Source Code for Module prompt.pdb

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003, 2004 Edward d'Auvergne                                  # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
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 21  ############################################################################### 
 22   
 23  import sys 
 24   
 25   
 26 -class PDB: 
 27 -    def __init__(self, relax): 
 28          """Class containing the function for loading a pdb file.""" 
 29   
 30          self.relax = relax 
 31   
 32   
 33 -    def pdb(self, run=None, file=None, dir=None, model=None, heteronuc='N', proton='H', load_seq=1): 
 34          """The pdb loading function. 
 35   
 36          Keyword Arguments 
 37          ~~~~~~~~~~~~~~~~~ 
 38   
 39          run:  The run to assign the structure to. 
 40   
 41          file:  The name of the PDB file. 
 42   
 43          dir:  The directory where the file is located. 
 44   
 45          model:  The PDB model number. 
 46   
 47          heteronuc:  The name of the heteronucleus as specified in the PDB file. 
 48   
 49          proton:  The name of the proton as specified in the PDB file. 
 50   
 51          load_seq:  A flag specifying whether the sequence should be loaded from the PDB file. 
 52   
 53   
 54          Description 
 55          ~~~~~~~~~~~ 
 56   
 57          To load a specific model from the PDB file, set the model flag to an integer i.  The 
 58          structure beginning with the line 'MODEL i' in the PDB file will be loaded.  Otherwise all 
 59          structures will be loaded starting from the model number 1. 
 60   
 61          To load the sequence from the PDB file, set the 'load_seq' flag to 1.  If the sequence has 
 62          previously been loaded, then this flag will be ignored. 
 63   
 64          Once the PDB structures are loaded, unit XH bond vectors will be calculated.  The vectors 
 65          are calculated using the atomic coordinates of the atoms specified by the arguments 
 66          heteronuc and proton.  If more than one model structure is loaded, the unit XH vectors for 
 67          each model will be calculated and the final unit XH vector will be taken as the average. 
 68   
 69   
 70          Example 
 71          ~~~~~~~ 
 72   
 73          To load all structures from the PDB file 'test.pdb' in the directory '~/pdb' for use in the 
 74          model-free analysis run 'm8' where the heteronucleus in the PDB file is 'N' and the proton 
 75          is 'H', type: 
 76   
 77          relax> pdb('m8', 'test.pdb', '~/pdb', 1, 'N', 'H') 
 78          relax> pdb(run='m8', file='test.pdb', dir='pdb', model=1, heteronuc='N', proton='H') 
 79   
 80   
 81          To load the 10th model from the file 'test.pdb', use: 
 82   
 83          relax> pdb('m1', 'test.pdb', model=10) 
 84          relax> pdb(run='m1', file='test.pdb', model=10) 
 85   
 86          """ 
 87   
 88          # Function intro text. 
 89          if self.relax.interpreter.intro: 
 90              text = sys.ps3 + "pdb(" 
 91              text = text + "run=" + `run` 
 92              text = text + ", file=" + `file` 
 93              text = text + ", dir=" + `dir` 
 94              text = text + ", model=" + `model` 
 95              text = text + ", heteronuc=" + `heteronuc` 
 96              text = text + ", proton=" + `proton` 
 97              text = text + ", load_seq=" + `load_seq` + ")" 
 98              print text 
 99   
100          # The run argument. 
101          if type(run) != str: 
102              raise RelaxStrError, ('run', run) 
103   
104          # File name. 
105          if type(file) != str: 
106              raise RelaxStrError, ('file name', file) 
107   
108          # Directory. 
109          if dir != None and type(dir) != str: 
110              raise RelaxNoneStrError, ('directory name', dir) 
111   
112          # The model argument. 
113          if model != None and type(model) != int: 
114              raise RelaxIntError, ('model', model) 
115   
116          # The heteronucleus argument. 
117          if type(heteronuc) != str: 
118              raise RelaxStrError, ('heteronucleus', heteronuc) 
119   
120          # The proton argument. 
121          if type(proton) != str: 
122              raise RelaxStrError, ('proton', proton) 
123   
124          # The load sequence argument. 
125          if type(load_seq) != int or (load_seq != 0 and load_seq != 1): 
126              raise RelaxBinError, ('load sequence flag', load_seq) 
127   
128          # Execute the functional code. 
129          self.relax.generic.pdb.load(run=run, file=file, dir=dir, model=model, heteronuc=heteronuc, proton=proton, load_seq=load_seq) 
130