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root/owl/trunk/proteinstructure/contactTypes.dat
Revision: 407
Committed: Tue Nov 20 18:41:56 2007 UTC (11 years, 10 months ago) by filippis
File size: 2657 byte(s)
Log Message:
contactTypes.dat 
-SC_CAGLY contact type added

SecStrucElement.java
-getSheetSerial method is now public

Pdb.java
-writeToDbFast added

Graph.java
-write_graph_to_db_fast
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-node_id, sssid, sheetSerial and turn are now also filled in

DbGraph.java
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-directionality is also taken into account now when reading edges

genDbGraph.java
-sequence separation added as option

createGraphDb.java added

Line User Rev File contents
1 duarte 326 # Contact types definitions:
2     # contact types names in lines starting with '>', then the contact type name and last the type: either "multi" or "single"
3     # then list of space separated atom names after each three letter aminoacid code
4     # lines starting with # are comments
5     > ALL multi
6     TRP: CE2 CA C O CB CG CD1 CD2 CH2 CZ3 CZ2 CE3 NE1 N
7     CYS: SG CB O CA C N
8     GLN: CA CG N NE2 OE1 CD C O CB
9     ALA: CA C N CB O
10     VAL: CG1 CB O C CA N CG2
11     LEU: N CA C O CB CG CD2 CD1
12     ASP: N CB OD2 CG CA C O OD1
13     SER: C N CA O CB OG
14     PRO: O C CB CG CA CD N
15     THR: CA N C CG2 OG1 CB O
16     PHE: O CE2 CE1 CG C N CA CB CD2 CD1 CZ
17     ARG: NH2 CZ NE CD CG C CA N NH1 CB O
18     LYS: C CA N O CB CG CD CE NZ
19     MET: CA O C CB CE N CG SD
20     HIS: CE1 CD2 ND1 CG CB O C CA N NE2
21     GLY: N CA C O
22     ILE: CG2 CD1 O N CA C CB CG1
23     GLU: C N CA OE2 OE1 CD CG CB O
24     ASN: ND2 OD1 CB O CG C CA N
25     TYR: CD2 CD1 OH CZ CE2 N CA C O CB CG CE1
26     > BB multi
27     TRP: CA N C O
28     CYS: CA N C O
29     GLN: CA N C O
30     ALA: CA N C O
31     VAL: CA N C O
32     LEU: CA N C O
33     ASP: CA N C O
34     SER: CA N C O
35     PRO: CA N C O
36     THR: CA N C O
37     PHE: CA N C O
38     ARG: CA N C O
39     LYS: CA N C O
40     MET: CA N C O
41     HIS: CA N C O
42     GLY: CA N C O
43     ILE: CA N C O
44     GLU: CA N C O
45     ASN: CA N C O
46     TYR: CA N C O
47     > SC multi
48     TRP: CE2 CB CG CD1 CD2 CH2 CZ3 CZ2 CE3 NE1
49     CYS: SG CB
50     GLN: CG NE2 OE1 CD CB
51     ALA: CB
52     VAL: CG1 CB CG2
53     LEU: CB CG CD2 CD1
54     ASP: CB OD2 CG OD1
55     SER: CB OG
56     PRO: CB CG CD
57     THR: CG2 OG1 CB
58     PHE: CE2 CE1 CG CB CD2 CD1 CZ
59     ARG: NH2 CZ NE CD CG NH1 CB
60     LYS: CB CG CD CE NZ
61     MET: CB CE CG SD
62     HIS: CE1 CD2 ND1 CG CB NE2
63     GLY:
64     ILE: CG2 CD1 CB CG1
65     GLU: OE2 OE1 CD CG CB
66     ASN: ND2 OD1 CB CG
67     TYR: CD2 CD1 OH CZ CE2 CB CG CE1
68 filippis 407 > SC_CAGLY multi
69     TRP: CE2 CB CG CD1 CD2 CH2 CZ3 CZ2 CE3 NE1
70     CYS: SG CB
71     GLN: CG NE2 OE1 CD CB
72     ALA: CB
73     VAL: CG1 CB CG2
74     LEU: CB CG CD2 CD1
75     ASP: CB OD2 CG OD1
76     SER: CB OG
77     PRO: CB CG CD
78     THR: CG2 OG1 CB
79     PHE: CE2 CE1 CG CB CD2 CD1 CZ
80     ARG: NH2 CZ NE CD CG NH1 CB
81     LYS: CB CG CD CE NZ
82     MET: CB CE CG SD
83     HIS: CE1 CD2 ND1 CG CB NE2
84     GLY: CA
85     ILE: CG2 CD1 CB CG1
86     GLU: OE2 OE1 CD CG CB
87     ASN: ND2 OD1 CB CG
88     TYR: CD2 CD1 OH CZ CE2 CB CG CE1
89 duarte 326 > Ca single
90     TRP: CA
91     CYS: CA
92     GLN: CA
93     ALA: CA
94     VAL: CA
95     LEU: CA
96     ASP: CA
97     SER: CA
98     PRO: CA
99     THR: CA
100     PHE: CA
101     ARG: CA
102     LYS: CA
103     MET: CA
104     HIS: CA
105     GLY: CA
106     ILE: CA
107     GLU: CA
108     ASN: CA
109     TYR: CA
110     > Cb single
111     TRP: CB
112     CYS: CB
113     GLN: CB
114     ALA: CB
115     VAL: CB
116     LEU: CB
117     ASP: CB
118     SER: CB
119     PRO: CB
120     THR: CB
121     PHE: CB
122     ARG: CB
123     LYS: CB
124     MET: CB
125     HIS: CB
126     GLY: CA
127     ILE: CB
128     GLU: CB
129     ASN: CB
130     TYR: CB
131     > Cg single
132     TRP: CD2
133     CYS: SG
134     GLN: CG
135     ALA:
136     VAL: CG1
137     LEU: CG
138     ASP: CG
139     SER: OG
140     PRO: CG
141     THR: OG1
142     PHE: CG
143     ARG: NE
144     LYS: CD
145     MET: CG
146     HIS: CG
147     GLY:
148     ILE: CG1
149     ASN: CG
150     GLU: CG
151     TYR: CG
152     > C single
153     TRP: C
154     CYS: C
155     GLN: C
156     ALA: C
157     VAL: C
158     LEU: C
159     ASP: C
160     SER: C
161     PRO: C
162     THR: C
163     PHE: C
164     ARG: C
165     LYS: C
166     MET: C
167     HIS: C
168     GLY: C
169     ILE: C
170     GLU: C
171     ASN: C
172     TYR: C