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Revision: 1.24
Committed: Tue Dec 11 10:05:10 2007 UTC (8 years, 9 months ago) by axeld
Branch: MAIN
CVS Tags: VERSION_3_2_0, HEAD
Changes since 1.23: +5 -0 lines
Log Message:
long time since last commit.

Line File contents
1 2007-03-29 Alexander V. Diemand <axeld@moltalk.org>
2
3 * Version 3.2 is clean rebuild on all supported platforms:
4 Linux (i386, x86_64), Windows, MacOS (ppc, i386)
5
6 2006-05-16 Alexander V. Diemand <axeld@moltalk.org>
7
8 * Version 3 introduces consistent naming of Classes: MT..
9
10 2006-05-16 Alexander V. Diemand <axeld@moltalk.org>
11
12 * checked in some bug fixes; tag: VERSION_2_2_2
13
14 2005-08-25 Alexander V. Diemand <axeld@moltalk.org>
15
16 * Library/MTPairwiseSequenceAlignment: added writeFastaToStream:
17 * Library/Residue: added mutateTo:
18
19 2005-06-22 Alexander V. Diemand <axeld@moltalk.org>
20
21 * Library/FileStream.oh: moved isFileCompressed: and checkFileStat:
22 from class StructureFactory to FileStream
23
24 2005-05-28 Alexander V. Diemand <axeld@moltalk.org>
25
26 * Library/AtomFactory.oh: new object factory added. This is being
27 used from PDBParser.m.
28
29 2005-04-07 Alexander V. Diemand <axeld@moltalk.org>
30
31 * Library/Structure.m: parsed descriptors of a structure are hold in
32 a dictionary and accessed through getDescriptorForKey: and
33 setDescriptor:withKey:. This removes a number of fields of class
34 Structure.
35 * Library/PDBParser.m: fills in descriptor dictionary in Structure
36
37 2005-02-12 Alexander V. Diemand <axeld@moltalk.org>
38
39 * Library/PDBParser.m: set default values for fields
40
41 2004-08-17 Alexander V. Diemand <axeld@moltalk.org>
42
43 * Library/PDBParser.m: respects the flag PDBPARSER_ALL_NMRMODELS and
44 loads all models in the file
45 * Library/Structure.oh: new methods added to access models in PDB files
46
47 2004-07-21 Alexander V. Diemand <axeld@moltalk.org>
48
49 * Library/privateResidue.m: added connectivity of MSE
50
51 2004-07-08 Alexander V. Diemand <axeld@moltalk.org>
52
53 * Library/Atom.m: bonds held in array now
54 * Library/Matrix.m: alignTo: moved here from Selection.m
55 * Library/Selection.m: alignTo: moved to Matrix.m
56 * Library/Residue.m : new methods previousResidue and nextResidue
57
58 2004-06-04 Alexander V. Diemand <axeld@moltalk.org>
59
60 * Library/PDBParser.m: better parsing of alternate sites
61
62 2004-05-25 Alexander V. Diemand <axeld@moltalk.org>
63
64 * Library/Vector.m: differenceTo: returns a Vector
65 * Library/Vector.m: angleBetween: checks acos(1.0) -> 0.0
66
67 2004-05-23 Alexander V. Diemand <axeld@moltalk.org>
68
69 * Library/Atom.m: bondTo: adds bond to both atoms
70
71 2004-05-10 Alexander V. Diemand <axeld@moltalk.org>
72
73 * Library/StructureFactory.oh: new flag to parse all alternate atoms
74 * PDBPARSER_ALL_ALTERNATE_ATOMS
75 * Library/PDBParser.m: parse only first of alternate atoms unless flag
76
77 2004-03-12 Alexander V. Diemand <axeld@moltalk.org>
78
79 * Library/String.m: new method -stringFromCharArray:
80 * Library/Structure.m: new method -addChain:
81
82 2004-02-20 Alexander V. Diemand <axeld@moltalk.org>
83
84 * Library/Residue.m: oneLetterCode returns 'X' in cases it cannot
85 * determine the real residue name
86 * Library/PDBParser.m: readHeader does not expect a valid PDB file
87 * header anymore
88
89 2004-01-22 Alexander V. Diemand <axeld@moltalk.org>
90
91 * Library/Chain.oh: store SEQRES as parsed from PDB files
92 * Library/PDBParser.m: parsing of SEQRES entries
93
94 2004-01-11 Alexander V. Diemand <axeld@moltalk.org>
95
96 * Library/PairwiseStrxAlignment.m: new TCoffee header
97 * Library/CompressedFileStream.oh: safe variants of stream creation
98 * Library/FileStream.oh: safe variants of stream creation, in default
99 * temporary directory
100
101 2004-01-09 Alexander V. Diemand <axeld@moltalk.org>
102
103 * Library/Atom.m: improved inference of element name from raw atom name
104
105 2004-01-02 Alexander V. Diemand <axeld@moltalk.org>
106
107 * Library/PDBParser.m: error message to stderr
108 * Library/privateResidue.m: error message to stderr
109
110 2003-12-31 Alexander V. Diemand <axeld@moltalk.org>
111
112 * Library/Chain.oh: added method -(NSNumber*)codeNumber
113
114 2003-12-04 Alexander V. Diemand <axeld@moltalk.org>
115
116 * Library/CompressedFileStream.oh: support for WIN32 added
117
118 2003-12-03 Alexander V. Diemand <axeld@moltalk.org>
119
120 * Library/privateStructure.m: write out a minimal header if storing
121 to PDB formatted file. Also store element and charge.
122
123 2003-11-28 Alexander V. Diemand <axeld@moltalk.org>
124
125 * Library/Residue.oh: new field name seqnum to remember position in
126 derived sequence. Setting of this value is side-effect of calling
127 Chain_getSequence or Chain_get3DSequence.
128
129 2003-11-27 Alexander V. Diemand <axeld@moltalk.org>
130
131 * Library/Atom.oh: added element and charge as fields to class Atom,
132 dropped method -type, new methods are -setCharge:, -setElement:,
133 -setElementWithName, -charge, -element, -elementName.
134 * Library/PDBParser.m: new flag is newfileformat if the file conforms
135 to PDB file format after 1996. This implies the parsing of segid,
136 atom charge and atom element name.
137
138 2003-11-18 Alexander V. Diemand <axeld@bioinformatics.org>
139
140 * Library/PairwiseStrxAlignment.m: -fromStreamAsTCoffee: expects the id
141 of the sequences in the format: <pdb code> + <chain id>, where chain id
142 is the numerical ascii value of the single char.
143
144 2003-11-07 Alexander V. Diemand <axeld@bioinformatics.org>
145
146 * Library/PDBParser.m Library/Chain.m: moved static vars into class
147 * Library/PairwiseStrxAlignment.m: bugs in dynamic programming fixed,
148 was depending on distance > 0.0 (becomes >=), we prefer the diagonal
149 move in the traceback.
150
151 2003-11-03 Alexander V. Diemand <axeld@bioinformatics.org>
152
153 * Library/Residue.m: -distanceCATo: returns -1.0 if distance cannot be
154 calculated (due to missing atoms)
155 * Library/Selection.m: -alignTo: does not align residue pairs which do
156 not have CA atoms
157 * Library/PDBParser.m: mkFloat(): now does read all 8 chars in numbers
158 * Library/Matrix44.oh: -chainWith: in-place multiplies the Matrix44
159 with the parameter Matrix44: M' = p_M * M
160 * Library/Coordinates.m: -transformBy and -rotateBy speedup with inlined
161 matrix calculations
162
163 2003-11-01 Alexander V. Diemand <axeld@bioinformatics.org>
164
165 * Library/Chain.m: -prepareResidueHash does accept the size of the
166 grid as a parameter
167
168 2003-10-22 Alexander V. Diemand <axeld@bioinformatics.org>
169
170 * Library/Residue.m: -isStandardAminoAcid is true for modified residues
171 * Library/MolTalk.oh: new definition MOLTALK_VERSION
172
173 2003-10-21 Alexander V. Diemand <axeld@bioinformatics.org>
174
175 * Library/PDBParser.m Library/Residue.oh Library/Residue.m: parsing of
176 MODRES entries enabled. They get stored directly in the modified
177 residue. Even if the PDB format requires a modified residue to be of
178 type heterogenous, I treat them like ordinary residues
179 * Library/privateStructure.m: saving of MODRES entries to PDB file
180
181 2003-10-21 Alexander V. Diemand <axeld@bioinformatics.org>
182
183 * Library/PDBParser.m: minor cleanups for speed
184 * Library/Residue.oh Library/Residue.m: atoms are held in array not
185 dictionary, gives quite some speed up
186
187 2003-10-20 Alexander V. Diemand <axeld@bioinformatics.org>
188
189 * Library/PDBParser.m: function mkInt now understands negative numbers
190 * Library/PDBParser.m: only consider atoms of first of alternate
191 locations for residues
192 * Library/Chain.m Library/Matrix.m Library/PairwiseStrxAlignment.m: make
193 it safe on SunOS by using basic mathematical functions like floor
194 instead of lround
195
196 2003-10-17 Alexander V. Diemand <axeld@bioinformatics.org>
197
198 * a lot: changed all retain,release,autorelease to macros
199 RETAIN,RELEASE,AUTORELEASE
200
201 * a lot: changed allocation of new NSAutoreleasePool to macro
202 CREATE_AUTORELEASE_POOL
203
204 * a lot: changed use of printf("%@",..) to printf("%s",..)
205
206 2003-09-28 Alexander V. Diemand <axeld@bioinformatics.org>
207
208 * Import into CVS on bioinformatics.org