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Update the vdw radii to the ones from Bondi #119

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Sep 26, 2018
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Update the vdw radii to the ones from Bondi #119

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d09a1e3
Update the vdw radii to the ones from Bondi
jbarnoud Sep 25, 2018
3679385
Add DOIs
jbarnoud Sep 26, 2018
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Update the vdw radii to the ones from Bondi 
remove useless import
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@jbarnoud
jbarnoud committed Sep 25, 2018
commit d09a1e3c806ad1a5d36d06d1bf7269576878110f
34 changes: 28 additions & 6 deletions vermouth/processors/make_bonds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,29 @@
from .processor import Processor
from ..utils import distance

COVALENT_RADII = {'H': 0.031, 'C': 0.076, 'N': 0.071, 'O': 0.066, 'S': 0.105}
# Van der Waals radii from A. Bondi, J. Phys. Chem., 68, 441-452, 1964.
# For hydrogen, we use R.S. Rowland & R. Taylor, J.Phys.Chem., 100, 7384-7391, 1996.
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VDW_RADII = { # in nm
'H': 0.120,
'He': 0.140,
'C': 0.170,
'N': 0.155,
'O': 0.152,
'F': 0.147,
'Ne': 0.154,
'Si': 0.210,
'P': 0.180,
'S': 0.180,
'Cl': 0.175,
'Ar': 0.188,
'As': 0.185,
'Se': 1.90,
'Br': 0.185,
'Kr': 0.202,
'Te': 0.206,
'I': 0.198,
'Xe': 0.216,
}
#VALENCES = {'H': 1, 'C': 4, 'N': 3, 'O': 2, 'S': 6}


Expand All @@ -36,7 +58,7 @@ def bonds_from_distance(system, fudge=1.1):
Creates edges between nodes of molecules in system based on a distance
criterion. Nodes in system must have `position` and `element` attributes.
The possible distance between nodes is determined by values in
`COVALENT_RADII`.
`VDW_RADII`.

Parameters
----------
Expand All @@ -53,7 +75,7 @@ def bonds_from_distance(system, fudge=1.1):
"""
system = nx.compose_all(system.molecules)
idx_to_nodenum = {idx: n for idx, n in enumerate(system)}
max_dist = max(COVALENT_RADII.values())
max_dist = max(VDW_RADII.get(node.get('element'), 0.2) for node in system.nodes.values())
positions = np.array([system.node[n]['position'] for n in system], dtype=float)
tree = KDTree(positions)
pairs = tree.query_pairs(2*max_dist*fudge) # eps=fudge-1?
Expand All @@ -65,11 +87,11 @@ def bonds_from_distance(system, fudge=1.1):
atom2 = system.node[node_idx2]
element1 = atom1['element']
element2 = atom2['element']
if element1 in COVALENT_RADII and element2 in COVALENT_RADII:
if element1 in VDW_RADII and element2 in VDW_RADII:
# Elements we do not know never make bonds.
dist = distance(atom1['position'], atom2['position'])
bond_distace = COVALENT_RADII[element1] + COVALENT_RADII[element2]
if dist <= bond_distace * fudge:
bond_distance = 0.5 * (VDW_RADII[element1] + VDW_RADII[element2])
if dist <= bond_distance * fudge:
system.add_edge(node_idx1, node_idx2, distance=dist)
return system

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