Casper Steinmann cstein

Cyclodextrin Structures

alpha-, beta- and gamma-cyclodextrin structures.

The structures are compatible with AMBER and for use with the GLYCAM force field.

	""" Builds a string of alpha-1,4-glucose residue names compatible with our
	efforts at AAU to build a GLYCAM-like force field

	author: Casper Steinmann
	email: [email protected]
	"""
	import argparse
	import numpy
	import numpy.random

	""" Compute Center of Mass distances between groups of residues """
	from typing import List

	import numpy as np
	import matplotlib
	import matplotlib.pyplot as plt

	import mdtraj
	""" Some notes on MD traj

	def twoint_kernel(
	RA, RB, RC, RD, lA, lB, lC, lD,
	aA, aB, aC, aD, cA, cB, cC, cD
	):
	""" Two-electron integral kernel

	Calculated with primitive gaussian type orbitals.

	This function implements equation 13 from:
	DOI: 10.1002/ejtc.36

	[
	{"name": "Imidazoles", "reactant": "[n+;H]", "product": "n"},
	{"name": "Amines", "reactant": "[N+;!H0]", "product": "N"},
	{"name": "Carboxylic acids and alcohols", "reactant": "[$([O-]);!$([O-][#7])]", "product": "O"},
	{"name": "Thiols", "reactant": "[S-;X1]", "product": "S"},
	{"name": "Sulfonamides", "reactant": "[$([N-;X2]S(=O)=O)]", "product": "N"},
	{"name": "Enamines", "reactant": "[$([N-;X2][C,N]=C)]", "product": "N"},
	{"name": "Tetrazoles", "reactant": "[n-]", "product": "[nH]"},
	{"name": "Sulfoxides", "reactant": "[$([S-]=O)]", "product": "S"},
	{"name": "Amides", "reactant": "[$([N-]C=O)]", "product": "N"}

	c1ccccc1 benzene
	c1ccccc1C methylbenzene
	c1ccccc1CC ethylbenzene
	c1ccccc1CCC propylbenzene
	c1ccccc1CCCC butylbenzene
	Cc1ccc(C)cc1 1-methyl-4-methylbenzene
	CCc1ccc(C)cc1 1-ethyl-4-methylbenzene
	CCCc1ccc(C)cc1 1-propyl-4-methylbenzene
	c1cc(C)ccc1CCCC 1-butyl-4-methylbenzene
	Cc1cc(C)ccc1 1-methyl-3-methylbenzene

	Resp charges for organic molecule

	&cntrl

	nmol = 7,
	ihfree = 0,
	iqopt = 2,
	qwt = 0.00050,

	&end

	from schrodinger import maestro
	from schrodinger import structure

	import PyQt5
	from PyQt5.QtWidgets import QFileDialog

	__doc__ = """
	Extracts QM region around molecule.
	"""
	#Name: QM/MM:Extract

	""" Script to generate appropriate QM, MM and QM/MM files """
	from operator import itemgetter
	import sys

	import numpy

	# shamelessly stolen from molecool
	aa2au = 1.8897261249935897 # bohr / AA

	# converts nuclear charge to atom label