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fixes for flake8

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edoapra 2021-10-29 15:08:48 -07:00
parent bc08e3879f
commit 28cfb44ed4
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GPG key ID: 472C4EBB4F3AEDFA
16 changed files with 145 additions and 144 deletions
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22
contrib/marat/nwchem-python/GenericAtom.py
View file

@ -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()
print(c.groupTag())

6
contrib/marat/nwchem-python/atom_params.py
View file

@ -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'))

24
contrib/marat/nwchem-python/generic_atom.py
View file

@ -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)

40
contrib/marat/nwchem-python/generic_residue.py
View file

@ -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)
# print(res0.toPDBrecord(atom_start=1))

82
contrib/marat/nwchem-python/my_system.py
View file

@ -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")
#

6
contrib/marat/nwchem-python/my_utils.py
View file

@ -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])

14
contrib/marat/nwchem-python/pdbparser.py
View file

@ -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

16
contrib/marat/nwchem-python/pdbrecord.py
View file

@ -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

22
contrib/marat/python/ResAtom.py
View file

@ -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

4
contrib/marat/python/Residue.py
View file

@ -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)
print(res0.toPDBrecord(id_atom=4))

6
contrib/marat/python/atom_dictionary.py
View file

@ -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'))

8
contrib/marat/python/myatom.py
View file

@ -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"
print("bondlength is", Atom.bondlength(a,b))
print("finished I am")

6
contrib/marat/python/myresidue.py
View file

@ -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
print(res0)

8
contrib/marat/python/mysystem.py
View file

@ -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
# print "added atom", a1.resid

19
contrib/marat/python/myvector.py
View file

@ -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

6
contrib/marat/python/myvector3.py
View file

@ -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()
print(c)
print("Length ", c.length())