Package: pygen-structures
pygen-structurespygen-structures(pigeon structures) is a Python utility which allows for the generation of 3 dimensional molecular structures which can be used in molecular dynamics or Monte Carlo simulations. Molecules are generated from a list of residues and patches in the format of the CHARMM forcefield, and can be written out as valid PSF and PDB files. The package can be used as a command line utility, or as a Python library.pygen-structurescan be installed usingpip(pip install pygen-structures), but relies uponRDKit, which is not pip-installable.RDKit can be installed in many ways, but the easiest way is to use thecondapackage manager. For full installation instructions, see the 'Installation' section of the readme. Python 3.6 and 3.7 are supported. To run the tests,pytestandOpenMMare required.In essence,pygen-structuresaims (eventually) to be a completepsfgenreplacement with more autonomous functionality. At present, structures for small molecules can be generated. This should make it significantly easier to perform combinatorial searches on particular sequence lengths and linkages. This requires no manual intervention provided the molecules of interest are reasonably small (small enough that embedding coordinates is possible, and that the secondary structure is not vitally important) and the residue/patch definitions already exist in the forcefield.InstallationThere are other ways to install the required dependencies, but the easiest way by far is to use conda. Instructions, include the installation of test dependencies, are outlined below:Install the conda package manager. Make sure the conda executable is in your PATH.Set up a conda environment with the relevant dependencies (or install them in your base distribution). This can be done with the following command:conda create -n pygen-structures -c rdkit -c omnia 'python>=3.6' 'rdkit>=2018.3' numpy 'openmm>=7.4' pytest.Activate the conda environment:conda activate pygen-structuresUse pip to installpygen-structuresin this environment:pip install pygen-structures.Installation complete! You will have to activate this environment usingconda activate pygen-structureseach time you want to use it.Test the installation:pytest --pyargs pygen_structuresTo install only the runtime dependencies, use the following command in step 2:conda create -n pygen-structures -c rdkit 'python>=3.6' 'rdkit>=2018.3' numpyCommand line usageCommand line usage for peptides is simple, and takes the following form:pygen-structures SEQUENCE -o OUTPUT_PREFIXSequences are specified using the one letter protein code by default, and terminal patches can be supplied by using hyphens as delimiters (e.g.NNEU-AFK-CT2, note that both termini must be supplied). D-amino acids need only be preceded by a lowercase 'd'.OUTPUT_PREFIX.psf and OUTPUT_PREFIX.pdb are created. If-ois not specified, the PDB file is written to stdout and no PSF file is generated.The histidine form used can be set using--histidine, and defaults to HSE.Patches can be supplied using--patches, the name of the patch, and the 0-based indices the patch is to be applied to (or 'FIRST'/'LAST').To generate more complex structures, such as sugars, the residue names should be supplied (hyphen delimited) and the-u/--use-charmm-namesoption selected. Some example usage is given below.--nameand--segidcontrol the names given in the COMPND record and the segment id respectively.ExamplesTo produce a simple peptide sequence, the one letter code can be used. To produce the peptide HIS-GLU-TYR, creatingHEY.psfandHEY.pdb:pygen-structures HEY -o HEYSupposing we think histidine should be protonated, we can change the protonation state of histidine by specifying a different histidine form:pygen-structures HEY -o HEY --histidine HSPOr we could use the three letter codes:pygen-structures -u HSP-GLU-TYR -o HEYFor the trisaccharide raffinose, we must use the residue codes. The default segid is PROT, so we can specify a more specific segid using the--segidflag, and set the name given in theCOMPNDheader using--name. The following command producesRAFF.psfandRAFF.pdb:pygen-structures -u AGLC-BFRU-AGAL --patches RAFF 0 1 2 --segid RAFF --name Raffinose -o RAFFWe can also make glycopeptides. To link alpha-glucose to an arginine residue (in this case, from an ALA-ASN-ALA peptide), we can use the NGLA patch. Note that because the protein residue is not the last in the chain, we have to apply the C-terminus patch manually.pygen-structures -u ALA-ASN-ALA-AGLC --patches CTER -2 NGLA 1 -1 -o ANA-NAGLCBy default, if parameters are missing then the files are not created and the missing parameters are written to stdout. Using the-vflag will disable verification.$ pygen-structures AdP -o AdP
Missing parameters:
bonds {('CPD1', 'CC')}
$ pygen-structures -v AdP -o AdP
$A different CHARMM distribution can be loaded using the-toption, with the path to the folder.pygen-structuresships with the latest CHARMM distribution (July 2019) at the time of writing, with some modifications to correct the D-amino acid parameters (these modifications are highlighted in the toppar README). The function which parses the folder will pick the latest versions of the parameter and topology files (36 over 27, 36m over 36), so if you plan on using an older version of the forcefield (this is not recommended) you will have to remove the newer versions and change the extensions to match the current conventions (.rtf, .prm).Library usageInformation about classes and functions for usage as a library can be found onthe project's ReadtheDocs page.ContributingContributions are welcome!Please read our Code of Conduct.