Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Implemented code for atom-typing to support the Alexandria force field. #2664

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Implemented code for atom-typing to support the Alexandria force field. #2664

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
1 change: 1 addition & 0 deletions data/CMakeLists.txt
View file
Open in desktop
@@ -1,6 +1,7 @@
# Open Babel data files

set(to_install
alexandria.prm
atomization-energies.txt
atomtyp.txt
babel_povray3.inc
Expand Down
509 changes: 509 additions & 0 deletions data/alexandria.prm
View file
Open in desktop

Large diffs are not rendered by default.

160 changes: 151 additions & 9 deletions data/bondtyp.txt
View file
Open in desktop
Expand Up @@ -31,49 +31,178 @@
#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
[X2,X3]1[#6]([#7]2)[#6][#6][#6]2[X2,X3][#6]([#7]3)[#6][#6][#6]3[X2,X3][#6]([#7]4)[#6][#6][#6]4[X2,X3][#6]([#7]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2

# N-methylmethanesulfinimidic-acid
[#6X4][#7X2][#16X3] 0 1 1 1 2 2
# amino--diaminomethylideneamino-methylidene--ethylazanium and analogs
[#6X3]([#7X3])([#7X3])([#7X2][#6X3]([#7X3])([#7X3]([#6]))) 0 1 1 0 2 1 0 3 2 3 4 1 4 5 1 4 6 2 6 7 1
# cyanoimino-methylene-azanide N#C-N-C#N
[#7X1][#6X2][#7X2][#6X2][#7X1] 0 1 3 1 2 1 2 3 1 3 4 3
# fulvene analogs
[#6X3]1([#6X3]([#1])([#1]))([#6X3][#6X3][#6X3][#6X3]1) 0 1 2 1 2 1 1 3 1 0 4 1 4 5 2 5 6 1 6 7 2 0 7 1
[#6X3]1([#7X2])([#6X3][#6X3][#6X3][#6X3]1) 0 1 2 0 2 1 2 3 2 3 4 1 4 5 2 0 5 1
# CR3-N=N-CH=CH
[#6X4][#7X2][#7X2][#6X3][#6X3] 0 1 1 1 2 2 2 3 1 3 4 2
#CR2=N-N=CH2
[#6X3][#7X2][#7X2][#6X3]([#1])([#1]) 0 1 2 1 2 1 2 3 2 3 4 1 3 5 1
# C2=N-NO2
[#6X3][#7X2][#7X3]([#8X1])([#8X1]) 0 1 2 1 2 1 2 3 1 2 4 2
#1-3-oxazole analogs
[#8X2]1[#6X3][#7X2][#6X3][#6X3]1 0 1 1 1 2 2 2 3 1 3 4 2 0 4 1
#N=C=N-C#N
[#7X1][#6X2][#7X2][#6X2][#7X1] 0 1 2 1 2 2 2 3 1 3 4 3
#pyridinium analogs
[#7X3]1([#6])([#6X3][#6X3][#6X3][#6X3][#6X3]1) 0 1 1 0 2 1 2 3 2 3 4 1 4 5 2 5 6 1 0 6 2
[#7X3]1([#1])([#6X3][#6X3][#6X3][#6X3][#6X3]1) 0 1 1 0 2 2 2 3 1 3 4 2 4 5 1 5 6 2 0 6 1
#Pyrrol-imine analogs
[#6X3]1([#7X2][#1,#6])([#7X2][#6X3][#6X3][#6X3]1) 0 1 2 1 2 1 0 3 1 3 4 2 4 5 1 5 6 2 0 6 1
#1H-pyrimidin-2-one analogs
[#6X3]1([#8X1])([#7X3][#6X3][#6X3][#6X3][#7X2]1) 0 1 2 0 2 1 2 3 1 3 4 2 4 5 1 5 6 2 0 6 1
# 5-methylideneimidazol-2-one analogs, 5-methylimidazol-4-one analogs
[#6X3]1([#8X1])([#7X3][#6X3]([#6X3])[#6X3][#7X2]1) 0 1 2 0 2 1 2 3 1 3 4 2 3 5 1 5 6 2 0 6 1
[#6X3]1([#8X1])([#7X2][#6X3][#7X2][#6X3]1) 0 1 2 0 2 1 2 3 2 3 4 1 4 5 2 0 5 1
# C/N-N=CH2
[#6X3]([#1])([#1])[#7X2][#7X2,#7X3,#6X3,#6X4] 0 1 1 0 2 1 0 3 2 3 4 1
# Imines
[#6X3]([#7X2][#1])([#7X3][#6X3]([#1])[#6X3]) 0 1 2 1 2 1 0 3 1 3 4 1 4 5 1 4 6 2
[#6X3]([#7X2][#1])([#7X2][#6X3]([#1])[#6X3]) 0 1 2 1 2 1 0 3 1 3 4 2 4 5 1 4 6 1
[#6X3]([#7X2][#1,#6])([#7X3])([*]) 0 1 2 1 2 1 0 3 1 0 4 1
# Azide
[#7D2][#7D2^1][#7D1] 0 1 2 1 2 2
# Nitro
[#8D1][#7D3^2]([#8D1])* 0 1 2 1 2 2 1 3 1

# [#8D1][#7D3^2]([#8D1])* 0 1 2 1 2 2 1 3 1; old code
[#8D1][#7D3^2]([#8D1])* 0 1 1 1 2 2 1 3 1
# nitronium
[#8X1][#7X2]([#8X1]) 0 1 2 1 2 2
# Dimethyl(methylidene)azanium and analogs
[#7X3]([#6X4])([#6X4])([#6X3]([#1])([#1])) 0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
[#7X3]([#6X3]([#7X3])([#7X3]))([#6X4])([#6X4]) 0 1 2 1 2 1 1 3 1 0 4 1 0 5 1
# N2O
[#7X1][#7X2][#8X1] 0 1 3 1 2 1
# nitroso R-N=O
[#8X1][#7X2][#7X2][#6X3] 0 1 2 1 2 1 2 3 2
[#8X1][#7X2]([*;!#6]) 0 1 2 1 2 1
[#8X1][#7X2]([#6X3]([*])([*])) 0 1 2 1 2 1 2 3 1 2 4 1
# H-N=P(-O)3
[#7X2]([#1])([#15X4]([#8X1])([#8X1])([#8X1])) 0 1 1 0 2 2 2 3 1 2 4 1 2 5 1
# NR2-C=C-C=O
[#7X3][#6X3][#6X3][#6X3][#8X1] 0 1 1 1 2 2 2 3 1 3 4 2
# NR2-C=C-C
[#7X3][#6X3][#6X3]([#6X4,#1])[#6X2] 0 1 1 1 2 2 2 3 1 2 4 1
# C=CH-NR-CR=O
[#6X3][#6X3]([#1])[#7X3][#6X3][#8X1] 0 1 2 1 2 1 1 3 1 3 4 1 4 5 2
# bis-methylamino-methylidene-methylazaniumyl--sulfate analogs
[#7X3]([#8X2])([#6X4])([#6X3]([#7X3])([#7X3])) 0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
# NO2H=CH-CR3
[#7X3]([#8X2])([#8X1])([#6X3][#6X4]) 0 1 1 0 2 1 0 3 2 3 4 1
# CR2=N-N(CR3)2
[#6X3][#7X2][#7X3]([#6X4])([#6X4]) 0 1 2 1 2 1 2 3 1 2 4 1
#1-2-4-thiadiazole
[#6X3]1([#7X2][#6X3]([#1])[#7X2][#16X2]1) 0 1 2 1 2 1 2 3 1 2 4 2 4 5 1 0 5 1
# cyanoimino-methylene-azanide N#C-N-C#N
#[#7X1][#6X2][#7X2][#6X2][#7X1] 0 1 3 1 2 1 2 3 1 3 4 3

# CR2=CH2
[#6X3]([#1])([#1])[#6X3] 0 1 1 0 2 1 0 3 2

#R-C#N-S
[#16X1][#7X2][#6X2] 0 1 1 1 2 3
# R(RO)S=O
[#16X3]([#8X1])([#8X2])([*!#8]) 0 1 2 0 2 1 0 3 1
#R-N=S=O
[#8X1][#16X2][#7X2][*] 0 1 2 1 2 2 2 3 1
[#8X1][#16X4]([#7X2][#1])([*])([*]) 0 1 2 1 2 2 2 3 1 1 4 1 1 5 1
# Sulfones
[#16D4]([#8D1])([#8D1])([*!#8])([*!#8]) 0 1 2 0 2 2 0 3 1 0 4 1
# Sulfates
[#16D4]([#8D1])([#8D1])([#8-,#8D1])([#8-,#8D1]) 0 1 2 0 2 2 0 3 1 0 4 1
# Thiosulfates
[#16D4]([#16D1])([#8D1])([#8-,#8])([#8-,#8]) 0 1 2 0 2 2 0 3 1 0 4 1
#[#16D4]([#16D1])([#8D1])([#8-,#8])([#8-,#8]) 0 1 2 0 2 2 0 3 1 0 4 1
[#16D4]([#16D1])([#8D1])([#8])([#8-,#8]) 0 1 1 0 2 2 0 3 2 0 4 1
# Sulfonyl analogs
[#16X3]([#8X1])([#8X1])([#6^2,#7^2]) 0 1 2 0 2 2 0 3 2
# Sulfinic acid and analogs
[#16X3]([#8X1])([#8X1,#8X2])([#6]) 0 1 2 0 2 1 0 3 1
# Sulfoxides
[#16D3]([#8D1])([*!#8])([*!#8]) 0 1 2 0 2 1 0 3 1
# Sulfite
[#16D3]([#8D1])([#8D1-])([#8D1-]) 0 1 2 0 2 1 0 3 1
# Sulfur trioxide
[#16D3^2]([#8D1])([#8D1])([#8D1]) 0 1 2 0 2 2 0 3 2
[#16D3^2]([#8D1])([#8D1])([#8D1]) 0 1 2 0 2 2 0 3 2
# Sulfites
[#16D3]([#8D1])([#8])([#8]) 0 1 2 0 2 1 0 3 1
# 1-Sulfinylethane and analogs C=S=O
[#8X1][#16X2][#6X3] 0 1 2 1 2 2
#H2C=S=O
[#16X4]([#8X1])([#6X3]([#1])([#1])) 0 1 2 0 2 2 2 3 1 2 4 1
# Sulfonic acid and sulfonic ester
[#16X4]([#8X1])([#8X1])([#8])* 0 1 2 0 2 2 0 3 1 0 4 1
# Disulfur monoxide
[#16D2]([#8D1])([#16D1]) 0 1 2 0 2 2
# Sulfmonoxides
[#16D2]([#8D1])([*!#8]) 0 1 2 0 2 1
# S=N-H
[#16X2,#16X4][#7X2][#1] 0 1 2 1 2 1
# Sulfur dioxide
[#16D2]([#8D1])([#8D1]) 0 1 2 0 2 2

# S=S=S, S=S
[#16X1][#16X2][#16X1] 0 1 2 1 2 2
[#16X1][#16X1] 0 1 2
# S=CH2
[#16X2][#6X3]([#1])([#1]) 0 1 2 1 2 1 1 3 1
# dimethyl-oxido-sulfanylidene-lambda5-phosphane and analogs
[#16X1][#15] 0 1 2
# dihydroxy-sulfanylidene--lambda4-sulfane and analogs
[#16X1;!-][#16X3,#16X4] 0 1 2
# thiopyrylium
[#16X2]1[#6X3][#6X3][#6X3]([#1])[#6X3][#6X3]1 0 1 1 1 2 2 2 3 1 3 4 1 3 5 2 5 6 1 0 6 2
# dithiol-1-ium analogs
[#16X2]1[#6X3][#6X3][#6X3][#16X2]1 0 1 2 1 2 1 2 3 2 3 4 1 0 4 1
# O=S=CR2
[#8X1][#16X2][#6X3] 0 1 2 1 2 2

# 4-methylidenetriphosphole
[#6X3]1([#6X3])([#15X2][#15X2][#15X2][#6X3]1) 0 1 2 0 2 1 2 3 2 3 4 1 4 5 2 0 5 1
# C=P-H
[#6X3]1([#15X2][#1])([#6X3][#15X2][#6X3][#15X2]1) 0 1 2 1 2 1 0 3 1 3 4 2 4 5 1 5 6 2 0 6 1
[#6X3]1[#15X2][#6X3][#6X3][#6X3]1 0 1 1 1 2 2 2 3 1 3 4 2 0 4 1
[#6X3,#6X2,#16X2][#15X2][#1] 0 1 2 1 2 1
# 3-4-dihydrophosphol-2-one analogs
[#6X3]1[#15X2][#6X3][#6X4][#6X4]1 0 1 1 1 2 2 2 3 1 3 4 1 0 4 1
# C=P-C
[#6X3][#15X2][#6;!r6] 0 1 2 1 2 1
#Phosphite
[#15D3]([#8D1])([#8D1])([#8D2]) 0 1 2 0 2 2 0 3 1

#Methylphosphinate and analogs
[#15X3^2]([#8X1;!-])([#8X1;!-])([#6]) 0 1 2 0 2 2 0 3 1
#oxophosphane
#[#15D2]([#8D1])([#1]) 0 1 2 0 2 1
[#15D2]([#8D1])([#1]) 0 1 2 0 2 1
#phosphaalkene and analogs
[#15X2;!R]([#6X3,#6X4])([#6X3]) 0 1 1 0 2 2
[#15X2]([#6X3;!H,#6X4])([#6X3;!H]) 0 1 1 0 2 2
# P=O
[#15X2][#8X1] 0 1 2

#Nitrosyl Hydride
[#7D2]([#8D1])([#1]) 0 1 2 0 2 1
#Nitrite
[#8X1][#7X2][#8X2][*] 0 1 2 1 2 1 2 3 1

# chloro-hydroxy-dioxidophosphanium; not working right now
#[#15X4]([#8X1])([#8X1])([#8X2])([*]) 0 1 1 0 2 1 0 3 1 0 4 1
#[#15X4]([#8X1])([#8X1])([#17])([*]) 0 1 1 0 2 1 0 3 1 0 4 1
# Phosphone
[#15D4]([#8D1])(*)(*)(*) 0 1 2 0 2 1 0 3 1 0 4 1

[#15X4]([#8X1])([*])([*])([*]) 0 1 2 0 2 1 0 3 1 0 4 1
# diphospholes and analogs
[#6][#15X2][#15X2][#6] 0 1 1 1 2 2 2 3 1
# C-P=O
[#15X2]([#8X1])([#6]) 0 1 2 0 2 1

# Carboxylic Acid, ester, etc.
[#6D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1
# Carbon dioxide
[#8D1][#6D2^1][#8D1] 0 1 2 1 2 2
# Carbon monoxide
[#8X1][#6X1] 0 1 3
# Amide C(=O)N - no negative charge on O (2aix_u1k.sdf)
[#6D3^2]([#8D1;!-])([#7])* 0 1 2 0 2 1 0 3 1
# Seleninic acid Se(=O)OH
Expand All @@ -86,14 +215,26 @@
# avoid aromatics (pdb_ligands_sdf/1yry_msg.sdf)
[CD3^2]([#16D1])([N])* 0 1 2 0 2 1 0 3 1

# C=C=C=CH2
[#6X3][#6X2][#6X2][#6X3]([#1])([#1]) 0 1 2 1 2 2 2 3 2 3 4 1 3 5 1
# allene C=C=C
# (this is problematic -- need to make sure the center carbon is sp)
[#6^2][#6D2^1][#6^2] 0 1 2 1 2 2

# ethenolate
[#6X3]([#1])([#1])[#6X3]([#8])([#1]) 0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
# acetylenoate
[#6X2]([#1])[#6X2]([#8]) 0 1 1 0 2 2 2 3 1

# ene-one C=C=O
[#6^2][#6D2^1][#8D1] 0 1 2 1 2 2

# isonitrile / isocyano
[#6D1][#7D2^1]* 0 1 3 1 2 1
# NR2 in ring with hybridized carbon neighbors, do not apply to aromatic N
# valence insted of degree used to fix pdb_ligands_sdf/3dcv_55e.sdf
[Nv2R][#6v3^2][#8v2] 0 1 2 1 2 1
[Nv2R][#6v3^2][Nv2] 0 1 2 1 2 1

# if three N are present in R-N-guanidine-ish, prefer double bond to the
# non-terminal N (i.e. D2 if present)
Expand All @@ -111,3 +252,4 @@

### other potential functional groups that may (or may not) be useful to add
# imidines ( N=C/N\C=N

3 changes: 3 additions & 0 deletions data/ringtyp.txt
View file
Open in desktop
Expand Up @@ -12,6 +12,9 @@
# #
##############################################################################

# 3 membered rings
RINGTYP thiirene S1C=C1

#
# 5 membered rings
#
Expand Down
1 change: 1 addition & 0 deletions src/CMakeLists.txt
View file
Open in desktop
Expand Up @@ -45,6 +45,7 @@ set(fingerprints
)

set(forcefields
forcefields/forcefieldalexandria.cpp
forcefields/forcefieldgaff.cpp
forcefields/forcefieldghemical.cpp
forcefields/forcefieldmmff94.cpp
Expand Down
48 changes: 46 additions & 2 deletions src/bondtyper.cpp
View file
Open in desktop
Expand Up @@ -115,8 +115,8 @@ namespace OpenBabel

OBSmartsPattern *currentPattern;
OBBond *b1, *b2;
OBAtom *a1,*a2, *a3;
double angle, dist1, dist2;
OBAtom *a1,*a2, *a3, *a4;
double angle, angle1, angle2, dist1, dist2;
vector<int> assignments;
vector<vector<int> > mlist;
vector<vector<int> >::iterator matches, l;
Expand Down Expand Up @@ -207,6 +207,50 @@ namespace OpenBabel
}
} // thione

// Imidazole [nD3]1c=[nD3]c=c1
OBSmartsPattern imidazolium; imidazolium.Init("[#7D3][#6][#7D3][#6][#6]");

if (imidazolium.Match(mol))
{
mlist = imidazolium.GetUMapList();
for (l = mlist.begin(); l != mlist.end(); ++l)
{
a1 = mol.GetAtom((*l)[1]);
a2 = mol.GetAtom((*l)[2]);
a2->SetFormalCharge(1);

angle1 = a2->AverageBondAngle();
dist1 = a1->GetDistance(a2);

if (angle1 > 115 && angle < 150 && dist1 < 1.72) {

if ( !a1->HasDoubleBond() ) {// no double bond already assigned
b1 = a1->GetBond(a2);

if (!b1 ) continue;
b1->SetBondOrder(2);
}
}

a3 = mol.GetAtom((*l)[3]);
a4 = mol.GetAtom((*l)[4]);

angle2 = a3->AverageBondAngle();
dist2 = a3->GetDistance(a4);

// imidazolium geometries ?
if (angle2 > 115 && angle2 < 150 && dist2 < 1.72) {

if ( !a3->HasDoubleBond() ) {// no double bond already assigned
b2 = a3->GetBond(a4);

if (!b2 ) continue;
b2->SetBondOrder(2);
}
}
}
} // imidazolium

// Isocyanate N=C=O or Isothiocyanate
bool dist1OK;
OBSmartsPattern isocyanate; isocyanate.Init("[#8,#16;D1][#6D2][#7D2]");
Expand Down
39 changes: 39 additions & 0 deletions src/forcefields/forcefieldalexandria.cpp
View file
Open in desktop
@@ -0,0 +1,39 @@
/**********************************************************************
forcefieldalexandria.cpp - Alexandria force field.

Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl>
Copyright (C) 2006-2007 by Tim Vandermeersch <tim.vandermeersch@gmail.com>
Copyright (C) 2021 by David van der Spoel <david.vanderspoel@icm.uu.se>

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/

#include <openbabel/babelconfig.h>

#include "forcefieldalexandria.h"

#include <cstdlib>

using namespace std;

namespace OpenBabel
{
//***********************************************
//Make a global instance
OBForceFieldAlexandria theForceFieldAlexandria("Alexandria", true);
//***********************************************

} // end namespace OpenBabel

//! \file forcefieldalexandria.cpp
//! \brief Alexandria force field
50 changes: 50 additions & 0 deletions src/forcefields/forcefieldalexandria.h
View file
Open in desktop
@@ -0,0 +1,50 @@
/**********************************************************************
forcefieldalexandriaf.h - Alexandria force field.

Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl>
Copyright (C) 2006 by Tim Vandermeersch <tim.vandermeersch@gmail.com>
Copyright (C) 2021 by David van der Spoel <david.vanderspoel@icm.uu.se>

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/

#include <vector>
#include <string>
#include <map>

#include <openbabel/forcefield.h>
#include <openbabel/base.h>
#include <openbabel/mol.h>

#include "forcefieldgaff.h"

namespace OpenBabel
{

// Class OBForceFieldAlexandria
// class introduction in forcefieldalexandria.cpp
class OBForceFieldAlexandria: public OBForceFieldGaff
{
public:
//! Constructor
explicit OBForceFieldAlexandria(const char* ID, bool IsDefault=true) : OBForceFieldGaff(ID, IsDefault)
{
SetPrmFile("alexandria.prm");
}

}; // class OBForceFieldAlexandria

}// namespace OpenBabel

//! \file forcefieldalexandria.h
//! \brief Alexandria force field