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DSSPparser/__init__.py

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+from .parser import parseDSSP
+from .pdbToxssp import pdbToxssp
+
+__all__ = ['parseDSSP', 'pdbToxssp']
+__version__ = '0.10'

DSSPparser/parser.py

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+# dssp file from http://www.cmbi.ru.nl/xssp/
+# parse protein secondary structure
+# reference by https://github.com/wilkelab/ProteinEvolutionToolbox/blob/master/python/dssp_parse.py
+# dssp format description in the https://swift.cmbi.umcn.nl/gv/dssp/DSSP_3.html
+# https://swift.cmbi.umcn.nl/gv/dssp/HTML/format.html
+
+
+import re
+import pandas as pd
+
+
+class parseDSSP(object):
+    '''parse dssp file
+    Arguments:
+        file {str} -- dssp file path
+    '''
+    def __init__(self, file):
+        # sequential residue number
+        self.resnum = []
+        # original PDB resname
+        self.inscode = []
+        self.chain = []
+        self.aa = []
+        self.struct = []
+        self.structdetails = []
+        self.bp1 = []
+        self.bp2 = []
+        self.acc = []
+        self.h_nho1 = []
+        self.h_ohn1 = []
+        self.h_nho2 = []
+        self.h_ohn2 = []
+        self.tco = []
+        self.kappa = []
+        self.alpha = []
+        self.phi = []
+        self.psi = []
+        self.xca = []
+        self.yca = []
+        self.zca = []
+        self.rcsb_given_chain = []
+        self.author_given_chain = []
+        self._file = file
+
+    def parse(self):
+        ''' parse line by line '''
+        input_handle = open(self._file, 'r')
+        flag = False
+        for line in input_handle:
+            if(re.search('#', line)):
+                flag = True
+                continue
+            if flag:
+                # RESIDUE
+                self.resnum.append(line[0:5].strip())
+                self.inscode.append(line[5:10].strip())
+                self.chain.append(line[10:12].strip())
+                # AA
+                self.aa.append(line[12:14].strip())
+                # S
+                self.struct.append(line[14:17])
+                self.structdetails.append(line[16:24])
+
+                self.bp1.append(line[24:29].strip())
+                self.bp2.append(line[29:34].strip())
+                # solvent accessibility
+                self.acc.append(line[34:38].strip())
+                # hydrogen bonds
+                self.h_nho1.append(line[38:50].strip())
+                self.h_ohn1.append(line[50:61].strip())
+                self.h_nho2.append(line[61:72].strip())
+                self.h_ohn2.append(line[72:83].strip())
+
+                self.tco.append(line[83:91].strip())
+
+                self.kappa.append(line[91:97].strip())
+                self.alpha.append(line[97:103].strip())
+                # IUPAC peptide backbone torsion angles
+                self.phi.append(line[103:109].strip())
+                self.psi.append(line[109:115].strip())
+                # author_given_chain
+                self.xca.append(line[115:122].strip())
+                self.yca.append(line[122:129].strip())
+                self.zca.append(line[129:136].strip())
+                # CHAIN AUTHCHAIN
+                self.rcsb_given_chain.append(line[136:153].strip())
+                self.author_given_chain.append(line[153:].strip())
+
+    def dictTodataframe(self):
+        ''' dict to dataframe
+        
+        Returns:
+            pandas.dataframe -- dataframe foramt 
+        '''
+
+        _dict = {'resnum': self.resnum, 'inscode': self.inscode, 'chain': self.chain, 'aa': self.aa, 'struct': self.struct, 'structdetails': self.structdetails, 
+                'bp1': self.bp1, 'bp2': self.bp2, 'acc': self.acc, 'h_nho1': self.h_nho1, 'h_ohn1': self.h_ohn1, 'h_nho2': self.h_nho2, 'h_ohn2': self.h_ohn2, 
+                'tco': self.tco, 'kappa': self.kappa, 'alpha': self.alpha, 'phi': self.phi, 'psi': self.psi, 'xca': self.xca, 'yca': self.yca, 'zca': self.zca, 
+                'rcsb_given_chain': self.rcsb_given_chain, 'author_given_chain': self.author_given_chain}
+        df = pd.DataFrame.from_dict(_dict)
+        return df
+
+    @property
+    def getResnums(self):
+        '''sequential resnumber, including chain breaks as extra residues
+        
+        Returns:
+            list -- resnums
+        '''
+
+        return self.resnum
+
+    @property
+    def getInsCode(self):
+        '''original PDB resname, not nec. sequential, may contain letters
+        
+        Returns:
+            list -- inscode
+        '''
+
+        return self.inscode
+
+    @property
+    def getChain(self):
+        '''one-letter chain ID, if any
+        
+        Returns:
+            list -- chain
+        '''
+
+        return self.chain
+
+    @property
+    def getAAs(self):
+        ''' amino acid sequence in one letter code
+        
+        Returns:
+            list -- aa
+        '''
+
+        return self.aa
+
+    @property
+    def getSecStruc(self):
+        '''secondary structure
+        
+        Returns:
+            list -- secstruc
+        '''
+
+        return self.struct
+
+    @property
+    def getSecStrucDetail(self):
+        '''3-turns/helix,4-turns/helix,5-turns/helix,geometrical bend,chirality,beta bridge label,beta bridge label
+        
+        Returns:
+            list -- secondary structure details
+        '''
+
+        return self.structdetails
+
+    @property
+    def getBP1(self):
+        '''beta bridge partner resnum
+        
+        Returns:
+            list -- bp1
+        '''
+
+        return self.bp1
+
+    @property
+    def getBP2(self):
+        '''beta bridge partner resnum,beta sheet label
+        
+        Returns:
+            list -- bp2
+        '''
+
+        return self.bp2
+
+    @property
+    def getACC(self):
+        '''solvent accessibility
+        
+        Returns:
+            list -- acc
+        '''
+
+        return self.acc
+
+    @property
+    def getH_NHO1(self):
+        '''hydrogen bonds
+        
+        Returns:
+            list -- h_nho1
+        '''
+
+        return self.h_nho1
+
+    @property
+    def getH_NHO2(self):
+        '''hydrogen bonds
+        
+        Returns:
+            list -- h_nho2
+        '''
+
+        return self.h_nho2
+
+    @property
+    def getH_OHN1(self):
+        '''hydrogen bonds
+        
+        Returns:
+            list -- h_ohn1
+        '''
+
+        return self.h_ohn1
+
+    @property
+    def getH_OHN2(self):
+        '''hydrogen bonds
+        
+        Returns:
+            list -- h_ohn2
+        '''
+
+        return self.h_ohn2
+
+    @property
+    def getTCO(self):
+        '''cosine of angle between C=O of residue I and C=O of residue I-1. For α-helices,TCO is near +1, for β-sheets TCO is near -1. Not used for structure definition.
+        
+        Returns:
+            list -- tco
+        '''
+
+        return self.tco
+
+    @property
+    def getKAPPA(self):
+        '''virtual bond angle (bend angle) defined by the three Cα atoms of residues I-2,I,I+2.Used to define bend (structure code 'S').
+        
+        Returns:
+            list -- [description]
+        '''
+
+        return self.kappa
+
+    @property
+    def getALPHA(self):
+        '''virtual torsion angle (dihedral angle) defined by the four Cα atoms of residues I-1,I,I+1,I+2.Used to define chirality (structure code '+' or '-').
+        
+        Returns:
+            list -- alpha
+        '''
+
+        return self.alpha
+
+    @property
+    def getPHI(self):
+        '''IUPAC peptide backbone torsion angles
+        
+        Returns:
+            list -- phi
+        '''
+
+        return self.phi
+
+    @property
+    def getPSI(self):
+        '''IUPAC peptide backbone torsion angles
+        
+        Returns:
+            list -- psi
+        '''
+
+        return self.psi
+
+    @property
+    def getX(self):
+        '''echo of Cα atom coordinates
+        
+        Returns:
+            list -- xca
+        '''
+
+        return self.xca
+
+    @property
+    def getY(self):
+        '''echo of Cα atom coordinates
+        
+        Returns:
+            list -- yca
+        '''
+
+        return self.yca
+
+    @property
+    def getZ(self):
+        '''echo of Cα atom coordinates
+        
+        Returns:
+            list -- zca
+        '''
+
+        return self.zca
+
+    @property
+    def getRcsbChain(self):
+        '''The rcsb-given and author-given chain ids respectively.
+        These will be the same for PDB files, but different for mmCIF files.
+        Also, in mmCIF files these ids can be longer than one character.
+
+        Returns:
+            list -- rcsb_given_chain
+        '''
+
+        return self.rcsb_given_chain
+
+    @property
+    def getAuthChain(self):
+        '''The rcsb-given and author-given chain ids respectively.
+        These will be the same for PDB files, but different for mmCIF files.
+        Also, in mmCIF files these ids can be longer than one character.
+        
+        Returns:
+            list -- author_given_chain
+        '''
+
+        return self.author_given_chain
+
+if __name__ == '__main__':
+    import sys
+    parse_ = parseDSSP(sys.argv[1])
+    parse_.parse()
+    # pddict = parse_.dictTodataframe()
+    # print(pddict)
+    print(parse_.getACC)
+