[Rdkit-discuss] Problem with reading/writing files?

2017-11-15 Thread Jan Halborg Jensen
The following code 1. energy-minizes a molecule and computes the energy 2. writes to coordinates to an sdf file, 3. reads it in and re-computes the energy But the two energies are off by 4 kcal/mol Any idea what I am doing wrong? Best regards, Jan from rdkit import Chem from rdkit.Chem import

Re: [Rdkit-discuss] Problem with reading/writing files?

2017-11-15 Thread Paolo Tosco
Dear Jan, you will need new_m = Chem.MolFromMolFile(file, removeHs=False) or hydrogens will be removed upon read. Cheers, p. On 11/15/17 13:50, Jan Halborg Jensen wrote: The following code 1. energy-minizes a molecule and computes the energy 2. writes to coordinates to an sdf file, 3. reads

[Rdkit-discuss] deglycosylation script

2017-11-15 Thread Axel Pahl
Dear fellow RDKitters, does someone have a script that he or she could share for the deglycosylation of chemical structures? Many thanks in advance. Kind regards, Axel -- Check out the vibrant tech community on one of

Re: [Rdkit-discuss] RPM distros

2017-11-15 Thread Tim Dudgeon
So this now seems to have been merged to master so I gave it a try: root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ .. -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) CUSTOM_INCHI_PA

Re: [Rdkit-discuss] RPM distros

2017-11-15 Thread Paolo Tosco
Hi Tim, It looks like you are missing the rpmbuild binary on the machine where you are trying to build the RPM. Issuing a yum install rpm-build as root should get it installed. Cheers, p. On 11/15/17 19:00, Tim Dudgeon wrote: So this now seems to have been merged to master so I gave it a

Re: [Rdkit-discuss] RPM distros

2017-11-15 Thread Tim Dudgeon
OK, makes sense, but I'm building on a Debian system. So neither 'yum install rpm-build' nor 'apt-get install rpm-build' doesn't work. So (sorry for the stupid question) can DEBs only be built on a Debian based system and RPMs om a Red Hat based system? On 15/11/2017 19:31, Paolo Tosco wrote

Re: [Rdkit-discuss] RPM distros

2017-11-15 Thread David Hall
apt install rpm should get you rpmbuild -David > On Nov 15, 2017, at 2:59 PM, Tim Dudgeon wrote: > > OK, makes sense, but I'm building on a Debian system. So neither 'yum install > rpm-build' nor 'apt-get install rpm-build' doesn't work. > > So (sorry for the stupid question) can DEBs only b

Re: [Rdkit-discuss] RPM distros

2017-11-15 Thread Tim Dudgeon
Thank you. I now have RPMs built: CPackRPM: Will use GENERATED spec file: /rdkit/build/_CPack_Packages/Linux/RPM/SPECS/rdkit-Runtime.spec CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Development.rpm generated. CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Extras.rpm ge