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Thomas Forest 4 years ago
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+# Implementation of the DSSP approach for secondary structure assignation
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+
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+Attempt to implement the historic 1983 version of DSSP (Define Secondary Structure of Proteins): Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers. 1983 222577-2637. PMID: 6667333; UI: 84128824.
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+
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+## Getting Started
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+
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+These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
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+
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+### Prerequisites
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+
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+You need to have **Python 3** and **Conda** on your machine, as it will be used to deploy the running environnement of DSSP.
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+This program has been tested for Python 3.7.4.
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+
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+### Installing
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+
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+Use conda to create the environnement
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+```
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+conda env create --file environment.yml
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+```
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+
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+Load your environnement
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+
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+```
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+conda activate dssp
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+```
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+
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+You should be ready to run the program, by calling, for example
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+```
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+python3 src/dssp.py data/1est.pdb
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+```
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+
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+## Author
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+
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+* **FOREST Thomas** - *M2BI* - [Univ-Paris-Diderot.fr](https://www.univ-paris-diderot.fr/) - thomas.forest@etu.univ-paris-diderot.fr
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+
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+## License
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+
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+This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details
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+
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+## Acknowledgments
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+
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+* Hat tip to anyone whose code was used
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+* Inspiration
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+* etc

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-HEADER    RIBONUCLEASE INHIBITOR                  09-MAY-94   1BTA
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-TITLE     THREE-DIMENSIONAL SOLUTION STRUCTURE AND 13C ASSIGNMENTS OF
3 
-TITLE    2 BARSTAR USING NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
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-COMPND    MOL_ID: 1;
5 
-COMPND   2 MOLECULE: BARSTAR;
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-COMPND   3 CHAIN: A;
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-COMPND   4 ENGINEERED: YES
8 
-SOURCE    MOL_ID: 1;
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-SOURCE   2 ORGANISM_SCIENTIFIC: BACILLUS AMYLOLIQUEFACIENS;
10 
-SOURCE   3 ORGANISM_TAXID: 1390
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-KEYWDS    RIBONUCLEASE INHIBITOR
12 
-EXPDTA    SOLUTION NMR
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-AUTHOR    M.J.LUBIENSKI,M.BYCROFT,S.M.V.FREUND,A.R.FERSHT
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-REVDAT   2   24-FEB-09 1BTA    1       VERSN
15 
-REVDAT   1   31-JUL-94 1BTA    0
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-JRNL        AUTH   M.J.LUBIENSKI,M.BYCROFT,S.M.FREUND,A.R.FERSHT
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-JRNL        TITL   THREE-DIMENSIONAL SOLUTION STRUCTURE AND 13C
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-JRNL        TITL 2 ASSIGNMENTS OF BARSTAR USING NUCLEAR MAGNETIC
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-JRNL        TITL 3 RESONANCE SPECTROSCOPY.
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-JRNL        REF    BIOCHEMISTRY                  V.  33  8866 1994
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-JRNL        REFN                   ISSN 0006-2960
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-JRNL        PMID   8043574
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-JRNL        DOI    10.1021/BI00196A003
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-REMARK   1
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-REMARK   1 REFERENCE 1
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-REMARK   1  AUTH   R.W.HARTLEY
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-REMARK   1  TITL   BARNASE AND BARSTAR: TWO SMALL PROTEINS TO FOLD
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-REMARK   1  TITL 2 AND FIT TOGETHER
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-REMARK   1  REF    TRENDS BIOCHEM.SCI.           V.  14   450 1989
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-REMARK   1  REFN                   ISSN 0968-0004
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-REMARK   2
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-REMARK   2 RESOLUTION. NOT APPLICABLE.
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-REMARK   3
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-REMARK   3 REFINEMENT.
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-REMARK   3   PROGRAM     : X-PLOR
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-REMARK   3   AUTHORS     : BRUNGER
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-REMARK   3
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-REMARK   3  OTHER REFINEMENT REMARKS: NULL
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-REMARK   4
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-REMARK   4 1BTA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
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-REMARK 100
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-REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
43 
-REMARK 210
44 
-REMARK 210 EXPERIMENTAL DETAILS
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-REMARK 210  EXPERIMENT TYPE                : NMR
46 
-REMARK 210  TEMPERATURE           (KELVIN) : NULL
47 
-REMARK 210  PH                             : NULL
48 
-REMARK 210  IONIC STRENGTH                 : NULL
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-REMARK 210  PRESSURE                       : NULL
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-REMARK 210  SAMPLE CONTENTS                : NULL
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-REMARK 210
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-REMARK 210  NMR EXPERIMENTS CONDUCTED      : NULL
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-REMARK 210  SPECTROMETER FIELD STRENGTH    : NULL
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-REMARK 210  SPECTROMETER MODEL             : NULL
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-REMARK 210  SPECTROMETER MANUFACTURER      : NULL
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-REMARK 210
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-REMARK 210  STRUCTURE DETERMINATION.
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-REMARK 210   SOFTWARE USED                 : NULL
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-REMARK 210   METHOD USED                   : NULL
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-REMARK 210
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-REMARK 210 CONFORMERS, NUMBER CALCULATED   : NULL
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-REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 1
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-REMARK 210 CONFORMERS, SELECTION CRITERIA  : NULL
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-REMARK 210
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-REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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-REMARK 210
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-REMARK 210 REMARK: NULL
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-REMARK 215
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-REMARK 215 NMR STUDY
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-REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
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-REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
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-REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
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-REMARK 215 THESE RECORDS ARE MEANINGLESS.
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-REMARK 500
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-REMARK 500 GEOMETRY AND STEREOCHEMISTRY
76 
-REMARK 500 SUBTOPIC: TORSION ANGLES
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-REMARK 500
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-REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
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-REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
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-REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
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-REMARK 500
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-REMARK 500 STANDARD TABLE:
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-REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
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-REMARK 500
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-REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
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-REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
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-REMARK 500
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-REMARK 500  M RES CSSEQI        PSI       PHI
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-REMARK 500    PRO A  27     -179.66    -57.36
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-REMARK 500    TYR A  30      105.85    -38.41
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-REMARK 500    GLU A  32        3.60     50.07
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-REMARK 500    TRP A  44      -66.63    177.13
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-REMARK 500    LEU A  62      -32.03    -33.51
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-REMARK 500    GLU A  64      106.99    -12.37
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-REMARK 500    ASN A  65       32.13     73.69
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-REMARK 500    ASP A  83       65.33   -109.29
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-REMARK 500    THR A  85       98.90    -52.92
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-REMARK 500
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-REMARK 500 REMARK: NULL
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-REMARK 500
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-REMARK 500 GEOMETRY AND STEREOCHEMISTRY
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-REMARK 500 SUBTOPIC: PLANAR GROUPS
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-REMARK 500
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-REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
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-REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
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-REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
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-REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
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-REMARK 500 AN RMSD GREATER THAN THIS VALUE
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-REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
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-REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
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-REMARK 500
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-REMARK 500  M RES CSSEQI        RMS     TYPE
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-REMARK 500    ARG A  11         0.17    SIDE_CHAIN
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-REMARK 500    ARG A  54         0.31    SIDE_CHAIN
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-REMARK 500    ARG A  75         0.11    SIDE_CHAIN
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-REMARK 500
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-REMARK 500 REMARK: NULL
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-REMARK 900
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-REMARK 900 RELATED ENTRIES
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-REMARK 900 RELATED ID: 1BTB   RELATED DB: PDB
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-DBREF  1BTA A    1    89  UNP    P11540   BARS_BACAM       1     89
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-SEQRES   1 A   89  LYS LYS ALA VAL ILE ASN GLY GLU GLN ILE ARG SER ILE
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-SEQRES   2 A   89  SER ASP LEU HIS GLN THR LEU LYS LYS GLU LEU ALA LEU
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-SEQRES   3 A   89  PRO GLU TYR TYR GLY GLU ASN LEU ASP ALA LEU TRP ASP
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-SEQRES   4 A   89  CYS LEU THR GLY TRP VAL GLU TYR PRO LEU VAL LEU GLU
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-SEQRES   5 A   89  TRP ARG GLN PHE GLU GLN SER LYS GLN LEU THR GLU ASN
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-SEQRES   6 A   89  GLY ALA GLU SER VAL LEU GLN VAL PHE ARG GLU ALA LYS
128 
-SEQRES   7 A   89  ALA GLU GLY CYS ASP ILE THR ILE ILE LEU SER
129 
-HELIX    1  H1 SER A   14  ALA A   25  1                                  12
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-HELIX    2  H2 ASN A   33  GLY A   43  1                                  11
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-HELIX    3  H3 PHE A   56  THR A   63  1                                   8
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-HELIX    4  H4 GLU A   68  GLY A   81  1                                  14
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-SHEET    1 SH1 3 LYS A   1  ASN A   6  0
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-SHEET    2 SH1 3 LEU A  49  ARG A  54  1
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-SHEET    3 SH1 3 ASP A  83  SER A  89  1
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-CISPEP   1 TYR A   47    PRO A   48          0         0.92
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-CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
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-ORIGX1      1.000000  0.000000  0.000000        0.00000
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-ORIGX2      0.000000  1.000000  0.000000        0.00000
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-ORIGX3      0.000000  0.000000  1.000000        0.00000
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-SCALE1      1.000000  0.000000  0.000000        0.00000
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-SCALE2      0.000000  1.000000  0.000000        0.00000
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-SCALE3      0.000000  0.000000  1.000000        0.00000
144 
-ATOM      1  N   LYS A   1      -8.655   5.770   8.371  1.00  1.40           N
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-ATOM      2  CA  LYS A   1      -7.542   5.187   9.163  1.00  0.52           C
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-ATOM      3  C   LYS A   1      -6.210   5.619   8.561  1.00  0.39           C
147 
-ATOM      4  O   LYS A   1      -6.156   6.468   7.693  1.00  0.33           O
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-ATOM      5  CB  LYS A   1      -7.641   3.666   9.159  1.00  1.53           C
149 
-ATOM      6  CG  LYS A   1      -7.750   3.179  10.602  1.00  2.38           C
150 
-ATOM      7  CD  LYS A   1      -9.158   3.466  11.126  1.00  3.11           C
151 
-ATOM      8  CE  LYS A   1      -9.145   4.744  11.965  1.00  3.58           C
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-ATOM      9  NZ  LYS A   1      -9.497   4.416  13.375  1.00  4.21           N
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-ATOM     25  N   LYS A   2      -5.128   5.066   9.028  1.00  0.51           N
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-ATOM     26  CA  LYS A   2      -3.813   5.485   8.490  1.00  0.44           C
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-ATOM     27  C   LYS A   2      -2.931   4.277   8.172  1.00  0.41           C
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-ATOM     28  O   LYS A   2      -3.040   3.218   8.757  1.00  0.58           O
157 
-ATOM     29  CB  LYS A   2      -3.138   6.383   9.534  1.00  0.63           C
158 
-ATOM     30  CG  LYS A   2      -1.624   6.134   9.604  1.00  1.04           C
159 
-ATOM     31  CD  LYS A   2      -0.967   7.224  10.453  1.00  0.93           C
160 
-ATOM     32  CE  LYS A   2       0.116   7.929   9.634  1.00  0.63           C
161 
-ATOM     33  NZ  LYS A   2       1.057   8.630  10.551  1.00  1.43           N
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-ATOM     47  N   ALA A   3      -2.040   4.474   7.250  1.00  0.27           N
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-ATOM     48  CA  ALA A   3      -1.086   3.403   6.848  1.00  0.30           C
164 
-ATOM     49  C   ALA A   3       0.316   4.013   6.751  1.00  0.30           C
165 
-ATOM     50  O   ALA A   3       0.469   5.207   6.586  1.00  0.54           O
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-ATOM     51  CB  ALA A   3      -1.491   2.834   5.486  1.00  0.34           C
167 
-ATOM     57  N   VAL A   4       1.342   3.214   6.860  1.00  0.30           N
168 
-ATOM     58  CA  VAL A   4       2.725   3.769   6.780  1.00  0.27           C
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-ATOM     59  C   VAL A   4       3.643   2.773   6.074  1.00  0.26           C
170 
-ATOM     60  O   VAL A   4       3.842   1.667   6.535  1.00  0.33           O
171 
-ATOM     61  CB  VAL A   4       3.250   4.021   8.194  1.00  0.30           C
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-ATOM     62  CG1 VAL A   4       4.617   4.709   8.122  1.00  0.35           C
173 
-ATOM     63  CG2 VAL A   4       2.262   4.915   8.946  1.00  0.35           C
174 
-ATOM     73  N   ILE A   5       4.210   3.153   4.961  1.00  0.23           N
175 
-ATOM     74  CA  ILE A   5       5.117   2.213   4.245  1.00  0.23           C
176 
-ATOM     75  C   ILE A   5       6.570   2.567   4.552  1.00  0.25           C
177 
-ATOM     76  O   ILE A   5       7.176   3.388   3.893  1.00  0.27           O
178 
-ATOM     77  CB  ILE A   5       4.879   2.300   2.742  1.00  0.23           C
179 
-ATOM     78  CG1 ILE A   5       3.360   2.231   2.478  1.00  0.23           C
180 
-ATOM     79  CG2 ILE A   5       5.620   1.142   2.061  1.00  0.24           C
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-ATOM     80  CD1 ILE A   5       3.034   1.246   1.346  1.00  0.22           C
182 
-ATOM     92  N   ASN A   6       7.134   1.947   5.547  1.00  0.27           N
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-ATOM     93  CA  ASN A   6       8.545   2.232   5.905  1.00  0.31           C
184 
-ATOM     94  C   ASN A   6       9.466   1.399   5.009  1.00  0.31           C
185 
-ATOM     95  O   ASN A   6       9.611   0.207   5.189  1.00  0.35           O
186 
-ATOM     96  CB  ASN A   6       8.759   1.859   7.370  1.00  0.37           C
187 
-ATOM     97  CG  ASN A   6       8.067   2.890   8.264  1.00  0.65           C
188 
-ATOM     98  OD1 ASN A   6       7.534   3.869   7.782  1.00  1.48           O
189 
-ATOM     99  ND2 ASN A   6       8.054   2.711   9.557  1.00  1.13           N
190 
-ATOM    106  N   GLY A   7      10.078   2.017   4.035  1.00  0.33           N
191 
-ATOM    107  CA  GLY A   7      10.976   1.261   3.114  1.00  0.36           C
192 
-ATOM    108  C   GLY A   7      12.182   0.718   3.879  1.00  0.35           C
193 
-ATOM    109  O   GLY A   7      12.583  -0.414   3.694  1.00  0.46           O
194 
-ATOM    113  N   GLU A   8      12.767   1.509   4.735  1.00  0.38           N
195 
-ATOM    114  CA  GLU A   8      13.946   1.022   5.505  1.00  0.43           C
196 
-ATOM    115  C   GLU A   8      13.659  -0.390   6.019  1.00  0.39           C
197 
-ATOM    116  O   GLU A   8      14.559  -1.170   6.260  1.00  0.45           O
198 
-ATOM    117  CB  GLU A   8      14.207   1.950   6.696  1.00  0.53           C
199 
-ATOM    118  CG  GLU A   8      14.064   3.409   6.256  1.00  1.39           C
200 
-ATOM    119  CD  GLU A   8      14.660   4.324   7.328  1.00  1.74           C
201 
-ATOM    120  OE1 GLU A   8      14.225   4.232   8.464  1.00  2.30           O
202 
-ATOM    121  OE2 GLU A   8      15.540   5.100   6.994  1.00  2.19           O
203 
-ATOM    128  N   GLN A   9      12.408  -0.720   6.195  1.00  0.35           N
204 
-ATOM    129  CA  GLN A   9      12.051  -2.069   6.699  1.00  0.38           C
205 
-ATOM    130  C   GLN A   9      11.745  -3.001   5.523  1.00  0.35           C
206 
-ATOM    131  O   GLN A   9      12.213  -4.121   5.468  1.00  0.40           O
207 
-ATOM    132  CB  GLN A   9      10.811  -1.937   7.578  1.00  0.43           C
208 
-ATOM    133  CG  GLN A   9      11.027  -0.819   8.600  1.00  0.50           C
209 
-ATOM    134  CD  GLN A   9      11.790  -1.365   9.805  1.00  1.06           C
210 
-ATOM    135  OE1 GLN A   9      12.979  -1.155   9.931  1.00  1.97           O
211 
-ATOM    136  NE2 GLN A   9      11.151  -2.059  10.705  1.00  1.49           N
212 
-ATOM    145  N   ILE A  10      10.952  -2.550   4.591  1.00  0.32           N
213 
-ATOM    146  CA  ILE A  10      10.597  -3.408   3.424  1.00  0.34           C
214 
-ATOM    147  C   ILE A  10      11.825  -4.171   2.934  1.00  0.31           C
215 
-ATOM    148  O   ILE A  10      12.893  -3.617   2.765  1.00  0.35           O
216 
-ATOM    149  CB  ILE A  10      10.059  -2.546   2.281  1.00  0.37           C
217 
-ATOM    150  CG1 ILE A  10       8.683  -2.005   2.655  1.00  0.51           C
218 
-ATOM    151  CG2 ILE A  10       9.933  -3.402   1.018  1.00  0.35           C
219 
-ATOM    152  CD1 ILE A  10       7.689  -3.158   2.715  1.00  0.78           C
220 
-ATOM    164  N   ARG A  11      11.668  -5.440   2.692  1.00  0.33           N
221 
-ATOM    165  CA  ARG A  11      12.794  -6.261   2.200  1.00  0.37           C
222 
-ATOM    166  C   ARG A  11      12.423  -6.834   0.830  1.00  0.39           C
223 
-ATOM    167  O   ARG A  11      13.251  -7.368   0.120  1.00  0.48           O
224 
-ATOM    168  CB  ARG A  11      13.035  -7.400   3.184  1.00  0.50           C
225 
-ATOM    169  CG  ARG A  11      13.677  -6.844   4.458  1.00  0.57           C
226 
-ATOM    170  CD  ARG A  11      15.105  -7.376   4.589  1.00  1.27           C
227 
-ATOM    171  NE  ARG A  11      15.489  -7.404   6.030  1.00  1.87           N
228 
-ATOM    172  CZ  ARG A  11      16.544  -8.065   6.417  1.00  2.53           C
229 
-ATOM    173  NH1 ARG A  11      16.881  -9.170   5.815  1.00  3.26           N
230 
-ATOM    174  NH2 ARG A  11      17.261  -7.620   7.412  1.00  2.99           N
231 
-ATOM    188  N   SER A  12      11.174  -6.725   0.458  1.00  0.37           N
232 
-ATOM    189  CA  SER A  12      10.732  -7.258  -0.860  1.00  0.45           C
233 
-ATOM    190  C   SER A  12       9.270  -6.869  -1.096  1.00  0.42           C
234 
-ATOM    191  O   SER A  12       8.619  -6.289  -0.242  1.00  0.37           O
235 
-ATOM    192  CB  SER A  12      10.862  -8.781  -0.865  1.00  0.56           C
236 
-ATOM    193  OG  SER A  12      11.282  -9.221   0.419  1.00  1.44           O
237 
-ATOM    199  N   ILE A  13       8.741  -7.185  -2.245  1.00  0.47           N
238 
-ATOM    200  CA  ILE A  13       7.324  -6.831  -2.520  1.00  0.46           C
239 
-ATOM    201  C   ILE A  13       6.445  -7.446  -1.435  1.00  0.41           C
240 
-ATOM    202  O   ILE A  13       5.579  -6.799  -0.887  1.00  0.36           O
241 
-ATOM    203  CB  ILE A  13       6.908  -7.370  -3.892  1.00  0.56           C
242 
-ATOM    204  CG1 ILE A  13       5.570  -6.749  -4.313  1.00  0.63           C
243 
-ATOM    205  CG2 ILE A  13       6.753  -8.888  -3.812  1.00  0.64           C
244 
-ATOM    206  CD1 ILE A  13       5.564  -5.246  -4.010  1.00  0.57           C
245 
-ATOM    218  N   SER A  14       6.669  -8.690  -1.109  1.00  0.46           N
246 
-ATOM    219  CA  SER A  14       5.851  -9.332  -0.047  1.00  0.44           C
247 
-ATOM    220  C   SER A  14       5.859  -8.424   1.179  1.00  0.37           C
248 
-ATOM    221  O   SER A  14       4.837  -8.162   1.781  1.00  0.35           O
249 
-ATOM    222  CB  SER A  14       6.453 -10.689   0.312  1.00  0.50           C
250 
-ATOM    223  OG  SER A  14       5.481 -11.469   0.996  1.00  1.07           O
251 
-ATOM    229  N   ASP A  15       7.009  -7.928   1.541  1.00  0.34           N
252 
-ATOM    230  CA  ASP A  15       7.097  -7.021   2.709  1.00  0.30           C
253 
-ATOM    231  C   ASP A  15       6.187  -5.819   2.475  1.00  0.24           C
254 
-ATOM    232  O   ASP A  15       5.470  -5.386   3.353  1.00  0.23           O
255 
-ATOM    233  CB  ASP A  15       8.536  -6.538   2.871  1.00  0.30           C
256 
-ATOM    234  CG  ASP A  15       9.056  -6.939   4.254  1.00  0.33           C
257 
-ATOM    235  OD1 ASP A  15       8.483  -7.843   4.840  1.00  1.17           O
258 
-ATOM    236  OD2 ASP A  15      10.015  -6.335   4.705  1.00  1.08           O
259 
-ATOM    241  N   LEU A  16       6.211  -5.283   1.288  1.00  0.25           N
260 
-ATOM    242  CA  LEU A  16       5.347  -4.111   0.980  1.00  0.23           C
261 
-ATOM    243  C   LEU A  16       3.898  -4.464   1.298  1.00  0.22           C
262 
-ATOM    244  O   LEU A  16       3.233  -3.804   2.073  1.00  0.21           O
263 
-ATOM    245  CB  LEU A  16       5.470  -3.779  -0.505  1.00  0.28           C
264 
-ATOM    246  CG  LEU A  16       4.802  -2.436  -0.784  1.00  0.31           C
265 
-ATOM    247  CD1 LEU A  16       5.341  -1.386   0.188  1.00  0.31           C
266 
-ATOM    248  CD2 LEU A  16       5.110  -2.013  -2.219  1.00  0.39           C
267 
-ATOM    260  N   HIS A  17       3.413  -5.509   0.701  1.00  0.22           N
268 
-ATOM    261  CA  HIS A  17       2.018  -5.941   0.944  1.00  0.22           C
269 
-ATOM    262  C   HIS A  17       1.874  -6.363   2.405  1.00  0.19           C
270 
-ATOM    263  O   HIS A  17       0.786  -6.432   2.941  1.00  0.19           O
271 
-ATOM    264  CB  HIS A  17       1.715  -7.120   0.024  1.00  0.26           C
272 
-ATOM    265  CG  HIS A  17       1.994  -6.716  -1.397  1.00  0.32           C
273 
-ATOM    266  ND1 HIS A  17       1.294  -5.699  -2.026  1.00  0.38           N
274 
-ATOM    267  CD2 HIS A  17       2.895  -7.181  -2.324  1.00  0.40           C
275 
-ATOM    268  CE1 HIS A  17       1.779  -5.586  -3.276  1.00  0.44           C
276 
-ATOM    269  NE2 HIS A  17       2.756  -6.465  -3.510  1.00  0.45           N
277 
-ATOM    277  N   GLN A  18       2.969  -6.639   3.055  1.00  0.19           N
278 
-ATOM    278  CA  GLN A  18       2.905  -7.047   4.475  1.00  0.19           C
279 
-ATOM    279  C   GLN A  18       2.501  -5.844   5.322  1.00  0.17           C
280 
-ATOM    280  O   GLN A  18       1.541  -5.888   6.067  1.00  0.18           O
281 
-ATOM    281  CB  GLN A  18       4.275  -7.553   4.927  1.00  0.21           C
282 
-ATOM    282  CG  GLN A  18       4.092  -8.654   5.975  1.00  0.55           C
283 
-ATOM    283  CD  GLN A  18       5.461  -9.139   6.452  1.00  1.31           C
284 
-ATOM    284  OE1 GLN A  18       6.390  -8.363   6.557  1.00  2.11           O
285 
-ATOM    285  NE2 GLN A  18       5.626 -10.399   6.749  1.00  2.02           N
286 
-ATOM    294  N   THR A  19       3.229  -4.764   5.217  1.00  0.17           N
287 
-ATOM    295  CA  THR A  19       2.882  -3.573   6.019  1.00  0.17           C
288 
-ATOM    296  C   THR A  19       1.519  -3.063   5.542  1.00  0.17           C
289 
-ATOM    297  O   THR A  19       0.682  -2.691   6.328  1.00  0.18           O
290 
-ATOM    298  CB  THR A  19       3.976  -2.492   5.860  1.00  0.20           C
291 
-ATOM    299  OG1 THR A  19       4.593  -2.276   7.121  1.00  0.22           O
292 
-ATOM    300  CG2 THR A  19       3.371  -1.165   5.396  1.00  0.21           C
293 
-ATOM    308  N   LEU A  20       1.286  -3.056   4.258  1.00  0.16           N
294 
-ATOM    309  CA  LEU A  20      -0.022  -2.590   3.751  1.00  0.18           C
295 
-ATOM    310  C   LEU A  20      -1.104  -3.472   4.365  1.00  0.17           C
296 
-ATOM    311  O   LEU A  20      -2.183  -3.040   4.683  1.00  0.24           O
297 
-ATOM    312  CB  LEU A  20      -0.050  -2.738   2.232  1.00  0.19           C
298 
-ATOM    313  CG  LEU A  20       0.878  -1.705   1.588  1.00  0.20           C
299 
-ATOM    314  CD1 LEU A  20       0.822  -1.851   0.068  1.00  0.23           C
300 
-ATOM    315  CD2 LEU A  20       0.434  -0.292   1.981  1.00  0.21           C
301 
-ATOM    327  N   LYS A  21      -0.794  -4.716   4.530  1.00  0.16           N
302 
-ATOM    328  CA  LYS A  21      -1.760  -5.680   5.122  1.00  0.16           C
303 
-ATOM    329  C   LYS A  21      -2.011  -5.324   6.586  1.00  0.17           C
304 
-ATOM    330  O   LYS A  21      -3.123  -5.365   7.059  1.00  0.19           O
305 
-ATOM    331  CB  LYS A  21      -1.173  -7.088   5.035  1.00  0.17           C
306 
-ATOM    332  CG  LYS A  21      -2.174  -8.100   5.593  1.00  0.29           C
307 
-ATOM    333  CD  LYS A  21      -1.414  -9.229   6.292  1.00  0.68           C
308 
-ATOM    334  CE  LYS A  21      -2.407 -10.255   6.837  1.00  1.26           C
309 
-ATOM    335  NZ  LYS A  21      -1.733 -11.101   7.860  1.00  1.94           N
310 
-ATOM    349  N   LYS A  22      -0.991  -4.980   7.317  1.00  0.18           N
311 
-ATOM    350  CA  LYS A  22      -1.204  -4.631   8.741  1.00  0.20           C
312 
-ATOM    351  C   LYS A  22      -2.006  -3.335   8.817  1.00  0.23           C
313 
-ATOM    352  O   LYS A  22      -3.074  -3.277   9.390  1.00  0.29           O
314 
-ATOM    353  CB  LYS A  22       0.142  -4.442   9.432  1.00  0.22           C
315 
-ATOM    354  CG  LYS A  22       0.148  -5.278  10.717  1.00  0.83           C
316 
-ATOM    355  CD  LYS A  22       1.553  -5.339  11.302  1.00  1.43           C
317 
-ATOM    356  CE  LYS A  22       1.494  -6.033  12.671  1.00  2.18           C
318 
-ATOM    357  NZ  LYS A  22       2.827  -6.602  13.001  1.00  2.84           N
319 
-ATOM    371  N   GLU A  23      -1.495  -2.303   8.219  1.00  0.22           N
320 
-ATOM    372  CA  GLU A  23      -2.195  -1.004   8.212  1.00  0.26           C
321 
-ATOM    373  C   GLU A  23      -3.621  -1.224   7.716  1.00  0.24           C
322 
-ATOM    374  O   GLU A  23      -4.587  -1.066   8.436  1.00  0.27           O
323 
-ATOM    375  CB  GLU A  23      -1.450  -0.080   7.250  1.00  0.29           C
324 
-ATOM    376  CG  GLU A  23      -0.006   0.098   7.725  1.00  0.35           C
325 
-ATOM    377  CD  GLU A  23       0.032   1.057   8.914  1.00  1.53           C
326 
-ATOM    378  OE1 GLU A  23      -1.026   1.364   9.438  1.00  2.29           O
327 
-ATOM    379  OE2 GLU A  23       1.120   1.471   9.280  1.00  2.27           O
328 
-ATOM    386  N   LEU A  24      -3.737  -1.599   6.480  1.00  0.23           N
329 
-ATOM    387  CA  LEU A  24      -5.066  -1.859   5.871  1.00  0.23           C
330 
-ATOM    388  C   LEU A  24      -5.767  -2.996   6.618  1.00  0.22           C
331 
-ATOM    389  O   LEU A  24      -6.953  -3.209   6.467  1.00  0.24           O
332 
-ATOM    390  CB  LEU A  24      -4.848  -2.277   4.418  1.00  0.21           C
333 
-ATOM    391  CG  LEU A  24      -4.150  -1.150   3.658  1.00  0.25           C
334 
-ATOM    392  CD1 LEU A  24      -3.120  -1.750   2.701  1.00  0.20           C
335 
-ATOM    393  CD2 LEU A  24      -5.184  -0.352   2.862  1.00  0.40           C
336 
-ATOM    405  N   ALA A  25      -5.043  -3.736   7.416  1.00  0.21           N
337 
-ATOM    406  CA  ALA A  25      -5.667  -4.860   8.158  1.00  0.22           C
338 
-ATOM    407  C   ALA A  25      -6.369  -5.796   7.170  1.00  0.21           C
339 
-ATOM    408  O   ALA A  25      -7.501  -6.191   7.366  1.00  0.23           O
340 
-ATOM    409  CB  ALA A  25      -6.670  -4.292   9.152  1.00  0.26           C
341 
-ATOM    415  N   LEU A  26      -5.693  -6.152   6.112  1.00  0.21           N
342 
-ATOM    416  CA  LEU A  26      -6.293  -7.062   5.095  1.00  0.24           C
343 
-ATOM    417  C   LEU A  26      -6.438  -8.468   5.690  1.00  0.28           C
344 
-ATOM    418  O   LEU A  26      -5.795  -8.792   6.669  1.00  0.30           O
345 
-ATOM    419  CB  LEU A  26      -5.371  -7.117   3.872  1.00  0.23           C
346 
-ATOM    420  CG  LEU A  26      -4.954  -5.697   3.483  1.00  0.21           C
347 
-ATOM    421  CD1 LEU A  26      -3.954  -5.751   2.337  1.00  0.26           C
348 
-ATOM    422  CD2 LEU A  26      -6.187  -4.909   3.043  1.00  0.23           C
349 
-ATOM    434  N   PRO A  27      -7.280  -9.262   5.077  1.00  0.34           N
350 
-ATOM    435  CA  PRO A  27      -7.526 -10.643   5.529  1.00  0.41           C
351 
-ATOM    436  C   PRO A  27      -6.221 -11.438   5.555  1.00  0.39           C
352 
-ATOM    437  O   PRO A  27      -5.165 -10.932   5.233  1.00  0.31           O
353 
-ATOM    438  CB  PRO A  27      -8.489 -11.230   4.490  1.00  0.48           C
354 
-ATOM    439  CG  PRO A  27      -8.880 -10.091   3.514  1.00  0.48           C
355 
-ATOM    440  CD  PRO A  27      -8.054  -8.852   3.890  1.00  0.38           C
356 
-ATOM    448  N   GLU A  28      -6.289 -12.685   5.931  1.00  0.50           N
357 
-ATOM    449  CA  GLU A  28      -5.058 -13.519   5.972  1.00  0.53           C
358 
-ATOM    450  C   GLU A  28      -4.729 -13.997   4.558  1.00  0.49           C
359 
-ATOM    451  O   GLU A  28      -3.622 -14.407   4.273  1.00  0.51           O
360 
-ATOM    452  CB  GLU A  28      -5.295 -14.732   6.871  1.00  0.67           C
361 
-ATOM    453  CG  GLU A  28      -5.557 -14.268   8.305  1.00  1.14           C
362 
-ATOM    454  CD  GLU A  28      -5.237 -15.405   9.276  1.00  1.65           C
363 
-ATOM    455  OE1 GLU A  28      -4.380 -16.210   8.953  1.00  2.31           O
364 
-ATOM    456  OE2 GLU A  28      -5.856 -15.452  10.327  1.00  2.20           O
365 
-ATOM    463  N   TYR A  29      -5.686 -13.952   3.671  1.00  0.47           N
366 
-ATOM    464  CA  TYR A  29      -5.426 -14.409   2.279  1.00  0.44           C
367 
-ATOM    465  C   TYR A  29      -5.020 -13.218   1.409  1.00  0.37           C
368 
-ATOM    466  O   TYR A  29      -4.999 -13.312   0.198  1.00  0.38           O
369 
-ATOM    467  CB  TYR A  29      -6.686 -15.061   1.704  1.00  0.51           C
370 
-ATOM    468  CG  TYR A  29      -7.900 -14.250   2.087  1.00  0.66           C
371 
-ATOM    469  CD1 TYR A  29      -8.300 -13.171   1.290  1.00  1.29           C
372 
-ATOM    470  CD2 TYR A  29      -8.627 -14.579   3.237  1.00  1.53           C
373 
-ATOM    471  CE1 TYR A  29      -9.428 -12.421   1.643  1.00  1.43           C
374 
-ATOM    472  CE2 TYR A  29      -9.756 -13.829   3.590  1.00  1.75           C
375 
-ATOM    473  CZ  TYR A  29     -10.156 -12.750   2.793  1.00  1.24           C
376 
-ATOM    474  OH  TYR A  29     -11.268 -12.011   3.140  1.00  1.57           O
377 
-ATOM    484  N   TYR A  30      -4.694 -12.103   2.017  1.00  0.32           N
378 
-ATOM    485  CA  TYR A  30      -4.275 -10.903   1.222  1.00  0.28           C
379 
-ATOM    486  C   TYR A  30      -3.419 -11.366   0.035  1.00  0.32           C
380 
-ATOM    487  O   TYR A  30      -2.281 -11.759   0.193  1.00  0.38           O
381 
-ATOM    488  CB  TYR A  30      -3.462  -9.958   2.121  1.00  0.29           C
382 
-ATOM    489  CG  TYR A  30      -3.006  -8.741   1.339  1.00  0.20           C
383 
-ATOM    490  CD1 TYR A  30      -3.750  -8.286   0.243  1.00  0.47           C
384 
-ATOM    491  CD2 TYR A  30      -1.832  -8.068   1.715  1.00  0.48           C
385 
-ATOM    492  CE1 TYR A  30      -3.319  -7.163  -0.477  1.00  0.49           C
386 
-ATOM    493  CE2 TYR A  30      -1.400  -6.943   0.995  1.00  0.49           C
387 
-ATOM    494  CZ  TYR A  30      -2.145  -6.493  -0.102  1.00  0.25           C
388 
-ATOM    495  OH  TYR A  30      -1.724  -5.388  -0.814  1.00  0.36           O
389 
-ATOM    505  N   GLY A  31      -3.974 -11.339  -1.151  1.00  0.39           N
390 
-ATOM    506  CA  GLY A  31      -3.215 -11.796  -2.357  1.00  0.51           C
391 
-ATOM    507  C   GLY A  31      -2.004 -10.892  -2.611  1.00  0.58           C
392 
-ATOM    508  O   GLY A  31      -1.214 -11.146  -3.495  1.00  1.36           O
393 
-ATOM    512  N   GLU A  32      -1.870  -9.835  -1.853  1.00  0.56           N
394 
-ATOM    513  CA  GLU A  32      -0.726  -8.877  -2.011  1.00  0.54           C
395 
-ATOM    514  C   GLU A  32      -0.533  -8.420  -3.470  1.00  0.54           C
396 
-ATOM    515  O   GLU A  32       0.377  -7.671  -3.760  1.00  0.59           O
397 
-ATOM    516  CB  GLU A  32       0.582  -9.491  -1.474  1.00  0.66           C
398 
-ATOM    517  CG  GLU A  32       0.741 -10.947  -1.915  1.00  1.51           C
399 
-ATOM    518  CD  GLU A  32       2.052 -11.506  -1.358  1.00  1.87           C
400 
-ATOM    519  OE1 GLU A  32       3.044 -10.799  -1.410  1.00  2.36           O
401 
-ATOM    520  OE2 GLU A  32       2.040 -12.632  -0.890  1.00  2.37           O
402 
-ATOM    527  N   ASN A  33      -1.373  -8.817  -4.389  1.00  0.51           N
403 
-ATOM    528  CA  ASN A  33      -1.203  -8.335  -5.792  1.00  0.53           C
404 
-ATOM    529  C   ASN A  33      -1.891  -6.977  -5.927  1.00  0.50           C
405 
-ATOM    530  O   ASN A  33      -2.423  -6.444  -4.974  1.00  0.56           O
406 
-ATOM    531  CB  ASN A  33      -1.811  -9.321  -6.806  1.00  0.54           C
407 
-ATOM    532  CG  ASN A  33      -2.420 -10.533  -6.096  1.00  0.62           C
408 
-ATOM    533  OD1 ASN A  33      -1.721 -11.465  -5.752  1.00  1.57           O
409 
-ATOM    534  ND2 ASN A  33      -3.703 -10.559  -5.864  1.00  0.82           N
410 
-ATOM    541  N   LEU A  34      -1.918  -6.429  -7.107  1.00  0.48           N
411 
-ATOM    542  CA  LEU A  34      -2.609  -5.125  -7.305  1.00  0.47           C
412 
-ATOM    543  C   LEU A  34      -4.108  -5.392  -7.331  1.00  0.40           C
413 
-ATOM    544  O   LEU A  34      -4.911  -4.621  -6.852  1.00  0.37           O
414 
-ATOM    545  CB  LEU A  34      -2.204  -4.539  -8.650  1.00  0.55           C
415 
-ATOM    546  CG  LEU A  34      -0.749  -4.072  -8.606  1.00  0.64           C
416 
-ATOM    547  CD1 LEU A  34      -0.358  -3.503  -9.971  1.00  0.82           C
417 
-ATOM    548  CD2 LEU A  34      -0.590  -2.986  -7.539  1.00  0.61           C
418 
-ATOM    560  N   ASP A  35      -4.469  -6.494  -7.911  1.00  0.39           N
419 
-ATOM    561  CA  ASP A  35      -5.897  -6.886  -8.018  1.00  0.36           C
420 
-ATOM    562  C   ASP A  35      -6.467  -7.173  -6.632  1.00  0.30           C
421 
-ATOM    563  O   ASP A  35      -7.614  -6.894  -6.351  1.00  0.28           O
422 
-ATOM    564  CB  ASP A  35      -5.975  -8.167  -8.833  1.00  0.38           C
423 
-ATOM    565  CG  ASP A  35      -5.683  -7.865 -10.303  1.00  0.43           C
424 
-ATOM    566  OD1 ASP A  35      -6.344  -7.000 -10.853  1.00  1.24           O
425 
-ATOM    567  OD2 ASP A  35      -4.803  -8.506 -10.856  1.00  1.06           O
426 
-ATOM    572  N   ALA A  36      -5.676  -7.742  -5.769  1.00  0.29           N
427 
-ATOM    573  CA  ALA A  36      -6.180  -8.058  -4.401  1.00  0.25           C
428 
-ATOM    574  C   ALA A  36      -6.124  -6.799  -3.563  1.00  0.22           C
429 
-ATOM    575  O   ALA A  36      -7.111  -6.353  -3.016  1.00  0.22           O
430 
-ATOM    576  CB  ALA A  36      -5.310  -9.125  -3.749  1.00  0.29           C
431 
-ATOM    582  N   LEU A  37      -4.967  -6.217  -3.477  1.00  0.21           N
432 
-ATOM    583  CA  LEU A  37      -4.820  -4.966  -2.697  1.00  0.19           C
433 
-ATOM    584  C   LEU A  37      -5.987  -4.058  -3.064  1.00  0.16           C
434 
-ATOM    585  O   LEU A  37      -6.706  -3.539  -2.224  1.00  0.16           O
435 
-ATOM    586  CB  LEU A  37      -3.502  -4.299  -3.095  1.00  0.21           C
436 
-ATOM    587  CG  LEU A  37      -3.539  -2.815  -2.724  1.00  0.20           C
437 
-ATOM    588  CD1 LEU A  37      -3.557  -2.667  -1.201  1.00  0.22           C
438 
-ATOM    589  CD2 LEU A  37      -2.302  -2.115  -3.290  1.00  0.24           C
439 
-ATOM    601  N   TRP A  38      -6.173  -3.884  -4.333  1.00  0.17           N
440 
-ATOM    602  CA  TRP A  38      -7.277  -3.046  -4.821  1.00  0.16           C
441 
-ATOM    603  C   TRP A  38      -8.577  -3.613  -4.303  1.00  0.16           C
442 
-ATOM    604  O   TRP A  38      -9.345  -2.951  -3.643  1.00  0.16           O
443 
-ATOM    605  CB  TRP A  38      -7.315  -3.093  -6.341  1.00  0.18           C
444 
-ATOM    606  CG  TRP A  38      -8.456  -2.267  -6.801  1.00  0.18           C
445 
-ATOM    607  CD1 TRP A  38      -9.708  -2.718  -6.963  1.00  0.21           C
446 
-ATOM    608  CD2 TRP A  38      -8.476  -0.860  -7.128  1.00  0.18           C
447 
-ATOM    609  NE1 TRP A  38     -10.508  -1.672  -7.389  1.00  0.23           N
448 
-ATOM    610  CE2 TRP A  38      -9.785  -0.502  -7.508  1.00  0.20           C
449 
-ATOM    611  CE3 TRP A  38      -7.487   0.125  -7.138  1.00  0.17           C
450 
-ATOM    612  CZ2 TRP A  38     -10.099   0.802  -7.885  1.00  0.22           C
451 
-ATOM    613  CZ3 TRP A  38      -7.785   1.430  -7.507  1.00  0.19           C
452 
-ATOM    614  CH2 TRP A  38      -9.093   1.778  -7.885  1.00  0.20           C
453 
-ATOM    625  N   ASP A  39      -8.815  -4.850  -4.599  1.00  0.17           N
454 
-ATOM    626  CA  ASP A  39     -10.061  -5.500  -4.130  1.00  0.18           C
455 
-ATOM    627  C   ASP A  39     -10.283  -5.117  -2.672  1.00  0.18           C
456 
-ATOM    628  O   ASP A  39     -11.394  -5.091  -2.182  1.00  0.21           O
457 
-ATOM    629  CB  ASP A  39      -9.927  -7.017  -4.254  1.00  0.21           C
458 
-ATOM    630  CG  ASP A  39     -10.613  -7.488  -5.537  1.00  0.29           C
459 
-ATOM    631  OD1 ASP A  39     -10.045  -7.286  -6.598  1.00  1.13           O
460 
-ATOM    632  OD2 ASP A  39     -11.695  -8.044  -5.438  1.00  1.06           O
461 
-ATOM    637  N   CYS A  40      -9.222  -4.807  -1.977  1.00  0.17           N
462 
-ATOM    638  CA  CYS A  40      -9.354  -4.412  -0.556  1.00  0.19           C
463 
-ATOM    639  C   CYS A  40      -9.797  -2.948  -0.466  1.00  0.19           C
464 
-ATOM    640  O   CYS A  40     -10.745  -2.623   0.218  1.00  0.23           O
465 
-ATOM    641  CB  CYS A  40      -8.001  -4.580   0.132  1.00  0.21           C
466 
-ATOM    642  SG  CYS A  40      -7.334  -6.221  -0.239  1.00  0.58           S
467 
-ATOM    648  N   LEU A  41      -9.117  -2.057  -1.142  1.00  0.17           N
468 
-ATOM    649  CA  LEU A  41      -9.497  -0.625  -1.076  1.00  0.18           C
469 
-ATOM    650  C   LEU A  41     -10.943  -0.424  -1.548  1.00  0.21           C
470 
-ATOM    651  O   LEU A  41     -11.729   0.247  -0.908  1.00  0.45           O
471 
-ATOM    652  CB  LEU A  41      -8.562   0.173  -1.981  1.00  0.17           C
472 
-ATOM    653  CG  LEU A  41      -7.117  -0.285  -1.776  1.00  0.19           C
473 
-ATOM    654  CD1 LEU A  41      -6.189   0.625  -2.567  1.00  0.18           C
474 
-ATOM    655  CD2 LEU A  41      -6.760  -0.219  -0.289  1.00  0.31           C
475 
-ATOM    667  N   THR A  42     -11.284  -0.971  -2.679  1.00  0.26           N
476 
-ATOM    668  CA  THR A  42     -12.650  -0.794  -3.226  1.00  0.28           C
477 
-ATOM    669  C   THR A  42     -13.665  -1.664  -2.479  1.00  0.32           C
478 
-ATOM    670  O   THR A  42     -14.826  -1.704  -2.836  1.00  0.55           O
479 
-ATOM    671  CB  THR A  42     -12.649  -1.174  -4.708  1.00  0.26           C
480 
-ATOM    672  OG1 THR A  42     -11.870  -2.347  -4.894  1.00  0.29           O
481 
-ATOM    673  CG2 THR A  42     -12.054  -0.026  -5.525  1.00  0.40           C
482 
-ATOM    681  N   GLY A  43     -13.262  -2.363  -1.452  1.00  0.27           N
483 
-ATOM    682  CA  GLY A  43     -14.258  -3.210  -0.729  1.00  0.31           C
484 
-ATOM    683  C   GLY A  43     -13.627  -3.900   0.484  1.00  0.27           C
485 
-ATOM    684  O   GLY A  43     -13.610  -5.112   0.574  1.00  0.32           O
486 
-ATOM    688  N   TRP A  44     -13.125  -3.148   1.425  1.00  0.25           N
487 
-ATOM    689  CA  TRP A  44     -12.519  -3.775   2.630  1.00  0.23           C
488 
-ATOM    690  C   TRP A  44     -11.944  -2.689   3.540  1.00  0.23           C
489 
-ATOM    691  O   TRP A  44     -12.415  -2.466   4.637  1.00  0.27           O
490 
-ATOM    692  CB  TRP A  44     -11.402  -4.721   2.201  1.00  0.24           C
491 
-ATOM    693  CG  TRP A  44     -10.808  -5.362   3.411  1.00  0.26           C
492 
-ATOM    694  CD1 TRP A  44      -9.735  -4.894   4.085  1.00  0.27           C
493 
-ATOM    695  CD2 TRP A  44     -11.233  -6.571   4.106  1.00  0.30           C
494 
-ATOM    696  NE1 TRP A  44      -9.470  -5.739   5.146  1.00  0.31           N
495 
-ATOM    697  CE2 TRP A  44     -10.366  -6.788   5.202  1.00  0.34           C
496 
-ATOM    698  CE3 TRP A  44     -12.274  -7.493   3.891  1.00  0.35           C
497 
-ATOM    699  CZ2 TRP A  44     -10.527  -7.879   6.058  1.00  0.41           C
498 
-ATOM    700  CZ3 TRP A  44     -12.439  -8.592   4.750  1.00  0.43           C
499 
-ATOM    701  CH2 TRP A  44     -11.567  -8.785   5.831  1.00  0.45           C
500 
-ATOM    712  N   VAL A  45     -10.925  -2.016   3.089  1.00  0.25           N
501 
-ATOM    713  CA  VAL A  45     -10.304  -0.949   3.912  1.00  0.26           C
502 
-ATOM    714  C   VAL A  45     -11.350   0.112   4.253  1.00  0.25           C
503 
-ATOM    715  O   VAL A  45     -12.264   0.362   3.493  1.00  0.37           O
504 
-ATOM    716  CB  VAL A  45      -9.165  -0.300   3.125  1.00  0.30           C
505 
-ATOM    717  CG1 VAL A  45      -8.436   0.706   4.017  1.00  0.42           C
506 
-ATOM    718  CG2 VAL A  45      -8.181  -1.377   2.661  1.00  0.28           C
507 
-ATOM    728  N   GLU A  46     -11.215   0.751   5.382  1.00  0.21           N
508 
-ATOM    729  CA  GLU A  46     -12.197   1.808   5.755  1.00  0.23           C
509 
-ATOM    730  C   GLU A  46     -11.566   3.177   5.505  1.00  0.22           C
510 
-ATOM    731  O   GLU A  46     -10.440   3.435   5.880  1.00  0.22           O
511 
-ATOM    732  CB  GLU A  46     -12.600   1.688   7.231  1.00  0.30           C
512 
-ATOM    733  CG  GLU A  46     -11.576   0.848   7.993  1.00  1.31           C
513 
-ATOM    734  CD  GLU A  46     -12.107   0.545   9.395  1.00  1.80           C
514 
-ATOM    735  OE1 GLU A  46     -13.089  -0.173   9.493  1.00  2.43           O
515 
-ATOM    736  OE2 GLU A  46     -11.524   1.036  10.347  1.00  2.28           O
516 
-ATOM    743  N   TYR A  47     -12.285   4.047   4.861  1.00  0.22           N
517 
-ATOM    744  CA  TYR A  47     -11.744   5.402   4.559  1.00  0.22           C
518 
-ATOM    745  C   TYR A  47     -12.564   6.446   5.329  1.00  0.26           C
519 
-ATOM    746  O   TYR A  47     -13.586   6.110   5.892  1.00  0.29           O
520 
-ATOM    747  CB  TYR A  47     -11.851   5.623   3.045  1.00  0.24           C
521 
-ATOM    748  CG  TYR A  47     -10.868   4.720   2.323  1.00  0.24           C
522 
-ATOM    749  CD1 TYR A  47      -9.830   4.081   3.021  1.00  1.25           C
523 
-ATOM    750  CD2 TYR A  47     -10.994   4.520   0.945  1.00  1.21           C
524 
-ATOM    751  CE1 TYR A  47      -8.935   3.251   2.342  1.00  1.27           C
525 
-ATOM    752  CE2 TYR A  47     -10.094   3.692   0.272  1.00  1.20           C
526 
-ATOM    753  CZ  TYR A  47      -9.067   3.058   0.970  1.00  0.29           C
527 
-ATOM    754  OH  TYR A  47      -8.181   2.239   0.301  1.00  0.34           O
528 
-ATOM    764  N   PRO A  48     -12.102   7.682   5.359  1.00  0.27           N
529 
-ATOM    765  CA  PRO A  48     -10.858   8.134   4.685  1.00  0.25           C
530 
-ATOM    766  C   PRO A  48      -9.620   7.409   5.219  1.00  0.22           C
531 
-ATOM    767  O   PRO A  48      -9.455   7.234   6.406  1.00  0.30           O
532 
-ATOM    768  CB  PRO A  48     -10.761   9.631   5.010  1.00  0.28           C
533 
-ATOM    769  CG  PRO A  48     -11.970  10.004   5.902  1.00  0.33           C
534 
-ATOM    770  CD  PRO A  48     -12.815   8.738   6.097  1.00  0.32           C
535 
-ATOM    778  N   LEU A  49      -8.744   7.000   4.338  1.00  0.20           N
536 
-ATOM    779  CA  LEU A  49      -7.502   6.298   4.775  1.00  0.19           C
537 
-ATOM    780  C   LEU A  49      -6.301   7.182   4.462  1.00  0.19           C
538 
-ATOM    781  O   LEU A  49      -6.335   7.998   3.567  1.00  0.20           O
539 
-ATOM    782  CB  LEU A  49      -7.362   4.977   3.994  1.00  0.18           C
540 
-ATOM    783  CG  LEU A  49      -5.885   4.560   3.861  1.00  0.17           C
541 
-ATOM    784  CD1 LEU A  49      -5.350   4.066   5.209  1.00  0.20           C
542 
-ATOM    785  CD2 LEU A  49      -5.759   3.447   2.816  1.00  0.16           C
543 
-ATOM    797  N   VAL A  50      -5.222   6.985   5.157  1.00  0.21           N
544 
-ATOM    798  CA  VAL A  50      -4.003   7.770   4.857  1.00  0.22           C
545 
-ATOM    799  C   VAL A  50      -2.919   6.786   4.408  1.00  0.20           C
546 
-ATOM    800  O   VAL A  50      -2.748   5.736   4.987  1.00  0.21           O
547 
-ATOM    801  CB  VAL A  50      -3.555   8.555   6.114  1.00  0.26           C
548 
-ATOM    802  CG1 VAL A  50      -2.135   8.158   6.542  1.00  0.26           C
549 
-ATOM    803  CG2 VAL A  50      -3.567  10.051   5.802  1.00  0.29           C
550 
-ATOM    813  N   LEU A  51      -2.167   7.122   3.409  1.00  0.19           N
551 
-ATOM    814  CA  LEU A  51      -1.081   6.210   2.976  1.00  0.18           C
552 
-ATOM    815  C   LEU A  51       0.228   6.969   3.109  1.00  0.18           C
553 
-ATOM    816  O   LEU A  51       0.745   7.517   2.155  1.00  0.20           O
554 
-ATOM    817  CB  LEU A  51      -1.267   5.748   1.523  1.00  0.17           C
555 
-ATOM    818  CG  LEU A  51      -0.106   4.823   1.149  1.00  0.19           C
556 
-ATOM    819  CD1 LEU A  51      -0.195   3.543   1.973  1.00  0.21           C
557 
-ATOM    820  CD2 LEU A  51      -0.185   4.451  -0.328  1.00  0.18           C
558 
-ATOM    832  N   GLU A  52       0.760   7.014   4.296  1.00  0.19           N
559 
-ATOM    833  CA  GLU A  52       2.031   7.743   4.505  1.00  0.21           C
560 
-ATOM    834  C   GLU A  52       3.158   6.861   3.988  1.00  0.19           C
561 
-ATOM    835  O   GLU A  52       3.789   6.122   4.721  1.00  0.19           O
562 
-ATOM    836  CB  GLU A  52       2.213   8.030   5.996  1.00  0.24           C
563 
-ATOM    837  CG  GLU A  52       3.642   8.508   6.256  1.00  0.30           C
564 
-ATOM    838  CD  GLU A  52       3.650   9.471   7.444  1.00  0.64           C
565 
-ATOM    839  OE1 GLU A  52       2.717   9.420   8.229  1.00  1.28           O
566 
-ATOM    840  OE2 GLU A  52       4.588  10.244   7.550  1.00  1.44           O
567 
-ATOM    847  N   TRP A  53       3.385   6.915   2.708  1.00  0.20           N
568 
-ATOM    848  CA  TRP A  53       4.436   6.072   2.099  1.00  0.20           C
569 
-ATOM    849  C   TRP A  53       5.813   6.694   2.321  1.00  0.24           C
570 
-ATOM    850  O   TRP A  53       6.142   7.720   1.760  1.00  0.38           O
571 
-ATOM    851  CB  TRP A  53       4.175   5.945   0.603  1.00  0.24           C
572 
-ATOM    852  CG  TRP A  53       4.807   4.689   0.123  1.00  0.23           C
573 
-ATOM    853  CD1 TRP A  53       6.084   4.326   0.376  1.00  0.25           C
574 
-ATOM    854  CD2 TRP A  53       4.223   3.620  -0.671  1.00  0.21           C
575 
-ATOM    855  NE1 TRP A  53       6.325   3.103  -0.214  1.00  0.26           N
576 
-ATOM    856  CE2 TRP A  53       5.210   2.627  -0.872  1.00  0.24           C
577 
-ATOM    857  CE3 TRP A  53       2.948   3.416  -1.234  1.00  0.21           C
578 
-ATOM    858  CZ2 TRP A  53       4.946   1.474  -1.601  1.00  0.25           C
579 
-ATOM    859  CZ3 TRP A  53       2.684   2.251  -1.974  1.00  0.23           C
580 
-ATOM    860  CH2 TRP A  53       3.682   1.284  -2.156  1.00  0.25           C
581 
-ATOM    871  N   ARG A  54       6.627   6.069   3.124  1.00  0.26           N
582 
-ATOM    872  CA  ARG A  54       7.992   6.607   3.371  1.00  0.35           C
583 
-ATOM    873  C   ARG A  54       8.988   5.823   2.515  1.00  0.49           C
584 
-ATOM    874  O   ARG A  54       8.781   4.663   2.219  1.00  1.33           O
585 
-ATOM    875  CB  ARG A  54       8.346   6.446   4.849  1.00  0.44           C
586 
-ATOM    876  CG  ARG A  54       8.545   7.825   5.481  1.00  0.88           C
587 
-ATOM    877  CD  ARG A  54       8.772   7.667   6.985  1.00  1.09           C
588 
-ATOM    878  NE  ARG A  54      10.009   8.396   7.382  1.00  1.40           N
589 
-ATOM    879  CZ  ARG A  54      10.254   8.632   8.637  1.00  1.87           C
590 
-ATOM    880  NH1 ARG A  54      10.719   7.683   9.399  1.00  2.47           N
591 
-ATOM    881  NH2 ARG A  54      10.035   9.816   9.133  1.00  2.46           N
592 
-ATOM    895  N   GLN A  55      10.062   6.439   2.107  1.00  0.53           N
593 
-ATOM    896  CA  GLN A  55      11.050   5.709   1.264  1.00  0.46           C
594 
-ATOM    897  C   GLN A  55      10.308   5.032   0.111  1.00  0.53           C
595 
-ATOM    898  O   GLN A  55      10.193   3.826   0.056  1.00  1.30           O
596 
-ATOM    899  CB  GLN A  55      11.759   4.650   2.111  1.00  0.55           C
597 
-ATOM    900  CG  GLN A  55      13.251   4.974   2.186  1.00  1.05           C
598 
-ATOM    901  CD  GLN A  55      13.542   5.750   3.472  1.00  1.22           C
599 
-ATOM    902  OE1 GLN A  55      12.710   5.822   4.354  1.00  1.82           O
600 
-ATOM    903  NE2 GLN A  55      14.698   6.338   3.616  1.00  1.89           N
601 
-ATOM    912  N   PHE A  56       9.791   5.807  -0.801  1.00  0.64           N
602 
-ATOM    913  CA  PHE A  56       9.035   5.228  -1.949  1.00  0.57           C
603 
-ATOM    914  C   PHE A  56      10.002   4.576  -2.944  1.00  0.71           C
604 
-ATOM    915  O   PHE A  56      10.000   3.374  -3.124  1.00  1.62           O
605 
-ATOM    916  CB  PHE A  56       8.267   6.356  -2.637  1.00  0.62           C
606 
-ATOM    917  CG  PHE A  56       7.213   5.805  -3.572  1.00  0.57           C
607 
-ATOM    918  CD1 PHE A  56       6.938   4.430  -3.629  1.00  1.37           C
608 
-ATOM    919  CD2 PHE A  56       6.504   6.690  -4.386  1.00  1.31           C
609 
-ATOM    920  CE1 PHE A  56       5.953   3.951  -4.507  1.00  1.40           C
610 
-ATOM    921  CE2 PHE A  56       5.522   6.212  -5.260  1.00  1.40           C
611 
-ATOM    922  CZ  PHE A  56       5.249   4.842  -5.323  1.00  0.79           C
612 
-ATOM    932  N   GLU A  57      10.824   5.355  -3.595  1.00  0.67           N
613 
-ATOM    933  CA  GLU A  57      11.784   4.768  -4.576  1.00  0.65           C
614 
-ATOM    934  C   GLU A  57      12.637   3.708  -3.882  1.00  0.58           C
615 
-ATOM    935  O   GLU A  57      13.002   2.709  -4.467  1.00  0.58           O
616 
-ATOM    936  CB  GLU A  57      12.703   5.861  -5.118  1.00  0.80           C
617 
-ATOM    937  CG  GLU A  57      11.991   6.634  -6.229  1.00  1.16           C
618 
-ATOM    938  CD  GLU A  57      12.794   7.891  -6.571  1.00  1.75           C
619 
-ATOM    939  OE1 GLU A  57      13.812   8.110  -5.935  1.00  2.34           O
620 
-ATOM    940  OE2 GLU A  57      12.378   8.612  -7.462  1.00  2.41           O
621 
-ATOM    947  N   GLN A  58      12.961   3.924  -2.638  1.00  0.58           N
622 
-ATOM    948  CA  GLN A  58      13.786   2.942  -1.899  1.00  0.60           C
623 
-ATOM    949  C   GLN A  58      12.982   1.655  -1.731  1.00  0.53           C
624 
-ATOM    950  O   GLN A  58      13.524   0.569  -1.730  1.00  0.56           O
625 
-ATOM    951  CB  GLN A  58      14.158   3.516  -0.530  1.00  0.69           C
626 
-ATOM    952  CG  GLN A  58      15.064   4.735  -0.723  1.00  0.94           C
627 
-ATOM    953  CD  GLN A  58      16.526   4.322  -0.542  1.00  1.56           C
628 
-ATOM    954  OE1 GLN A  58      16.810   3.268  -0.008  1.00  2.34           O
629 
-ATOM    955  NE2 GLN A  58      17.472   5.114  -0.966  1.00  1.94           N
630 
-ATOM    964  N   SER A  59      11.685   1.773  -1.611  1.00  0.52           N
631 
-ATOM    965  CA  SER A  59      10.829   0.560  -1.473  1.00  0.52           C
632 
-ATOM    966  C   SER A  59      10.318   0.172  -2.859  1.00  0.44           C
633 
-ATOM    967  O   SER A  59       9.371  -0.576  -3.002  1.00  0.48           O
634 
-ATOM    968  CB  SER A  59       9.639   0.859  -0.562  1.00  0.65           C
635 
-ATOM    969  OG  SER A  59       9.861   0.266   0.709  1.00  1.39           O
636 
-ATOM    975  N   LYS A  60      10.954   0.675  -3.881  1.00  0.41           N
637 
-ATOM    976  CA  LYS A  60      10.532   0.342  -5.266  1.00  0.42           C
638 
-ATOM    977  C   LYS A  60      11.614  -0.520  -5.922  1.00  0.44           C
639 
-ATOM    978  O   LYS A  60      11.326  -1.436  -6.666  1.00  0.55           O
640 
-ATOM    979  CB  LYS A  60      10.356   1.636  -6.062  1.00  0.51           C
641 
-ATOM    980  CG  LYS A  60       9.518   1.361  -7.311  1.00  1.03           C
642 
-ATOM    981  CD  LYS A  60       9.317   2.665  -8.084  1.00  1.61           C
643 
-ATOM    982  CE  LYS A  60       9.529   2.412  -9.575  1.00  2.36           C
644 
-ATOM    983  NZ  LYS A  60      10.507   3.397 -10.112  1.00  3.11           N
645 
-ATOM    997  N   GLN A  61      12.860  -0.228  -5.655  1.00  0.51           N
646 
-ATOM    998  CA  GLN A  61      13.963  -1.020  -6.264  1.00  0.62           C
647 
-ATOM    999  C   GLN A  61      14.010  -2.425  -5.651  1.00  0.60           C
648 
-ATOM   1000  O   GLN A  61      13.841  -3.416  -6.332  1.00  0.66           O
649 
-ATOM   1001  CB  GLN A  61      15.297  -0.315  -6.006  1.00  0.73           C
650 
-ATOM   1002  CG  GLN A  61      15.326   1.021  -6.751  1.00  1.14           C
651 
-ATOM   1003  CD  GLN A  61      16.704   1.221  -7.385  1.00  1.66           C
652 
-ATOM   1004  OE1 GLN A  61      17.499   0.303  -7.440  1.00  2.16           O
653 
-ATOM   1005  NE2 GLN A  61      17.024   2.390  -7.868  1.00  2.39           N
654 
-ATOM   1014  N   LEU A  62      14.264  -2.497  -4.372  1.00  0.64           N
655 
-ATOM   1015  CA  LEU A  62      14.358  -3.820  -3.661  1.00  0.71           C
656 
-ATOM   1016  C   LEU A  62      13.391  -4.833  -4.276  1.00  0.67           C
657 
-ATOM   1017  O   LEU A  62      13.653  -6.019  -4.302  1.00  0.94           O
658 
-ATOM   1018  CB  LEU A  62      13.995  -3.678  -2.170  1.00  0.78           C
659 
-ATOM   1019  CG  LEU A  62      13.609  -2.241  -1.817  1.00  0.78           C
660 
-ATOM   1020  CD1 LEU A  62      12.330  -1.844  -2.561  1.00  0.66           C
661 
-ATOM   1021  CD2 LEU A  62      13.367  -2.146  -0.310  1.00  0.94           C
662 
-ATOM   1033  N   THR A  63      12.276  -4.379  -4.770  1.00  0.58           N
663 
-ATOM   1034  CA  THR A  63      11.298  -5.309  -5.376  1.00  0.70           C
664 
-ATOM   1035  C   THR A  63      10.933  -4.785  -6.761  1.00  0.81           C
665 
-ATOM   1036  O   THR A  63       9.802  -4.445  -7.030  1.00  0.89           O
666 
-ATOM   1037  CB  THR A  63      10.042  -5.450  -4.482  1.00  0.65           C
667 
-ATOM   1038  OG1 THR A  63       8.893  -5.599  -5.300  1.00  0.72           O
668 
-ATOM   1039  CG2 THR A  63       9.848  -4.231  -3.559  1.00  0.52           C
669 
-ATOM   1047  N   GLU A  64      11.921  -4.721  -7.629  1.00  0.95           N
670 
-ATOM   1048  CA  GLU A  64      11.731  -4.227  -9.035  1.00  1.21           C
671 
-ATOM   1049  C   GLU A  64      10.247  -4.117  -9.389  1.00  1.18           C
672 
-ATOM   1050  O   GLU A  64       9.570  -5.108  -9.578  1.00  1.53           O
673 
-ATOM   1051  CB  GLU A  64      12.403  -5.214  -9.993  1.00  1.55           C
674 
-ATOM   1052  CG  GLU A  64      12.903  -4.472 -11.231  1.00  1.91           C
675 
-ATOM   1053  CD  GLU A  64      14.052  -5.257 -11.865  1.00  2.44           C
676 
-ATOM   1054  OE1 GLU A  64      14.291  -6.373 -11.432  1.00  3.09           O
677 
-ATOM   1055  OE2 GLU A  64      14.675  -4.730 -12.771  1.00  2.79           O
678 
-ATOM   1062  N   ASN A  65       9.732  -2.920  -9.470  1.00  1.70           N
679 
-ATOM   1063  CA  ASN A  65       8.289  -2.761  -9.802  1.00  1.68           C
680 
-ATOM   1064  C   ASN A  65       7.456  -3.157  -8.582  1.00  0.85           C
681 
-ATOM   1065  O   ASN A  65       6.375  -3.697  -8.706  1.00  1.09           O
682 
-ATOM   1066  CB  ASN A  65       7.944  -3.685 -10.974  1.00  2.27           C
683 
-ATOM   1067  CG  ASN A  65       6.828  -3.063 -11.814  1.00  2.89           C
684 
-ATOM   1068  OD1 ASN A  65       6.854  -1.884 -12.103  1.00  3.24           O
685 
-ATOM   1069  ND2 ASN A  65       5.844  -3.815 -12.224  1.00  3.66           N
686 
-ATOM   1076  N   GLY A  66       7.968  -2.928  -7.401  1.00  0.56           N
687 
-ATOM   1077  CA  GLY A  66       7.225  -3.330  -6.177  1.00  1.20           C
688 
-ATOM   1078  C   GLY A  66       6.279  -2.227  -5.680  1.00  0.91           C
689 
-ATOM   1079  O   GLY A  66       5.073  -2.381  -5.677  1.00  1.26           O
690 
-ATOM   1083  N   ALA A  67       6.826  -1.155  -5.185  1.00  0.39           N
691 
-ATOM   1084  CA  ALA A  67       5.996  -0.071  -4.590  1.00  0.46           C
692 
-ATOM   1085  C   ALA A  67       5.313   0.846  -5.615  1.00  0.34           C
693 
-ATOM   1086  O   ALA A  67       4.352   1.513  -5.286  1.00  0.53           O
694 
-ATOM   1087  CB  ALA A  67       6.909   0.777  -3.713  1.00  0.64           C
695 
-ATOM   1093  N   GLU A  68       5.778   0.935  -6.823  1.00  0.27           N
696 
-ATOM   1094  CA  GLU A  68       5.129   1.851  -7.769  1.00  0.38           C
697 
-ATOM   1095  C   GLU A  68       3.751   1.292  -8.176  1.00  0.39           C
698 
-ATOM   1096  O   GLU A  68       2.884   2.021  -8.617  1.00  0.49           O
699 
-ATOM   1097  CB  GLU A  68       6.069   2.020  -8.971  1.00  0.51           C
700 
-ATOM   1098  CG  GLU A  68       5.274   2.020 -10.258  1.00  1.38           C
701 
-ATOM   1099  CD  GLU A  68       6.148   2.521 -11.410  1.00  1.57           C
702 
-ATOM   1100  OE1 GLU A  68       6.989   3.370 -11.165  1.00  1.83           O
703 
-ATOM   1101  OE2 GLU A  68       5.961   2.047 -12.518  1.00  2.27           O
704 
-ATOM   1108  N   SER A  69       3.544   0.011  -8.034  1.00  0.39           N
705 
-ATOM   1109  CA  SER A  69       2.227  -0.585  -8.417  1.00  0.47           C
706 
-ATOM   1110  C   SER A  69       1.196  -0.382  -7.297  1.00  0.37           C
707 
-ATOM   1111  O   SER A  69       0.120   0.157  -7.510  1.00  0.35           O
708 
-ATOM   1112  CB  SER A  69       2.405  -2.082  -8.669  1.00  0.58           C
709 
-ATOM   1113  OG  SER A  69       2.127  -2.366 -10.033  1.00  0.90           O
710 
-ATOM   1119  N   VAL A  70       1.509  -0.818  -6.106  1.00  0.34           N
711 
-ATOM   1120  CA  VAL A  70       0.544  -0.662  -4.984  1.00  0.27           C
712 
-ATOM   1121  C   VAL A  70       0.107   0.793  -4.912  1.00  0.20           C
713 
-ATOM   1122  O   VAL A  70      -1.057   1.098  -4.748  1.00  0.20           O
714 
-ATOM   1123  CB  VAL A  70       1.215  -1.063  -3.671  1.00  0.31           C
715 
-ATOM   1124  CG1 VAL A  70       0.288  -0.737  -2.499  1.00  0.29           C
716 
-ATOM   1125  CG2 VAL A  70       1.504  -2.565  -3.687  1.00  0.41           C
717 
-ATOM   1135  N   LEU A  71       1.033   1.696  -5.048  1.00  0.24           N
718 
-ATOM   1136  CA  LEU A  71       0.663   3.134  -5.002  1.00  0.23           C
719 
-ATOM   1137  C   LEU A  71      -0.340   3.411  -6.113  1.00  0.23           C
720 
-ATOM   1138  O   LEU A  71      -1.335   4.061  -5.909  1.00  0.23           O
721 
-ATOM   1139  CB  LEU A  71       1.897   3.996  -5.229  1.00  0.30           C
722 
-ATOM   1140  CG  LEU A  71       1.476   5.464  -5.305  1.00  0.35           C
723 
-ATOM   1141  CD1 LEU A  71       1.177   5.986  -3.899  1.00  0.36           C
724 
-ATOM   1142  CD2 LEU A  71       2.605   6.290  -5.924  1.00  0.43           C
725 
-ATOM   1154  N   GLN A  72      -0.083   2.914  -7.289  1.00  0.28           N
726 
-ATOM   1155  CA  GLN A  72      -1.027   3.138  -8.419  1.00  0.30           C
727 
-ATOM   1156  C   GLN A  72      -2.417   2.716  -7.977  1.00  0.25           C
728 
-ATOM   1157  O   GLN A  72      -3.408   3.314  -8.334  1.00  0.25           O
729 
-ATOM   1158  CB  GLN A  72      -0.583   2.279  -9.617  1.00  0.35           C
730 
-ATOM   1159  CG  GLN A  72      -1.789   1.868 -10.473  1.00  1.18           C
731 
-ATOM   1160  CD  GLN A  72      -1.304   1.317 -11.813  1.00  1.42           C
732 
-ATOM   1161  OE1 GLN A  72      -1.069   2.064 -12.742  1.00  1.78           O
733 
-ATOM   1162  NE2 GLN A  72      -1.144   0.029 -11.955  1.00  1.97           N
734 
-ATOM   1171  N   VAL A  73      -2.487   1.666  -7.230  1.00  0.23           N
735 
-ATOM   1172  CA  VAL A  73      -3.797   1.162  -6.774  1.00  0.20           C
736 
-ATOM   1173  C   VAL A  73      -4.352   2.055  -5.661  1.00  0.16           C
737 
-ATOM   1174  O   VAL A  73      -5.547   2.201  -5.514  1.00  0.16           O
738 
-ATOM   1175  CB  VAL A  73      -3.590  -0.254  -6.268  1.00  0.21           C
739 
-ATOM   1176  CG1 VAL A  73      -4.840  -0.752  -5.547  1.00  0.20           C
740 
-ATOM   1177  CG2 VAL A  73      -3.258  -1.151  -7.468  1.00  0.26           C
741 
-ATOM   1187  N   PHE A  74      -3.501   2.649  -4.873  1.00  0.15           N
742 
-ATOM   1188  CA  PHE A  74      -4.001   3.529  -3.773  1.00  0.14           C
743 
-ATOM   1189  C   PHE A  74      -4.501   4.858  -4.358  1.00  0.16           C
744 
-ATOM   1190  O   PHE A  74      -5.460   5.440  -3.887  1.00  0.18           O
745 
-ATOM   1191  CB  PHE A  74      -2.868   3.807  -2.778  1.00  0.14           C
746 
-ATOM   1192  CG  PHE A  74      -2.926   2.806  -1.651  1.00  0.12           C
747 
-ATOM   1193  CD1 PHE A  74      -3.895   2.932  -0.650  1.00  0.16           C
748 
-ATOM   1194  CD2 PHE A  74      -2.007   1.751  -1.608  1.00  0.16           C
749 
-ATOM   1195  CE1 PHE A  74      -3.946   2.003   0.395  1.00  0.18           C
750 
-ATOM   1196  CE2 PHE A  74      -2.058   0.822  -0.563  1.00  0.19           C
751 
-ATOM   1197  CZ  PHE A  74      -3.027   0.949   0.439  1.00  0.19           C
752 
-ATOM   1207  N   ARG A  75      -3.859   5.334  -5.388  1.00  0.19           N
753 
-ATOM   1208  CA  ARG A  75      -4.271   6.610  -6.018  1.00  0.23           C
754 
-ATOM   1209  C   ARG A  75      -5.453   6.341  -6.929  1.00  0.24           C
755 
-ATOM   1210  O   ARG A  75      -6.368   7.124  -7.030  1.00  0.33           O
756 
-ATOM   1211  CB  ARG A  75      -3.119   7.150  -6.851  1.00  0.26           C
757 
-ATOM   1212  CG  ARG A  75      -1.995   7.625  -5.930  1.00  0.54           C
758 
-ATOM   1213  CD  ARG A  75      -1.790   9.130  -6.107  1.00  1.28           C
759 
-ATOM   1214  NE  ARG A  75      -1.186   9.394  -7.445  1.00  1.38           N
760 
-ATOM   1215  CZ  ARG A  75      -1.177  10.604  -7.930  1.00  1.76           C
761 
-ATOM   1216  NH1 ARG A  75      -1.310  11.627  -7.134  1.00  2.43           N
762 
-ATOM   1217  NH2 ARG A  75      -1.032  10.790  -9.212  1.00  2.43           N
763 
-ATOM   1231  N   GLU A  76      -5.429   5.219  -7.581  1.00  0.22           N
764 
-ATOM   1232  CA  GLU A  76      -6.544   4.838  -8.482  1.00  0.23           C
765 
-ATOM   1233  C   GLU A  76      -7.787   4.692  -7.616  1.00  0.21           C
766 
-ATOM   1234  O   GLU A  76      -8.839   5.219  -7.917  1.00  0.23           O
767 
-ATOM   1235  CB  GLU A  76      -6.206   3.501  -9.129  1.00  0.24           C
768 
-ATOM   1236  CG  GLU A  76      -5.555   3.723 -10.494  1.00  0.30           C
769 
-ATOM   1237  CD  GLU A  76      -6.631   4.058 -11.527  1.00  0.89           C
770 
-ATOM   1238  OE1 GLU A  76      -7.781   3.734 -11.282  1.00  1.65           O
771 
-ATOM   1239  OE2 GLU A  76      -6.286   4.632 -12.547  1.00  1.48           O
772 
-ATOM   1246  N   ALA A  77      -7.653   4.005  -6.512  1.00  0.18           N
773 
-ATOM   1247  CA  ALA A  77      -8.796   3.857  -5.591  1.00  0.17           C
774 
-ATOM   1248  C   ALA A  77      -9.143   5.259  -5.113  1.00  0.19           C
775 
-ATOM   1249  O   ALA A  77     -10.294   5.632  -5.003  1.00  0.20           O
776 
-ATOM   1250  CB  ALA A  77      -8.403   2.975  -4.403  1.00  0.17           C
777 
-ATOM   1256  N   LYS A  78      -8.133   6.059  -4.876  1.00  0.21           N
778 
-ATOM   1257  CA  LYS A  78      -8.377   7.464  -4.462  1.00  0.24           C
779 
-ATOM   1258  C   LYS A  78      -9.200   8.121  -5.560  1.00  0.28           C
780 
-ATOM   1259  O   LYS A  78      -9.990   9.016  -5.336  1.00  0.32           O
781 
-ATOM   1260  CB  LYS A  78      -7.038   8.187  -4.372  1.00  0.26           C
782 
-ATOM   1261  CG  LYS A  78      -7.077   9.218  -3.247  1.00  0.32           C
783 
-ATOM   1262  CD  LYS A  78      -7.173  10.619  -3.855  1.00  0.70           C
784 
-ATOM   1263  CE  LYS A  78      -7.216  11.663  -2.738  1.00  0.99           C
785 
-ATOM   1264  NZ  LYS A  78      -6.353  12.821  -3.109  1.00  1.50           N
786 
-ATOM   1278  N   ALA A  79      -8.984   7.664  -6.756  1.00  0.28           N
787 
-ATOM   1279  CA  ALA A  79      -9.690   8.204  -7.933  1.00  0.33           C
788 
-ATOM   1280  C   ALA A  79     -11.110   7.645  -7.972  1.00  0.32           C
789 
-ATOM   1281  O   ALA A  79     -12.027   8.262  -8.477  1.00  0.38           O
790 
-ATOM   1282  CB  ALA A  79      -8.920   7.757  -9.173  1.00  0.35           C
791 
-ATOM   1288  N   GLU A  80     -11.285   6.472  -7.440  1.00  0.28           N
792 
-ATOM   1289  CA  GLU A  80     -12.620   5.829  -7.425  1.00  0.29           C
793 
-ATOM   1290  C   GLU A  80     -13.585   6.626  -6.544  1.00  0.37           C
794 
-ATOM   1291  O   GLU A  80     -14.762   6.332  -6.476  1.00  0.68           O
795 
-ATOM   1292  CB  GLU A  80     -12.466   4.417  -6.865  1.00  0.32           C
796 
-ATOM   1293  CG  GLU A  80     -12.076   3.469  -7.995  1.00  0.45           C
797 
-ATOM   1294  CD  GLU A  80     -13.336   2.876  -8.627  1.00  0.67           C
798 
-ATOM   1295  OE1 GLU A  80     -13.927   3.543  -9.460  1.00  1.40           O
799 
-ATOM   1296  OE2 GLU A  80     -13.688   1.764  -8.269  1.00  1.30           O
800 
-ATOM   1303  N   GLY A  81     -13.098   7.621  -5.858  1.00  0.39           N
801 
-ATOM   1304  CA  GLY A  81     -13.987   8.421  -4.973  1.00  0.45           C
802 
-ATOM   1305  C   GLY A  81     -13.572   8.186  -3.522  1.00  0.39           C
803 
-ATOM   1306  O   GLY A  81     -13.963   8.908  -2.626  1.00  0.45           O
804 
-ATOM   1310  N   CYS A  82     -12.776   7.179  -3.288  1.00  0.41           N
805 
-ATOM   1311  CA  CYS A  82     -12.322   6.888  -1.905  1.00  0.38           C
806 
-ATOM   1312  C   CYS A  82     -11.476   8.057  -1.395  1.00  0.38           C
807 
-ATOM   1313  O   CYS A  82     -10.977   8.854  -2.164  1.00  0.49           O
808 
-ATOM   1314  CB  CYS A  82     -11.480   5.614  -1.920  1.00  0.39           C
809 
-ATOM   1315  SG  CYS A  82     -12.566   4.168  -1.820  1.00  0.63           S
810 
-ATOM   1321  N   ASP A  83     -11.316   8.173  -0.105  1.00  0.32           N
811 
-ATOM   1322  CA  ASP A  83     -10.510   9.298   0.444  1.00  0.37           C
812 
-ATOM   1323  C   ASP A  83      -9.188   8.769   1.009  1.00  0.36           C
813 
-ATOM   1324  O   ASP A  83      -8.935   8.844   2.195  1.00  0.57           O
814 
-ATOM   1325  CB  ASP A  83     -11.305   9.984   1.553  1.00  0.42           C
815 
-ATOM   1326  CG  ASP A  83     -10.709  11.364   1.834  1.00  0.53           C
816 
-ATOM   1327  OD1 ASP A  83      -9.782  11.437   2.624  1.00  1.11           O
817 
-ATOM   1328  OD2 ASP A  83     -11.191  12.324   1.255  1.00  1.30           O
818 
-ATOM   1333  N   ILE A  84      -8.339   8.244   0.168  1.00  0.33           N
819 
-ATOM   1334  CA  ILE A  84      -7.028   7.720   0.652  1.00  0.31           C
820 
-ATOM   1335  C   ILE A  84      -5.965   8.818   0.503  1.00  0.34           C
821 
-ATOM   1336  O   ILE A  84      -5.289   8.905  -0.503  1.00  0.67           O
822 
-ATOM   1337  CB  ILE A  84      -6.622   6.513  -0.191  1.00  0.30           C
823 
-ATOM   1338  CG1 ILE A  84      -7.546   5.345   0.117  1.00  0.50           C
824 
-ATOM   1339  CG2 ILE A  84      -5.182   6.114   0.131  1.00  0.28           C
825 
-ATOM   1340  CD1 ILE A  84      -8.049   4.762  -1.198  1.00  0.34           C
826 
-ATOM   1352  N   THR A  85      -5.813   9.657   1.490  1.00  0.49           N
827 
-ATOM   1353  CA  THR A  85      -4.796  10.748   1.400  1.00  0.50           C
828 
-ATOM   1354  C   THR A  85      -3.430  10.156   1.047  1.00  0.47           C
829 
-ATOM   1355  O   THR A  85      -2.721   9.661   1.897  1.00  0.60           O
830 
-ATOM   1356  CB  THR A  85      -4.702  11.468   2.749  1.00  0.61           C
831 
-ATOM   1357  OG1 THR A  85      -5.862  12.265   2.940  1.00  0.76           O
832 
-ATOM   1358  CG2 THR A  85      -3.458  12.361   2.773  1.00  0.55           C
833 
-ATOM   1366  N   ILE A  86      -3.051  10.211  -0.200  1.00  0.41           N
834 
-ATOM   1367  CA  ILE A  86      -1.727   9.654  -0.602  1.00  0.40           C
835 
-ATOM   1368  C   ILE A  86      -0.610  10.583  -0.118  1.00  0.44           C
836 
-ATOM   1369  O   ILE A  86      -0.489  11.706  -0.564  1.00  0.59           O
837 
-ATOM   1370  CB  ILE A  86      -1.665   9.540  -2.126  1.00  0.38           C
838 
-ATOM   1371  CG1 ILE A  86      -2.821   8.668  -2.620  1.00  0.74           C
839 
-ATOM   1372  CG2 ILE A  86      -0.331   8.915  -2.540  1.00  0.93           C
840 
-ATOM   1373  CD1 ILE A  86      -2.613   7.223  -2.166  1.00  0.32           C
841 
-ATOM   1385  N   ILE A  87       0.212  10.123   0.786  1.00  0.39           N
842 
-ATOM   1386  CA  ILE A  87       1.322  10.982   1.287  1.00  0.44           C
843 
-ATOM   1387  C   ILE A  87       2.659  10.368   0.860  1.00  0.44           C
844 
-ATOM   1388  O   ILE A  87       3.132   9.413   1.442  1.00  0.55           O
845 
-ATOM   1389  CB  ILE A  87       1.247  11.073   2.813  1.00  0.46           C
846 
-ATOM   1390  CG1 ILE A  87       0.091  11.995   3.208  1.00  0.57           C
847 
-ATOM   1391  CG2 ILE A  87       2.556  11.640   3.362  1.00  0.55           C
848 
-ATOM   1392  CD1 ILE A  87      -0.237  11.800   4.689  1.00  0.61           C
849 
-ATOM   1404  N   LEU A  88       3.259  10.902  -0.170  1.00  0.50           N
850 
-ATOM   1405  CA  LEU A  88       4.552  10.348  -0.662  1.00  0.52           C
851 
-ATOM   1406  C   LEU A  88       5.728  11.146  -0.093  1.00  0.56           C
852 
-ATOM   1407  O   LEU A  88       5.984  12.263  -0.495  1.00  0.80           O
853 
-ATOM   1408  CB  LEU A  88       4.558  10.413  -2.173  1.00  0.59           C
854 
-ATOM   1409  CG  LEU A  88       3.653   9.297  -2.669  1.00  0.82           C
855 
-ATOM   1410  CD1 LEU A  88       2.691   9.851  -3.697  1.00  0.94           C
856 
-ATOM   1411  CD2 LEU A  88       4.496   8.193  -3.286  1.00  1.57           C
857 
-ATOM   1423  N   SER A  89       6.445  10.581   0.841  1.00  0.55           N
858 
-ATOM   1424  CA  SER A  89       7.604  11.308   1.435  1.00  0.62           C
859 
-ATOM   1425  C   SER A  89       8.908  10.659   0.968  1.00  0.85           C
860 
-ATOM   1426  O   SER A  89       8.935   9.445   0.852  1.00  1.41           O
861 
-ATOM   1427  CB  SER A  89       7.520  11.241   2.961  1.00  0.87           C
862 
-ATOM   1428  OG  SER A  89       7.246  12.538   3.473  1.00  1.64           O
863 
-ATOM   1429  OXT SER A  89       9.859  11.388   0.735  1.00  1.52           O
864 
-TER    1435      SER A  89
865 
-MASTER       97    1    0    4    3    0    0    6 1434    1    0    7
866 
-END

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src/__pycache__/chem.cpython-37.pyc View File


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+ 0 - 498
src/chem.py~ View File 

@@ -1,498 +0,0 @@
1 
-import math
2 
-#from structure import *
3 
-from geom import *
4 
-
5 
-class Atom:
6 
-
7 
-    def dist_atoms(self, atom2):
8 
-        return(math.sqrt((self.coord_x-atom2.coord_x)**2 +
9 
-                         (self.coord_y-atom2.coord_y)**2 +
10 
-                         (self.coord_z-atom2.coord_z)**2))
11 
-
12 
-
13 
-    def __init__(self, atom_id, atom_name, res_name, chain_id,
14 
-                 res_seq_nb, insertion_code, coordinates):
15 
-        self.atom_id = atom_id
16 
-        self.atom_name = atom_name
17 
-        self.res_name = res_name
18 
-        self.chain_id = chain_id
19 
-        self.res_seq_nb = res_seq_nb
20 
-        self.insertion_code = insertion_code
21 
-        self.coord_x = coordinates[0]
22 
-        self.coord_y = coordinates[1]
23 
-        self.coord_z = coordinates[2]
24 
-        self.coords = coordinates
25 
-
26 
-class Structure:
27 
-    def __init__(self, res):
28 
-        self.res = res
29 
-
30 
-class Turn(Structure):
31 
-
32 
-    def __init__(self, turn_type, res):
33 
-        self.turn_type = turn_type
34 
-        Structure.res = res
35 
-
36 
-class Bridge(Structure):
37 
-
38 
-    def __init__(self, bridge_type, res_num, res_partner, indices):
39 
-        self.bridge_type = bridge_type
40 
-        self.res_num = res_num
41 
-        self.res_partner = res_partner
42 
-        Structure.res = res_num
43 
-        self.i = indices[0]
44 
-        self.j = indices[1]
45 
-
46 
-class Helix(Structure):
47 
-
48 
-    def __init__(self, residues, res_num, helix_type):
49 
-        self.residues = residues
50 
-        self.res_num = res_num
51 
-        Structure.res = res_num
52 
-        self.helix_type = helix_type
53 
-
54 
-
55 
-class Residue:
56 
-    def __init__(self, atoms_list, indice):
57 
-        self.atoms = {}
58 
-        for atom in atoms_list:
59 
-            self.atoms[atom.atom_name] = atom
60 
-            self.resid = atom.res_seq_nb
61 
-            self.res_name = atom.res_name
62 
-            self.res_letter = self.get_amino_letter(atom.res_name)
63 
-            self.chain_id = atom.chain_id
64 
-            self.insertion_code = atom.insertion_code
65 
-            self.indice = indice
66 
-
67 
-    def get_amino_letter(self, res_name):
68 
-        code3 = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLU', 'GLN', 'GLY',
69 
-                 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER',
70 
-                 'THR', 'TRP', 'TYR', 'VAL']
71 
-
72 
-
73 
-        code1 = ['A','R','N','D','C','E','Q','G','H','I','L','K','M','F','P',
74 
-                 'S','T','W','Y','V']
75 
-
76 
-        return code1[code3.index(res_name)]
77 
-
78 
-    def h_bond(self, res2):
79 
-        if("H" not in res2.atoms.keys()):
80 
-            return(False)
81 
-        # dimensionnal factor, in kcal/mole
82 
-        f = 332
83 
-        # partial charges
84 
-        q1 = 0.42
85 
-        q2 = 0.20
86 
-        # distance between O-N atoms, in angströms
87 
-        r_ON = self.atoms["O"].dist_atoms(res2.atoms["N"])
88 
-        # distance between C-H atoms, in angströms
89 
-        r_CH = self.atoms["C"].dist_atoms(res2.atoms["H"])
90 
-        # distance between O-H atoms, in angströms
91 
-        r_OH = self.atoms["O"].dist_atoms(res2.atoms["H"])
92 
-        # distance between C-N atoms, in angströms
93 
-        r_CN = self.atoms["C"].dist_atoms(res2.atoms["N"])
94 
-        # electrostatic interaction energy, in kcal/mole
95 
-        E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f
96 
-        return(E)
97 
-
98 
-    def get_turns(self, residues):
99 
-        """
100 
-        Get all the turns from a specific residue.
101 
-        """
102 
-        turns = {}
103 
-        i = residues.index(self)
104 
-        k = 0
105 
-        for j in range(3,6):
106 
-                if(i+j<len(residues)):
107 
-                    if(self.h_bond(residues[i+j])<-0.5):
108 
-                        k = j
109 
-        if k != 0:
110 
-            #print(k,"TURN", residues[i].resid, residues[i+k].resid)
111 
-            return Turn(k,residues[i].resid)
112 
-
113 
-        return False
114 
-
115 
-    def get_bends(self, residues):
116 
-        i = residues.index(self)
117 
-        if i >=2 and i <len(residues)-2:
118 
-            angle = math.degrees(vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords),
119 
-                                                              position_vector(residues[i-2].atoms["CA"].coords)),
120 
-                                               vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
121 
-                                                              position_vector(residues[i].atoms["CA"].coords))))
122 
-            if(angle>70):
123 
-                return [angle, 'S']
124 
-            return [angle, '']
125 
-        else:
126 
-            return [360.0, '']
127 
-
128 
-    def get_bridges(self, residues):
129 
-        bridges = {}
130 
-        bridge = {}
131 
-        strongest_bridge = {}
132 
-        i = residues.index(self)
133 
-        if(i >= 1 and i < len(residues)-4):
134 
-            E_min = 0
135 
-            for j in range(i+2,len(residues)-1):
136 
-                # select triplet with the minimal energy
137 
-
138 
-                if(residues[i-1].h_bond(residues[j])<-0.5
139 
-                   and residues[j].h_bond(residues[i+1])<-0.5):
140 
-                    bridge = {'res1':residues[i-1].h_bond(residues[j]),
141 
-                              'res2':residues[j].h_bond(residues[i+1]),
142 
-                              'ipos':residues[i].resid,
143 
-                              'jpos':residues[j].resid,
144 
-                              'btype':"para"}
145 
-
146 
-                if(residues[j-1].h_bond(residues[i])<-0.5
147 
-                   and residues[i].h_bond(residues[j+1])<-0.5):
148 
-                    bridge = {'res1':residues[j-1].h_bond(residues[i]),
149 
-                              'res2':residues[i].h_bond(residues[j+1]),
150 
-                              'ipos':residues[i].resid,
151 
-                              'jpos':residues[j].resid,
152 
-                              'btype':"para"}
153 
-
154 
-                if(residues[i].h_bond(residues[j])<-0.5
155 
-                   and residues[j].h_bond(residues[i])<-0.5):
156 
-                    bridge = {'res1':residues[i].h_bond(residues[j]),
157 
-                              'res2':residues[j].h_bond(residues[i]),
158 
-                              'ipos':residues[i].resid,
159 
-                              'jpos':residues[j].resid,
160 
-                              'btype':"anti"}
161 
-
162 
-                if(residues[i-1].h_bond(residues[j+1])<-0.5
163 
-                   and residues[j-1].h_bond(residues[i+1])<-0.5):
164 
-                    bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
165 
-                              'res2':residues[j-1].h_bond(residues[i+1]),
166 
-                              'ipos':residues[i].resid,
167 
-                              'jpos':residues[j].resid,
168 
-                              'btype':"anti"}
169 
-
170 
-                if(bridge):
171 
-                    if(bridge['res1']+bridge['res2']<E_min):
172 
-                        E_min = bridge['res1']+bridge['res2']
173 
-                        strongest_bridge = bridge
174 
-                        bridge = {}
175 
-                        coord_bridge = [i,j]
176 
-            # finally add the strongest bridge at i and j pos
177 
-            if(strongest_bridge):
178 
-                bridges[coord_bridge[0]] = (Bridge(strongest_bridge['btype'],
179 
-                                                   strongest_bridge['ipos'],
180 
-                                                   strongest_bridge['jpos']))
181 
-
182 
-                bridges[coord_bridge[1]] = (Bridge(strongest_bridge['btype'],
183 
-                                                   strongest_bridge['jpos'],
184 
-                                                   strongest_bridge['ipos']))
185 
-        if(len(bridges)>0):
186 
-            return(bridges[coord_bridge[0]])
187 
-        else:
188 
-            return(False)
189 
-
190 
-    def get_helix(self, residues):
191 
-        """
192 
-        Return if there is an helix at a given residue,
193 
-        as well as its type.
194 
-        """
195 
-        i = residues.index(self)
196 
-        # if there are no turns or it is the first residue, skip
197 
-        if i == 0:
198 
-            return False
199 
-
200 
-        if(self.get_turns(residues) and residues[i-1].get_turns(residues)):
201 
-            #print(self.get_turns(residues).turn_type,"- HELIX at", residues[i].indice)
202 
-            return(self.get_turns(residues).turn_type, residues[i].indice)
203 
-        return(False)
204 
-
205 
-    def get_ladder(self, residues):
206 
-        #ladders = {}
207 
-        i = residues.index(self)
208 
-        if i != 0:
209 
-            if self.get_bridges(residues):
210 
-                if (residues[i-1].get_bridges(residues)):
211 
-                    local_bridge = self.get_bridges(residues)
212 
-                    consec_bridge = residues[i-1].get_bridges(residues)
213 
-                    if local_bridge.bridge_type == consec_bridge.bridge_type:
214 
-                        #print("ladder", consec_bridge.res_num, local_bridge.res_num)
215 
-                        ladder = {'start':consec_bridge.res_num,
216 
-                                  'end':local_bridge.res_num,
217 
-                                  'bridges':[consec_bridge, local_bridge]}
218 
-                        return ladder
219 
-        return False
220 
-
221 
-    def get_tco(self, residues):
222 
-        i = residues.index(self)
223 
-        if(i!=0):
224 
-            res2 = residues[i-1]
225 
-            CO_res1 = vector_from_pos(self.atoms["C"].coords,
226 
-                                      self.atoms["O"].coords)
227 
-            CO_res2 = vector_from_pos(res2.atoms["C"].coords,
228 
-                                      res2.atoms["O"].coords)
229 
-            angle = vector_angles(CO_res1, CO_res2)
230 
-        else:
231 
-            angle = math.pi/2
232 
-        return(math.cos(angle))
233 
-
234 
-    def get_chirality(self, residues):
235 
-        i = residues.index(self)
236 
-        if (i >=1 and i < len(residues)-2):
237 
-            chirality = {}
238 
-            angle = calc_dihedral(residues[i-1].atoms["CA"].coords,
239 
-                                  residues[i].atoms["CA"].coords,
240 
-                                  residues[i+1].atoms["CA"].coords,
241 
-                                  residues[i+2].atoms["CA"].coords)
242 
-
243 
-            if(angle>0 and angle<=180):
244 
-                sign="+"
245 
-
246 
-            if(angle<=0 and angle > -180):
247 
-                sign="-"
248 
-
249 
-        else:
250 
-            angle = 360.0
251 
-            sign = ''
252 
-
253 
-        return [angle, sign]
254 
-
255 
-    def get_phi_psi(self, residues):
256 
-        i = residues.index(self)
257 
-        if(i==0):
258 
-            phi = 360.0
259 
-        else:
260 
-            phi = calc_dihedral(residues[i-1].atoms["C"].coords,
261 
-                                residues[i].atoms["N"].coords,
262 
-                                residues[i].atoms["CA"].coords,
263 
-                                residues[i].atoms["C"].coords)
264 
-        if(i==len(residues)-1):
265 
-            psi = 360.0
266 
-        else:
267 
-            psi = calc_dihedral(residues[i].atoms["N"].coords,
268 
-                                residues[i].atoms["CA"].coords,
269 
-                                residues[i].atoms["C"].coords,
270 
-                                residues[i+1].atoms["N"].coords)
271 
-
272 
-        return((phi, psi))
273 
-def get_bridges(residues):
274 
-    bridges = {}
275 
-    bridge = {}
276 
-    strongest_bridge = {}
277 
-    for i in range(1,len(residues)-4):
278 
-        E_min = 0
279 
-        for j in range(i+2,len(residues)-1):
280 
-            # select triplet with the minimal energy
281 
-
282 
-            if(residues[i-1].h_bond(residues[j])<-0.5
283 
-               and residues[j].h_bond(residues[i+1])<-0.5):
284 
-                bridge = {'res1':residues[i-1].h_bond(residues[j]),
285 
-                          'res2':residues[j].h_bond(residues[i+1]),
286 
-                          'ipos':residues[i].resid,
287 
-                          'jpos':residues[j].resid,
288 
-                          'i':residues[i].indice,
289 
-                          'j':residues[j].indice,
290 
-                          'btype':"para"}
291 
-
292 
-            if(residues[j-1].h_bond(residues[i])<-0.5
293 
-               and residues[i].h_bond(residues[j+1])<-0.5):
294 
-                bridge = {'res1':residues[j-1].h_bond(residues[i]),
295 
-                          'res2':residues[i].h_bond(residues[j+1]),
296 
-                          'ipos':residues[i].resid,
297 
-                          'jpos':residues[j].resid,
298 
-                          'i':residues[i].indice,
299 
-                          'j':residues[j].indice,
300 
-                          'btype':"para"}
301 
-
302 
-            if(residues[i].h_bond(residues[j])<-0.5
303 
-               and residues[j].h_bond(residues[i])<-0.5):
304 
-                bridge = {'res1':residues[i].h_bond(residues[j]),
305 
-                          'res2':residues[j].h_bond(residues[i]),
306 
-                          'ipos':residues[i].resid,
307 
-                          'jpos':residues[j].resid,
308 
-                          'i':residues[i].indice,
309 
-                          'j':residues[j].indice,
310 
-                          'btype':"anti"}
311 
-
312 
-            if(residues[i-1].h_bond(residues[j+1])<-0.5
313 
-               and residues[j-1].h_bond(residues[i+1])<-0.5):
314 
-                bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
315 
-                          'res2':residues[j-1].h_bond(residues[i+1]),
316 
-                          'ipos':residues[i].resid,
317 
-                          'jpos':residues[j].resid,
318 
-                          'i':residues[i].indice,
319 
-                          'j':residues[j].indice,
320 
-                          'btype':"anti"}
321 
-
322 
-            if(bridge):
323 
-                if(bridge['res1']+bridge['res2']<E_min):
324 
-                    E_min = bridge['res1']+bridge['res2']
325 
-                    strongest_bridge = bridge
326 
-                    coord_bridge = [i,j]
327 
-                    bridge = {}
328 
-
329 
-        # finally add the strongest bridge at i and j pos
330 
-        if(strongest_bridge):
331 
-
332 
-            bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'],
333 
-                                                     strongest_bridge['ipos'],
334 
-                                                     strongest_bridge['jpos'],
335 
-                                                     [strongest_bridge['i'],
336 
-                                                      strongest_bridge['j']]))
337 
-
338 
-            bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'],
339 
-                                                     strongest_bridge['ipos'],
340 
-                                                     strongest_bridge['jpos'],
341 
-                                                     [strongest_bridge['i'],
342 
-                                                      strongest_bridge['j']]))
343 
-    if(len(bridges)>0):
344 
-        return(bridges)
345 
-    else:
346 
-        return(False)
347 
-
348 
-def get_ladders(bridges, residues):
349 
-    ladders = {}
350 
-    i = 1
351 
-    while i < len(residues):
352 
-        k = 1
353 
-        if i in bridges.keys():
354 
-            temp_bridges = [bridges[i]]
355 
-            while ((i+k in bridges.keys()) and
356 
-                   (bridges[i].bridge_type == bridges[i+k].bridge_type)):
357 
-                temp_bridges.append(bridges[i+k])
358 
-                k+=1
359 
-        if k>1:
360 
-            #print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
361 
-            ladders[i] = {'start':bridges[i].res_num,
362 
-                          'end':bridges[i+k-1].res_num,
363 
-                          'bridges':temp_bridges,
364 
-                          'i':i,
365 
-                          'j':i+k-1}
366 
-            i+=k-1
367 
-        else:
368 
-            i+=1
369 
-    return ladders
370 
-
371 
-def connected_ladders(ladd_1, ladd_2):
372 
-    links = []
373 
-    for bridge in ladd_1['bridges']:
374 
-        if bridge.res_partner in res_list(ladd_2):
375 
-            return ladd_2
376 
-
377 
-    return False
378 
-
379 
-def connected_ladders2(ladd_1, ladd_2):
380 
-    links = []
381 
-    for bridge in ladd_1['bridges']:
382 
-        if bridge.res_partner in res_list(ladd_2):
383 
-            return([ladd_1['i'], ladd_1['j'], bridge.i, bridge.j,
384 
-                    ladd_2['i'], ladd_2['j']])
385 
-            #return ladd_2
386 
-
387 
-    return False
388 
-
389 
-
390 
-def get_sheets(ladders):
391 
-    """
392 
-    Bridges between ladders.
393 
-    Check if 1 bridge between one ladder and one or more other ladders.
394 
-    Iterate over all residues of one ladder and check if bridge with other residues
395 
-    of the other ladders.
396 
-    """
397 
-    ladds = [ elem for elem in ladders.values() ]
398 
-    sheets = {}
399 
-
400 
-    corresp = {}
401 
-    for ladd1 in ladds:
402 
-        for ladd2 in ladds:
403 
-            if connected_ladders(ladd1, ladd2)!=False:
404 
-                corresp_list = [ elem for elem in corresp.keys() ]
405 
-                if ladd1['i'] not in corresp_list and ladd2['i'] not in corresp_list:
406 
-                    ind = len(sheets.keys())
407 
-                    sheets[ind] = []
408 
-                    sheets[ind].append(ladd1)
409 
-                    sheets[ind].append(ladd2)
410 
-                    corresp[ladd1['i']] = ind
411 
-                    corresp[ladd2['i']] = ind
412 
-                elif ladd2 not in corresp_list and ladd1 in corresp_list:
413 
-                    sheets[corresp[ladd1['i']]].append(ladd2)
414 
-                    corresp[ladd2['i']] = corresp[ladd1['i']]
415 
-                elif ladd1 not in corresp_list and ladd2 in corresp_list:
416 
-                    sheets[corresp[ladd2['i']]].append(ladd1)
417 
-                    corresp[ladd1['i']] = corresp[ladd2['i']]
418 
-
419 
-    return sheets
420 
-
421 
-def get_sheets2(ladders):
422 
-    """
423 
-    Bridges between ladders.
424 
-    Check if 1 bridge between one ladder and one or more other ladders.
425 
-    Iterate over all residues of one ladder and check if bridge with other residues
426 
-    of the other ladders.
427 
-    """
428 
-    sheets = {}
429 
-    for ladder in ladders:
430 
-        for ladd2 in ladders:
431 
-            if connected_ladders(ladders[ladder], ladders[ladd2]):
432 
-                bridge_i = connected_ladders2(ladders[ladder], ladders[ladd2])[2]
433 
-                bridge_j = connected_ladders2(ladders[ladder], ladders[ladd2])[3]
434 
-                print("ladder",ladders[ladder]['i'], ladders[ladder]['j'],"bridge",bridge_i, bridge_j,
435 
-                      "ladder 2",ladders[ladd2]['i'], ladders[ladd2]['j'])
436 
-
437 
-
438 
-def res_list(ladder):
439 
-    # TODO : method in ladder class
440 
-    l=[]
441 
-    for i in range(ladder['i'], ladder['j']):
442 
-        l.append(i)
443 
-    return(l)
444 
-
445 
-def build_turns_patterns(residues):
446 
-    turns_3 = {}
447 
-    turns_4 = {}
448 
-    turns_5 = {}
449 
-    for i,res in enumerate(residues):
450 
-        turn = residues[i].get_turns(residues)
451 
-        if(turn):
452 
-            for k in range(turn.turn_type):
453 
-                if turn.turn_type == 3:
454 
-                    turns_3[i+1+k] = turn.turn_type
455 
-                if turn.turn_type == 4:
456 
-                    turns_4[i+1+k] = turn.turn_type
457 
-                if turn.turn_type == 5:
458 
-                    turns_5[i+1+k] = turn.turn_type
459 
-    return[turns_3, turns_4, turns_5]
460 
-
461 
-def build_helix_patterns(residues):
462 
-    helix_3 = {}
463 
-    helix_4 = {}
464 
-    helix_5 = {}
465 
-    for i,res in enumerate(residues):
466 
-        helix = residues[i].get_helix(residues)
467 
-        if(helix):
468 
-            helix_type = residues[i].get_helix(residues)[0]
469 
-            helix_pos = residues[i].get_helix(residues)[1]
470 
-            #print("TYPE", helix_type)
471 
-            for k in range(helix_type):
472 
-                if helix_type == 3:
473 
-                    helix_3[i+1+k] = "G"
474 
-                if helix_type == 4:
475 
-                    helix_4[i+1+k] = "H"
476 
-                if helix_type == 5:
477 
-                    helix_5[i+1+k] = "I"
478 
-        #print(helix_3)
479 
-    return[helix_3, helix_4, helix_5]
480 
-
481 
-def print_helix_pattern(residues, res, helix):
482 
-    i = residues.index(res)+1
483 
-    if i in helix.keys():
484 
-        return (helix[i])
485 
-    else:
486 
-        return(' ')
487 
-
488 
-def print_turn_pattern(residues, res, turns):
489 
-    i = residues.index(res)+1
490 
-    if i in turns.keys() and not i-1 in turns.keys():
491 
-        return(">")
492 
-    elif i in turns.keys() and i-1 in turns.keys():
493 
-        return(turns[i])
494 
-    elif i not in turns.keys() and i-1 in turns.keys():
495 
-        return("<")
496 
-    else:
497 
-        return(' ')
498 
-

+ 42 - 0
src/pdb.py View File 

@@ -6,10 +6,39 @@ import pymol
6 6
7 7 
 class PDBFile:
8 8 
     def get_content(self, filename):
9 
+        """Get content of a PDB file
10 
+
11 
+        Parameters
12 
+        ----------
13 
+        filename : str
14 
+            The name of the file to be parsed.
15 
+
16 
+        This function is used to get the raw content
17 
+        of the PDB file.
18 
+
19 
+        Returns
20 
+        -------
21 
+        list
22 
+            List of lines of the PDB file.
23 
+        """
9 24 
         with open(filename) as f:
10 25 
             return(f.readlines())
11 26
12 27 
     def get_header(self):
28 
+        """Returns header of a PDB file
29 
+
30 
+        Parameters
31 
+        ----------
32 
+        self : PDBFile
33 
+            The instance of PDB File to get the header from.
34 
+
35 
+        This function is used to get the header of the PDB file.
36 
+
37 
+        Returns
38 
+        -------
39 
+        dict
40 
+            A field-formatted metadata header.
41 
+        """
13 42 
         metadata = {}
14 43 
         for line in self.rawLines:
15 44 
             # no need to continue if meta are complete
 
@@ -28,6 +57,19 @@ class PDBFile:
28 57 
         return(metadata)
29 58
30 59 
     def get_atoms(self, filename):
60 
+        """Get all atoms inside a PDB file.
61 
+
62 
+        Parameters
63 
+        ----------
64 
+        self : PDBFile
65 
+            The instance of PDB File to get the header from.
66 
+        filename :
67 
+            The name of the file. Used to be sent to
68 
+            add_hydrogens(), as it will be used by PyMOL lib.
69 
+
70 
+        This function is used to parse all ATOM lines and
71 
+        create residues accordingly.
72 
+        """
31 73 
         self.atoms = []
32 74 
         self.residues = []
33 75 
         temp_atoms = []