jbellamycarter

#!/usr/bin/env python3
# -*- coding:utf-8 -*-

import requests
import re

def _version_to_tuple(tag):
    """Converts major.minor.patch software version numbers to tuple.
    Tolerates numbers starting with 'v' and alpha/beta post-numbering
    

jbellamycarter

jbellamycarter

#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Copyright 2020 Jedd Bellamy-Carter
# MIT License

"""CIU IWAT solver.
Fit CIU data using intensity-weighted average arrival-time to a 
four-parameter sigmoid curve. Optionally generates plot of fit.

INPUT: Standard CIU data representation. 

jbellamycarter

:: This batch script will execute CCSCalc for the provided PDB file
:: and save the output in a file ending in "_ccscalc_out.txt".
::
:: Run with `Start-Process ccscalc_run_script.bat PDB_FILE_PATH` in PowerShell
:: or `ccscalc_run_script.bat PDB_FILE_PATH` in command prompt.
:: Save associated file `types_oplsaa.txt` in `DriftScope\docs\atom_types` directory

SETLOCAL
SET pdb_file=%1
SET atom_types="C:\DriftScope\docs\atom_types\types_oplsaa.txt"

jbellamycarter

# PyMol start-up script with personal settings for visualisation
# Jedd Bellamy-Carter
set antialias, 2
#set ray_trace_mode, 1
set ray_interior_color, white
set cartoon_highlight_color, white
set cartoon_discrete_colors, on
set cartoon_side_chain_helper, on
set cartoon_dumbbell_length, 1.0
set cartoon_dumbbell_width, 0.2

jbellamycarter

def all_atom_rmsd(ref, traj):
    """Calculate the all-atom RMSD for a trajectory against reference.
    Assumes that the same structure is being compared with all atoms
    in the same order. `traj` can be a single frame or a full trajectory.
    
    Parameters
    ----------
    ref : list or ndarray
        xyz coordinates for the reference positions (Nx3)
    traj : list or ndarray

jbellamycarter

"""
PyMol plugin that splits difficult multimolecule PDBs, such as those generated
by SwissDock or CHARMM simulations.

Writes a new file that treats each 'molecule' as a model which can then be parsed
by Pymol as 'states'. 

Copyright 2018 Jedd Bellamy-Carter
Released under the terms of the MIT License (https://opensource.org/licenses/MIT)
"""

jbellamycarter

# Run: git config --global core.excludesfile ~/.gitignore_global
# Created by https://www.gitignore.io/api/tex,linux,macos,python,backup,windows,archives,libreoffice,microsoftoffice
# Edit at https://www.gitignore.io/?templates=tex,linux,macos,python,backup,windows,archives,libreoffice,microsoftoffice

### Archives ###
# It's better to unpack these files and commit the raw source because
# git has its own built in compression methods.
*.7z
*.jar
*.rar

jbellamycarter

from collections import OrderedDict
# Uses OrderedDict for maintaining insertion order pre-Python3.7

class PDB():
    """
    Class for parsing PDB files that follow the accepted format
    https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM

    Extracts ATOM and HETATM records. 
    HETATM with HOH resname are removed.

jbellamycarter

def all_atom_rmsd(ref, traj):
    """Calculate the all-atom RMSD for a trajectory against reference.
    Assumes that the same structure is being compared with all atoms
    in the same order. `traj` can be a single frame or a full trajectory.
    
    Parameters
    ----------
    ref : list or ndarray
        xyz coordinates for the reference positions (Nx3)
    traj : list or ndarray