the command line or in python?
System details
>>> import sys
>>> print(sys.version)
2.7.6 (default, Nov 23 2017, 15:49:48)
[GCC 4.8.4]
and Ubuntu
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 14.04.5 LTS
Release: 14.04
Codename: trusty
ps If it is of any interest I want to run a piece of python code called, take_elementary_step
updates python
asked Feb 27 at 16:36
user1945827
17611
I installed RDkit following instructions from the following website using the following line of code,
sudo apt-get install python-rdkit librdkit1 rdkit-data
But when I check the version using the following code (in python), following instructions from this webpage
>>> import rdkit
>>> from rdkit import rdBase
>>> rdBase.rdkitVersion
'2013.09.1'
I don't get the latest version.
How can I update this version, either in ubuntu at the command line or in python?
System details
>>> import sys
>>> print(sys.version)
2.7.6 (default, Nov 23 2017, 15:49:48)
[GCC 4.8.4]
and Ubuntu
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 14.04.5 LTS
Release: 14.04
Codename: trusty
ps If it is of any interest I want to run a piece of python code called, take_elementary_step
updates python
updates python
asked Feb 27 at 16:36
user1945827
17611
asked Feb 27 at 16:36
user1945827
17611
edited Feb 27 at 19:11
asked Feb 27 at 16:36
user1945827
17611
asked Feb 27 at 16:36
user1945827
17611
asked Feb 27 at 16:36
user1945827
17611
17611
Ubuntu repositories don't always have the latest version. The version it has is always the most compatible. That means it should work with the version of Ubuntu you have.
– user68186
Feb 27 at 17:21
It works with my Ubuntu but not with the code I'm trying to run. The author tells me (twitter exchange) that the rdkit version is too low.
– user1945827
Feb 27 at 19:13
add a comment |Â
Ubuntu repositories don't always have the latest version. The version it has is always the most compatible. That means it should work with the version of Ubuntu you have.
– user68186
Feb 27 at 17:21
It works with my Ubuntu but not with the code I'm trying to run. The author tells me (twitter exchange) that the rdkit version is too low.
– user1945827
Feb 27 at 19:13
Ubuntu repositories don't always have the latest version. The version it has is always the most compatible. That means it should work with the version of Ubuntu you have.
– user68186
Feb 27 at 17:21
Ubuntu repositories don't always have the latest version. The version it has is always the most compatible. That means it should work with the version of Ubuntu you have.
– user68186
Feb 27 at 17:21
It works with my Ubuntu but not with the code I'm trying to run. The author tells me (twitter exchange) that the rdkit version is too low.
– user1945827
Feb 27 at 19:13
It works with my Ubuntu but not with the code I'm trying to run. The author tells me (twitter exchange) that the rdkit version is too low.
– user1945827
Feb 27 at 19:13
add a comment |Â
2 Answers
2
active
oldest
votes
up vote
2
down vote
accepted
To update RDKit, you'd have to compile it from source. This doesn't appear to be trivial to do.
This said, I have grabbed the rdkit source code from Ubuntu Bionic (in development, but this is the latest from Debian), and backported it within a PPA to Trusty and Xenial.
You can do the following to install the updated version of python-rdkit (I am still working on adapting this package to work with the latest RDKit, but I can't guarantee I'll provide ongoing updates):
sudo apt-get remove python-rdkit
sudo apt-get autoremove
sudo add-apt-repository ppa:teward/python-rdkit
sudo apt-get update
sudo apt-get install python-rdkit
While this also will clean out other obsolete packages and such, it should then install a newer version of RDkit (from March 2016).
(I'm still working to see if there's a newer RDKit package somewhere though...)
answered Mar 1 at 14:52
Thomas Ward♦
41.6k23113166
1
Note that I have verified these steps work in a clean environment. This installs the March 2016 version - the latest available in Debian.
– Thomas Ward♦
Mar 1 at 15:19
add a comment |Â
up vote
0
down vote
If i search for rdkit with
apt search rdkit
I get "python-rdkit/xenial 201503-3 amd64" as one of the entries. The version number says 201503-3.
I just tried installing it like you, by running
sudo apt install python-rdkit
When i import and check the version:
>>> rdkit.rdBase.rdkitVersion
'2015.03.1'
That is a more recent version than yours atleast, so maybe try reinstalling?
Also notice that this is for python 2.7.12
answered Feb 27 at 17:15
user3430996
728
1
You're using Xenial. OP is on Trusty.
– Thomas Ward♦
Feb 27 at 19:15
I got python-rdkit/trusty,now 201309-1 amd64 [installed] when I ran your code. When I ran sudo apt install python-rdkit there was no difference with respect to version.
– user1945827
Feb 27 at 19:18
1
@user1945827 Note that the answer here was for Xenial, and not Trusty. You are on Trusty so you have to install viapip/PyPI, and not the repositories. See my answer.
– Thomas Ward♦
Feb 27 at 19:18
@ThomasWard when i search via pip i get version 2009: "rdkit (2009.Q1b1)", so im not so sure that that is the answer.
– user3430996
Feb 27 at 19:54
@mrfred489 I see the same search. But, when I look at PyPI itself, there's no versions uploaded to PyPI for it. (And I checked the rdkit site, it's non-trivial to build it since the python part is just a python wrapper around the C libraries that rdkit actually is)
– Thomas Ward♦
Feb 27 at 19:58
add a comment |Â
2 Answers
2
active
oldest
votes
2 Answers
2
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
2
down vote
accepted
To update RDKit, you'd have to compile it from source. This doesn't appear to be trivial to do.
This said, I have grabbed the rdkit source code from Ubuntu Bionic (in development, but this is the latest from Debian), and backported it within a PPA to Trusty and Xenial.
You can do the following to install the updated version of python-rdkit (I am still working on adapting this package to work with the latest RDKit, but I can't guarantee I'll provide ongoing updates):
sudo apt-get remove python-rdkit
sudo apt-get autoremove
sudo add-apt-repository ppa:teward/python-rdkit
sudo apt-get update
sudo apt-get install python-rdkit
While this also will clean out other obsolete packages and such, it should then install a newer version of RDkit (from March 2016).
(I'm still working to see if there's a newer RDKit package somewhere though...)
answered Mar 1 at 14:52
Thomas Ward♦
41.6k23113166
1
Note that I have verified these steps work in a clean environment. This installs the March 2016 version - the latest available in Debian.
– Thomas Ward♦
Mar 1 at 15:19
add a comment |Â
up vote
2
down vote
accepted
To update RDKit, you'd have to compile it from source. This doesn't appear to be trivial to do.
This said, I have grabbed the rdkit source code from Ubuntu Bionic (in development, but this is the latest from Debian), and backported it within a PPA to Trusty and Xenial.
You can do the following to install the updated version of python-rdkit (I am still working on adapting this package to work with the latest RDKit, but I can't guarantee I'll provide ongoing updates):
sudo apt-get remove python-rdkit
sudo apt-get autoremove
sudo add-apt-repository ppa:teward/python-rdkit
sudo apt-get update
sudo apt-get install python-rdkit
While this also will clean out other obsolete packages and such, it should then install a newer version of RDkit (from March 2016).
(I'm still working to see if there's a newer RDKit package somewhere though...)
answered Mar 1 at 14:52
Thomas Ward♦
41.6k23113166
1
Note that I have verified these steps work in a clean environment. This installs the March 2016 version - the latest available in Debian.
– Thomas Ward♦
Mar 1 at 15:19
add a comment |Â
up vote
2
down vote
accepted
up vote
2
down vote
accepted
To update RDKit, you'd have to compile it from source. This doesn't appear to be trivial to do.
This said, I have grabbed the rdkit source code from Ubuntu Bionic (in development, but this is the latest from Debian), and backported it within a PPA to Trusty and Xenial.
You can do the following to install the updated version of python-rdkit (I am still working on adapting this package to work with the latest RDKit, but I can't guarantee I'll provide ongoing updates):
sudo apt-get remove python-rdkit
sudo apt-get autoremove
sudo add-apt-repository ppa:teward/python-rdkit
sudo apt-get update
sudo apt-get install python-rdkit
While this also will clean out other obsolete packages and such, it should then install a newer version of RDkit (from March 2016).
(I'm still working to see if there's a newer RDKit package somewhere though...)
answered Mar 1 at 14:52
Thomas Ward♦
41.6k23113166
To update RDKit, you'd have to compile it from source. This doesn't appear to be trivial to do.
This said, I have grabbed the rdkit source code from Ubuntu Bionic (in development, but this is the latest from Debian), and backported it within a PPA to Trusty and Xenial.
You can do the following to install the updated version of python-rdkit (I am still working on adapting this package to work with the latest RDKit, but I can't guarantee I'll provide ongoing updates):
sudo apt-get remove python-rdkit
sudo apt-get autoremove
sudo add-apt-repository ppa:teward/python-rdkit
sudo apt-get update
sudo apt-get install python-rdkit
While this also will clean out other obsolete packages and such, it should then install a newer version of RDkit (from March 2016).
(I'm still working to see if there's a newer RDKit package somewhere though...)
answered Mar 1 at 14:52
Thomas Ward♦
41.6k23113166
answered Mar 1 at 14:52
Thomas Ward♦
41.6k23113166
answered Mar 1 at 14:52
Thomas Ward♦
41.6k23113166
answered Mar 1 at 14:52
Thomas Ward♦
41.6k23113166
41.6k23113166
1
Note that I have verified these steps work in a clean environment. This installs the March 2016 version - the latest available in Debian.
– Thomas Ward♦
Mar 1 at 15:19
add a comment |Â
1
Note that I have verified these steps work in a clean environment. This installs the March 2016 version - the latest available in Debian.
– Thomas Ward♦
Mar 1 at 15:19
1
1
Note that I have verified these steps work in a clean environment. This installs the March 2016 version - the latest available in Debian.
– Thomas Ward♦
Mar 1 at 15:19
Note that I have verified these steps work in a clean environment. This installs the March 2016 version - the latest available in Debian.
– Thomas Ward♦
Mar 1 at 15:19
add a comment |Â
up vote
0
down vote
If i search for rdkit with
apt search rdkit
I get "python-rdkit/xenial 201503-3 amd64" as one of the entries. The version number says 201503-3.
I just tried installing it like you, by running
sudo apt install python-rdkit
When i import and check the version:
>>> rdkit.rdBase.rdkitVersion
'2015.03.1'
That is a more recent version than yours atleast, so maybe try reinstalling?
Also notice that this is for python 2.7.12
answered Feb 27 at 17:15
user3430996
728
1
You're using Xenial. OP is on Trusty.
– Thomas Ward♦
Feb 27 at 19:15
I got python-rdkit/trusty,now 201309-1 amd64 [installed] when I ran your code. When I ran sudo apt install python-rdkit there was no difference with respect to version.
– user1945827
Feb 27 at 19:18
1
@user1945827 Note that the answer here was for Xenial, and not Trusty. You are on Trusty so you have to install viapip/PyPI, and not the repositories. See my answer.
– Thomas Ward♦
Feb 27 at 19:18
@ThomasWard when i search via pip i get version 2009: "rdkit (2009.Q1b1)", so im not so sure that that is the answer.
– user3430996
Feb 27 at 19:54
@mrfred489 I see the same search. But, when I look at PyPI itself, there's no versions uploaded to PyPI for it. (And I checked the rdkit site, it's non-trivial to build it since the python part is just a python wrapper around the C libraries that rdkit actually is)
– Thomas Ward♦
Feb 27 at 19:58
add a comment |Â
up vote
0
down vote
If i search for rdkit with
apt search rdkit
I get "python-rdkit/xenial 201503-3 amd64" as one of the entries. The version number says 201503-3.
I just tried installing it like you, by running
sudo apt install python-rdkit
When i import and check the version:
>>> rdkit.rdBase.rdkitVersion
'2015.03.1'
That is a more recent version than yours atleast, so maybe try reinstalling?
Also notice that this is for python 2.7.12
answered Feb 27 at 17:15
user3430996
728
1
You're using Xenial. OP is on Trusty.
– Thomas Ward♦
Feb 27 at 19:15
I got python-rdkit/trusty,now 201309-1 amd64 [installed] when I ran your code. When I ran sudo apt install python-rdkit there was no difference with respect to version.
– user1945827
Feb 27 at 19:18
1
@user1945827 Note that the answer here was for Xenial, and not Trusty. You are on Trusty so you have to install viapip/PyPI, and not the repositories. See my answer.
– Thomas Ward♦
Feb 27 at 19:18
@ThomasWard when i search via pip i get version 2009: "rdkit (2009.Q1b1)", so im not so sure that that is the answer.
– user3430996
Feb 27 at 19:54
@mrfred489 I see the same search. But, when I look at PyPI itself, there's no versions uploaded to PyPI for it. (And I checked the rdkit site, it's non-trivial to build it since the python part is just a python wrapper around the C libraries that rdkit actually is)
– Thomas Ward♦
Feb 27 at 19:58
add a comment |Â
up vote
0
down vote
up vote
0
down vote
If i search for rdkit with
apt search rdkit
I get "python-rdkit/xenial 201503-3 amd64" as one of the entries. The version number says 201503-3.
I just tried installing it like you, by running
sudo apt install python-rdkit
When i import and check the version:
>>> rdkit.rdBase.rdkitVersion
'2015.03.1'
That is a more recent version than yours atleast, so maybe try reinstalling?
Also notice that this is for python 2.7.12
answered Feb 27 at 17:15
user3430996
728
If i search for rdkit with
apt search rdkit
I get "python-rdkit/xenial 201503-3 amd64" as one of the entries. The version number says 201503-3.
I just tried installing it like you, by running
sudo apt install python-rdkit
When i import and check the version:
>>> rdkit.rdBase.rdkitVersion
'2015.03.1'
That is a more recent version than yours atleast, so maybe try reinstalling?
Also notice that this is for python 2.7.12
answered Feb 27 at 17:15
user3430996
728
answered Feb 27 at 17:15
user3430996
728
answered Feb 27 at 17:15
user3430996
728
answered Feb 27 at 17:15
user3430996
728
728
1
You're using Xenial. OP is on Trusty.
– Thomas Ward♦
Feb 27 at 19:15
I got python-rdkit/trusty,now 201309-1 amd64 [installed] when I ran your code. When I ran sudo apt install python-rdkit there was no difference with respect to version.
– user1945827
Feb 27 at 19:18
1
@user1945827 Note that the answer here was for Xenial, and not Trusty. You are on Trusty so you have to install viapip/PyPI, and not the repositories. See my answer.
– Thomas Ward♦
Feb 27 at 19:18
@ThomasWard when i search via pip i get version 2009: "rdkit (2009.Q1b1)", so im not so sure that that is the answer.
– user3430996
Feb 27 at 19:54
@mrfred489 I see the same search. But, when I look at PyPI itself, there's no versions uploaded to PyPI for it. (And I checked the rdkit site, it's non-trivial to build it since the python part is just a python wrapper around the C libraries that rdkit actually is)
– Thomas Ward♦
Feb 27 at 19:58
add a comment |Â
1
You're using Xenial. OP is on Trusty.
– Thomas Ward♦
Feb 27 at 19:15
I got python-rdkit/trusty,now 201309-1 amd64 [installed] when I ran your code. When I ran sudo apt install python-rdkit there was no difference with respect to version.
– user1945827
Feb 27 at 19:18
1
@user1945827 Note that the answer here was for Xenial, and not Trusty. You are on Trusty so you have to install viapip/PyPI, and not the repositories. See my answer.
– Thomas Ward♦
Feb 27 at 19:18
@ThomasWard when i search via pip i get version 2009: "rdkit (2009.Q1b1)", so im not so sure that that is the answer.
– user3430996
Feb 27 at 19:54
@mrfred489 I see the same search. But, when I look at PyPI itself, there's no versions uploaded to PyPI for it. (And I checked the rdkit site, it's non-trivial to build it since the python part is just a python wrapper around the C libraries that rdkit actually is)
– Thomas Ward♦
Feb 27 at 19:58
1
1
You're using Xenial. OP is on Trusty.
– Thomas Ward♦
Feb 27 at 19:15
You're using Xenial. OP is on Trusty.
– Thomas Ward♦
Feb 27 at 19:15
I got python-rdkit/trusty,now 201309-1 amd64 [installed] when I ran your code. When I ran sudo apt install python-rdkit there was no difference with respect to version.
– user1945827
Feb 27 at 19:18
I got python-rdkit/trusty,now 201309-1 amd64 [installed] when I ran your code. When I ran sudo apt install python-rdkit there was no difference with respect to version.
– user1945827
Feb 27 at 19:18
1
1
@user1945827 Note that the answer here was for Xenial, and not Trusty. You are on Trusty so you have to install via
pip/PyPI, and not the repositories. See my answer.– Thomas Ward♦
Feb 27 at 19:18
@user1945827 Note that the answer here was for Xenial, and not Trusty. You are on Trusty so you have to install via
pip/PyPI, and not the repositories. See my answer.– Thomas Ward♦
Feb 27 at 19:18
@ThomasWard when i search via pip i get version 2009: "rdkit (2009.Q1b1)", so im not so sure that that is the answer.
– user3430996
Feb 27 at 19:54
@ThomasWard when i search via pip i get version 2009: "rdkit (2009.Q1b1)", so im not so sure that that is the answer.
– user3430996
Feb 27 at 19:54
@mrfred489 I see the same search. But, when I look at PyPI itself, there's no versions uploaded to PyPI for it. (And I checked the rdkit site, it's non-trivial to build it since the python part is just a python wrapper around the C libraries that rdkit actually is)
– Thomas Ward♦
Feb 27 at 19:58
@mrfred489 I see the same search. But, when I look at PyPI itself, there's no versions uploaded to PyPI for it. (And I checked the rdkit site, it's non-trivial to build it since the python part is just a python wrapper around the C libraries that rdkit actually is)
– Thomas Ward♦
Feb 27 at 19:58
add a comment |Â
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Ubuntu repositories don't always have the latest version. The version it has is always the most compatible. That means it should work with the version of Ubuntu you have.
– user68186
Feb 27 at 17:21
It works with my Ubuntu but not with the code I'm trying to run. The author tells me (twitter exchange) that the rdkit version is too low.
– user1945827
Feb 27 at 19:13