Hi All,
I have been working on a python code that i am running in pymol. This code
takes in two files, one of which is a multi-model ligand pdb file that has
already been run through autodock vina. Therefore, each model within the
pdb file has a remark saying: "REMARK VINA RESULT:" followed by the binding
energy and RMSD values.
The goal of my code is to iterate through the atoms within different states
of the ligand and run some calculations--which is currently working very
well. However, i would like to add some other capabilities to the code,
including being able to take the autodock vina binding energy result into
account.
Due to the ability of iterating through the states of the pdb file as well
as running other pymol commands on these files, i am using the pymol
command 'cmd.load()' to import the files instead of the python command of
'open()'.
Looking through pymol archives i saw a brief mention that when opening a
pdb file with cmd.load(), it ignores and thus does not store any line that
starts with "REMARK"... is this always the case? or is there an option that
allows the user to store the information that is in the remarks?
The few solutions i have found online regarding being able to access the
information in a REMARK statement all take in the file with open(), and
proceed to look if the line has a certain string. This seems very
cumbersome, as the files i am working with will have anywhere from 20 to
100 models and i would have to go about a very convoluted process to get
each state's binding energy. Also, as far as my understanding goes, if you
use open() to read the file, you will not be able to run other pymol
commands on the file (such as cmd.iterate_state, cmd.pseudoatom, etc) which
are vital for my code.
So i am currently at a standstill when it comes to reading and storing the
binding affinities for each state of the multi-model pdb file. It would be
great if i could just create a list that contained all of the binding
affinities. Are there any ideas out there to help remedy this problem?
Thanks very much,
Rene
--
*Rene Francolini*
Carnegie Mellon University
M.S. Computational Biology 2016
B.S. Biological Sciences 2015
------
LinkedIn: www.linkedin.com/in/rfrancolini
Email: rene.francol...@gmail.com
Phone: (973) 303-5203
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