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#!/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 | |
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#!/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. |
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:: 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" |
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# 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 |
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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 |
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""" | |
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) | |
""" |
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# 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 |
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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. |
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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 |
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