Get Buch hbonds

import molsysmt as msm

molsys = msm.convert(msm.systems['chicken villin HP35']['chicken_villin_HP35.h5msm'])

hbonds, distance = msm.hbonds.get_buch_hbonds(molsys)

hbonds

array([[[ 42,  43,  91],
        [ 51,  52,  90],
        [ 80,  81,  90],
        [ 92,  93,  47],
        [112, 113,  58],
        [130, 132,  79],
        [130, 133,  78],
        [134, 135,  70],
        [144, 145,  85],
        [160, 161,  97],
        [180, 181, 117],
        [187, 188, 165],
        [218, 219,  64],
        [233, 234,  63],
        [236, 238,  28],
        [239, 240,  28],
        [239, 241,  63],
        [253, 254, 212],
        [263, 264, 209],
        [283, 284, 223],
        [293, 294, 258],
        [307, 308, 268],
        [383, 384, 330],
        [401, 402, 530],
        [401, 403, 529],
        [405, 406, 330],
        [419, 421, 312],
        [422, 423, 345],
        [439, 440, 364],
        [453, 454, 388],
        [472, 473, 410],
        [490, 492,   1],
        [490, 493, 559],
        [494, 495, 458],
        [512, 513, 435],
        [512, 514, 427],
        [512, 515, 477],
        [516, 517, 444],
        [531, 532, 458],
        [549, 550, 149]]])

distance

Magnitude

[[0.19900184899743265 0.1592068665023842 0.1890973375327663 0.20613839228599634 0.18360413105937268 0.19072421648800025 0.17168940393130158 0.19033877025065687 0.20429170693579443 0.1801211447594014 0.19193856762798467 0.19313254218204326 0.18154159603983389 0.18365466864633762 0.19502046022774844 0.1878008390980677 0.1776581909942343 0.21942750833075667 0.18543787343025933 0.21186451615597585 0.20569050719939008 0.20363263300367979 0.2109751681965716 0.17315926287016672 0.1984504114762396 0.2005732411095738 0.17853138665143908 0.18927051194783365 0.19304897717338138 0.18621129797789518 0.19133047834885888 0.18645105933091424 0.1777470038487362 0.19041938113064577 0.18692091200312963 0.1804259183575564 0.18477119540899792 0.17978267900340797 0.21460729773509604 0.17574799614241132]]

Units

nanometer

molsys = msm.convert(msm.systems['Barnase-Barstar']['barnase_barstar.h5msm'])

msm.info(molsys, element='molecule')

index	name	type	n atoms	n groups	n components	chain index	entity index	entity name
0	BARNASE	protein	1727	110	1	0	0	protein 0
1	BARSTAR	protein	1432	89	1	0	1	protein 1

hbonds, distance = msm.hbonds.get_buch_hbonds(molsys, selection='molecule_name=="BARNASE"',
                                              selection_2='molecule_name=="BARSTAR"')

hbonds

array([[[ 431,  432, 2361],
        [ 431,  434, 2400],
        [ 583,  584, 2442],
        [ 858,  859, 2296],
        [ 876,  878, 2969],
        [ 879,  881, 2969],
        [ 882,  883, 2297],
        [1253, 1254, 2361],
        [1253, 1255, 2412],
        [1256, 1258, 2361],
        [1256, 1258, 2362],
        [1311, 1312, 2362],
        [1317, 1318, 2362],
        [1610, 1611, 2237],
        [2267, 2268,  896]]])