che696_examples

Several Python scripts to serve as examples for ChE 696 individual projects

Copyright

Copyright (c) 2018, hbmayes, MIT license

Acknowledgements

Project based on a Cookiecutter project forked from the Computational Chemistry Python Cookiecutter

Installation

1. Make sure python is installed. Python >=3.5 is recommended. The package is meant to be python 2.7 compatible, but primarily tested with Python 3.5 and 3.6. There are many ways to install python. We recommend http://conda.pydata.org/miniconda.html

2. From the base folder where you would like the set of files (a new folder will be created, by default called md_utils):

      git clone https://github.com/team-mayes/che696_examples.git
   

3. To allow the scripts to be found anywhere on your computer using your terminal screen, making sure the following folder exists (make it if it does not) and in your .bashrc or .bash_profile path, and remember to source that file after an update:

      $HOME/.local/bin
   

4. To make a tarball to allow installation:

   a. From the main directory of your project, run:

         python setup.py sdist   
   

   b. The step above will create the directory 'dist' in the main directory if it does not yet exist, and also a tarball, where the * in the name will be replaced by the current version of the package:

         dist/che696_examples-*.tar.gz
   

   c. To install this package on your local computer, run:

         pip install dist/che696_examples-*.tar.gz --user
   

   d. You can also copy the tarball to any other machine (same type of computer or not) and similarly install with pip, just changing the directory name where the tarball exists, as needed. e. If you are upgrading the package after the initial install, just add the '--upgrade' flag:

         pip install --upgrade dist/che696_examples-*.tar.gz --user
   

Example

1. To see if the installation worked, try running one of the scripts with the help option. All scripts in this package have such an option, which will briefly tell you about the code, e.g.::

       add_to_each_line -h
   

2. Following the help instructions, give it a try!

When the whole git repository is cloned, there will be example input files in the tests/test_data folder.

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Scripts

add_to_each_line

• Reads in a file and adds a beginning and/or end to each line. The first argument must be the name of the file to be read.

col_stats

• Given a csv file with columns of data, returns the min, max, avg, and std dev per column. Optionally, it can return the maximum value from each column plus a "buffer" length (useful for preparing CP2K input). It can optionally prepare histograms of non-numerical data.

fill_tpl

• Fills in a template file with parameter values. See example *.tpl template files and *.ini configurations files in tests/test_data/fill_tpl.

pdb_edit

• Creates a new version of a pdb file applying options such as renumbering molecules.
  • use the option "add_element_types = true" to fill in the column of element types (created originally because VMD dropped them for the protein section; CP2K wants them)
    • by default, it will check all atoms. You can specify a range on which to perform this action with 'first_atom_add_element' and 'last_atom_add_element'
    • it will only add the element type if it is in the internal atom_type/element dictionary (a warning will show if a type is not in the dictionary). Otherwise, it will leave those columns as they originally were.
    • by default, it loads a dictionary I made based on charmm atom types (charmm_atom_type,element; one per line). The user can specify a different dictionary file with "atom_type_element_dict_file"
  • if the user specifies a 'first_wat_atom' and 'last_wat_atom', the program will check that the atoms are printed in the order OH2, H1, H2
    • when using this option, if the first protein atom is not 1 (numbering begins at 1, like in a PDB, not 0, like VMD index), use the option "last_prot_atom = " to indicate the first protein atom num
    • this options requires inputting the last protein atom id (add "last_prot_atom = X" to the configuration file, where X is the integer (decimal) atom number)
  • by default, the output pdb name of a pdb file called 'struct.pdb' will be 'struct_new.pdb'. You can specify a new name with the keyword 'new_pdb_name'
  • by default, the output directory will be the same as that for the input pdb. This can be changed with the 'output_directory' keyword
  • the program will renumber atoms starting from 1 (using hex for atom numbers greater than 99999), using a dictionary to change order if a csv dictionary of "old,new" indexes is specified with 'atom_reorder_old_new_file'
  • the program will renumber molecules starting from 1 if 'mol_renum_flag = True' is included in the configuration file. Molecules may also be renumbered with by specifying a csv dictionary of "old,new" indexes with 'mol_renum_old_new_file'

tex_add_spell

• Adds a word to a Hunspell-type dictionary file.