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* data/element.txt, data/atomtyp.txt: Minor changes. Allow boron
to have 4 bonds and adjust implicit valence for several elements.
This commit is contained in:
Geoffrey Hutchison
@@ -1,4 +1,10 @@
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2008-12-12 Geoffrey Hutchison <babel@geoffhutchison.net>
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* data/element.txt, data/atomtyp.txt: Minor changes. Allow boron
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to have 4 bonds and adjust implicit valence for several elements.
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2008-12-02 Chris Morley
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* src/tokenst.cpp, include/openbabel/tokenst.h: Add function
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to ignore istream up to a specified string.
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@@ -11,7 +17,6 @@
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fixes from Sergey Trepalin. Performs better, but still some
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memory leaks.
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2008-12-01 Geoffrey Hutchison <babel@geoffhutchison.net>
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* src/formats/pdbformat.cpp: Add support for reading CRYST1
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+164
-156
@@ -77,163 +77,171 @@ static const char AtomTypeData[] = {
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0x67,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,0x5B,0x24,0x28,0x5B,0x4E,
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||||
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||||
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||||
0x53,0x5D,0x29,0x5D,0x09,0x09,0x09,0x09,0x4E,0x61,0x6D,0x0A,0x45,0x58,0x54,
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|
||||
0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x09,0x09,0x09,0x4E,0x74,0x72,
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||||
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|
||||
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|
||||
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||||
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||||
0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,0x5B,0x24,0x28,0x43,0x28,0x3D,
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x5D,0x09,0x09,0x09,0x4F,0x2E,0x63,0x6F,
|
||||
0x32,0x20,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,0x5B,0x23,0x31,0x35,0x5D,
|
||||
0x09,0x09,0x09,0x09,0x09,0x50,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,0x5B,
|
||||
0x23,0x31,0x35,0x58,0x34,0x2B,0x5D,0x09,0x09,0x09,0x09,0x50,0x33,0x2B,0x0A,
|
||||
0x45,0x58,0x54,0x54,0x59,0x50,0x09,0x5B,0x23,0x31,0x35,0x3B,0x24,0x28,0x5B,
|
||||
0x23,0x31,0x35,0x44,0x34,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,
|
||||
0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,
|
||||
0x09,0x50,0x61,0x63,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,
|
||||
0x35,0x3B,0x24,0x28,0x5B,0x23,0x31,0x35,0x44,0x33,0x5D,0x28,0x7E,0x5B,0x4F,
|
||||
0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x09,0x09,0x50,
|
||||
0x61,0x63,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,0x5B,0x23,0x31,0x36,0x5D,
|
||||
0x09,0x09,0x09,0x09,0x09,0x53,0x33,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,
|
||||
0x5B,0x23,0x31,0x36,0x44,0x33,0x2B,0x2C,0x23,0x31,0x36,0x58,0x33,0x2B,0x5D,
|
||||
0x09,0x09,0x09,0x09,0x53,0x33,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,
|
||||
0x5B,0x23,0x31,0x36,0x3B,0x73,0x2C,0x24,0x28,0x5B,0x53,0x44,0x31,0x5D,0x3D,
|
||||
0x2A,0x29,0x5D,0x09,0x09,0x09,0x53,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
|
||||
0x09,0x5B,0x23,0x31,0x36,0x44,0x34,0x3B,0x24,0x28,0x53,0x28,0x3D,0x4F,0x29,
|
||||
0x28,0x3D,0x4F,0x29,0x29,0x5D,0x09,0x09,0x09,0x53,0x6F,0x32,0x0A,0x45,0x58,
|
||||
0x54,0x54,0x59,0x50,0x09,0x5B,0x23,0x31,0x36,0x44,0x33,0x3B,0x24,0x28,0x53,
|
||||
0x28,0x3D,0x4F,0x29,0x29,0x5D,0x09,0x09,0x09,0x53,0x6F,0x78,0x0A,0x45,0x58,
|
||||
0x54,0x54,0x59,0x50,0x09,0x5B,0x23,0x31,0x36,0x3B,0x24,0x28,0x5B,0x23,0x31,
|
||||
0x36,0x44,0x34,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,0x7E,0x5B,
|
||||
0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x09,0x53,
|
||||
0x61,0x63,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,0x5B,0x23,0x31,0x36,0x3B,
|
||||
0x24,0x28,0x5B,0x23,0x31,0x36,0x44,0x33,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,
|
||||
0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x09,0x09,0x53,0x61,0x63,
|
||||
0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,0x5B,0x23,0x35,0x5D,0x09,0x09,0x09,
|
||||
0x09,0x09,0x42,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x09,0x5B,0x23,0x35,
|
||||
0x44,0x34,0x5D,0x09,0x09,0x09,0x09,0x09,0x42,0x33,0x0A,0x00};
|
||||
|
||||
} // namespace OpenBabel
|
||||
#endif // OB_ATOMTYP_H
|
||||
|
||||
+19
-7
@@ -53,6 +53,8 @@ INTHYB [Te] 3 # sp3 hybridization Te
|
||||
#
|
||||
#IMPLICIT VALENCE RULES
|
||||
#
|
||||
IMPVAL [#5] 3 # Generic boron
|
||||
|
||||
IMPVAL [#6^3] 4
|
||||
IMPVAL [#6^2] 3
|
||||
IMPVAL [#6^1] 2
|
||||
@@ -61,11 +63,6 @@ IMPVAL [#6^2-] 2
|
||||
IMPVAL [#6^1-] 1 #CM for isocyanides
|
||||
IMPVAL [c+] 2
|
||||
|
||||
IMPVAL [#8] 2
|
||||
IMPVAL [#8-] 1
|
||||
IMPVAL [#8+] 3
|
||||
IMPVAL [$([#8]=*)] 1
|
||||
|
||||
IMPVAL [N^3] 3
|
||||
IMPVAL [N^3+] 4
|
||||
IMPVAL [N^2] 3
|
||||
@@ -86,9 +83,15 @@ IMPVAL [n] 2
|
||||
IMPVAL [n-] 2
|
||||
IMPVAL [n+] 3
|
||||
|
||||
IMPVAL [#8] 2 # Generic O
|
||||
IMPVAL [#8-] 1
|
||||
IMPVAL [#8+] 3
|
||||
IMPVAL [$([#8]=*)] 1
|
||||
|
||||
IMPVAL [#9D0] 1
|
||||
IMPVAL [#9D0-] 0 #[F-]
|
||||
|
||||
IMPVAL [#13] 3 # generic Al
|
||||
IMPVAL [#14] 4 # regular sp3 Si
|
||||
|
||||
IMPVAL [#15D4] 4
|
||||
@@ -110,13 +113,22 @@ IMPVAL [$([#16D2](=O)-O)] 3 # e.g. O[S]=O
|
||||
|
||||
IMPVAL [#17D0] 1
|
||||
IMPVAL [#17D0-] 0 #[Cl-]
|
||||
|
||||
IMPVAL [#31] 3
|
||||
IMPVAL [#32] 4
|
||||
|
||||
IMPVAL [#33] 3
|
||||
IMPVAL [as] 3
|
||||
|
||||
IMPVAL [#34] 2
|
||||
|
||||
IMPVAL [#35D0] 1
|
||||
IMPVAL [#35D0-] 0 #[Br-]
|
||||
|
||||
IMPVAL [#52] 2
|
||||
IMPVAL [#53D0] 1
|
||||
IMPVAL [#53D0-] 0 #[I-]
|
||||
|
||||
IMPVAL [#5] 3
|
||||
IMPVAL [as] 3
|
||||
#
|
||||
#EXTERNAL TYPE RULES
|
||||
#
|
||||
|
||||
+1
-1
@@ -40,7 +40,7 @@ static const char ElementData[] = {
|
||||
0x33,0x32,0x32,0x37,0x09,0x30,0x09,0x30,0x2E,0x37,0x36,0x09,0x31,0x2E,0x30,
|
||||
0x30,0x09,0x30,0x2E,0x30,0x30,0x09,0x42,0x65,0x72,0x79,0x6C,0x6C,0x69,0x75,
|
||||
0x6D,0x0A,0x35,0x09,0x42,0x09,0x32,0x2E,0x30,0x31,0x09,0x30,0x2E,0x38,0x32,
|
||||
0x09,0x30,0x2E,0x38,0x32,0x09,0x31,0x2E,0x38,0x09,0x33,0x09,0x31,0x30,0x2E,
|
||||
0x09,0x30,0x2E,0x38,0x32,0x09,0x31,0x2E,0x38,0x09,0x34,0x09,0x31,0x30,0x2E,
|
||||
0x38,0x31,0x31,0x09,0x32,0x2E,0x30,0x34,0x09,0x38,0x2E,0x32,0x39,0x38,0x30,
|
||||
0x09,0x30,0x2E,0x32,0x37,0x39,0x37,0x32,0x33,0x09,0x31,0x2E,0x30,0x30,0x09,
|
||||
0x30,0x2E,0x37,0x31,0x09,0x30,0x2E,0x37,0x31,0x09,0x42,0x6F,0x72,0x6F,0x6E,
|
||||
|
||||
+1
-1
@@ -35,7 +35,7 @@
|
||||
2 He 0.0 0.32 0.32 1.4 0 4.002602 0.0 24.5874 0 0.85 1.00 1.00 Helium
|
||||
3 Li 0.97 1.34 1.34 2.2 1 6.941 0.98 5.3917 0.618049 0.80 0.50 1.00 Lithium
|
||||
4 Be 1.47 0.90 0.90 1.9 2 9.012182 1.57 9.3227 0 0.76 1.00 0.00 Beryllium
|
||||
5 B 2.01 0.82 0.82 1.8 3 10.811 2.04 8.2980 0.279723 1.00 0.71 0.71 Boron
|
||||
5 B 2.01 0.82 0.82 1.8 4 10.811 2.04 8.2980 0.279723 1.00 0.71 0.71 Boron
|
||||
6 C 2.50 0.77 0.77 1.7 4 12.0107 2.55 11.2603 1.262118 0.50 0.50 0.50 Carbon
|
||||
7 N 3.07 0.75 0.75 1.6 4 14.0067 3.04 14.5341 -0.07 0.05 0.05 1.00 Nitrogen
|
||||
8 O 3.50 0.73 0.73 1.55 2 15.9994 3.44 13.6181 1.4611120 1.00 0.05 0.05 Oxygen
|
||||
|
||||
Reference in New Issue
Block a user