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[Jmol-commits] SF.net SVN: jmol:[17116] trunk/Jmol/src/org/jmol/minimize
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From: <ha...@us...> - 2012-05-09 18:10:11
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Revision: 17116
http://jmol.svn.sourceforge.net/jmol/?rev=17116&view=rev
Author: hansonr
Date: 2012-05-09 18:10:04 +0000 (Wed, 09 May 2012)
Log Message:
-----------
refactoring
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/minimize/Minimizer.java
trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java
trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
Removed Paths:
-------------
trunk/Jmol/src/org/jmol/minimize/forcefield/UFF.txt
Modified: trunk/Jmol/src/org/jmol/minimize/Minimizer.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/Minimizer.java 2012-05-09 18:09:32 UTC (rev 17115)
+++ trunk/Jmol/src/org/jmol/minimize/Minimizer.java 2012-05-09 18:10:04 UTC (rev 17116)
@@ -445,11 +445,6 @@
return pFF;
}
- public List<String[]> getAtomTypes() {
- getForceField();
- return (pFF == null ? null : pFF.getAtomTypes());
- }
-
/* ***************************************************************
* Minimization thead support
****************************************************************/
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java 2012-05-09 18:09:32 UTC (rev 17115)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java 2012-05-09 18:10:04 UTC (rev 17116)
@@ -56,7 +56,7 @@
return calc.getUnit();
}
- public abstract List<String[]> getAtomTypes();
+ protected abstract List<String[]> getAtomTypes();
protected abstract Map<String, FFParam> getFFParameters();
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java 2012-05-09 18:09:32 UTC (rev 17115)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java 2012-05-09 18:10:04 UTC (rev 17116)
@@ -47,6 +47,11 @@
private BitSet bsAromatic;
@Override
+ public void clear() {
+ bsAromatic = null;
+ }
+
+ @Override
public boolean setModel(Minimizer m, BitSet bsElements, int elemnoMax) {
super.setModel(m);
Logger.info("minimize: setting atom types...");
@@ -181,7 +186,7 @@
// open UFF.txt
URL url = null;
- String fileName = "UFF.txt";
+ String fileName = "uff/UFF.txt";
BufferedReader br = null;
try {
if ((url = this.getClass().getResource(fileName)) == null) {
@@ -264,7 +269,7 @@
public List<String[]> getAtomTypes() {
List<String[]> types = new ArrayList<String[]>(); //!< external atom type rules
URL url = null;
- String fileName = "UFF.txt";
+ String fileName = "uff/UFF.txt";
try {
if ((url = this.getClass().getResource(fileName)) == null) {
System.err.println("Couldn't find file: " + fileName);
@@ -292,7 +297,7 @@
+ fileName);
}
- Logger.info(types.size() + " force field parameters read");
+ Logger.info(types.size() + " UFF parameters read");
return (types.size() > 0 ? types : null);
}
@@ -403,9 +408,4 @@
Token.tokenExpressionEnd},
};
- @Override
- public void clear() {
- bsAromatic = null;
- }
-
}
Deleted: trunk/Jmol/src/org/jmol/minimize/forcefield/UFF.txt
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/UFF.txt 2012-05-09 18:09:32 UTC (rev 17115)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/UFF.txt 2012-05-09 18:10:04 UTC (rev 17116)
@@ -1,281 +0,0 @@
-#
-# Open Babel file: UFF.prm
-#
-# Force field parameters for UFF, the Universal Force Field
-# Used by OBForceField and OBUFFForceField
-#
-# J. Am. Chem. Soc. (1992) 114(25) p. 10024-10035.
-# The parameters in this file are taken from the UFF implementation in RDKit
-# http://rdkit.org/
-#
-# Atom typing rules are based on UFF published atom descriptions
-# atom [SMARTS] [atomtype] [description]
-# These must be sorted according to the element and complexity
-# of the type rule (i.e., generic rules first, more specific rules later)
-#
-# MODIFIED 3/2008 by Bob Hanson for Jmol (bh)
-#
-# Parameters follow later
-# param Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
-
-atom [#1] H_ Generic hydrogen
-atom [#1D2] H_b Bridging hydrogen
-atom [#2] He4+4 Helium
-atom [#3] Li Lithium
-atom [#4] Be3+2 Generic Be
-atom [#5] B_2 Trigonal planar boron
-atom [#5D4] B_3 Tetrahedral boron
-atom [#6] C_3 Generic sp3 C
-atom [C^2] C_2 sp2 non-aromatic C=
-atom [C+1] C_2+ trivalent C (cation) // bh added Jmol 12.0.RC9
-atom [C-1] C_3 trivalent C (anion) // bh added Jmol 12.0.RC9
-atom [CA1] C_2 allylic C (anion or cation) // bh added Jmol 12.0.RC9
-atom [C^1] C_1 sp hybridized C
-atom [c] C_R aromatic C
-atom [#7] N_3 Generic sp3 N
-atom [NA1] N_2 allylic N or amide // bh added Jmol 12.0.RC9
-atom [N^2] N_2 sp2 non-aromatic N // bh was [ND2], but this improperly treats N-oxides
-atom [N^1] N_1 sp hybridized N // bh was [ND1], but this is more specifically sp
-atom [n] N_R aromatic N
-atom [#8] O_3 generic, sp3 hybridized O
-#atom [#8] O_3_z sp3 hybridized O for zeolites
-atom [O^2] O_2 sp2 hybridized O
-atom [O^1] O_1 sp hybridized O
-atom [o] O_R aromatic O
-atom [#9] F_ generic F
-atom [#10] Ne4+4
-atom [#11] Na
-atom [#12] Mg3+2
-atom [#13] Al3
-atom [#14] Si3
-atom [#15+5] P_3+5 formal charge +5
-#atom [#15] P_3+q Organometallic phosphine ligands
-atom [#15] P_3+3 generic phosphorus
-atom [#16] S_3+2 generic S
-atom [#16+4] S_3+4 S+4
-atom [#16+6] S_3+6 S+6
-atom [S^2] S_2 non-aromatic sp2 S
-atom [s] S_R aromatic S
-atom [#17] Cl
-atom [#18] Ar4+4
-atom [#19] K_
-atom [#20] Ca6+2
-atom [#21] Sc3+3
-atom [#22] Ti6+4 generic Ti (6-valent)
-atom [#22D3] Ti3+4
-atom [#23] V_3+5
-atom [#24] Cr6+3
-atom [#25] Mn6+2
-atom [#26] Fe6+2 generic Fe (6-valent)
-atom [#26D3] Fe3+2
-atom [#27] Co6+3
-atom [#28] Ni4+2
-atom [#29] Cu3+1
-atom [#30] Zn3+2
-atom [#31] Ga3+3
-atom [#32] Ge3
-atom [#33] As3+3
-atom [#34] Se3+2
-atom [#35] Br
-atom [#36] Kr4+4
-atom [#37] Rb
-atom [#38] Sr6+2
-atom [#39] Y_3+3
-atom [#40] Zr3+4
-atom [#41] Nb3+5
-atom [#42] Mo6+6 generic Mo (6-valent)
-atom [#42D3] Mo3+6 trivalent Mo
-atom [#43] Tc6+5
-atom [#44] Ru6+2
-atom [#45] Rh6+3
-atom [#46] Pd4+2
-atom [#47] Ag1+1
-atom [#48] Cd3+2
-atom [#49] In3+3
-atom [#50] Sn3
-atom [#51] Sb3+3
-atom [#52] Te3+2
-atom [#53] I_
-atom [#54] Xe4+4
-atom [#55] Cs
-atom [#56] Ba6+2
-atom [#57] La3+3
-atom [#58] Ce6+3
-atom [#59] Pr6+3
-atom [#60] Nd6+3
-atom [#61] Pm6+3
-atom [#62] Sm6+3
-atom [#63] Eu6+3
-atom [#64] Gd6+3
-atom [#65] Tb6+3
-atom [#66] Dy6+3
-atom [#67] Ho6+3
-atom [#68] Er6+3
-atom [#69] Tm6+3
-atom [#70] Yb6+3
-atom [#71] Lu6+3
-atom [#72] Hf3+4
-atom [#73] Ta3+5
-atom [#74] W_6+6 generic W (6-valent)
-atom [#74D3+4] W_3+4
-atom [#74D3+6] W_3+6
-atom [#75] Re6+5 generic Re (6-valent)
-atom [#75D3] Re3+7 trivalent Re
-atom [#76] Os6+6
-atom [#77] Ir6+3
-atom [#78] Pt4+2
-atom [#79] Au4+3
-atom [#80] Hg1+2
-atom [#81] Tl3+3
-atom [#82] Pb3
-atom [#83] Bi3+3
-atom [#84] Po3+2
-atom [#85] At
-atom [#86] Rn4+4
-atom [#87] Fr
-atom [#88] Ra6+2
-atom [#89] Ac6+3
-atom [#90] Th6+4
-atom [#91] Pa6+4
-atom [#92] U_6+4
-atom [#93] Np6+4
-atom [#94] Pu6+4
-atom [#95] Am6+4
-atom [#96] Cm6+3
-atom [#97] Bk6+3
-atom [#98] Cf6+3
-atom [#99] Es6+3
-atom [#100] Fm6+3
-atom [#101] Md6+3
-atom [#102] No6+3
-atom [#103] Lw6+3
-
-# Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
-param H_ 0.354 180 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
-param H_b 0.46 83.5 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
-param He4+4 0.849 90 2.362 0.056 15.24 0.098 0 0 9.66 14.92 1.3
-param Li 1.336 180 2.451 0.025 12 1.026 0 2 3.006 2.386 1.557
-param Be3+2 1.074 109.47 2.745 0.085 12 1.565 0 2 4.877 4.443 1.24
-param B_3 0.838 109.47 4.083 0.18 12.052 1.755 0 2 5.11 4.75 0.822
-param B_2 0.828 120 4.083 0.18 12.052 1.755 0 2 5.11 4.75 0.822
-param C_3 0.757 109.47 3.851 0.105 12.73 1.912 2.119 2 5.343 5.063 0.759
-param C_R 0.729 120 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
-param C_2 0.732 120 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
-param C_2+ 0.732 120 6.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
-param C_1 0.706 180 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
-param N_3 0.7 106.7 3.66 0.069 13.407 2.544 0.45 2 6.899 5.88 0.715
-param N_R 0.699 120 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715
-param N_2 0.685 111.2 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715
-param N_1 0.656 180 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715
-param O_3 0.658 104.51 3.5 0.06 14.085 2.3 0.018 2 8.741 6.682 0.669
-param O_3_z 0.528 146 3.5 0.06 14.085 2.3 0.018 2 8.741 6.682 0.669
-param O_R 0.68 110 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669
-param O_2 0.634 120 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669
-param O_1 0.639 180 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669
-param F_ 0.668 180 3.364 0.05 14.762 1.735 0 2 10.874 7.474 0.706
-param Ne4+4 0.92 90 3.243 0.042 15.44 0.194 0 2 11.04 10.55 1.768
-param Na 1.539 180 2.983 0.03 12 1.081 0 1.25 2.843 2.296 2.085
-param Mg3+2 1.421 109.47 3.021 0.111 12 1.787 0 1.25 3.951 3.693 1.5
-param Al3 1.244 109.47 4.499 0.505 11.278 1.792 0 1.25 4.06 3.59 1.201
-param Si3 1.117 109.47 4.295 0.402 12.175 2.323 1.225 1.25 4.168 3.487 1.176
-param P_3+3 1.101 93.8 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102
-param P_3+5 1.056 109.47 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102
-param P_3+q 1.056 109.47 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102
-param S_3+2 1.064 92.1 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047
-param S_3+4 1.049 103.2 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047
-param S_3+6 1.027 109.47 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047
-param S_R 1.077 92.2 4.035 0.274 13.969 2.703 0 1.25 6.928 4.486 1.047
-param S_2 0.854 120 4.035 0.274 13.969 2.703 0 1.25 6.928 4.486 1.047
-param Cl 1.044 180 3.947 0.227 14.866 2.348 0 1.25 8.564 4.946 0.994
-param Ar4+4 1.032 90 3.868 0.185 15.763 0.3 0 1.25 9.465 6.355 2.108
-param K_ 1.953 180 3.812 0.035 12 1.165 0 0.7 2.421 1.92 2.586
-param Ca6+2 1.761 90 3.399 0.238 12 2.141 0 0.7 3.231 2.88 2
-param Sc3+3 1.513 109.47 3.295 0.019 12 2.592 0 0.7 3.395 3.08 1.75
-param Ti3+4 1.412 109.47 3.175 0.017 12 2.659 0 0.7 3.47 3.38 1.607
-param Ti6+4 1.412 90 3.175 0.017 12 2.659 0 0.7 3.47 3.38 1.607
-param V_3+5 1.402 109.47 3.144 0.016 12 2.679 0 0.7 3.65 3.41 1.47
-param Cr6+3 1.345 90 3.023 0.015 12 2.463 0 0.7 3.415 3.865 1.402
-param Mn6+2 1.382 90 2.961 0.013 12 2.43 0 0.7 3.325 4.105 1.533
-param Fe3+2 1.27 109.47 2.912 0.013 12 2.43 0 0.7 3.76 4.14 1.393
-param Fe6+2 1.335 90 2.912 0.013 12 2.43 0 0.7 3.76 4.14 1.393
-param Co6+3 1.241 90 2.872 0.014 12 2.43 0 0.7 4.105 4.175 1.406
-param Ni4+2 1.164 90 2.834 0.015 12 2.43 0 0.7 4.465 4.205 1.398
-param Cu3+1 1.302 109.47 3.495 0.005 12 1.756 0 0.7 4.2 4.22 1.434
-param Zn3+2 1.193 109.47 2.763 0.124 12 1.308 0 0.7 5.106 4.285 1.4
-param Ga3+3 1.26 109.47 4.383 0.415 11 1.821 0 0.7 3.641 3.16 1.211
-param Ge3 1.197 109.47 4.28 0.379 12 2.789 0.701 0.7 4.051 3.438 1.189
-param As3+3 1.211 92.1 4.23 0.309 13 2.864 1.5 0.7 5.188 3.809 1.204
-param Se3+2 1.19 90.6 4.205 0.291 14 2.764 0.335 0.7 6.428 4.131 1.224
-param Br 1.192 180 4.189 0.251 15 2.519 0 0.7 7.79 4.425 1.141
-param Kr4+4 1.147 90 4.141 0.22 16 0.452 0 0.7 8.505 5.715 2.27
-param Rb 2.26 180 4.114 0.04 12 1.592 0 0.2 2.331 1.846 2.77
-param Sr6+2 2.052 90 3.641 0.235 12 2.449 0 0.2 3.024 2.44 2.415
-param Y_3+3 1.698 109.47 3.345 0.072 12 3.257 0 0.2 3.83 2.81 1.998
-param Zr3+4 1.564 109.47 3.124 0.069 12 3.667 0 0.2 3.4 3.55 1.758
-param Nb3+5 1.473 109.47 3.165 0.059 12 3.618 0 0.2 3.55 3.38 1.603
-param Mo6+6 1.467 90 3.052 0.056 12 3.4 0 0.2 3.465 3.755 1.53
-param Mo3+6 1.484 109.47 3.052 0.056 12 3.4 0 0.2 3.465 3.755 1.53
-param Tc6+5 1.322 90 2.998 0.048 12 3.4 0 0.2 3.29 3.99 1.5
-param Ru6+2 1.478 90 2.963 0.056 12 3.4 0 0.2 3.575 4.015 1.5
-param Rh6+3 1.332 90 2.929 0.053 12 3.5 0 0.2 3.975 4.005 1.509
-param Pd4+2 1.338 90 2.899 0.048 12 3.21 0 0.2 4.32 4 1.544
-param Ag1+1 1.386 180 3.148 0.036 12 1.956 0 0.2 4.436 3.134 1.622
-param Cd3+2 1.403 109.47 2.848 0.228 12 1.65 0 0.2 5.034 3.957 1.6
-param In3+3 1.459 109.47 4.463 0.599 11 2.07 0 0.2 3.506 2.896 1.404
-param Sn3 1.398 109.47 4.392 0.567 12 2.961 0.199 0.2 3.987 3.124 1.354
-param Sb3+3 1.407 91.6 4.42 0.449 13 2.704 1.1 0.2 4.899 3.342 1.404
-param Te3+2 1.386 90.25 4.47 0.398 14 2.882 0.3 0.2 5.816 3.526 1.38
-param I_ 1.382 180 4.5 0.339 15 2.65 0 0.2 6.822 3.762 1.333
-param Xe4+4 1.267 90 4.404 0.332 12 0.556 0 0.2 7.595 4.975 2.459
-param Cs 2.57 180 4.517 0.045 12 1.573 0 0.1 2.183 1.711 2.984
-param Ba6+2 2.277 90 3.703 0.364 12 2.727 0 0.1 2.814 2.396 2.442
-param La3+3 1.943 109.47 3.522 0.017 12 3.3 0 0.1 2.8355 2.7415 2.071
-param Ce6+3 1.841 90 3.556 0.013 12 3.3 0 0.1 2.774 2.692 1.925
-param Pr6+3 1.823 90 3.606 0.01 12 3.3 0 0.1 2.858 2.564 2.007
-param Nd6+3 1.816 90 3.575 0.01 12 3.3 0 0.1 2.8685 2.6205 2.007
-param Pm6+3 1.801 90 3.547 0.009 12 3.3 0 0.1 2.881 2.673 2
-param Sm6+3 1.78 90 3.52 0.008 12 3.3 0 0.1 2.9115 2.7195 1.978
-param Eu6+3 1.771 90 3.493 0.008 12 3.3 0 0.1 2.8785 2.7875 2.227
-param Gd6+3 1.735 90 3.368 0.009 12 3.3 0 0.1 3.1665 2.9745 1.968
-param Tb6+3 1.732 90 3.451 0.007 12 3.3 0 0.1 3.018 2.834 1.954
-param Dy6+3 1.71 90 3.428 0.007 12 3.3 0 0.1 3.0555 2.8715 1.934
-param Ho6+3 1.696 90 3.409 0.007 12 3.416 0 0.1 3.127 2.891 1.925
-param Er6+3 1.673 90 3.391 0.007 12 3.3 0 0.1 3.1865 2.9145 1.915
-param Tm6+3 1.66 90 3.374 0.006 12 3.3 0 0.1 3.2514 2.9329 2
-param Yb6+3 1.637 90 3.355 0.228 12 2.618 0 0.1 3.2889 2.965 2.158
-param Lu6+3 1.671 90 3.64 0.041 12 3.271 0 0.1 2.9629 2.4629 1.896
-param Hf3+4 1.611 109.47 3.141 0.072 12 3.921 0 0.1 3.7 3.4 1.759
-param Ta3+5 1.511 109.47 3.17 0.081 12 4.075 0 0.1 5.1 2.85 1.605
-param W_6+6 1.392 90 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538
-param W_3+4 1.526 109.47 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538
-param W_3+6 1.38 109.47 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538
-param Re6+5 1.372 90 2.954 0.066 12 3.7 0 0.1 3.96 3.92 1.6
-param Re3+7 1.314 109.47 2.954 0.066 12 3.7 0 0.1 3.96 3.92 1.6
-param Os6+6 1.372 90 3.12 0.037 12 3.7 0 0.1 5.14 3.63 1.7
-param Ir6+3 1.371 90 2.84 0.073 12 3.731 0 0.1 5 4 1.866
-param Pt4+2 1.364 90 2.754 0.08 12 3.382 0 0.1 4.79 4.43 1.557
-param Au4+3 1.262 90 3.293 0.039 12 2.625 0 0.1 4.894 2.586 1.618
-param Hg1+2 1.34 180 2.705 0.385 12 1.75 0 0.1 6.27 4.16 1.6
-param Tl3+3 1.518 120 4.347 0.68 11 2.068 0 0.1 3.2 2.9 1.53
-param Pb3 1.459 109.47 4.297 0.663 12 2.846 0.1 0.1 3.9 3.53 1.444
-param Bi3+3 1.512 90 4.37 0.518 13 2.47 1 0.1 4.69 3.74 1.514
-param Po3+2 1.5 90 4.709 0.325 14 2.33 0.3 0.1 4.21 4.21 1.48
-param At 1.545 180 4.75 0.284 15 2.24 0 0.1 4.75 4.75 1.47
-param Rn4+4 1.42 90 4.765 0.248 16 0.583 0 0.1 5.37 5.37 2.2
-param Fr 2.88 180 4.9 0.05 12 1.847 0 0 2 2 2.3
-param Ra6+2 2.512 90 3.677 0.404 12 2.92 0 0 2.843 2.434 2.2
-param Ac6+3 1.983 90 3.478 0.033 12 3.9 0 0 2.835 2.835 2.108
-param Th6+4 1.721 90 3.396 0.026 12 4.202 0 0 3.175 2.905 2.018
-param Pa6+4 1.711 90 3.424 0.022 12 3.9 0 0 2.985 2.905 1.8
-param U_6+4 1.684 90 3.395 0.022 12 3.9 0 0 3.341 2.853 1.713
-param Np6+4 1.666 90 3.424 0.019 12 3.9 0 0 3.549 2.717 1.8
-param Pu6+4 1.657 90 3.424 0.016 12 3.9 0 0 3.243 2.819 1.84
-param Am6+4 1.66 90 3.381 0.014 12 3.9 0 0 2.9895 3.0035 1.942
-param Cm6+3 1.801 90 3.326 0.013 12 3.9 0 0 2.8315 3.1895 1.9
-param Bk6+3 1.761 90 3.339 0.013 12 3.9 0 0 3.1935 3.0355 1.9
-param Cf6+3 1.75 90 3.313 0.013 12 3.9 0 0 3.197 3.101 1.9
-param Es6+3 1.724 90 3.299 0.012 12 3.9 0 0 3.333 3.089 1.9
-param Fm6+3 1.712 90 3.286 0.012 12 3.9 0 0 3.4 3.1 1.9
-param Md6+3 1.689 90 3.274 0.011 12 3.9 0 0 3.47 3.11 1.9
-param No6+3 1.679 90 3.248 0.011 12 3.9 0 0 3.475 3.175 1.9
-param Lw6+3 1.698 90 3.236 0.011 12 3.9 0 0 3.5 3.2 1.9
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