From 28cfb44ed4a71d6e3ea40805c8e551b4ab7178fa Mon Sep 17 00:00:00 2001 From: edoapra Date: Fri, 29 Oct 2021 15:08:48 -0700 Subject: [PATCH] fixes for flake8 --- contrib/marat/nwchem-python/GenericAtom.py | 22 ++--- contrib/marat/nwchem-python/atom_params.py | 6 +- contrib/marat/nwchem-python/generic_atom.py | 24 +++--- .../marat/nwchem-python/generic_residue.py | 40 ++++----- contrib/marat/nwchem-python/my_system.py | 82 +++++++++---------- contrib/marat/nwchem-python/my_utils.py | 6 +- contrib/marat/nwchem-python/pdbparser.py | 14 ++-- contrib/marat/nwchem-python/pdbrecord.py | 16 ++-- contrib/marat/python/ResAtom.py | 22 ++--- contrib/marat/python/Residue.py | 4 +- contrib/marat/python/atom_dictionary.py | 6 +- contrib/marat/python/myatom.py | 8 +- contrib/marat/python/myresidue.py | 6 +- contrib/marat/python/mysystem.py | 8 +- contrib/marat/python/myvector.py | 19 +++-- contrib/marat/python/myvector3.py | 6 +- 16 files changed, 145 insertions(+), 144 deletions(-) diff --git a/contrib/marat/nwchem-python/GenericAtom.py b/contrib/marat/nwchem-python/GenericAtom.py index 69e88fe526..4ec00b2d51 100644 --- a/contrib/marat/nwchem-python/GenericAtom.py +++ b/contrib/marat/nwchem-python/GenericAtom.py @@ -21,8 +21,8 @@ class GenericAtom(object): if d: if type(d) is not type({}): - print "wrong type ", type(d) - print "expecting", type({}) + print("wrong type ", type(d)) + print("expecting", type({})) sys.exit(1) else: self.dct = d @@ -77,15 +77,15 @@ if __name__ == '__main__': aline4="ATOM 2 O1 -0.985 -1.156 1.840 -0.80 O" a=GenericAtom.fromPDBrecord(aline2) - print a.groupTag() - print a.coord - print a.dct + print(a.groupTag()) + print(a.coord) + print(a.dct ) b=GenericAtom.fromPDBrecord(aline3) - print b.coord - print b.dct - print GenericAtom.bondlength(a,b),GenericAtom.bonded(a,b) - print a.covRadius()+b.covRadius() + print(b.coord) + print(b.dct ) + print(GenericAtom.bondlength(a,b),GenericAtom.bonded(a,b)) + print(a.covRadius()+b.covRadius()) c=GenericAtom.fromPDBrecord(aline1) - print GenericAtom.bondlength(a,c),GenericAtom.bonded(a,c) + print(GenericAtom.bondlength(a,c),GenericAtom.bonded(a,c)) c=GenericAtom.fromPDBrecord(aline4) - print c.groupTag() \ No newline at end of file + print(c.groupTag()) diff --git a/contrib/marat/nwchem-python/atom_params.py b/contrib/marat/nwchem-python/atom_params.py index b62d011489..facf8e4b5e 100644 --- a/contrib/marat/nwchem-python/atom_params.py +++ b/contrib/marat/nwchem-python/atom_params.py @@ -41,7 +41,7 @@ class AtomParams(): try: return d[s1.group(1)],s1.group(1) except KeyError: - print "Cannot match name", a + print("Cannot match name", a) sys.exit(1) @staticmethod @@ -517,7 +517,7 @@ class AtomParams(): if __name__ == '__main__': - print AtomParams.fullName(' H1 ') - print AtomParams.vdwRadius('h') + print(AtomParams.fullName(' H1 ')) + print(AtomParams.vdwRadius('h')) diff --git a/contrib/marat/nwchem-python/generic_atom.py b/contrib/marat/nwchem-python/generic_atom.py index da81e85f2e..4abbc56f9b 100644 --- a/contrib/marat/nwchem-python/generic_atom.py +++ b/contrib/marat/nwchem-python/generic_atom.py @@ -22,8 +22,8 @@ class GenericAtom(object): if d: if type(d) is not type({}): - print "wrong type ", type(d) - print "expecting", type({}) + print("wrong type ", type(d)) + print("expecting", type({})) sys.exit(1) else: self.dct = d @@ -145,20 +145,20 @@ if __name__ == '__main__': # aline4="ATOM 2 O1 -0.985 -1.156 1.840 -0.80 O" # # a=GenericAtom.fromPDBrecord(aline2) -# print a.groupTag() -# print a.coord -# print a.dct +# print(a.groupTag()) +# print(a.coord) +# print(a.dct ) # b=GenericAtom.fromPDBrecord(aline3) -# print b.coord -# print b.dct -# print GenericAtom.bondlength(a,b),GenericAtom.bonded(a,b) -# print a.covRadius()+b.covRadius() +# print(b.coord) +# print(b.dct ) +# print(GenericAtom.bondlength(a,b),GenericAtom.bonded(a,b)) +# print(a.covRadius()+b.covRadius()) # c=GenericAtom.fromPDBrecord(aline1) -# print GenericAtom.bondlength(a,c),GenericAtom.bonded(a,c) +# print(GenericAtom.bondlength(a,c),GenericAtom.bonded(a,c)) # c=GenericAtom.fromPDBrecord(aline4) -# print c.groupTag() +# print(c.groupTag()) aline6="O1 -0.985 -1.156 1.140 0.0 0.0 " aline5="O1 -0.985 -1.156 " d=GenericAtom.fromXYZrecord(aline6) d.translate([1.0,1.0,1.0]) - print d + print(d) diff --git a/contrib/marat/nwchem-python/generic_residue.py b/contrib/marat/nwchem-python/generic_residue.py index baf63b8379..7e541195df 100644 --- a/contrib/marat/nwchem-python/generic_residue.py +++ b/contrib/marat/nwchem-python/generic_residue.py @@ -179,7 +179,7 @@ class GenericResidue(object): r = GenericAtom.bondlength(a1, a2) if r < rOH: plist.append([a1,a2]) -# print "plist",plist +# print("plist",plist) for a1,a2 in plist: if a1.elemName()=='H': res1,res2=res2,res1 @@ -217,7 +217,7 @@ class GenericResidue(object): r = GenericAtom.bondlength(a1, a2) if r < rOH: plist.append([a1,a2]) -# print "plist",plist +# print("plist",plist) for a1,a2 in plist: if a1.elemName()=='H': res1,res2=res2,res1 @@ -277,7 +277,7 @@ class GenericResidue(object): # return False # a3 = res2.get_bonded(a2, 'O')[0] # angle = GenericAtom.angle(a1, a2, a3) -# print r,angle +# print(r,angle) # return angle>OHO @staticmethod @@ -286,7 +286,7 @@ class GenericResidue(object): for a1 in res1.byFilter(): for a2 in res2.byFilter(): dr=min(dr,GenericAtom.bondlength(a1, a2)) - print dr,a1.name(),a2.name() + print(dr,a1.name(),a2.name()) return dr def byElement(self,name): @@ -309,33 +309,33 @@ if __name__ == '__main__': # aline2 = "ATOM 1 I1 IO3 1 -1.555 -0.350 0.333 1.39 I" # # res0 = GenericResidue() -# print res0 +# print(res0) # a = GenericAtom.fromPDBrecord(aline2) -# print a +# print(a) # res0.AddAtom(a) -# print res0.size() +# print(res0.size()) res0 = GenericResidue.fromPDBfile("io3.pdb") - print res0 + print(res0) res1 = GenericResidue.fromPDBfile("h2o-1.pdb") - print res1.signature() - print res0.signature() + print(res1.signature()) + print(res0.signature()) res1.guess_name() - print res1.name + print(res1.name) res0.guess_name() - print res0.name + print(res0.name) - print "distance test" + print("distance test") (r,a1,a2)=GenericResidue.distance(res0, res1) - print r, a1.name(), a2.name() - print res1.get_bonded(a2, "O") + print(r, a1.name(), a2.name()) + print(res1.get_bonded(a2, "O")) name = None - print (filter(lambda a: name is None or a.elemName()==name,res1.atoms )) - print GenericResidue.hbonded(res0,res1) - print "HERE COMES PDB RECORD" - print res0.toPDBrecord(1) + print((filter(lambda a: name is None or a.elemName()==name,res1.atoms ))) + print(GenericResidue.hbonded(res0,res1)) + print("HERE COMES PDB RECORD") + print(res0.toPDBrecord(1)) # b = ResAtom.fromPDBrecord(aline1) # res0.AddAtom(a) # res0.AddAtom(b) -# print res0.toPDBrecord(atom_start=1) \ No newline at end of file +# print(res0.toPDBrecord(atom_start=1)) diff --git a/contrib/marat/nwchem-python/my_system.py b/contrib/marat/nwchem-python/my_system.py index f63901a808..4330c5e442 100644 --- a/contrib/marat/nwchem-python/my_system.py +++ b/contrib/marat/nwchem-python/my_system.py @@ -126,10 +126,10 @@ class MySystem(object): G=nx.MultiDiGraph() for i,r in enumerate(self.reslist): G.add_node(i+1,name=r.name) - print G.nodes() + print(G.nodes()) solvent = [n for n,d in G.nodes_iter(data=True) if d['name'] in ['WAT','HOH','WTR' ]] solute = [n for n,d in G.nodes_iter(data=True) if d['name'] not in ['WAT','HOH','WTR' ]] - print "solute",solute + print("solute",solute) nr = len(self.reslist) for i in range(nr): @@ -149,18 +149,18 @@ class MySystem(object): if GenericResidue.spec_bonded(ri, rj): G.add_edge(j+1,i+1,name="special") - print "all",[(u,v) for u,v,d in G.edges_iter(data=True)] + print("all",[(u,v) for u,v,d in G.edges_iter(data=True)] ) esolute = [(u,v,d) for u,v,d in G.edges_iter(data=True) if (u in solute or v in solute) and d['name']=='hbond' ] - print "solute-solute",esolute + print("solute-solute",esolute) esolute2 = [(u,v) for u,v,d in G.edges_iter(data=True) if (u in solute or v in solute) and d['name']=='hbond2' ] - print "double solute",esolute2 + print("double solute",esolute2) esolvent= [(u,v) for u,v,d in G.edges_iter(data=True) if (u in solvent and v in solvent) and d['name']=='hbond'] - print "solvent-solvent",esolvent + print("solvent-solvent",esolvent ) especial= [(u,v) for u,v,d in G.edges_iter(data=True) if d['name']=='special' ] - print especial + print(especial ) G=nx.relabel_nodes(G,lambda x: str(x)) pos0=nx.spectral_layout(G) @@ -188,7 +188,7 @@ class MySystem(object): # T=nx.dfs_tree(G) # print(sorted(T.edges(data=True))) nx.write_dot(G,"shell.dot") -# print "density=",nx.density(G) +# print("density=",nx.density(G)) nx.write_gml(G, "test.gml") # plt.show() # display # return G @@ -200,10 +200,10 @@ class MySystem(object): G=nx.MultiGraph() for i,r in enumerate(self.reslist): G.add_node(i+1,name=r.name) - print G.nodes() + print(G.nodes()) solvent = [n for n,d in G.nodes_iter(data=True) if d['name'] in ['WAT','HOH','WTR' ]] solute = [n for n,d in G.nodes_iter(data=True) if d['name'] not in ['WAT','HOH','WTR' ]] - print "solute",solute + print("solute",solute) h = self.hbond_matrix1() nr = numpy.size(h,0) @@ -217,18 +217,18 @@ class MySystem(object): elif GenericResidue.spec_bonded(self.reslist[i], self.reslist[j]): G.add_edge(i+1,j+1,name="special") - print "all",[(u,v) for u,v,d in G.edges_iter(data=True)] + print("all",[(u,v) for u,v,d in G.edges_iter(data=True)] ) esolute = [(u,v) for u,v,d in G.edges_iter(data=True) if (u in solute or v in solute) and d['name']=='hbond' ] - print esolute + print(esolute) esolute2 = [(u,v) for u,v,d in G.edges_iter(data=True) if (u in solute or v in solute) and d['name']=='hbond2' ] - print esolute2 + print(esolute2) esolvent= [(u,v) for u,v,d in G.edges_iter(data=True) if (u in solvent and v in solvent) and d['name']=='hbond'] - print esolvent + print(esolvent ) especial= [(u,v) for u,v,d in G.edges_iter(data=True) if d['name']=='special' ] - print especial + print(especial ) pos0=nx.spectral_layout(G) pos=nx.spring_layout(G,iterations=500,pos=pos0) @@ -254,7 +254,7 @@ class MySystem(object): # T=nx.dfs_tree(G) # print(sorted(T.edges(data=True))) # nx.write_dot(G,"shell.dot") -# print "density=",nx.density(G) +# print("density=",nx.density(G)) # plt.show() # display # return G @@ -311,7 +311,7 @@ class MySystem(object): G=nx.Graph() for i,r in enumerate(self.reslist): G.add_node(i+1,name=r.name) - print G.nodes() + print(G.nodes()) h = self.hbond_matrix() @@ -319,7 +319,7 @@ class MySystem(object): for i in range(nr): for j in range(i+1,nr): if GenericResidue.touching(self.reslist[i], self.reslist[j],2.8): - print 'adding edge',i+1,j+1 + print('adding edge',i+1,j+1) G.add_edge(i+1,j+1,name="special") # pos0=nx.spectral_layout(G) @@ -415,8 +415,8 @@ class MySystem(object): def info(self): for tag,res in self.residues.iteritems(): - print tag - print res + print(tag ) + print(res ) if __name__ == '__main__': # sim0 = MySystem("test") @@ -430,23 +430,23 @@ if __name__ == '__main__': # sim1 = MySystem.from_file("w10-11.xyz") - print sim1.num_hbonds(rOH=2.18, HOH=138) + print(sim1.num_hbonds(rOH=2.18, HOH=138)) # sim1.create_graph_directed("test.png") # sim1.toPDBfile("shell-1.pdb") # sim1.create_graph("shell.png") # G=sim1.graph() -# print nx.density(G) -# print sim1.num_hbonds()[0] +# print(nx.density(G)) +# print(sim1.num_hbonds()[0]) # dm=sim1.dist_matrix(2.8) # chain0=[0] # level=2 # chain1=[] -# print dm +# print(dm) # for i in chain0: # for j in range(i+1,25): # if dm[i][j]==1: # chain1.append([i,j]) -# print chain1 +# print(chain1) # # chain0=chain1 # chain1=[] @@ -455,7 +455,7 @@ if __name__ == '__main__': # for j in range(i+1,25): # if dm[i][j]==1: # chain1.append([i,j]) -# print chain1 +# print(chain1) # # slist=set() # while len(slist)<15: @@ -469,7 +469,7 @@ if __name__ == '__main__': # for i,s in enumerate(slist): # filename = "cw9-%d.pdb"%(i) # comment="-".join(["%s" % el for el in s]) -# print s,filename,comment +# print(s,filename,comment) # sim1.toPDBfile1(filename,s,comment) # it = iter(slist) @@ -479,7 +479,7 @@ if __name__ == '__main__': # nx.draw_spring(H) # plt.show() - print "finished" + print("finished") sys.exit(0) @@ -488,17 +488,17 @@ if __name__ == '__main__': # sim2 = MySystem.fromPDBfile("test.pdb") # sim3 = MySystem.fromXYZfile("w2-test.xyz") # sim3.groupAtoms() -# print sim1.residues["XYZ"] +# print(sim1.residues["XYZ"]) # sim1.connectAtoms() # G=nx.Graph(hbond) # # for i in range(nr): -# print i+1, hbond[i], sum(hbond[i]) +# print(i+1, hbond[i], sum(hbond[i])) # -# print nx.connected_components(G) -# print nx.clustering(G) +# print(nx.connected_components(G)) +# print(nx.clustering(G)) # nx.write_dot(G,'file.dot') # pos=nx.spring_layout(G) # colors=range(20) @@ -506,10 +506,10 @@ if __name__ == '__main__': # nx.draw_spring(G) # plt.show() # plt.savefig("path.png") -# print "looking for cliques" -# print list(nx.find_cliques(G)) -# print nx.number_connected_components(G) -# print sorted(nx.degree(G).values()) +# print("looking for cliques") +# print(list(nx.find_cliques(G))) +# print(nx.number_connected_components(G)) +# print(sorted(nx.degree(G).values())) # # sim1.toPDBfile("mytest.pdb") # try: @@ -520,22 +520,22 @@ if __name__ == '__main__': # # L=nx.generalized_laplacian(G) # e=eigenvalues(L) -# print e -# print "pagerank" +# print(e) +# print("pagerank") # d= nx.degree(G) # for w in sorted(d, key=d.get, reverse=True): -# print w, d[w] +# print(w, d[w]) # T=nx.minimum_spanning_tree(G) # print(sorted(T.edges(data=True))) # print(nx.cycle_basis(G)) # nx.draw_spring(G) # plt.show() -# print len(hbond) +# print(len(hbond)) # sim1.info() # r=list(sim1.residues.itervalues()) -# print r +# print(r) # sim1 = MySystem.fromPDBfile("test.pdb") # diff --git a/contrib/marat/nwchem-python/my_utils.py b/contrib/marat/nwchem-python/my_utils.py index 3dc191203d..c0266c05bd 100644 --- a/contrib/marat/nwchem-python/my_utils.py +++ b/contrib/marat/nwchem-python/my_utils.py @@ -37,13 +37,13 @@ def extract_random_clusters(filename,nres,prefix=None,nconf=15,with_residues=Non reslist.add(tuple(sorted(alist))) - print reslist + print(reslist) for i,s in enumerate(reslist): filename = "%s-%d.pdb"%(prefix,i) comment="-".join(["%s" % el for el in s]) sim1.toPDBfile1(filename,s,comment) - print "generated cluster",s,"as",filename + print("generated cluster",s,"as",filename) @@ -63,4 +63,4 @@ def make_unique(seq, idfun=None): if __name__ == '__main__': extract_random_clusters("shell-1.pdb",11,with_residues=[0,1,2]) - \ No newline at end of file + diff --git a/contrib/marat/nwchem-python/pdbparser.py b/contrib/marat/nwchem-python/pdbparser.py index 192f4b6061..ed9c19eb26 100644 --- a/contrib/marat/nwchem-python/pdbparser.py +++ b/contrib/marat/nwchem-python/pdbparser.py @@ -28,7 +28,7 @@ class PDBAtomParser(object): @staticmethod def record(name,buf): -# print inspect.getsource(PDBAtomParser.recordName) +# print(inspect.getsource(PDBAtomParser.recordName) ) ir=PDBAtomParser.irec[name] atype=PDBAtomParser.atype[name] value = buf[ir[0]:ir[1]] @@ -82,11 +82,11 @@ if __name__ == '__main__': aline2="ATOM 588 GLU -13.363 -4.163 -2.372 1.00 0.00" aline3="ATTM 588 GLU -13.363 -4.163 -2.372 1.00 0.00" - print PDBAtomParser.record("name",aline2) - print PDBAtomParser.record("name",aline1) - print PDBAtomParser.getDict(aline1) - print PDBAtomParser.getDict(aline2) - print PDBAtomParser.getDict(aline3) + print(PDBAtomParser.record("name",aline2) ) + print(PDBAtomParser.record("name",aline1) ) + print(PDBAtomParser.getDict(aline1)) + print(PDBAtomParser.getDict(aline2)) + print(PDBAtomParser.getDict(aline3)) # 1 - 6 Record name "ATOM " @@ -120,4 +120,4 @@ if __name__ == '__main__': # ATOM 294 2HG GLU 18 -13.518 -3.769 0.084 1.00 0.00 H - \ No newline at end of file + diff --git a/contrib/marat/nwchem-python/pdbrecord.py b/contrib/marat/nwchem-python/pdbrecord.py index b32a370cbd..82373c5026 100644 --- a/contrib/marat/nwchem-python/pdbrecord.py +++ b/contrib/marat/nwchem-python/pdbrecord.py @@ -32,7 +32,7 @@ class PDBAtomRecord(object): returns value of the "name" field in the provided "buf" buffer always returns None value if buffer is not of ATOM or HETATM type ''' -# print inspect.getsource(PDBAtomRecord.fieldName) +# print(inspect.getsource(PDBAtomRecord.fieldName) ) if not PDBAtomRecord.test(buf): return None ir=PDBAtomRecord.irec[name] @@ -91,12 +91,12 @@ if __name__ == '__main__': aline2="ATOM 588 GLU -13.363 -4.163 -2.372 1.00 0.00" aline3="ATTM 588 GLU -13.363 -4.163 -2.372 1.00 0.00" - print PDBAtomRecord.field("name",'') - print PDBAtomRecord.field("name",aline3) - print PDBAtomRecord.dct(aline1) - print PDBAtomRecord.dct(aline2) - print PDBAtomRecord.dct(aline3) - print PDBAtomRecord.dct('') + print(PDBAtomRecord.field("name",'') ) + print(PDBAtomRecord.field("name",aline3) ) + print(PDBAtomRecord.dct(aline1)) + print(PDBAtomRecord.dct(aline2)) + print(PDBAtomRecord.dct(aline3)) + print(PDBAtomRecord.dct('')) # 1 - 6 Record name "ATOM " @@ -130,4 +130,4 @@ if __name__ == '__main__': # ATOM 294 2HG GLU 18 -13.518 -3.769 0.084 1.00 0.00 H - \ No newline at end of file + diff --git a/contrib/marat/python/ResAtom.py b/contrib/marat/python/ResAtom.py index d4c5f4a49c..efb9c6c507 100644 --- a/contrib/marat/python/ResAtom.py +++ b/contrib/marat/python/ResAtom.py @@ -99,25 +99,25 @@ class ResAtom(Atom): if __name__ == '__main__': - print "creating first atom" + print("creating first atom") aline1="ATOM 588 1HG GLU 18 -13.363 -4.163 -2.372 1.00 0.00 H" - print aline1 + print(aline1) a = ResAtom.fromPDBrecord(aline1) - print "it should come out as this" - print a + print("it should come out as this") + print(a) aline2="ATOM 589 2HG GLU 18 -12.634 -3.023 -3.475 1.00 0.00 H" - print "creating second atom" + print("creating second atom") aline2="ATOM 589 2HG GLU 18 -12.634 -3.023 -3.475 1.00 0.00 H" - print aline2 + print(aline2) b = ResAtom.fromPDBrecord(aline2) - print "it should come out as this" - print b + print("it should come out as this") + print(b) - print "The distance between these two atoms is", Atom.bondlength(a, b) + print("The distance between these two atoms is", Atom.bondlength(a, b)) - print "PDB record for second atom with starting index 5 and resid 23" - print b.toPDBrecord(id_atom=5,id_res=23) + print("PDB record for second atom with starting index 5 and resid 23" ) + print(b.toPDBrecord(id_atom=5,id_res=23)) # PDB ATOM RECORD FORMAT diff --git a/contrib/marat/python/Residue.py b/contrib/marat/python/Residue.py index d91f5dbee1..adb1637876 100644 --- a/contrib/marat/python/Residue.py +++ b/contrib/marat/python/Residue.py @@ -48,7 +48,7 @@ class Residue: self.name = a.resname else: if a.resname != self.name: - print "different names for the same residue index" + print("different names for the same residue index") sys.exit(1) self.atoms.append(a) @@ -61,4 +61,4 @@ if __name__ == '__main__': b = ResAtom.fromPDBrecord(aline1) res0.AddAtom(a) res0.AddAtom(b) - print res0.toPDBrecord(id_atom=4) \ No newline at end of file + print(res0.toPDBrecord(id_atom=4)) diff --git a/contrib/marat/python/atom_dictionary.py b/contrib/marat/python/atom_dictionary.py index ae20e688db..6e4d86d79a 100644 --- a/contrib/marat/python/atom_dictionary.py +++ b/contrib/marat/python/atom_dictionary.py @@ -41,7 +41,7 @@ class AtomDictionary(): try: return d[s1.group(1)],s1.group(1) except KeyError: - print "Cannot match name", a + print("Cannot match name", a) sys.exit(1) @staticmethod @@ -517,7 +517,7 @@ class AtomDictionary(): if __name__ == '__main__': - print AtomDictionary.fullName(' H1 ') - print AtomDictionary.vdwRadius('h') + print(AtomDictionary.fullName(' H1 ')) + print(AtomDictionary.vdwRadius('h')) diff --git a/contrib/marat/python/myatom.py b/contrib/marat/python/myatom.py index 3ccc5d6803..b2f25c307a 100644 --- a/contrib/marat/python/myatom.py +++ b/contrib/marat/python/myatom.py @@ -65,12 +65,12 @@ if __name__ == '__main__': try: b = Atom.fromPDBrecord(aline1) except SystemExit: - print "error reading PDB line" + print("error reading PDB line") sys.exit(1) try: a = Atom.fromPDBrecord(aline2) except SystemExit: - print "error reading PDB line" + print("error reading PDB line") sys.exit(1) - print "bondlength is", Atom.bondlength(a,b) - print "finished I am" \ No newline at end of file + print("bondlength is", Atom.bondlength(a,b)) + print("finished I am") diff --git a/contrib/marat/python/myresidue.py b/contrib/marat/python/myresidue.py index 47db0a9401..172a51e145 100644 --- a/contrib/marat/python/myresidue.py +++ b/contrib/marat/python/myresidue.py @@ -26,7 +26,7 @@ class MyResidue: def AddAtom(self,a1): self.atoms.append(a1) - print self.atoms + print(self.atoms) if __name__ == '__main__': res0 = MyResidue("test") @@ -36,9 +36,9 @@ if __name__ == '__main__': try: b = Atom.fromPDBrecord(aline1) except SystemExit: - print "error reading PDB line" + print("error reading PDB line") sys.exit(1) res0.AddAtom(b) # a = Atom.fromPDBrecord(aline2) # sim0.AddAtom(a) - print res0 \ No newline at end of file + print(res0) diff --git a/contrib/marat/python/mysystem.py b/contrib/marat/python/mysystem.py index 7c1356c09d..a11204e214 100644 --- a/contrib/marat/python/mysystem.py +++ b/contrib/marat/python/mysystem.py @@ -56,13 +56,13 @@ if __name__ == '__main__': try: b = ResAtom.fromPDBrecord(aline1) except SystemExit: - print "error reading PDB line" + print("error reading PDB line") sys.exit(1) sim0.AddAtom(b) a = ResAtom.fromPDBrecord(aline2) sim0.AddAtom(a) sim1 = MySystem.fromPDBfile("test.pdb") - print sim1.residues + print(sim1.residues) # def AddAtom1(self,a1): @@ -73,7 +73,7 @@ if __name__ == '__main__': # rmap[a1.resid]["atoms"]=[] # rmap[a1.resid]["name"]=a1.resname # if rmap[a1.resid]["name"]!=a1.resname: -# print "different names for the same residue index" +# print("different names for the same residue index") # sys.exit(1) # rmap[a1.resid]["atoms"].append(a1) -# print "added atom", a1.resid \ No newline at end of file +# print "added atom", a1.resid diff --git a/contrib/marat/python/myvector.py b/contrib/marat/python/myvector.py index c03746c5a8..44dd965b67 100644 --- a/contrib/marat/python/myvector.py +++ b/contrib/marat/python/myvector.py @@ -5,6 +5,7 @@ Created on Feb 4, 2012 ''' import math from numpy import array +from functools import reduce class Vector: def __init__(self, coord=[],name="Vector"): @@ -24,7 +25,7 @@ class Vector: __rmul__ = __mul__ def __repr__(self): - return `self.coord` + return repr(self.coord) def norm1(self, start=0): return reduce(lambda x,y: x + abs(y), self.coord, start) @@ -45,17 +46,17 @@ class Vector: def test(): x = Vector([2, 4, 6]) - print x + 3, 3 + x - print x * 4, 4 * x - print x.norm1(), x.prod() + print(x + 3, 3 + x) + print(x * 4, 4 * x) + print(x.norm1(), x.prod()) y = Vector([1, 2, 3]) - print x + y - print x * y - print x * y * 2 - print x * y * x + print(x + y) + print(x * y) + print(x * y * 2) + print(x * y * x) z = Vector([1,1,1]) - print z.length(), math.sqrt(3.0), z.size + print(z.length(), math.sqrt(3.0), z.size) if __name__ == '__main__': test() # run my self-test code diff --git a/contrib/marat/python/myvector3.py b/contrib/marat/python/myvector3.py index bdc99486bd..b9804f51e2 100644 --- a/contrib/marat/python/myvector3.py +++ b/contrib/marat/python/myvector3.py @@ -51,7 +51,7 @@ class Vector(object): if __name__ == '__main__': a = Vector(1.0,1.0,0.0) b = Vector(1.0,1.0,0.0) - print a + print(a) c=a-b - print c - print "Length ", c.length() \ No newline at end of file + print(c) + print("Length ", c.length())