Package: py2sambvca
py2sambvcaSimple thin client to interface python scripts with SambVca catalytic pocket Fortran calculator.Installationpy2sambvcais available on PyPI and can be installed like so:pipinstallpy2sambvcapy2sambvcahaszeroexternal dependencies.Downloading and CompilingSambVcapy2sambvcacan read and write input and output files forSambVcawithout the actual program in place, but in order to run input files you must have an executablesambvca21.exe(or similar) somewhere on your machine.You can download the source codeon theSambVcawebserverand compile it usinggfortran.By default,py2sambvcaexpects the executable to be present in thecwdand namedsambvca21.exeon Windows orsambvca21.xon Unix-based systems. optionally, the filepath to your executable can be specified as shown below.UsageAfter installation,py2sambvcacan be added to a Python script viaimportand instantiated:frompy2sambvcaimportp2snhc_p2s=p2s("test/data/nhc.xyz",[22],[5],[1],path_to_sambvcax="sambvca21.exe",)The required input parameters are shown below:xyz_filepath(str): Location of .xyz molecular coordinates file for writing input datasphere_center_atom_ids(list): ID of atoms defining the sphere centerz_ax_atom_ids(list): ID of atoms for z-axisxz_plane_atoms_ids(list): ID of atoms for xz-planeThe following parameters are optional and will be filled with default values if not specified:atoms_to_delete_ids(list): ID of atoms to be deleted (default None)sphere_radius(float): Sphere radius in Angstrom (default 3.5)displacement(float): Displacement of oriented molecule from sphere center in Angstrom (default 0.0)mesh_size(float): Mesh size for numerical integration (default 0.10)remove_H(int): 0/1 Do not remove/remove H atoms from Vbur calculation (default 1)orient_z(int): 0/1 Molecule oriented along negative/positive Z-axis (default 1)write_surf_files(int): 0/1 Do not write/write files for top and bottom surfaces (default 1)path_to_sambvcax(str): Path to the SambVca executable. Only needed to use py2sambvca.calc()(default "sambvca.exe")working_dir(path): Path to the working directory where the output and input files are generated (default os.getcwd())verbose(int): 0 for no output, 1 for some output, 2 for the most output (default 1)radii_table(dict or str): a dictionary of atomic symbols and their radii (angstroms), or "default" for the radii used in the original implementationFrom here, running can be done stepwise or with a single function:nhc_p2s.run()# equivalent tonhc_p2s.write_input()nhc_p2s.calc()nhc_p2s.parse_output()nhc_p2s.clean_files()All values for the total complex, quadrants, and octants are available through getters:Total ValuesQuadrant ValuesOctant Valuesget_free_volume()get_quadrant_free_volume()get_octant_free_volume()get_buried_volume()get_quadrant_buried_volume()get_octant_buried_volume()get_exact_volume()not availablenot availableget_total_volume()get_quadrant_total_volume()get_octant_total_volume()get_percent_buried_volume()get_quadrant_percent_buried_volume()get_octant_percent_buried_volume()get_percent_free_volume()get_quadrant_percent_free_volume()get_octant_percent_free_volume()get_percent_total_volume()not availablenot availableResults can also be accessed through a general getter method:get(),get_quadrant_result(), andget_octant_result().All results can also be directly accessed through dictionaries, returned from a call torun()orparse_output()and available throughp2s.total_results,p2s.quadrant_results, andp2s.octant_results.In case there is something else you are looking for, you can use a general purposeget_regex()function to return the line containing a pattern.ExamplesHere are a couple repositories usingpy2sambvcaas a Python package or extending its source code, check them out:Metal-organic framework stability analysis by Hiu KiMOF Stability ML by Ruihan WangSee AlsoKjell Jorner'smorfeuspackage re-implements the original buried volume algorithm directly in PythonLicensepy2sambvcais available under the GNU GPLv3 in accordance with the base Fortran code which is available under the same license and can be retreieved here:https://www.molnac.unisa.it/OMtools/sambvca2.1/download/download.htmlThe original fortran program (sambvca21.f) is also included in thetestdirectory for testing purposes. It is still under the same terms of the GNU license:This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.The results obtained from using the source code shall be used for scientific purposes only, excluding industrial or commercial purposes. To use the SambVca suite for industrial or commercial purposes, contact lcavallo|@|unisa.it.Proper acknowledgement shall be made to the author of the source code in publications resulting from the use of it in its original form or modified.The results from using the source code are provided "AS IS" without warranty of any kind.CitationPlease cite theSambVcaunderlying Fortran tool according to the guidelines on the buried volume webserver:https://www.molnac.unisa.it/OMtools/sambvca2.1/help/help.htmlpy2sambvcahas been uploaded to Figshare and may be cited as: Burns, J. figshare. 2020, DOI:10.6084/m9.figshare.12846707