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: css@bio.aau.dk | |
""" | |
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"} |
title | docking score | SMILES | |
---|---|---|---|
S01 | -9.61916 | CC1=CC=C(C(=O)N2CN(C([NH3+])=O)N(C(=O)[O-])C2=O)C=C1 | |
S02 | -9.6052 | NC1CN(C([NH3+])=O)C(=O)N1C(=O)[O-] | |
S03 | -8.84833 | CNC(=O)C1=CN(C(=O)[O-])CN(C([NH3+])=O)C1 | |
S04 | -8.92497 | CC1=CC=CC=C1NN1C(=O)N(C(=O)[O-])C2=C1C=CC=C2F |
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 |